title: Inactivation of CDK2 is synthetic lethal to MYCN-overexpressing cancer cells

first: Richard

last: Volckmann

summary: Two genes have a synthetic lethal relationship when silencing or inhibition of one gene is only lethal in the context of a mutation or activation of the second gene. This situation offers an attractive therapeutic strategy, as inhibition of such a gene will only trigger cell death in tumor cells with an activated second oncogene but spare normal cells without activation of the second oncogene. Here we present evidence that CDK2 is synthetic lethal to neuroblastoma cells with MYCN amplification and overexpression. Neuroblastomas are childhood tumors with an often lethal outcome. Twenty percent of the tumors have MYCN amplification and these tumors are ultimately refractory to any therapy. Targeted silencing of CDK2 by three RNA interference techniques induced apoptosis in MYCN-amplified neuroblastoma cell lines, but not in MYCN single copy cells. Silencing of MYCN abrogated this apoptotic response in MYCN-amplified cells. Inversely, silencing of CDK2 in MYCN single copy cells did not trigger apoptosis, unless a MYCN transgene was activated. The MYCN induced apoptosis after CDK2 silencing was accompanied by nuclear stabilization of P53 and mRNA profiling showed up-regulation of P53 target genes. Silencing of P53 rescued the cells from MYCN-driven apoptosis. The synthetic lethality of CDK2 silencing in MYCN activated neuroblastoma cells can also be triggered by inhibition of CDK2 with a small molecule drug. Treatment of neuroblastoma cells with Roscovitine, a CDK inhibitor, at clinically achievable concentrations induced MYCN-dependent apoptosis. The synthetic lethal relation between CDK2 and MYCN indicates CDK2 inhibitors as potential MYCN-selective cancer therapeutics.

overall_design: CDK2 shRNA in a tet repressor system was stably transfected in the IMR32 cell line. Time course analysis was performed in triplicate after induction of CDK2 shRNA at 5 time points.

last: Molenaar

last: Koster

first: Rogier

last: Versteeg


title: Expression data from human brain anterior cingulate cortex - including control samples and samples with major depression disorders (26 samples BA25_F)

status: Public on May 16 2014

city: Pittsburgh

first: Etienne

last: Sibille

state: PA

address: 450 Technology Drive, Suite 231

department: Psychiatry

country: USA

institute: University of Pittsburgh

summary: Major depressive disorder is a heterogeneous illness with a mostly uncharacterized pathology. Large scale gene expression (transcriptome) analysis and genome-wide association studies (GWAS) for single nucleotide polymorphisms have generated a considerable amount of gene- and disease-related information, but heterogeneity and various sources of noise have limited the discovery of disease mechanisms. As systematic dataset integration is becoming essential, we developed methods and performed meta-clustering of gene coexpression links in 11 transcriptome studies from postmortem brains of human subjects with major depressive disorder (MDD) and non-psychiatric control subjects. We next sought enrichment in the top 50 meta-analyzed coexpression modules for genes otherwise identified by GWAS for various sets of disorders. One coexpression module of 88 genes was consistently and significantly associated with GWAS for MDD, other neuropsychiatric disorders and brain functions, and for medical illnesses with elevated clinical risk of depression, but not for other diseases (See publication for details).

overall_design: 26 total samples in 13 pairs were analyzed in postmortem tissue from the anterior cingulate cortex.


title: Expression data from human brain dorsolateral prefrontal cortex - including control samples and samples with major depression disorders (28 samples BA9_M)

overall_design: 28 total samples in 14 pairs were analyzed in postmortem tissue from the dorsolateral prefrontal cortex.


title: Expression data from human brain dorsolateral prefrontal cortex - including control samples and samples with major depression disorders (30 samples BA9_F)

overall_design: 30 total samples in 15 pairs were analyzed in postmortem tissue from the dorsolateral prefrontal cortex.


title: Expression data from human brain anterior cingulate cortex - including control samples and samples with major depression disorders (32 samples MD1_ACC)

overall_design: 32 total samples in 16 pairs were analyzed in postmortem tissue from the anterior cingulate cortex.


title: Transcriptomic analysis of human breast and prostate cancer cell lines on lysophosphatidic acid (LPA) stimulation

city: Lyon

first: Olivier

last: Peyruchaud

state: Rhone Alpes

address: UFR de medicine Lyon Est (Domaine Laennec), 7-11 Rue Guillaume Paradin

country: France

institute: INSERM U1033

summary:
LPA is a natural bioactive lipid with growth factor-like functions due to activation of series of six G protein-coupled receptors (LPA1-6).
In this study we determine the LPA induced early-gene expression profile in three unrelated human cancer cell lines (MDA-MB-231, MCF7, PC3) with an objective to identify potential biomarker/s specifically upregulated through the activation of LPA receptor type 1 (LPA1)

overall_design: MDA-MB-231, MCF7, PC3 cells were serum starved for 24h and then stimulated with LPA (1µM) for 45min. The controls were the serum starved unstimulated cells. Two replicates for each sample were included in this study. Microarray analysis was performed using a high-density oligonucleotide array (GeneChip Human Genome U133 plus 2.0 array, Affymetrix)

first: Marion

last: David

first: Debashish

last: Sahay


title: Expression data from human brain amygdala - including control samples and samples with major depression disorders (28 samples MD1_AMY)

overall_design: 28 total samples in 14 pairs were analyzed in postmortem tissue from the amygdala.


title: Expression data from human brain anterior cingulate cortex - including control samples and samples with major depression disorders (24 samples BA25_M)

overall_design: 24 total samples in 12 pairs were analyzed in postmortem tissue from the anterior cingulate cortex.


title: siPools: highly complex but accurately defined siRNA pools eliminate Off-target effects (HuGene-2_0)

status: Public on May 15 2014

city: Regensburg

first: Julia

middle: C

last: Engelmann

address: Josef-Engert-Str. 9

department: Statistical Bioinformatics

country: Germany

institute: University of Regensburg

summary:
Short interfering RNAs (siRNA) are widely used as tool for gene inactivation in basic research and therapeutic applications. One of the major shortcomings of siRNA experiments are sequence-specific Off-target effects. Such effects are largely unpredictable because siRNAs can affect partially complementary sequences and function like microRNAs (miRNAs), which inhibit gene expression on mRNA stability or translational levels.
Here we demonstrate that novel, enzymatically generated siRNA pools - referred to as siPools - containing up to 60 accurately defined siRNAs eliminate Off-target effects. This is achieved by the low concentration of each individual siRNA diluting sequence-specific Off-target effects below detection limits. In fact, whole transcriptome analyses reveal that single siRNA transfections can severely affect global gene expression. However, when complex siRNA pools are transfected, almost no transcriptome alterations are observed. Taken together, we present enzymatically-produced complex but accurately defined siRNA pools with potent On-target silencing but without detectable Off-target effects.

overall_design: dsRNA fragments of more than 30bp length may trigger interferon response in mammalian cells, depending on the cell type as well as length and concentration of the dsRNA. To demonstrate that complex siRNA pools (siPools) do not contain trace amounts of such longer dsRNA species and therefore do not trigger interferon response, MCF7 cells which exhibit sensitive interferon response, were transfected with a siPool targeting human SCYL1, consisting of 60 siRNA at a total siRNA concentration of 3nM. As positive control, MCF7 cells were transfected with an RNAseIII generated mixture of dsRNAs (esiRNAs) at equal concentration (weight/volume). Mock transfected cells served as negative control. Every sample was tested in biological triplicates. Total RNA was extract 48h after transfection for affimetrix expression analysis.

first: Michael

last: Hannus

first: Michaela

last: Beitzinger

first: Marie-Theresa

last: Weickert

first: Rainer

last: Spang

first: Stefan

first: Gunter

last: Meister


title: Molecular effects of EtOH and Nicotine on normal human oral keratinocytes

status: Public on May 14 2014

city: Los Angeles

first: Yong

last: Kim

state: CA

address: 10833 Le Conte Ave, 73-022 CHS

institute: UCLA

summary: We have performed gene expression microarry analysis to profile molecular alterations in normal human oral keratinocytes that are induced by EtOH and/or nicotine. Our goal is to examine molecular signatures that are dysregulated by EtOH or nicotine and define the effects of co-use of alcohol and nicotine on normal oral epithelial cells and potentially on carcinogenesis.

overall_design: Primary normal human oral keratinocytes were cultured and treated with various dose of EtOH (0, 20 and 50 mM) and cotreated with various dose of nicotine (0, 0.5 and 1uM) for 24 hours. Total RNA was isolated and subjected to gene expression microarray analysis using Affymetrix Human Genome 2.0 plus.

first: Jeffrey

middle: J


title: siPools: highly complex but accurately defined siRNA pools eliminate Off-target effects

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

overall_design: Refer to individual Series


title: Gene expression data from mouse hemopoietic stem cells (LSKs), promyelocytes, myelocytes and granulocytes.

city: Camperdown

first: Justin

last: Wong

state: NSW

address: Building 93 Royal Prince Alfred Hospital

country: Australia

institute: Centenary Institute

summary:
Differentiation of hemopoietic stem cells into granulocytes is characterized by distinct changes in the transcriptome.
We analyzed mRNA expression in primary murine myeloid cells at four successive stages of hemopoietic differentiation; Lin- Sca1+ cKit+ stem/progenitor cells (LSKs), promyelocytes, myelocytes and granulocytes.

overall_design: Using fluorescence–activated cell sorting, we isolated primary murine myeloid cells at four successive stages of hemopoietic differentiation; Lin- Sca1+ cKit+ stem/progenitor cells (LSK), promyelocytes, myelocytes and granulocytes.

first: Jeff

last: Holst


title: Expression profile for overproduction of ArT

status: Public on May 13 2014

city: State College

first: Thomas

middle: K.

last: Wood

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

institute: Pennsylvania State University

summary:
Toxin-antitoxin (TA) systems are ubiquitous throughout bacterial and archaeal genomes.  TA systems consist of a stable toxin that inhibits growth and a labile antitoxin that prevents toxicity of the toxin.
Here we made an artificial TA system (arT/arA) and performed a DNA microarray study for overproduction of the toxin.

overall_design: arT was overexpressed in Escherichia coli BW25113 and compared to the empty vector.

first: Soo

middle: W

last: Valerie

first: Cheng

last: Hsin-Yao

first: Kwan

last: Brian

first: Wood

middle: K

last: Thomas


title: Intrahepatic miRNA/mRNA expression in non-responders to pegylated interferon plus ribavirin combination therapy for chronic hepatitis C

city: Bunkyo-ku

first: Kaoru

last: Mogushi

state: Tokyo

address: 2-1-1 Hongo

department: Intractable Disease Research Center

country: Japan

institute: Juntendo University

summary: Despite advance in interferon-based treatment for chronic hepatitis C, difficult-to-treat patients remain in existence yet. To identify key genes involved in difficult-to-treat characteristics, gene expression patterns of miRNA and RNA were analyzed by profiling pretreatment liver tissues from five sustained virological responders (SVR), three relapsers (R) and four non-responders (NR). Expression levels of miRNA and mRNA were compared between SVR/R and NR groups by using microarray, respectively. Quantitative real-time reverse-transcriptase polymerase chain reaction and statistical analyses validated genes with significantly differential expression levels in 50 liver tissues: proliferation-, inflammation- and anti-apoptosis-related mRNA expression levels increased significantly in NR, compared to SVR/R. Of miRNA with significantly differential expression levels on microarray, several miRNA were correlated inversely with those significant mRNA. In vitro studies by using miRNA inhibitors and mimics verified the inverse correlation between the miRNA and mRNA. These findings enhance our understanding of the difficult-to-treat molecular mechanism and identification of target molecules for novel treatments.

