title: Colon gene expression signatures in mice mono-associated with IBD-associated micro-organisms

status: Public on Aug 22 2015

city: Jouy en Josas

first: Thomas

middle: Walter

last: Hoffmann

address: Domaine de Vilvert

department: UMR 1319 MICALIS

institute: INRA Jouy en Josas

summary: Studying host-microbiota interactions is fundamental to understand mechanisms involved in intestinal inflammation and inflammatory bowel diseases. In this work, we studied these interactions in mice mono-associated with 4 bacteria and 2 yeasts, all representative of intestinal microbiota and/or associated with IBD pathogenesis: Bacteroides thetaiotaomicron, adhesive-invasive Escherichia coli (AIEC), Ruminococcus gnavus, Roseburia intestinalis, Saccharomyces boulardii and Candida albicans. Transcriptomics analyses showed that B. thetaiotaomicron had the highest immunological effect, being able to almost recapitulate the effects of a whole microbiota, and particularly induced Treg pathways. Furthermore, this analysis also pointed out the effects of E. coli AIEC LF82 on IDO activation and of S. boulardii on angiogenesis, as well as major effects of R. gnavus on metabolism. This work therefore reveals information on the role of each micro-organism and proposes several tracks to follow to better understand IBD pathogenesis and identify therapeutic targets

overall_design: 6 mono-associations + 2 controls (germ-free and conventionalized mice), with 5 to 7 mice per group.

middle: W

first: Hang-Phuong

last: Pham

first: Marco

last: Moroldo

first: Philippe

last: Langella

first: Harry

last: Sokol


title: Gene expression analysis of spinal cord microglia in atopic diathesis model mice.

status: Public on Jul 09 2015

city: Fukuoka

first: Ryo

last: Yamasaki

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-Ku

department: Neurology

country: Japan

institute: Kyushu University

summary: To elucidate differential gene expression pattern in atopic diathesis model mice spinal cord microglia compared to normal mice.

overall_design: Sort microglia from atopic diathesis model mice and control mice, extract RNA and subjected to RNA array assay.

first: Takayuki

last: Fujii

first: Bing

last: Wang

first: Mizuho

last: Kido

first: Jun-ichi

last: Kira


title: L1000 Connectivity Map perturbational profiles from Broad Institute LINCS Center for Transcriptomics LINCS PHASE *II* (n=354,123; updated March 30, 2017)

status: Public on Jul 15 2015

city: Cambridge

first: Aravind

last: Subramanian

state: MA

address: 415 Main Street

country: USA

institute: The Broad Institute

summary:
The Library of Integrated Cellular Signatures (LINCS) is an NIH program which funds the generation of perturbational profiles across multiple cell and perturbation types, as well as read-outs, at a massive scale. The LINCS Center for Transcriptomics at the Broad Institute uses the L1000 high-throughput gene-expression assay to build a Connectivity Map which seeks to enable the discovery of functional connections between drugs, genes and diseases through analysis of patterns induced by common gene-expression changes.

The platform is GPL20573: Broad Institute Human L1000 epsilon
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL20573

For questions or assistance with this dataset, please email the CMap support team at: clue@broadinstitute.org

overall_design: LINCS aims to enable a functional understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The Broad Institute LINCS Center for Transcriptomics contributes to this collaborative effort by application of the Connectivity Map concept. In brief, the study design involves the generation of a compendium of transcriptional expression data from cultured human cells treated with small-molecule and genetic loss/gain of function perturbagens. These measurements are made using the L1000 high-throughput gene-expression assay that enables data generation at an unprecedented scale.  The data are processed through a computational system, that converts raw fluorescence intensities into differential gene expression signatures. The data at each stage of the pre-processing are available: Level 1 (LXB) - raw, unprocessed flow cytometry data from Luminex scanners. One LXB file is generated for each well of a 384-well plate, and each file contains a fluorescence intensity value for every observed analyte in the well. Level 2 (GEX) - gene expression values per 1,000 genes after deconvolution from Luminex beads. Level 3 (Q2NORM) - gene expression profiles of both directly measured landmark transcripts plus inferred genes. Normalized using invariant set scaling followed by quantile normalization. Level 4 (Z-SCORES) - signatures with differentially expressed genes computed by robust z-scores for each profile relative to control (PC relative to plate population as control; VC relative to vehicle control)


title: Gene expression profiling of fibroblasts harboring POC1A mutation

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: POC1A encodes a WD repeat protein localizing to centrioles and spindle poles and associated with Short stature, onychodysplasia, facial dysmorphism and hypotrichosis (SOFT) syndrome (OMIM #614813). In our study, we reported on two patients with primordial dwarfism (PD) from the same family. We utilized Whole Exome Sequencing (WES) in the patients to screen all PD related genes and to define putative novel candidate genes. A novel homozygous p.T120A missense mutation was detected in POC1A, a known causative gene of SOFT syndrome, and confirmed using Sanger sequencing. To confirm the pathogenicity of the detected mutation, primary fibroblast cultures obtained from the patients and a control individual were used. Gene expression profiles of the fibroblast cultures were taken.

overall_design: We performed gene expression arrays on fibroblasts cultured from patients with SOFT syndrome and POC1A mutation and compared their expression profiles to that of control fibroblast cells.

first: Mustafa

last: Ozen

middle: J

first: Yiqun

last: Zhang


title: Role of areca nut induced TGF-β and epithelial mesenchymal interaction in pathogenesis of precancerous Oral submucous fibrosis

status: Public on Jul 06 2015

city: Bangalore

first: Neeraj

last: KUMAR

address: Indian Institute of Science Bangalore

department: MRDG

country: India

institute: Indian Institute of Science Bangalore

summary: To understand the role of areca nut and TGF-β induced gene expression changes in fibroblasts and its contibution in the manifestation of Oral submucous fibrosis, we studied gene expression profile in primary human gingival fibroblast (hGF) cells following treatment with areca nut, TGF-β and both together.

overall_design: Control Vs Areca nut 5 µg/ml water extract (5H) (2), Contro Vs TGF-β (2), Control Vs Areca nut (5 µg/ml)  and TGF-β (5 ng/ml) (5H+T) (2).     (2)- Biological duplicates.

first: Ila

last: Pant

last: Kumar

first: Imran

last: Khan

first: S

middle: G

last: Rao

first: Paturu

last: Kondaiah


title: Acute lung injury results from innate sensing of viruses by an ER stress pathway

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: Incursions of new pathogenic viruses into humans from animal reservoirs are occurring with alarming frequency. The molecular underpinnings of immune recognition, host responses, and pathogenesis in this setting arepoorly understood. We studied pandemic influenza viruses to determine the mechanism by which increasing glycosylation during evolution of surface proteins facilitates diminished pathogenicity in adapted viruses. ER stressduring infection with poorly glycosylated pandemic strains activated the unfolded protein response, leading to inflammation, acute lung injury, and mortality. Seasonal strains or viruses engineered to mimic adapted viruses displaying excess glycans on the hemagglutinin did not cause ER stress, allowing preservation of the lungs and survival. We propose that ER stress resultingfrom recognition of non-adapted viruses is utilized to discriminate “non-self” at the level of protein-processing and to activate immune responses, with unintended consequences on pathogenesis. Understanding this mechanism should improve strategies for treating acute lung injury from zoonotic viral infections.

overall_design: Lung transcription analysis of Influenza A virus infected mice.

first: Eike

middle: R

last: Hrincius

first: Swantje

last: Ledmann

first: Peter

last: Vogel

first: Shane

last: Gansebom

first: Amali

middle: E

last: Samarasinghe

first: Dahui

last: You

first: Stephania

middle: A

last: Cormier

first: Jonathan

last: McCullers


title: Candidates for bile acid-dependent PPARα-target genes in mouse intestinal cells

status: Public on Aug 01 2015

first: Satoru

last: Koyanagi

address: 3-1-1 Maidashi, Higashi-ku

department: Pharmaceutics

summary: In addition to their role as a digestive detergent, bile acids have the ability to modulate the expression of genes. The intestinal content of cholic acids (CA) fluctuated in response to the daily feeding-fasting cycle; therefore, we hypothesized that the temporal accumulation of CA may affect the expression of genes in intestinal epithelial cells. To screen bile acid-regulated genes, we performed oligonucleotide microarray analyses using RNA isolated from the CA-treated intestinal cells of mice. Several types of genes were screened as candidates for bile acid-regulated genes. They included genes that encoded lipid metabolism-related proteins, receptors, transcriptional factors, and plasma-membrane transporters.

overall_design: Total 2 samples were derived from [1] vehicle (0.05% DMSO and 0.25% ethanol)-treated intestinal epithelial cells of mice and [2] cholic acid (CA)-treated intestinal epithelial cells of mice.

first: Ayako

last: Okamura

first: Adila

last: Dilxiat

first: Naoki

last: Kusunose

first: Naoya

last: Matsunaga

first: Shigehiro

last: Ohdo


title: Gene expression profiling of IOERT exposed MCF10A breast epithelial cells

city: Cefalù

first: Valentina

last: Bravatà

address: Contrada Pietrapollastra Pisciotto

country: Italy

institute: IBSBC CNR

summary: Intraoperative Electron Radiation Therapy (IOERT) is a therapeutic technique that delivers a single high dose of ionizing radiation (IR) directly to the tumor bed during cancer surgery. The main goal of IOERT is to counteract tumor growth by acting on residual cancer cells in the site at high risk for recurrence as well as to preserve healthy surrounding tissue from the side effects of radiation therapy. The high IR dose used during IOERT treatment induces a strong stress response resulting in the activation of pro- and anti-proliferative cell signaling pathways in both tumor and normal cells. The radiobiology of healthy tissue response to IR is a topic of interest which may contribute to avoid the impairment of normal tissue/organ function and to decrease the risks of secondary cancers. In this study, we examined changes in gene expression in MCF10A breast epithelial cell line exposed to 9Gy and 23Gy high single dose of IR delivered by IOERT.

overall_design: Changes in gene expression in MCF10A breast epithelial cell line exposed to 9Gy and 23Gy high single dose of IR (named MCF10A_9Gy and MCF10A_23Gy respectively), were analyzed as two-color hybridizations using Agilent Technologies whole human genome 4x44K microarrays


title: Restoration of mesenchymal retinal pigmented epithelial cells by TGFbeta pathway inhibitors

city: Santa Barbara

first: Monte

middle: J.

last: Radeke

state: CA

address: Neuroscience Research Institiute

department: Neuroscience Research Institute

institute: University of California, Santa Barbara

summary: Age-related macular degeneration (AMD) is a leading cause of blindness. Most vision loss occurs following the transition from a disease of deposit formation and inflammation to a disease of neovascular fibrosis and/or cell death. Here, we investigate how protracted wound stimulus leads to seminal changes in gene expression and the onset of a self-sustained state of wound response in retinal pigmented epithelial (RPE) cells. Using a human fetal RPE cell culture model and a systems level transcriptome analysis, we show that prolonged subconfluent culture resulting from  repeated passage, leads to terminal acquisition of a mesenchymal-like phenotype post-confluence accompanied by altered expression of >40% of the transcriptome. In contrast, at subconfluence <5% of transcripts have >2-fold expression changes after repeated passage. Protein-protein interaction analysis reveals a core set of genes comprising two interconnected modules with functions pertaining to wound response and cell division.  Among the wound response genes are the TGF-beta pathway activators: TGFB1, TGFG2, INHBA, INHBB, GDF6, CTGF, and THBS1. Small molecule inhibition of TGFBR1/ACVR1B mediated signaling both forestalls and reverses the passage-dependent loss of epithelial potential. Moreover, a disproportionate number of RPE wound response genes have altered expression in neovascular and geographic AMD; including key members of the TGF-beta pathway. In conclusiton, in RPE cells the switch to a terminal mesenchymal-like state following protracted or repeated wound stimulus is driven by activation of a self-perpetuating TGF-beta feedback loop. Targeted inhibition of TGF-beta signaling may be an effective approach towards retarding AMD progression and producing RPE cells in quantity for research and cell based therapies.

