title: The transcriptional repressor BLIMP1 curbs host-defenses by suppressing expression of the chemokine CCL8

city: Worcester

first: Daniel

middle: R

last: Caffrey

state: MA

address: 364 Plantation St

institute: UMASS Medical School

summary: The transcriptional repressor BLIMP1 is a master regulator of B and T cell differentiation. To examine the role of BLIMP1 in innate immunity we used a conditional knockout (CKO) of Blimp1 in myeloid cells and found that Blimp1 CKO mice were protected from lethal infection induced by Listeria monocytogenes. Transcriptome analysis of Blimp1 CKO macrophages identified the murine chemokine (C-C motif) ligand 8, CCL8 as a direct target of Blimp1-mediated transcriptional repression in these cells. BLIMP1-deficient macrophages expressed elevated levels of Ccl8 and consequently Blimp1 CKO mice had higher levels of circulating CCL8 resulting in increased neutrophils in the peripheral blood, promoting a more aggressive anti-bacterial response. Mice lacking the Ccl8 gene were more susceptible to L. monocytogenes infection than wild type mice. While CCL8 failed to recruit neutrophils directly, it was chemotactic for γ/δ T cells and CCL8-responsive γ/δ T cells were enriched for IL-17F. Finally, CCL8-mediated enhanced clearance of L. monocytogenes was dependent on γ/δ T cells. Collectively, these data reveal an important role for BLIMP1 in modulating host-defenses by suppressing expression of the chemokine CCL8.

overall_design: RNA (5μg) was isolated from WT and Blimp1 CKO BMDM untreated or infected for 2 hours with L.monocytogenes (MOI=5). Three biological replicates were performed for each experimental condition. The gene chip mouse genome 430 2.0 Array (Affymetrix) was used.  Biological replicates were normalized using the GCRMA method and analyzed using various Bioconductor tools.

first: Martina

last: Severa

first: Katherine

last: Fitzgerald


title: The human AlkB homologue 4 interacts with proteins associated with transcription (expression)

status: Public on Dec 01 2013

city: Oslo

first: Leonardo

middle: A.

last: Meza-Zepeda

address: Ullernchausseen 70

department: Dept. of Tumor Biology

country: Norway

institute: The Norwegian Radium Hospital

summary: The Fe(II)- and 2-oxoglutarate (2OG)-dependent dioxygenase AlkB from E. coli is a demethylase which repairs alkyl lesions in DNA, as well as RNA, through a direct reversal mechanism. Humans possess nine AlkB homologues (ALKBH1-8 and FTO). ALKBH2 and ALKBH3 display demethylase activities corresponding to that of AlkB, and both ALKBH8 and FTO are RNA modification enzymes. The biochemical functions of the rest of the homologues are still unknown. To increase our knowledge on the functions of ALKBH4 and ALKBH7 we have here performed yeast two-hybrid screens to identify interaction partners of the two proteins. While no high-confidence hits were detected in the case of ALKBH7, several proteins associated with chromatin and/or involved in transcription were found to interact with ALKBH4. For all interaction partners, the regions mediating binding to ALKBH4 comprised domains previously reported to be involved in interaction with DNA or chromatin. Furthermore, some of these partners showed nuclear co-localization with ALKBH4. However, the global gene expression pattern was only marginally altered upon ALKBH4 over-expression, and larger effects were observed in the case of ALKBH7. Although the molecular function of both proteins remains to be revealed, our findings suggest a role for ALKBH4 in regulation of gene expression or chromatin state and support the previous association of ALKBH7 with spermatogenesis.

overall_design: Gene expression profiling of ALKBH4 and ALKBH7 over-expression

first: Linn

middle: G

last: Bjornstad

first: Trine

middle: J

last: Meza

first: Marit

last: Otterlei

first: Solveig

middle: M

last: Olafsrud

middle: A

first: Pal

middle: O

last: Falnes


title: Deciphering genomic alterations in colorectal cancer through transcriptional subtype-based network analysis

status: Public on Dec 22 2013

city: Nashville

first: Jing

last: Zhu

state: TN

country: USA

institute: Vanderbilt University

summary: High-throughput genomic studies have identified thousands of genetic alterations in colorectal cancer (CRC). Distinguishing driver from passenger mutations is critical for developing rational therapeutic strategies. Because only a few transcriptional subtypes exist in previously studied tumor types, we hypothesize that highly heterogeneous genomic alterations may converge to a limited number of distinct mechanisms that drive unique gene expression patterns in different transcriptional subtypes. In this study, we defined transcriptional subtypes for CRC and identified driver networks/pathways for each subtype, respectively. Applying consensus clustering to a patient cohort with 1173 samples identified three transcriptional subtypes, which were validated in an independent cohort with 485 samples. The three subtypes were characterized by different transcriptional programs related to normal adult colon, early colon embryonic development, and epithelial mesenchymal transition, respectively. They also showed statistically different clinical outcomes. For each subtype, we mapped somatic mutation and copy number variation data onto an integrated signaling network and identified subtype-specific driver networks using a random walk-based strategy. We found that genomic alterations in the Wnt signaling pathway were common among all three subtypes; however, unique combinations of pathway alterations including Wnt, VEGF, Notch and TGF-beta drove distinct molecular and clinical phenotypes in different CRC subtypes. Our results provide a coherent and integrated picture of human CRC that links genomic alterations to molecular and clinical consequences, and which provides insights for the development of personalized therapeutic strategies for different CRC subtypes.

overall_design: To characterize the embryonic development of colon, we conducted a time course microarray study using the inbred C57BL/6 (Jackson Laboratories, Bar Harbor, ME) mice. Seven samples corresponding to the mouse colonic development from E13.5 to E18.5 and adult (eight week post-natal) were collected. RNA samples were submitted to the Vanderbilt Functional Genomics Shared Resource (FSGR, http://array.mc.vanderbilt.edu), where RNA was hybridized to the Affymetrix Mouse Genome 430 2.0 GeneChip Expression Arrays (Santa Clara, CA) according to manufacturer’s instructions. The RMA algorithm was used for data normalization. Mouse gene symbols were mapped to human gene symbols by the Human and Mouse Orthology list available from the Mouse Genome Informatics (http://www.informatics.jax.org/).

first: Jeffrey

middle: L

last: Franklin

first: Robert

last: Coffey

first: Bing

last: Zhang


title: Array_data_MEF_Kera_Coculture

status: Public on Nov 26 2013

city: Heidelberg

first: Peter

last: Angel

address: Im Neuenheimer Feld 280

department: Signal Transduction and Growth Control

country: Germany

institute: German Cancer Research Center

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Genome-wide analysis of keratinocyte gene expression during their course of differentiation in presence or absence of JNK1,2-deficient or wildtype immortalized mouse embryonic fibroblasts (MEFs)

summary: Analysis of keratinocyte differentiation in presence or absence of fibroblast-derived JNK-dependent soluble factors in vitro. The hypothesis tested in the present study was that JNK-dependent fibroblast-derived soluble factors promote an efficient keratinocyte differentiation. Results provide important information about reduced expression of a subset of differentiation associated genes in keratinocytes in the absence of JNK-dependent fibroblast-derived soluble factors.

overall_design: In vitro transwell co-culture experiments were performed using jnk1-/-jnk2-/- or wildtype immortalized mouse embryonic fibroblasts (MEFs) and differentiating primary normal human epidermal keratinocytes (NHEK) over a time course of 6 days. Total RNA was obtained from NHEK prior to cultivation with MEFs (day 0) and every second day (days 2, 4, and 6) during co-culture. MEFs have been described previously in Sabapathy et al. (2004) Mol Cell 15:713-25.

first: Marion

last: Schumacher

first: Bettina

last: Füssel

first: Zbigniew

last: Rogon


title: The human AlkB homologue 4 interacts with proteins associated with transcription

type:
Expression profiling by array
Methylation profiling by array


title: Differential gene expression in CD11b+ splenocytes from mice subject to social threat vs. control (II)

city: Los Angeles

first: Steve

last: Cole

state: CA

address: 11-934 Factor Bldg, UCLA

department: Medicine

institute: UCLA School of Medicine

summary:
Gene expression profiling was carried out on splenocyte mRNA samples collected from 6 animals subject to repeated social threat and 6 animals subject to non-threatening control conditions (pooled into 3 groups of 2).  The primary research question is whether gene expression differs in CD11b+ splenocytes from animals exposed to social threat vs non-threatening control conditions.
Keywords: Risk prediction

overall_design:
Gene expression profiling was carried out on splenocyte mRNA samples collected from 6 animals subject to repeated social threat and 6 animals subject to non-threatening control conditions (pooled into 3 groups of 2).  The primary research question is whether gene expression differs in CD11b+ splenocytes from animals exposed to social threat vs non-threatening control conditions.
This study provides an additional body of data from the same general protocol used in Series GSE16661, and will support more extensive analyses than the original study.


title: Transcript abundance comparison between BALB/c ears inoculated with Leishmania mexicana and Leishmania mexicana plus promastigote secretory gel (PSG)

status: Public on Dec 17 2013

city: London

first: Emilie

middle: De La Llave

last: Giraud

address: Keppel Street

department: IID

country: United Kingdom

institute: London School of Hygiene and Tropical Medicine

summary: To determine the modulation of gene expression of  Leishmania mexicana(M379)-inoculated BALB/c ears  in the presence of promastigote secretory gel (PSG)

overall_design: A genome-wide transcriptional analysis was performed by comparing the gene expression profiles of Leishmania mexicana- inoculated BALB/c ears and Leishmania mexicana plus PSG BALB/c ears.  Leishmania mexicana amastigotes were purified from mouse cutaneous lesions and transformed in vitro in metacycic promastigotes (MT). After 6, 24 and 48 hours, ears were collected and processed for RNA extraction. Three Biological replicates per condition were run.

first: Rod

last: Dillon

first: Paul

last: Bates

first: Matthew

last: Rogers


title: Reversible mRNA and miRNA expression patterns in the transcriptome of Rasless fibroblasts

status: Public on Nov 27 2013

city: Salamanca

first: Alicia

middle: Ginel

last: Picardo

state: Select a State or Province

address: Campus Miguel de Unamuno

country: Spain

institute: Cic, Salamanca

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

summary:
Analysis of the transcriptional profiles of mRNA and microRNA in Rasless fibroblasts. 4-Hydroxy-tamoxifen (4-OHT) treatment triggers removal of K-Ras expression in [H-Ras-/-;N-Ras-/-;K-Raslox/lox;RERTert/ert ] mouse fibroblasts (named K-Raslox) generating “Rasless” MEFs which are unable to proliferate, but recover proliferative ability after ectopic expression of constitutively active downstream kinases such as BRAF and MEK1.
Using Affymetrix microarrays, we compared the transcriptional profiles of Rasless fibroblasts to those of K-Raslox (MEFs lacking only H-Ras and N-Ras). We also compared the transcriptional profile of Rasless cells with those of BRAF and MEK1-transfected Rasless cells which recovered proliferative ability. Re-entry of the Rasless cells into cell cycle progression through ectopic expression of activated BRAF or MEK1 resulted in full reversion of most transcriptional alterations identified in cells lacking the three canonical Ras proteins.