overall_design: Moderated t-statistics based on the empirical Bayes approach were performed to identify mRNA or miRNA differentially expressed between SVRs/relapses and NVRs using the “limma” package from BioConductor software (http://www.bioconductor.org/) under R statistical software version 2.12.1 (http://www.r-project.org/). Because of multiple hypothesis testing, p values were adjusted by the Benjamini-Hochberg false discovery rate (FDR) method. Related miRNA expression data are in GSE45179.

first: Akihito

last: Tsubota

first: Ken

last: Miyaguchi

first: Rie

last: Agata

first: Yoko

last: Yumoto

first: Yoshihisa

last: Namiki

first: Keisuke

last: Nagatsuma

first: Hiroshi

last: Tanaka

first: Norio

last: Tada


title: Identification of nuclear-enriched miRNAs during mouse granulopoiesis

type:
Expression profiling by array
Other


title: Induction of hepatocellular carcinoma through activation of stromal cells in Pdgf-c transgenic mice

status: Public on May 12 2014

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary: Liver cirrhosis is a strong risk factor for the development of hepatocellular carcinoma (HCC), yet the mechanisms by which cirrhosis predisposes patients to tumorigenesis are not well understood. Transgenic mice expressing platelet-derived growth factor C (Pdgf-c) under the control of the albumin promoter provide a unique animal model that mimics the step-wise disease progression in humans from fibrosis to HCC. The livers of Pdgf-c Tg mice show evidence of liver injury, including inflammation, proliferation, fibrosis and steatosis, and as the mice age, angiogenesis and dysplasia. Eighty-five percent of these mice develop HCC spontaneously, and have reduced survival that is related to their liver pathology. Through measurement of protein, RNA, and histological markers, we provide evidence to support the hypothesis that changes in liver stromal cells play an essential role in tumorigenesis in this model. A paracrine signaling model is proposed where ectopic expression of Pdgf-c in hepatocytes results in activation of hepatic stellate cells, which subsequently activates endothelial and Kupffer cells. Activation of these non-parenchymal cells promotes the release of hepatocyte growth factors that, together with changes in extracellular matrix, lead to the formation of HCC. Pdgf-c Tg mice provide a useful pre-clinical model in which to test novel drugs for chronic liver disease and HCC that focus on blocking the processes that alter the liver's fibrotic microenvironment.

overall_design: Two strains of mice, C57BL/6 and C57/BL6 Pdgf-c transgenic, were analyzed to see if liver stromal cells play an essential role in tumorigenesis.

first: Jocelyn

middle: H

last: Wright

first: Melissa

middle: M

last: Johnson

first: Matthew

last: Yeh

first: Renay

middle: L

last: Bauer

first: Kelly

last: Hudkins

first: Deb

middle: G

last: Gilbertson

first: Theodor

last: Bammler

first: Richard

middle: P

last: Beyer

first: Nelson

last: Fausto

first: Jean

middle: S

last: Campbell


title: Gene expression data of pHGG tumor samples

city: Heidelberg

first: Marcel

last: Kool

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

institute: German Cancer Research Center DKFZ

summary:
Pediatric high-grade gliomas (pHGGs) harboring the K27M mutation of H3F3A (histone H3.3) are characterized by global reduction of the repressive histone mark H3K27me3 and DNA hypomethylation.
Analysis of K27M-induced changes on H3K27me3 occupancy and DNA methylation at differentially expresed genes (K27M vs. wild-type H3.3) in primary pHGG tumor samples.

overall_design: 22 glioblastoma samples from pHGG patients were selected for RNA extraction and hybridization on Affymetrix Affymetrix Human Genome U133 Plus 2.0 Arrays. Expression profiling data of 17 pHHGs are part of our previous study (GSE36245 or GSE34824).

first: Sebastian

last: Bender

first: Yujie

last: Tang

first: Anders

last: Lindroth

first: Christoph

last: Plass

first: Yoon-Jae

last: Cho

first: Stefan

last: Pfister


title: SOX9 overexpression in melanoma

status: Public on May 09 2014

city: Geneva

first: Phil

middle: Fang

last: Cheng

address: Rue Gabrielle-Perret-Gentil 4

department: Oncology

country: Switzerland

institute: Hopitaux universitaires de Geneve

summary: SOX9 is generally not expressed in melanomas with a high proliferative capacity but is expressed in melanomas with a high invasive capacity. Here we overexpress full length SOX9 in M010817, a melanoma cell culture with high proliferative capacity but low invasive capacity.

overall_design: 3x Control vector. 3x SOX9 overexpression

first: P

middle: F


title: Genes expression of cervical squamous cell carcinoma, CaSki cells, treated with or without recombinant TGF-b1 (2 ng/mL)

city: Kyoto

first: Budiman

last: Kharma

state: Kyoto

address: 54 Kawahara-cho, Shogoin, Sakyo-ku

department: Gynecology and Obstetrics

institute: Kyoto University Graduate School of Medicine

summary:
Aggressive local invasion is the major way of spread in uterine cervical squamous cell carcinoma (CSCC). Although TGF-b facilitates invasion of various types of cancer cells, the role of TGF-b pathway in CSCC is unclear.
Through array-based analysis, immunohistochemical staining of human endometrial cancer tissue, it is shown that interaction between CSCC cells and surrounding cancer asscocited fibroblasts (CAFs) activates TGF-b via TSP-1 secretion to facilitate CSCC invade, resulting in up-regulation of pSMAD3 in CSCC cells to promote invasion. These results suggest that activation of TGF-b induced by the interaction between CSCC cells and CAFs could play a key role in the initiation of tumor spreads.

overall_design: We used microarrays to clarify the changes of gene expression along with recombinant TGF-b1 treatment and to confirm whether there are any changes on genes expression related to TGF-b pathway.

first: Michikazu

last: Nagura

first: Noriomi

last: Matsumura

first: Tsukasa

last: Baba

first: Ryusuke

last: Murakami

first: Junzo

last: Hamanishi

first: Ken

last: Yamaguchi

first: Kaoru

last: Abiko

first: Masafumi

last: Koshiyama

first: Masaki

last: Mandai

first: Susan

last: Murphy

first: Ikuo

last: Konishi


title: Aging-induced differential methylation in human PBMCs occurs with but often without change in expression of the associated gene (DNA Methylation)

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: Aging is a progressive process that results in the accumulation of intra- and extracellular alterations that in turn contribute to a reduction in health. Age-related changes in DNA methylation have been reported before and may be responsible for aging-induced changes in gene expression, although a causal relationship has yet to be shown. Using genome-wide assays, we analyzed age-induced changes in DNA methylation and their effect on gene expression with and without transient induction with the synthetic transcription modulating agent WY14,643. To demonstrate feasibility of the approach, we isolated peripheral blood mononucleated cells (PBMCs) from five young and five old healthy male volunteers and cultured them with or without WY14,643. Infinium 450K BeadChip and Affymetrix Human Gene 1.1 ST expression array analysis revealed significant differential methylation of at least 5 % (ΔYO > 5 %) at 10,625 CpG sites between young and old subjects, but only a subset of the associated genes were also differentially expressed. Age-related differential methylation of previously reported epigenetic biomarkers of aging including ELOVL2, FHL2, PENK, and KLF14 was confirmed in our study, but these genes did not display an age-related change in gene expression in PBMCs. Bioinformatic analysis revealed that differentially methylated genes that lack an age-related expression change predominantly represent genes involved in carcinogenesis and developmental processes, and expression of most of these genes were silenced in PBMCs. No changes in DNA methylation were found in genes displaying transiently induced changes in gene expression. In conclusion, aging-induced differential methylation often targets developmental genes and occurs mostly without change in gene expression.

overall_design: Peripheral blood mononuclear cells were isolated from 10 volunteers (5 young 5 old), treated with the synthetic PPARalpha agonists WY14,643 or control for 13 hrs, and subjected to genome-wide DNA methylation and gene expression analysis. This entry contains the DNA methylation data.

first: Wilma

middle: T

last: Steegenga

first: Tiffany

last: Morris

first: Mark

middle: V

last: Boekschoten

first: Michael

last: Müller


title: Expression data from EGFR WT or EGFR mutant NSCLC with or without erlotinib

city: South San Francisco

first: Ho-June

last: Lee

address: 1 DNA way

department: Discovery Oncology

institute: Genentech

summary:
Non-small cell lung cancers (NSCLCs) harboring activating EGFR mutants show dramatic responses to EGFR TKIs, such as erlotinib and geffitinib. However, nearly all patients show relapse within 1 year after initial treatment.
We used microarrays to detail global gene expression changes in EGFR mutant cells vs. WT cells responding to erlotinib.

overall_design: 4 EGFR mutant and 4 WT NSCLC cells were treated with or without erlotinib for 24 hr, followed by RNA extraction and hybridization on Affymetrix microarrays.

first: Pan

last: Du


title: Identification of targets regulated by SELP in HSC

city: cambridge

first: yaoyu

last: chen

state: Massachusetts

address: 250 Mass ave

department: ONC

institute: NIBR

summary:
To understand the underlying mechanism by which Alox15 gene is required by HSCs, we performed a comparative DNA microarray analysis using total RNA isolated from wild type Lin-Sca-1+c-Kit+, SELP-/- Lin-Sca-1+c-Kit+. The result was validated by quantitative real-time PCR analysis of wild type Lin-Sca-1+c-Kit+ and SELP-/- Lin-Sca-1+c-Kit+.
Cancer stem cells are responsible for the initiation and maintenance of some types of cancer, and few effective target genes in these stem cells have been identified. Here we show that the selp is essential for the survival of leukemia stem cells (LSCs) in BCR-ABL-induced chronic myeloid leukemia (CML). To understand the underlying mechanism through which SELP regulates the function of HSCs, the gene expression profiles between WT and Selp-/- HSCs were compared.

first: Yaoyu

last: Chen

first: Yi

last: Shan

first: Shaoguang

last: Li


title: Antagonism between the Master Regulators of Differentiation Ensures the Discreteness and Robustness of Cell Fates

status: Public on May 08 2014

first: Eisuke

last: Nishida

address: Kitashirakawa, Sakyo-ku

department: Department of Cell and Developmental Biology

institute: Graduate School of Biostudies, Kyoto University

summary:
The discreteness of cell fates is an inherent and fundamental feature of multicellular organisms. Here we show that cross-antagonistic mechanisms of actions of MyoD and PPARg, which are the master regulators of muscle and adipose differentiation, respectively, confer the robustness to the integrity of cell differentiation. Simultaneous expression of MyoD and PPARg in mesenchymal stem/stromal cells led to the generation of a mixture of multinucleated myotubes and lipid-filled adipocytes. Interestingly, hybrid cells, i.e., lipid-filled myotubes, were not generated, suggesting that these differentiation programs are mutually exclusive. Mechanistically, while exogenously expressed MyoD was rapidly degraded in adipocytes through ubiquitin-proteasome pathways, exogenously expressed PPARg was not down-regulated in myotubes. In PPARg-expressing myotubes, PPARg-dependent histone hyperacetylation was inhibited in a subset of adipogenic gene loci, including that of C/EBPa, an essential effector of PPARg. Thus, the cross-repressive interactions between MyoD- and PPARg-induced differentiation programs ensure the discrete cell fate decisions.
To gain insights into the mechanisms by which adipogenic differentiation is inhibited in PPARg-expressing myotubes, we performed microarray analysis to compare gene expression profiles of the myotube-enriched (M) fraction and the adipocyte-enriched (A) fraction. M fraction and A fraction were obtained by fractionating a mixture of myotubes and adipocytes, which was generated by simultaneous expression of MyoD and PPARg, according to  cell size.