overall_design: Transcriptome profiles were determined from 44 human fetal RPE cultures of varying passage number, seeding density, culture maturity, and/or growth factor or small molecule treatment. Probes were labeled with Cy3 or Cy5 and Agilent whole genome microarrays were hybridized with a pair of Cy3 and Cy5 probes. After background subtraction and LOWESS correction to adjust for dye-dependent effects the net intensity values were determined as described in the Data Processing section and the entire data set was quantile normalized. The values reported in the Series Matrix are the quantile normalized net intensity values of the gene specific probes.

first: Carolyn

middle: M

first: Pete

last: Coffey

first: Lincoln

middle: V

last: Johnson


title: TLR4 Signaling Is a Major Mediator of the Female Tract Response to Seminal Fluid in Mice

status: Public on Jul 01 2015

city: Adelaide

first: John

last: Schjenken

state: South Australia

address: The Robinson Research Institute and School of Paediatrics and Reproductive Health. Level 6. Medical School North. Frome Road

country: Australia

institute: The University of Adelaide

summary: To examine the effect of seminal fluid on the whole genome expression profile of endometrial tissue following mating, RNA was extracted from endometrial tissue collected 8 h after CBAF1 females were mated with intact Balb/c males and compared to RNA from endometrial tissue of females mated with seminal fluid deficient SVX/VAS Balb/c males. This comparison controlled for ovarian hormone status, exposure to the male and mating activity, and the neuroendocrine response to cervical and vaginal stimulus at mating, so that changes in endometrial gene expression could be attributed specifically to contact with seminal fluid. The endometrial RNA from n=16 individual females was pooled into four independent biological replicates per treatment group (n=4 endometrial samples per replicate) and expression profiles were analyzed by Affymetrix microarray. Seminal fluid exposure induced a clear difference in the profile of genes expressed in the endometrium with a total of 335 genes were differentially regulated with a fold-change greater than 1.5 and p<0.05. Of these, 190 genes were upregulated and 145 genes were downregulated following contact with seminal fluid. Bioinformatics analysis revealed TLR4 signaling as a strongly predicted upstream regulator activated by the differentially expressed genes.Additional experiments confirmed the role of TLR4 with the absence of TLR4 in TLR4 null mice resulting in a failure for seminal fluid to induce endometrial Csf3, Cxcl2, Il6 and Tnf expression. This study provides evidence that TLR4 contributes to seminal fluid modulation of the periconception immune environment. Activation of TLR4 signaling by microbial or endogenous components of seminal fluid is thus implicated as a key element of the female tract response to seminal fluid at the outset of pregnancy in mice.

overall_design: Endometrial RNA collected 8 h following coitus from n=16 individual females was pooled into four independent biological replicates per treatment group (n=4 endometrial samples per replicate) and expression profiles were analyzed by Affymetrix microarray. Microarray analysis was performed using Affymetrix Mouse Gene 2.0 ST Arrays at the Adelaide Microarray Centre (Adelaide, Australia). Total RNA (300 ng) was labelled using the GeneChip® WT PLUS Reagent Kit according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA). Microarray data was analyzed using Partek Genomics Suite version 6.6). Briefly, .cel files were imported using RMA background correction, following GC content correction and mean probe summarization. Differentially expressed probes were defined as ≥1.50-fold change, t-test p <0.05.  To investigate gene pathways and upstream regulators activated by seminal fluid following mating, differentially expressed genes were analyzed using Ingenuity Pathway Analysis (IPA) version 18488943 Build 308606M (IPA, Ingenuity Systems, Redwood City, CA).

first: Sarah

last: Robertson

first: David

last: Sharkey

first: Danielle

last: Glynn


title: Effects of glucose on gene expression in cultured vascular smooth muscle cells

city: Lund

first: Sebastian

last: Albinsson

address: BMC D12

country: Sweden

institute: Lund University

summary:
Hyperglycemia can contribute to the detrimental effects of diabetes in the vasculature.
To better understand the role of glucose for the effects on vascular smooth muscle cells we investigated gene expression in high and low glucose conditions

overall_design: Mouse aortic smooth muscle cells in passage 3-4 were cultured for 14 days in DMEM 10%FCS supplemented with 1.7mM or 25 mM glucose. RNA was isolated using Qiagen mRNeasy according to standard protocol

first: Thi

middle: H

last: Tran


title: Multiple influences of UNBS1450 on histiocytic lymphoma cell line U937  A high throughput transcriptomic analysis

city: Seoul

first: Marc

last: Diederich

address: Gwanak-ro, Gwanak-gu, 1

department: College of Pharmacy

country: South Korea

institute: Seoul National University

summary: Analysis of the effect of UNBS1450 on U937 cells at different time points. This study attemps to elucidate early effect of the compound in this cell line at times preceding the accumulation of apoptotic markers

overall_design: We used 8 experimental conditions, comparing UNBS-treated cells to untreated ones after 0, 3, 6 and 9 hours of treatment. Four biological replicates were done, including dye-swaps.

first: Florian

last: Muller

first: Claudia

last: Cerella

first: Anthoula

last: Gaigneaux

first: Flavia

last: Radogna

first: Elodie

last: Viry

first: Sebastien

last: Chateauvieux

first: Mario

last: Dicato


title: Eicosapentaenoic and docosahexaenoic acid-enriched high fat diet delays the development of fatty liver in mice.

status: Public on Jun 30 2015

city: Gothenburg

first: Nikulkumar

middle: Kirtilal

last: Soni

state: Vastra Gotaland

address: Kemivagen 10

department: Department of Biology and Biological Engineering

institute: Chalmers University of Technology

summary:
To investigate the effects of quality of fat in a high fat diet (HFD) over time on hepatic lipid storage and transcriptome in mice.
In this dataset, we include the expression data obtained from dissected mouse liver after being fed with Control, HFD-EPA/DHA and HFD-corn oil diet for 8 and 12 weeks.

overall_design: In total, 24 samples were analyzed. Based on hierarchical clustering and scatter plots, one microarray from the HFD-corn oil group at 8 weeks was removed from subsequent analyses. The Piano package was used for Gene Set Enrichment Analysis (GSEA) to identify the total number of genes regulated and the direction of regulation. Gene Ontology (GO) terms were annotated to each probe-set after performing GSEA. The reporter algorithm was used to analyse the functional enrichment level of individual GO term. Heatmaps were generated using the  log10p-values to visualize enriched GO biological processes (BPs) terms.

middle: K

first: Britt

last: Gabrielsson


title: Differential gene expression to VEGF in aorta from wild-type and C17S PKARI knock-in mice

status: Public on Jun 24 2015

city: London

first: Matthew

last: Arno

state: LONDON

address: 150 Stamford Street

department: Genomics Centre

country: United Kingdom

institute: King's College London

summary:
Angiogenesis is essential for tissue development, wound healing and tissue perfusion, with its dysregulation linked-to tumorigenesis, rheumatoid arthritis and heart disease. Here we show pro-angiogenic stimuli couple to NADPH oxidase-dependent generation of oxidants that catalyse an activating intermolecular-disulphide between regulatory-RIα subunits of protein kinase A (PKA), which stimulates PKA-dependent ERK signalling. This is crucial to blood vessel growth as 'redox-dead' Cys17Ser RIα knock-in mice fully resistant to PKA disulphide-activation have deficient angiogenesis in models of hind limb ischaemia and tumour-implant growth. Disulphide-activation of PKA represents a new therapeutic target in diseases with aberrant angiogenesis.
The aim of this study was to identify unique differences in gene expression that may account for decreased angiogenesis in C17S PKARI knock-in mice compared with their littermate wild-types observed in cell and whole animal studies

overall_design: Freshly isolated mouse aortic vessels from 3 C17S PKARI knock-in or 3 littermate wild-types were used in this study. Each vessel was divided in two rings and either left untreated or treated with VEGF.

first: Joseph

last: Burgoyne

first: Philip

last: Eaton


title: Expression data from E12.5 and E14.5 mouse embryonic gonad of wild type (WT) and Wnt-4 knock-out (KO) mice. [MG_U74Av2]

city: Oulu

first: Florence

last: Naillat

address: Aapistie 5A

country: Finland

institute: Oulu University

summary:
Wnt-4 signaling is critical for embryonic female sexual development. When Wnt-4 gene is deleted during embryonic development, the knock-out females present a partial sex reversal.
We used microarrays to detail the global programme of gene expression underlying sexual development and identified distinct classes of up and down-regulated genes during this process.

overall_design: Mouse embryonic gonad from wild type and Wnt-4 knock-out mice (male and female) were selected at two stages of sex determination for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain homogeneous populations of embryonic gonad at each developmental stage in order to increase the temporal resolution of expression profiles. To that end, we hand-selected embryos according to morphological criteria at two time-points: E 12.5 and E14.5.

first: Seppo

last: Vainio


title: caArray_jacks-00113: Murine KRASLA lung cancer gene expression

status: Public on Jun 26 2015

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

summary:
Tumors from 5-6 month old KrasLA mice were dissected. Gene expression analysis on U74A affy chips. 19 normal lungs from age matched controls were also includeed
**NOTE: Migrated from caArray 1.x, identifier='gov.nih.nci.ncicb.caarray:Experiment:1015897590231167:1'

overall_design:
jacks-00113
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: mg_u74av2
Organism: Mus musculus (ncbitax)
Tissue Sites: Lung
Material Types: synthetic_DNA, synthetic_RNA, organism_part
Disease States: normal lung, lung cancer


title: Therapeutic antiviral T cells noncytopathically clear persistently infected microglia after conversion into antigen-presenting cells

status: Public on Jun 22 2015

city: Bethesda

first: Kory

last: Johnson

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

summary: Several viruses can infect the mammalian nervous system and induce neurological dysfunction. Adoptive immunotherapy (AI) is an approach that involves administration of antiviral T cells and has shown promise in clinical studies for the treatment of peripheral virus infections in humans such as cytomegalovirus, Epstein-Barr virus, and adenovirus, among others. Clearance of neurotropic infections, on the other hand, is particularly challenging because the central nervous system (CNS) is relatively intolerant of immunopathological reactions. Therefore, it is essential to develop and mechanistically understand therapies that noncytopathically eradicate pathogens from the CNS. Here, we used mice persistently infected from birth with lymphocytic choriomeningitis virus (LCMV) to demonstrate that therapeutic antiviral T cells can completely purge the persistently infected brain without causing blood brain barrier breakdown or tissue damage. Mechanistically, this is accomplished through a tailored release of chemoattractants that recruit antiviral T cells, but few pathogenic innate immune cells such as neutrophils and inflammatory monocytes. Upon arrival, T cells enlisted the support of nearly all brain resident myeloid cells (microglia) by converting them into CD11c+ antigen-presenting cells (APCs) – a cell population also found in the brain of a human immunodeficiency virus infected patient. Two-photon imaging studies revealed that antiviral CD8+ and CD4+ T cells interacted directly with CD11c+ microglia and induced STAT1 signaling, but did not initiate programmed cell death. We propose that noncytopathic CNS viral clearance can be achieved by therapeutic antiviral T cells reliant on restricted chemoattractant production and interactions with apoptosis-resistant microglia.

