title: Expression data from RUNX1S291fs-mutant and/or Ezh2 conditional knockout Lineage-c-Kit+Sca-1+ (LSK) cells

status: Public on Sep 04 2013

summary: Recent studies have showed that loss-of-function mutations of EZH2, a catalytic component of polycomb repressive complex 2, are often associated with RUNX1 mutations in myelodysplastic syndrome (MDS) patients.  We established a novel MDS model mouse by transducing a RUNX1S291fs mutant in hematopoietic stem cells followed by deletion of Ezh2 and found that Ezh2 loss significantly promoted RUNX1S291fs-induced MDS.

overall_design: We retrovirally transduced RUNX1S291fs or empty-control into either Cre-ERT;Ezh2wt/wt or Cre-ERT;Ezh2flox/flox (CD45.2+) HSCs.  The transduced cells were transplanted into lethally irradiated recipient mice together with life-saving CD45.1+ wild-type bone marrow cells.  After deletion of Ezh2, gene expression analysis were performed on pooled bone marrow LSK cells isolated from WT, Ezh2Δ/Δ, RUNX1S291fs, and RUNX1S291fs/Ezh2Δ/Δ mice (n=2-4) and two distinct RUNX1S291fs/Ezh2Δ/Δ-MDS mouse.


title: The Dynamics of Diverse Segmental Amplifications in Populations of Saccharomyces cerevisiae Adapting to Strong Selection

status: Public on Sep 25 2013

city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

country: USA

institute: University of Washington

type: Genome variation profiling by genome tiling array

summary: Population adaptation to strong selection can occur through the sequential or parallel accumulation of competing beneficial mutations. The dynamics, diversity and rate of fixation of beneficial mutations within and between populations are still poorly understood. To study how the mutational landscape varies across populations during adaptation, we performed experimental evolution on seven parallel populations of Saccharomyces cerevisiae continuously cultured in limiting sulfate medium. By combining qPCR, array CGH, restriction digestion and CHEF gels, and whole genome sequencing, we followed the trajectory of evolution to determine the identity and fate of beneficial mutations. Over a period of 200 generations, the yeast populations displayed parallel evolutionary dynamics that are driven by the coexistence of independent beneficial mutations. Selective amplifications rapidly evolve under this selection pressure, in particular common inverted amplifications containing the sulfate transporter gene SUL1. Compared to single clones, detailed analysis of the populations uncovers a greater complexity whereby multiple subpopulations arise and compete despite a strong selection. The most common evolutionary adaptation to strong selection in these populations grown in sulfate limitation is determined by clonal interference, with adaptive variants both persisting and replacing one another.

overall_design: These are CGH arrays.  Each experiment compares the DNA content of an experimentally evolved strain with its ancestor.

first: Celia

last: Payen

first: Bonny

last: Brewer

middle: J


title: Gene expression profiling of ElonginA knocked-down Hela cells in the presence of Doxorubicin

status: Public on Sep 03 2013

city: Bunkyo-ku

first: Junya

last: Kawauchi

state: Tokyo

address: Yushima 1-5-45

department: Medical Research Institute

country: Japan

institute: Tokyo Medical & Dental University

summary: Transcriptional elongation factor Elongin A exhibits an activity to repress the temporary pause of RNA polymerase II (RNAPII) on the DNA template, resulting in increase of mRNA synthesis in vitro. However, actual elongation ability of Elongin A in mammalian cells has not been determined yet. To elucidate the practical transcriptional role of mammalian Elongin A in vivo, we carried out whole genome expression analysis using Elongin A knocked-down HeLa cells.

overall_design: Gene expression in Elongin A knocked-down HeLa cells was measured at 2 hours after doxorubicin treatment (1microM).

first: Shigetaka

last: Kitajima


title: Cardiac mesenchymal progenitors from postmortem cardiac tissue retained cellular characterization

status: Public on Aug 28 2013

city: Kyoto

first: Satoshi

last: Gojo

address: 465 Kajii-cho, Kamigyo-ku

institute: Kyoto Prefectural University of Medicine

summary:
Background and Objective: Currently, the cells for transplantation were derived from either autologous or allogeneic tissue. The former has a drawback that the quality of donor cells could depend on the patient’s condition, and the quantity could also be limited. To solve these problems, we investigated the potential of allogeneic cardiac mesenchymal progenitors (CMPs) derived from postmortem heart, which might be an immunological privileged like bone marrow-derived mesenchymal progenitors.

Materials and Methods: We examined whether viable CMPs could be isolated from murine postmortem cardiac tissue that was harvested 24 hours postmortem. After two to three weeks propagation with high dose of basic fibroblast growth factor, we performed the cellular characteristics analyses, which included proliferation and differentiation property flow cytometric analyses, and microarray analyses.

Results: Postmortem CMPs had longer lag phase after seeding than CMPs from living tissues, but they demonstrated the similar characteristics in all above examinations. In addition, global gene expression analysis by microarray indicated the similar characteristics between the cell derived from postmortem and living tissue.

Conclusion: These results indicate allogeneic postmortem CMPs could have promising potential for cell transplantation as clinical applications, because of circumventing the issue of brain death.

overall_design: The samples were collected fom living or postmortem cardiac tissue (24 hr at 4C). We generated cardiac mesenchymal progenitors (CMPs) from these cardiac tissue, and compared global gene expression by AgilentMouse GE 8x60k Microarray. Adult, or fetal mouse heart RNAs were used as positive control. Adult mouse total heart RNAs were purchased from Clontech. Fetal mouse heart was extracted from fetus which is embryonic day 16.5 C57BL/6 strain. Tg means Transgenic mouse (C57BL/6-Tg(Myh6-EGFP)MG2).

first: Daisuek

last: Kami

first: Tomoya

last: Kitani

first: Midori

last: Nakata


title: CSE-induced hydorogen sulfide improves glucose homeostasis and inhibits beta-cell failure in high-fat diet mice

status: Public on Sep 02 2013

city: Yufu

first: Toshihide

last: Kimura

state: Oita

address: 1-1 Idaigaoka, Hasamamachi

department: Department of Pharmacology

institute: Oita University, Faculty of Medicine

summary:
CSE knockout (CSE-KO)mice at age 6 months were fed a high fat diet (HFD) for 8 weeks.we determined the effects of CSE knockdown on beta-cell function and mass in islets from the mice. After 8 weeks of the HFD,blood glucose levels were drasically increaced in CSE-KO mice compared with WT mice.
To assess the effect of HFD on gene expression in CSE-KO mice,we performed a comparative DNA microarray analysis

overall_design: 2 samples analysis.control is CSE-WT(HFD+)

first: Mitsuhiro

last: Okamoto

first: Mami

last: Yamaoka

first: Masahiro

last: Takei

first: Tomomi

last: Ando

first: Shigeki

last: Taniguchi

first: Isao

last: Ishii

first: Kazuo

last: Tohya

first: Toshimasa

last: Ishizaki

first: Ichiro

last: Niki


title: H4K16 acetylation marks active genes and enhancers of embryonic stem cells, but does not alter chromatin compaction [Agilent array]

status: Public on Aug 23 2013

city: Edinburgh

first: Gillian

last: Taylor

address: MRC HGU Crewe Road South

country: United Kingdom

institute: IGMM

summary: We report that acetylation of H4K16 is a new marker of active enhancers and that some enhancers are marked by H3K4me1, MOF and H4K16ac but not by acetylated H3K27 or p300, suggesting that they are novel p300-independent regulatory elements.

overall_design: Gene expression in undifferentiated 46c (sox1-gfp) ES cells, and gfp FACS sorted cells after 5 days of differentiation to neural progenitor cells with NB27 and Neuro2 medium supplements.  3 biological replicates  were performed for each sample.

