title: Expression analysis of common myeloid progenitors (CMPs) expressing Hes1

status: Public on May 01 2014

city: Tokyo

first: Fumio

last: Nakahara

address: 4-6-1 Shirokanedai, Minato-ku

department: Division of Cellular Therapy, Advanced Clinical Research Center

institute: The Institute of Medical Science, The University of Tokyo

summary: High levels of Hes1 expression are frequently found in BCR-ABL-positive chronic myelogenous leukemia in blast crisis (CML-BC). In mouse bone marrow transplantation (BMT) models, co-expression of BCR-ABL and Hes1 induces CML-BC–like disease; however the underlying mechanism remained elusive. Here, based on gene expression analysis, we show that MMP-9 is upregulated by Hes1 in common myeloid progenitors (CMPs). Analysis of promoter activity demonstrated that Hes1 upregulated MMP-9 by activating NF-kB. Analysis of 20 samples from CML-BC patients showed that MMP-9 was highly expressed in three, with two exhibiting high levels of Hes1 expression. Interestingly, MMP-9 deficiency impaired the cobblestone area-forming ability of CMPs expressing BCR-ABL and Hes1 that were in conjunction with a stromal cell layer. In addition, these CMPs secreted MMP-9, promoting the release of soluble Kit-ligand (sKitL) from stromal cells, thereby enhancing proliferation of the leukemic cells. In accordance, mice transplanted with CMPs expressing BCR-ABL and Hes1 exhibited high levels of sKitL as well as MMP-9 in the serum. Importantly, MMP-9 deficiency impaired the development of CML-BC–like disease induced by BCR-ABL and Hes1 in mouse BMT models. The present results suggest that Hes1 promotes the development of CML-BC, partly through MMP-9 upregulation in leukemic cells.

overall_design: Common myeloid progenitors (CMPs; Lineage negative, c-Kit positive, Sca-1 negative, Fc-gamma-receptor low, CD34 positive fraction) were sorted with a FACSAria cell sorter (Becton Dickinson). Retroviruses were generated by transfecting Plat-E packaging cells with retrovirus vector pMYs-Hes1-IRES-GFP or empty vector (pMYs-IRES-GFP) using FuGENE 6 (Roche Diagnostics). Infection of retrovirus harboring Hes1 (pMYs-Hes1-IRES-GFP) or empty vector (pMYs-IRES-GFP) into progenitors was performed using RetroNectin (Takara Bio).  Hes1-transfected CMPs and Mock-transduced CMPs were isolated 36 hours after infection with a FACSAria cell sorter. One sample of Hes1-transfected CMPs and one sample of mock-transduced CMPs were analyzed with GeneChip Mouse Genome 430 2.0 Array.

first: Hiroyuki

last: Aburatani

first: Toshio

last: Kitamura


title: Integrin α3b1-dependent gene expression in MDA-MB-231 breast  cancer cells

status: Public on May 02 2014

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

country: USA

institute: SUNY-University at Albany

summary:
Gene-level and exon-level analysis of gene expression in MDA-MB-231 cells that stably express control shRNA or integrin α3-targeting shRNA.
The laminin-332-binding integrin α3b1 is expressed highly in many breast cancer cells, but its roles in regulating gene expression programs that promote breast cancer progression have not been explored.  In order to identify genes that are regulated by α3b1 in human breast cancer cells, we used a lentiviral approach to express an α3-targeting shRNA to suppress integrin α3b1 in MDA-MB-231 cells, and we identified subsequent changes in gene expression and alternate exon useage.

overall_design: We used the Affymetrix Human Exon 1.0 ST platform to analyze biological replicates of MDA-MB-231 cells that were transduced with lentivirus to stably express either control shRNA or α3-targeting shRNA.  Array data was processed by Affymetrix Exon Array Computational Tool.

first: C

middle: M

last: DiPersio

first: Sita

last: Subbaram


title: BAC-trap studies of Purkinje cells in normal and FMR1 mutant mice

city: Houston

first: Chad

middle: A.

last: Shaw

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: BCM

summary:
The molecular mechanism(s) leading to Purkinje neuron loss in the neurodegenerative disorder Fragile X-Associated Tremor/Ataxia Syndrome (FXTAS) are limited by the complex morphology of this cell type. Purkinje neurons are notoriously difficult to isolate and maintain in culture presenting considerable difficultly to identify molecular changes in response to riboCGG repeat-containing mRNA that induces neurotoxicity in FXTAS. Several studies have uncovered a number of RNA binding proteins involved in translation that aberrantly interact with the toxic RNA; however, whether these interactions alter the translational profile of cells has not been investigated. Here we employ bacTRAP translational profiling to demonstrate that Purkinje neurons ectopically expressing 90 CGG repeats exhibit a dramatic change in their translational profile even prior to the onset of riboCGG-induced phenotypes. This approach identified nearly 500 transcripts that are differentially associated with ribosomes in r(CGG)90-expressing mice. Functional annotation cluster analysis revealed broad ontologies enriched in the r(CGG)90 list, including RNA binding and response to stress. Intriguingly, a transcript for the Tardbp gene, implicated in a number of other neurodegenerative disorders, exhibits altered association with ribosomes in the presence of r(CGG)90 repeats. We therefore tested and showed that reduced association of Tardbp mRNA with the ribosomes results in a loss of TDP-43 protein expression in r(CGG)90–expressing Purkinje neurons. Furthermore, we showed that TDP-43 could modulate the rCGG repeat-mediated toxicity in a Drosophila model that we developed previously. These findings together suggest translational dysregulation may be an underlying mechanism of riboCGG-induced neurotoxicity and provide insight into the pathogenicity of FXTASBAC-trap studies of Purkinje cels in normal and mutant mice
Looking for cell type specific gene expression differences caused by mutation in FMR1 using BAC-Trap RNA capture assay. A cutoff value of 4.5 for mean probe_set mean across all 18 hybridizations was used to determine a cutoff for expression in Purkinje cells.  This 16040 corresponded to a mean value of at least 3.4323 in the 4week time point.

overall_design: L7CGG90Fmr1:Pcp2 BAC (r(CGG)90 BAC) and wild-type:L7/Pcp2 BAC (WT BAC) transgenic mice used in this study have a 50% C57B6 and 50% FVB genetic background and were derived from the same parents by crossing L7CGG90Fmr1 heterozygote transgenics (100% C57B6 background) with L7/Pcp2eEGFPL10a BAC homozygous transgenics (100% FVB background). All mice reported were F1 progeny and were therefore hemizygous for one or both transgenes. Littermate wild-type mice were used for all experiments whenever possible.

first: Jocelyn

last: Galloway

first: Deena

last: Parghbi

first: Mickael

last: Poidevin

first: Peng

last: Jin

first: Edward

last: Chen

first: David

last: Nelson


title: Restoring Systemic GDF11 Levels Reverses Age-Related Dysfunction in Mouse Skeletal Muscle

status: Public on May 08 2014

city: Boston

first: Amy

middle: J

last: Wagers

state: MA

address: One Joslin place

department: Stem Cell and Regenerative Biology

institute: Joslin diabetes center and Harvard University

summary:
In this study, we investigated signaling pathways in Skeletal muscle precursors that are altered with aging and age-related deficits in muscle regenerative potential. We performed fluorescence activated cell sorting (FACS) to obtain highly purified skeletal muscle satellite cells from young, middle-aged and old mice.
Parabiosis experiments indicate that impaired regeneration in aged mice is reversible by exposure to a young circulation, suggesting that young blood contains humoral "rejuvenating" factors that can restore regenerative function. Here, we demonstrate that the circulating protein growth differentiation factor 11 (GDF11) is a rejuvenating factor for skeletal muscle. Supplementation of systemic GDF11 levels, which normally decline with age, by heterochronic parabiosis or systemic delivery of recombinant protein, reversed functional impairments and restored genomic integrity in aged muscle stem cells (satellite cells). Increased GDF11 levels in aged mice also improved muscle structural and functional features and increased strength and endurance exercise capacity. These data indicate that GDF11 systemically regulates muscle aging and may be therapeutically useful for reversing age-related skeletal muscle and stem cell dysfunction.

overall_design: We used  Affymetrix Mouse Genome array to identify global transcriptional changes associated with age in skeletal muscle precursors.

first: Manisha

last: Sinha

first: Young

middle: C

last: Jang

first: Juhyun

last: Oh

first: Danika

last: Khong

first: Elizabeth

middle: Y

last: Wu

first: Rohan

last: Manohar

first: Christine

last: Miller

first: Samuel

middle: G

last: Regalado

first: Francesco

last: Loffredo

first: James

middle: R

last: Pancoast

first: Michael

middle: F

last: Hirshman

first: Jessica

last: Lebowitz

first: Jennifer

middle: L

last: Shadrach

first: Massimiliano

last: Cerletti

first: Mi

last: Kim

first: Thomas

last: Serwold

first: Laurie

last: Goodyear

first: Bernard

last: Rosner

first: Richard

middle: T

last: Lee


title: Expression data from PML-RARα transgenic mouse APL(acute promyelocyte leukemia) cells

city: Shanghai

first: Jiang

last: Zhu

address: 197, rui-jin 2nd Road

country: China

institute: Shanghai institute of hematology

summary:
The differentiation of leukemia stem cells (LSCs) is generally regarded as a one-way alterative process to self-renewal. However, how differentiation impacts LSC stemness has largely been unexplored. Here we show that before reaching terminal differentiation (TD), apical LSCs of mouse acute promyelocytic leukemia passed through a partial differentiation (PD) stage, wherein the leukemia cells re-initiated leukemia via de-differentiation albeit at a reduced rate. Notably, while retinoic acid (RA) preferentially drove the transition of LSC to PD, monocytic Irf8 skewed PD cells to terminal maturation over de-differentiation and/or expansion. Remarkably, the combined use of RA and Irf8 induction depleted the total leukemogenic potential, which indicates that discrete stage- or lineage-specific mechanisms elaborate a step-wise LSC differentiation.
We used microarrays to detail the global programme of gene expression indicating the molecular mechanisms unerlying the the process of LSC step-wise differentiation.

overall_design: Retroviral GFP-labled mouse APL cells (bone marrow sample) were repopulated in vivo through transplantation into syngenic recipients. At the proper time points, the GFP positive APL bone marrow cells were collected and sorted for UNSC, UNPD and UNTD samples through FACS. RA-PD and RA-TD cells were sorted from bone marrow tissue treated with ATRA (all trans retinoic acid) for 5 days. The freshly isolated samples were then lysed for RNA extration. Each sample had two biological replicates.

first: Fei

last: Ding

first: Jing

first: XiangZhen

last: Liu


title: Gene expression profiling of small intestinal epithelia in AP-1B KO mice

city: Tsuruoka

first: Shinji

last: Fukuda

state: Yamagata

address: 246-2 Mizukami, Kakuganji

department: Institute for Advanced Biosciences

country: Japan

institute: Keio University

summary: To elucidate the function of AP-1B in small intestinal epithelia, which is well known as one of the components of the AP-1 clathrin adaptor complex, gene expression profiling of AP-1B KO mice was performed.

overall_design: Small intestine of AP-1B +/- and -/- mice were dissected and soaked in Hank's Buffered Salt Solution (HBSS) (GIBCO) containing 30 mM EDTA. After incubation on ice for 20 min, IECs were isolated by manipulation with a fine needle under stereomicroscopic monitoring (n=2).