overall_design: 6 Mouse Microglia-sorted Brain Samples: 3 (-) AI, 3 (+) AI.

first: Jasmin

last: Herz

first: Dorian

middle: B

last: McGavern


title: Functional screen for novel regulators of murine hematopoietic stem cell in vivo repopulating activity

first: David

last: Finkelstein

summary: Although Hematopoietic Stem Cell Transplantation (HSCT) routinely treats hematologic disease, many patients experience adverse outcomes.  Understanding the molecular regulation of HSC engraftment is paramount to improving HSCT regimens.  Here, we executed a large-scale transplant-based functional screen for novel regulators of HSC repopulation..  Of  >50 gene candidates tested, 18 were required for in vivo hematopoietic repopulation and two were detrimental to repopulation, as their loss enhanced this activity.  Each Hit was validated in a second screen.  Eleven Hits have never before been implicated in HSC biology.  We further show that one novel Hit, Foxa3, is required for optimal engraftment as Foxa3-/- bone marrow is defective in both primary and secondary hematopoietic reconstitution.  We also present evidence that Foxa3 is a novel pioneer factor in HSC.   Each gene identified in our screen is a window into the cellular mechanisms that control hematopoietic reconstitution.  Thus, this work represents a resource to the community to better understand these processes

overall_design: 3 FOXA3 KO samples are compared to 3 wt samples

first: Per

last: Holmfeldt

first: Miguel

last: Ganuza

first: Himangi

last: Marathe

first: Trent

last: Hall

first: Jennifer

last: Pardieck

first: Angelica

middle: C

last: Saulsberry

first: Alba

last: Cico

first: Ludovic

last: Gaut

first: Shannon

last: McKinney-Freeman


title: caArray_green-00155: Global expression profiling identifies signatures of tumor virulence in MMTV-PyMT-transgenic mice

status: Public on Jun 20 2015

summary:
Comparison the gene expression profiles of mouse mammary tumors derived from MMTV-PyMT transgenic in five different strains including FVB/NJ, I/LnJ F1, NZB/B1NJ F1, MOLF/Ei F1 and LP/J F1 and identification of signatures of tumor virulence.
**NOTE: Migrated from caArray 1.x, identifier='gov.nih.nci.ncicb.caarray:Experiment:1015897560599049:1'

overall_design:
green-00155
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: mg_u74av2
Organism: Mus musculus (ncbitax)
Material Types: organism_part, synthetic_RNA, whole_organism, total_RNA
Disease States: Mouse mammary tumor


title: Discrete Functions of Rev-erba Couple Metabolism to the Clock [array]

status: Public on Jun 16 2015

city: Philadelphia

first: Bin

last: Fang

address: 3400 Civic Center Blvd, Bldg 42

institute: University of Pennsylvania

summary: Circadian and metabolic physiology are intricately intertwined, as illustrated by Rev-erb , a transcription factor (TF) that functions both as a core repressive component of the cell autonomous clock and as a regulator of metabolic genes.  Here we show that Rev-erb  modulates the clock and metabolism by different genomic mechanisms. Clock control requires Rev-erb  to bind directly to the genome at its cognate sites, where it competes with activating ROR TFs. By contrast, Rev-erb  regulates metabolic genes primarily by recruiting the HDAC3 corepressor to sites to which it is tethered by cell type-specific transcription factors.  Thus, direct competition between Rev-erb  and ROR TFs provides a universal mechanism for self-sustained control of molecular clock across all tissues, whereas Rev-erb  utilizes lineage-determining factors to convey a tissue-specific epigenomic rhythm that regulates metabolism tailored to the specific need of that tissue.

overall_design: Gene expressions in wild type and RORs depleted mouse livers were compared using Affymetrix MoGene2.0st array. Four biological replicates were used for each condition.

first: Yuxiang

last: Zhang

first: Matthew

last: Emmett

first: Manashree

last: Damle

first: Zheng

last: Sun

first: Dan

last: Feng

first: Sean

last: Armour

first: Jarrett

last: Remsberg

last: Jager

first: Raymond

last: Soccio

last: Steger

first: Mitchell

last: Lazar


title: Expression data from fetal mouse lung from mothers fed high fibre or acetate

status: Public on Jun 29 2015

city: Clayton

first: Charles

last: Mackay

state: VIC

address: Wellington st

institute: Monash University

summary: We used microarrays to detail the global programme of gene expression in the fetal lung late in gestation, from mothers that had been fed normal chow, high fibre, or acetate in the drinking water. The experiment was designed to examine the hypothesis that metabolites of the mother i.e. acetate could cross the placenta and influence gene transcription in the fetus. Diets used were "Normal chow" (NC) (8720310), or "High-fiber" (SF11-025) (Specialty feeds, Perth, Australia. Acetate (200 mM) was provided in the drinking water and refreshed three times per week.

overall_design: Gene expression in the lung may be affected by metabolites in utero. We examined whole lung of E21 fetuses from high-fiber fed mothers, normal chow fed mothers and acetate in drinking water fed mothers. Added fibre in the diet, or acetate in drinking water, would allow simple comparison with normal chow fed mothers, to determine whether fibre/acetate affected gene transcription in the fetal lung.

first: Alison

last: Thorburn


title: Nuclear Factor κB inducing kinase activation as a mechanism of pancreatic beta cell failure in obesity

status: Public on Jun 18 2015

city: Sydney

first: Jianmin

last: Wu

state: NSW

address: 370 Victoria Street Darlinghurst

department: Cancer Division

institute: Garvan Institute of Medical Research

summary:
The NF-κB pathway is a master regulator of inflammatory processes and is implicated in insulin resistance and pancreatic beta cell dysfunction in the metabolic syndrome. While canonical NF-κB signaling is well studied, there is little information on the divergent non-canonical NF-κB pathway in the context of pancreatic islet dysfunction in diabetes. Here, we demonstrate that pharmacological activation of the non-canonical NF-κB inducing kinase (NIK) disrupts glucose homeostasis in zebrafish in vivo. Further, we identify NIK as a critical negative regulator of beta cell function as pharmacological NIK activation results in impaired glucose-stimulated insulin secretion in mouse and human islets. NIK levels are elevated in pancreatic islets isolated from diet-induced obese (DIO) mice, which exhibit increased processing of non-canonical NF-κB components p100 to p52, and accumulation of RelB. Tumor necrosis factor α (TNFα) and receptor activator of NF-κB ligand (RANKL), two ligands associated with diabetes, induce NIK in islets. Mice with constitutive beta cell intrinsic NIK activation present impaired insulin secretion with DIO. NIK activation triggers the non-canonical NF-κB transcriptional network to induce genes identified in human type 2 diabetes genome-wide association studies linked to beta cell failure. These studies reveal that NIK contributes a central mechanism for beta cell failure in diet-induced obesity.
We identify a role for Nuclear Factor inducing κB (NIK) in pancreatic beta cell failure. NIK activation disrupts glucose homeostasis in zebrafish in vivo and impairs glucose-stimulated insulin secretion in mouse and human islets in vitro. NIK activation also perturbs beta cell insulin secretion in a diet-induced obesity mouse model. These studies reveal that NIK contributes a central mechanism for beta cell failure in obesity.

overall_design: To uncover the role of NIK in pancreatic beta cells, we performed a gene expression microarray analysis comparing pancreatic islets with constitutive beta cell intrinsicNIK activation from the 16 week old mice (beta cell specific TRAF2 and TRAF2 knockout mice) to their controls (n=3 per group).

first: Elisabeth

last: Malle

first: Nathan

last: Zammit

first: Stacey

middle: N

last: Walters

first: Yen

last: Koay

first: Bernice

last: Tan

first: Jeanette

last: Villanueva

first: Robert

last: Brink

first: Tom

last: Loudovaris

first: James

last: Cantley

first: Shelli

last: McAlpine

first: Daniel

last: Hesselson

first: Shane

middle: T

last: Grey


title: Hepatic gene expression profiling in AHNAK KO mice

status: Public on Jun 23 2015

first: Je Kyung

last: Seong

department: Veterinary Medicine

summary: To identify molecular mechanism underlying the protection from diet-induced hepatic steatosis in AHNAK deficiency mice, we examined microarray analysis with liver sample from HFD-fed AHNAK KO and WT mice.

overall_design: Two-condition experiment, regular chow (CD) -fed WT vs. CD-fed AHNAK KO and High fat diet(HFD)-fed WT vs. HFD-fed AHNAK KO mice.  Biological replicates: 3 control,  One replicate per array.

first: Je

first: Yo

last: Kim


title: Microarray analysis of committed cDC progenitors

status: Public on Jun 08 2015

city: St Louis

first: Gary

last: Grajales-Reyes

state: Mo

address: Room 7766, CSRB

department: Immunology

institute: Washington University in St. Louis

summary: Analysis of stage-specific gene expression in Zbtb46GFP/+ pre-CD8 DCs, pre-CD4 DCs, CD24 cDCs and CD172a cDCs

overall_design: Bone Marrow and Splenocytes were harvested from 8-10 littermate Zbtb46GFP/+ mice and sorted to >95% purity on the FACS AriaFusion.

first: Kenneth

last: Murphy


title: The effects of leptin deficiency on cold-induced energy expenditure

status: Public on Jun 15 2015

city: Olsztyn

first: Monika

last: Kaczmarek

address: Tuwima 10

country: Poland

institute: Institute of Animal Reproduction and Food Research, Polish Academy of Sciences

summary: At 24 °C Lep-/- mice are hyperphagic compared to the Lep+/+ mice. Reducing the ambient temperature from 24 to 6 °C (3 °C per day) was accompanied by a graded parallel increase in food intake in both control and Lep-/- mice. The rate of increase in food intake per degree Celsius reduction in ambient temperature by the control mice and Lep-/- mice was essentially indistinguishable. Since the body composition of Lep+/+ and Lep-/- mice was unchanged during cold exposure, thermogenesis is fueled solely by food intake. Accordingly, we predicted that the same changes in gene expression associated with the central regulation of thermogenesis by the hypothalamus must occur in both Lep+/+ and Lep-/- mice during the transition from 24 to 6 °C.

overall_design: Microarray analysis of gene expression was performed on hypothalamic tissue dissected from Lep-/- and Lep+/+ mice kept at different temperature conditions, that is, in mice maintained at 24°C and in mice in which the ambient temperature had been reduced to 6 °C over 6 days.

first: Julia

last: Jaroslawska

first: Leslie

middle: P

last: Kozak


title: Radiosensitive hematopoietic cells determine the extent of skin inflammation in experimental epidermolysis bullosa acquisita

city: Lübeck

first: Saleh

middle: M.