first: Ragnhild

last: Eskeland

first: Madapura

middle: M

last: Pradeepa

first: Wendy

last: Bickmore


title: Age-associated gene expression in normal breast tissue mirrors qualitative age-at-incidence patterns for breast cancer

status: Public on Aug 31 2013

city: Chapel Hill

first: Melissa

last: Troester

state: NC

address: 135 Dauer Drive, CB 7435

department: Epidemiology

institute: University of North Carolina at Chapel Hill

summary: Background: Age is the strongest breast cancer risk factor, with overall breast cancer risk increasing steadily beginning at approximately 30 years of age. However, while breast cancer risk is lower among younger women, young women’s breast cancer may be more aggressive. Though several genomic and epidemiologic studies have shown higher prevalence of aggressive, estrogen-receptor negative breast cancer in younger women, the age-related gene expression that predisposes to these tumors is poorly understood. Characterizing age-related patterns of gene expression in normal breast tissues may provide insights on etiology of distinct breast cancer subtypes that arise from these tissues. Methods: To identify age-related changes in normal breast tissue, 96 tissue specimens from reduction mammoplasty patients aged 14 to 70 were assayed by gene expression microarray. Results: Significant associations between gene expression levels and age were identified for 802 probes (481 increased, 321 decreased with increasing age). Enriched functions included ‘aging of cells’, ‘shape change’, and ‘chemotaxis’, and enriched pathways included Wnt/beta-catenin signaling, Ephrin Receptor Signaling, and JAK/Stat Signaling. Applying the age-associated genes to publicly available tumor datasets, the age-associated pathways defined two groups of tumors with distinct survival. Conclusion: The hazard rates of young-like tumors mirrored that of high grade tumors in the Surveillance, Epidemiology and End Results Program, providing a biological link between normal aging and age-related tumor aggressiveness. Impact: These data show that studies of normal tissue gene expression can yield important insights about the pathways and biological pressures that are relevant during tumor etiology and progression.

overall_design: reference x sample

first: Jason

middle: R

last: Pirone

first: Monica

middle: D

last: Arcy

middle: A


title: Small RNA-seq and gene expression analysis reveal a miRNA profile of cancer-susceptibility in ATM deficient human mammary epithelial cells (mRNA)

status: Public on Aug 22 2013

city: RTP

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: Deficiencies in the ATM gene are the underlying cause for ataxia telangiectasia, a congenital syndrome characterized by neurological, motor and immunological defects, as well as a predisposition to cancer risks. MicroRNAs (miRNAs) are small regulators of post-transcriptional gene expression and a useful tool for cancer diagnosis, staging, and prediction of therapeutic responses to clinical regimens. In particular, miRNAs have been used to develop signatures for breast cancer profiling.  We are interested in the consequences of ATM deficiency on miRNA expression in breast epithelial cells and the potential contribution to cancer predisposition. In this study we investigate the effects of ATM loss on the miRNA expression and related gene expression changes in normal human mammary epithelial cells (HME-CC). We have identified 81 significantly differently expressed miRNAs in the ATM-deficient HME-CCs using small RNA sequencing. Many of these differentially expressed miRNAs have been described and implicated in tumorigenesis and proliferation. These changes include down-regulation of tumor suppressor miRNAs, such as hsa-miR-29c and hsa-miR-16, as well as the over-expression of pro-oncogenic miRNAs hsa-miR-93 and hsa-mir-221. All 81 miRNAs were combined with genome wide gene expression profiles to investigate possible targets of miRNA regulation. We identified messenger RNA (mRNA) targets of these miRNAs that were also significantly regulated after the depletion of ATM. Predicted targets included many genes implicated in cancer formation and progression, including SOCS1 and the proto-oncogene MAF. Integrated analysis of miRNA and mRNA expression allows us to build a more complete understanding of the pathways and networks involved in the breast cancer predisposition observed in individuals deficient in ATM. This study highlights miRNA and predicted mRNA target expression changes in ATM-deficient HME-CCs and suggests a mechanism for the breast cancer-prone phenotype seen in ATM deficient cells and patients. Additionally, this study provides preliminary data for defining miRNA profiles that may be used prognostic biomarkers for breast cancer predisposition.

overall_design:
Examination of small RNA population in human mammary epithelial cell lines. Each condition was preformed in triplicate.

This submission represents the transcriptome component of study.

first: Jill

middle: E

last: Hesse

first: Liwen

last: Liu

first: Cynthia

middle: L

last: Innes

first: Richard

middle: S

last: Paules


title: Effects of supernatants of USP2 knockdown HL-60 cells and mock transfected HL60 cells on differentiated 3T3-L1 cells

status: Public on Aug 27 2013

city: Ebetsu

first: Hiroshi

last: Kitamura

address: 582 Midorimachi, Bunkyodai

department: School of Veterinary Medicine

institute: Rakuno Gakuen University

summary: Ubiquitin specifc protease (USP) 2 modulates various cellular responces including carcinogenesis, spermatogenesis, and glucose metabolism. So far, we established USP2 knockdown HL-60 cells to explore roles of USP2 in macrophages. In this experiment, we investigated whether USP2 knockdown HL-60 cells more prominently modulate function of adipocytes compared with control cells.

overall_design: USP2 knock down(KD) HL-60 cells and mock vector-transfected mock control cells were differentiated into macrophage-like cells in the presence of 30nM of phorbol 12-myristate 13-acetate for 5 days. Subseqently, supernatants of the USP2 KD cells and control cells were added to differentiated 3T3-L1 cells for 3 and 6 hrs. Total RNA was isolated from the supernatant-treated 3T3-L1 cells, and subjected to microarray analysis. Duplicate samples were prepared for each cell and time point.

first: Yoshinori

last: Shimamoto

last: Naoe


title: Ficolin-1 is upregulated in leukocytes and glomeruli from microscopic polyangiitis patients

status: Public on Aug 18 2013

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: To search for new markers of active lesions that might help better understand the molecular basis of MPA and aid in its diagnosis, DNA microarray analysis was performed with peripheral blood mononuclear cells (PBMCs).

overall_design: A total of 12 sets of two color arrays were performed and each individual array included a target sample and a control sample.

last: Nojima


title: Effect of cigarette smoke on gene expression in mammary epithelial cells [gene expression]

status: Public on Aug 12 2013

city: Baltimore

first: Francescopaolo

last: Di Cello

state: MD

address: 1650 Orleans Street

institute: The Johns Hopkin University School of Medicine

summary: Recent epidemiological studies demonstrate that both active and involuntary exposure to tobacco smoke increases the risk of breast cancer. Little is known, however, about the molecular mechanisms by which tobacco smoke contributes to breast carcinogenesis. To investigate these mechanisms we have analyzed gene expression and methylation in MCF 10A mammary epithelial cells chronically exposed to aqueous cigarette smoke extract (CSE).

overall_design: CSE was prepared weekly and added to the cell cultures at a concentration equivalent to 0.001 cigarettes/ml. Two clones were isolated after 13 weeks of treatment and expanded in the same concentration of CSE for 8 additional weeks. Mock-treated samples were prepared in parallel.

last: Zahnow


title: The inducuction of UPR target genes in response to zinc depletion and serum starvation in HeLa cells.

status: Public on Aug 09 2013

city: Tokyo

first: Kengo

last: Homma

address: 3-1, 7-Chome, Hongo, Bunkyo-ku

department: Graduate School of Pharmaceutical Sciences

institute: The University of Tokyo

summary: Zinc is an essential trace element, and impaired zinc homeostasis is implicated in the pathogenesis of various human diseases. However, the mechanisms cells use to respond to zinc deficiency are poorly understood. We previously reported that amyotrophic lateral sclerosis (ALS)-linked pathogenic mutants of SOD1 cause chronic ER stress through specific interactions with Derlin-1, which is a component of the ER-associated degradation machinery. Moreover, we recently demonstrated that this interaction is common to ALS-linked SOD1 mutants, and SOD1WT comprises a masked Derlin-1-binding region. We found that under serum starved and zinc-deficient conditions, SOD1WT adopts a mutant-like conformation that exposes the Derlin-1-binding region, suggesting that SOD1-Derlin-1 interaction may contribute to induce ER stress under these conditions.  Using RNA microarrays, we revealed that the zinc depletion and serum starvation  induce the expression of the unfolded protein response (UPR) target genes, including HSPA5/BiP, SEL1L, DNAJC3/p58, and ARMET. We conclude that SOD1 has a novel function as a molecular switch that activates the ER stress response under zinc-deficient conditions

overall_design: HeLa cells were treated with 8µM TPEN for 9h or exposured to 36h of serum starvation with or without 30µM zinc.Then the total RNA was isolated from cells using the Isogen reagent (Wako) following the manufacturer's recommendations.