first: Koji

last: Hase

first: Hiroshi

last: Ohno


title: Gene expression changes induced by Evi1 withdrawal in Evi1 dependent myeloid clone C6

city: Hannover

first: Adrian

last: Schwarzer

address: Carl-Neuberg-Str. 1

department: Experimental Hematology

country: Germany

institute: Hannover Medical School

summary: The transcription factor Evi1 is essential for the formation and maintenance of hematopoietic stem cells, and induces clonal dominance with malignant progression upon constitutive activation by chromosomal rearrangements or transgene integration events. To understand the immediate and adaptive response of primary murine hematopoietic cells to the transcriptional upregulation of Evi1, we developed an inducible lentiviral vector system with a robust expression switch. We found that Evi1 delays differentiation and promotes survival in myeloid culture conditions, orchestrating a battery of genes involved in stemness (Aldh1a1, Ly6a [Sca1], Abca1, Epcam, among others). Importantly, Evi1 suppresses Cyclins and Cyclin-dependent kinases (Cdk), while it upregulates Cdk inhibitors, inducing quiescence in various proliferation-inducing cytokine conditions and operating in a strictly dose-dependent manner. Hematopoietic cells with persisting Evi1-induction tend to adopt a relatively low expression level. We thus classify Evi1 as a dormancy-inducing oncogene, likely requiring epigenetic and genetic compensation for cell expansion and malignant progression.

overall_design: Evi1 dependent myeloid clone C6 cells expressing a Doxycyclin inducible codon-optimized murine Evi1 were harvested at day 2 after DOX withdrawal and compared to C6 cells under Doxycyclin 1 ug/ml

first: Olga

last: Kustikova


title: Subtype-dependent prognostic relevance of an interferon-induced pathway metagene in human node negative breast cancer

city: Milan

first: Maurizio

last: Callari

address: Via Amadeo, 42

country: Italy

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

summary: We identified and validated the pivotal role for a metagene containing IFN-induced genes in association to higher metastatic potential as a function of the specific molecular subtype

overall_design: Fresh frozen primary tumors were collected at the time of diagnosis from 123 patients with operable breast cancer previously untreated and undergoing radical or conservative surgery at the Istituto Nazionale Tumori of Milano (INTM) between1990 and 1998. All patients were pathologically defined as axillary node negative and were not submitted to any type of adjuvant systemic treatment until relapse. Patients were selected in order to have a comparable pattern of classical risk factors (age, tumor size).

first: Maria

last: Daidone


title: Hematopoietic stem cell quiescence attenuates DNA damage repair and response contributing to age-dependent DNA damage accumulation

city: Stanford

first: Jun

last: Seita

state: CA

address: Lokey Stem Cell Building #G3101, 265 Campus Drive

department: Institute for Stem Cell Biology and Regenerative Medicine

institute: Stanford University

type:
Expression profiling by array
Third-party reanalysis

summary: Comprehensive analysis of gene expression in hematopoietic stem and progenitor cells from young and old mice.

overall_design: Gene expression profiling of young and old mouse hematopoietic stem and progenitor cells by Gene Expression Commons system.

first: Isabel

last: Beerman

first: Matthew

middle: A

last: Inlay

first: Irving

last: Weissman

first: Derrick

last: Rossi


title: Exon array expression profiling: DYRK1A acts as transcriptional activator

city: Paris

first: Suk Min

last: JANG

address: 25 rue du Dr-Roux

department: Biologie Development

country: France

institute: Institut Pasteur

summary:
Transcriptome analysis of depletion of DYRK1A in HeLa cells
Global gene expression profiling has shown upregulation of many genes in the context of DYRK1A depletion in HeLa cells. Many of these genes deregulated by DYRK1A are involved in immune response system.

overall_design: Transcriptome analysis of siRNA against DYRK1A transfected in HeLa cells on GeneChip® Human Exon 1.0 ST Arrays (Affimetrix). Control HeLa cells have been transfected with the same concentration of siRNA non-targeting (siNT). Experiment has been done experimental triplicates.

first: Suk

last: Jang

first: Saliha

last: Azebi

first: Guillaume

last: Soubigou

first: Christian

last: Muchardt


title: Regulation of gene expression by Set-beta in rat retinal ganglion cells

status: Public on Apr 30 2014

city: Farmington

first: Ephraim

last: Trakhtenberg

state: CT

address: 263 Farmington Ave. RM L4005

department: Neuroscience

institute: University of Connecticut School of Medicine

summary: The goal of this experiment was to investigate the molecular mechanism of how Set-beta regulates neurite growth. Set-beta’s subcellular localization is regulated by posttranslational modifications. We found that Set-beta suppresses neurite growth of purified postnatal rat retinal ganglion cell (RGC) primary neurons when it is overexpressed in the nucleus, whereas recruiting Set-beta to cellular membrane by fusing myr-tag to its N-terminus promotes neurite growth. Here, we transfected purified by immunopanning postnatal rat RGC with wild-type Set-beta which localizes to the nucleus, myr-Set-beta which is recruited to cellular membranes, and mCherry control, and analyzed with microarrays Set-beta’s subcellular localization-dependent effects on gene expression. We found that wild-type Set-β regulated expression of significantly more genes than myr-Set-β, consistent with wild-type Set-β’s nuclear localization and previously described roles in regulating transcription. These data reveal potential downstream gene effectors regulating neurite growth, and specific candidate genes could be validated and tested in future experiments.

overall_design: Acutely purified by immunopanning postnatal day 4 (P4) retinal ganglion cells (RGCs) transfected with mCherry, wild-type Set-β, and myr-Set-β, and co-transfected with pMAX-GFP (Lonza) constructs, were plated at high density on uncoated glass Lab-Tek II chamber slides (Thermo Fisher Scientific). The following morning, after gentle trituration, GFP-positive cells were FACS-isolated at 37°C in PBS with BD FACSAria I cell sorter at 20 psi using a 130 µm nozzle; GFP-negative threshold was set by first processing untransfected RGCs. Cells were gated on a FSC-A versus SSC-A plot to exclude dead cells and/or debris, and aggregates were removed using single cell gating with FSC-H versus FSC-W and SSC-H versus SSC-W plots. Immediately after isolation, GFP-positive cells were diluted in pre-equilibrated growth medium, centrifuged 15 minutes at 80 g, resuspended in growth medium in a 48-well tissue culture plastic plate as above, and cultured 2 more days in growth medium, as above. The Quick-RNA MicroPrep kit (R1050, Zymo Research) was used for RNA extraction 3 days after transfection, according to the manufacturer's instructions. Total RNA were used as input for the whole transcriptome amplification Ovation Pico WTA System V2 kit (3302-12, NuGEN), the cDNA product was quantified with Nanodrop 8000 Spectrophotometer (Thermo Scientific) and its quality was examined with a Bioanalyzer 2100 using the Nano 6000 kit (Agilent). 5 µg of cDNA product from each sample was used as input for fragmentation and labeling using the Encore Biotin Module kit (4200-12, NuGEN); the fragmentation product quality was tested as above. The labeled product was hybridized to whole genome GeneChip Rat Gene 2.0 ST Arrays (Affymetrix). The staining, washing and scanning of the arrays was carried out using a Fluidics 450 station, GeneChip Operating Software and GeneChip Scanner 3000 7G (Affymetrix). Image intensities were analyzed with Expression Console (Affymetrix) from CEL files for quality control using standard GeneChip Rat Gene 2.0 ST Array control probes (Affymetrix), and to determine the RMA expression values and for annotations. RMA expression values were normalized to the median for each sample.

first: Yan

last: Wang

first: Melina

middle: I

last: Morkin

first: Stephanie

last: Fernandez

first: Gregory

last: Mlacker

first: Jesse

last: Shechter

first: Xiongfei

last: Liu

first: Karan

middle: H

last: Patel

first: Allison

last: Lapins

first: Steven

last: Yang

first: Susan

last: Dombrowski

first: Jeffrey

last: Goldberg


title: Expression profiling in control and YY1 knockout mouse intestinal crypt epithelia

status: Public on Apr 29 2014

city: Piscataway

first: Michael

middle: P

last: Verzi

state: NJ

address: 145 Bevier Road

department: Genetics

institute: Rutgers, the State University of New Jersey

summary: Crypts were isolated from either control or YY1f/f; Vil-Cre-ERT2 mice treated with tamoxifen for 4 days to induce knockout

overall_design: Jejunal crypt epithelia were isolated and processed for microarray

first: Ansu

last: Perekatt

first: Mike


title: Gene expression profiles in HepG2 cells exposed to atorvastatin

status: Public on Apr 26 2014

city: Oslo

first: Camilla

last: Stormo

address: Kirkeveien 166

country: Norway

institute: Oslo University Hospital

summary:
In the exon array data set, gene level analysis was performed on HepG2 cells exposed to atorvastatin.
No genes were found to be statistically significantly differentially expressed upon atorvastatin treatment.

overall_design: 3 control and 3 atorvastatin treated HepG2 samples were analysed. Genes with an FDR≤5% after Benjamini-Hochberg correction was considered as differentially expressed.

first: Ole

middle: K

last: Olstad

first: Marianne

last: Kringen

first: Robert

last: Lyle

first: Daniel

last: Sachse

first: Jens

last: Berg

first: Armin

last: Piehler


title: Expression data from human THP-1 monocytes stimulated with increasing concentrations of arachidonic (AA) or oleic acid (OA).

status: Public on Apr 27 2014

city: Irapuato

first: Gertrud

last: Lund

state: Guanajuato

address: Km 9.6 del Libramiento Norte Carretera Irapuato-León SN

department: Genetic Engineering

country: Mexico

institute: CINVESTAV Irapuato

summary:
Previous data indicated tha AA and OA modify global DNA methylation. This study analyzes the impact of these fatty acids on expression as a complement to array-based DNA methylation data.
In this dataset, we include the expression data obtained from THP-1 monocyte stimulated with 1, 10 or 100uM AA or OA for 24h.

overall_design: RNA extracted from the same cells used for array-based DNA methylation analysis (see corresponding data in published article) was used to produce expression data by Affymetrix Human Exon 1.0 ST v2 Array

first: Guillermo

last: Silva-Martinez

first: Silvio

last: Zaina


title: Expression data from WT and Snail1 knockout (KO) embryonic endothelial cells (ECs)

status: Public on Apr 24 2014

city: Ann Arbor

first: Zhaoqiu

last: Wu

state: MI

address: 210 Washtenaw Ave

department: Life Sciences Institute

institute: University of Michigan

summary: Snail1 is a master factor of epithelial to mesenchymal transitioin (EMT), however, its role in embryonic vascular development is largely undefined. We used microarrays to compare the global programme of gene expression between cultured WT and Snai1 KO embyronic ECs.

overall_design: ECs isolated from E10.5 Snail1f/f embryos were infected with adeno-βGal or -Cre to generate WT and Snail1 KO ECs. RNA were collected for Affymetrix microarrays.

first: Stephen

last: Weiss


title: Expression data from kidneys of diabetic WT and T3-/- mice

status: Public on Apr 25 2014

city: Roma

first: Ivan

last: Arisi

address: viale Regina Elena 295

department: Bioinformatics Facility

institute: European Brain Research Institute

summary: Activation of A Disintegrin and A Metalloprotease Domain17 (ADAM17) is involved in nephropathy, but the role of this metalloprotease and its inhibitor TIMP3 in diabetic kidney disease is unclear. We used microarray profiling to find genes differentially expressed in the 2 genotypes which could explain the more severe diabetic kidney disease features observed in T3-/- mice compared to the WT littermates.

overall_design: Total RNA was extracted from 3 WT and 3 Timp3-/- diabetic kidneys

first: Loredana

last: Fiorentino

first: Massimo

last: Federici


title: Regulation of gene expressions in vivo by anti-VEGF and anti-Notch therapy [Mouse430_2]

city: Oxford

first: Francesca

last: Buffa

address: The Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

summary: U87-EV human glioblastoma xenograft tumours is therapeutically treated by bevacizumab, a humanized anti-human VEGF mAb, or dibenzazepine (DBZ) when tumour is established in BALB/c SCID mice. At the end point, collect tumour samples and extracted total RNA for microarray to investigate the gene profile changes compared to control. These include the genes from human tumour cells and mouse host stroma cells.