last: Ibrahim

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Dermatology

country: Germany

institute: Universität zu Lübeck

summary:
Animal models have enhanced our understanding of the pathogenesis of autoimmune diseases. For these models, genetically identical, inbred mice have commonly been used. Different inbred mouse strains, however, show a high variability in disease manifestation. Identifying the factors that influence this disease variability could provide unrecognized insights into pathogenesis. We established a novel antibody transfer-induced model of epidermolysis bullosa acquisita (EBA), an autoimmune disease characterized by (muco)-cutaneous blistering caused by anti-type VII collagen (COL7) autoantibodies. Blistering after anti-COL7 IgG (directed against the von-Willebrand-factor A like domain 2) transfer showed clear variability among inbred mouse strains; i.e. severe cutaneous blistering and inflammation in C57Bl/6J, and absence of skin lesions in MRL/MpJ mice. The transfer of anti-COL7 IgG into irradiated, EBA-resistant MRL/MpJ mice, rescued by transplantation with bone marrow from EBA-susceptible B6.AK-H2k mice, induced blistering. To the contrary, irradiated EBA-susceptible B6.AK-H2k mice that were rescued using MRL/MpJ bone marrow were devoid of blistering. In vitro, immune complex activation of neutrophils from C57Bl/6J or MRL/MpJ mice showed an impaired ROS release from the latter, whereas no differences were observed after PMA activation. This finding was paralleled by divergent expression profiles of immune-complex activated neutrophils from either C57Bl/6J or MRL/MpJ mice. Collectively, we demonstrate that radiosensitive cells determine the varying extent of skin inflammation and blistering in the end-stage effector phase of EBA.
We used microarray to differentiate between the molecular response for the immune complex stimulated neutrophils in MRL/MpJ and C57Bl/6J mice

overall_design: To unravel the molecular basis for the different response to immune complex (IC) stimulation between MRL/MpJ and C57Bl/6J mice, the cells were activated using IC, and differential expression using microarray was compared between resting or activated neutrophils from MRL/MpJ or C57Bl/6J mice.

first: Yask

last: Gupta

first: Ralf

last: Ludwig


title: Effect of mutating androgen receptor phosphorylation site Tyr-267

status: Public on Jun 10 2015

city: Chapel Hill

first: Office of Genomics Research

last: UNC Lineberger Comprehensive Cancer Center

state: NC

address: 125 Mason Farm Road, CB #7599 5105-5106 Marsico Hall

institute: University of North Carolina at Chapel Hill

summary: Reactivation of androgen receptor (AR) may drive recurrent prostate cancer in castrate patients.  Ack1 tyrosine kinase is overexpressed in prostate cancer and promotes castrate resistant xenograft tumor growth and enhances androgen target gene expression and AR recruitment to enhancers.  Ack1 phosphorylates AR at Tyr-267 in the N-terminal transactivation domain.  In this study, the role of this phosphorylation site was investigated by characterizing the phosphorylation site mutant in the context of full length and truncated AR lacking the ligand-binding domain.  The Y267F mutant showed decreased transactivation of reporters.  Expression of wild type full length and truncated AR in LNCaP cells increased cell proliferation in androgen-depleted conditions and increased colony formation.  However, the Y267F mutant of full length and truncated AR was defective in stimulating cell proliferation.  The full length AR Y267F mutant was defective in nuclear translocation induced by androgen or Ack1 kinase.  The truncated AR was constitutively localized to the nucleus.  Chromatin immunoprecipitation analysis showed that it was recruited to the target enhancers without androgen.  The truncated Y267F AR mutant did not exhibit constitutive nuclear localization and androgen enhancer binding activity.  Expression of AR responsive genes in cells expressing truncated AR wt and AR-Y267F mutant under androgen deprived conditions was assessed by microarray gene expression analysis.  The AR pathway score was increased in cells expressing truncated AR wt and decreased in cells expressing truncated AR-Y267F.  These results support the concept that phosphorylation of Tyr-267 is required for AR nuclear translocation and recruitment and DNA binding  and transcription of AR responsive genes.

overall_design: Gene expression profiling was performed using RNA samples from LNCaP cells expressing truncated AR-wt and truncated AR-Y267F growing in androgen deprived conditions.  The RNA sample from vector control cells were used as reference sample.  Two biological replicates were used per each cell line.

first: Young

last: Whang

first: Mehmet

last: Karaca


title: Development of gene expression signatures for subconfluent and overconfluent HT-1080 fibrosarcoma cell line

status: Public on Jun 04 2015

city: Nagoya

first: Atsushi

last: Enomoto

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

department: Department of Pathology

institute: Nagoya University Graduate School of Medicine

summary: We investigated the changes in gene expression profile between subconfluent (80%) and overconfluent HT-1080 fibrosarcoma cell line.

overall_design: We have employed whole genome microarray expression profiling as a discovery platform to identify genes expression profiles in HT-1080 cells. Total RNAs from subconfluent (HT-1080_80%) and overconfluent (HT-1080_overconfluent) HT-1080 cells were harvested and subjected to the microarray analysis.

first: Nobuhisa

last: Nakamura


title: Expression data from Lineage-c-Kit+Sca-1+ (LSK) and megakaryocyte/erythroid progenitor (MEP) cells isolated from WT, Ezh2Δ/Δ, JAK2V617F, and JAK2V617F/Ezh2Δ/Δ mice

city: Kumamoto

first: Goro

last: Sashida

state: Kumamoto

address: 2-2-1 Honjo, Chuo-ku

department: IRCMS

institute: Kumamoto University

summary: Loss-of-function mutations in EZH2 are associated with worse outcomes in patients with primary myelofibrosis (PMF).  To understand how EZH2 insufficiency is involved in the pathogenesis of PMF, we generated mice compound for Ezh2 conditional deletion and a JAK2V617F transgene.

overall_design: The total bone marrow cells isolated from Cre-ERT2, Ezh2flox/flox;Cre-ERT2, JAK2V617F;Cre-ERT2 and JAK2V617F;Ezh2flox/flox;Cre-ERT2 mice were transplanted into lethally irradiated CD45.1+ wild-type recipient mice. As we deleted Ezh2 at four weeks post transplantation, we performed gene-expression analysis of LSKs and MEPs isolated from the recipient mice at 2 months post transplantation.

last: Iwama


title: Expression data from Lineage-c-Kit+Sca-1+ (LSK) and megakaryocyte/erythroid progenitor (MEP) cells isolated from JAK2V617F/Ezh2Δ/Δ mice post JQ1 treatment

overall_design: The total bone marrow cells isolated from JAK2V617F;Ezh2flox/flox;Cre-ERT2 mice were transplanted into lethally irradiated CD45.1+ wild-type recipient mice. Post the deletion of Ezh2, we administered JAK2V617F/Ezh2Δ/Δ mice with JQ1 or control DMSO for two weeks, and performed gene-expression analysis of bone marrow LSKs and MEPs immediately after completion of JQ1 treatment.


title: Gene expression profile in sciatic nerve from presymptomatic SOD1G93A Amyotrophic Lateral Sclerosis animal model

city: Sao Paulo

first: Jessica

middle: Ruivo

last: Maximino

state: SP

address: Av. Dr. Arnaldo, 455

department: Neurology

country: Brazil

institute: University of Sao Paulo (FMUSP)

summary: Microarray analyses using a whole mouse genome platform were employed in the evaluation of gene expression pattern of sciatic nerves of transgenic SOD1(G93A) mice and their littermate controls at presymptomatic age of 60 days.

overall_design: Sciatic nerve from SOD1G93A and Non transgenic controls from 60 days were used in the experiments. 4 biological replicates were used. A reference sample, comprised by RNA from different neonatal organs (heart, liver, kidney) were used in the hybridations.

first: Chrystian

middle: J

last: Alves

first: Gerson

last: Chadi


title: Understanding the role of EZH2 insufficiency in the pathogenesis of PMF

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

overall_design: Refer to individual Series


title: Gene expression profiling of mouse mast cells exposed to different cancer cell supernatants

status: Public on Jun 01 2015

city: Munich

first: Georgios

last: Stathopoulos

state: Bayern

address: Max-Lebsche-Platz

department: Comprehensive Pneumology Center

institute: Helmholz Zentrum Munich

summary: Naïve mast cells were cultured from murine bone marrow using incubation with IL-3 alone (samples 1-4) or IL-3 and KITL (samples 5-8).

overall_design: IL-3 only or IL-3/KITL-matured bone marrow-derived mast cells were exposed to non-conditioned, or various mouse tumor cell line conditioned media.

first: Nikolaos

middle: I

last: Kanellakis


title: Genomic Analysis Reveals Distinct Mechanisms and Functional Classes of SOX10-Regulated Genes in Melanocytes [gene expression]

status: Public on Jul 03 2015

first: Laura

middle: L

last: Baxter

address: 35A Convent Drive

department: NHGRI

institute: NIH

summary:
We performed ChIP-Seq analysis of SOX10, histone H3 lysine 27 acetylation (H3K27ac) and H3K27 trimethylation (H3K27me3) in melanocytes to profile the genomic binding sites of SOX10 and the chromatin landscape. In parallel, we generated Sox10 haploinsufficient cell lines using gene knockout approaches and conducted microarray gene expression analysis to identify functional gene targets of SOX10 transcriptional regulation in melanocytes. We demonstrate that SOX10 predominantly engages “open” chromatin, binds to melanocyte enhancer elements and plays a central role in transcriptional activation and repression of functionally distinct classes of genes. Furthermore, we identified cis-regulatory sequence motifs of putative co-regulatory transcription factors that define SOX10-activated and SOX10-repressed target genes. Our results uncover novel mechanisms and roles of SOX10 in global transcriptional regulation of diverse regulatory pathways in the melanocyte lineage.
These results indicated that SOX10 plays a role in activation and repression of distinct classes of genes.

overall_design: Microarray gene expression analysis in Sox10 haploinsufficient immortal melanocyte cell lines derived from 3-day-old Sox10LacZ/+; Ink4a-Arf null mice. Syngeneic control cells were melan-Ink4a-Arf-1.

first: Temesgen

middle: D

last: Fufa

first: Melissa

last: Harris

first: Dawn

middle: E

last: Watkins-Chow

first: Denise

last: Levy

first: David

middle: U

last: Gorkin

first: Lingyun

last: Song

first: Alexias

last: Safi

first: Gregory

last: Crawford

first: Elena

last: Sviderskaya

first: Dorothy

last: Bennett

first: Andrew

middle: S

last: McCallion

first: Stacie

last: Loftus

first: William

last: Pavan


title: Comparison of mouse cancer cell line global gene expression [MG2]

summary: We compared different mouse cancer cell lines to identify their unique cell signatures.

overall_design: Samples from different cancer cell lines were analyzed using Genespring 12.5 GX to obtain the  data.


title: Gene expression profiling of P53/R26 +/+ (n=2) versus P53/R26-Zeb2tg/tg (n=3) thymic tumors

status: Public on May 23 2015

city: Ghent

first: Kaat

last: Durinck

address: Corneel Heymanslaan 10

department: Biomolecular Medicine

country: Belgium

institute: Center for Medical Genetics

summary: Early T-cell precursor leukemia (ETP-ALL) is a high-risk subtype of human leukemia that is poorly understood at the molecular level. Here, we report translocations targeting the zinc finger E-box binding transcription factor ZEB2 as a new and recurrent genetic lesion in immature/ETP-ALL. Using a conditional gain-of-function mouse model, we demonstrate that sustained Zeb2 expression perturbs normal T-cell differentiation and initiates T-cell leukemia. Moreover, Zeb2 driven mouse leukemia exhibit some features of the human immature/ETPALL gene expression signature, as well as an enhanced leukemia-initiation potential and activated JAK/STAT signaling through transcriptional activation of IL7R. This study reveals ZEB2 as a novel oncogene in the biology of immature/ETP-ALL and paves the way towards pre-clinical studies of novel compounds for the treatment of this aggressive subtype of human T-ALL using our Zeb2 driven mouse model.