overall_design: Microarray analysis was performed using mRNA isolated from C3H10T1/2 cells. We used five samples: non-infected cells, control lentivirus-infected cells, HA-PPARg-infected cells, and cells co-infected with Myc-MyoD and HA-PPARg and then fractionated accroding to cell size (M-fraction and A-fraction). Total RNA was prepared using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction. Other procedures including hybridization to the Mouse Gene 1.0 ST array (Affymetrix) were performed according to Affymetrix protocols. The affymetrix outputs (CEL files) were imported into GeneSpring GX 11.0.2 (Agilent Technologies) microarray analysis software for presentation of the expression profiles. Probe intensities were normalized, and expression signals of all genes (probe sets) were calculated using RMA (robust multi-array analysis, as implemented in GeneSpring GX).

first: Kazunori

last: Sunadome


title: Macrophage-restricted Interleukin-10 receptor-, but not IL-10 deficiency causes severe spontaneous colitis

city: Rehovot

first: Gilgi

last: Friedlander

address: Hertzel st

country: Israel

institute: Weizmann Institute of Science

summary: Interleukin-10 (IL-10) is a pleiotropic anti-inflammatory cytokine produced and sensed by most hematopoietic cells. Genome wide association studies and experimental animal models point at a central role of the IL-10 axis in Inflammatory Bowel Diseases. Here we investigated the importance of intestinal macrophage production of IL-10 and their IL-10 exposure, as well as the existence of an IL-10-based autocrine regulatory loop in the gut. Specifically, we generated mice harboring IL-10 or IL-10 receptor (IL-10Rα) mutations in intestinal lamina propria-resident chemokine receptor CX3CR1hi-expressingmacrophages. We found macrophage-derived IL-10 dispensable for gut homeostasis and maintenance of colonic T regulatory cells. In contrast, loss of IL-10 receptor expression impaired the critical conditioning of these monocyte-derived macrophages, but resulted in spontaneous development of severe colitis. Collectively, our results highlight IL-10 as a critical homeostatic macrophage-conditioning factor in the colon and define intestinal CX3CR1hi macrophages as a decisive factor that determines gut health or inflammation.

overall_design: Microarray of resident macrophages sorted from colons of Interleukin-10 deficeint mice and macrophage-restricted interleukin-10 receptor deficient mice versus colonic resident macrophages of wild type mice

first: Ehud

last: Zigmond

first: Biana

last: Bernshtein

first: Catherine

middle: R

last: Walker

first: Simon

last: Yona

first: Ki-Wook

last: Kim

first: Ori

last: Brenner

first: Rita

last: Krauthgamer

first: Chen

last: Varol

first: Werner

last: Mueller

first: Steffen

last: Jung


title: Expression data from Hepatosplenic T cell lymphoma patient samples and normal spleen as control.

status: Public on May 10 2014

city: Leuven

first: Julio

last: Finalet

address: Herestraat 49

country: Belgium

institute: KULeuven

summary: Hepatosplenic T-cell lymphoma (HSTL) is an aggressive lymphoma cytogenetically characterized by isochromosome 7q   [i(7)(q10)], of which the molecular consequences remain unknown. We report here results of an integrative genomic and transcriptomic (expression microarray and RNA-sequencing) study of six HSTL cases with i(7)(q10) and three cases with ring 7   [r(7)], a rare variant aberration. Using high resolution array CGH, we prove that HSTL is characterized by the common loss of a 34.88 Mb region at 7p22.1p14.1 (3506316-38406226 bp) and duplication/amplification of a 38.77 Mb region at 7q22.11q31.1 (86259620-124892276 bp). Our data indicate that i(7)(q10)/r(7)-associated loss of 7p22.1p14.1 is a critical event in the development of HSTL, while gain of 7q sequences drives progression of the disease and underlies its intrinsic chemoresistance. Loss of 7p22.1p14.1 does not target a postulated tumor suppressor gene but unexpectedly enhances the expression of CHN2 from the remaining 7p allele, resulting in overexpression of β2-chimerin and dysregulation of a pathway involving RAC1 and NFATC2 with a cell proliferation response. Gain of 7q leads to increased expression of critical genes, including RUNDC3B, PPP1R9A and ABCB1, a known multidrug resistance gene. RNA-sequencing did not identify any additional recurrent mutations or gene fusions, suggesting that i(7)(q10) is the only driver event in this tumor. Our study confirms the previously described gene expression profile of HSTL and identifies a set of 24 genes, including three located on chromosome 7 (CHN2, ABCB1 and PPP1R9A), distinguishing HSTL from other malignancies

overall_design: overall design

last: Ferreiro

first: Leila

last: Rouhigharabaei

first: Helena

last: Urbankova

first: Jo-Anne

last: van der Krogt

first: Lucienne

last: Michaux

first: Shashirekha

last: Shetty

first: Laszlo

last: Krenacs

first: Thomas

last: Tousseyn

first: Pascale

last: De Paepe

first: Anne

last: Uyttebroeck

first: Gregor

last: Verhoef

first: Tom

last: Taghon

first: Peter

last: Vandenberghe

first: Jan

last: Cools

first: Iwona

last: Wlodarska


title: Aging-induced differential methylation in human PBMCs occurs with but often without change in expression of the associated gene

first: Guido

last: Hooiveld

type:
Expression profiling by array
Methylation profiling by array


title: Immune regulation by low doses of the DNA methyltransferase inhibitor 5-azacitidine in common human epithelial cancers [methylation]

city: Baltimore

first: Stephen

last: Baylin

state: Maryland

address: 1650 Orleans St CRB I RM 541

institute: Johns Hopkins UniversityJohns Hopkins Medical Institutions

summary:
Epigenetic therapy is emerging as a potential therapy for solid tumors. To investigate its mechanism of action, we performed integrative expression and methylation analysis of 63 cancer cell lines (breast, colorectal, and ovarian) after treatment with the DNA methyltransferase inhibitor 5-azacitidine (AZA). Gene Set Enrichment Analysis demonstrated significant enrichment for immunomodulatory pathways in all three cancers (14.4-31.3%) including interferon signaling, antigen processing and presentation, and cytokines/chemokines. Strong upregulation of cancer testis antigens was also observed.
An AZA IMmune gene set (AIMs) derived from the union of these immunomodulatory pathway genes classified primary tumors from all three types, into “high” and “low” AIM gene expression subsets in tumor expression data from both TCGA and GEO (GSE42284, GSE10893, and GSE26712 for the colon, breast, and ovarian samples, respectively). Samples from selected patient biopsies showed upregulation of AIM genes after treatment with epigenetic therapy. These results point to a broad immune stimulatory role for DNA demethylating drugs in multiple cancers.

overall_design: A total of 338 samples were analyzed.

first: Huili

last: Li

first: Katherine

middle: B

last: Chiappinelli

first: Angela

middle: A

last: Guzzetta

first: Ray-Whay

middle: C

last: Yen

first: Rajita

last: Vatapalli

first: Cynthia

last: Zahnow

first: Nita

last: Ahuja


title: Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels [Bisulfite-array]

city: Chicago

first: Nicholas

middle: E

last: Banovich

state: IL

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

institute: University of Chicago

type: Methylation profiling by genome tiling array

summary: DNA methylation is an important epigenetic regulator of gene expression. Recent studies have revealed widespread associations between genetic variation and methylation levels. However, the mechanistic links between genetic variation and methylation remain unclear. To begin addressing this gap, we collected methylation data at ~300,000 loci in lymphoblastoid cell lines (LCLs) from 64 HapMap Yoruba individuals, and genome-wide bisulfite sequence data in ten of these individuals. We identified (at an FDR of 10%) 13,915 *cis* methylation QTLs (meQTLs), i.e., CpG sites in which changes in DNA methylation are associated with genetic variation at proximal loci. We found that meQTLs are frequently associated with changes in methylation at multiple CpGs across regions of up to 3 kb. Interestingly, meQTLs are also frequently associated with variation in other properties of gene regulation, including histone modifications, DNase I accessibility, chromatin accessibility, and expression levels of nearby genes. These observations suggest that genetic variants may lead to coordinated molecular changes in all of these regulatory phenotypes. One plausible driver of coordinated changes in different regulatory mechanisms is variation in transcription factor (TF) binding. Indeed, we found that SNPs that change predicted TF binding affinities are significantly enriched for associations with DNA methylation at nearby CpGs.

overall_design: Bisulfite converted DNA from 64 individuals was hybridized to the Illumina Infinium HumanMethylation450 BeadChip

first: Xun

last: Lan

first: Bryce

last: van de Geijn

first: Graham

last: McVicker

first: Jacob

last: Degner

first: John

middle: D

last: Blischak

first: Jonathan

last: Pritchard

first: Yoav

last: Gilad


title: Immune regulation by low doses of the DNA methyltransferase inhibitor 5-azacitidine in common human epithelial cancers


title: Nfatc1 enhances stem cell contribution to squamous skin tumors

status: Public on May 06 2014

city: New Haven

first: Valerie

last: Horsley

state: CT

address: 266 Whitney Avenue

department: Department of Molecular, Cellular and Developmental Biology

institute: Yale University

summary:
We find that epithelial-specific deletion of Nfatc1 decreases skin tumor susceptibility in mice subjected to DMBA/TPA carcinogenesis. To probe the molecular mechanisms by which Nfatc1 may regulate tumorigenesis, we identify gene expression changes associated with constitutive NFATc1 activation in primary mouse keratinocytes.
Constitutively active NFATc1 activity in primary mouse keratinocytes to investigate how Nfatc1 regulates tumor initiation in the skin.

overall_design: Primary mouse keratinocytes were infected with retroviruses encoding a recombinant human NFATc1 containing mutations in the autoinhibitory domain that render it constitutively active (CAC1). Keratinocytes infected with retroviruses generated from an empty MSCV reotroviral vector were used as a control. Three biological replicates were performed.

first: Jill

last: Goldstein


title: Deactivation of Hepatic Stellate Cells during Liver Fibrosis Resolution in Mice

status: Public on May 05 2014

city: New York

first: Robert

last: Schwabe

state: NY

address: 1150 St. Nicholas Ave, Room 415

institute: Columbia University

summary:
Gene expression of mouse hepatic stellate cells was characterized under the following conditions:
Quiescent (isolated from normal mouse liver) and reverted (isolated from mouse liver treated with 4
injections of carbontetrachloride followed by 45 day rest period)
Affymetrix Mouse 1.0ST  gene expression measurements were
used to characterize the transcriptomic basis in quiescent hepatic stellate cells, isolated from normal liver,
and reverted hepatic stellate cells, isolated from liver treated with 4 injections of CCl4 followed by a 45 day
rest period.

overall_design:
Gene expression of mouse hepatic stellate cells was characterized under the following conditions:
A. Quiescent control hepatic stellate cells (n=4).
B. Reverted hepatic stellate cells (n=4).