overall_design: 5 control, 5 dibenzazepine-treated, and 4 bevacizumab-treated samples

first: Adrian

last: Harris


title: Comparison of Treg and Teff cells in healthy and COPD smokers.

status: Public on Apr 19 2014

city: Philadelphia

first: Wissam

last: Chatila

state: PA

address: 3500 N. Broad St.

institute: Temple University

summary: Rationale:  COPD is characterized by an abnormal regulatory T cell (Treg) response and increases in Th1 and Th17 cell responses.  It is unclear if dysregulation of miRNAs within Treg alters the adaptive immunophenotype in COPD.   Objectives: To compare the miRNA profile of COPD Treg cells with that of healthy controls and to explore the function of differentially expressed miRNAs.      Methods:  Treg cells (CD4+CD25+CD49-CD127-) and T effector (CD4+CD25-) cells were obtained from the peripheral blood of 4 nonsmokers, 4 healthy current smokers, and 4 COPD current smokers for analysis of miRNA expression, matching them for age and sex. We assessed expression initially by microarray analysis on the Illumina miRNA platform then conducted real time RT-PCR validation of the microarray results.

overall_design: 24 samples were analyzed. 8 from each patient group of healthy Normal, Healthy Smoker, and COPD Smoker.


title: Expression variation between VHLR200w homozygous verse wildtype control

status: Public on Apr 23 2014

city: Chicago

first: Xu

last: Zhang

state: Illinois

address: 820 South Wood St

institute: University of Illinois at Chicago

summary: Hypoxia may cause pulmonary and brain edema, pulmonary hypertension, aberrant metabolism and early mortality. To better understand pathological processes associated with hypoxia, we examined gene expression in Chuvash polycythemia (CP) blood mononuclear cells. CP is a congenital disorder of up-regulated hypoxic response at normoxia wherein VHLR200W homozygosity leads to elevated hypoxia inducible factor (HIF)-1 and HIF-2 levels, thromboses, pulmonary hypertension, lower systemic blood pressure (SBP) and increased mortality. VHLR200W homozygotes are often treated by phlebotomy resulting in iron deficiency, allowing us to evaluate an interaction of augmented hypoxia sensing with iron deficiency.

overall_design: Expression was profiled for 8 VHLR200W homozygotes (CP21, CP23, CP26_2, CP37, CP40, CP43, CP45, CP46) and 17 VHL wildtype individuals (CP48, CP49, CP50, CP51, CP52, CP53, CP55, CP57, CP58, CP59, CP61, CP62, CP63, CP65, CP66, CP67_2, CP68), matched for normal iron status as reflected in serum ferritin concentration. Additional studies including 16 VHLR200W homozygotes with low ferritin (CP22, CP24, CP25, CP28, CP29, CP30, CP31, CP32, CP34, CP35, CP36, CP39, CP41, CP42, CP44, CP47) indicated that iron deficiency generally affects the induction effect of VHLR200W. Two wildtype individuals (CP54, CP56) had no serum ferritin concentration record and two wildtype individuals (CP60, CP64) were defined as iron deficiency subject, which were not included in further expression analysis.

first: Wei

first: Shwu-Fan

last: Ma

first: Galina

last: Miasniakova

first: Adelina

last: Sergueeva

first: Tatiana

last: Ammosova

first: Min

last: Xu

first: Sergei

last: Nekhai

first: Josef

last: Prchal

first: Michael

last: Wade

first: Joe

last: Garcia

first: Roberto

last: Machado

first: Victor

last: Gordeuk


title: Expression data from quiescent and activated neural stem cells from the adult mouse V-SVZ niche

status: Public on May 07 2014

city: NYC

first: Fiona

last: Doetsch

address: 630 West 168th St

institute: Columbia University

summary: RNA was purified from GFAP::GFP+CD133+ and GFAP::GFP+CD133+EGFR+ cells isolated from the adult mouse V-SVZ niche (GFAP::GFP mice, Jackson Mice Stock number 003257)

overall_design: 6 samples consisting of two conditions of three biological replicates each were analyzed

first: Paolo

last: Codega

first: Violeta

last: Silva-Vargas

first: Alex

last: Paul

first: Angel

last: Maldonado-Soto

first: Annina

last: DeLeo

first: Erika

last: Pastrana


title: The Cellular and Molecular Origin of Tumor-associated Macrophages

status: Public on Apr 18 2014

city: New York

first: Willey

last: Liao

address: 101 Avenue of the Americas

department: Bioinformatics

institute: New York Genome Center

summary: Long recognized as an evolutionarily ancient cell type involved in tissue homeostasis and immune defense against pathogens, macrophages are being rediscovered as regulators of several diseases including cancer.  Here we show that in mice, mammary tumor growth induces the accumulation of tumor-associated macrophages (TAMs) that are phenotypically and functionally distinct from mammary tissue macrophages (MTMs). TAMs express the adhesion molecule Vcam1 and proliferate upon their differentiation from inflammatory monocytes, but do not exhibit an “alternatively activated” phenotype. TAM differentiation depends on the transcriptional regulator of Notch signaling, RBPJ; and TAM, but not MTM, depletion restores tumor-infiltrating cytotoxic T cell responses and suppresses tumor growth.  These findings reveal the ontogeny of TAMs and a discrete tumor-elicited inflammatory response, which may provide new opportunities for cancer immunotherapy.

overall_design:
MMTV-PyMT mice (Jackson Laboratory) were backcrossed to the C57BL/6 background for 10 generations.  Rbpjfl/fl mice were provided by Tasuku Honjo and crossed to CD11ccre mice provided by Boris Reizis. Littermate controls were used in all experiments when possible.  All mice were maintained in a specific pathogen-free facility and animal experimentation was conducted in accordance with institutional guidelines.
In the MMTV-PyMT spontaneous mammary tumor model, we found the key Notch transcriptional regulator, RBPJ, to be required for TAM terminal differentiation from inflammatory monocytes. The bulk myeloid cell population that remains in CD11cCreRbpj fl/fl mice (the cells in "Rbpj KO" samples), represents monocytes that have begun their differentiation into macrophages, but are unable to terminally differentiate due to the lack of Rbpj.

first: Ruth

last: Franklin

first: Will

first: Abira

last: Sarkar

first: Myoungjoo

last: Kim

last: Bivona

first: Kang

last: Liu

first: Eric

last: Pamer

first: Ming

middle: O

last: Li


title: Hes6 expression is controlled by c-Myc and the AR to promote E2F1 activity and poor outcome in castrate-resistant prostate cancer (cMyc ChIP-seq)

status: Public on Apr 17 2014

city: Cambridge

first: Roslin

last: Russell

address: Robinson Way

institute: Cambridge Research Institute, Cancer Research UK

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Hes6 is a transcription co-factor that is associated with stem cell characteristics in neural tissue, but its role in cancer remains uncertain. Here we show that Hes6 is controlled by c-Myc and the AR and can drive castration resistance in xenografts of the androgen-dependent LNCaP prostate cancer cell line model. Hes6 activates a cell cycle enhancing transcriptional network that maintains tumour growth in the absence of circulating androgen but with maintained nuclear AR. We demonstrate interaction between E2F1, the AR and Hes6 and show the co-dependency of these factors in the castration-resistant setting. In the clinical setting, we have discovered a Hes6-associated signature that predicts poor outcome in prostate cancer, which could be pharmacologically targeted.

overall_design: Myc ChIPseq on LNCaP cells.

first: Alastair

middle: D

last: Lamb

first: Antonio

last: Ramos-Montoya


title: A luteal phase deficiency model in normal women: structural and functional responses to varying concentrations of progesterone

city: Porto Alegre

first: Ricardo

last: Savaris

state: Rs

address: Rua Ramro Barcelos 2350/1124

department: Ginecologia e Obstetrícia

country: Brazil

institute: Universidade Federal do Rio Grande do Sul

summary: Progesterone (P) action is essential for embryo implantation, but the P concentration required for normal receptivity remains unclear. We use an in vivo model in normal women that abolishes detectable endogenous P production, allowing experimental provision of P. Endometrial samples on the 10th day of varying doses of P exposure are compared structurally and functionally with each other and with mid-secretory endometrium of natural cycles, using histological and microarray analysis. At 2.5mg/day of P, a delayed appearance of morphological features is seen. Higher sub-physiological levels of P result in normal morphology, but aberrant gene expression. These studies prove that low P levels can result in histological delay, consistent with clinical expectations. However, P levels required for consistent histological delay are lower than those seen in all ovulatory women. These studies also demonstrate that gene expression abnormalities can occur at higher sub-physiological P concentrations, without a change in morphology, a functional-morphological disassociation. The expression of some endometrial receptivity associated genes is multiphasic, with peak expression between the lowest and highest doses, suggesting sustained supraphysiological doses seen in fertility treatment cycles may not be optimal. These findings provide a scientific underpinning to previous studies that questioned the value of endometrial morphology as a marker for receptive endometrium and suggest potential new strategies for understanding endometrial P action.

overall_design: Total RNA obtained endometrium of women treated with progesterone at different doses (2.5 mg (n=4); 5 mg (n=4); 10mg (n=5_); 40 mg (n=5); Control no drug (n=9))

first: S

last: Young


title: Expression data from the transplanted mouse islets into hyperglycemic and normoglycemic mice at 6 hours post-transplantation

city: Yokohama

first: nobuaki

last: shiraki

address: 4259-B-25 Nagatsuta-cho, Midori-ku

department: School of Life Science and Technology

institute: Tokyo Institute of Technology

summary:
insulin treatment protects islets from the initial rapid loss that is usually observed after transplantation and positively affects the outcome of islet transplantation in Akita mice.
To study the molecular mechanism underlying the improved islet survival, expression profile analyses was performed to analyze the differences between the grafts transplanted into hyperglycemic and normoglycemic mice at 6 hours post-transplantation

overall_design: Cells were harvested at grafts for RNA extraction and hybridization on Affymetrix microarrays. We performed gene expression profiles of the transplanted mouse islets into hyperglycemic and normoglycemic mice at 6 hours post-transplantation

first: Nobuaki

last: Shiraki

first: Tomonori

last: Tsuyama


title: Gene expression profile alone is inadequate in predicting complete response in multiple myeloma

status: Public on Apr 21 2014

city: Boston

first: Nikhil

last: Munshi

address: 450 Brookline Ave, DB106

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary:
We have analyzed gene expression microarray datasets from four different clinical trials to assess accuracy of gene expression based signature in predicting treatment complete response in patients with multiple myeloma. Two of four datasets were made available via The Intergroupe Francophone du Myélome (IFM) group, and remaining two datasets were downloaded from NCBI GEO portal with accession IDs: GSE19784 (HOVON65/GMMG-HD4 trial) and GSE9782 (APEX/SUMMIT trial). Analysis UUID: datasets_archive--2afcd42a-7e12-11e3-9145-5fcc1e060548--15-Jan-2014-12-23-44-CST.
Following dataset provides gene expression microarray dataset for IFM-2005 trial involving 67 newly diagnosed patients with MM. A second and larger dataset involving 136 newly diagnosed patients with MM from IFM-2005 trial can be accessed via NCBI GSE ID: GSE39754.

overall_design: CD-138 purified plasma cells from 67 newly diagnosed patients with MM were profiled using Affymetrix Exon-1.0 ST microarray platform. Pre-processing and normalization of dataset was carried out using dChip (http://www.hsph.harvard.edu/cli/complab/dchip/exon.htm#expressio) and R package - aroma.affymetrx (http://www.aroma-project.org/vignettes/FIRMA-HumanExonArrayAnalsis). Patients subsequently received bortezomib based induction therapy, followed by autologus stem cell transplant. Post-induction treatment response is attached in metadata file.