overall_design: Conditional Zeb2 knockin mouse model was developed and crossed into p53 null background. Murine T-cell leukemia/lymphoma tumors developed both in the p53 null control and the p53 null Zeb2 transgenic group. In this experiment, gene expression profiling was performed on these murine leukemias to determine the transcriptional program associated with sustained Zeb2 expression in the context of P53 null driven murine T cell leukemogenesis.

first: Steven

last: Goossens

first: Pieter

last: Van Vlierberghe

first: Joni

last: Van der Meulen

first: Jody

last: Haigh


title: Expression data from a mouse small cell lung cancer (SCLC) cell line, KP1, transfected with Notch-ICD

status: Public on May 21 2015

city: Stanford

first: Julien

last: Sage

address: 265 Campus Drive, SIM1 G2078

department: Pediatrics

institute: Stanford University

summary:
Transient transfection of activated Notch1 (Notch1-ICD) decreases cellular proliferation and reduces the expression of a subset of neuroendocrine genes.
We used microarrays to identify the gene expression changes 48 hours after overexpression of Notch1-ICD.

overall_design: mSCLC cells transfected with Notch1-ICD-ires-GFP were FACS sorted for GFP+ cells 48 hours after transfection. RNA was then extracted and hybridized to Affymetrix GeneChip® Mouse Gene 2.0 ST array.

first: Jing

last: Lim


title: Differential in vivo tumorigenicity of distinct subpopulations from a luminal-like breast cancer model

status: Public on May 26 2015

city: Oslo

first: Nirma

last: Skrbo

address: Ullernchauseen 70

department: Dep of Genetics

country: Norway

institute: Oslo University Hospital

type:
Expression profiling by array
SNP genotyping by SNP array


title: DHA effect on endothelial cells (HUVEC) under proinflammatory condition

status: Public on May 20 2015

city: Baronissi (SA)

first: Rosanna

last: Martinelli

address: Via Allende

department: Medicine and Surgery

institute: Salerno University

summary: Transcriptional profiling of Human Umbilical Vein Endothelial Cells (HUVEC) comparing untreated control cells with IL-1-treated cells with or without pre-treatment with DHA.

overall_design: Three condition experiment: DHA treated HUVEC  cells (25 µmol/L DHA for 48 hours) vs control; IL-1 treated HUVEC  cells (5ng/ml for 3 hours)  vs control; HUVEC treated with 25 µmol/L DHA for 48 hours and then stimulated with 5 ng/mL IL-1β for 3 hours. For each condition, 3 replicates


title: Gene expression data from spinal cord of DRa1-mMOG-35-55 or Vehicle treated DR*1501-Tg mice with EAE

status: Public on May 13 2015

city: portland

first: Arthur

last: Vandenbark

state: OR

address: 3181 SW Sam Jackson Park Rd

institute: Oregon Health and Science University

summary: To evaluate DRα1-mMOG-35-55 effects on CNS inflammation during Experimental allergic encephalomyelitis (EAE) in a more comprehensive manner, we performed microarray analysis on spinal cords from DRα1-mMOG-35-55- vs. Vehicle-treated DR*1501-Tg mice with EAE.  EAE was induced with mMOG-35-55/CFA/Ptx and mice were treated with DRα1-mMOG-35-55 (100ug daily x 3) or Vehicle ,after disease onset at a clinical score of 2.  Twenty four hr after the last treatment, total RNA was isolated from spinal cords and gene expression profiles from pooled RNA were analyzed using the Mouse Gene 2.0 ST Affymetrix GeneChip system

overall_design: RNA was isolated from spinal cords of 3 DRa1-mMOG-35-55 treated mice and 3 Vehicle treated mice,and pooled in to two groups SCV - for Vheicle treatment and SCA - for DRa1-mMOG-35-55 treatment


title: Post-natal development of brown adipocytes in white fat: Phases independent and dependent of the ambient temperature

status: Public on May 03 2015

first: Monika

middle: M

last: Kaczmarek

summary: Decreased ambient temperature, from birth to weaning, significantly reduced fat mass (FM) and adiposity in developing mice. Changes in FM content in 10 day-old mice raised at 17°C were not accompanied by precocious induction of brown adipocytes in inguinal white adipose tissue (WAT). Brown phenotype was induced in 21 day-old mice independently of ambient temperature (17°C or 29°C) however the expression of Ucp1 and other brown fat biomarker genes was greater in animals raised at 17°C suggesting increased adaptive thermogenesis. Accordingly, we predict that the induction of brown adipocytes in WAT follows a strict developmental program and the number of potential brown adipocytes in WAT is determined genetically.

overall_design: Microarray analysis of gene expression was performed on inguinal white adipose tissue dissected from 10 and 21 day-old mice kept at different temperature conditions, that is, in mice maintained at 17°C or 29oC during early post-natal development.

first: Agnieszka

last: Chabowska-Kita

first: Leslie

last: Kozak


title: Disruption of Cytochrome c Oxidase Function Induces Warburg Effect and Metabolic Reprogramming

status: Public on May 05 2015

first: Dawei

middle: W

last: Dong

state: Pennsylvania

address: 3620 Hamilton Walk

department: Biomedical Sciences

institute: University of Pennsylvania

summary: Defects in mitochondrial oxidative phosphorylation complexes, altered bioenergetics and metabolic shift are often seen in cancers. Here we show a role for the dysfunction of electron transport chain component, cytochrome c oxidase (CcO) in cancer progression. We show that genetic silencing of the CcO complex by shRNA expression and loss of CcO activity in multiple cell types from the mouse and human sources resulted in metabolic shift to glycolysis, loss of anchorage dependent growth and acquired invasive phenotypes. Disruption of CcO complex caused loss of transmembrane potential and induction of Ca2+/Calcineurin-mediated retrograde signaling. Propagation of this signaling, includes activation of PI3-kinase, IGF1R and Akt, Ca2+ sensitive transcription factors and also, TGF1, MMP16, periostin that are involved in oncogenic progression. Whole genome expression analysis showed up regulation of genes involved in cell signaling, extracellular matrix interactions, cell morphogenesis, cell motility and migration. The transcription profiles reveal extensive similarity to retrograde signaling initiated by partial mtDNA depletion, though distinct differences are observed in signaling induced by CcO dysfunction. The possible CcO dysfunction as a biomarker for cancer progression was supported by data showing that esophageal tumors from human patients show reduced CcO subunits IVi1 and Vb in regions that were previously shown to be hypoxic core of the tumors. Our results show that mitochondrial electron transport chain defect initiates a retrograde signaling. These results suggest that a defect in CcO complex can potentially induce tumor progression.

overall_design: Total RNA from control and CcO IVi1 silenced cells was extract. Three independent samples were generated for control and silenced, respectively.

first: Satish

last: Srinivasan

first: Manti

last: Guha

first: Kelly

middle: A

last: Whelan

first: Gordon

last: Ruthel

first: Yasuto

last: Uchikado

first: Shoji

last: Natsugoe

first: Hiroshi

last: Nakagawa

first: Narayan

middle: G

last: Avadhani


title: The p53 Target Gene Siva Enables Tumorigenesis

status: Public on May 15 2015

first: Stephano

last: Spano Mello

address: 269 Campus Drive

summary: Siva is a p53target gene essential for p53-dependent apoptosis, although it can also promote proliferation through inhibition of p53 in some settings. Thus, the role of Siva in tumorigenesis remains unclear. Surprisingly, we find that Siva loss inhibits non-small cell lung cancer (NSCLC) development, suggesting that Siva facilitates tumorigenesis. Similarly, Siva knockdown in mouse and human NSCLC cell lines decreases proliferation and transformation. To gain an understanding of the molecular basis for the reduced proliferation and transformation resulting from Siva knockdown, we performed gene expression profiling experiments on LSZ4 and LSZ2 cells after Siva knockdown by lentiviral transduction with each of the two previously characterized shRNAs (shSiva1 and shSiva2) and each of two control shRNAs (shLacZ and shGFP). Hierarchical clustering revealed a notable difference in gene expression profiles between Siva knockdown and control samples. Differentially expressed genes were analyzed for enrichment in Gene Ontology (GO) terms using GeneSpring Analysis. We found that the most enriched GO terms included immune regulation – consistent with Siva’s known role in regulating NFкB signaling – as well as cell migration and metabolic processes.

overall_design: RNA from LSZ2 and LSZ4 non small cell lung cancer cells expressing control (shGFP1, shLacz) or Siva (shSiva1, shSiva2) hairpins was used.  A total of seven control samples and eight test samples using different cell lines and hairpins were used.

first: Jeanine

last: Van Nostrand

last: Mello

first: Laura

last: Attardi


title: Characterization of Anatomical, Macromolecular, and Gene Expression Changes in the Retinal and Retinal Pigmented Epithelium of the nm3342 Mouse: A Potential Model of Serous Retinal Detachment

status: Public on May 16 2015

city: Santa Barbara

first: Steven

middle: K

last: Fisher

address: BLDG. 571 Lagoon Rd.

department: Neuroscience Research Institute

institute: University of California, Santa Barbara

summary: To characterize gene expression changes in mice following serous retinal detachments, we employed whole genome microarray expression profiling as a tool to identify genes with the potential effects on the neural retina as well as retinal pigmented epithelium.   Total RNA was harvested from nm3342 (mutant) and age-matched wild-type (C57Bl/6J) mice at P30 or P365 for examination using microarray analysis.

overall_design: Retinas and retinal pigmented epithelium was harvested from both age-matched mutant and wild-type mice.

first: Gabriel

last: Luna

first: Qirui

last: Hu


title: Transcriptomic analysis reveals novel mechanistic insight into murine biological responses to multi-walled carbon nanotubes in lungs and cultured lung epithelia cells

city: Ottawa

first: Sarah

last: Labib

state: Ontario

address: 204b-50 Colombine

country: Canada

institute: Health Canada


title: Gene expression profiles of FGF-treated prostate cancer cells

status: Public on May 29 2015

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: Fibroblast growth factor 23 (FGF23) is a member of endocrine FGF subfamily, which includes FGF19, FGF21 and FGF23. We explored the question of whether different FGF ligands are activating the same transcriptional program in prostate cancer (PCa) cells or whether there are unique or partially overlapping activities as well.

overall_design:
We stimulated biological duplicates of LNCaP cells with FGF2 (classical FGF), FGF19 or FGF23 and collected mRNAs after 24 hrs. We then carried out expression array analysis using Agilent expression arrays.
Multiple group comparisons

first: Michael

last: Ittmann


title: CCR2+ vs. CCR2- murine hematopoietic stem cells

status: Public on May 01 2015

city: Charlestown

first: Kamila

last: Naxerova

state: MA

address: 149 13th Street

department: Center For Systems Biology

institute: Massachusetts General Hospital / Harvard Medical School

summary: Comparative analysis of FACS-sorted CCR2- and CCR2+ HSC in the steady state. CCR2+ HSC have fourfold higher proliferative rates than CCR2- HSC, are are biased towards the myeloid lineage and dominate the migratory HSC population.