first: Juliane

last: Troeger

first: Ingmar

last: Mederacke

first: Geum-Youn

last: Gwak

first: Dianne

last: Dapito

first: Xueru

last: Mu

first: Christine

last: Hsu

first: Jean-Philippe

last: Pradere

first: Richard

last: Friedman


title: Epigenetic Analysis of ASD in AMA

city: Bronx

first: Esther

last: Berko

address: 1301 Morris Park Ave

department: Genetics

institute: Albert Einstein College of Medicine

summary: DNA from ectodermal cells of individuals with an Autism Spectrum Disorder born to mothers aged 35 and older was analzyed for discovery of differentially methylated regions and comethylation modules associated with ASD

overall_design: DNA from 48 individuals with ASD and DNA from 48 typically developing controls (all born to mothers older than 35) was isolated, bisulphite converte, and hybridized to the Illumina 450K array.

last: Greally


title: CD24 targets

city: Birmingham

first: Lizhong

last: Wang

address: 740 20th St S

institute: UAB

summary: Gene expression were identified with or without CD24 gene silencing in Du145 cells.

overall_design: RNA isolated from 5 independent cultures of Scramble control, 3 cultures of CD24-ShRNA1 and 2 cultures of CD24-ShRNA2 were tested using Affimatrx Human U133 Plus 2.0 microarrays.

first: Yang

last: Liu


title: Expression data from 70 gastric cancer patients

city: Shanghai

first: Hua

last: Dong

address: 199 Liangjing Rd.

country: China

institute: astrazeneca

summary: To explore the spectrum of genetic aberrations of Chinese gastric cancer, 70 samples were further profiled by Affymetrix Hu133Plus2 arrays for mRNA expression

overall_design: 70 gastric cancer frozen tumor tissues were selected for RNA extraction and hybridization on Affymetrix microarrays. All these samples have been also profiled using Agilent 244K array CGH technology.

first: Ziliang

last: Qian

first: Guanshan

last: Zhu

first: Jiafu

last: Ji

first: Qunsheng


title: Array CGH and expression data from gastric cancer patients

type: Genome variation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Dynamic tumor growth patterns in a novel murine model of colorectal cancer

status: Public on May 03 2014

city: Madison

first: Terrah

middle: Jean

last: Paul Olson

state: WI

address: 600 Highland Ave.

department: Surgery

institute: University of Wisconsin School of Medicine and Public Health

summary:
Colorectal cancer often arises from adenomatous polyps.  Polyps can grow and progress to cancer, but may also remain static in size, regress, or resolve.  Prediciting which progress to cancer and which remain benign is difficult.  We developed a long-lived murine model of colorectal cancer with tumors that can be followed by colonoscopy.  Our aim was to assess whether these tumors have similar growth patterns and histologic fates to human colorectal polyps to identify features to aid in risk stratification of colonic tumors.
Long-lived Apc^Min/+ mice were treated with 4% dextran sodium sulfate to promote colonic tumorigenesis.  Tumor growth patterns were characterized by serial colonoscopy, and pathology was determined.  Serial biopsies of tumors were obtained for immunohistochemistry and gene expression profiling by microarray analysis with Affymetrix Whole Genome array.  Tumors (n=424) grew, remained static, regressed, or resolved over time with different relative frequencies.  Newly developed tumors demonstrated dynamic growth patterns with higher rates of growth and resolution, while more established tumors tended to remain static in size.  Colonic tumors were hyperplastic lesions (3%), adenomas (73%), intramucosal carcinomas (20%), or adenocarcinomas (3%).  Differentially expressed genes between adenomas and intramucosal carcinomas were identified.  We did not identify differentially expressed genes between early and late biopsies from the same tumor.  This novel murine model of intestinal tumorigenesis develops colonic tumors that can be monitored by serial colonoscopy, mirror growth patterns seen in human colorectal polyps, and progress to colorectal cancer.  Further characterization of cellular and molecular features are needed to determine which features can be used to risk-stratify polyps for progress to colorectal cancer and potentially guide prevention strategies.

overall_design: F1 (SWR x C57BL/6) Apc^Min/+ mice who had been given two treatments of 4% dextran sodium sulfate in drinking water at weaning underwent colonoscopy around 80 days of age.  Those with distal colonic tumors amenable to biopsy had two biopsies taken at that time.  Tumors were monitored by colonoscopy every 14 days.  Every 28 days, two additional biopsies were taken of each tumor.  This protocol was repeated until mice were moribund.  Six tumors were removed after sacrifice.  The earliest and latest biopsies of each tumor were selected for RNA extraction and Affymetrix hybridization.

middle: J

last: Halberg


title: Astrocyte-encoded positional cues maintain sensorimotor circuit integrity

status: Public on May 02 2014

city: San Francisco

first: David

last: Rowitch

address: 35 Medical Center Way, RMB 932D

department: Institute for Regenerative Medicine

institute: University of California-San Francisco

summary: Astrocytes, the most abundant cells in the central nervous system, promote synapse formation and help refine neural connectivity. Although they are allocated to spatially distinct regional domains during development, it is unknown whether region-restricted astrocytes are functionally heterogeneous. Here we show that postnatal spinal cord astrocytes express several region-specific genes, and that ventral astrocyte-encoded Semaphorin3a (Sema3a) is required for proper motor neuron and sensory neuron circuit organization. Loss of astrocyte-encoded Sema3a led to dysregulated α−motor neuron axon initial segment orientation, markedly abnormal synaptic inputs, and selective death of α−but not of adjacent γ−motor neurons. Additionally, a subset of TrkA+ sensory afferents projected to ectopic ventral positions.  These findings demonstrate that stable maintenance of a positional cue by developing astrocytes influences multiple aspects of sensorimotor circuit formation. More generally, they suggest that regional astrocyte heterogeneity may help to coordinate postnatal neural circuit refinement.

overall_design: 12 total samples consisting of three biological replicates each of flow sorted postnatal day 7 dorsal spinal cord astrocytes, ventral spinal cord astrocytes, dorsal SC non astrocytes, and ventral SC non astrocytes

first: A

last: Molofsky

first: D

middle: H


title: Gene expresssion changes in pancreatic islets of 11 weeks old IKK2-CApdx-1 mice compared to control and Pdx-1+/- mice

city: Ulm

first: Karlheinz

last: Holzmann

address: Helmholtzstreet 8/1

department: Medical Faculty

institute: Ulm University

summary: Canonical IKK/NF-κB signaling is a master regulator of inflammation and innate immunity and has been implicated in the pathogenesis of T1D. To investigate the impact of NF-κB activation on β-cell homeostasis and diabetes development, we generated a transgenic gain-of-function mouse model allowing conditional NF-κB activation via expression of IKK2-CA  (constitutively active IKK2 allele) in β-cells using the tetracycline-regulated gene expression system. Pdx-1-tTA (knockin model generating Pdx-1 haploinsufficiency) driver mice were used for β-cell specific transgene expression. Double transgenic IKK2-CA-pdx-1 mice develop a full-blown immune-mediated diabetes.To identify gene expression changes underlying this diabetes development pancreatic islets of diabetic IKK2-CA-Pdx-1, PDX-1 +/- and control mice were prepared and isolated total RNA was used for microarray analysis.

overall_design: Pancreatic islets were isolated from 11 weeks old control (n=5), Pdx-1+/- (n=4) and  IKK2-CApdx-1 (n=5) mice, total RNA was extracted with RNeasy mini kit (QIAGEN). Microarray analyses were performed using 200 ng total RNA as starting material and 5.5 µg ssDNA per hybridization (GeneChip Fluidics Station 450; Affymetrix, Santa Clara, CA). The total RNAs were amplified and labeled following the Whole Transcript (WT) Sense Target Labeling Assay (http://www.affymetrix.com). Labeled ssDNA was hybridized to Mouse Gene 1.0 ST Affymetrix GeneChip arrays (Affymetrix, Santa Clara, CA). The chips were scanned with a Affymetrix GeneChip Scanner 3000 and subsequent images analyzed using Affymetrix® Expression Console Software (Affymetrix). Probe level data were obtained using the robust multichip average (RMA) normalization algorithm.

first: Bernd

last: Baumann

first: Thomas

last: Wirth

first: Heba

last: Salem


title: In Vitro Transformation of Primary Human CD34+ Cells by AML Fusion Oncogenes: Early Gene Expression Profiling Reveals Possible Drug Target in AML

status: Public on May 01 2014

city: Saint Louis

first: Anmaar

last: Abdul-Nabi

state: Missouri

address: 660 South Euclid Avenue.  PO box 8118

department: Pathology and Immunology

institute: Washington University in Saint louis

summary: Different fusion oncogenes in acute myeloid leukemia (AML) have distinct clinical and laboratory features suggesting different modes of malignant transformation. Here we compare the in vitro effects of representatives of major groups of AML fusion oncogenes on primary human CD34+ cells.

overall_design: For the 3 d and 8 d time points, the oncogenes were retrovirally expressed in primary human CD34+ cells, with cells transduced with empty retroviral vector as controls. As retroviral transduction requires days, for the 6 h time point the oncogenes were expressed from a pTracer-CMV/Bsd plasmid using nucleofection. Cells nucleofected with empty pTracer-CMV/Bsd vector were used as a control.

first: Abdul-Nabi

middle: M

last: Anmaar

first: Yassin

last: Enas

first: Yaseen

last: Nabeel


title: Hypoxia/Anoxia

status: Public on May 04 2014

city: Uppsala

first: Mårten

last: Fryknäs

address: Akademiska sjh ingång 61

department: Medical sciencies

country: Sweden

institute: Uppsala university

summary: The environment inside even a small tumor is characterized by total (anoxia) or partial oxygen deprivation, hypoxia. It has been shown that radiotherapy and some conventional chemotherapies may be less effective in hypoxia, and therefore it is important to investigate how different drugs act in different microenvironments. In the associated study we performed a large screening of the effects of 19 clinically used or experimental chemotherapeutic drugs on four different cell lines in conditions of normoxia, hypoxia and anoxia. A panel of 19 commercially available drugs: 5-fluorouracil, acriflavine, bortezomib, cisplatin, digitoxin, digoxin, docetaxel, doxorubicin, etoposide, gemcitabine, irinotecan, melphalan, mitomycin c, rapamycin, sorafenib, thalidomide, tirapazamine, topotecan and vincristine were tested for cytotoxic activity on the cancer cell lines A2780 (ovarian), ACHN (renal), MCF-7 (breast), H69 (SCLC) and U-937 (lymphoma). Parallel aliquots of the cells were grown at different oxygen pressures and after 72 hours of drug exposure viability was measured with the fluorometric microculture cytotoxicity assay (FMCA). Sorafenib, irinotecan and docetaxel were in general more effective in an oxygenated environment, while cisplatin, mitomycin c and tirapazamine were more effective in a low oxygen environment. Surprisingly, hypoxia in H69 and MCF-7 cells mostly rendered higher drug sensitivity. In contrast ACHN appeared more sensitive to hypoxia, giving slower proliferating cells, and consequently, was more resistant to most drugs. Gene expression analysis was performed on MCF-7 cells after 90 hours in either anoxic or hypoxic conditions, and compared to cells grown in a regular cell incubator. The gene expression analysis was performed to validate that the cells were hypoxic/anoxic and showed the characteristic hypoxia response.