platform_organism:
Mus musculus
synthetic construct

overall_design:
Pre-confluent cell cultures corresponding to the different Ras genotypes were harvested for extraction of total RNA and miRNA samples, and subsequent hybridization on Affymetrix microarrays. The different sets of experimental mRNA samples analyzed here included (i) 8 samples K-Raslox (proliferating cells expressing only K-Ras, considered as Control): 4 biological replicates, technical duplicates each; (ii) 7 samples Rasless: the same cells after treatment with 4-OHT for 12 days (to become non-proliferating fibroblasts), including 4 biological replicates and technical duplicates from 3 of them; (iii) 3 samples BRAF-rescued MEFs (Rasless cells harboring activated BRAF constructs, with regained proliferative ability): 3 biological replicates; (iv) 3 samples MEK1-rescued MEFs (Rasless cells harboring activated MEK1 constructs, with regained proliferative ability): 3 biological replicates; and their respective controls harbouring the vempty vectors (v) 2 samples Hygromycin-resistant (control for BRAF-transfected Rasless cells) including 2 biological replicates, and (vi) 4 samples Puromycin-resistant (control for MEK1-transfected Rasless cells) including 2 biological replicates, technical duplicates each. The gene expression study contains a total of 27 samples.
Regarding the miRNA expression study, the experimental samples analyzed included (i) 4 samples samples K-Raslox (used as Control): 2 biological replicates, technical duplicates each; (ii) 8 samples Rasless: the same cells after treatment with 4-OHT for 6 days (2 biological replicates, technical duplicates each) and 12 days (2 biological replicates, technical duplicates each); (iii) 4 samples BRAF-rescued, including 2 biological replicates, technical duplicates each; (iv) 4 samples MEK1-rescued,including 2 biological replicates, technical duplicates each, and (v) 4 samples Puromycin-resistant empty vector, containing 2 biological replicates, technical duplicates each. The miRNA expression study contains a total of 24 samples.

first: Sami

last: Azrak

last: Ginel-Picardo

first: Eugenio

last: Santos


title: Expression data from mDCT cell-line over-expressing hMR

status: Public on Nov 23 2013

city: Tokyo

first: Kohei

last: Ueda

country: Japan

institute: The University of Tokyo

summary:
Target gene of mineralocorticoid receptor (MR) is comparatively unknown, although distal convoluted tubule (DCT) expresses MR in in vivo.
We used microarray and immortalized murine DCT cell-line overexpressing human MR with treatment of aldosterone to elucidate target genes of MR in DCT.

overall_design: mDCT overexpresses human MR by lipofection and is treated for 3 hours with ethanol (g1), or 10^-9 M aldosterone (g2), or 10^-7 M aldosterone (g3), or 10^-7 M aldosterone with pretreatment of 5 x 10^-6 M spironolactone (g4) for 2 hours.


title: Exon array analysis for SFEBq differentiation-defective clones and good clones

status: Public on Dec 03 2013

city: Kyoto

first: Shinya

last: Yamanaka

address: 53 Kawahara-machi, Shogoin, Sakyo-ku

institute: Center for iPS Cell Research and Applicaton (CiRA), Kyoto University

summary: It remains controversial whether human induced pluripotent stem cells (hiPSCs) are distinct from human embryonic stem cells (hESCs) in their molecular signatures and differentiation properties. We examined the gene expression and DNA methylation of 49 hiPSC and 10 hESC lines and identified no molecular signatures that distinguished hiPSCs from hESCs. Comparisons of the in vitro directed neural differentiation of 40 hiPSC and four hESC lines showed that most hiPSC clones were comparable to hESCs. However, in seven hiPSC clones, significant amount of undifferentiated cells persisted even after neural differentiation and resulted in teratoma formation when transplantated into mouse brains. These differentiation-defective hiPSC clones were marked by higher expression of several genes, including those expressed from long terminal repeats of human endogenous retroviruses. These data demonstrated that many hiPSC clones are indistinguishable from hESCs, while some defective hiPSC clones need to be eliminated prior to their application for regenerative medicine.

overall_design: We extracted total RNA from 3 differentiation-defective clones, 3 good clones and 2 somatic cells, and hybridized them to Affymetrix exon arrays.

first: M

last: Koyanagi-Aoi

first: Y

last: Sato


title: Expression data from murine irf4-/- and irf4+/+ mature B cells purified by magnetic cell separation

status: Public on Nov 22 2013

city: New York

first: Ulf

last: Klein

state: NY

address: 1130 St. Nicholas Avenue

department: Herbert Irving Comprehensive Cancer Center

institute: Columbia University

summary: Gene expression profiling of murine irf4-/- and irf4+/+ splenic B cells identifies genes regulated by the transcription factor IRF4 in quiescent mature B cells.

overall_design: B cells from 12-week old irf4-/- and irf4+/+ littermate mice were isolated by magnetic depletion of non-B cells from splenic mononuclear cells. RNA was isolated. Labeled cRNA was hybridized to microarrays and genes specifically expressed in irf4-/- vs. irf4+/+ samples.

first: Giorgia

last: Simonetti


title: miRNA profiling of control and ischemic samples in vitro and in vivo

status: Public on Nov 21 2013

city: Leicester

first: Dalbir

middle: Kaur

last: Dhiraj

state: Leicestershire

address: Lancaster Road

department: MRC Toxicology Unit

institute: Medical Research Council

summary: miRNA microarray profiling of primary cortical neurons exposed to 4h oxygen and glucose deprivation  (OGD) in vitro. RNA samples collected at 8h post-OGD terminaion. miRNAs were also profiled in mice exposed to 3- vessel occlusion model of stroke. RNA samples collected from contralateral (control) and ipsilateral (infarct) sides of the brain following 24h of reperfusion.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Comparison of control and ischemic samples across 3 biological replicates for both in vitro and in vivo samples. In vitro cultures consisted of primary cortical neurons derived from E17 rat Wistar embryos. In vivo samples were obtained from C57bl/6 mice exposed to three-vessel occlusion.

first: Elvina

last: Crysanthou


title: Gene expression profile of patients affected by Metachromatic Leukodystrophy (MLD)

city: Milan

first: Martina

last: Cesani

address: via Olgettina 58

country: Italy

institute: TIGET-HSR

summary: The genome-wide analysis of T lympocytes from 24 MLD patients and a corresponding number of matched controls reveals a list of differentially expressed genes that can be used to build classifiers that correctly classify not only patients and controls with high sensitivity and specificity, but also MLD patients into early- and late-onset clinical classes. Among the most differentially expressed genes, the class of metallothioneins shows a consistent and significant over-expression, confirmed also in affected tissues of patients and mouse models of MLD and other Lysosomal Storage Disorders, indicating metallothioneins a novel dynamic biomarker of disease progression and treatment response in this class of diseases. Moreover, gene onthology analysis performed on the microarray data suggest an involvement of stress response- and autophagy-related pathways as pathological mechanisms in MLD.

overall_design: Total RNA extracted from T-lymphocytes of 24 MLD patients and 24 age-and sex-matched controls

first: Alessandra

last: Biffi

first: Clemens

last: Scherzer


title: Runx3 function in splenic NK cells (IL-2 or IL-15)

status: Public on Nov 18 2013

city: Rehovot

first: Joseph

last: Lotem

department: Molecular genetics

country: Israel

institute: Weizmann institute of science

summary: NK cells are innate immune cells that recognize and kill foreign, virally-infected and tumor cells without the need for prior immunization. NK expansion following viral infection is IL-2 or IL-15-dependent.

overall_design: To identify Runx3 responsive genes, NK cells were isolated from spleen of WT and Runx3-/- mice . Ten samples (5 WT and 5 Runx3-/-)  of freshly isolated NK cells  were separately obtained from individual mice. Cells were cultured for 7 days  with IL-2 or IL-15.

first: Ditsa

last: Levanon

first: Dena

last: Leshkowitz

first: Yoram

last: Groner


title: Essential functions for ID proteins at multiple checkpoints in natural killer T cell development

status: Public on Nov 19 2013

city: Chicago

first: Barbara

last: Kee

state: Illinois

address: 924 E57th st

department: Pathology

institute: The University of Chicago

summary: Thymic iNKT cell development is divided into four stages (stage 0-3) that are characterised, in C57BL/6 mouse strain, by the differential expression of surface markers, such as CD24, CD44 and NK1.1. During transition from immature to mature iNKT cell subsets, gene expression is tightly regulated. Here, we used microarray analysis to detail the influence of the transcriptional regulator ID3 during iNKT cell maturation in the thymus.

overall_design: Stage 1 (Tet+CD24-CD44-NK1.1-) and Stage 2 (Tet+CD24-CD44+NK1.1-) iNKT cells from WT and Id3KO thymi were FACS sorted for RNA extraction and Affymetrix hybridisation.

first: Mikael

last: Sigvardsson


title: Comparison of gene expression in motor pools with differential vulnerability in ALS

status: Public on Nov 15 2013

first: Krista

middle: Joan

last: Spiller

state: New York

address: 630 W 168th street

summary: ALS is a uniformly fatal neurodegenerative disease in which motor neurons in the spinal cord and brain stem are selectively lost. Individual motor - groups of motor neurons innervating single muscles - show widely varying degrees of disease resistance: in the final stages of ALS, nearly all voluntary movement is lost but eye movement and eliminative and sexual functions remain relatively unimpaired. These functions are controlled by motor neurons of the oculomotor (III), trochlear (IV) and abducens (VI) nuclei in the midbrain and brainstem, and by Onuf’s nucleus in the lumbosacral spinal cord, respectively. Correspondingly, in ALS autopsies the oculomotor and Onuf’s nuclei are almost completely preserved. We used microarray profiling of isolated wildtype mouse motor neurons to identify genes whose expression was characteristic of both oculomotor and Onuf’s nuclei but not of vulnerable lumbar spinal neurons, or vice versa.

overall_design: Three wild-type C57BL/6J  P7 male animals were perfused with 30% sucrose, lumbosacral spinal cord and midbrain regions were rapidly recovered, embedded in OCT compound, and frozen in liquid nitrogen. 12 µm-thick cryosections were mounted on RNAse-free, PEN-foil covered glass slides (Zeiss), fixed for 2 min in 100% EtOH, rinsed in 50% EtOH, stained with 1% cresyl violet for 2 min, rinsed with 50% EtOH, dehydrated in graded solutions of ethanol and air dried prior to LCM using PALM Microbeam system (Zeiss). From each animal, ~200 DL, L5, and oculomotor motor neurons were collected directly in lysis buffer.  RNA was purified using Absolutely RNA, NanoPrep kit (Stratagene, La Jolla, CA). RNA integrity was assessed on the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).  At least 1.5 ng of purified RNA was the starting material used in the WT-Ovation Pico RNA Amplification System (Nugen, San Carlos,CA) with the FL-Ovation cDNA Biotin Module V2 (Nugen) to generate labeled probe. 10 µg of biotinylated cRNA from three independent samples for each motor neuron group isolated by LCM was hybridized to on Affymetrix (Santa Clara, CA) Mouse Genome 430 2.0 Arrays. Gene ontology and pathway analysis was performed using DAVID Bioinformatics Resources 6.7 (National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD).

first: Artem

last: Kaplan

first: Kevin

middle: C

last: Kanning

first: Christopher

middle: E

last: Henderson


title: Antigen availability determines CD8+ T cell-dendritic cell interaction kinetics and T cell fate decisions.

city: Cambridge

first: Gabriela

last: Alexe

address: 415 Main St.