overall_design: Comparison of pooled CCR2- and CCR2+ HSC (bone marrow from 20 mice pooled for each sample), three biological replicates each.

first: Partha

last: Dutta


title: Expression data from decitabine-treated and non-treated BR5FVB1-Akt cells

status: Public on Jun 03 2015

city: Boston

middle: Solomon

last: Goldberg

address: 450 Brookline Avenue

department: Cancer Immunology and AIDS

institute: Dana-Farber Cancer Institute

summary:
The DNA methyl transferase inhibitor decitabine regulates gene expression in cancer cells.
We used microarrays to detail the globle programming of gene expression, and identified a distinct class of immunoregulartory genes up-regulated upon decitabine treatment in ovarian cancer cells.

overall_design: BR5FVB1-Akt cells were treated with or without 10 uM of dectiabine for 72 hours. Total RNA was extracted and whole-transcript gene arry (Mouse gene ST 2.0) was performed.

first: Lei

last: Wang


title: Target genes of BRG1 in human embryonic stem cells

status: Public on Apr 28 2015

city: RTP

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: BRG1-SWI/SNF complex is an important chromatin remodeling complex that involved in various biological processes. Here we described the genome-wide binding of histone acetylation upon BRG1 depletion in human embryonic stem cells.

overall_design: Human embryonic stem cells were treated with either scrambled siRNA or siRNA against BRG1 for 48 h, and each treatment has three replicates.

first: Yuan


title: Gene expression signature of gemcitabine resistance in human gastric cancer cell line

city: Sendai

first: yuriko

last: saiki

state: Miyagi

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

department: Molecular Pathology

institute: Tohoku University School of Medicine

summary: We examined the microarray-based expression profiles of the cells to identify genes associated with gemcitabine resistance

overall_design: Using a set of parental and gemcitabine resistant cell line, MKN28 and RMKN28, we studied mRNA transcription levels by microarray analysis to see if there are any of the key molecules for development of acquisition of the GEM resistance.

first: Y

last: Saiki

first: A

last: Horii


title: Transcriptomic analysis of mouse lung tissue exposed to multiwalled carbon nanotubes (Mitsui7)

summary: There is great interest in substituting animal with in vitro experimentation in human health risk assessment, but there are rather few comparisons of in vitro and in vivo biological responses to engineered nanomaterials (ENM).  We used high-content genomics tools, to compare in vivo pulmonary responses of multiwalled carbon nanotubes (MWCNT) to those in vitro in cultured lung epithelial cells at the global transcriptomic level. Mice were exposed via a single intratracheal instillation to 18, 54 or 162 μg of Mitsui7 and samples were collected at 24 hours post-instillation.

overall_design: This experiment examined the pulmonary transcriptional response of female C57BL/6 mice exposed to Mitsui7 multiwalled carbon nanotubes at three doses: D1 (18 μg), D2 (54 μg), D3 (162 μg), and vehicle control. Each dose group was examined 24 hours post-exposure. Each dose group had 6 biological replicates. There were a total of 22 samples included in the final analysis using a two-color reference design.

first: Andrew

last: Williams

first: Sabina

last: Halappanavar


title: Transcriptomic analysis of cultured lung epithelial cells exposed to multiwalled carbon nanotubes (Mitsui7)

summary: There is great interest in substituting animal with in vitro experimentation in human health risk assessment, but there are rather few comparisons of in vitro and in vivo biological responses to engineered nanomaterials (ENM).  We used high-content genomics tools, to compare in vivo pulmonary responses of multiwalled carbon nanotubes (MWCNT) to those in vitro in cultured lung epithelial cells at the global transcriptomic level. Mouse lung epithelial cells were incubated with 12.5, 25 and 100 μg/ml of Mitsui7 and harvested at 24 hours post-exposure.

overall_design: This experiment examined the mouse lung epithelial cell line FE1's response following exposure to Mitsui7 multiwalled carbon nanotubes at three doses: D1 (12.5 μg/ml), D2 (25 μg/ml), D3 (100 μg/ml), and vehicle control. Each dose group was examined 24 hours post-exposure. Each dose group had 6 biological replicates. There were a total of 22 samples included in the final analysis using a two-color reference design.


title: An alternative pluripotent state confers interspecies chimaeric competency [Microarray]

status: Public on May 06 2015

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

summary: Here we show that by simple modulation of extrinsic signaling pathways, a new class of pluripotent stem cells, referred to as intrinsic state-epiblast stem cells (IS-EPIs), could be efficiently derived from different stages of the early embryo. IS-EPIs share features of primed pluripotency yet are distinct from EpiSCs in their molecular characteristics and ability to colonize post-implantation embryos. We performed Microarray analysis and compared global gene expression pattern among amplified RNA samples from  ESCs, EpiSCS, IS-EPIs as well as in vivo isolated Epiblasts.

overall_design: Examination of global gene expression profiles multiple pluripotent stem cell types

first: Jun

last: Wu


title: Nociceptor HDAC4 regulates inflammatory pain

status: Public on Apr 23 2015

city: Woodbury

first: Megan

last: Crow

state: New York

address: 500 Sunnyside Blvd

institute: Cold Spring Harbor Laboratory

summary: Transcriptional alterations are characteristic of persistent pain states but the key regulators remain elusive. Using a conditional knockout (cKO) strategy in mice we sought to determine whether loss of the transcriptional co-repressor histone deacetylase four (HDAC4) would have implications for sensory neuron transcription and nociception. HDAC4 was found to be largely dispensable for transcriptional regulation of naïve sensory neurons but was required for transcriptional responses after injury, with Calca and Trpv1 expression consistently downregulated in HDAC4 cKO compared to littermate controls (0.2-0.44 fold). This downregulation corresponded to reduced sensitivity to capsaicin in vitro (76% +/- 4.4% wildtype capsaicin responders vs 56.9% +/- 4.7% cKO responders) and to reduced thermal hypersensitivity in the complete Freund’s adjuvant model of inflammatory pain (1.3-1.4 fold improvement). These data indicate that HDAC4 is a novel inflammatory pain mediator and may be a good therapeutic target, capable of orchestrating the regulation of multiple downstream effectors.

overall_design: Total RNA was extracted from HDAC4 cKO and HDAC4 fl/fl naïve adult lumbar dorsal root ganglia (n=3/group). mRNA expression was compared using Affymetrix Mouse Gene Arrays (Mouse Gene 2.0ST) run on a GeneChip Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner.

first: Stephen

middle: B

last: McMahon


title: Mechanisms of haptoglobin protection against hemoglobin peroxidation triggered endothelial damage

status: Public on Apr 30 2015

city: Zurich

first: Christian

middle: Andreas

last: Schaer

address: Raemistrasse 100

country: Switzerland

institute: University Hospital Zurich

summary:
Extracellular hemoglobin (Hb) has been recognized as a disease trigger in hemolytic conditions such as sickle cell disease, malaria and blood transfusion. In vivo, many of the adverse effects of free Hb can be attenuated by the Hb scavenger acute phase protein haptoglobin (Hp). The primary physiologic disturbances that can be caused be free Hb are found within the cardiovascular system and Hb triggered oxidative toxicity towards the endothelium has been promoted as a potential mechanism. The molecular mechanisms of this toxicity as well as of the protective activities of Hp are not yet clear. Within this study we systematically investigated the structural, biochemical and cell biologic nature of Hb toxicity in an endothelial cell system under peroxidative stress.
We identified two principal mechanisms of oxidative Hb toxicity that are mediated by globin degradation products and by modified lipoprotein species, respectively. The two damage pathways trigger diverse and discriminative inflammatory and cytotoxic responses. Hp provides structural stabilization of Hb and shields Hb’s oxidative reactions with lipoproteins providing dramatic protection against both pathways of toxicity. By these mechanisms Hp shifts Hb’s destructive pseudo-peroxidative reaction into a potential anti-oxidative function during peroxidative stress.

overall_design:
HPAEC: A two color common reference design was chosen with 4-8 independent biological replicates of each condition. Each experimental sample (Cy5 labeled) was hybridized against a non-treated reference sample (Cy3 labeled).
HUVEC: A two color common reference design was chosen with 3-4 independent biological replicates of each condition. Each experimental sample (Cy5 labeled) was hybridized against a non-treated reference sample (Cy3 labeled).

first: Dominik


title: Differential in vivo tumorigenicity of distinct subpopulations from a luminal-like breast cancer model (expression)

first: Nirma

last: Skrbo

summary: The cellular heterogeneity of one patient derived orthotopic breast cancer xenograft model (PDBCX) was investigated using flow cytometry , combined with assessment of in vivo tumorigenicity and whole genome expression profiling. Epithelial cell adhesion molecule (EpCAM) was revealed as a highly specific cell surface marker of the human tumor cell population in both xenografts.   Based on expression patterns observed in primary tumor tissue, SSEA-4 and CD24 were chosen as markers to further subdivide the luminal tumor cells into four subpopulations. FACS sorting was used to isolate four cell subpopulations.   Results: In vivo tumorigenicity assay showed that SSEA-4+/CD24+ cells were non-tumorigenic, while the three other subpopulations were tumorigenic. Tumors resulting from the SSEA-4+/CD24- subpopulation of luminal cancer cells, did not express CD24, while tumors arising from the SSEA-4-/CD24-, and SSEA-4-/CD24+ populations both recapitulated the original tumor containing all four subpopulations. Whole genome expression analysis revealed distinct transcriptional profiles, and 44 genes were significantly differentially expressed when comparing the tumorigenic vs non-tumorigenic populations. Several interesting genes putatively suppressing the cancer cells ability to initiate tumors in vivo were upregulated in the non-tumorigenic population. We here show that tumor initiating cells within one primary tumor evidently included more than one phenotype. Furthermore, with respect to cell surface marker expression, one of the subpopulations produced tumors unlike both the originating cells, and the original tumor.   Discussion: Our results imply that subpopulations from one primary tumor can give rise to dissimilar daughter tumors. These tumors may not necessarily respond to the same targeted treatment, and thereby represent a therapy escape mechanism. This study highlights that to remove the risk of breast cancer recurrence, inhibition of the molecules critical for driving the tumor progression in several tumor cell subpopulations might be essential

overall_design: Gene expression was measured in four cell subpopulations isolated from Patient derived human luminal-like breast cancer xenograft. Four replicates from  three subpopulations and three replicates from one subpopulation.

first: Geir-Olav

last: Hjortland

first: Alexandr

last: Kristian

first: Lina

last: Prasmickaite

first: Ruth

last: Holm

first: Olav

last: Engebråten

first: Therese

last: Sørlie

first: Gunhild

last: Mælandsmo

first: Kristin

last: Andersen


title: Gene expression in the heart of mouse with myocardial infarction

status: Public on Apr 25 2015

city: Luxembourg

first: Yvan

last: Devaux

address: 120 route d'Arlon

country: Luxembourg

institute: LIH

summary: To investigate the function of genes in heart, we performed gene expression microarray for the hearts of 4 sham-operated mice and 4 anterior interventricular artery ligated mice.