first: Hidenori

last: Ichijo


title: Gene expression in Caco-2 cells co-cultured with bacteria in an apical anaerobic environment

status: Public on Aug 19 2013

city: Palmerston North

first: Wayne

last: Young

address: Tennent Drive

country: New Zealand

institute: AgResearch

summary: Transcriptional profiling of Caco-2 cells co-cultured with Faecalibacterium prausnitzii DSM17677, Lactobacilus rhamnosus HN001, UV-killed F. prausnitzii, or no bacteria in an apical anaerobic environment for four hours.

overall_design: 2 colour microarray, reference design. Biological replicates: 6 per treatment group.

first: Dulantha

last: Ulluwishewa


title: Developmental changes in the in vitro activated regenerative activity of primitive mammary epithelial cells

status: Public on Aug 13 2013

city: Vancouver

first: Maisam

last: Makarem

state: BC

country: Canada

institute: BC Cancer Research Center

summary:
Many normal adult tissues contain rare stem cells with extensive self-maintaining regenerative potential. During development, the stem cells of the hematopoietic and neural systems undergo intrinsically specified changes in their self-renewal potential. In the mouse, mammary stem cells with transplantable regenerative activity are first detectable a few days before birth. They share some phenotypic properties with their adult counterparts but are enriched in a subpopulation that displays a distinct gene expression profile. Here we show that fetal mammary epithelial cells have a greater direct and inducible growth potential than their adult counterparts. The latter feature is revealed in a novel culture system that enables large numbers of mammary stem cells with serially transplantable activity as well as in vitro clonogenic progenitors to be produced within 7 days from single fetal or adult input cells. We further show that these responses are highly dependent on novel factors produced by fibroblasts. These findings provide new avenues for elucidating mechanisms that regulate normal mammary epithelial stem cell properties at the single-cell level, how these change during development, and how their perturbation may contribute to transformation.
We used microarrays to compare the transcriptome of E18.5 fetal and adult MRU-enriched mammary cells.

overall_design: Three biological replicates each of CD31-CD45-Ter119-BP-1-EpCAM+CD49f+ adult basal cells and CD31-CD45-Ter119-EpCAM++CD49f+ fetal cells were sorted. RNA was extracted and hybridized to the Agilent One-Color Gene Expression Arrays .

first: Nagarajan

last: Kannan

first: Long

middle: V

last: Nguyen

first: David

last: Knapp

first: Sneha

last: Balani

first: Michael

last: Prater

first: John

last: Stingl

first: Afshin

last: Raouf

first: Oksana

last: Nemirovsky

first: Peter

last: Eirew

first: Connie

last: Eaves


title: Gene expression data from Dstncorn1 mutant, rescued and WT cornea after genetic ablation of Srf from the corneal epithelium

status: Public on Aug 10 2013

city: Madison

first: Sakae

last: Ikeda

state: WI

address: 425G Henry Mall

department: Medical Genetics

institute: University of Wisconsin - Madison

summary:
The purpose of this study is to characterize gene expression changes that occur when conditional knock-out of Srf rescues mutant phenotypes in the cornea of Dstncorn1 mice.
This study uses a unique model combining genetic and genomic approaches to identify genes that are regulated by SRF.

overall_design: Three biological replicates were used for each of the three groups (mutant, rescued and WT). Each biological replicate consisted of 10 pooled corneas from five mice.

first: Sharolyn

last: Kawakami-Schulz


title: Laughter specific genes and laughter sensitive genes

status: Public on Aug 02 2013

city: Tsurumi-ku, Yokohama

first: Miyo

last: Hori

state: Kanagawa

address: 1-1-43, Suehiro-cho

department: Business Development

institute: DNA Chip Research Inc.

summary:
The changes of mRNA expression levels were analyzed in peripheral leukocytes after laughing with or without "Effective laugh maker" training.

Keywords: stress response

overall_design: Relative changes in gene expression accompanied with laughter before/after laughing training. Over-expressed and under-expressed genes were discriminated in "Effective laugh maker" training responder group.

first: Takashi

last: Hayashi


title: Consequences of perinatal bisphenol A exposure in a mouse model of multiple sclerosis

status: Public on Aug 01 2013

city: College Station

first: Candice

last: Brinkmeyer-Langford

state: TX

address: TAMU MS4458

institute: Texas A&M University

summary: Multiple sclerosis (MS) is a complex disease influenced by genetic and environmental contributing factors.  Endocrine disrupting compounds (EDCs) such as bisphenol A (BPA) affect gene expression and hormone-regulated systems throughout the body.  We investigated the effects of BPA on Theiler’s-virus induced demyelination (TVID), a mouse model of MS.  Perinatal BPA exposure, combined with viral infection, resulted in a decreased level of viral antibodies, accelerated the onset of TVID symptoms, increased inflammation in both the spinal cord and digestive tract, and amplified immune-related gene expression changes induced by viral infection. These results demonstrate the effect of BPA on the trajectory of TVID, and illustrate how multiple factors collectively influence autoimmune disease.

overall_design: For microarray: 7 samples


title: Expression data from the hearts of a mouse model of spontaneous myocardial infarction

status: Public on Sep 01 2013

city: Cambridge

first: D. R.

last: Mani

state: MA

address: 7 Cambridge Center

institute: The Broad Institute of MIT and Harvard

summary: Mice with homozygous null mutations in the HDL receptor (SR-BI) and apoE genes (SR-BI KO/apoE double KO (dKO) mice) spontaneously develop occlusive, atherosclerotic coronary artery disease (CAD) and die prematurely (50% mortality at 42 days of age) on standard chow diet feeding. Microarray analysis was performed to investigate the changes in gene expression profiles during the development of spontaneous severe CAD, which includes myocardial infarction and heart failure. These data will provide new insights in understanding the pathophysiology of CAD.

overall_design: The whole Hearts from dKO or SR-BI+/- apoE-/- (HET) mice (n=9-12) were harvested at 21, 31 and 43 days of age, and analyzed using Affymetrix microarrays. dKO mice do not show detectable signs of CAD at 21 days of age, small myocardial infarction (MI) and heart failure at 31 days of age, and extensive MI and severe heart failure at 43 days of age (50% mortality at 42 days of age). Each mouse was assigned to one array. SR-BI+/- apoE-/- mice (HET) which do not develop detectable signs of CAD on chow diet were used as controls.The data also include those from probucol treated dKO and HET mice (n=2-8).

first: Kosuke

last: Tsukamoto

first: D

first: Songwen

last: Zhang

first: Monty

last: Krieger


title: IkB-like protein NFKBIZ regulates NF-kB signaling and is critical for survival of ABC DLBCL (MALT inhibition)

status: Public on Jul 22 2013

city: Münster

last: Grau

state: Nordrhein-Westfalen

address: Albert-Schweitzer-Campus 1

department: Faculty of Medicine

country: Germany

institute: University of Münster

summary:
Constitutive activation of the nuclear factor-kappa B (NF-kB) pathway is a hallmark of the activated B-cell-like (ABC) subtype of diffuse large B-cell lymphoma (DLBCL). Recurrent mutations of NF-kB regulators that cause constitutive activity of this oncogenic pathway have been identified. However, it remains unclear how specific target genes are regulated. We identified the IkB-like protein NFKBIZ that binds NF-kB subunits and enhances transactivation of some NF-kB target genes while repressing others, to be upregulated in ACB compared to GCB DLBCL primary patient samples (p=5.1 x 10^-37). Knockdown of NFKBIZ by RNA interference was toxic to ABC but not GCB DLBCL cell lines. Gene expression profiling following NFKBIZ knockdown significantly downregulated a large number of NF-kB target genes, suggesting a central role in regulating NF-kB signaling. To further investigate the molecular mechanisms of how NFKBIZ mediates NF-kB signaling in ABC DLBCL, we performed immunoprecipitations and detected an interaction of NFKBIZ with both p50 and p52 NF-kB subunits, indicating that both the canonical and non-canonical NF-kB pathways are regulated by NFKBIZ. Collectively, our data imply that NFKBIZ is required for NF-kB signaling in ABC DLBCL and thus might represent a promising molecular target for future therapies.