overall_design:
Microarray based mRNA profiling was used to charactarize cells grown in hypoxia and anoxia.
In the associated study we performed a large screening of the effects of 19 clinically used or experimental chemotherapeutic drugs on four different cell lines in conditions of normoxia, hypoxia and anoxia. We fin that hypoxia/anoxia render cancer cells both more resistant and more sensistive, depending of the type of drug used. The gene expression analysis was performed to validate that the cells really were hypoxic/anoxic and showed the characteristic hypoxia response. The cell line used for the gene expression analysis was MCF-7.

first: Marten

last: Fryknas


title: Distinct Stromal Cell Factor Combinations Can Separately Control Hematopoietic Stem Cell Survival, Proliferation and Self-Renewal

city: Vancouver

first: Connie

last: Eaves

state: British Columbia

address: 675 West 10th Avenue

department: Terry Fox Laboratory

country: Canada

institute: BC Cancer Agency

summary: Hematopoietic stem cells (HSCs) are identified by their ability to sustain prolonged blood cell production in vivo, although recent evidence suggests that durable self-renewal (DSR) is shared by HSC subtypes with distinct self-perpetuating differentiation programs. Net expansions of DSR-HSCs occur in vivo, but molecularly defined conditions that support similar responses in vitro are lacking. We hypothesized that this might require a combination of factors that differentially promote HSC viability, proliferation and self-renewal. We now demonstrate that HSC survival and maintenance of DSR potential is variably supported by different Steel factor (SF)-containing cocktails with similar HSC-mitogenic activities. In addition, stromal cells produce other factors, including nerve growth factor and collagen 1, that can antagonize the apoptosis of initially quiescent adult HSCs and, in combination with SF and interleukin-11, produce >15-fold net expansions of DSR-HSCs ex vivo within 7 days. These findings suggest a new molecular basis for HSC control and expansion.

overall_design: Adult mouse bone marrow CD45+EPCR+CD48-CD150+ cells were used in a total of 4 conditions (fresh, 6 hour stimulation with SF+IL-11+UG26 CM, UG26 CM only, SF+IL-11) with 2 technical replicates per condition.

first: Stefan

last: Wohrer

last: Knapp


title: Epigenetic and in vivo comparison of diverse mesenchymal stromal cell sources reveals an endochonrdal signature for human hematopoietic niche formation

status: Public on Apr 30 2014

city: Stanford

first: Andreas

last: Reinisch

address: 265 Campus Drive

department: Institute for Stem Cell Biology and Regenerative Medicine

institute: Stanford University

summary: Despite similarities in morphology, phenotype and in vitro behavior, Mesenchymal Stromal Cells (MSC) form various tissue sources show striking differences in their in vivo potential to form bone, cartilage and hematopoietic support tissue.  Comparing four commonly use MSC sources (bone marrow (BM), white adipose tissue (WAT), umbilical cord (UC) and skin) we found only bone marrow (BM)-derived MSCs capable of endochondral ossification and marrow attraction. To gain mechanistic insights explaining this differences we analyzed gene expression characteristics of MSC from all four tissue sources using  Affymetrix Genechip Human Gene 2.0 ST Array.

overall_design: MSCs from BM, WAT, UC and skin were isolated using plastic adherence. Cells were expanded in standard alpha-MEM supplemented with pooled human platelet lysate fully replacing fetal bovine serum. MSCs were subcutaneously implanted into immune-compromised mice to comparatively evaluate bone formation and subsequent bone marrow attraction. In parallel we have isolated RNA from all sources to analyze tissue source specific gene expression profile.

first: Nathalie

last: Etchart

first: Nicole

last: Hofmann

first: Daniel

last: Thomas

first: Margareta

last: Fruehwirth

first: Subarna

last: Sinha

first: Udo

last: Hartwig

first: Christine

last: Beham-Schmid

first: Slave

last: Trajanoski

first: Qiong

last: Lin

first: Wolfgang

last: Wagner

first: Christian

last: Dullin

first: Frauke

last: Alves

first: Katharina

last: Schallmoser

first: Michael

last: Andreeff

first: Dirk

last: Strunk


title: Expression Array analysis of MTAP in HT080 cells

city: Philadelphia

first: warren

last: kruger

address: 333 Cottman Ave.

institute: Fox Chase Cancer Center

summary:
Methylthioadenosine Phosphorylase (MTAP) is a tumor suppressor gene that encodes an enzyme responsible for the catabolism of the polyamine byproduct 5′deoxy-5′-methylthioadenosine (MTA).  To elucidate the mechanism by which MTAP inhibits tumor formation, we have created isogenic MTAP+ and MTAP- HT1080 fibrosarcoma cells.
In this experiment we have performed expression array analysis on MTAP-, MTAP+, and MTAP+ cells treated with the MTAP inhibitor MT-DADMe-ImmA.

overall_design: Three biological replicates of each sample were grown and analyzed.  M- is MTAP-. M+ is MTAP+, and M+I is MTAP treated with inhibitor (48 hours).

first: Warren

last: Kruger

first: Baiqing

last: Tan

last: Slifker

first: Yue-Sheng

last: Li


title: Expression data from NEAT1 regulated genes with or without polyI:C

status: Public on May 07 2014

city: 4-6-1, Komaba, Meguroku

first: Takahide

last: Kohro

institute: LSBM, RCAST

summary:
Although thousands of long non-coding RNAs (lncRNAs) are localized in the nucleus, only a few dozen have been functionally characterized.
We found that nuclear paraspeckle assembly transcript 1 (NEAT1), an essential lncRNA for the formation of nuclear body paraspeckles, is induced by poly I:C stimulation, resulting in excess formation of paraspeckles.
Using microarray analysis, we investigated whether NEAT1 induction followed by excess formation of paraspeckles was involved in poly I:C-inducible gene expression.

overall_design: We want to know the NEAT1-regulated genes. To the end, HeLa TO cells with and without poly I:C stimulation and NEAT1-knock down cells with and without poly I:C stimulation and cells transfected with mock plasmid or Neat1v2 expression plasmid alone  were used for RNA extraction and hybridization on Affymetrix microarrays.

first: Katsutoshi

last: Imamura

first: Naoto

last: Imamachi

first: Gen

last: Akizuki

first: Michiko

last: Kumakura

first: Atsushi

last: Kawaguchi

first: Kyosuke

last: Nagata

first: Akihisa

last: Kato

first: Yasushi

first: Hiroki

last: Sato

first: Misako

last: Yoneda

first: Chieko

last: Kai

first: Tetsushi

last: Yada

first: Kiyomi

last: Kaneki

first: Tsuyoshi

last: Inoue

first: Mika

last: Kobayashi

first: Tatsuhiko

last: Kodama

first: Youichiro

last: Wada

first: Kazuhisa

last: Sekimizu

first: Nobuyoshi

last: Akimitsu


title: Identification of GNG7 as An Epigenetically Silenced Gene in Head and Neck Cancer by Gene Expression Profiling

first: Joseph

last: Califano

state: MD

address: 1550 Orleans Street

department: School of Medicine

institute: The Johns Hopkins University

summary: Silencing of tumor suppressor genes plays a vital role in head and neck carcinogenesis. Aberrant hypermethylation in the promoter region of some known or putative tumor suppressor genes (TSGs) occurs frequently during the development of various cancers including head and neck squamous cell carcinoma (HNSCC). In this study we used an expanded mRNA expression profiling approach followed by microarray expression analysis to identify epigenetically inactivated genes in HNSCC. Two HNSCC cell lines were treated with 5-aza-2’-deoxycytidine followed by microarray analysis to identify epigenetically silenced genes in HNSCC. 1960, 614, and 427 genes were upregulated in HNSCC cell lines JHU-012, JHU-011 and the combination of both cell lines, respectively. HNSCC tumor and normal mucosal samples were used for gene profiling by a 47K mRNA gene expression array and we found, 7140 genes were downregulated in HNSCC tumors compared to normal mucosa as determined by microarray analysis and were integrated with cell line data. Integrative analysis defined 126 candidate genes, of which only seven genes showed differentially methylation in tumors and no methylation in normal mucosa after bisulfite sequencing. After validation by QMSP, one gene, GNG7, was confirmed as being highly methylated in tumors and unmethylated in normal mucosal and salivary rinse samples demonstrating cancer-specific methylation in HNSCC tissues. TXNIP and TUSC2 were partially methylated in tumors and normal salivary rinses but unmethylated in normal mucosa. We concluded GNG7 as a highly specific promoter methylated gene associated with HNSCC. In addition, TXNIP and TUSC2 are also potential biomarkers for HNSCC.

overall_design: We performed pharmacological unmasking analysis on two HNSCC cancer cell lines JHU-O11 and JHU-O12 by treating cells with or without 5-aza-dC, followed by RNA extraction and microarray analysis using Affymetrix U133 Plus 2.0. The array data were analyzed by initially dChip and then SAM. We performed a four-phase strategy to obtain the unmasked genes in the cells treated with 5-aza and downregulated genes in primary tumors. In the first phase, we compared the cell lines, either JHU-012 or JHU-011, before treatment to the cell lines treated with 5-aza, in order to identify genes that were reexpressed ≥ 2 fold. We found 1960 genes that were upregulated by 5-aza-dC in JHU-O12 cell line. SAM output was obtained at a delta value of 2.05 with a false discovery rate (FDR) of 10% and the d-score cut-off was 1.17.  614 reexpressed genes were found  in 5 aza-treated JHU-O11 (SAM output; delta: 2.089, FDR%: 10, d-score cut-off: 2.8). 427 genes were commonly upregulated in both cell lines when the cell lines were normalized  and analyzed together (SAM output; delta: 1.44, FDR%: 10, d-score cut-off: 1.88). In the second phase of our analysis, we further extracted RNA and performed the 47K mRNA expression array analysis on 13 primary HNSCC tumors samples and 5 normal mucosa samples from non-cancer control patients. After initial dChip and SAM analysis (SAM output; delta: 1.247, FDR%: 5.24, d-score cut-off:0.24), we found 7140 downregulated genes in primary HNSCC tumors compared with normal mucosa. In the third phase, we investigated these three data sets: a) SAM output of 1960 upregulated genes after 5-aza treatment of JHU-012 vs SAM output of 7140 downregulated genes in primary HNSCC: We found that 210 genes that were upregulated by 5-aza-dC in the JHU-O12 cell line and showed downregulation in tumor samples, b) SAM output of 614 upregulated genes after 5-aza treatment of JHU-011 vs SAM output of 7140 downregulated genes in primary HNSCC: We found 79 genes that were upregulated by 5-aza-dC in the JHU-O11 cell line and showed downregulation in tumor samples, c) SAM output from analyzing both cell lines together in the same SAM computation, of 427 upregulated genes after 5-aza treatment of JHU-011 and JHU-012 vs SAM output of 7140 downregulated genes in primary HNSCC: We found 44 genes that were upregulated by 5-aza-dC in JHU-O11 and JHU-012 cell lines and showed downregulation in tumor samples, suggesting that methylation might be involved in gene downregulation.    In the fourth phase of our strategy, we rank-ordered the results of upregulated genes obtained from these 3 data sets and found 126 common genes. We then examined promoter regions of the 126 genes for CpG islands and performed bisulfite sequencing analysis of the promoter region of these genes. We found that 7 genes showed a differential methylation pattern between normal and neoplastic samples. After validation of these genes in a cohort of 33 HNSCC patients and normal salivary and mucosal samples from healthy people by QMSP, we found 3 genes of interest.