overall_design: 4 mice were subjected to permanent occlusion of the anterior interventricular artery while 4 mice were subjected to the identical surgical procedure without coronary ligation. 24 hours after the permanent occlusion, mice were sacrificed and the ventricles of heart were harvested for RNA isolation. Total RNAs were labelled and hybridised on Agilent Mouse SurePrint G3 Array. One sample per array.


title: Generation of neural progenitor cells by chemical cocktails and hypoxia

status: Public on Apr 27 2015

city: Shanghai

first: Lin

last: Cheng

address: Yueyang Road 320

country: China

institute: New Building #1003, SIBCB

summary: Neural progenitor cells (NPCs) can be induced from somatic cells by defined factors. Here we report that NPCs can be generated from mouse embryonic fibroblasts by a chemical cocktail, namely VCR (V, VPA, an inhibitor of HDACs; C, CHIR99021, an inhibitor of GSK-3 kinases and R, Repsox, an inhibitor of TGF-β pathways), under a physiological hypoxic condition. These chemical-induced NPCs (ciNPCs) resemble mouse brain-derived NPCs regarding their proliferative and self-renewing abilities, gene expression profiles, and multipotency for different neuroectodermal lineages in vitro and in vivo. Further experiments reveal that alternative cocktails with inhibitors of histone deacetylation, glycogen synthase kinase, and TGF-β pathways show similar efficacies for ciNPC induction. Moreover, ciNPCs can also be induced from mouse tail-tip fibroblasts and human urinary cells with the same chemical cocktail VCR. Thus our study demonstrates that lineage-specific conversion of somatic cells to NPCs could be achieved by chemical cocktails without introducing exogenous factors.

overall_design: To access the exact identity of ciNPCs, we extracted mRNA from mouse brain-derived NPCs (as control NPCs), MEFs, ciNPCs at passage 5 and passage 13 and compared the global gene expression patterns of these cells by microarray analysis.

first: Wenxiang

last: Hu

first: Binlong

last: Qiu

first: Jian

last: Zhao

first: Yongchun

last: Yu

first: Wuqiang

last: Guan

first: Min

last: Wang

first: Wuzhou

last: Yang

first: Gang

last: Pei


title: Alterations in gene expression following knockdown of thioredoxin 1 (TR1) with stable viral transduction

city: Salt Lake City

first: Philip

last: Moos

state: UT

department: Pharmacology & Toxicology

country: USA

institute: University of Utah

summary:
This experiment was to determine if we could observe changes in gene expression following the attenuation of one of the primary redox regulators of cells - thioredoxin reductase 1. The experiment was set up with two cell lines that expressed different basal levels of TR1.
LOX cells represent an aggressive melanoma in xenograft models and are high expressors of TR1 while SK Mel-28 cells represent a non-aggressive melanoma in xenografts adn are low expressors of TR1.

overall_design:
The experimental design was to set up direct comparisons for melanoma cells with the induction of a control miRNA or the miRNA directed against TR1 - with an evaluation of the uninduced situation.
Melanoma cell lines stabily transfected with tetracyclin-inducible microRNA - directed at either control, or to TR1.


title: Lineage conversion induced by pluripotency factors involves transient passage through  an iPSC stage

first: Ori

last: Bar-Nur

address: 185 Cambridge st.

department: Center of Regenerative medicine

institute: Harvard University

summary: Brief expression of pluripotency-associated factors such as Oct4, Klf4, Sox2 and c-Myc (OKSM), in combination with differentiation-inducing signals, has been reported to trigger transdifferentiation of fibroblasts into other cell types. Here we show that OKSM expression in mouse fibroblasts gives rise to both induced pluripotent stem cells (iPSCs) and induced neural stem cells (iNSCs) under conditions previously shown to induce only iNSCs. Fibroblast-derived iNSC colonies silenced retroviral transgenes and reactivated silenced X chromosomes, both hallmarks of pluripotent stem cells. Moreover, lineage tracing with an Oct4-CreER labeling system demonstrated that virtually all iNSC colonies originated from cells transiently expressing Oct4, whereas ablation of Oct4+ cells prevented iNSC formation. Lastly, an alternative transdifferentiation cocktail that lacks Oct4 and was reportedly unable to support induced pluripotency yielded iPSCs and iNSCs carrying the Oct4-CreER-derived lineage label. Together, these data suggest that iNSC generation from fibroblasts using OKSM and other pluripotency-related reprogramming factors requires passage through a transient iPSC state.

overall_design: 5 samples were anlyzed in total, 2 induced pluripotent stem cell (iPSC) lines ,  1 brain-derived neural stem cell (NSC) line and 2 induced NSC lines (iNSCs)

first: Konrad

last: Hochedlinger


title: Loss of TET2 in hematopoietic cells leads to DNA hypermethylation of active enhancers and induction of leukemogenesis [Agilent]

city: Dundee

first: Kasper

middle: Dindler

last: Rasmussen

address: Dow Street

department: Division of Molecular, Cellular, and Developmental Biology (MCDB)

institute: School of Life Sciences, University of Dundee

summary: DNA methylation is tightly regulated throughout mammalian development and altered DNA methylation patterns are a general hallmark of cancer. The methylcytosine dioxygenase TET2 is frequently mutated in hematological disorders, including acute myeloid leukemia (AML), and has been suggested to protect CpG islands and promoters from aberrant DNA methylation. In this study, we present a novel Tet2-dependent leukemia mouse model that closely recapitulates gene expression profiles and hallmarks of human AML1-ETO induced AML. Using this model, we show that the primary effect of Tet2 loss in pre-leukemic hematopoietic cells is progressive and widespread DNA hypermethylation affecting up to 25% of active enhancer elements. In contrast, CpG island and promoter methylation does not change in a Tet2-dependent manner, but increase relative to population doublings. We confirm this specific enhancer hypermethylation phenotype in human AML patients with TET2 mutations. Analysis of immediate gene expression changes reveals rapid deregulation of a large number of genes implicated in tumorigenesis, including many downregulated tumor suppressor genes. Hence, we propose that TET2 prevents leukemic transformation by protecting enhancers from aberrant DNA methylation, and that it is the combined silencing of several tumor suppressor genes in TET2-mutated hematopoietic cells that contribute to increased stem cell proliferation and leukemogenesis.

overall_design: Gene expression profiles (Agilent SurePrint G3 Mouse GE 8x60K arrays)  of FACS-sorted in vivo GMP cells (Lin-cKit+Sca1-CD16/32+CD150-) isolated from bone marrow of recipient mice one month after transplantation of WT bone marrow or splenic cells from two independent moribond Tet2-/-:AE leukemic mice (LeuA/AE1), or LeuB/AE3)

first: Guangshuai

last: Jia

first: Jens

middle: V

last: Johansen

first: Marianne

middle: T

last: Pedersen

first: Nicolas

last: Rapin

first: Frederik

middle: O

last: Bagger

first: Bo

last: Porse

first: Olivier

last: Bernard

first: Jesper

last: Christensen

first: Kristian

last: Helin


title: Loss of TET2 in hematopoietic cells leads to DNA hypermethylation of active enhancers and induction of leukemogenesis (Affymetrix)

status: Public on Apr 22 2015

overall_design: Gene expression profiles from Tet2-/-;AML1-ETO and Tet2fl/fl;AML1-ETO in vitro-grown hematopoietic cells were compared using GeneChip Mouse Gene ST 2.0 Arrays (Affymetrix). Expression changes were investigated at early (passage 2) and late (passage 10) timepoints after Tet2 disruption.


title: Impact of conditional autophagy knockout on cytotoxic CD8 T cells at day 7 and day 8 after influenza infection

city: Victoria

first: Julian

middle: J.

last: Lum

state: BC

address: 2410 Lee Avenue

department: Deeley Research Centre

institute: BC Cancer Agency

summary: To investigate the role of autophagy on cytotoxic CD8 T cells, we developed a new mouse that expresses an Atg5 gene with loxP sites up- and downstream of the exon 3, Cre-recombinase, T cell receptor specific for the OVA peptide SIINFEKL and the congenic marker Thy1.1. These cells were adoptively transferred into wild type mice followed by influenza-OVA infection and induction of Atg5 knockout at day 5 after infection. Tracking the kinetic of the cells show, that the Atg5 knockout cells do not expand as much as the control cells and they experience complete contraction within few days. No memory population is established. To investigate differences in Atg5 knockout cells versus control cells we sorted the donor cells at the peak of immune response and investigated their gene expression profile via microarray analysis.

overall_design: 10.000 naive CD8 T cells were isolated from the spleens of transgenic mice (untreated) and were adoptively transferred into naive wild type mice. On the next day these mice got intranasally infected with 15 plaque forming units of Influenza strain A/PR8-OVA. At day 5 to 8, Atg5 knockout was induced by intraperitoneal tamoxifen administration. At day 7 and 8, donor cells were sorted from spleens, RNA was isolated and investigated via microarray. Three groups of transgenic cells were compared in two independent experiments: Atg5 knockout cells were compared to two groups of control cells: 1. heterozygously Atg5 loxP expressing cells and 2. homozygously Atg5 loxP expressing cell that lacked the expression of Cre-recombinase.

first: Katrin

last: Schlie

middle: J


title: Mito-protective autophagy is impaired in erythroid cells of aged mtDNA-mutator mice

status: Public on Apr 21 2015

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

summary: Somatic mitochondrial DNA (mtDNA) mutations contribute to the pathogenesis of age-related disorders, including myelodysplastic syndromes (MDS). The accumulation of mitochondria harboring mtDNA mutations in patients with these disorders suggests a failure of normal mitochondrial quality-control systems. The mtDNA-mutator mice acquire somatic mtDNA mutations via a targeted defect in the proofreading function of the mtDNA polymerase, PolgA, and develop macrocytic anemia similar to that of patients with MDS. We observed an unexpected defect in clearance of dysfunctional mitochondria at specific stages during erythroid maturation in hematopoietic cells from aged mtDNA-mutator mice. Mechanistically, aberrant activation of mechanistic target of rapamycin signaling and phosphorylation of uncoordinated 51-like kinase (ULK) 1 in mtDNA-mutator mice resulted in proteasome mediated degradation of ULK1 and inhibition of autophagy in erythroid cells. To directly evaluate the consequence of inhibiting autophagy on mitochondrial function in erythroid cells harboring mtDNA mutations in vivo, we deleted Atg7 from erythroid progenitors of wildtype and mtDNA-mutator mice. Genetic disruption of autophagy did not cause anemia in wild-type mice but accelerated the decline in mitochondrial respiration and development of macrocytic anemia in mtDNA-mutator mice. These findings highlight a pathological feedback loop that explains how dysfunctional mitochondria can escape autophagy-mediated degradation and propagate in cells predisposed to somatic mtDNA mutations, leading to disease.