The complete dataset is comprised of three experiments with the male HBL-1 ABC DLBCL cell line: a) 8 paired GEP measurements after NFKBIZ inhibition by shRNA, b) 6 paired GEP measurements after applying the MLN inhibitor and c) 4 two-color measurements after applying a MALT inhibitor.

overall_design: This dataset includes 4 two-color measurements of the male HBL-1 ABC DLBCL cell line after applying a MALT inhibitor.

first: Georg

last: Lenz


title: Effect of cigarette smoke on gene expression in mammary epithelial cells

first: Francescopaolo

last: Di Cello

type:
Methylation profiling by array
Expression profiling by array

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

overall_design: Refer to individual Series


title: Differential expression of genes in spinal cord folowing experimental autoimmune encephalomyelitis (EAE) in mice.

city: Melbourne

first: Victoria

middle: Mary

last: Perreau

state: Victoria

address: Parkville

department: Center for Neuroscience

country: Australia

institute: University of Melbourne

summary: Microarrays were used to identify genes that were differently expressed in mouse spinal cord as a resut of experimental autoimmune encephalomyelitis (EAE),  which is a model for demyelinating disease.

overall_design: Mice were injected with PLP peptide or vechicle.

first: Vilija

middle: G

last: Jokubaitis

first: Melissa

last: Gresle

first: Helmut

last: Butzkueven

first: Trevor

last: Kilpatrick

first: Tania

last: Cipriani


title: An oncogenic Kras expression signature identified by cross-species

city: Palo Alto

first: Dedeepya

last: Vaka

address: 265 Campus Drive

department: Pediatrics

institute: Stanford

summary:
Mouse lung cancers were generated using the KrasLA model, in which a latent mutated Kras2 allele (resulting in the amino acid substitution G12D) is sporadically activated through spontaneous homologous recombination. These mice develop lung adenomas with full penetrance; over time, the tumors acquire morphologic characteristics reminiscent of those of human adenocarcinoma, such as nuclear atypia and a high mitotic index.
KrasLA2 mice on a 129svJae background were crossed with wild type C57B/6J mice to obtain F1 progeny.  The initial report of this mouse model described two alleles, KrasLA1 and KrasLA2.  All expression profiles in this study were generated using the KrasLA2 mice.  We call the model KrasLA throughout for simplicity.   Mice bearing the KrasLA latent allele were allowed to develop to 5-6 month of age and sacrificed by cervical dislocation. Lungs were removed and placed in RNAlaterTM solution (Ambion).  Individual tumors large enough to be easily dissected (3mm-8mm) were removed and cut into 2 pieces. One piece was placed in formalin to be used for histological analysis while the other piece was stored at -80 for RNA/DNA extraction.

overall_design: Gene expression profiling was perfomed on lung tumors derived from KrasLA mouse (n = 31) and normal mouse lung samples (n = 19).

first: A

last: Sweet-Cordero

first: S

last: Mukherjee

last: Subramanian

first: H

last: You

first: J

last: Roix

first: C

last: Ladd-Acosta

last: Mesirov

first: T

last: Golub

last: Jacks


title: Differentially expressed gene profiles according to physical status of human papillomavirus integration in cervical cancer

status: Public on Jul 28 2013

city: Goyang-si

first: Hye-Jin

last: Shin

state: Gyeonggi-do

address: 323 Ilsan-ro, Ilsandong-gu

department: Research Institute and Hospital

country: South Korea

institute: National Cancer Center

summary: Integration of human papillomavirus (HPV) DNA into the host genome is a critical aetiological event in the progression from normal cervix to intraepithelial neoplasm, and finally to invasive cervical cancer. In this study, we want to know how HPV DNA physical status relates to treatment outcome for cervical carcinomas.

overall_design: Cervical cancer samples were compared with normal sample. And also, we divided 39 cervical cancer patients into four groups according to HPV DNA physical status and investigated differentially expressed gene profiles in these groups using Agilent two-color experiment.

first: Joo-Young

last: Kim


title: siRNA Knockdown of SWI/SNF complex proteins in prostate cancer cell lines

status: Public on Jul 20 2013

city: Ann Arbor

first: Matthew

last: Iyer

state: MI

address: 5316 CCGC 0940 1400 E. Medical Center Drive

department: Michigan Center for Translational Pathology

institute: University of Michigan

summary: Here we performed transcriptional profiling of the prostate cancer cell lines LNCaP and 22Rv1 comparing non-targeting siRNA treatment versus siRNAs targeting SWI/SNF complex proteins (SMARCA2, SMARCA4, and SMARCB1). Goal was to determine the effect of SWI/SNF knockdown on gene expression in prostate cancer.

overall_design: Two-condition experiment: non-targeting siRNA versus SWI/SNF-siRNA treated cells. Three SWI/SNF proteins were targeted: SMARCA2, SMARCA4, and SMARB1. Biological replicates: 1 control replicate, 2 treatment replicates per SWI/SNF protein.  Technical replicates: 1 replicate per SWI/SNF protein. Cell lines: 22Rv1 and LNCaP.

first: Xiaojun

last: Jing

middle: K

first: John

last: Prensner


title: Prostate cancer cell lines: non-targeting siRNA versus SChLAP1-siRNA treated

summary: SChLAP1 is a novel long non-coding RNA expressed in prostate cancer. Here we performed transcriptional profiling of the prostate cancer cell lines LNCaP and 22Rv1 comparing non-targeting siRNA treatment versus SChLAP1-siRNA treatment. Goal was to determine the effect of SChLAP1 knockdown on gene expression in prostate cancer.

overall_design: Two-condition experiment: non-targeting siRNA versus SChLAP1 siRNA treated cells. Biological replicates: 1 control replicate, 2 treatment replicates.  Technical replicates: 3 replicates per SChLAP1 siRNA.  Cell lines: 22Rv1 and LNCaP.

first: Xiaojung


title: Gene expression signatures of dasatinib-treated chronic myeloid leukemia patients with resistance to imatinib

status: Public on Jul 31 2013

city: New York

first: Angela

middle: A.

last: Fachel

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

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

summary: Dasatinib has demonstrated efficacy in patients with chronic-phase chronic myeloid leukemia (CML) who had resistance or intolerance to imatinib. However, some patients also develop resistance or intolerance to dasatinib. To identify potential molecular pathways involved in primary resistance to dasatinib in CML, we analyzed gene expression profiles of mononuclear cells of 7 imatinib-resistant patients, collected before and after 1-year dasatinib treatment. Large-scale gene expression was measured with Agilent microarrays covering protein-coding genes and long (>200 nt) noncoding RNAs (lncRNAs). Sets of genes and lncRNAs significantly differentially expressed (>1.5 fold-change; q value ≤10%) were identified. Ingenuity Pathway Analysis pointed to a number of functions, canonical pathways and gene networks that were significantly enriched with differentially expressed genes. In addition to protein-coding genes, lncRNAs have been recently implicated in pathways leading to tumorigenesis. Our data point to new possible regulatory elements involved in dasatinib resistance in CML.

overall_design:
This SuperSeries is composed of the SubSeries listed below.
Refer to individual Series.


title: Expression data from left versus right mouse entorhinal cortex (EC).