first: Stephane

last: Minvielle

first: Florence

last: Magrangeas

first: Herve

last: Avet-Loiseau

first: Philippe

last: Moreau

first: Cheng

first: Samirkumar

middle: B

last: Amin


title: Hes6 expression is controlled by c-Myc and the AR to promote E2F1 activity and poor outcome in castrate-resistant prostate cancer (E2F1 ChIP-seq)

overall_design: E2F1 ChIPseq on LNCaP cells.


title: Diverse intracellular pathogens activate Type III Interferon expression from peroxisomes

status: Public on Apr 15 2014

first: Jonathan

last: Kagan

address: 300 Longwood Ave, Enders 649

institute: Children's Hospital Boston

summary:
Detection of viral RNA in the cytosol of infected cells depends on RIG-I-lilke recptors that use MAVS as an adapter protein to activate antiviral gene expression. MAVS is
tail-anchored on mitochondria, mitochondria-associated membranes and peroxisomes. As peroxisomal membrane proteins can be mistargeted to mitochondria in the absence
of peroxisomes, we hypothesized that MAVS-dependent antiviral gene expression is activated more efficiently in this instance. Pex19 deficient skin firoblasts derived from a
Zellweger syndrome patient lack peroxisomes. We introduced wild type Pex19 into these cells to restore peroxisome formation and assessed alterations in
the gene expression profile of these cells after reovirus infection.

overall_design: 6 samples: 9 and 16 hrs after reovirus infection at an MOI of 100 total RNA was extracted from Pex19 reconstituted and deficient cell lines. Gene expression data was compared to uninfected cells.

first: Evelyn

last: Dixit


title: Identification of targets regulated by MLL1 in response to HSP90 inhibitors

city: cambridge

first: yaoyu

last: chen

state: Massachusetts

address: 250 Mass ave

department: ONC

institute: NIBR

summary: MLL1 WT or KO MEF with and without HSP90 inhibitor treatment

overall_design: MEF cells were seeded in 6-well plates for 3d with 100ng/ml doxycycline prior to treatment with 0.1% DMSO or 100nM AUY922 for 3h

first: Jinyun

last: Chen


title: Zbtb20-mediated repression of genes in developing CA1 pyramidal neurons

status: Public on Apr 11 2014

city: Odense

first: Mads

last: Thomassen

address: Soender Boulevard 9

department: Clinical Genetics (KKA)

country: Denmark

institute: Odense University Hospital

summary: The transcriptional repressor Zbtb20 is essential for specification of hippocampal CA1 pyramidal neurons. Moreover, ectopic expression of Zbtb20 is sufficient to transform subicular and retrosplenial areas of D6/Zbtb20S mice to CA1. We used microarrays to identify genes that are repressed by Zbtb20 in developing CA1 pyramidal neurons in the CA1-transformed cortex of D6/Zbtb20S mice.

overall_design: For RNA extraction and hybridization on Affymetrix microarrays, we isolated the CA1-transformed subiculum and retrosplenial cortex from postnatal day 1 D6/Zbtb20S mice, as well as corresponding areas from their wildtype littermates. Total RNA was extracted using the RNeasy Lipid Tissue Mini Kit (Qiagen). Each RNA sample represents a pool of RNA obtained from dissected tissues of seven animals.

first: Jakob

middle: V

last: Nielsen

first: Jens

last: Noraberg

first: Torben

last: Kruse

first: Niels

last: Jensen


title: Expression data from 5 paired of gastric cancer tissues and gastric normal tissues

status: Public on Apr 16 2014

city: Changchun

first: Jihan

last: Wang

address: 126, Xinmin Street

institute: Jilin University

summary: In this dataset, we include the expression data obtained from gastric cancer tissues and gastric normal tissues to determine the differentially expressed genes in gastric cancer tissues

overall_design: 10 tissues (5 paired of gastric cancer vs.normal tissues) were analysed. We generated the following pairwise comparisons:C1 VS.N1;C2 VS.N2;C3 VS.N3;C4 VS.N4;C5 VS.N5; genes with a fold-change ≥2 were selected

first: Fan

last: Li


title: Inflammation induced repression of Foxp3-bound chromatin in regulatory T cells [microarray]

status: Public on Apr 12 2014

first: Aaron

last: Arvey

institute: Memorial Sloan-Kettering Cancer Center

summary:
The transcription factor Foxp3 is indispensable for the ability of regulatory T (Treg) cells to suppress fatal inflammation. Here, we characterized the role of Foxp3 in chromatin remodeling and regulation of gene expression in actively suppressing Treg cells in an inflammatory setting. Although genome-wide Foxp3 occupancy of DNA regulatory elements was similar in resting and in vivo activated Treg cells, Foxp3-bound enhancers were poised for repression only in activated Treg cells. Following activation, Foxp3-bound sites showed reduced chromatin accessibility and selective H3K27 tri-methylation, which was associated with Ezh2 recruitment and downregulation of nearby gene expression. Thus, Foxp3 poises its targets for repression by facilitating formation of repressive chromatin in regulatory T cells upon their activation in response to inflammatory cues.

The supplementary file GSE55705_dt_expr.txt is a matrix for Treg expression data from platform GPL1261 that includes co-normalized data from GSE40685.

overall_design: array expression

first: Joris

last: van der Veeken

first: Robert

middle: M

last: Samstein

first: Alexander

last: Rudensky


title: Comparative Iron Oxide Nanoparticle Cellular Dosimetry and Response in Mice by the Inhalation and Liquid Cell Culture Exposure Routes

city: Corvallis

first: Susan

middle: C.

last: Tilton

state: OR

address: 1007 ALS Bldg

department: AG Envr & Molec Toxicology

institute: Oregon State University

summary:
To identify the molecular impact of SPIO nanoparticle inhalation exposure on lung tissue.
Transcriptional responses were measured by global microarray analysis of mouse lung.

overall_design: Male Balb/c mice were exposed to aerosolized SPIO nanoparticles using a nano-aerosol generation and inhalation system . Exposure was performed using two groups of 30 male Balb/c mices (60 total).  One group of 30 was exposed to aerosolized SPIO nanopartic

middle: C

first: Brian

last: Thrall


title: Ectopic Expression data of TLX1 in Hematopoietic Progenitors in TLX1 Transgenic Mice Deficient in DNA-PK

status: Public on Apr 05 2014

city: North York

first: Yan Zhen

last: Zheng

address: 2075 Bayview Avenue

country: Canada

institute: Sunnybrook Research Institute

summary:
The noncluster homeodomain containing gene, HOX11/TLX1 (TLX1) is detected at the breakpoint of the t(10;14)(q24;q11) chromosome translocation in patients with T cell Acute Lymphoblastic leukemia (T-ALL). This translocation results in the inappropriate expression of TLX1 in T cells. The oncogenic potential of TLX1 was demonstrated in IgHµ-TLX1Tg mice, which developed mature B cell lymphoma after a long latency period suggesting the requirement of additional mutations to initiate malignancy.
To determine whether dysregulation of genes involved in the DNA damage response contributed to tumor progression, we crossed IgHµ-TLX1Tg mice with PrkdcScid/Scid mice; To identify the molecular pathways dysregulated in the earliest stages of TLX1-induced transformation, we used Affimetrix microarrays to compare gene expression profiling of premaliganant thymocytes (6~8 weeks old): DN1, DN2 and DN3 stages from HOX11 transgenic PrkdcScid/Scid (HOXSCID) mice with the same stage thymocytes from the sex and age matched control PrkdcScid/Scid (SCID) mice.  Expression analysis of IgH-TLX1TgPrkdcScid/Scid thymocytes revealed dysregulated expression of cell cycle, apoptotic, mitotic spindle and anaphase-promoting complex genes in double negative (DN) 2 and DN3 stage thymocytes. Moreover, DN1, DN2 and DN3 TLX1-expressing thymocytes showed downregulated expression of ribosomal and mitochondria ribosomal protein genes.

overall_design: Four groups of double mutant IgH-HOX11TgPrkdcScid/Scid mice and four groups of  control PrkdcScid/Scid mice were sacrificed at the age of 6~8 weeks and the fresh thymocytes were FACS sorted by markers CD25 and CD44 to DN1, DN2 and DN3 stages. To minimize the sample variability caused by individual differences among animals, about 2 ~5 the same phenotype, stage and sex thymocytes were pooled (total 104 ~ 105 cells) and used as one sample each for RNA extraction and hybridization on Affymetrix microarrays.

first: Yanzhen

first: Konstantin

last: Krutikov

first: Edwin

first: Margaret

last: Hough


title: Expression data from CD4+ T cells of germ free mice, SPF IQI mice and SPF C57BL/6 mice depletd with Uhrf1 (by Cd4Cre-Uhrf1flox/flox)

status: Public on Apr 07 2014

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

institute: RIKEN

summary: Commensal bacteria shapes gut immune system. Colonization bacteria increase the frequency of regulatory T cells, however, the molecular mechanisms has not yet been unknown. To reveal the mechanism, we isolated Treg cells and Non-Treg cells and performed the global expression analysis.

overall_design: Colonic lamina propria cells were isolated from mice described above. Treg cells and Non-Treg cells (also called as Tconv cells) were sorted by FACS AriaIII

first: T

first: Y

last: Furusawa

last: Obata

first: K

last: Hase


title: CMPF alters expression of genes related to metabolism in isolated mouse islets

status: Public on Apr 01 2014

city: Toronto

first: Michael

last: Wheeler

state: Ontario

address: 1 King's College Circle

department: Physiology

institute: University of Toronto

summary: CMPF is elevated in diabetes and is associated with impaired insulin secretion. We used microarrays to determine the effect of CMPF on gene expression in isolated islets.

overall_design: Isolated islets from male CD1 mice were treated for 24h with vehicle control or 200uM CMPF.

first: Kacey

middle: J

last: Prentice


title: Context-dependent actions of Exendin-4 on β-cell function and dynamic changes in islet gene expression over time in vivo

city: Coventry

last: Khan

address: Gibbet Hill Road

department: Life Sciences

institute: University of Warwick

summary: GLP-1 analogues, such as exendin-4, preserve functional β-cell mass in various model systems and are revolutionising management of type 2 diabetes. Yet, comparatively little is known about effectiveness in the face of severe β-cell depletion. Moreover, direct and sequential effects of exendin-4 on islet-specific gene expression over time in vivo are not well characterised. To address these issues and others, we have examined the time-dependent effects of exendin-4 treatment on β-cell mass regulation alongside accompanying changes in islet gene expression in vivo. Context-dependent actions were assessed by comparing effects on normal islets and also following massive toxigenetic β-cell ablation in pIns-MYCERTAM transgenic mice in vivo. Despite over 90% loss of β-cell mass, exendin-4 treatment normalised blood glucose and insulin levels in hyperglycaemic mice, though benefits rapidly waned on withdrawal of treatment. As exendin-4 did not arrest the decline in β-cell mass or turnover in this study, we could directly isolate effects on function of surviving β-cells. Improved glucose homeostasis was associated with dynamic changes in multiple islet genes and pathways in vivo favouring glucose-stimulated insulin secretion, such as Irs2, Pdx1, Sox4, glucokinase, and glycolysis pathway. Several key growth pathways and epigenetic regulators were also differentially expressed. Thus, even in the face of extensive β-cell loss exendin-4 can markedly improve hyperglycaemia by differential gene expression in surviving islet cells.

overall_design:
Activation of MYCERTAM was achieved through administration of 1mg of 4 hydroxytamoxifen (4OHT; Sigma-Aldrich, St. Louis, MO) by daily intraperitoneal injection. To assess the effect of exendin-4 on MYCER-induced hyperglycaemia, mice were given either twice-daily subcutaneous (sc) injections of exendin-4 (50ug/kg dissolved in 5mls water), or equivalent volumes of water vehicle, starting 2 days prior to 4OHT injections. For microarray analyses parallel mouse experiments were set up using 8-12 week old pIns-MYCERTAM male mice either treated with 4OHT or vehicle (peanut oil) and exendin-4 or vehicle, as described, for 4, 8, 16, 32 and 72 hours (n=3 for each time point and for each of four conditions; 4OHT and exendin-4 treated, peanut oil and exendin-4 treated, 4OHT and water treated, peanut oil and water treated).