first: Semra

last: Demokan

first: Alice

last: Chuang

first: Xiaofei

last: Chang

first: Tanbir

last: Khan

first: Ian

last: Smith

first: Kavita

last: Pattani

first: Santanu

last: Dasgupta

first: Shahnaz

last: Begum

first: Zubair

first: Nanette

last: Liegeois

first: William

last: Westra

first: David

last: Sidransky

first: Wayne

last: Koch


title: Gene expression in the mouse embryonic small intestinal epithelium in the presence or absence of GATA4 and GATA6

city: Milwaukee

first: Michele

last: Battle

address: 8701 Watertown Plank Rd

department: Cell Biology, Neurobiology, and Anatomy

institute: Medical College of Wisconsin

summary: Gene expression was compared between E18.5 Gata4Gata6 double conditional knockout (cKO) small intestinal epithelium and E18.5 control mouse small intestinal epithleium.

overall_design: E18.5 mouse small intestine was collected from control and Gata4Gata6 double conditional knockout mice. Epithelial cells were isolated, and RNA was prepared.  Affymetrix Mouse Gene 1.0 gene arrays were used to interrogate gene expression.  Data was analyzed using dChip software.


title: Cross-species gene expression analysis of species-specific differences in preclinical assessment of pharmaceutical compounds (human)

city: Nottingham

first: John

last: Okyere

address: BioCity Nottingham

country: United Kingdom

institute: CrossGen Limited

summary: Significant qualitative and quantitative differences exist between humans and the animal models used in research. However, significant quantitative and qualitative differences exist between humans and the animal models used in research. This is as a result of genetic variation between human and the laboratory animal. Therefore the development of a system that would allow the assessment of all molecular differences between species after drug exposure would have a significant impact on drug evaluation for toxicity and efficacy. Here we describe a cross-species microarray methodology that identifies and selects orthologous probes after cross-species sequence comparison to develop an orthologous cross-species gene expression analysis tool. The assumptions made by the use of this orthologous gene expression strategy for cross-species extrapolation is that; conserved changes in gene expression equate to conserved pharmacodynamic endpoints. This assumption is supported by the fact that evolution and selection have maintained the structure and function of many biochemical pathways over time, resulting in the conservation of many important processes. We demonstrate this difference using a cross-species methodology by investigating species specific differences of the peroxisome proliferator activator receptor (PPAR) alpha in rat and human.

overall_design: Human primary hepatocytes were treated with 30µ, 100µ EMD and 0.1% DMSO as vehicle control. All samples were incubated at 24hr and 72hr intervals before RNA extractions and hybridization onto Affymetrix human microarrays.

first: J

last: Oppon

first: D

last: Dzidzienyo

first: L

last: Sharma

first: G

last: Ball


title: Riding the spermatogenic wave: Profiling gene expression within neonatal germ and Sertoli cells during a synchronized initial wave of spermatogenesis

city: Pullman

first: Michael

last: Griswold

address: 100 Dairy Rd.

department: School of Molecular Biosciences

institute: Washington State University

summary: WIN 18,446/RA treatment of neonatal mice was used to synchronize the initial wave of spermatogenesis and identify novel messages expressed within either germ or Sertoli cells as spermatogonia enter meiosis.

overall_design: germ cell-specific (Stra8-cre: RiboTag; or Ngn3-cre:RiboTag) and Sertoli cell-specific (Amh-Cre: RiboTag)

first: Elizabeth

last: Evans


title: Identification of WISP1 as an important survival factor in human mesenchymal stem cells

city: Würzburg

first: Katrin

last: Schlegelmilch

address: Brettreichstr. 11

department: Orthopedic Centre for Musculoskeletal Research

institute: University of Würzburg

summary: WNT-induced secreted protein 1 (WISP1/CCN4), a member of the CCN protein family, acts as a downstream factor of the canonical WNT-signaling pathway. A dysregulated expression of WISP1 often reflects its oncogenic potential by inhibition of apoptosis, a necessary form of cell death that protect cell populations for transformation into malignant phenotypes. WISP1-signaling is also known to affect proliferation and differentiation of human mesenchymal stem cells (hMSCs), which are fundamental for the constitution and maintenance of the musculoskeletal system. Our study emphasizes the importance of WISP1-signaling for cell survival of primary human cells. Therefore, we established a successful down-regulation of endogenous WISP1 transcripts through gene silencing in hMSCs. We were able to demonstrate the consequence of cell death immediately after WISP1 down-regulation took place. Bioinformatical analyses of subsequent performed microarrays from WISP1 down-regulated vs. control samples confirmed this observation. We uncovered several clusters of differential expressed genes important for cellular apoptosis induction and immuno-regulatory processes, thereby indicating TRAIL-induced and p53-mediated apoptosis as well as IFNbeta-signaling. Since all of them act as potent inhibitors for malignant cell growth, in vitro knowledge about the connection with WISP1-signaling could help to find new therapeutic approaches concerning cancerogenesis and tumor growth in musculoskeletal tissues.

overall_design:
We established a successful down-regulation of endogenous WISP1 transcripts through gene silencing in hMSCs.
Knock-down versus controls.

first: Alexander

last: Keller

first: Viola

last: Zehe

first: Sylvia

last: Hondke

first: Ludger

last: Klein-Hitpass

first: Norbert

last: Schütze


title: Cross-species gene expression analysis of species-specific differences in preclinical assessment of pharmaceutical compounds

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus


title: Expression data from AstraZeneca internal cell lines

status: Public on Apr 28 2014

city: Macclesfield

first: Mark

last: Wappett

address: Alderley Park

department: Oncology

institute: AstraZeneca

summary: Full legacy gene expression dataset run internally

overall_design: Gene expression data from various panels and experiments was collected, QC'd and normalised in tandem to provide a full summary dataset of the cell line expression data generated internally


title: Expression data from human hair follicle after doxorubicin treatment

city: Boston

first: Andrey

last: Sharov

address: 609 Albans St, J-405

institute: Boston University

summary: Chemotheraputic drugs are able to affect both neoplastic and normal rapidly proliferating cells. We used microarray analysis to identify molecular signatures of the early phase in the response of human hair follicles to chemotheraputic drug, doxorubicin.

overall_design: Human hair follicles were cultured in Williams E medium and were treated with 1 uM Doxorubicin HCl or vehicle control solution for 1 hour. 3 hours after treatmnet hair bulbs were disected for RNA isolation and RNA was analysed using Affymetrix Human Genome U133A 2.0 array.  processing 3 hours after completion of the DXR treatment. Total RNA was isolated from the hair follicle bulbs using TriIzol® Reagent (Invitrogen, San Diego, CA). All experiments were performed using at least three replicates, and RNA isolated from three experimental and control samples was pooled and processed for microarray analyses using one sample of pooled RNA per experimental and control group.

first: Tatyana

last: Sharova


title: Six homeoproteins and a linc-RNA cooperate at the fast MYH locus to lock terminal fast myofibre phenotype

status: Public on Apr 27 2014

city: Paris

first: iori

last: sakakibara

address: 22 rue Méchain

institute: Cochin institut

summary: Thousands of long intergenic noncoding RNAs (lincRNAs) are encoded by the mammalian genome, which were reported to have multiple biological functions as transcriptional activators acting in cis 1 or trans 2, transcriptional repressors 3,4 or miRNAs decoys 5,6. However, the function of most lincRNAs has not yet been identified in vivo. Here, we demonstrate a role for linc-MYH, a novel long intergenic noncoding RNA, in adult fast-type myofibre specialization. Skeletal myofibre fast and slow phenotypes are established through differential expression of numerous fibre-specific genes7. We show linc-MYH and the fast MYH genes share a common enhancer located in the fast MYH genes locus and regulated by the Six1 homeoproteins. Muscle-specific Six1 mutant mice show increased expression of slow-type genes, and downregulation of linc-MYH and fast-type genes. linc-MYH function revealed by in vivo knockdown and wide transcriptomic analysis, is in fine to prevent expression of genes ensuring slow muscle contractile properties, and to increase fast-type muscle gene expression in fast-type myofibres. Thus, formation of efficient fast sarcomeric units and appropriate Ca++ cycling and excitation/contraction/relaxation coupling in fast- myofibres is achieved through the coordiante control of fast MYHs and linc-MYH expression by a Six bound enhancer.

overall_design:
Ten μg of shRNA-expressing vector were introduced into TA muscles of 8 week-old mice by electroporation. Two weeks following electroporation, TA myofibres expressing GFP were dissected under a Nikon SMZ1500 stereo microscope and frozen in liquid nitrogen before processing. The efficiency of each shRNA was established by determination of linc-MYH transcript levels in TA muscles transfected by each shlincMYH. The shRNA against 5'- TTCTGCTCACCACCTACAATT-3' sequence was selected for the knockdown experiment. After validation of RNA quality with the Bioanalyzer 2100 (using Agilent RNA6000 nano chip kit), 50 ng of total RNA were reverse transcribed following the Ovation PicoSL WTA System (Nugen). Briefly, the resulting double-strand cDNA was used for amplification based on SPIA technology. After purification according to Nugen protocol, 5 μg of single strand DNA was used for generation of Sens Target DNA using Ovation Exon Module kit (Nugen). 2.5 μg of Sens Target DNA were fragmented and labelled with biotin using Encore Biotin Module kit (Nugen). After control of fragmentation using Bioanalyzer 2100, the cDNA was then hybridized to GeneChip® Mouse Gene 1.0 ST (Affymetrix) at 45°C for 17 hours. After overnight hybridization, the ChIPs were washed using the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G. The scanned images were then analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files) and metrics for Quality Controls. The analysis of some of these metrics and the study of the distribution of raw data show no outlier experiment.
Gastrocnemius muscles were collected from cSix1 KO and control mice. Total RNAs were extracted by Trizol Reagent (Invitrogen) according to manufacturer's instruction. After validation of RNA quality with the Bioanalyzer 2100 (using Agilent RNA6000 nano chip kit), 50 ng of total RNA were reverse transcribed following the Ovation PicoSL WTA System (Nugen). Briefly, the resulting double-strand cDNA was used for amplification based on SPIA technology. After purification according to Nugen protocol, 5 μg of single strand DNA was used for generation of Sens Target DNA using Ovation Exon Module kit (Nugen). 2.5 μg of Sens Target DNA were fragmented and labelled with biotin using Encore Biotin Module kit (Nugen). After control of fragmentation using Bioanalyzer 2100, the cDNA was then hybridized to GeneChip® Mouse Gene 1.0 ST (Affymetrix) at 45°C for 17 hours. After overnight hybridization, the ChIPs were washed using the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G. The scanned images were then analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files) and metrics for Quality Controls. The analysis of some of these metrics and the study of the distribution of raw data show no outlier experiment.

first: Iori

last: Sakakibara

first: Marc

last: Santolini

first: Pascal

last: Maire


title: Expression data from rejection and non-rejection kidney transplant patients

status: Public on Apr 26 2014

first: Bruce

middle: Maxwell

last: McManus

state: BC

address: 1081 Burrard Street

department: UBC James Hogg Research Centre

institute: PROOF Centre of Excellence

summary: Acute renal allograft rejection is an important complication in kidney transplantation. Accurate diagnosis of rejection events is necessary for timely response and treatment. We illustrate the usefulness and biological relevance of selected multivariate approaches to detect rejection from genomic and proteomic signals. The data was used to study gene expression changes using whole genome microarray analysis of peripheral blood from subjects with acute rejection (n=20) and non-rejecting controls (n=20) to obtain insight into the molecular and biological causation of acute renal allograft rejection when combined with proteomics (iTRAQ) data for the same patients/time-points.