department: Computational Biology and Bioinformatics

institute: Broad Institute

overall_design: This experiment compares the transciptional changes in antigen specific murine CD8 T cells (P14 T cells) after exposure in vivo to dendritic cells (DC) pulsed with low dose cognate peptide (1uM KAVYNFATC), high dose cognate peptide (100uM KAVYNFATC) or no antigen. Splenic dendritic cells were freshly isolated, peptide pulsed, washed and then adoptively transferred s.c. to the right footpad of C57BL/6 hosts.  After 18h, freshly isolated P14 CD8 T cells were labelled with CMFDA and adoptively transferred iv.  Two hours after T cell transfer, anti-L selectin antibody was given iv.  At 12 and 24 hours, recipients were sacrificed and The right popliteal LN was harvested at 12 or 24h post T cell transfer and a single cell suspension was created and stained with PE CD4, B220 and CD19 (dump channel). Cells were then sorted on a FacsARIA for being non-doublets, CMFDA positive and dump channel negative.  The experiment was conducted for 39 samples out of which 35 passsed transcriptional quality control tests. The phenotypic distribution for the 35 samples includes:   (1) high dose (100uM KAVYNFATC ) cognate peptide pulsed samples harvested at 12h post T cell transfer: 6  biological replicates  (2) high dose (100uM KAVYNFATC ) cognate peptide pulsed samples harvested at 24h post T cell transfer: 7  biological replicates   (3) low dose (1uM KAVYNFATC) cognate peptide pulsed samples harvested at 12h post T cell transfer: 6  biological replicates  (4) low dose (1uM KAVYNFATC) cognate peptide pulsed samples harvested at 24h post T cell transfer: 9  biological replicates  (5) no antigen pulsed samples harvested at 12h post T cell transfer: 3  biological replicates  (6) no antigen pulsed samples harvested at 24h post T cell transfer: 4  biological replicates.

first: Sarah

last: Henrickson


title: Microarray Studies on the STAT5A MUTANT.

status: Public on Nov 12 2013

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

summary: Stat5+/- mice were bred into the C57BL/6 background. Stat5+/- mice were intercrossed and mouse embryonic fibroblasts (MEFs) were isolated from 12.5-13.5-day WT or Stat5-/- fetuses. The retroviral-expression vector carrying a DNA binding domain mutant Stat5A (E437/E438?AA) or tyrosine-phosphorylated Stat5A Y694F mutation based on an MSCV-IRES-GFP backbone (gift from Richard Moriggl, Ludwig-Boltzmann Institute, Vienna, Austria) was infected into Stat5-/- MEFs. FACS was used to select GFP+ cells. After 5 hours starvation in serum free medium with 0.1% of BSA, MEFs were treated with growth hormone for 2 hours. Total cellular RNA from each group of the MEFs was extracted with TRIzol reagent (Invitrogen) according to the manufacturer's instructions. Microarray analyses were performed using Affymetrix Mouse Genome 430 2.0 GeneChips (Affymetrix, Santa Clara, CA) (four groups, biological replicates for each group). Expression values were determined with GeneChip Operating Software (GCOS) v1.1.1 software. RMA signals were summarized using GeneSpring GX 10.0.1 (Agilent) and normalized by quantile normalization. All data analysis was performed with GeneSpring software GX 10.01.

overall_design: Total 4 groups (EA, EA_GH, YF, YF_GH), biological duplicate replication for each group


title: Compare RNA profile between LPS+CPN and LPS+CPN+GGOH treated peritoneal macrophages

city: Dallas

first: jinyong

last: kim

state: tx

address: 5332 Harry Hines Blvd

department: Molecular Genetics

institute: UT southwestern medical Institute

summary: To find out genes regulated by geranylgeraniol (GGOH) treatment in peritoneal macrophage, we compared gene expression of cells treated with 200ng ml LPS and 250 micromolar compactin versus 200ng ml LPS, 250 micromolar compactin and 100micromolar GGOH.

overall_design: To find out upregulated or downregulated genes regulated by GGOH treatment in peritoneal macrophage (LPS+CPN treated cell).

first: Jinyong

last: Kim


title: Expression data from peritoneal macrophages stimulated with trehalose-6,6'-dimycolate (TDM)

status: Public on Nov 14 2013

city: Bunkyo-ku

first: Chikara

last: Komiya

state: Tokyo

address: 1-5-45 Yushima

department: Molecular Endocrinology and Metabolism

institute: Tokyo Medical and Dental University

summary:
Macrophage-inducible C-type lectin (Mincle, Clec4e) is a pathogen sensor that recognizes pathogenic fungi and Mycobactrium tuberculosis. We perfomed microarray analysis using peritoneal macrophages stimulated with TDM, a mycobacterial cell wall glycolipid that is known to be a Mincle ligand.
Many chemokine and cytokine genes were upregulated in wildtype macrophages stimulated with TDM. Upregulation of these genes were completely abolishd in Mincle KO macrophages.

overall_design: Peritoneal macrophages from WT and Mincle KO mice were stimulated with TDM or vehicle for 24 h (3 samples each). Microarray analysis was performed using Affymetrix Mouse 430 2.0.

first: Takahisa

last: Matsuda

first: Miyako

last: Tanaka

first: Takayoshi

last: Suganami

first: Yoshihiro

last: Ogawa


title: Analyses of mIRNA transcript level following exposure to triptolide

city: Minneapolis

first: Aaron

last: Sarver

state: MN

address: 425 East River Road

department: Masonic Cancer Center

institute: University of Minnesota

summary: Analyses of mirna transcript levels following exposure to the drug triptolide in vitro and prodrug minnelide in xenograft pancreatic tumor mouse models.

overall_design: Response of pancreatic adenocarcinoma cell lines to minelide in vitro and exposure to its prodrug triptolide in SCID mouse tumors derived from the same cell lines.


title: p53 reactivation in liver tumors

status: Public on Nov 11 2013

first: Edward

middle: R.

last: Kastenhuber

address: 1275 York Ave

department: Cancer Biology & Genetics

institute: Memorial Sloan-Kettering Cancer Center

summary: We induced liver tumors by transforming liver progenitor cells (LPC) with retroviruses expressing oncogenic Ras coupled to tetracycline transactivator  together with an inducible shRNA targeting p53. Transformed LPCs were orthotopical transplanted into recipient livers and after tumor onset mice were fed with either  Doxycycline containing chow or normal chow. 8 days later tumors were harvested and RNA was extracted.

overall_design: RNA was extracted using Trizol. For microarray experiment, HrasV12 driven liver tumors harboring tet-off shp53 were treated with Doxycycline for 0 day (p53 OFF, as control) or 8 days (p53 ON). Samples were assessed by Affymetrix 430 2.0 mouse microarray.

first: Darjus

last: Tschaharganeh

first: Wen

last: Xue

first: Scott

last: Lowe


title: Expression data from E11.5 mouse branchial arch 1 (BA1) - comparison between Ezh2lox/lox and Wnt1Cre Ezh2lox/lox embryos

status: Public on Nov 09 2013

city: Zurich

first: Michal

last: Okoniewski

state: Zurich

address: Binzmühlestrasse 130

country: Switzerland

institute: ETH Zurich

summary: Conditional ablation of Ezh2 in the neural crest lineage results in loss of the neural crest-derived mesenchymal derivatives. In this data sheet we determine gene expression analysis in Ezh2lox/lox and Wnt1Cre Ezh2lox/lox in E11.5 mouse BA1 cells.

overall_design: Conditional ablation of Ezh2 in the neural crest lineage was achieved by crossing Wnt1creEzh2lox/wt mice with Ezh2lox/lox mouse lines. We analyzed a total of 6 samples including 3 biological replicates from Ezh2lox/lox embryos and 3 biological replicates from Wnt1cre Ezh2lox/lox embryos.

first: Daniel

last: Schwarz

first: Lukas

last: Sommer


title: Expression data from three HEK293 derivatives with or without doxycycline

city: New Orleans

first: Tadahide

last: Izumi

state: LA

address: 533 Bolivar Street

department: Otolaryngology

institute: Louisiana State University Health Sciences Center

summary:
To examine the effect of wtAPE1 and ubiquitin-APE1 fusion proteins on global gene expression. Total RNA from HEK293 derivatives that express vector alone (ctl), wt-APE1, or ubiquitin-APE1 fusion in the presence of doxycycline were analyzed.

Three HEK293 derivatives expressing none (vector), wtAPE1, or Ub-APE1 fusion linked at APE1's 24th Lys were incubated with/without doxycycline (dox) 2 µg/ml for 16 hr. Each -/+ dox cultures were triplicated. Total RNA was extracted (Qiagen) and then analyzed by LSU's bioinformatics core. The quality and quantity of total RNA was assessed using an ND-1000 Spectrophometer (NanoDrop, Wilmington, DE), NanoChip assay and Bioanalyzer 2100 (Agilent). All samples were of high integrity with RIN # greater than 7 and A260/280 greater than 1.8. Procedures for cDNA synthesis, sense target labeling, and hybridization were carried out as described at http://media.affymetrix.com/support/technical/appnotes/wt_appnote.pdf (Affymetrix, Redwood City, CA). All experiments were performed using GeneChip Exon 1.0 ST Arrays and Whole Transcript Sense Target labeling Assay (version 4, Affymetrix). Overnight hybridization of fragmented single-stranded DNA was carried out in an Affymetrix GeneChip Hybridization Oven 640, then washed and stained with streptavidin-phycoerythrin using GeneChip 450 Microfluidics Station (Affymetrix). Chips were scanned with an Affymetrix High Resolution 3000 (G7) scanner. Signal and background intensities were quantitated by pixel intensity using Affymetrix GeneChip Operating Software (GCOS 1.4). Array quality control assessment was carried out using Robust Multi-chip Analysis (RMA) workflow for Core probesets in Expression Console (Affymetrix). Gene-level analysis for differential gene expression was analyzed in GeneSpring 7.3x (Agilent Technologies) using the sample CHP files. The RMA method was used for the background correction, normalization and average expression measures for the probesets. An expression filter (20th percentile cutoff) was applied to remove genes with low signal intensity values. For differential gene expression analysis, the Welch ANOVA test with asymptotic p-value computation was applied and transcripts with p-value (< 0.05) and fold change (2.0 fold) were selected.

overall_design: Three cell lines (HEK293/pcDNA-FRT empty vector, HEK293/pcDNA-FRT wtAPE1, HEK293/pcDNA-FRT ubAPE1), +/- 2µg/ml doxycycline for 16 h. Triplicates of each cell line/condition. Replicates were averaged.

first: C

middle: S

last: Busso

first: T


title: Effect of W805EC nanoemulsion (NE) on global gene transcription in JawsII dendritic cells in vitro

city: Ann Arbor

first: Paul

middle: Edward

last: Makidon

state: MI

address: 9340 MSRB III, 1150 W. Medical Center Dr.

department: Internal Medicine

institute: University of Michigan

summary:
Nanoemulsion adjuvant affects immune gene expression in dendritic cells.
Microarray was used to asses global changes in gene expression in JAWS II dendritic cells  upon treatment with nanoemulsion (NE) adjuvant W805EC

overall_design: JawsII cell were incubated with NE formulation for 6 and 24 hours, and RNA was extracted for Affymetrix hybridization

first: Anna

middle: U

last: Bielinska


title: Expression data from Sh2b3 Knock-out NOTCH1-induced leukemias

status: Public on Nov 06 2013

first: Alberto

last: Ambesi-Impiombato

department: ICG

summary:
To formally address the tumor suppressor activity of Sh2b3 in vivo, we tested the interaction between oncogenic NOTCH1 and Sh2b3 loss in a retroviral- transduction bone marrow transplantation model of NOTCH-induced T-ALL
Forced expression of activated NOTCH1 in this model typically results in full leukemia transformation 5-10 weeks later.