status: Public on Jul 30 2013

first: Diego

last: Berman

state: NY

department: Pathology and Cell Biology

institute: Columbia University

summary:
The entorhinal cortex of the mouse seems to be sensitive to molecular mechanisms that have been linked to the pathology of Alzheimer's disease. In this microarray study we are interested in comparing the expression profile of the left versus the right EC of the mouse, in order to understand if there is a significant difference in gene expression that might reveal any insights into the differential activation of these areas.
We used microarrays to detail the global programme of gene expression underlying a possible lateralization of the EC in the mouse brain (left versus right EC).

overall_design: The left and the right entorhinal cortices of 6 month-old C57BL/6 wild-type mice was dissected out by following anatomical landmarks and guided by the Mouse Brain Paxinos and Franklin’s atlas. Samples were immediately processed for RNA extraction by using the RNeasy Kit from QIAGEN according to manufacturer’s instructions. Before running the microarrays, RNA quality and integrity was monitored on an Agilent BioAnalyzer. Samples were then run on Affymetrix Genechip Mouse gene 2.0 ST arrays following Affymetrix’s standard procedures (n=3 per cortical hemisphere). Microarrays data were analyzed through the use of Ingenuity® iReport (Ingenuity® Systems, www.ingenuity.com).

first: Usman

last: Khan

first: Li

last: Liu

first: Frank

last: Provenzano

first: Caterina

last: Profaci

first: Richard

last: Sloan

last: Mayeux

first: Karen

last: Duff

first: Scott

last: Small


title: Overexpression of SChLAP1 versus LACZ in RWPE cells

summary: SChLAP1 is a novel long non-coding RNA expressed in prostate cancer. Here we performed transcriptional profiling of the benign immortalized prostate cell line RWPE overexpressing two isoforms of the SChLAP-1 lncRNA compared with RWPE overexpressing LACZ. Our goal was to determine the effect of SChLAP1 overexpression on gene expression in prostate cells.

overall_design: Two-condition experiment: RWPE overexpressing SChLAP1 versus RWPE overexpressing LACZ. Biological replicates: 1 control replicate, 2 experimental replicates.  Technical replicates: 2 replicates per SChLAP1 isoform.  Cell lines: RWPE.


title: SChLAP-1, a long non-coding RNA, antagonizes the SWI/SNF complex and coordinates aggressive prostate cancer.


title: Gene expression profiles in islets from pancreatectomized mice

status: Public on Jul 18 2013

city: Yokohama

first: Jun

last: Shirakawa

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

institute: Yokohama City university

summary: To obtain comprehensive profile of gene expression following a pancreatectomy, we performed microarray analysis of genes expressed in islets of C57BL/6J mice 3 days after  60% pancreatectomy or sham operation.

overall_design: gene expression in mouse pancreatic islets was measured at 3 days after 60% pancreatectomy or sham operation.


title: Development of gene expression signatures for LGR5hi and LGR5lo ISCs in response to gamma-irradiation

city: Ulm

first: Hans

last: Kestler

address: Albert-Einstein-Allee 11

department: Research Group Bioinformatics and Systems Biology

institute: University of Ulm

summary: To check gene expression signatures for LGR5hi and LGR5lo ISCs in response to gamma-irradiation, we performed whole genome microarray on  LGR5hi and LGR5lo ISCs purified from irradiated mice or non-irradiated mice

overall_design: Radiation induced gene expression in LGR5hi and LGR5lo ISCs of LGR5-GFPki mice was measured at 3 hours after exposure to 12Gy γ-irradiation or non-irradiation.


title: A comparative gene expression profiling of spondyloarthropathy and rheumatoid arthritis using oligonucleotide based microarrays

status: Public on Jul 15 2013

city: Bangalore

first: Akhilesh

last: Pandey

email: pandey@jhmi.edu, arivusudar@ibioinformatics.org, sameerkumar.iob@gmail.com, microarray@ibioinformatics.org

state: Karnataka

address: UnitI, Discoverer building, ITPL

country: India

institute: Institute of Bioinformatics

summary:
Comparative gene expression profiling of mononuclear cells from synovial fluid samples of rheumatoid arthritis (RA) and
spondyloarthropathy (SpA) cases was performed. A total of 72 transcripts were found to be differentially expressed in RA compared
to SpA, with p-value threshold of 0.05 and using the Benjamini-Hochberg False Discovery rate multiple comparison corrections.
From the list, 57 transcripts were found to be upregulated in RA as compared to SpA and 15 downregulated by a fold
change cut-off of 1.5-fold.

overall_design: The proposed study carried out mRNA expression profiling of mononuclear cells from synovial fluid samples of seven RA and five SpA cases. We have used 4X44K and 1X44K arrays from Agilent Technologies platform. Based on the RNA integrity, selected molecules were processed further using single-color microarray based gene expression. The raw data files obtained from this study were eventually analyzed with R package of the BioConductor suite.


title: Overexpression of GATA1 confers resistance to chemotherapy in acute megakaryocytic leukemia

status: Public on Jul 01 2013

city: Detroit

first: Yubin

last: Ge

address: 110 East Warren Ave.

institute: Karmanos Cancer Institute

summary: Gene expression study of shRNA knockdown of GATA1 in the megakaryoblastic cell line Meg01.

overall_design: Cell culture samples from two Meg01 clones (GATA1 4-14 and GATA1 5-13) were compared against a negative control infection sample (GATA1-neg). Two dye-swap microarrays were completed for each clone.

first: Alan

last: Dombkowski

first: Jeffrey

last: Taub


title: Protein coding gene expression profile of dasatinib-treated chronic myeloid leukemia patients with resistance to imatinib

overall_design: Dasatinib pre-treatment and 1-yr post-treatment samples from 3 responders (R) or 4 non-responders (NR) chronic myeloid leukemia (CML) patients were investigated. We analyzed expression of Pre-treatment R vs. Pre-treatment NR; Pre-treatment R vs. Post-treatment NR; Pre-treatment NR vs. Post-treatment NR.

first: Rosana

last: Silveira

first: Yuri

middle: B

last: Moreira

first: Carmino

last: De Souza

first: Fernando

middle: F

last: Costa

first: Sergio

last: Verjovski-Almeida

first: Katia

last: Pagnano


title: Role of HGF in epithelial-stromal cell interactions during progression from benign breast disease to ductal carcinoma in situ