overall_design: 40 Samples

first: Paul

last: Keown

first: W

last: McMaster


title: Regulation of gene expressions in vivo by anti-VEGF therapy

status: Public on Apr 25 2014

city: Oxford

first: Francesca

last: Buffa

address: The Weatherall Institute of Molecular Medicine

institute: University of Oxford

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

overall_design: 3 control samples versus 3-bevacizumab treated samples

first: Adrian

last: Harris


title: Regulation of gene expressions in vivo by anti-VEGF and anti-Notch therapy [HG-U133_Plus_2]

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

overall_design: 3 control samples, 3 dibenzazepine-treated samples, 3 bevacizumab-treated samples


title: Microglial response to Aβ and prostaglandin-E2 EP4 receptor activation

first: Katrin

last: Andreasson

address: 1201 Welch Road, MSLS P210

department: Neurology and Neurological Sciences

summary:
A persistent and non-resolving inflammatory response to accumulating Aβ peptide species is a cardinal feature in the development of Alzheimer's disease (AD). In response to accumulating Aβ peptide species, microglia, the innate immune cells of the brain, generate a toxic inflammatory response that accelerates synaptic and neuronal injury. Many pro-inflammatory signaling pathways are linked to progression of neurodegeneration. However, endogenous anti-inflammatory pathways capable of suppressing Aβ-induced inflammation represent a relatively unexplored area.
Here we hypothesized that signaling through the prostaglandin-E2 (PGE2) EP4 receptor potently suppresses microglial inflammatory responses to Aβ42 peptides. In cultured microglial cells, EP4 stimulation attenuated levels of Aβ42-induced inflammatory factors and potentiated phagocytosis of Aβ42. Microarray analysis was performed and demonstrated that EP4 stimulation broadly opposed Aβ42-driven gene expression changes in microglia, with enrichment for targets of IRF1, IRF7, and NF-κB transcription factors.

overall_design: Primary microglia were isolated from the brains of postnatal day 7 C57BL/6J mouse pups using the Neural Tissue Dissociation Kit (P), MACS Separation Columns (LS), and magnetic CD11b Microbeads from Miltenyi Biotec (Auburn, CA). Microglia from three separate litters of pups were maintained as three independent biological replicates for each treatment. After being cultured for three days, microglia were treated with oligomeric Aβ42 (10uM) and/or the specific EP4 agonist AE1-329 (100nM) for 6 hours. These 4 treatment conditions (Aβ + AE1, Aβ alone, AE1 alone, and vehicle alone) and 3 independent biological replicates per treatment gave us 12 total samples. After 6 hours of treatment, RNA was isolated from the microglia for microarray analysis.

first: Nathaniel

last: Woodling

middle: I


title: Gene expression profiling of wild type and CCR2-/- mice post chikungunya infection

status: Public on Apr 23 2014

city: SÃO PAULO

first: Helder

middle: I.

last: Nakaya

state: SÃO PAULO

address: AVENIDA PROFESSOR LINEU PRESTES, 580, Block 17

country: Brazil

institute: Universidade de São Paulo

summary: A number of inhibitors of chemokine CCL2 and its receptor CCR2 are in development and may find application for treating a range of inflammatory conditions, including autoimmune and viral arthritides.  Herein we sought to determine the effect of CCR2 deficiency on arthritis caused by an arthritogenic alphavirus, Chikungunya virus.

overall_design: Chikungunya virus (LR2006-OPY1) was injected subcutaneously into the hind foot of either CCR2 knockout or wild-type control mice (n=4-6). At day 0 and d7 post infection, RNA from the feet was harvested, the RNA was pooled (4-6 feet per time point per mouse strain) and gene expression analysis was performed using Mouse Gene ST arrays (Affymetrix).

first: Yee

middle: S

last: Poo

first: Joy

last: Gardner

first: Thibaut

last: Larcher

first: Wayne

last: Schroder

first: Thuy

last: Le

first: Lee

last: Major

first: Andreas

last: Suhrbier


title: Transcriptional regulation by infliximab therapy in kawasaki disease patients with immunoglobulin resistance

city: Sagamihara Kanagawa

first: Yoshihito

last: Ogihara

address: 1-15-1 Kitasato Minami-ku

department: Pediatrics

institute: Kitasato University

summary: Infliximab (IFX) has been reported as the further therapy in intravenous immunoglobulin G (IVIG)-resistant Kawasaki disease (KD) patients. IFX is a monoclonal antibody that blocks the pro-inflammatory cytokine tumor necrosis factor (TNF)-α, but how IFX affect KD vasculitis is unknown. We investigated expression profiling of whole blood cells to elucidate the molecular mechanisms of the effectiveness of IFX therapy and to find characteristic biomarker and an important target in refractory KD. Methods: Refractory KD patients who failed to respond to repeated intravenous immunoglobulin G (IVIG) infusions had received a single infusion of IFX as third therapy. To validate specifically transcripts abundance for IFX therapy, we detected the altered transcripts expression and signaling pathways of whole blood mRNA in these IFX-responsive patients (n=8) using Affymetrix array, comparing initial IVIG-responsive patients (n=6).Results: A total of 1,388 transcripts abundance were significantly altered before and after IFX treatment. These transcripts abundance in IFX had Nucleotide-binding oligomerization domain pathway that play a role in activation of NFκB and IL-1 signaling pathway outside the field of TNF-α signaling pathway. Fifty transcripts including Peptidase inhibitor-3 (PI3), Matrix metalloproteinase-8 (MMP8), Chemokine (C-C motif) receptor-2 (CCR2) and Pentraxin-3 (PTX3) were significantly down-regulated in IFX. Conclusion: We demonstrated that the inhibition of TNF-α by IFX have affected various molecular mechanism materially for IVIG-resistant KD patients.

overall_design: 28 samples of pre- and post-treatment in IFX-responsive patients (n=8) and IVIG-responsive patients (n=6).


title: Effects of KAT2B and WDR5 depletion on hepatocyte gene expression

status: Public on Apr 21 2014

city: Odense M

first: Kim

last: Ravnskjaer

address: Campusvej 55

department: Department of Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary:
During fasting, increases in circulating pancreatic glucagon maintain glucose balance by up-regulating hepatic gluconeogenesis. Triggering of the cAMP pathway stimulates the gluconeogenic program through the phosphorylation of CREB and via the de-phosphorylation of the CREB coactivator CRTC2. Hormonal and nutrient signals are also thought to modulate gluconeogenic genes by promoting epigenetic changes that facilitate assembly of the transcriptional machinery, although the nature of these modifications is unclear. Here we show that histone H3 acetylation at Lys 9 (H3K9Ac) is elevated over gluconeogenic genes during fasting and in diabetes, where it contributes to increases in hepatic glucose production. Following its dephosphorylation, CRTC2 promoted increases in H3K9Ac by mediating the recruitment of the lysine acetyltransferase 2B (KAT2B) and WD repeat-containing protein 5 (WDR5), a core subunit of histone methyltransferase (HMT) complexes. In turn, KAT2B and WDR5 stimulated the gluconeogenic program through a self-reinforcing cycle whereby increases in H3K9Ac further potentiated CRTC2 occupancy at CREB binding sites.  Breaking this cycle, by depletion of KAT2B or WDR5, decreased gluconeogenic gene expression.  As administration of a small molecule KAT2B antagonist lowered circulating blood glucose concentrations in insulin resistance, our results demonstrate how this enzyme may be a useful target for diabetes treatment.
A subset of cAMP responsive genes depend on specific recruitment of KAT2B (pcaf), which in concert with WDR5 acetylates H3K9. By selectively depleting hepatocytes for KAT2B or WDR5 prior to glucagon stimulation we explore, which genes rely on KAT2B and WDR5 activity.

overall_design: mKAT2B or mWDR5 were knocked down in primary mouse hepatocytes using adenoviral transduction with appropriate shRNAs. Control cells were transduced with a non-specific (NS) shRNA. 72 hours post transduction some cells were stimulated for 90 minutes with 100nM glucagon and others with PBS. Total RNA was purified and subjected to micro-RNA analysis. All samples are pools of RNA from three sepearate dishes. One replicate is included for  most samples.

first: Marc

last: Montminy


title: leukemia propagating cells rebuild an evolving niche in response to therapy

city: shanghai

first: dengli

last: hong

address: Chongqing South Road 280

institute: Shanghai Jiao-Tong University School of Medicine

summary:
Residence of cancer-propagating cells (CPCs) within preferential microenvironmental niches has a major part in evading therapy. However, the nature of niches involved and the mechanisms protecting CPCs remain largely unknown. We addressed these issues in mouse transplantation models of acute lymphoblastic leukemia (ALL). When the engrafted leukemic cells substantially damaged adjacent vascular structures and endosteal linings in the bone marrow (BM), after chemotherapy small foci of CPCs were retained, surrounded by sheaths of supporting cells that comprise a novel niche. We investigated patients’ BM biopsies and found evidence of a similar process in patients receiving induction-therapy. The efficacy of chemotherapy was enhanced by interfering with the niche formation or niche-CPC interaction. We therefore identified a therapy-induced niche that protects CPCs.
We used microarrays to compare the  gene expression profile of ALL cell line (Nalm-6) from model (A0D) mice and rediduel cells from Ara-C treatment for 2 days (A2D) mice.

overall_design: Engrafted NALM-6-GFP+ cells from A0D mice and residual cells from A2D mice were flow sorted. Total RNA was isolated using RNeasy micro kit (Qiagen). Biotinylated cRNA was hybridized using HGU133Plus 2.0 GeneChip arrays (Affymetrix).

first: Dengli

last: Hong

first: Caiwen

last: Duan


title: Expression data from Rheumatoid Arthritis synovial tissue samples

status: Public on Apr 22 2014

city: South San Francisco

first: Sarah

middle: K

last: Kummerfeld

address: 1 DNA Way

institute: Genentech

summary:
Rheumatoid arthritis (RA) is a complex and clinically heterogeneous autoimmune disease.
Microarray analysis of 83 synovial samples provides insight into the expression-level differences between patients at the site of disease activity.

overall_design: Synovial samples from Rheumatoid Arthritis patients were obtained during joint resection and profiled using microarrays.