overall_design: We performed microarray gene expression analysis of Sh2b3 wild type and Sh2b3–/– NOTCH1 induced leukemias

first: Arianne

last: Perez-Garcia

first: Michael

last: Hadler

first: Isaura

last: Rigo

first: Charles

last: LeDuc

first: Kara

last: Kelly

first: Chaim

last: Jalas

first: Elisabeth

last: Paietta

first: Janis

last: Racevskis

first: Jacob

last: Rowe

first: Martin

last: Tallman

first: Maddalena

last: Paganin

first: Giuseppe

last: Basso

first: Wei

last: Tong

first: Wendy

middle: K

last: Chung

first: Adolfo

last: Ferrando


title: Expression data of the endothelial-to-hematopoietic transition in E8.5 concepti

city: Oxford

first: Stephen

last: Taylor

address: Headington

institute: CBRG

summary:
During development a specialised subset of endothelial cells, the haemogenic endothelium, undergo an endothelial-to-haematopoietic transition. This process critically involves the transcription factor Runx1. Here we have isolated a specific subpopulation of endothelial cells using a Runx1 enhancer-reporter transgenic mouse line (23GFP). We have compared the gene expression profile of this population to non-23GFP expressing endothelial cells and CD41 expressing haematopoietic progenitor cells to assess whether 23GFP expression marks a biologically distinct subset of endothelium.
We used affymetrix microarrays to detail the global programme of gene expression underlying the different populations and identified a distinct expression profile of the 23GFP expressing endothelium.

overall_design: 23GFP transgenic mouse embryos were dissected free of the ectoplacental cone at embryonic day E8.5, pooled, and sorted into 23GFP- and 23GFP+ endothelial (VE-Cad+ Ter119- CD45- CD41-) and CD41+ haematopoietic cells (VE-Cad+ Ter119-CD45-CD41+23GFP+) cells by FACS. Triplicate samples for each cell population were analysed. cDNA synthesis, fragmentation, and hybridisation were performed by the Stanford Protein and Nucleic Acid Facility.

first: Marella

last: de Bruijn

first: Gemma

last: Swiers


title: Expression data from ATRA-treated endometrial stromal cells

status: Public on Nov 05 2013

city: Xi'an

first: Jingjing

last: Ma

address: No. 127 Changlexi Road

country: China

institute: Fourth Military Medical University

summary:
Decidualization is critical for the embryonic implantation and successful pregnancy. ATRA can suppress in-vitro decidualization of human endometrial stromal cells (hESCs) induced by MPA and estrogen treatment. However, the mechanism by which RA suppressed estrogen and progesterone induced decidualization of mESCs is not clear.
We used microarrays to investigate the mechanism by which all-trans RA (ATRA) regulates the decidualization of endometrial stroma cells (mESCs).

overall_design: mESCs were isolated at day 4 of pregnancy and cultured with administration of E2 and P4 in the presence or absence of ATRA for 72h.


title: Gene expression data of  brown-like adipocytes from Lgr4 homozygous mutant SVF

status: Public on Nov 07 2013

city: Shanghai

first: ruixin

last: liu

address: 2nd Ruijin Road, Building 11, 925

institute: ruixin liu

summary:
Obesity has become a global health problem. Brown adipose tissue (BAT), specialized for energy expenditure through thermogenesis, potently counteracts obesity. Recently, BAT is also identified in human adults. We found that Lgr4 homozygous mutant (Lgr4m/m) mice display reduced adiposity and exhibit brown-like adipocytes in their WAT depots with higher expression of uncoupling protein 1 (Ucp1). Furthermore, Lgr4 ablation potentiates brown adipocyte differentiation from stromal vascular fraction (SVF) of epididymal WAT (eWAT) in vitro.
We used microarrays to emxamine the gene expression profiles of the brown-like adipocytes differentiated from SVF of wild-type and Lgr4 mutant mice. We identified distinct gene expression profiles of these two groups.

overall_design: To demonstrate Lgr4 ablation can potentiate the differentiation of SVF from eWAT toward brown-like adipocytes in vitro, we isolated SVF from epididymal white adipose tissue (eWAT) of  wild-type (WT) and Lgr4 mutant mice. We then plated SVF cells in 12-well plate, and  differentiated them to brown adipocytes, followed by RNA extraction and hybridization with Affymetrix microarrays.

first: Jiqiu

last: Wang

first: Ruixin

last: Liu

first: Maopei

last: Chen

first: Guang

last: Ning


title: Gene expression changes induced by overexpression of IDH1mut in the sorted mouse bone marrow cells

city: Hannover

first: Anuhar

last: Chaturvedi

address: Cral Neuberg Strasse-1

department: Hematology, Hemostasis, Oncology and Stem Cell Transplantation

institute: Hannover Medical School

summary: Mutations in the enzymes IDH1 and IDH2 have been identified in a wide variety of tumors like glioma, chondrosarcoma, thyroid cancer, lymphoma, melanoma, and in acute myeloid leukemia. Mutated IDH1/2 produces the metabolite 2-hydroxyglutarate (2HG), which interferes with epigenetic regulation of gene expression, and thus may promote tumorigenesis.

overall_design: HoxA9 immortalized bone marrow cells from C57BJ/6 mice were transduced with either empty vector or pSF91-IDH1wt-IRES-EGFP, or pSF91-IDH1mut-IRES-GFP and transplanted in irradiated recipient mice. Four weeks after transplantation, GFP+ cells were sorted from mouse bone marrow, from which total RNA was extracted and subjected to microarray analysis.

first: Michael

last: Heuser


title: microRNA differential regulations gradually mediate genomic instability during cervical intraepithelial neoplasia progression.

status: Public on Nov 02 2013

first: Wenjuan

last: Mo

address: No. 220 Handan Road

department: School of Life Science

institute: Fudan University

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

summary: In most cases human papillomavirus (HPV) infections are cleared from the cervical cells by the immune system itself, but in a few cases, where there is persistent HPV infection, it can lead to cervical intraepithelial neoplasia (CIN) progression and ultimately invasive cervical carcinoma. The cytopathic effect is in general accompanied by chronic inflammation, which produces inflammation cytokines that contribute to DNA damage, and at the same time, aberrations occurred in the host DNA repair mechanisms, thus lead to HPV genomic integration into the host cells which propels cell immortalization. In this study, we reported the genome-wide expression profiles of both microRNAs (miRNAs) and mRNAs from 24 cervical samples with consecutive stages of normal, CIN I (mild dysplasia) and CIN III (severe dysplasia and carcinoma in situ), and presented the SIG++ algorithm which is founded on the evolution process of intermolecular regulation change during disease progression, to identify the significant change of miRNA-mRNA regulations rather than the expression change, across different disease stages, thereupon elucidating the molecular mechanisms of increasing host genomic instability as disease progresses. As reconstructing miRNA differential networks, we found that at each stage of CIN, there respectively exists specific miRNA regulations mediating chronic inflammation persistence, genome instability and cell survival, which coordinately carrys out the integration of HPV genomes into the host cell genomes, and finally results in cell immortalization. Beyond the specific implications for cervical carcinogenesis, this work establishes a new framework for studying the biology of miRNAs in pathogenesis from the perspective of miRNA differential regulation, and helps ensure the comprehensiveness of miRNA-mediated genetic regulatory pathways.

overall_design: There are totally 24 clinical samples in this study comprises three stages: 7 normal cervix samples (HPV-), 9 CIN I samples (HPV+) and CIN III samples (HPV+), where normal refers to the adjacent tissue of early lesions. For each sample, its total RNA was extracted and purified, then separately hybridized to Illumina HumanHT-12 V4.0 expression beadchip (gene symbol) and Illumina Human v2 MicroRNA Expression BeadChip, for examining the expression profiles of mRNAs and miRNAs, respectively.

first: Chao

first: Yan

last: Zhang

first: Hong

last: Lu


title: Association of maternal mRNA with the spindle in mouse oocytes

city: Philadelphia

first: Edward

last: Romasko

state: PA

address: 3307 N Broad St

institute: Temple University

type:
Expression profiling by array
Other

summary: The oocytes of many species, both invertebrate and vertebrate, contain a large collection of localized determinants in the form of proteins and translationally inactive maternal mRNAs. However, it is unknown whether mouse oocytes contain localized MmRNA determinants and what mechanisms might be responsible for their control. We collected intact MII oocytes, enucleated MII oocyte cytoplasts (with the spindle removed), and spindle-chromosome complexes which had been microsurgically removed. RNA was extracted, amplified, labeled, and applied to microarrays to determine if any MmRNA determinants were localized to the SCC.

overall_design: We used microarrays to determine whether maternal mRNAs in mouse oocytes are enriched in the meiotic spindle

first: Keith

last: Latham

first: Uros

last: Midic

first: Dasari

last: Amarnath


title: Transcriptomic responses to high water temperature in Pacific salmon [2008]

status: Public on Nov 01 2013

city: Vancouver

first: Ken

last: Jeffries

state: British Columbia

address: 2424 Main Mall

country: Canada

institute: University of British Columbia

summary: Characterizing a common cellular stress response (CSR) to high water temperature across species and populations is necessary for identifying the capacity of Pacific salmon (Oncorhynchus spp.) to persist in current and future climate warming scenarios, especially for populations at the southern periphery of their species' distributions. In this study, populations of wild adult pink (O. gorbuscha) and sockeye (O. nerka) salmon from the Fraser River, British Columbia, Canada, were experimentally treated to an ecologically relevant 'cool' or 'warm' water temperature to uncover common transcriptomic responses to elevated water temperature.

sample_organism:
Oncorhynchus gorbuscha
Oncorhynchus nerka

overall_design: Ninety-eight samples from three separate temperature exposure studies were analyzed on ninety-eight microarrays, using a common reference design, with multiple biological replicates for each temperature condition for each year of the experiment.

first: Scott

middle: G

last: Hinch

first: Thomas

last: Sierocinski

first: Paul

last: Pavlidis

first: Kristi

last: Miller


title: Runx3 function in splenic NK cells

first: Joseph

last: Lotem

institute: Weizmann institute of science

summary: NK cells are innate immune cells that recognize and kill foreign, virally-infected and tumor cells without the need for prior immunization. NK expansion following viral infection is IL-2 or IL-15-dependent.

overall_design: To identify Runx3 responsive genes, NK cells were isolated from spleen of WT and Runx3-/- mice . Six samples (3 WT and 3 Runx3-/-)  of freshly isolated NK cells (resting) were separately obtained from individual mice.

first: Ditsa

last: Levanon

first: Dena

last: Leshkowitz

first: Yoram

last: Groner


title: Senescence gene signature of radiation fibrosis

first: Uma

middle: T

last: Shankavaram

address: 9000 Rockville Pike

department: NCI

institute: NIH

summary:
Radiation lung injury is characterized by early inflammation and late fibrosis. The causes underlying the chronic, progressive nature of radiation injury are poorly understood.  Here, we report that the gene expression of irradiated lung tissue correlates with that observed in the lungs in aged animals. We demonstrate that NOX4 expression and superoxide elaboration is increased in irradiated lungs and pneumocytes in a dose dependent fashion.
We used microarrays to detail the global programme of gene expression and report that irradiated lung tissue correlates with that observed in the lungs in aged animals.

overall_design: Female C57Bl/Ncr mice, aged 10 weeks were treated with/ without radiation to the thorax with a X-RAD 320 x-ray irradiator at a dose rate of 2.61 Gy/minute. An age-matched cohort of mice received no IR while additional cohorts received 5 Gy in a single dose, 17.5 Gy in a single dose. RNA was extracted and hybridization done on Affymetrix Mouse430_2 microarrays.