status: Public on Jul 12 2013

city: Chapel Hill

first: Melissa

last: Troester

address: 135 Dauer Drive, CB 7435

institute: University of North Carolina at Chapel Hill

summary: ABSTRACT: Introduction: Basal-like and luminal breast cancers have distinct stromal-epithelial interactions, which likely play a role in progression to invasive cancer. However, little is known about how stromal-epithelial interactions evolve in benign and pre-invasive lesions.Methods: To study epithelial-stroma interactions in basal-like breast cancer progression, we cocultured reduction mammoplasty fibroblasts with the isogenic MCF10 series of cell lines (representing benign/normal, atypical hyperplasia, and ductal carcinoma in situ). We used gene expression microarrays to identify pathways induced by coculture in premalignant cells (MCF10DCIS) compared to normal and benign (MCF10A and MCF10AT1). Relevant pathways were then (1) targeted in vitro and effects on morphogenesis were evaluated and (2) evaluated in vivo for associations with basal-like subtype. Results: Our results show that premalignant MCF10DCIS cells express characteristic gene expression patterns of invasive basal-like microenvironments.  Furthermore, while HGF secretion is upregulated (relative to normal, MCF10A levels) when fibroblasts are cocultured with either atypical (MCF10AT cells) or premalignant (MCF10DCIS) cells, only MCF10DCIS cells upregulate the HGF receptor, MET. In 3-dimensional cultures, upregulation of HGF/MET in MCF10DCIS cells induced morphological changes suggestive of invasive potential, and these changes were reversed by antibody-based blocking of HGF signaling. These results are relevant to in vivo progression because high expression of a novel MCF10DCIS-derived HGF signature was correlated with basal-like subtype among invasive cancers, with approximately 86% of basal-like cancers highly expressing the HGF signature. Conclusions: In this study we document coordinated and complementary changes in HGF secretion and MET expression in epithelium and stroma in pre-invasive lesions. These results suggest that targeting stroma-derived HGF signaling in early carcinogenesis may block progression of basal-like precursor lesions.Introduction: In breast cancers, the basal-like subtype has high levels of genomic instability relative to other breast cancer subtypes with many basal-like-specific regions of aberration. There is evidence that this genomic instability extends to smaller scale genomic aberrations as well, as shown by a previously described micro-event in the PTEN gene in the Basal-like SUM149 breast cancer cell line. Methods: We sought to identify if small regions of genomic change exist by using a high density, gene centric Comparative Genomic Hybridizations (CGH) array on both cell lines and primary tumors. A custom Agilent tiling array for CGH (244,000 probes, 200bp tiling resolution) was created to identify small regions of genomic change and was focused on previously identified basal-like-specific, and general cancer genes. Tumor genomic DNA from 94 patients and 2 breast cancer cell lines was labeled and hybridized to these arrays. Aberrations were called using SWITCHdna and the smallest 25% of SWITCHdna-defined genomic segments being called micro-aberrations (<64 contiguous probes, ~ <15kb). Results: Our data showed that primary tumor breast cancer genomes frequently contained areas of small-scale copy number gains and losses, termed micro-aberrations, which are undetectable using lower-density genome-wide platforms. The basal-like subtype exhibited the highest incidence of these events. These micro-aberrations sometimes altered expression of the involved gene as suggested by data from microarray and mRNA-seq studies. We confirmed the presence of the PTEN micro-amplification in SUM149 and by mRNA-seq showed that this resulted in loss of expression of all exons downstream of this event. Micro-aberrations disproportionately affected the 5’ regions of the affected genes, including the promoter region, and a high frequency of micro-aberrations was associated with poor survival outcomes. Conclusion: Using a high probe density, gene-centric aCGH microarray, we present evidence of small-scale genomic aberrations that contribute to gene inactivation, and thus, genomic instability and tumor formation through a mechanism not detected using conventional copy number analyses.

overall_design: reference x sample

first: Patricia

last: Casbas-Hernandez


title: Transcriptome Profiling of Lgr5-expressing ovarian surface epithelium cells

status: Public on Dec 04 2013

city: Singapore

first: Nick

last: Barker

address: 8A Biomedical Grove, Immunos

country: Singapore

institute: A*STAR Institute of Medical Biology

summary:
Transcriptome profiling using Affymetrix GeneChip arrays was performed on sorted populations of Lgr5-expressing mouse ovarian surface epithelium.
The ovary surface epithelium (OSE) undergoes ovulatory tear-and-remodelling throughout life. Resident stem cells drive such tissue homeostasis in many adult epithelia, but their existence in the ovary has yet to be definitively proven. Lgr5 marks stem cells in multiple epithelia. Here we use reporter mice and Single Molecule Florescent-in-Situ-Hybridization (FISH) to document candidate Lgr5+ stem cells within the mouse ovary and associated structures. Lgr5 is broadly expressed during ovary organogenesis, but becomes limited to the OSE in early neonate life. In adults, Lgr5 expression is predominantly restricted to proliferative regions of the OSE and fimbria- mesovarian junction. Using conditional in vivo lineage tracing we identify embryonic and early neonate Lgr5+ populations as stem/progenitor cells contributing to the development of adult OSE and granulosa cell lineages, as well as the epithelia of the mesovarian and oviduct including its distal opening, fimbria. Long-term lineage tracing reveals that adult OSE-resident Lgr5+ populations contribute to epithelial homeostasis and OSE regenerative repair in vivo. Thus, Lgr5 is a marker of stem/progenitor cells of the ovary and tubal epithelia.

overall_design: Ovarian surface epithelium from pooled batches of Lgr5-eGFP-CreERT2 mice (n=8, per array) were sorted for cells expressing either high or low EGFP. Total RNA from three technical replicates per sorted population (Lgr5-high or Lgr5-low) was extracted with the RNeasy Micro Kit (QIAGEN), DNaseI-treated, and amplified with the Ovation Pico WTA V2 (NuGEN Technologies). Single-stranded cDNA amplification products were purified using QIAquick PCR Purification Kit (QIAGEN). cDNA was biotinylated using the Encore Biotin Module (NuGEN Technologies). Biotiylated cDNA was hybridized to Affymetrix Mouse Genechip ST 2.0 expression arrays.


title: RAP1 protects from obesity, diabetes and metabolic syndrome through its extra telomeric role regulating gene expression (young mouse liver)

status: Public on Jun 21 2013

city: Madrid

first: Paula

last: Martinez

state: Madrid

address: Melchor Fernandez Almagro 3

country: Spain

institute: CNIO

summary: RAP1 is one of the components of shelterin, the capping complex at chromosome ends or telomeres. Unlike other shelterins, however, RAP1 is not essential for preventing telomere fusions. RAP1 also binds along chromosome arms, where it is proposed to regulate gene expression. To investigate the non-telomeric roles of RAP1 in vivo, we generated a RAP1 whole-body knock-out mouse model. Unexpectedly, these mice presented an early onset of obesity, which was particularly severe in females and was aggravated under a high-fat diet. Rap1-deficient mice showed abnormal accumulation of fat in abdominal depots and developed signs of type II diabetes and metabolic syndrome, including hepatic steatosis and high fasting plasma levels of insulin, glucose, cholesterol, and alanine transaminase. Gene expression analyses of the liver and visceral white fat from Rap1-deficient mice before the onset of obesity indicated deregulation of key metabolic transcriptional programs including fatty acid metabolism, PPARa signalling and glucose metabolism. Transcriptome and Western blotting analyses in liver further identified Ppara and Pgc1a and their target genes as the key metabolic pathways affected by Rap1 deletion. Finally, we show here that RAP1 binds to Ppara and Pgc1a loci and modulates their transcription. These findings underscore an unprecedented role for a telomere-binding protein in the regulation of metabolism.

overall_design: 2 condition experiment: WT versus Rap1 knockout. Tissue: liver. 4 biological replicates per genotype. Mice were 10 weeks old.

last: Martínez

first: Gonzalo

last: Gómez-López

last: García

first: Juana

last: Flores

first: María

last: Blasco


title: RAP1 protects from obesity, diabetes and metabolic syndrome through its extra telomeric role regulating gene expression (old mouse liver)

overall_design: 2 condition experiment: WT versus Rap1 knockout. Tissue: liver. 3 biological replicates per genotype. Mice were 30 weeks old.


title: RAP1 protects from obesity, diabetes and metabolic syndrome through its extra telomeric role regulating gene expression (young mouse white fat)

overall_design: 2 condition experiment: WT versus Rap1 knockout. Tissue: white gonadal fat. 4 biological replicates per genotype. Mice were 10 weeks old.


title: VEGF-A stimulated gene expression in human liver sinusoidal endothelial cells

status: Public on Jun 01 2013

city: Birmingham

first: Ian

last: Rowe

address: Edgbaston

department: Hepatitis C Virus Research Group

institute: University of Birmingham

summary: Transcriptomic analysis of VEGF-A stimulated liver sinusoidal endothelial cell gene expression.  Untreated cells were compared to those treated with VEGF-A.  VEGF-A stimulation is critical for normal LSEC phenotype, and the response to liver injury

overall_design: Two conditions: untreated vs. VEGF-A treated.  LSEC from 2 donors were pooled.  4 technical repeats.

first: Sarah

last: Durant


title: Expression changes between loricrin knockout and wildtype P0

status: Public on Jun 28 2013

city: Aurora

first: Dennis

middle: R.

last: Roop

state: Colorado

department: Dermatology

institute: University of Colorado

summary: The loss of loricrin, a major component of the cornified envelope, results in a delay of epidermal barrier formation. Therefore, the living layers of the epidermis are aberrantly exposed to late-stage amniotic fluid, which may serve as the signal to upregulate genes that functionally compensate for the loss of loricrin. Consistent with this hypothesis, metabolomic studies revealed marked changes in amniotic fluid between E14.5 and E16.5 dpc. In addition, we discovered that the Nrf2/Keap1 pathway detects these compositional changes and directly upregulates the expression of genes involved in the compensatory response, thus ensuring postnatal survival. In support of this finding, we demonstrate that genetically blocking the Nrf2 pathway abolishes the compensatory response, and preemptively activating Nrf2 pharmacologically rescues the delay in barrier formation in utero. Our findings reveal that the functions of Nrf2 and the composition of amniotic fluid have co-evolved to ensure the formation of a functional barrier.