overall_design: We used microarrays to identify expression profiles and pathways that are differentially activated or suppressed in Ter119+ bone marrow cells isolated from phlebotomized wildtype or Polg mutant mice

first: XiuJie

last: Li-Harms

first: Mondira

last: Kundu


title: Differential adipose tissue gene expression profiles in abacavir treated patients that may contribute to cardiovascular risk: a microarray study

status: Public on Apr 16 2015

city: Birmingham

first: Mohsen

last: Shahmanesh

address: Vincent Drive

department: School of Clinical and Experimental Medicine, College of Medical and Dental Sciences

institute: University of Birmingham

summary:
Objective: to compare changes in gene expression by microarray from subcutaneous adipose tissue from HIV treatment naïve patients treated with efavirenz based regimens containing abacavir (ABC), tenofavir (TDF) or zidovidine (AZT). There were significant divergence between ABC and the other two groups 6 months after treatment in genes controlling cell adhesion and environmental information processin, with some convergence at 18 months. Compared to HIV negative controls the ABC group, but not AZT or TDF, showed enrichment of genes controlling adherence junction at six months and 184 months (adjusted p <0.05), and cell matrix adhesion (adjusted p<3.4E-0.5) at 6 months. Tight junction (p=0.03), gap junction (p<0.05) and leukocyte transendothelial migration (p=0.03) were over-expressed in ABC compared to TDF at 6 m. Enrichment pathways and individual genes controlling cell adhesion and environmental information processing were specifically dysregulated in the ABC group compared with the other treatments, There was little difference between AZT and TDF.
Conclusion: After initiating treatment, there is divergence in the expression of genes controlling cell adhesion and environmental information processing between ABC and both TDF and AZT in subcutaneous adipose tissue. If similar changes are taking place in other tissues including the coronary vasculature, they may contribute to the observed increased risk of cardiovascular events reported in patients recently started on abacavir-containing regimens.

overall_design: 31 HIV treatment naïve patients were randomised to receive either zidovidine (AZT)/lamivudine or tenofavir (TDF)/emtricitabine in fixed dose preparations. Both groups also received efavirenz. Patients were tested before treatment (AZT n=15, TDF n=16) and at 6 (AZT n=9, TDF n=12) and 18-24 (AZT n= 8, TDF n=9) months after starting therapy. Tests included extensive biochemical tests, tests of body fat distribution and subcutaneous fat biopsies. 15 HIV negative patients were similarly tested. Patients and controls were matched for age, ethnicity, gender, weight, BMI, pretreatment CD4 count, viral load, and family history of cardiovascular disease and diabetes. In a second part of the study patients on their initial antiretroviral regimen containihg abacavir (ABC)/lamivudine plus efavirenz for 6 months (n=9) and 184 months (n=10) were similarly tested. the ABC-treated group were matched in all the listed characteristice with the other two groups. None of the patients had ever experienced an AIDS-defining disease or developed lipodystrophy over the study period. Fat biopsies were snap frozen until assayed. Microarray methods: RNA was extracted for microarray and array data generated using a Qiagen RNeasy Lipid Tissue Mini Kit. Total RNA was converted into labeled cDNA using the WT-Ovation Pico RNA Amplification System and samples were hybridized to an Agilent Whole Human Genome Microarray 4x44K (AMADID 014850, Agilent Technologies). The Agilent arrays were scanned with the Agilent Technologies DNA Microarray Scanner G2505C with default settings. Scanned images were extracted and initial quality control performed in Agilent Feature Extraction (AFE) software version 10.7.3.1. Additional quality assessment was performed using the R arrayQualityMetrics package. As no major experimental problems could be detected, all microarrays were included in subsequent analysis steps. The dataset was read into R and processed using the Agi4x44PreProcess package with options to use the AFE Processed Signal as foreground signal and BG Used signal as background adjusted signal. The data were then normalized by the quantile method using the limma function normalize Between Arrays.  Probeset filtering was performed using the Agi4x44PreProcess filter method using AFE provided flags to identify features with quantification errors of the signal, reducing the 45,015 features on the Agilent Whole Human Genome Microarray 4x44K array by 38%, or 17,264 features. Residual technical batch effects were corrected using the ComBat method implemented in the SVA R package.Since patients were not randomised to the ABC treatment all samples were treated as unrelated. Gene expression differences between treatment arms were assessed using the linear modeling features implemented in the limma package in R. Multiple testing across contrasts was performed using the limma global method with Benjamini-Hochberg approach for control of false discovery rate (FDR). Gene set enrichment analysis of GO terms and KEGG pathways was performed using the conditional hypergeometric test implemented in the GOstats R package. Statistical significance of gene set enrichment was performed using the Benjamini-Hochberg correction method implemented in the EMA R package .

first: Kenneth

last: Phillips

first: Meg

last: Boothby

first: Jeremy

last: Tomllinson


title: Analysis of mir-17~92 targets in motor neurons

status: Public on Apr 14 2015

city: Taipei

first: Jun-An

last: Chen

address: 128 Academia Road, Section 2

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

summary: To identify mir-17~92 targets in MNs, a set of target candidate genes from the intersection of upregulated genes found only in the mir-17~92 KO MNs that were predicted to be direct targets of mir-17~92 by TargetScan.

overall_design: Motor neurons in the spinal cord from WT ; Hb9::GFP and mir-17~92 -/- ; Hb9::GFP embryos at E12.5 were isolated by FACS. Subsequently, both WT and KO motor neurons (GFPon) and non motor neurons (GFPoff) transcriptome were analyzed by Agilent SurePrint G3 Mouse GE 8x60K Microarray (Agilent-G4858A-028005).

first: Ya-Lin

last: Lu


title: The Fitness Consequences of Aneuploidy Are Driven by Condition-Dependent Gene Effects

status: Public on Apr 12 2015

city: Seattle

first: Maitreya

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

institute: University of Washington

summary: Aneuploidy is a hallmark of tumor cells, and yet the precise relationship between aneuploidy and a cell’s proliferative ability, or cellular fitness, has remained elusive. In this study, we have combined a detailed analysis of aneuploid clones isolated from laboratory-evolved populations of Saccharomyces cerevisiae with a systematic, genome-wide screen for the fitness effects of telomeric amplifications to address the relationship between aneuploidy and cellular fitness. We found that aneuploid clones rise to high population frequencies in nutrient-limited evolution experiments and show increased fitness relative to wild type. Direct competition experiments confirmed that three out of four aneuploid events isolated from evolved populations were themselves sufficient to improve fitness. To expand the scope beyond this small number of exemplars, we created a genome-wide collection of >1,800 diploid yeast strains, each containing a different telomeric amplicon (Tamp), ranging in size from 0.4 to 1,000 kb. Using pooled competition experiments in nutrient-limited chemostats followed by high-throughput sequencing of strain-identifying barcodes, we determined the fitness effects of these >1,800 Tamps under three different conditions. Our data revealed that the fitness landscape explored by telomeric amplifications is much broader than that explored by single-gene amplifications. As also observed in the evolved clones, we found the fitness effects of most Tamps to be condition specific, with a minority showing common effects in all three conditions. By integrating our data with previous work that examined the fitness effects of single-gene amplifications genome-wide, we found that a small number of genes within each Tamp are centrally responsible for each Tamp’s fitness effects. Our genome-wide Tamp screen confirmed that telomeric amplifications identified in laboratory-evolved populations generally increased fitness. Our results show that Tamps are mutations that produce large, typically condition-dependent changes in fitness that are important drivers of increased fitness in asexually evolving populations.

overall_design: Each of these arrays is a Comparative Genomic Hybridization experiment to detect copy number differences between a reference strain and a strain of interest.

first: Anna

last: Sunshine


title: Comparison of Ly6D- common lymphoid progenitors (CLPs) from OcnCre;iDTR control and mutant mice.

status: Public on Apr 10 2015

first: Vionnie

middle: W. C.

last: Yu

address: 185 Cambridge St

department: Center for Regenerative Medicine

institute: Massachusetts General Hospital/Harvard University

summary: We performed gene expression microarray comparing Ly6D- CLPs isolated from OcnCre;iDTR control and mutant mice by flow cytometry.

overall_design: Ly6D- CLPs were isolated from the bone marrow of OcnCre;iDTR control or mutant mice by flow cytometry and subjected to Affymetrix microarray comparison of gene expression. Markers used to define Ly6D- CLP by flow cytometry was: LineageLo, cKit+, Sca+, CD127+, Thy1.2-, Ly6D-

first: David

last: Scadden


title: Gene Array Data from p0 Mouse pup; ascending and descending aortas; fibulin-4 knockout and control

city: Saint Louis

first: Jessica

last: Wagenseil

state: MO

address: 1 Brookings Dr.  Box 1185

department: Mechanical Engineering and Materials Sciences

institute: Washington University

summary:
Fibulin-4 plays an essential role in elastic fiber formation, though it's exact function is unclear. Mice lacking the fibulin-4 gene develop cutis laxa with thoracic aortic aneurysms and have narrowed descending aortic diamaters, dying shortly after birth. Another model that disrupt elastic fiber formation, elastin gene knockeds, are also perinatally lethal and have narrowed descending aortas but do not develop thoracic aneurysms.
We hypothesized that there may be altered gene expression to explain the altered anatomy based on aortic tissue location we observed, which may provide therapeutic target(s)

overall_design: Ascending and descending aortas of p0 mouse pups were dissected, pooled in groups of eight, and homogenized to isolate RNA and we used microarrays on the pooled samples to identify genes that had expression significantly changed.

first: Jesse

last: Procknow


title: G-CSF mobilizes CD34+ regulatory monocytes that inhibit Graft-versus-Host Disease

status: Public on Apr 01 2015

city: London

first: Stephen

last: Henderson

address: Paul O'Gorman Building

department: Cancer Institute

institute: UCL

summary:
Administration of G-CSF mobilizes a unique population of CD11b+Ly6C+CD34+mature monocytes that can inhibit GVHD in murine models of BMT via an iNOS-dependent mechanism.  The transcriptional profiles of flow sorted lineage-CD11b+CD34+ cells from G-CSF treated mice were compared with conventional splenic Ly6C+ and Ly6C- monocytes, progenitor cells and cultured myeloid-derived suppressor cells.  Further comparisons were made with lineage-CD11b+CD34+ cells from G-CSF treated mice that had been grown in culture or that were derived from iNOS ko mice.
We used microarrays to detail the global programme of gene expression underlying diffrenetiation of each of these cell types

overall_design: Lin-CD11b+CD34+ populations were isolated directly from the spleens of G-CSF-treated C57BL/6 mice or iNOS ko mice.  In untreated C57BL/6 mice, Lin-CD11b+CD115+Ly6C+ and Lin-CD11b+CD115+Ly6C- monocytes were isolated from the spleen and Lin-CD117+CD115+CD135-Ly6C+CD11b- common monocyte progenitors were isolated from the bone marrow.  Myeloid-derived suppressor cells (Ly6C+CD11b+ cells derived from G-CSF, GM-CSF and IL-13 cultured C57BL/6 bone marrow) were also isolated and compared with the above populations.  Lin-CD11b+CD34+ spleen cells derived from G-CSF-treated C57BL/6 mice were cultured for 3 days in Flt3 ligand and SCF and then compared to the original input population.

first: Marie

last: Rubio

first: Ronjon

last: Chakraverty


title: Gene expression profile of a MDH2-mutated tumor

status: Public on Apr 08 2015

city: MADRID

first: ALBERTO

middle: CASCÓN

last: SORIANO

state: MADRID

address: C/MELCHOR FERNÁNDEZ ALMAGRO Nº3

department: HUMAN GENETICS

country: Spain

institute: CENTRO NACIONAL DE INVESTIGACIONES ONCOLÓGICAS

summary: Transcriptional analysis of one primary paraganglioma

overall_design: One sample (primary paraganglioma) were hybridized onto a cDNA microarray in order to investigate differentially expressed genes

first: A

last: Cascón

first: I

last: Comino-Méndez