first: Deborah

last: Citrin

first: Eun

middle: J

last: Chung


title: Transcriptional programs controlled by NGF signaling in developing mouse dorsal root ganglia neurons

city: Baltimore

first: David

middle: D

last: Ginty

address: 725 N. Wolf ST

department: Neuroscience

institute: HHMI/Johns Hopkins Univ

summary: During embryogenesis, nociceptive sensory neurons of the dorsal root ganglia depend intimately on Nerve Growth Factor (NGF) for neuronal survival, maturation and target innervation.  NGF is a secreted molecular signal synthesized by neuronal target tissues.  In developing nociceptors, NGF engages the receptor tyrosine kinase TrkA to activate a gene transcriptional program involving the regulation of hundreds of transcripts.  To identify NGF-dependent genes in developing mouse nociceptors, we have designed and performed two separate microarray screens to compare gene expression profiles of DRG neurons either with or lacking NGF signaling.

overall_design: For the first screen comparing DRGs of Bax−/− and Ngf−/−; Bax−/− mice, DRGs were dissected and pooled from E14.5 Ngf−/−; Bax−/− and Bax−/− embryos.  Total RNA was extracted and directly subjected to microarray analysis.  For the second screen comparing mouse DRG explants grown in the presence or absence of NGF, E13.5 mouse DRG explants were cultured for two days with 50 ng/ml of either NGF or NT3.  Total RNA was extracted and then subjected to microarray analysis.

first: Kenji

last: Mandai


title: Transcriptomic responses to high water temperature in Pacific salmon [2009]

middle: M


title: Gene expression in liver tissue from Ghrh-KO and normal (wild-type) mice

city: Boston

first: William

middle: R

last: Swindell

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard University

summary: The hypothalamus has recently emerged as a key regulator of metabolism and aging in mammals. We have examined the impact of targeted disruption of hypothalamic hypophysiotropic peptide: Growth Hormone-releasing Hormone (GHRH) in mice on longevity, and the putative mechanisms of delayed aging. GHRH knockout (KO) mice are remarkably long-lived and in comparison to genetically normal (wild type) animals exhibiting major shifts in the expression of genes related to xenobiotic detoxification, stress resistance, and insulin signaling. These mutant mice also have increased adiponectin levels and alterations in glucose homeostasis consistent with the removal of the counter-insulin effects of GH. While these effects overlap with those of caloric restriction (CR), we show that effects of CR and the GHRH mutation are additive, with lifespan of GHRH-KO mutants further increased by CR. We conclude that GHRH-KO mice feature perturbations in a network of signaling pathways related to stress resistance, metabolic control and inflammation, and therefore provide a new model that can be used to explore links between GHRH repression, downregulation of the somatotropic axis, and extended longevity.

overall_design: Hepatic tissue was obtained from 3 Ghrh-KO mice and 3 control (wild-type) mice (males). Expression in each sample was profiled using Affymetrix Mouse Genome 430 2.0 arrays.

first: Liou

last: Sun


title: VEGF Isoform Transcriptome Changes in the E9.5 Murine Forebrain

city: Grand Forks

first: Jacob

middle: Thomas

last: Cain

state: ND

address: 10 Cornell St Stop 9019

department: Biology

institute: University of North Dakota

type:
Expression profiling by array
Third-party reanalysis

summary: Regulation of neural stem cell (NSC) fate decisions is critical during the transition from a multicellular mammalian forebrain neuroepithelium to the multilayered neocortex. Forebrain development requires coordinated vascular investment alongside NSC differentiation. Vascular endothelial growth factor A (Vegf) has proven to be a pleiotrophic gene whose multiple protein isoforms regulate a broad range of effects in neurovascular systems. To test the hypothesis that the Vegf isoforms (120, 164, and 188) are required for normal forebrain development, we analyzed the forebrain transcriptome of mice expressing specific Vegf isoforms, Vegf120, VegfF188, or a combination of Vegf120/188. Transcriptome analysis identified differentially expressed genes in embryonic day (E) 9.5 forebrain, a time point preceding dramatic neuroepithelial expansion and vascular investment in the telencephalon. Meta-analysis identified gene pathways linked to chromosome-level modifications, cell fate regulation, and neurogenesis that were altered in Vegf isoform mice.

overall_design:
Twelve E9.5 wildtype forebrain samples were compared to four E9.5 Vegf120 mouse forebrains, four E9.5 Vegf188 mouse forebrains, three E9.5 Vegf120/188 mouse forebrains, and four E11.5 wild type forebrains using the Mouse 430. 2.0 Affymetrix GeneChip.
This study comprises of new samples and reanalysis of Samples from GSE30767 and GSE8091.

first: J

first: M

middle: A

last: Berosik

first: S

last: Snyder

first: N

middle: F

last: Crawford

middle: I

last: Nour

first: G

last: Schaubhut

first: D

last: Darland


title: Zfp322a regulates mouse ES cell pluripotency and enhances reprogramming efficiency [Expression]

status: Public on Oct 31 2013

city: Singapore

first: Qiang

last: Wu

address: 8 Medical Drive

department: Biochemistry

country: Singapore

institute: National University of Singapore

summary: Embryonic stem (ES) cells derived from the inner cell mass (ICM) of blastocysts are characterised by their ability to self-renew and their potential to differentiate into many different cell types. Recent studies have shown that zinc finger proteins are crucial for maintaining pluripotent ES cells. Mouse zinc finger protein 322a (Zfp322a) is expressed in the ICM of early mouse embryos. However, little is known regarding the role of Zfp322a in the pluripotentcy maintenance of ES cells. Here, we report that Zfp322a is required for ES cell identity since depletion of Zfp322a directs ES cells towards differentiation. Chromatin immunoprecipitation (ChIP) and dual-luciferase reporter assays revealed that Zfp322a binds to Oct4 and Nanog promoters and regulates their transcription. These data along with the results obtained from our ChIP-seq experiment showed that Zfp322a is an essential component of the ES cell transcription regulatory network. Targets which are directly regulated by Zfp322a were identified by correlating the gene expression profile of Zfp322a RNAi-treated ES cells with the ChIP-seq results. These experiments revealed that Zfp322a inhibits ES cell differentiation by suppressing MAPK pathway. Additionally, Zfp322a is found to be a novel reprogramming factor that can replace Sox2 in the classical Yamanaka’s factors (OSKM). It can be even used in combination with Yamanaka’s factors and that addition leads to a higher reprogramming efficiency and to acceleration of the onset of the reprogramming process. Together, our results demonstrate that Zfp322a is a novel essential component of the transcription factor network which maintains the identity of ES cells.

overall_design: Zfp322a depleted (RNAi) E14 mES cells were used for RNA extraction and hybridization on Affymetrix microarrays. We compared these microarray samples with the corresponding wild type (control RNAi cells).

first: Hui

last: Ma

first: Hui-Min

last: Ng

first: Xiuwen

last: Teh

first: Hu

last: Li

first: Yun-Hwa

last: Lee

first: Yew-Mei

last: Chong

first: Yuin-Han

last: Loh

first: James

last: Collins

first: Bo

last: Feng

first: Henry

last: Yang


title: Transcriptomic responses to high water temperature in Pacific salmon [2007]

first: Ken

last: Jeffries

first: Scott

last: Hinch

first: Thomas

last: Sierocinski

first: Paul

last: Pavlidis

first: Kristi

last: Miller


title: Fracture healing in osteoporotic mice

status: Public on Oct 25 2013

city: Wuerzburg

first: Julia

last: Dotterweich

address: Friedrich-Bergius-Ring 15

department: Orthopedic Center for Musculoskeletal Research

institute: University of Wuerzburg

summary: Genome-wide comparative gene expression analysis of callus tissue of osteoporotic mice (Col1a1-Krm2 and Lrp5-/-) and wild-type were performed to identify candidate genes that might be responsible for the impaired fracture healing observed in Col1a1-Krm2 and Lrp5-/- mice.

overall_design: To investigate bone healing in osteoporosis, we performed fracture healing studies in wild-type mice (C57BL/6 genetic background) and the low bone mass strains Col1a1-Krm2 and Lrp5-/- (Schulze et al., 2010; Kato et al., 2002). Osteotomy was set in femora of female mice and stabilized by a semi-rigid fixator to allow fast bone healing (Röntgen et al., 2010). 21 days post surgery we analyzed the fracture calli by biochemical/histological methods, as well as micro-computed tomography, and observed impaired fracture healing in Col1a1-Krm2 and Lrp5-/- mice in comparison to wild-type. To identify genes that may be responsible for the impaired healing in osteoporotic mice, we performed microarray analysis of three independent callus samples of each genotype. The callus tissue was taken 10 days after surgery, because extensive bone formation took place at this point.

first: P

last: Benisch

first: A

last: Ignatius

first: V

last: Röntgen

last: Liedert

first: M

last: Amling

first: T

last: Schinke

first: F

last: Jakob

first: R

last: Ebert

first: L

last: Klein-Hitpass


title: Impact of ectopic expression of SNAIL2, ZEB2, ZEB1 or TWIST1 on BRAF-target genes in the  murine melanocytic melan-a cell line

status: Public on Oct 29 2013

city: Lyon

first: stéphane

last: ansieau

address: 28 rue Laennec

department: Centre Léon Bérard

country: France

institute: Inserm U590

summary: We have demonstrated that the oncogenic activation of B-RAF (using a truncated delta-BRAF-ER version inducible with tamoxifen) in the melan-a melanocyte cell line triggers the activation of Zeb1 and Twist1 at the expanse of Zeb2 and Snail2. Enforced maintenance of Zeb2 or Snail2 expression reduces the B-RAF oncogenic potential while ectopic expression of Zeb1 or Twist1 cooperates with B-RAF in melan-a cell transformation. To get an insight into the properties of these embryonic transcription factors, gene expression profiles of melan-a-derived cell lines either expressing a non-activated B-RAF (- tamoxifen) or an activated BRAF (+ tamoxifen) alone or in combination with Snail2, Zeb2, Twist1 or Zeb1 have been established.

overall_design:
Melan-a cells were transduced with an activated version of BRAF(delta-BRAF-ER, inducible with tamoxifen) alone or in combination with SNAIL2, ZEB2, ZEB1 or TWIST1. Gene expression profiles before or following BRAF activation (alone or in combination with the embryonic transcription factors) were determined.
Ectopic expression of SNAIL2, ZEB2, ZEB1 or TWIST1 on BRAF-target genes in the  murine melanocytic melan-a cell line.

first: Julie

last: Caramel

first: Severine

last: Croze

first: Anne

last: Wierinckx

first: Geoffrey

last: Richard

first: Alain

last: Puisieux

first: Stéphane

last: Ansieau


title: Expression profiling of Ebf2- and Ebf2- stromal cells in mouse bone marrow

status: Public on Oct 24 2013

city: Huddinge

first: HONG

last: QIAN

state: Stockholms Lan

address: Neo, HERM, Floor 7, Hälsovägen 7,

department: Department of Medicine

country: Sweden

institute: Karolinska Institute

summary:
To identify the true molecular features of the Ebf2+ cells, we performed microarray analysis of freshly sorted CD45-TER119-Ebf2+ and Ebf2- cells. This allowed for the detection of 1968 genes that were 2-fold differentially expressed in Ebf2+ and Ebf2- cells. Among these, 1075 genes were upregulated and 893 genes including Ebf2, were downregulated in the Ebf2- as compared to the Ebf2+ cells. These include Nov, Fmod, Ndn, Dcn, Ctgf, Angiopoietin like-1(Angptl1), Fn1 and Jag1, some of which has been reported to be expressed in culture-selected MSCs. Furthermore, consistent with antigen expression analysis by FACS, the Ebf2+ cells highly expressed transcripts of Pdgfra, Pdgfrb, Sca1/Ly6a, Thy1 and Itga7 and Itgav, that have been suggested to be linked to MSCs. Nestin was mainly expressed in the Ebf2+ cells whereas it was hardly detectable in the Ebf2- cells. Altogether, molecularly, the Ebf2+ cells displayed features of a MSC.
Ebf2 expression is not restricted to committed osteoblast progenitor cells but rather marks a multipotent mesenchymal progenitor cell population in adult mouse BM. These cells do not appear to be completely overlapping with the previous reported MSC populations. The findings provide new insights into the in vivo cellular identity and molecular properties of BM mesenchymal stem and progenitor cells.