overall_design: 1 sample with one replicate for each genotype was performed for both loricrin knockout and wildtype


title: Analysis of Drug Resistant Cell Lines

status: Public on Jun 22 2013

city: Thousand Oaks

first: Dan

last: Baker

state: CA

address: 1 Amgen Center Drive

department: Molecular Sciences

institute: Amgen Inc.

summary:
Analysis of Drug transports as a mechanism of resistance to aurora kinase inhibition
Parental and Taxol-resistant cell lines are compared for gene expression profile differences.

overall_design: 2 samples, fluor reversed


title: Pruning of the adipocyte cistrome by hematopoietic master regulator PU.1 (expression)

status: Public on Jun 27 2013

city: Philadelphia

first: Joanna

last: DiSpirito

state: PA

address: Smilow Center for Translational Research, 3400 Civic Center Boulevard

department: IDOM

institute: University of Pennsylvania

summary: Master transcription factors are the gatekeepers of lineage identity. As such, they have been a major focus of efforts to manipulate cell fate for therapeutic purposes. The ETS transcription factor PU.1 has a potent ability to confer macrophage phenotypes on cells already committed to a different lineage, but how it overcomes the presence of other master regulators is not known. The nuclear receptor PPARγ is the master regulator of the adipose lineage, and its genomic binding pattern is well characterized in adipocytes. Here, we show that when expressed at macrophage levels in mature adipocytes, PU.1 bound a large fraction of its macrophage sites, where it induced chromatin opening and the expression of macrophage target genes. Strikingly, PU.1 markedly reduced the genomic binding of PPARγ without changing its abundance. PU.1 expression repressed genes with nearby adipocyte-specific PPARγ binding sites, while a common macrophage-adipocyte gene expression program was retained. Together, these data reveal unexpected lability within the adipocyte PPARγ cistrome and show that even in terminally differentiated cells, PU.1 can remodel the cistrome of another master regulator.

overall_design: Microarray expression profiling was performed on 3T3-L1 adipocytes from two treatment groups: (1) adipocytes transduced with a control adenovirus expressing beta-galactosidase (LACZ-Ads) and (2) adipocytes transduced with an adenovirus expressing full-length murine PU.1 cDNA (PU.1-Ads). Each sample group consists of four biological replicates which are here defined as separate differentiations of mature 3T3-L1 adipocytes and adenoviral infections. Each replicate was hybridized to an individual array for a total of eight arrays.

first: J

first: B

last: Fang

first: F

last: Wang

first: M

last: Lazar


title: RAP1 protects from obesity, diabetes and metabolic syndrome through its extra telomeric role regulating gene expression

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

overall_design: Refer to individual Series


title: Activation of TGF-beta pathway by areca nut constituents: A possible cause of Oral submucous fibrosis.

status: Public on May 22 2013

first: Neeraj

last: KUMAR

address: Indian Institute of Science Bangalore

department: MRDG

institute: Indian Institute of Science Bangalore

summary: To understand the role of areca nut constituents in manifestation of Oral submucous fibrosis, we studied gene expression profile in epithelial cells following areca nut water extract treatment. A comaprison with TGF-beta induced gene expression changes were performed as epithelial cells were predicted to be source of TGF-beta.

overall_design: Control Vs Areca nut 5 ug/ml water extract (5H) (2), Contro Vs TGF-beta (2), Control Vs ALK5 (TbetaRI inhibitor) (2), Control Vs 5H + ALK5 inhibitor (2). (2)- Biological duplicates.

first: Imran

last: Khan

last: Kumar

first: Sivakrishna

last: Narra

first: Paturu

last: Kondaiah


title: Human monocyte-derived dendritic cells treated with U0126 or SB203580

status: Public on May 03 2013

first: Angel

last: Corbí

address: Ramiro de Maeztu 9

department: Molecular Microbiology and Infection Biology

institute: Consejo Superior de Investigaciones Científicas

summary:
Identification of MEK-ERK or p38MAPK dependent genes in human monocyte derived dendritic cells.
Dendritic cells (DC) promote tolerance or immunity depending on their maturation state. Previous studies have revealed that DC maturation is enhanced or accelerated upon MEK-ERK signaling pathway inhibition. We have now determined the contribution of MEK-ERK activation to the profile of gene expression of human immature monocyte-derived dendritic cells (MDDC) and peripheral blood myeloid DC. ERK inhibition altered the expression of genes that mediate CCL19-directed migration (CCR7) and LDL binding (CD36, SCARB1, OLR1, CXCL16) by immature DC. Besides, ERK upregulated CCL2 expression while impaired the expression of DC maturation markers (RUNX3, ITGB7, IDO1). MEK-ERK-regulated genes exhibited an over-representation of cognate sequences for the Aryl Hydrocarbon Receptor (AhR) transcription factor, and we show that AhR mediates some of the ERK-dependent transcriptional effects in DC. Therefore, MEK-ERK signaling pathway regulates antigen capture, lymph node homing and the acquisition of maturation-associated genes, and its contribution to the maintenance of the immature state of MDDC and myeloid DC is partly dependent on the activity of AhR. Since pharmacological modulation of the MEK-ERK signaling pathway has been proposed as a potential therapeutic strategy for cancer, our findings indicate that ERK inhibitors might influence the generation of anti-tumor responses through regulation of critical DC effector functions.

overall_design: Human peripheral blood monocytes from three independent healthy donors (DC4, DC5 and DC7) were isolated by anti-CD14-labeled magnetic microbeads. CD14+ monocytes were cultured for 5 days in RPMI 10% FCS containing GM-CSF and IL-4 to generate immature monocyte-derived dendritic cells (MDDC). Immature MDDC were exposed to MEK inhibitor, U0126, or p38MAPK inhibitor, SB203580 for 1 hour and a final dose of GM-CSF and IL-4 were added to the culture. Cells were collected for analysis after 4, 10 or 24 hours.Total RNA from each condition was extracted using the All prep DNA/RNA/protein mini kit (Qiagen) and hybridized to an Agilent Human Whole Genome  (4x44) Oligo Microarray. All experimental procedures were performed following manufacturer instructions.

last: Corbi

first: Noemi

last: Aguilera-Montilla


title: Development of gene expression signatures to characterize evolution of hASC cells isolated and maintained xenogeneic-free

status: Public on Apr 24 2013

city: Logroño

first: Andrés

last: Sanz-García

state: La Rioja

address: C/ Luis de Ulloa 20

institute: University of La Rioja

summary: Human adipose stem cells (hASCs) play a crucial role in the fields of regenerative medicine and tissue engineering for different reasons: the abundance of adipose tissue, their easy harvesting, the ability to multipotent differentiation and the fact that they do not trigger allogeneic blood response or secrete cytokines that act as immunosuppressants. The vast majority of protocols use animal origin reagents, with the underlying risk of transmitting infections by non-human pathogens. We have designed a protocol to isolate and maintain the properties of hASCs avoiding xenogeneic reagents. These changes not only preserve hASCs morphology, but also increase cell proliferation and maintain their stem cell marker profile. On the other hand, human serum albumin (HSA), Tryple® and human Serum (HS), do not affect hASCs multipotent differentiation ability. The amendments introduced do not trigger modifications in the transcriptional profile of hASCs, alterations in key biochemical pathways or malignization. Thus, we have proven that it is possible to isolate and maintain hASCs avoiding animal reagents and, at the same time, preserving crucial culture parameters during long term culture. Thereby we have revealed a novel and effective tool for the improvement of clinical, cell-based therapies.

overall_design: Gene expression in human adipose stem cells isolated and maintained with human reagents were measured immediately after their isolation, and at passages 1, 3 and 5. Pools from the same 8 healthy donors were used to measure the 4 points of growth.