!Sample_data_processing = After the quality control step, the following 8 samples out of 60 showing poor reproducibility were excluded from our further study: GSM930242, GSM930247, GSM930251, GSM930263, GSM930264, GSM930289, GSM930291, GSM930298.

first: James

last: Young

first: Yi-Fang

last: Wang

first: Sam

last: Robson

first: Sylvie

last: Abouna

first: Asta

last: Laiho

first: Attilla

last: Gyenesei

first: Leena

last: Kytömäki

last: Hermann

first: Martin

last: Weickert

first: Albert

last: Barberà

first: Stella

last: Pelengaris


title: Identification of spondylarthropathy-specific genes in BALB/c mice with proteoglycan-induced spondylitis (PGIS)

first: Tibor

last: Glant

state: IL

address: 1735 West Harrison

department: Orthopedic Surgery

institute: Rush University Medical Center

summary:
BALB/c mice develop peripheral arthritis (PGIA) and spondyloarthropathy (PGIS) upon repeated intraperitoneal injections of human cartilage proteoglycan (PG) aggrecan. The aim of the present study was to identify spondylitis-specific genes by comparing intervertebral disc (IVD) RNA samples from spondyloarthropathic and naïve BALB/c mice.

Keywords: Genetic modification

overall_design: We compared the gene expression data of 5 spondyloarthropathic and 3 naïve (control) mice.

first: Balint

last: Farkas

first: Ferenc

last: Boldizsar

first: Oktavia

last: Tarjanyi

first: Anna

last: Laszlo


title: Gene expression changes in CD4+ thymocytes upon removal of Cullin3

first: Rebecca

last: Mathew

address: GCIS, 929 E 57th Street

institute: The University of Chicago

summary:
We report gene expression changes in Cul3 deficient thymic CD4+ T cells
We used microarrays to detail the global programme of gene expression changes upon removal of Cul3 during thymic development

overall_design: CD25-, CD1dPBS57-, gdTCR - CD4+ Single positive cells from thymocytes of CD4Cre-Cul3fl/fl (LM) and CD4 Cre+Cul3fl/fl (KO) were sort purified and total RNA was extracted using Trizol and analysed by microarray.

first: Ai-ping

last: Mao

first: Andrew

last: Chiang

first: Clara

last: Bertozzi-Villa

first: Jeffrey

last: Bunker

first: Seth

last: Scanlon

first: Benjamin

last: McDonald

first: Michael

middle: G

last: Constantinides

first: Kristin

last: Hollister

last: Singer

first: Alexander

last: Dent

first: Aaron

middle: R

last: Dinner

last: Bendelac


title: NRROS negatively regulates ROS in phagocytes during host defense and autoimmunity

status: Public on Mar 31 2014

city: South San Francisco

first: Jason

last: Hackney

address: 1 DNA Way

department: Department of Bioinformatics and Computational Biology

institute: Genentech, Inc.

summary:
Production of reactive oxygen species (ROS) is one of the important antimicrobial mechanisms of phagocytic cells. Enhanced oxidative burst requires these cells to be primed with agents such as IFNg and LPS with a synergistic effect of these agents on the level of the burst. However, excessive ROS generation will lead to tissue damage and has been implicated in a variety of inflammatory and autoimmune disease. Therefore, this process needs to be tightly regulated. In order to understand the genes regulating this process, we will treat bone marrow derived macrophages with above mentioned priming agents and study the gene expression.
We used microarrays to determine the changes in gene expression that occur in bone marrow derived macrophages after treatment with IFNg, LPS, or a combination of IFNg and LPS

overall_design: Four condition experiment; Biological replicates: four replicates per condition

first: Rajkumar

last: Noubade

first: Kit

last: Wong

first: Naruhisa

last: Ota

first: Sascha

last: Rutz

first: Celine

last: Eidenschenk

first: Jiabing

last: Ding

first: Patricia

last: Valdez

first: Ivan

last: Peng

last: Sebrell

first: Patrick

last: Caplazi

last: DeVoss

first: Robert

last: Soriano

first: Zora

last: Modrusan

first: Tao

last: Sai

first: Wenjun

last: Ouyang


title: Expression data from cultured primary mouse dermal fibroblasts

status: Public on Mar 28 2014

city: Charlottesville

first: Yongde

last: Bao

state: VA

department: MIC

institute: UVa

summary:
In previous investigations, we detected that growth of melanoma cells in mice depleted for adam9 is enhanced. This resulted from molecular alterations in stromal cells cross-communicating to tumor cells and from constitutively altered expression of some molecules, e.g., TIMP1 in stromal fibroblasts lacking adam9.
We used microarray analysis to identify the gene expression alterations occurring in stromal cells upon adam9 deletion which lead to the molecular alterations observed and contribute to the tumor phenotype.

overall_design: Primary fibroblasts from adam9 KO and WT mice were cultured in standard conditions to address constitutive gene alterations.

first: Paola

last: Zigrino

first: Anna

last: Abety


title: Therapeutic potential of spleen tyrosine kinase inhibition for treatment of high-risk precursor B-cell acute lymphoblastic leukemia

status: Public on Mar 29 2014

first: Paul

last: Kowalski

address: PGCRL - 686 Bay St

department: Developmental and Stem Cell Biology

institute: The Hospital for Sick Children

summary:
This study revealed pathogenic role of pre-BCR-independent SYK activation in high-risk B-ALL.
Intensified and central nervous system (CNS)-directed chemotherapy has significantly improved outcomes for pediatric B-acute lymphoblastic leukemia (B-ALL), but confers significant late-effect morbidities. Moreover, many patients suffer relapses, underscoring the need to develop novel, molecularly targeted B-ALL therapies. Using a mouse model, we showed that leukemic B-cells require pre-B-cell receptor (pre-BCR)-independent spleen tyrosine kinase (SYK) signaling in vivo. In diagnostic samples from human B-ALL patients, SYK and downstream targets were phosphorylated regardless of pre-BCR expression or genetic subtype. Two small molecule SYK inhibitors, fostamatinib and BAY61-3606, attenuated growth of 69 B-ALL samples, including high-risk (HR) subtypes. Orally administered fostamatinib significantly reduced high disease burden after xenotransplantation of HR B-ALL samples into immune-deficient mice, and decreased leukemia dissemination into spleen, liver, kidneys and the CNS of recipients. Thus, SYK activation sustains growth of multiple HR B-ALL subtypes, suggesting that SYK inhibitors may improve outcomes for HR and relapsed B-ALL.

overall_design: B-cell leukemia samples (3) from a mutant mouse model were compared to sorted or cultured preB or proB cells from normal mice using Affymetrix GeneChip arrays.

first: Jayne

middle: S

last: Danska

middle: E


title: Gene expression analyses of PR action in the uteri of SRC-2 mutant mice

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: Ovarian estrogen (E2) and progesterone (P4) are indispensable for embryo-implantation and endometrial stromal decidualization; however, the molecular mechanisms that underpin these reproductive processes are unclear. Steroid receptor coregulator-2 (SRC-2) belongs to the multifunctional SRC/p160 family which also includes SRC-1 and SRC-3.  Sharing strong sequence homology, all three SRCs exert diverse regulatory effects by modulating the transcriptional potency of nuclear receptor family members, including the estrogen and progesterone receptor (ER and PR respectively).  Importantly, absence of SRC-2 in PR positive cells in the epithelial, stromal, and myometrial compartments of the murine uterus results in a striking infertility defect. This reproductive phenotype highlights a key role for SRC-2 in uterine function which is not shared with other coregulators. Intriguingly, abrogation of uterine SRC-2 does not block embryo apposition or attachment to the apical surface of luminal epithelial cells of the endometrium but rather prevents P4-dependent local decidualization of the sub-epithelial stroma.  Remarkably, epithelial-specific ablation of SRC-2 in the murine uterus does not compromise endometrial functionality, again underscoring the unique importance of stromal derived SRC-2 in uterine function. The stromal decidualization defect resulting from SRC-2 ablation is reflected at the molecular level by a marked attenuation in P4 responsive target genes known to be critical for P4 dependent decidualization (i.e. ERBB receptor feedback inhibitor 1, Follistatin and Fkbp5).  Conversely, the induction of E2 or P4 target genes involved in embryo implantation (i.e. leukemia inhibitory factor (LIF) and Indian hedgehog (Ihh) respectively) is not affected by SRC-2’s absence.  As with mouse studies, decidualization of primary human stromal cells (HESCs) in culture is blocked by SRC-2 knockdown; however, HESC decidualization is unaffected by knockdown of SRC-1 or SRC-3.  As a consequence of SRC-2 knockdown, molecular studies disclose a striking decrease in the induction of a subset of P4 target genes (i.e. WNT4 and FKBP5) which are essential for the stromal-epithelioid transformation step, the cellular hallmark of endometrial decidualization.  Collectively, these studies not only showcase the evolutionary importance of SRC-2 in endometrial biology but also suggest that deregulation of this coregulator may underpin a spectrum of hormone-dependent uterine pathologies such as endometriosis and endometrial cancer.

overall_design:
Microarray analysis was performed on mouse uteri using eighteen SRC-2flox/flox (SRC-2f/f) and eighteen PRCre/+ SRC-2flox/flox (SRC-2d/d) mice. Mice were ovariectomized at 6 weeks and after 2 weeks mice were either treated with sesame oil (vehicle) or 1 mg of P4. RNA from three mice per genotype per treatment were pooled and assigned as one sample (three samples per genotype per treatment).
multiple group comparison

first: Ramakrishna

last: Kommagani

first: Bert

last: O'Malley


title: Comparative transcriptome analysis of DFAT cells after the treatment with Y-27632 and the transfection of Mkl1 siRNA

city: Shinjuku-ku

first: Hiroyuki

last: NOBUSUE

state: Tokyo

address: 35 Shinanomachi

department: Institute for Advanced Medical Research

institute: Keio University School of Medicine

summary:
Cellular differentiation is regulated through activation and repression of defined transcription factors. A hallmark of differentiation is a pronounced change in cell shape, which is determined by dynamics of the actin cytoskeleton. In de-differentiated fat (DFAT) cells and 3T3-L1 cells, we showed that treatment with the ROCK inhibitor Y-27632, by inducing remodeling of the actin cytoskelton, causes adipocyte differentiation. In addition, we found that depletion of MKL1, an actin binding transcriptional coactivator, elicits adipogenesis.
To investigate whether regulation of MKL1 by actin cytoskeleton dynamics drives adipocyte differentiation, we compared the gene expression changes resulting from DFAT cells after treatment with Y-27632 and transfection of Mkl1 siRNA.

overall_design: Using Affymetrix mouse genome array, we compared global gene expression profiles in DFAT cells after treatment with Y-27632 and transfection with Mkl1 siRNA to search for particular biological functions in genes of which expression intensities were increased and decreased.

last: Nobusue

first: Hideyuki

last: Saya


title: SIRT4 KO livers microarray

first: Gaelle

last: Laurent

state: MA

address: 250 Longwood Avenue

department: Cell Biology

institute: Harvard Medical School

summary: Sirtuins are a family of protein deacetylases, deacylases, and ADP-ribosyltransferases that regulate life span, control the onset of  numerous age-associated diseases, and mediate metabolic homeostasis. We have uncovered a novel role for the mitochondrial  sirtuin SIRT4 in the regulation of hepatic lipid metabolism during changes in nutrient availability. We show that SIRT4 levels  decrease in the liver during fasting and that SIRT4 null mice display increased expression of hepatic peroxisome proliferator activated  receptor   (PPAR ) target genes associated with fatty acid catabolism. Accordingly, primary hepatocytes from SIRT4  knockout (KO) mice exhibit higher rates of fatty acid oxidation than wild-type hepatocytes, and SIRT4 overexpression decreases  fatty acid oxidation rates. The enhanced fatty acid oxidation observed in SIRT4 KO hepatocytes requires functional SIRT1, demonstrating a clear cross talk between mitochondrial and nuclear sirtuins. Thus, SIRT4 is a new component of mitochondrial signaling in the liver and functions as an important regulator of lipid metabolism.