overall_design: RNA was extracted from 1,000 or 2000 purified adult bone marrow cells using the RNAeasy microkit. RNA was labeled and amplified by dual amplification and hybridized to Affymetrix microarray MOE430_2, according to AffymetrixTM GeneChip Expression Analysis Technical Manual. Probe level expression values were calculated using the RMA algorithm.

first: Hong

last: Qian

first: Aurora

last: Badaloni

first: Francesca

last: Chiara

first: Jenny

last: Stjernberg

first: Naresh

last: Polisetti

first: Kristian

last: Nihlberg

first: G

last: Consalez

first: Mikael

last: Sigvardsson


title: Gene Expression in wild type and CCR5 knockout mice with lung metastasis

city: Chapel Hill

first: Hendrik

middle: Wilhelm

last: van Deventer

state: NC

address: 170 Manning Drive

department: Medicine

institute: University of North Carolina Chapel Hill

summary: We have shown that  C57BL/6J CCR5 knockout mice develop 30.4% ± 8.6% fewer B16 F10 lung nodules compared to wild type mice after the intravenous injection of 100,000 B16 F10 cells.  We sought to understand this phenomenon by comparing gene expression in the lungs of these mice at 6, 24, and 48 hours after tumor injection.

overall_design: There were 6 groups or conditions (CCR5 - 6 hours, WT - 6 hours, CCR5 - 24 hours, WT - 24 hours, CCR5 - 48 hours, WT - 48 hour); each group had 4 to 5 mice.  All of the mice were injected with 100,000 B16 F10 melanoma cells by tail vein.  At the designated time, the mice were anesthetized with Avertin and their lungs were perfused with  PBS.  After this, the lungs were harvested and snap frozen in liquid nitrogen.  They were kept at minus 80 degrees C until processing.  mRNA was extracted as described below and equivalent amounts of mRNA (by weight) was pooled by group.

middle: W

first: Jonathan

last: Serody

last: P-Y Ting


title: Regulation of Gamma globin gene expression by AT2 and its associated proteins through the cAMP response element.

city: Chicago

first: Subhradip

last: Karmakar

state: IL

address: 900 E 57th Street

institute: U of Chicago

summary: The upstream Gg-globin cAMP-response element (G-CRE) plays a role in regulating Gg-globin expression through binding of CREB1, cJun and ATF2. In this study we identified the ATF2 DNA-binding partners. ATF2 knockdown resulted in a significant reduction of g-globin expression accompanied by decreased ATF2 binding to the G-CRE. By contrast, stably expressed ATF2 in K562 cells increased g-globin, which was reduced by ATF2 knockdown. Moreover, a similar role for ATF2 on g-globin expression was observed in primary erythroid progenitors. To understand the role of ATF2 in g-globin expression, chromatographically purified G-CRE/ATF2-interacting proteins were subjected to mass spectrometry analysis; binding partners included CREB1, cJun, Brg1, and histone deacetylases among others. Co-immunoprecipitation and chromatin immunoprecipitation assay demonstrated interaction of these proteins with ATF2 in CD34+ cells undergoing erythroid differentiation which was correlated with g-globin expression during development. These results suggest synergism between developmental stage-specific recruitments of the ATF2 protein complex and expression of g-globin during erythropoiesis. Microarray studies in K562 cells support additional roles for ATF2 in hematopoiesis and chromatin remodeling

overall_design: Total RNA was isolated from K562 cells in culture following transfection with scrambled siRNA or ATF2 siRNA following which RNA was isolated and gene expression monitored

first: B

last: Pace


title: TCTP is an androgen-regulated gene implicated in prostate cancer

status: Public on Oct 23 2013

city: Oslo

first: Margrethe

last: Storm

address: Blindernveien 31

institute: University of Oslo

summary: TCTP has been implicated in a plethora of important cellular processes related to cell growth, cell cycle progression, malignant transformation and inhibition of apoptosis. In addition to these intracellular functions, TCTP has extracellular functions and plays an important role in immune cells. TCTP expression was previously shown to be deregulated in prostate cancer, but its function in prostate cancer cells is largely unknown. Here we show that TCTP expression is regulated by androgens in LNCaP prostate cancer cells in vitro as well as human prostate cancer xenografts in vivo. Knockdown of TCTP reduced colony formation and increased apoptosis in LNCaP cells, implicating it as an important factor for prostate cancer cell growth. Global gene expression profiling in TCTP knockdown LNCaP cells showed that several interferon regulated genes are regulated by TCTP, suggesting that it may have a role in regulating immune function in prostate cancer. In addition, recombinant TCTP treatment increased colony formation in LNCaP cells suggesting that secreted TCTP may function as a proliferative factor in prostate cancer. These results suggest that TCTP may have a role in prostate cancer development.

overall_design: A total of 6 samples were analyzed. These consisted of three biological replicates for each treatment. The samples transfected with siRNA against Luciferase (siLuc) served as controls.

first: Mari

last: Kaarbø

first: Su

last: Qu

first: Håkon

last: Wæhre

first: Bjørn

last: Risberg

first: Håvard

middle: E

last: Danielsen

first: Fahri

last: Saatcioglu


title: Expression data from differentiating Flk1- and Flk1+ ES cells expressing Snail during Wnt inhibition

city: Saint Louis

first: Jennifer

last: Gill

state: MO

address: 660 South Euclid Ave.

department: Pathology/Immunology

institute: Washington University School of Medicine

summary:
ES cells differentiated in the presence of the Wnt inhibitor DKK1 fail to express the transcription factor Snail and undergo EMT or mesoderm differentiation.  We generated an ES cell line, A2.snail, that induced Snail expression upon addition of doxycycline addition.
Microarrays were used to gain a global picture of Flk1- and Flk1+ cells generated one day after Snail was expressed during Wnt inhibition.

overall_design: A2.snail ES cells, which express Snail upon addition of doxycycline, were differentiated as embryoid bodies in differentiation media and DKK1.  Snail-induced cultures uniquely develop a select population of Flk1+ cells.  Total RNA was harvested from sorted control (no doxycycline) Flk1- cells and sorted Snail-induced (doxycycline at day 2) Flk1- and Flk1+ cells at day 3 of differentiation.

first: Ellen

last: Langer

first: Robert

middle: C

last: Lindsley

first: Mi

last: Cai

first: Theresa

middle: L

last: Murphy

first: Michael

last: Kyba

first: Kenneth


title: Transcriptomic responses to high water temperature in Pacific salmon

first: Ken

last: Jeffries

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

overall_design: Refer to individual Series

first: Scott

last: Hinch

first: Thomas

last: Sierocinski

first: Paul

last: Pavlidis

first: Kristi

last: Miller


title: Genome-wide profiling of the activity-dependent hippocampal transcriptome

city: Berlin

first: Nils

last: Blüthgen

address: Chariteplatz 1

department: Institute of Pathology

institute: Charite Universitätsmedizin Berlin

summary: Activity-dependent gene expression is central for sculpting neuronal connectivity in the brain. Despite the importance for synaptic plasticity, a comprehensive analysis of the temporal changes in the transcriptomic response to neuronal activity is lacking. In a genome wide survey we identified genes that were induced at 1, 4, 8, or 24 hours following neuronal activity in the hippocampus.

overall_design: 3 month old male mice were injected with kainic acid or isotonic saline solution. Animals were sacrificed by cervical luxation 1, 2, 4, 8, or 24 h after onset of the first seizure, and RNA  was extracted  from the hippocampal region.

first: Guido

last: Hermey

first: Claudia

last: Mahlke

first: Jakob

last: Gutzmann

first: Jörg

last: Schreiber

first: Dietmar

last: Kuhl


title: Genome-wide cheater screen reveals safeguards for cell cooperation during embryogenesis

status: Public on Oct 21 2013

city: New York

middle: P.

last: Zwaka

address: 1425 Madison Ave

institute: Icahn School of Medicine at Mt. Sinai

summary: Ensuring cooperation among formerly autonomous cells has been a central challenge in the evolution of multicellular organisms. One solution is monoclonality, but this option does not eliminate genetic and epigenetic variability, leaving room for exploitative behavior. We therefore hypothesized that embryonic development must be protected by robust regulatory mechanisms that prevent aberrant clones from superseding wild-type cells. Using a genome-wide screen in murine induced pluripotent stem cells, we identified a network of genes (centered on p53, topoisomerase 1, and olfactory receptors) whose downregulation caused the cells to replace wild-type cells, both in vitro and in the mouse embryo—without perturbing normal development. These genes thus appear to fulfill an unexpected role in fostering cell cooperation.

overall_design: We mixed knockdown (Top1 or p53) and mock embryonic stem cells and collected mRNA on day 4 of coculture, while cells were in the growth phase. These conditions allowed direct comparisons within a single cell type rather than a mixture of different cell types as seen under differentiation conditions. To extract information specific to cell cooperation as opposed to canonical p53 and Top1 functions, we compared results obtained from our mixed (1:4) culture with those obtained after mixing mRNA (also 1:4) from p53- or Top1-knockdown cells and mock cells that were grown homotypically.

first: T

middle: P

first: Marion

last: Dejosez


title: Expression profiling of ProB and PreB cells in Ebf1 heterozygous mouse bone marrow

status: Public on Oct 18 2013

first: HONG

last: QIAN

summary:
Loss of one allele of Ebf1 impairs pre-B cell (B220+CD19+CD43low/negIgM-) expansion. In order to better understand the underlying cause of the reduced pre-B cell compartment in Ebf1+/- mice, we sorted pro-B (B220+CD19+CD43highIgM- ) as well as pre-B cells from Wt and Ebf1 heterozygote mutant mice and performed Affymetrix based microarray gene expression analysis.
While the overall gene expression patterns as well as Pax5 expression in Wt and Ebf1 pro-B cells were similar, gene set enrichment (GSE) analysis of the microarray data suggested a reduced expression of cell division (p<0.001) and mitosis (p<0.001) genes in the Ebf1+/- pre-B cells as compared to their Wt counterparts. This in combination with rather normal expression of B-lineage genes in Ebf1+/- pre-B cells opens for the possibility that the phenotypic loss of pre-B cells in Ebf1+/- mice could be a result of reduced expansion of progenitors rather than by a differentiation block.

overall_design: RNA was extracted from 20,000 or 25000 purified adult bone marrow cells using the RNAeasy microkit. RNA was labeled and amplified by dual amplification and hybridized to Affymetrix microarray MOE430_2, according to AffymetrixTM GeneChip Expression Analysis Technical Manual. Probe level expression values were calculated using the RMA algorithm.