first: Glynn

last: Dennis Jr

first: Cécile

last: Holweg

first: David

last: Choy

first: Francesca

last: Setiadi

first: Jason

last: Hackney

first: Peter

last: Haverty

first: Houston

last: Gilbert

first: Wei

middle: Y

last: Lin

first: Lauri

last: Diehl

first: Sally

last: Fischer

first: An

last: Song

last: Musselman

first: Micki

last: Klearman

first: Cem

last: Gabay

first: Arthur

last: Kavanaugh

first: Judith

last: Endres

last: Fox

first: Flavius

last: Martin

first: Michael

last: Townsend


title: Fosb gene products contribute to excitotoxic microglial activation by regulating the expression of complement C5a receptors in microglia

status: Public on Apr 18 2014

city: Fukuoka

first: Yusaku

last: Nakabeppu

state: Fukuoka

address: 3-1-1 Maidashi Higashi-ku

department: Department of Immunobiology and Neuroscience

institute: Medical Institute of Bioregulation, Kyushu University

summary: The Fosb gene encodes subunits of the activator protein-1 transcription factor complex. Two mature mRNAs, Fosb and ΔFosb, encoding full-length FOSB and ΔFOSB proteins respectively, are formed by alternative splicing of Fosb mRNA. Fosb products are expressed in several brain regions. Moreover, Fosb-null mice exhibit depressive-like behaviors and adult-onset spontaneous epilepsy, demonstrating important roles in neurological and psychiatric disorders. Study of Fosb products has focused almost exclusively on neurons; their function in glial cells remains to be explored. In this study, we found that microglia express equivalent levels of Fosb and ΔFosb mRNAs to hippocampal neurons and, using microarray analysis, we identified six microglial genes whose expression is dependent on Fosb products. Of these genes, we focused on C5ar1 and C5ar2, which encode receptors for complement C5a. In isolated Fosb-null microglia, chemotactic responsiveness toward the truncated form of C5a was significantly lower than that in wild-type cells. Fosb-null mice were significantly resistant to kainate-induced seizures compared with wild-type mice. C5ar1 mRNA levels and C5aR1 immunoreactivity were increased in wild-type hippocampus 24 hours after kainate administration; however, such induction was significantly reduced in Fosb-null hippocampus. Furthermore, microglial activation after kainate administration was significantly diminished in Fosb-null hippocampus, as shown by significant reductions in CD68 immunoreactivity, morphological change and reduced levels of Il6 and Tnf mRNAs, although no change in the number of Iba-1-positive cells was observed. These findings demonstrate that, under excitotoxicity, Fosb products contribute to a neuroinflammatory response in the hippocampus through regulation of microglial C5ar1 and C5ar2 expression.

overall_design: fosB+/G mice with a null-mutant allele, fosBG, were established and maintained by backcrossing to C57BL/6J. To yield homozygous mutant mice, fosB+/G (N20 generation) mice were intercrossed. C57BL/6J mice were used as wild-type control.

first: Hiroko

last: Nomaru


title: Expression data from undifferentiated human ES cell line, khES3, grown using complete, methionine, leucine or lysine deprived media and ES cell derived endoderm

status: Public on Apr 17 2014

city: Yokohama

first: nobuaki

last: shiraki

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

department: School of Life Science and Technology

institute: Tokyo Institute of Technology

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

overall_design: Refer to individual Series


title: Alternative Splicing of MBD2 Supports Self-Renewal in Human Pluripotent Stem Cells

status: Public on Apr 19 2014

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic


title: Expression profiling of lung T cell subsets from wild-type and Serpinb1a-/- mice

city: Cambridge

first: Scott

last: Davis

state: MA

address: 200 Technology Square, Suite 602

department: Tempero DPU

institute: GSK

summary: The aim of this study was to identify differential gene expression in lung T cell subsets upon germline Serpinb1a ablation.

overall_design:
CD8-CD19- lymphocytes enriched by negative selection from digested lungs of naïve, 9-12 week old wild-type 129S6 mice or Serpinb1a homozygous null mice were FACS sorted into CD4+ CCR6+ effector/ memory T cells, gd T cells, or CD4+ CD25hiCD127low regulatory T cells. FACS sorted cells were collected into RLT buffer (Qiagen) directly, lysed, and total mRNA was isolated using Quiagen's RNeasy mini kit.
Wild-type vs. Serpinb1a-/- gd+ T cells, CD4+ CCR6+ effector/ memory T cells, or CD4+ CD25hiCD127low regulatory T cells

first: Eileen

last: Remold-O'Donnell

first: Picheng

last: Zhao

first: Mark

last: Sundrud


title: Expression profiling by array of 44 adrenocortical carcinomas

status: Public on Apr 29 2014

first: Nabila

last: Elarouci

address: 14 rue Corvisart

department: Recherche

institute: Ligue Nationale contre le Cancer

summary: Gene expression profiles of adrenocortical carcinomas were analyzed using Affymetrix Human Gene 2.0 ST Array to identify homogeneous molecular subgroups

overall_design: Gene expression profiles of 44 adrenocortical carcinomas were hybridized using Affymetrix Human Gene 2.0 ST Array

first: Eric

last: Letouzé

first: Aurélien

last: De Reynie

first: Windy

last: Luscap

first: Barreau

last: Olivia

first: Guillaume

last: Assié

first: Jérome

last: Bertherat


title: CDDP treated KYSE140

status: Public on Apr 15 2014

city: Beijing

first: Yang

last: Xu

address: No.17 Panjiayuan Nanli, Chaoyang district

institute: Cancer Hospital

summary: We used microarrays to detail the gene expression profiles of KYSE140 cell line to identify distinct up and down-regulated genes during treatment with cisplatin.

overall_design: KYSE140 cell line were treated with 10 mM cisplatin for 12 hrs and selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to gene expression profiles of KYSE 140 cell line treated with cisplatin.


title: Gene expression signatures in motor neuron disease fibroblasts reveal dysregulation of metabolism, hypoxia-response and RNA processing functions

status: Public on Apr 16 2014

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

institute: University of Sheffield

summary:
Amyotrophic lateral sclerosis and primary lateral sclerosis are two syndromic variants within the motor neurone disease spectrum. Whilst primary lateral sclerosis is associated with loss of upper motor neurons and a more benign disease course up to 17yrs,  amyotrophic lateral sclerosis is caused by loss of both upper and lower motor neurons and has an average disease course of 2-3 years. The majority of cases are sporadic, thereby limiting the availability of cellular models for investigating pathogenic disease mechanisms.
The aim of the present study was to evaluate fibroblasts as a cellular model for  sporadic amyotrophic lateral sclerosis and primary lateral sclerosis, to establish whether disease-related dysregulated biological processes recapitulate those seen in the central nervous system and to elucidate pathways that distinguish between the two disease phenotypes.

overall_design: We used microarray analysis to determine the differences in gene expression between fibroblasts derived from skin biopsies taken from sporadic amyotrophic lateral sclerosis and primary lateral sclerosis neurologically normal human controls

first: Rohini

last: Raman

last: Allen

first: Emily

last: Goodall

first: Shelley

last: Kramer

first: Lize-Linde

last: Polger

first: Marta

last: Milo

first: Hannah

last: Hollinger

first: Theresa

last: Walsh

first: Robin

last: Highley

first: Simon

last: Olpin

first: Christopher

last: McDermott

first: Pamela

last: Shaw

first: Janine

last: Kirby


title: A retinoblastoma allele that is mutated at its common E2F interaction site inhibits cell proliferation in gene targeted mice

status: Public on Apr 14 2014

city: London

first: Fred

last: Dick

state: ON

address: Cancer Research Labs 790 Commissioners Road East

institute: Western University

summary: The retinoblastoma protein (pRB) is best known for regulating cell proliferation through E2F transcription factors. In this report we investigate the properties of a targeted mutation that disrupts pRB interactions with the transactivation domain of E2Fs. Mice that carry this mutation endogenously (Rb1∆G) are defective in regulating E2F target genes. Surprisingly, cell cycle regulation in Rb1∆G/∆G MEFs strongly resembles that of wild type. In a serum deprivation induced cell cycle exit, Rb1∆G/∆G MEFs display a similar magnitude of E2F target gene derepression as Rb1-/-, even though Rb1∆G/∆G cells exit the cell cycle normally. Interestingly, cell cycle arrest in Rb1∆G/∆G MEFs is responsive to p16 expression, indicating that the ΔG-pRB protein can be activated in G1 to arrest proliferation through non-E2F mechanisms. Some Rb1∆G/∆G mice die neonatally with a muscle degeneration phenotype, while the others live a normal lifespan with no evidence of spontaneous tumor formation. Histological analysis reveals discrete examples of hyperplasia in the mammary epithelium, but most tissues appear normal while being accompanied by derepression of pRB regulated E2F targets. This suggests that non-E2F, pRB dependent pathways may have a more relevant role in proliferative control than previously identified.

overall_design: Total RNA was extracted from littermate paired WT, ∆G and null MEFs induced to enter quiencense by Serum deprivation. Expresssion levels were analyzed by Affymetrix GeneChip Mouse Gene 1.0ST Array. Relative expression was determined by BRB-Array Tools software to generate RMA values.

first: Michael

last: Thwaites

last: Cantalupo

first: Frederick


title: Expression data from undifferentiated human ES cell line, khES3, grown using complete or methionine deprived media and ES cell derived endoderm

first: nobuaki

last: shiraki

summary:
In undifferentiated human ES cells, 5hr Met deprivation (delta Met) led to decreased proliferation, and prolonged 24hr Met deprivation resulted in G0-G1 phase cell cycle arrest, which then led to apoptosis.
We used microarrays to detail the molecular mechanism of cell-death caused by Met deprivation in undifferentiated ES cells and checked the difference of Met cycle relate gene expression between undifferentiated human ES cells and ES cell derived endoderm.

overall_design: Cells were harvested at undifferentiated or differentiated stages for RNA extraction and hybridization on Affymetrix microarrays. We performed gene expression profiles of undifferentiated khES3 cells cultured in complete (compl) or Met-deprived conditions (deltaMet) for 5 or 24 hr.  And 0hr untreated cells and endoderm cells were used as a comparison

first: Nobuaki

last: Shiraki

first: Tomonori

last: Tsuyama


title: Dynamic Gene Expression Response to TGF-β Stimulation in Multipotent Progenitors and Common Dendritic Cell Progenitors

city: Aachen

first: Martin

last: Zenke

state: NRW

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

institute: Institute for Biomedical Engineering

summary: Multipotent progenitors (MPP) and common dendritic cell progenitors (CDP) were obtained from mouse bone marrow, followed by in vitro culture with a specific cytokine cocktail and FACS sorting (Felker et al., 2010; Seré et al., 2012). Cells were treated with 10 ng/ml recombinant human TGF-β1 (R&D Systems, Minneapolis, USA) for 2, 4, 8, 12 and 24 h as described (Felker et al., 2010) or left untreated.

overall_design:
Untreated multipotent progenitor (MPP)
- MPP_0h_1
- MPP_0h_2
- MPP_0h_3
TGF-beta1 treated (2 hours) MPP
- MPP_2h_1
- MPP_2h_2
- MPP_2h_3
TGF-beta1 treated (4 hours) MPP
- MPP_4h_1
- MPP_4h_2
- MPP_4h_3
TGF-beta1 treated (8 hours) MPP
- MPP_8h_1
- MPP_8h_2
- MPP_8h_3
TGF-beta1 treated (12 hours) MPP
- MPP_12h_1
- MPP_12h_2
- MPP_12h_3
TGF-beta1 treated (24 hours) MPP
- MPP_24h_1
- MPP_24h_2
- MPP_24h_3

Untreated common dendritic cell progenitor (CDP)
- CDP_0h_1
- CDP_0h_2
- CDP_0h_3
TGF-beta1 treated (2 hours) CDP
- CDP_2h_1
- CDP_2h_2
- CDP_2h_3
TGF-beta1 treated (4 hours) CDP
- CDP_4h_1
- CDP_4h_2
- CDP_4h_3
TGF-beta1 treated (8 hours) CDP
- CDP_8h_1
- CDP_8h_2
- CDP_8h_3
TGF-beta1 treated (12 hours) CDP
- CDP_12h_1
- CDP_12h_2
- CDP_12h_3
TGF-beta1 treated (24 hours) CDP
- CDP_24h_1
- CDP_24h_2
- CDP_24h_3

first: Kristin

last: Seré

first: Qiong

last: Lin

first: Bert

last: Smeets

first: Kurt

last: Hoffmann

first: Holger

last: Fröhlich