overall_design: SIRT4 knockout (KO) and wild-type (WT) littermates (male; n   6 per genotype; 7- to 8-month-old littermates) were  sacrificed after a 16-h overnight fast. Samples were individually hybridized on Affymetrix Mouse Genome 430 2.0 GeneChips by the Biopolymers Facility (Harvard Medical School).

first: Gaëlle

first: Vincent

last: de Boer

first: Lydia

middle: W

last: Finley

first: Meredith

last: Sweeney

first: Hong

last: Lu

first: Thaddeus

middle: T

last: Schug

first: Yana

last: Cen

first: Seung

last: Jeong

first: Xiaoling

last: Li

first: Anthony

middle: A

last: Sauve

first: Marcia

last: Haigis


title: Integrated analysis identifies key determinants of embryonic stem cell identity and homeostasis

status: Public on Mar 26 2014

city: RTP

first: Raja

last: Jothi

state: NC

address: 111 TW Alexander Drive; A314

department: National Institute of Environmental Health Sciences

institute: National Institutes of Health

summary: Despite RNAi-based screens to uncover genes controlling embryonic stem cell (ESC) identity, the pluripotency network remains poorly characterized, as does the precise molecular mechanisms underlying the balance between self-renewal and differentiation. Here we carried out a systematic meta-analysis of published gene expression data to rank-order genes based on their likelihood of regulating ESC identity. Not only did our analysis correctly rank known pluripotency-associated genes atop the list, but it also helped unearth many novel determinants of ESC identity including several components of functionally distinct complexes, as determined using RNAi. We focus on our top-hit Nucleolin, and characterize its mechanistic role in the maintenance of ESC homeostasis by shielding from differentiation-inducing redox imbalance-induced oxidative stress. Notably, we identify a conceptually novel mechanism involving a Nucleolin-dependent bistable switch regulating the homeostatic balance between self-renewal and differentiation in ESCs. Our gene ranks represent a rich and valuable resource for uncovering novel ESC regulators.

overall_design: Microarray gene expression profiling in E14Tg2a mESCs after transfection with indicated siRNAs: Ncl siRNA #1 (Invitrogen, 17975-MSS206961) Ncl siRNA #2 (Invitrogen, 17975-MSS275939), and Control siRNA duplex targeting firefly luciferase.

first: Senthilkumar

last: Cinghu

first: Sailu

last: Yellaboina


title: Tumor repressor protein 53 and steroid hormones provide a new paradigm for ovarian cancer metastases

status: Public on Mar 21 2014

first: JoAnne

last: Richards

address: One Baylor Plaza

department: Molecular and Cellular Biology

summary: The functional status of the tumor repressor protein (TP53 or TRP53) is a defining feature of ovarian cancer. Mutant or null alleles of TP53 are expressed in greater than 90% of all high-grade serous adenocarcinomas. Wild type TP53 is elevated in low-grade serous adenocarcinomas in women and in our Pten/Kras/Amhr2-Cre mutant mouse model. Disruption of the Trp53 gene in this mouse model did not lead to high-grade ovarian cancer but did increase expression of estrogen receptor alpha (ERalpha; ESR1) and markedly enhanced the responsiveness of these cells to estrogen. Specifically, when Trp53 positive and Trp53 null mutant mice were treated with estradiol or vehicle, only the Trp53 null and Esr1 positive tumors respond vigorously to estradiol in vivo and exhibit features characteristic of high-grade type ovarian cancer: invasive growth into the ovarian stroma, rampant metastases to the peritoneal cavity and signs of genomic instability. Estrogen promoted and progesterone suppressed the growth of Trp53 null ovarian tumors and tumor cells injected intraperitoneally (IP), subcutaneously (SC) or when grown in matrigel. Exposure of the Trp53 depleted cells to estrogen also has a profound impact on the tumor microenvironment and immune-related events. These results led to the new paradigm that TRP53 status is related to the susceptibility of transformed ovarian surface epithelial (OSE) cells to estradiol-induced metastases and genomic instability. This novel finding is relevant not only for women during their reproductive years but also for women on hormone (estradiol) replacement therapies.

overall_design: A direct comparison of ovarian surface epithelia cells from two different genotype mice

first: Lisa

middle: K

last: Mullany

first: Zhilin

last: Liu

first: Kwong-Kwok

last: Wong

first: Victoria

last: Deneke

first: Yi

last: Ren

first: Alan

last: Herron


title: Transcriptome analysis in host defense during high multiplicity mycobacterial infection

city: San Diego

first: Jay

last: Zhang

state: Southport

address: Gold Coast Campus

country: Australia

institute: Griffith Health Institute

summary: This experiment is to compare the transcription patterns of mouse macrophages (J774A.1) infected with BCG, H37Ra and M. smegmatis under high multiplicity of infection (MOI). Through the global transcriptome profiling study, we define a pathogen specific host gene expression pattern and indicate that SRC likely plays a central role in regulating multiple unique signaling pathways activated by MTB infection. Mycobacterium tuberculosis (MTB) infects an estimated one-third of the global population and is one of the main causes of mortality due to an infectious agent.

overall_design: high multiplicity mycobacterial infection of BCG, H37Ra and M.semg


title: Gene expression in mouse hematopoietic stem and multi-potent progenitor cells with temporally defined divisional histories

status: Public on Mar 20 2014

city: New York

first: Jiajing

last: Qiu

state: NY

address: 1468 Madison Ave, ANBG bldg 24-10

department: Hematology/Oncology Department of Medicine

institute: Icahn School of Medicine at Mount Sinai

summary:
Homeostatic hematopoietice stem cells (HSCs) with greater divisional history lose repopulating potential after very few cell divisions. Divisional history overrides both phenotype and immediate quiescence in determining functional activity. In GFP label retaining system GFP is progressively diluted when cells proceed through a cascade of divisions.
We used a GFP label retaining system and performed microarray expression analyses to track the changes in the gene expression profile of bone marrow (BM) LSK cells that relates to divisional history during homeostasis.

overall_design: Chromatins are dynamically labeled in a double transgenic mouse (huCD34-tTA X Tet-O-H2B-GFP) by the expression of GFP tagged Histone2B. The expression is driven by a human CD34 promoter active specifically in all bone marrow (BM) hematopoietic stem and multi-potent progenitor cells. This is a pulse/chase Tet-off system where cells constantly label with GFP.  Upon administration of Doxycyclin (Dox) to GFP labeled animals, further labeling is stopped during the chase period. With each round of cell division, the newly synthesized endogenous H2B will dilute H2B-GFP by one-half, whereas cells that don’t divide will retain GFP labeling. Therefore, the level of GFP reflects how many times cells have divided over the  period of Dox treatment (chase).  Animals were treated with Dox for 12 weeks starting at the age of 6-8 weeks. After chase, BM Lineage negative, Sca1+, Kit+ (LSK) cells with varying GFP levels were sorted for mRNA extraction. GFP levels were ranked from 0 to 4 based on the kinetic analysis of GFP fully labeled LSK cells and obvious peaks in the GFP histogram of LSK cells after Dox treatment. There is approximately 1-2 cell divisions between each level of GFP.

first: Kateri

last: Moore


title: Acute Effects Caused by the Rodent Non-Genotoxic Carcinogen Diethylhexylphthalate

status: Public on Mar 17 2014

city: Bracknell

first: Richard

last: Currie

address: Jealotts Hill

institute: Syngenta International Research Centre

summary: Acute effects caused by the non-genotoxic carcinogen and peroxisome proliferator (PP) diethylhexylphthalate (DEHP) in the mouse liver

overall_design: Mice (n = 6) were dosed by oral gavage (10 ml/kg body weight) with the non-genotoxic carcinogen diethylhexylphthalate (DEHP), every 24 h for 3 days (1150 mg/kg/day), or with an equivalent volume of vehicle control (corn oil).


title: Immunotherapy Targets in Tumors

status: Public on Mar 14 2014

first: John

last: Walker

state: CA

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

summary: Recent work has shown that cytotoxic T cells play a central role in immune-mediated control of cancers1-3, and monoclonal antibodies that target inhibitory receptors on T cells can induce significant clinical benefit in patients despite advanced disease4-6. However, many of the regulatory pathways that result in loss of T cell function within immunosuppressive tumors remain unknown. Here we show that such regulatory mechanisms can be systematically discovered in vivo in the tumor microenvironment. We devised a pool shRNA screening approach aimed at identifying genes that block the function of tumor-infiltrating CD8 T cells. We postulated that shRNAs targeting key inhibitors would enable robust T cell infiltration and proliferation in tumors, despite multiple inhibitory signals. Candidate shRNAs were discovered by transfer of shRNA-transduced T cells into tumor-bearing mice, followed by deep sequencing to quantify the representation of all hairpins in tumors and lymphoid organs. A subset of shRNAs induced T cell accumulation in tumors but not the spleen, demonstrating feasibility of discovering shRNAs with differential action across tissues. One of the targets was Ppp2r2d, a regulatory subunit of the family of PP2A phosphatases7. Control shRNA-transduced T cells underwent apoptosis upon recognition of melanoma cells, while Ppp2r2d shRNA-transduced T cells accumulated in tumors due to enhanced proliferation and reduced apoptosis. Ppp2r2d shRNAexpressing T cells also significantly delayed tumor growth. This in vivo approach has wide applications to dissect complex immune functions in relevant tissue microenvironments.

overall_design: OT-I derived T cells were transduced with shRNA's and adoptively transferred to B16 tumor bearing mice. Following incubation the T cells were purified from either tumors or spleens. The shRNA's targeted either a control gene (LacZ) or one of 5 selected genes found to regulate the presence of T cells in tumors vs in spleen

first: Penghui

last: Zhou

first: Donald

last: Shaffer

first: Diana

last: Alvarez Arias

first: Yukoh

last: Nakazaki

first: Wouter

last: Pos

first: Alexis

last: Torres

first: Viviana

last: Cremasco

first: Stephanie

last: Dougan

first: Glenn

last: Cowley

first: Kutlu

last: Elpek

first: Jennifer

last: Brogdon

last: Lamb

first: Shannon

last: Turley

first: Hidde

middle: L

last: Ploegh

first: David

last: Root

first: J

last: Love

last: Dranoff

first: Nir

last: Hacohen

first: Harvey

last: Cantor

first: Kai

last: Wucherpfennig


title: Transcription profiling of mouse liver by array

city: Research Triangle Park

first: Mitch

last: Rosen

address: MD 72

institute: U.S. EPA

summary: PPARα-null and wild-type male mice treated with PFHxS or PFNA

overall_design: PPARα-null and wild-type male mice at 6-9 months of age were dosed by gavage for 7 consecutive days with either 0, 3, or 10 mg/kg  PFHxS, or 1 or 3 mg/kg PFNA (#394459, Sigma-Aldrich, St, Louis, MO) in water.  PFHxS was kindly provided by 3M Corp (St. Paul, MN).  Four biological replicates consisting of individual animals were included in each dose group.  Dose levels reflected exposures that produce hepatomegaly in adult mice without inducing overt toxicity.


title: Generating mouse model with predominant naïve or innate memory phenotype CD4+ T cells

city: Ithaca

first: Weishan

last: Huang

state: New York

address: C5 121, Cornell U.