first: Josefine

last: Ahsberg

first: Jonas

last: Ungerbäck

first: Tobias

last: Strid

first: Eva

last: Welinder

first: Jenny

last: Stjernberg

first: Malin

last: Larsso

first: Hong

last: Qian

first: Mikael

last: Sigvardsson


title: Comparison of microRNA Profiling Platforms (BeadChip)

status: Public on Oct 22 2013

city: Toronto

first: Shirley

last: Tam

state: Ontario

address: 661 University Avenue, Suite 510, MaRS Building, West Tower

department: Genome Technologies

institute: Ontario Institute for Cancer Research

summary: Global miRNA expression profiling of human malignancies is gaining popularity in both basic and clinically driven research. But to date, the majority of such analyses have used microarrays and quantitative real-time PCR.  With the introduction of digital count technologies, such as next-generation sequencing (NGS) and the NanoString nCounter System, we have at our disposal, many more options. To make effective use of these different platforms, the strengths and pitfalls of several miRNA profiling technologies were assessed, including a microarray platform, NGS technologies and the NanoString nCounter System.  These results were compared to gold-standard quantitative real-time PCR.

overall_design: Comparison of non-small cell lung cancer cell lines grown in vitro (n = 5) and in vivo (n = 5) as xenograft models.

first: Richard

last: de Borja

first: Ming-Sound

last: Tsao

first: John

last: McPherson


title: Gene expression analysis of a series of HER2+ of breast tumors

city: Amsterdam

first: Jelle

middle: Johannes

last: ten Hoeve

address: Plesmanlaan 121

department: Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

summary:
Abstract

Motivation
Breast cancer is a heterogeneous disease with distinct subtypes. Even within these subtypes differences at the molecular level are present which are reflected in variable responses to chemotherapy. We set out to identify genes associated with chemotherapy resistance by analyzing a set of HER2-positive breast cancers.
Methods
We collected, gene expression profiled and analyzed 60 HER2-positive breast tumor biopsies, obtained from patients scheduled to undergo neoadjuvant therapy. In addition to conventional supervised approaches for the detection of reporters of resistance, we report on a novel approach specifically tailored to the detection of small groups of resistant samples that show aberrant gene expression patterns.
Results
We propose a novel analytical approach that takes heterogeneity in response into account. We show that this approach is more powerful than classical approaches for detecting small subgroups of samples showing aberrant expression in a controlled setting. We applied this approach to our 60 breast cancer samples prior to neoadjuvant chemotherapy, and generated candidate response reporter lists for each subtype.
Discussion
Using a novel analytical approach we report on the mRNA gene expression analysis of a cohort of breast cancers prior to neoadjuvant chemotherapy. An important characteristic of this approach is that it takes heterogeneity in neoadjuvant treatment response into account. Such approaches are needed to identify biomarkers for predicting treatment response.

overall_design: We collected, gene expression profiled and analyzed 60 breast tumor biopsies, obtained from patients scheduled to undergo neoadjuvant therapy.

first: Jorma

last: de Ronde

first: Esther

last: Lips

first: Lennart

last: Mulder

first: Guillem

last: Rigaill

first: Andrew

last: Vincent

last: Wesseling

first: Marja

last: Nieuwland

first: Ron

last: Kerkhoven

first: Marie-Jeanne

last: Vrancken Peeters

first: Gabe

last: Sonke

first: Sjoerd

last: Rodenhuis

first: Lodewyk

last: Wessels


title: Expression data from mouse cerebral cortex

city: Durham

first: Douglas

last: Marchuk

address: 213 Research Dr, 277 CARL

institute: DUKE Univ

summary:
Differential gene expression of cerebral cortex might be responsible for distinct neurovascular developments between different mouse strains
We used Affymetrix microarray to explore the global gene expression patterns of mouse cerebral cortex of different mouse strains at two developmental stages

overall_design: Cerebral cortex from two mouse strains [C57BL/6J(B6) and C3H/J (C3H)] at post-natal day 1 (p1) and post-natal 11 weeks (11 wk) were harvested for microarray experiments

first: Pei-Lun

last: Chu


title: Latent gammaherpesvirus 68 infection induces distinct transcriptional changes in different organs

first: Ramnik

last: Xavier

address: 185 Cambridge Street

institute: Massachusetts General Hospital

summary: Previous studies identified a role for latent herpesvirus infection in cross-protection to infection and exacerbation of chronic inflammatory diseases. Here, we compared the gene expression signature from livers, spleens and brains of mice infected with wild-type gammaherpesvirus 68 (MHV68), a mutant virus defective in the establishment of latency (ORF73.stop) or mockulum. We identified over 600 genes differentially expressed in organs of mice latently infected with MHV68 and found distinct sets of genes linked to different pathways were altered in spleen compared to liver. Several of the most differentially expressed latency-specific genes (e.g. IFNγ, Cxcl9, Ccl5) are associated with known latency-specific phenotypes.

overall_design: RNA was extracted from livers, spleens and brains of 7-9 week old male C57Bl/6 mice infected with gammaherpesvirus 68 (MHV68), a virus defective in establishment of latency (ORF73.stop) or mockulum. RNA from 3-4 mice per treatment was pooled and analyzed by M430 2.0 Affymetrix Gene Chip. Three biologic replicates were analyzed for all conditions, except mock livers, for which four biologic replicates were analyzed.

first: Gautam

last: Goel

first: Susan

last: Canny

first: Herbert

last: Virgin


title: Expression Data from Leukemia Patients Supporting Personalized Functional Cancer Genomics Analyses

status: Public on Oct 04 2013

city: Portland

first: Daniel

last: Bottomly

address: 3181 Sam Jackson Park Rd.

institute: OHSU

summary: A set of expression samples used to support a personalized genomics analysis with regards to functional assays (e.g. siRNA or small molecule screens)

overall_design: 50 patient samples from a variety of disease types and several tissues


title: Variants at multiple loci implicated in both innate and adaptive immune responses are associated with Sjögren’s syndrome

status: Public on Oct 06 2013

city: Oklahoma City

first: Kathy

last: Sivils

state: OK

address: 825 NE 13th St.

department: Arthritis and Clinical Immunology

institute: Oklahoma Medical Research Fondation

summary: This is a genome-wide association study performed in Sjogrens syndrome in which gene expression data was used in conjunction with genotype data to perform expression quantitative trait loci (eQTL) analysis.

overall_design: This is a case/control study.

first: Christopher

last: Lessard


title: Expression data from subpopulations of Apc1638N/+ intestinal adeno tumors versus Apc1638N/+ / KRAS v12G intestinal adenocarcinomas tumors

status: Public on Oct 01 2013

city: Rotterdam

first: Andreas

last: Kremer

address: Dr. Molewaterplein 50

department: Bioinformatics

institute: Erasmus MC

summary: Constitutive activation of the Wnt pathway leads to adenoma formation, an obligatory step towards intestinal cancer. In view of the established role of Wnt in regulating stemness, we attempted the isolation of cancer stem cells (CSCs) from Apc- and Apc/KRAS-mutant intestinal tumours. Whereas CSCs are present in malignant Apc/KRAS–mutant carcinomas, they appear to be very rare (<10-6) in the benign Apc–mutant adenomas. In contrast, the Lin-CD24hiCD29+ subpopulation of adenocarcinoma cells appear to be enriched in CSCs with increased levels of active -catenin. Expression profiling analysis of the CSC-enriched subpopulation confirmed their enhanced Wnt activity and revealed additional differential expression of other signalling pathways, growth factor binding proteins, and extracellular matrix components. As expected, genes characteristic of the Paneth cell lineage (e.g. defensins) are co-expressed together with stem cell genes (e.g. Lgr5) within the CSC-enriched subpopulation. This is of interest as it may indicate a cancer stem cell niche role for tumor-derived Paneth-like cells, similar to their role in supporting Lgr5+ stem cells in the normal intestinal crypt. Overall, our results indicate that oncogenic KRAS activation in Apc-driven tumours results in the expansion of the CSCs compartment by increasing b-catenin intracellular stabilization.

overall_design: To identify molecular differences between stem-like and more differentiated (bulk) tumour cells from Apc1638N/+ and Apc1638N/+/KRASV12G intestinal adenomas and adenocarcinomas, we isolated total RNA from 104 Lin-CD24hiCD29+, Lin-CD24medCD29+/Lin-CD24loCD29+  and Lin- (bulk) tumour cells from 5 individual mice of each genotype (Apc1638N/+ and Apc1638N/+/KRASV12G). Total RNA samples were then employed to hybridize oligonucleotide microarrays (Affymetrix Mouse Genome 430A 2.0 Array) according to conventional protocols.

first: Mehrnaz

last: Ghazvini

first: Petra

last: Sonneveld

first: Patrick

last: Franken

first: Andrea

last: Sacchetti

first: Yaser

last: Atlasi

first: Sabrin

last: Roth

first: Rosalie

last: Joosten

last: Smits

first: Riccardo

last: Fodde


title: Expression of CD39 and CD45RO on CD4+CD25hi T cells identifies human naïve (G3) and effector Treg (G2), and distinguishes them from activated non-Treg cells (Tresp).

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

institute: University of Cambridge

summary: Human responder T-cells (Tresp) and 2 lineages of regulatory T cells (Tregs), namely G2 and G3, were isolated by flow sorting based on their immunoreacitivities against specific cell surface markers and their gene expression profiles were interrogated using Affymetrix Exon 1.0 ST Arrays

overall_design: Comparison of gene expression profiles between responder T-cells, G2 Tregs and G3 Tregs

first: Ling

middle: Y

last: Ye

first: Huji

last: Xu

first: Jane

last: Goodall


title: TWEAK-treated time course in Pan02 cells

city: Watertown

first: Mary

last: Simcox

address: 500 Arsenal St

institute: Forma Therapeutics

summary: Tumor necrosis factor-related weak inducer of apoptosis, TWEAK, is a TNF superfamily member that mediates signaling through its receptor fibroblast growth factor inducible-14, Fn14. In tumor cell lines, TWEAK induces proliferation, survival and NF-kappaB signaling and gene expression that promote tumor growth and suppress antitumor immune responses. Anti-TWEAK antibody, RG7212, inhibits tumor growth in vivo with decreases in pathway activation markers and modulation of tumor, blood and spleen immune cell composition. Candidate response prediction markers, including Fn14, have been identified in mouse models. Phase I pharmacodynamic data from patients are consistent with preclinical results. TWEAK:Fn14 signaling is upregulated in human cancer and pathway activation induces tumor proliferation and survival signaling. Blockade with anti-TWEAK mAb, RG7212, inhibits tumor growth in multiple models in mice. TWEAK induces changes that suppress anti-tumor immune responses and RG7212 blocks these effects resulting in changes in tumor immune cell composition and decreases in cytokines that promote immunosuppression. Antitumor efficacy in mice was observed in a range of Fn14 expressing models with pathway activation and expressing either wild-type or mutant p53, BRAF or KRAS suggesting both a patient selection strategy and potential broad clinical applicability. Preclinical mechanism of action hypotheses are supported by Phase I clinical data, with decreases in proliferation markers and increased tumor T cell infiltration.

overall_design: Pan02 cells untreated or treated with 1090-TW (TWEAK) for 4 hours, 8 hours, or 24 hours.  Four replicates for each condition were performed.

first: Windy

middle: D

last: Berkofsky-Fessler

first: Holly

last: Hilton

first: Saumya

last: Pant


title: Stem Cell Quiescence acts as a tumor suppressor mechanism in hair follicle initiated squamous tumors

status: Public on Oct 30 2013

city: Los Angeles

first: William

last: Lowry

state: CA

address: 621 Charles Young

institute: UCLA

summary: In some organs, adult stem cells are uniquely poised to serve as cancer cells of origin1-4.  It is unclear, however, whether tumorigenesis is influenced by the activation state of the adult stem cell.  Hair follicle stem cells (HFSCs) act as cancer cells of origin for cutaneous squamous cell carcinoma (SCC) and undergo defined cycles of quiescence and activation.  The data presented here show that HFSCs are unable to initiate tumors during the quiescent phase of the hair cycle, indicating that the mechanisms that keep HFSCs dormant are dominant to the gain of oncogenes (Ras) or the loss of tumor suppressors (p53). Furthermore, Pten activity is necessary for quiescence based tumor suppression, as its deletion alleviates tumor suppression  without affecting proliferation.  These data demonstrate that stem cell quiescence is a form of tumor suppression in HFSCs, and that Pten plays a role in maintaining quiescence in the presence of tumorigenic stimuli. This experiment includes RNA profiling of hair follicle stem cells at various stages of tumorigenesis

overall_design:
Briefly: HFSCs were lineage traced with YFP allele, FACS isolated from various genotypes, and then profiled by Affymetrix microarray
Cell Isolation and FACS:
Whole dorsal and ventral mouse K15-CrePR; LSLYFP, K15-CrePR; KrasG12D; LSLYFP and K15-CrePR; KrasG12D; Ptenff; LSLYFP was extracted, diced and digested with collagenase (20mg/ml) for 2 hours at 37C, then an equal volume of .25% trypsin was added and digestion continued for an additional hour at 37C.  Digested tissue was mechanically dispersed via pipette and filtered with a 100uM cell strainer, collected at 300g and washed twice with PBS. The cells were then filtered through a 40uM cell strainer and FACS processed.  YFP+ and YFP- cell populations were collected in RNA lysis buffer (Stratagene) and stored at -80C.
Gene expression profiling
Microarray analyses by GeneSpring software were performed

first: Andrew

last: White


title: Gene expression profiling of anterior and posterior palatal tissue from Tgfbr2 mutant mouse models

first: Richard

last: Pelikan

state: Oklahoma

address: 825 NE 13th St

department: Genes & Human Disease Research Program

institute: Oklahoma Medical Research Foundation

summary: The overall goal of this project is to investigate the role of TGF-beta signaling in epithelial cells as it pertains to the orientation of muscle fibers in the soft palate during embryogenesis. Here, we first conducted gene expression profiling of the anterior and posterior portions of the palate from wild-type mice. In addition, we also conducted gene expression profiling of the posterior palate in mutant mice with an epithelium-specific conditional inactivation of the Tgfbr2 gene. The latter mice provide a model of submucosal cleft palate, which is a congenital birth defect commonly observed in many syndromic conditions.

overall_design: To investigate the adverse effects of dysfunctional TGF-Beta signaling on tissue-tissue interaction between the palatal epithelium and myofibers during palatogenesis, we analyzed mice with an epithelial cell-specific conditional inactivation of Tgfbr2 (Tgfbr2fl/fl;K14-Cre). We performed microarray analyses of anterior palatal tissue and posterior palatal tissue of E15.5 Tgfbr2fl/fl control mice (n=5, each region), and posterior palatal tissue of Tgfbr2fl/fl;K14-Cre mutant mice, collected at embryonic day 15.5 (n=5). Control samples and mutant samples are from separate litters.

first: Jun-ichi

last: Iwata

first: Akiko

last: Suzuki

first: Yang

last: Chai


title: Gene expression in Dupuytren's disease

city: Clayton

first: Carl

last: Sprung

address: 27-31 Wright St

department: MIMR

country: Australia

institute: Monash University

summary:
Dupuytren's disease (DD) is a classic example of pathological fibrosis which results in a debilitating disorder affecting a large sector of the human population. It is characterized by excessive local proliferation of fibroblasts and over-production of collagen and other components of the extracellular matrix (ECM) in the palmar fascia. The fibrosis progressively results in contracture of elements between the palmar fascia and skin causing flexion deformity or clawing of the fingers and a severe reduction in hand function. While much is known about the pathogenesis and surgical treatment of DD, little is known about the factors that cause its onset and progression, despite many years of research. Gene expression patterns in DD patients now offers the potential to identify genes that direct the pathogenesis of DD.

In this study, we used primary cultures of fibroblasts derived from excisional biopsies of fibrotic tissue from DD patients to compare the gene expression profiles on a genome-wide basis with normal control fibroblasts. Our investigations have identified genes that may be involved with DD pathogenesis including some which are directly relevant to fibrosis. In particular, these include significantly reduced expression levels of three matrix metallopeptidases (MMP1, MMP3, MMP16), follistatin, and STAT1, and significantly increased expression levels of fibroblast growth factors (FGF9, FGF11), a number of collagen genes and other ECM genes in DD patient samples. Many of these gene products are known to be involved in fibrosis, tumour formation and in the normal processes of tissue remodelling. In addition, alternative splicing was identified in some DD-associated genes. These highly sensitive genomic investigations provide new insight into the molecular mechanisms that may underpin the development and progression of DD.

overall_design: Four exon arrays of DD primary fibroblasts derived from fibrotic tissue were compared to fibroblasts derived from skin punch biopsies from individuals who did not show DD symptoms.

middle: N

first: Helen

middle: B

last: Forrester

first: Peter

last: Temple-Smith


title: Expression analysis of murine primary and derived orthotopic SEOC tumors

city: Frederick

first: Ludmila

last: Szabova

state: MD

address: 1050 Boyles Street

department: CAPR

institute: Frederick National Laboratory for Cancer Research

summary:
We previously generated  genetically engineered mouse (GEM) models based on perturbation of Tp53, Rb with or without Brca1 or Brca2 that develop serous epithelial ovarian cancer (SEOC) closely resembling the human disease on  histologic and molecular levels. We have adapted these GEM models to orthotopic allografts that uniformly develop tumors with short latency in immunocompetent recipients and are ideally suited for routine preclinical studies. To monitor passaged tumors at the molecular level, we analyzed transcriptional profiles of a set of primary SEOC and matching derived passaged tumors. We have merged this dataset with previously published ( doi:  10.1158/0008-5472.CAN-11-3834; PMID 22617326) dataset of murine primary ovarian tumors from our GEM models (GSE46169) and merged and compared them to expression profiles of human dataset published previously (doi:  10.1038/nature10166).
The high mortality rate from ovarian cancers can be attributed to late-stage diagnosis and lack of effective treatment. Despite enormous effort to develop better targeted therapies, platinum-based chemotherapy still remains the standard of care for ovarian cancer patients, and resistance occurs at a high rate. One of the rate limiting factors for translation of new drug discoveries into clinical treatments has been the lack of suitable preclinical cancer models with high predictive value. We previously generated  genetically engineered mouse (GEM) models based on perturbation of Tp53, Rb with or without Brca1 or Brca2 that develop serous epithelial ovarian cancer (SEOC) closely resembling the human disease on  histologic and molecular levels. Here, we describe an adaptation of these GEM models to orthotopic allografts that uniformly develop tumors with short latency and are ideally suited for routine preclinical studies.

overall_design: RNA was isolated from flash frozen ovarian tumors using Trizol and Qiagen RNeasy columns


title: Phrenic neuronal determinants screen in M.Musculus [1]

city: London

first: Eric

last: Blanc

address: New Hunt's House

department: MRC Centre for Developmental Neurobiology

institute: King's College London

summary:
Expression response after induction of putative phrenic neuronal determinants in ES cells was compared to a pre-determined list of genes over-expressed in FACS-sorted phrenic cells.
Transcription factor Pou3f1 was identified as a major determinant of phrenic identity.

overall_design: Cells type individually compared to the overall expression to identify differentially expressed genes patterns

first: Carolina

last: Barcellos-Machado

first: Ivo

last: Lieberam


title: Human Mesothelioma MicroRNA Study Part 1

city: Stanford

first: Ming

last: Zheng

address: Room L212, Lane Bldg

institute: Stanford University

summary: MicroRNA expression profiles of malignant pleural mesothelioma (MPM) specimens were analyzed to identify novel microRNA that are potentially involved in the oncogenic transformation of human pleural cells.  In addition to several novel MPM-associated microRNAs, we observed that the expression level of microRNA-1 was significantly lower in tumors as compared to normal pleural specimens.  Subsequently, pre-mir of microRNA-1 was introduced into MPM cell lines to overexpress this microRNA.  Phenotypic changes of these altered cells were assayed.  The cellular proliferation rate was significantly inhibited after overexpression of microRNA-1.  Early and late apoptosis were measured by Annexin V and TUNEL assays, respectively.  Taken together, these data suggested that overexpression of microRNA-1 induced apoptosis in these MPM cell lines, acting as a tumor suppressor.  We confirmed our observations by assessing in the transduced MPM cells cell cycle-related genes, pro-apoptotic and anti-apoptotic genes, which all showed coordinated, significant changes characteristic of the apoptotic phenotype. Thus, further investigation and validation of our microRNA database of MPM may elucidate previously unrecognized molecular pathways and/ or mechanisms by identifying novel microRNAs that are involved in malignant transformation.  Our study has now found microRNA-1 to be one of these MPM-associated microRNAs, with potential pathogenic and therapeutic significance.

overall_design: MicroRNA microarray transcriptional profiling studies of 25 MPM primary tumors as well 6 normal pleural samples from an unmatched patient cohort as normal comparators were performed.

first: Chuong

last: Hoang

first: Yue

last: Xu


title: Expression and Metabolic Profiles in a Panel of Five Neural Tube Defect Mouse Models

status: Public on Sep 30 2013

city: seattle

first: Joseph

last: Nadeau

state: WA

address: 720 Broadway

institute: Pacific Northwest Research Institute

summary: Neural tube defects (NTDs) are serious birth defects with an estimated worldwide incidence of 1 per 1,000 live births. The multifactorial nature of NTDs in humans has made it difficult to elucidate pathogenesis mechanisms. However, a strong relationship has been established between folate-homocysteine metabolism and NTD risk. Prevention of a substantial proportion of fetal NTDs can be achieved through maternal folic acid (FA) supplementation. However the mechanism by which FA exerts its beneficial effect remains unclear. METHODS: To improve our understanding of the underlying mechanisms of NTD pathogenesis and the ways in which folate exerts its beneficial effect, we analyzed mRNA profiles as well as folate and vitamin B12 levels in five NTD mouse mutants whose response to dietary FA was previously established. RESULTS: Differentially expressed genes representing the effect of each NTD-causing mutation were identified and associated with biologic pathways. Interestingly, the panel of NTD mutants collectively revealed pathways related to two nuclear receptors, retinoid X receptor (RXR) and pregnane X receptor (PXR), suggesting that these pathways may be related to a shared mechanism of NTD development. Moreover, the NTD-causing mutations that were associated with FA responsiveness had expression profiles that were related to folate-homocysteine metabolic pathways. These pathways were not strongly associated with mutants that do not respond to FA supplementation, implying that FA may be beneficial when the NTD mutation affects pathways related to folate-homocysteine metabolism.

overall_design: 5 groups of NTD mutants were studied. From each mutant group Heterozygous (test) and wild-type (control) female pups were used for this study at 6-8 weeks of age. 4 biological replicates were used for each of the test and control groups of each mutant. All mice used for the experiments  were fasted 4-5 hours before dissection. A total of 36 samples were analyzed.

first: Ghunwa

last: Nakouzi

first: Patricia

middle: M

last: DiBello

first: Donald

last: Jacobsen

middle: H