department: Microbiology & Immunology

institute: Cornell University

summary:
Innate memory phenotype (IMP) CD4+ T cells are non-conventional αβ T cells exhibiting features of innate immune cells, characterized as CD44high and CD62Llow in periphery. It is recently reported by our group that bone marrow chimeric mice lacking thymic MHCI expression develop predominantly IMP CD8+ T cells, while those lacking hematopoietic MHCI develop predominantly naïve CD8+ T cells. Here we perform hirarchical clustering analysis and found that CD4+ T cells share similar property: chimeras lacking thymic MHCII gave rise to predominantly CD4+ T cells that resemble IMP CD4+ T cells observed in WT mice, and vice versa, chimeras lacking hematopoietic MHCII had a majority of naïve-like CD4+ T cells resembling naïveCD4+ T cells seen in WT mice.
We used microarrays to compare the global programme of gene expression to determine whether the hematopoietic MHCII selected CD4+ T cells are IMP, and whether the thymic MHCII selected CD4+ T cells are naïve CD4+ T cells as observed in WT mice. Through hierarchical clustering and analysis of global gene differential expression, we determined that hematopoietic MHCII dependent IMP CD4+ T cells generated from WT bone marrow transplanted into irradiated MHCII-/- recipients, resemble IMP CD4+ T cells in WT mice, while naïve CD4+ T cells generated from MHCII-/- bone marrow transplanted into irradiated WT recipients, resemble naïve CD4+ T cells in WT mice.

overall_design: Cell Sorting was performed using a Cytopeia Influx Cell Sorter. Chimeric IMP (CD45.1+TCRβ+CD4+CD44highCD62Llow) CD4+ T cells were sorted from splenocytes of CD45.1+WT→CD45.2+MHCII-/- chimeras (WM IMP CD4), and chimeric naïve (CD45.2+TCRβ+CD4+CD44lowCD62Lhigh) CD4+ T cells were sorted from splenocytes of CD45.2+MHCII-/- → CD45.1+WT chimeras (MW naïve CD4) respectively, 8 weeks post transplantation.  WT IMP (TCRβ+CD4+CD44highCD62Llow) and naïve (TCRβ+CD4+CD44lowCD62Lhigh) CD4+ T cells were sorted from splenocytes of 8-week old WT mice.

first: Qian

last: Qi

first: Avery

last: August


title: Heme regulates the development of iron-recycling macrophages from monocytes (sorted splenocytes)

city: St. Louis

first: MALAY

last: HALDAR

state: MO

address: 7751 charing square lane

department: Pathology and Immunology

institute: Washington University in St. Louis

summary:
Splenic red pulp macrophages (RPM) degrade senescent erythrocytes and recycle heme-associated iron. The transcription factor Spic is selectively expressed by RPM and is required for their development, but the physiologic stimulus inducing Spic is unknown. Here, we report that Spic also regulated the development of F4/80+VCAM+ bone marrow macrophages (BMM) and that Spic expression in BMM and RPM development was induced by heme, a metabolite of erythrocyte degradation. Pathologic hemolysis induced loss of RPM and BMM due to excess heme but induced Spic in monocytes to generate new RPM and BMM. Spic expression in monocytes was constitutively inhibited by the transcriptional repressor Bach1. Heme induced proteasome-dependent BACH1 degradation and rapid Spic derepression. Further, cysteine-proline dipeptide motifs in BACH1 that mediate heme-dependent degradation were necessary for Spic induction by heme. These findings are the first example of metabolite-driven differentiation of a tissue-resident macrophage subset and provide new insight into iron homeostasis.

Global gene expression pattern of Spic+ monocytes, Spic- monocytes, and Spic high red pulp macrophages were compared by sorting these cells from Spic(igfp/+) splenocytes and performing microarray-based gene expression profiling.

overall_design: Splenocytes were prepared from Spic(igfp/+) mice and were first negatively selected for CD4, CD8, and B220 by MACS (Miltenyi Biotech) purification using the respective microbeads. Negatively selected splenocytes were then stained with anti-CD11b and anti-Ly6c and sorted for Spic+ monocytes (CD11b+Ly6c+Spic+) and Spic- monocytes (CD11b+Ly6c+Spic-). Purified RPM were obtained by staining splenocytes with anti-F4/80 and sorting for F4/80 hi Spic-EGFP hi cells.

first: Malay

last: Haldar

first: Masako

last: Kohyama

first: Kenneth

last: Murphy


title: Oncogenic Nras has a bimodal effect on hematopoietic stem cells promoting proliferation and self-renewal

city: Memphis

first: Shann-Ching

last: Chen

state: TN

address: 262 Danny Thomas Place

department: Pathology

institute: St. Jude Children's Research Hospital

summary: Pre-leukemic mutations are thought to promote clonal expansion of hematopoietic stem cells (HSCs) by increasing self-renewal and competitiveness. However, mutations that increase HSC proliferation tend to reduce competitiveness and self-renewal potential, raising the question of how a mutant HSC can sustainably outcompete wild-type HSCs. Activating mutations in NRAS are prevalent in human myeloproliferative disease and leukemia. Here we show that a single allele of oncogenic NrasG12D increases HSC proliferation but also increases reconstituting and self-renewal potential upon serial transplantation in irradiated mice, all without immortalizing HSCs or causing leukemia in our experiments. NrasG12D also confers long-term self-renewal potential upon multipotent progenitors. To explore the mechanism by which NrasG12D promotes HSC proliferation and self-renewal we assessed HSC cell cycle kinetics using H2B-GFP label retention. We found that NrasG12D had a bimodal effect on HSCs, increasing the proliferation of some HSCs while increasing the quiescence and competitiveness of other HSCs. One signal can therefore increase HSC proliferation, competitiveness, and self-renewal through a bimodal effect that promotes proliferation in some HSCs and quiescence in others.

overall_design: 12 RNA samples from mouse bone marrows were analyzed. There are three biological replicates for each subtype.

first: Qing

last: Li

first: Natacha

last: Bohin

first: Tiffany

last: Wen

first: Jeffery

last: Magee

first: Kevin

last: Shannon

first: Sean

last: Morrison


title: Effect of CSF1R inhibition in tumor macrophages on gene expression in metastatic epithelial cells

status: Public on Mar 13 2014

city: Columbus

first: Haritha

last: Mathsyaraja

address: 460 W12th Ave

institute: The Ohio State University

summary: Metastasis is the primary cause of mortality in breast cancer patients. Tumor associated macrophages (TAMs) are active collaborators in mediating several steps of the tumor metastatic cascade, but the molecular details governing this collaboration remain ill-defined.  Colony Stimulating Factor 1 (CSF1), a factor critical for macrophage differentiation and survival, functions to recruit TAMs to the primary tumor site, and anti-CSF1 therapies are in clinical trials.In this study, we tested the effect of inhibiting CSF1 signaling in macrophages on gene expression in metastatic tumor cells in mouse models of breast cancer metastasis. Tumor cells were sorted from lung metastases from control and CSF1R inhibitor treated mice. Several pro-tumor processes were significantly affected by CSF1R inhibitor treatment, including angiogenesis and tumor cell proliferation. In addition, a 29 gene signature derived from this data could retrospectively predict survival in a cohort of luminal B breast cancer patients. Collectievly, our results highlight the utility of employing CSF1R inhibitors for the treatment of metastatic breast cancer.

overall_design: GFP tagged MVT1 metastatic mammary tumor cells were injected intravenously into FVB/N mice. Mice were gavaged with the CSF1R inhibitor GW2580 or vehicle starting one week post injection. GFP tagged tumor cells were sorted from metastatic tumor bearing lungs 1 and 2 weeks post injection from 2 vehicle treated mice for each. These are denoted 1_week_WT and 2_week_WT respectively. GFP tagged tumor cells were simultaneously sorted from mice gavaged with GW2580. These samples are denoted 2_week_GW. RNA was extracted and gene expression profiling was performed using the Affymetrix Mouse Genome 430 2.0 Array platform.

first: Michael

last: Ostrowski

first: Lianbo

last: Yu


title: Expression data from mouse protein iPS cells compared to mouse embryonic stem cells and mouse hepatocyte.

status: Public on Mar 08 2014

city: Belmont

first: Kwang-Soo

last: Kim

address: 115 Mill St.

institute: McLean Hospital/Harvard Medical School

summary:
Increased genomic integrity an improved protein-based iPS cell method compared to current viral induced strategies
We used microarrays to detail the global gene expression of protein-based iPS cells

overall_design: Total RNAs were prepared from mH, mES, miPS cells usingTRIzol reagent (Invitrogen, Carlsbad, CA) and their cDNAs were allowed to hybridize to Affymetrix Mouse Expression Array 430 containing over 43,000 mouse transcripts at the Harvard Partners Center for Genomics and Genetics.


title: Expression data from adult ATII and E18 Bipotent progenitor cells in the mouse lung

status: Public on Mar 07 2014

city: Stanford

first: Mark

last: Krasnow

state: Ca

address: Beckman Center, B400 279 W. Campus Dr.

institute: Stanford University

summary: Alveoli are thin-walled sacs that serve as the gas exchange units of the lung.  They are affected in devastating lung diseases including COPD, Idiopathic Pulmonary Fibrosis, and the major form (adenocarcinoma) of lung cancer, the leading cause of cancer deaths.  The alveolar epithelium is composed of two morphologically distinct cell types:  alveolar type (AT) 1 cells, exquisitely thin cells across which oxygen diffuses to reach the blood, and AT2 cells, specialized surfactant-secreting cells.  Classical studies suggested that AT1 cells arise from AT2 cells during development and following injury, but more recent studies suggest other sources.  Here we use histological and marker analysis, lineage tracing, and clonal analysis in mice to identify alveolar progenitor and stem cells and map their locations and potential in vivo.  The results show that AT1 and AT2 cells arise independently during development from a bipotential progenitor.  After birth, new AT1 cells derive from rare, long-lived, self-renewing AT2 cells, each producing a slowly expanding clonal focus of regenerated alveoli contiguous with the founder AT2 cell.  This stem cell function of AT2 cells is broadly activated by diffuse AT1 cell injury, and AT2 self-renewal can be induced in vitro by EGF ligands and permanently activated in vivo by AT2 cell-specific targeting of the oncogenic KrasG12D allele, efficiently transforming AT2 cells into monoclonal adenomatous tumors that rapidly enlarge and prove fatal.  Thus, there is a developmental switch in alveolar progenitor cells after birth, when mature AT2 cells function as facultative stem cells that contribute to local alveolar renewal, repair, and cancer.  We propose that short-range signals from dying AT1 cells regulate AT2 stem cell activity: a signal transduced by EGFR-KRAS controls AT2 self-renewal and is hijacked during oncogenic transformation, and a separate signal controls reprogramming to AT1 cell fate.

overall_design: To compare expression between ATII and E18 BP populations, RNA was isolated from either population purified by FACS.  Two populations are analyzed with 3 biological replicates per population.

first: Douglas

last: Brownfield

first: Tushar

last: Desai


title: Cell autonomous and non-autonomous interactions of a western-style diet and the vitamin D receptor in intestinal homeostasis and tumorigenesis

status: Public on Mar 12 2014

city: Bronx

first: Leonard

middle: H

last: Augenlicht

address: 1300 Morris Park Ave

department: Medicine and Cell Biology

institute: Albert Einstein College of Medicine

summary:
These data suggest that co-culture with macrophages increases expression of NDRG-1 in epithelial cell lines.  The finding is confirmed in 2 human epithelial cell lines, and in tissue derived from mice genetically and dietetically altered to increase macrophage infiltration of the small and large intestinal epithelium.  NDRG1 is identified as a potential mediator of macrophage effects on tumorigenesis in the large and small intestine.
Array data is part of a larger study involving the effects of Vitamin D, in concert with macrophages, on intestinal homeostasis and tumorigenesis.

overall_design: Cells from mouse epithelial cell line CT26 were cultured either alone, or with RAW macrophages in a system which allowed no physical contact but exchange of soluble factors between the cell types.  The experiment was peformed twice.

first: Donghai

last: Wang


title: A mouse model of HIES reveals pro and anti-inflammatory functions of STAT3

status: Public on Mar 06 2014

city: Bethesda

first: Arian

middle: Dominic John

last: Laurence

state: MD

address: 9000 Rockville Pike, Building 10, Room13C120-11B

department: MIIB

institute: NIAMS

summary: Mutations of STAT3 underlie the autosomal dominant form of hyper-immunoglobulin E syndrome (HIES). STAT3 has critical roles in immune cells and thus, hematopoietic stem cell transplantation (HSCT), might be a reasonable therapeutic strategy in this disease.  However, STAT3 also has critical functions in non-hematopoietic cells and dissecting the protean roles of STAT3 is limited by the lethality associated with germline deletion of Stat3.  Thus, predicting the efficacy of HSCT for HIES is difficult. To begin to dissect the importance of STAT3 in hematopoietic and non-hematopoietic cells as it relates to HIES, we generated a mouse model of this disease.  We found that these transgenic mice recapitulate multiple aspects of HIES, including elevated serum IgE and failure to generate Th17 cells.  We found that these mice were susceptible to bacterial infection that was partially corrected by HSCT using wild type bone marrow, emphasizing the role played by the epithelium in the pathophysiology of HIES.

overall_design: The effect of IL-6 and IL-10 on BM-DC gene expression was investigated in cell derived from wild type or mut-Stat3 mice

first: Scott

last: Steward-Tharp

first: Yuka

last: Kanno

first: Alex

last: Kotlyar

first: Alejandro

last: Villarino

first: Giuseppe

last: Sciume

first: Stefan

last: Kuchen

first: Wolfgang

last: Resch

first: Elizabeth

last: Wohlfert

first: Kan

last: Jiang

first: Kiyoshi

last: Hirahara

first: Golnaz

last: Vahedi

first: Hong-wei

last: Sun

first: Lionel

last: Feigenbaum

first: Joshua

middle: D

last: Milner

first: Steven

last: Holland

first: Fiona

last: Powrie

first: Rafael

last: Casellas

first: John

last: O'Shea


title: MicroRNA levels in non-transformed and transformed lung cells

status: Public on Mar 11 2014

city: Newark

first: Melissa

middle: B.

last: Rogers

state: NJ

address: 185 south orange ave.

department: Biochem. & Molec. Biology

institute: Rutgers NJMS

summary:
MicroRNA levels in non-transformed BEAS-2B bronchial epithelial cells, two lines of mycoplasma transformed BEAS-2B cells, and A549 lung adenocarcinoma cells were measured.
Microarray analyses of 1145 microRNAs in A549 lung adenocarcinoma cells and two other transformed lung cell types relative to BEAS-2B bronchial epithelial cells were performed.  106 miRNAs were down-regulated and 69 miRNAs were up-regulated in all three transformed lines

overall_design: The control cells were the human non-transformed BEAS-2B cells (Lechner JF, LaVeck MA. A serum-free method for culturing normal human bronchial epithelial cells at clonal density. J. Tissue Culture Methods 9: 43-48, 1985).  The BEAStra1 and BEAStra2 cells were replicate populations of BEAS-2B cells that were transformed following infection with mycoplasma (Jiang, S., Zhang, S., Langenfeld, J., Lo, S.C., and Rogers, M.B., Mycoplasma infection transforms normal lung cells and induces bone morphogenetic protein 2 expression by post-transcriptional mechanisms. J Cell Biochem. 104(2): 580-594, 2007).  A459 lung adenocarcinoma cells were derived from a human lung tumor (Giard DJ, et al. In vitro cultivation of human tumors: establishment of cell lines derived from a series of solid tumors. J. Natl. Cancer Inst. 51: 1417-1423, 1973. PubMed: 4357758).

middle: B

first: Annette

last: Lee

first: Diane

last: Garsetti


title: Molecular Adaptations of Striatal Spiny Projection Neurons During Levodopa-Induced Dyskinesia

status: Public on Mar 03 2014

city: Cambridge

first: Myriam

last: Heiman

state: Massachusetts

address: 43 Vassar St

department: Department of Brain and Cognitive Sciences

institute: Massachusetts Institute of Technology

summary: L-3,4-dihydroxyphenylalanine (levodopa) treatment is the major pharmacotherapy for Parkinson's disease. However, almost all patients receiving levodopa eventually develop debilitating involuntary movements (dyskinesia). While it is known that striatal spiny projection neurons (SPNs) are involved in the genesis of this movement disorder, the molecular basis of dyskinesia is not understood. In this study, we identify distinct cell-type-specific gene expression changes that occur in sub-classes of SPNs upon induction of a parkinsonian lesion followed by chronic levodopa treatment. We identify several hundred genes whose expression is correlated with levodopa dose, many of which are under the control of AP-1 and ERK signaling. In spite of homeostatic adaptations involving several signaling modulators, AP-1-dependent gene expression remains highly dysregulated in direct pathway SPNs (dSPNs) upon chronic levodopa treatment. We also discuss which molecular pathways are most likely to dampen abnormal dopaminoceptive signaling in spiny projection neurons, hence providing potential targets for antidyskinetic treatments in Parkinson's disease.

overall_design: To profile the cell-type-specific responses of striatal spiny projection neurons (SPNs) to striatal dopamine depletion, we conducted TRAP analysis of the two major classes of these neurons: dSPNs that express the dopamine receptor 1a (Drd1a), and iSPNs that express the dopamine receptor 2 (Drd2). To disrupt dopamine innervation to both of these SPN populations that reside in the striatum, we injected the neurotoxin 6-hydroxydopamine (6-OHDA), unilaterally, in the medial forebrain bundle (MFB) in hemizygous Drd1-TRAP and Drd2-TRAP adult (9-14 weeks) male mice (kept on a C57BL/6J genetic background). This lesion procedure causes nigral dopamine cell death within a few days, along with a widespread and near-complete loss of dopaminergic innervation to the entire dorsal striatum on one side of the brain (a hemiparkinsonian model).      We first examined the effects of dopamine depletion alone, compared to a mock lesion (ascorbate / saline injected).  We then examined the effects of chronic levodopa treatment upon the molecular profiles of dopamine- depleted dSPNs and iSPNs, with two dose regimens.   The ‘high-dose’ L-DOPA regimen (3 mg/kg on days 1-3, followed by 6 mg/kg on days 4-9) was expected to induce severe dyskinesia in all MFB-lesioned mice. The low-dose L-DOPA regimen (1 mg/kg on days 1-3, followed by 2 mg/kg on days 4-9) was expected to reverse limb use asymmetry without causing conspicuous dyskinesias. To equalize the effects of stress and handling across all groups, including control groups, all mice were equally handled and thus received saline injections when not receiving levodopa injections.  Each treatment group contained 7-10 replicates.     TRAP-purified mRNAs from either Drd1a- or Drd2-expressing SPNs were reverse-transcribed, amplified, and used to interrogate Affymetrix 430_2.0 GeneChip microarrays.

first: Adrian

last: Heilbut

first: Veronica

last: Francardo

first: Ruth

last: Kulicke

first: Robert

last: Fenster

first: Eric

last: Kolaczyk

first: Jill

middle: P

last: Mesirov

first: D

last: Surmeier

first: M

last: Cenci

first: Paul

last: Greengard


title: Isolation and genomic characterization of cancer stem cells in head and neck cancer

status: Public on Mar 02 2014

city: Royal Oak

first: Bryan

last: Thibodeau

state: MI

address: 3811 West 13 Mile Road

department: BioBank

institute: Beaumont Research Institute

summary:
This study investigated the use of three different established cell sorting strategies to isolate and characterize stem cells from head and neck cancer cell lines.
Five low passage cell lines were subjected to cell sorting based on Hoechst side population, Aldefluor and CD44 expression. Isolated cell populations were studied for gene expression, radiosensitivity and chemosensitivity to cis-platin and paclitaxel
Each sorting method identified a different set of genes associated with different Gene Ontology categories with mitosis being the only common category. CD44 associated gene changes were almost exclusively associated with cell cycle and in particular mitosis. There were no significant differences in radiosensitivity or cis-platin sensitivity of stem or non-stem cells but CD44 isolated stem cells were more resistant to paclitaxel

overall_design: Five head and neck cell lines were used to isolate cancer stem cells by 3 isolation methods. For each isolation method, cancer stem cell enriched populations (n=5) were compared to cancer stem cell depleted populations (n=5). The resulting gene expression patterns were compared among the 3 isolation methods.

first: George

last: Wilson

first: Brian

last: Marples

first: Sandra

last: Galoforo

first: Timothy

last: Geddes

first: Reidar

last: Grenman

first: Jan

last: Akervall


title: Prognostic value of gene signatures and proliferation in lymph node negative breast cancer

status: Public on Mar 05 2014

city: Stavanger

first: Kristin

last: Jonsdottir

address: Torgveien 25b

department: Dep. of Pathology

institute: Stavanger university Hospital

summary: Analyses whether, and if so, gene expression can add prognostic information in the subgroups of patients with tumours with low or high proliferative activity. As proliferation measured with MAI and PPH3 has repeatedly been shown to be the best prognosticator in node-negative breast cancer (high sensitivity, little overtreatment).

overall_design: Total RNA were extracted from 94 lymph node negative breast cancer patients

first: Janssen

last: Emiel


title: Expression data from exposure of BAT and WAT at 6 and 28 degrees C

status: Public on Mar 01 2014

city: London

first: Myrsini

last: Kaforou

address: Norfolk Place

institute: Imperial College London

summary:
We run microarrays from three per group Sv129 female mice, ten weeks old, which were maintained at 28°C (warm conditions) or 6° C (cold stimulated) for ten days, while standard animal house temperature is 22 °C.
After ten days, three types of tissue were collected: Brown Adipose Tissue (BAT), Mesenteric (visceral) White Adipose Tissue (MES) and Posterior Subcutaneous White Adipose Tissue (WAT)

overall_design: Different adipose tissue depots were taken for RNA extraction and hybridization on Affymetrix microarrays. We sought to determine the differences between white and brown adipose tissues at different temperatures

last: Christian

first: Meritxell

last: Rosell

first: A

last: Frontini

first: S

last: Cinti

first: G

last: Montana


title: Comparison of gene expression profiles of naïve and in vitro effector CD8+ T cells from wild-type and BATF-/- mice

city: Boston

first: R. Anthony

last: Barnitz

address: 450 Brookline Ave.

department: Department of Pediatric Oncology

institute: Dana-Farbert Cancer Institute, Harvard Medical School

summary: The transcription factor BATF is required for Th17 and TFH differentiation. Here, we show that BATF also has a fundamental role in regulating effector CD8+ T cell differentiation.  BATF-deficient CD8+ T cells show profound defects in effector expansion and undergo proliferative and metabolic catastrophe early after antigen encounter.  BATF, together with IRF4 and Jun proteins, binds to and promotes early expression of genes encoding lineage-specific transcription-factors (T-bet and Blimp-1) and cytokine receptors, while paradoxically repressing genes encoding effector molecules (IFNg and granzyme B). Thus, BATF amplifies TCR-dependent transcription factor expression and augments inflammatory signal propagation but restrains effector gene expression.  This checkpoint prevents irreversible commitment to an effector fate until a critical threshold of downstream transcriptional activity has been achieved.

overall_design: P14 TCR transgenic CD8+ T cells from wild-type or BATF-/- mice were examined either as naïve cells or after 3 days of in vitro stimulation with antibodies to CD3 and CD28 in the presence of IL-2

first: R

first: W

middle: N

last: Haining

first: E

last: Wherry