first: Escobedo-Lucea

last: Carmen

first: Sanz-Garcia

last: Andres


title: Molecular Basis of Renal Adaptation in a Murine Model of Congenital Obstructive Nephropathy

status: Public on Jun 18 2013

city: Columbus

first: Ashley

last: Jackson

state: OH

address: 700 Children's Dr

department: Molecular and Human Genetics

institute: Nationwide Children's Hospital

summary: Congenital obstructive nephropathy is a common cause of chronic kidney disease and a leading indication for renal transplant in children. The cellular and molecular responses of the kidney to congenital obstruction are incompletely characterized. In this study, we evaluated global transcription in kidneys with graded hydronephrosis in the megabladder (mgb-/-) mouse to better understand the pathophysiology of congenital obstructive nephropathy. Three primary pathways associated with kidney remodeling/repair were induced in mgb-/- kidneys independent of the degree of hydronephrosis. These pathways included retinoid signaling, steroid hormone metabolism, and renal response to injury. Urothelial proliferation and the expression of genes with roles in the integrity and maintenance of the renal urothelium were selectively increased in mgb-/- kidneys. Ngal/Lcn2, a marker of acute kidney injury, was elevated in 36% of kidneys with higher grades of hydronephrosis. Evaluation of Ngalhigh versus Ngallow kidneys identified the expression of several novel candidate markers of renal injury. This study indicates that the development of progressive hydronephrosis in mgb-/- mice results in renal adaptation that includes significant changes in the morphology and potential functionality of the renal urothelium. These observations will permit the development of novel biomarkers and therapeutic approaches to progressive renal injury in the context of congenital obstruction.

overall_design: Gene expression was measured in control, mild, moderate and severely hydronephrotic megabladder mouse kidneys. A total of 6 control kidneys were compared to 18 mutant kidneys from age-matched male animals.

first: Brian

last: Becknell

last: Carpenter

first: Jordan

last: Allen

first: Michael

last: Wilhide

first: Susan

last: Ingraham

first: David

last: Hains

first: Kirk

last: McHugh


title: Effect of NDRG1 deletion and hypoxia in mouse placenta

status: Public on Apr 26 2013

city: Pittsburgh

first: Jacob

last: Larkin

address: 240 Craft Ave.

department: OB/GYN/Reproductive Sciences

institute: University of Pittsburgh

summary: We sought to identify changes in placental gene expression that may contribute to the phenotype of NDRG1-deficient embryos, and to define the contribution of hypoxia and fetal sex to these changes. We therefore used high-density oligonucleotide microarrays to interrogate differences in placental gene expression, stratified by fetal sex, Ndrg1 status (WT vs KO) and oxygenation (21% vs 12%).

overall_design: C57Bl6/J mice heterozygous for NDRG1-null allele were bred and separated next day (E0.5), and give ad libitum access to standard chow and water with 12h light:dark cycle. Pregnant dams were sacrificed at E15.5 by cervical dislocation following isoflurane anesthesia. Following sacrifice, embryos and placentas were collected, NDRG1 genotype and sex were determined by PCR of fetal tissue, and RNA was extracted from placental tissue following removal of membranes.

first: Yoel

last: Sadovsky


title: Gene expression changes in the olfactory bulb of mice induced by exposure to diesel exhaust are dependent on animal rearing environment

status: Public on Apr 18 2013

city: Shiga

first: Satoshi

last: Yokota

address: 1-1-1 Noji-Higashi, Kusatsu

institute: Ritsumeikan University

summary: There is an emerging concern that particulate air pollution increases the risk of cranial nerve disease onset. Small nanoparticles, mainly derived from diesel exhaust particles reach the olfactory bulb by their nasal depositions. It has been reported that diesel exhaust inhalation causes inflammation of the olfactory bulb and other brain regions. However, these toxicological studies have not evaluated animal rearing environment. We hypothesized that rearing environment can change mice phenotypes and thus might alter toxicological study results. In this study, we exposed mice to diesel exhaust inhalation at 90 micro g/m3, 8 hours/day, for 28 consecutive days after rearing in a standard cage or environmental enrichment conditions. Microarray analysis found that expression levels of 112 genes were changed by diesel exhaust inhalation. Functional analysis using Gene Ontology revealed that the dysregulated genes were involved in inflammation and immune response. This result was supported by pathway analysis. Quantitative RT-PCR analysis confirmed 10 genes. Interestingly, background gene expression of the olfactory bulb of mice reared in a standard cage environment was changed by diesel exhaust inhalation, whereas there was no significant effect of diesel exhaust exposure on gene expression levels of mice reared with environmental enrichment. The results indicate for the first time that the effect of diesel exhaust exposure on gene expression of the olfactory bulb was influenced by rearing environment. Rearing environment, such as environmental enrichment, may be an important contributive factor to causation in evaluating still undefined toxic environmental substances such as diesel exhaust.

overall_design: RNA sample was taken from olfactory bulb of 56-day-old mouse received diesel exhaust (DE) inhalation at 90 micro g/m3, 8 hours/day, for 28 consecutive days, while control RNA was taken from mouse received clean air, after rearing in a standard cage or environmental enrichment conditions. Comparisons among groups were made by one-color method with normalized data from Cy3 channels for data analysis.

first: Hiroshi

last: Hori

first: Masakazu

last: Umezawa

first: Natsuko

last: Kubota

first: Rikio

last: Niki

first: Shinya

last: Yanagita

first: Ken

last: Takeda


title: CD4+T cells activation

status: Public on Apr 10 2013

city: Kunming

first: Hua-Tang

last: Zhang

state: Yunnan

address: No.32 Jiaochang Donglu

department: key laboratory of animal models and human diseases mechanisms

country: China

institute: Kunming Institute of Zoology, Chinese Academy of Science

summary: Aanlysis of human resting CD4+T cells and cells activated by two different methods: CD4+ T cells unstimulated (be susceptible but not support to HIV-1) and stimulated either by CD3/CD28 costimulation (reversed susceptibility and resisted to HIV-1) or by PHA/IL-2 for six days (be susceptible and support to HIV-1) to investigate potential mechanism of reversing susceptible to HIV-1.

overall_design: We measured gene expression in resting human CD4+T cells and cells activated by two methods for six days which could induce different effects to HIV-1. Three independent experiments were performed at each treatments using different donors for each experiment.


title: EWS/ATF1 activates Fos and induces soft tissue sarcomas from neural crest-derived cells [Agilent].

status: Public on Apr 04 2013

city: Tokyo

first: Yasuhiro

last: Yamada

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Molecular Pathology

institute: University of Tokyo

summary: Clear cell sarcoma (CCS) is an aggressive soft tissue malignant tumor characterized by a unique t(12; 22) translocation, leading to the expression of a chimeric EWS/ATF1 fusion gene.  However, little is known about the mechanisms underlying how EWS/ATF1 is involved in the development of CCSs.  In addition, the cells of origin for CCSs remain to be determined.  We generated EWS/ATF1-inducible mice, and examined the effects of EWS/ATF1 expression in adult cells.  We show that the forced expression of EWS/ATF1 results in the development of EWS/ATF1-dependent sarcomas in mice.  The histology of EWS/ATF1-induced sarcomas resembles that of CCSs and EWS/ATF1-induced tumor cells express CCS-markers, such as S100, Sox10, and Mitf.  A lineage tracing experiment revealed that such sarcomas are derived from neural crest-lineage cells.  Finally, we found that EWS/ATF1 directly induces Fos in an ERK-independent manner, and demonstrated that the increased Fos expression is important for the active cell proliferation in not only EWS/ATF1-induced sarcomas, but also in human CCSs.  Our results indicate that FOS, as well as EWS/ATF1 itself, could be a promising therapeutic target for the treatment of EWS/ATF1-related sarcomas.

overall_design: Tumor cell lines were established from soft tissue sarcomas in EWS/ATF1-induced mice. Because these cell lines contain doxycycline-inducible EWS/ATF1 alleles, EWS/ATF1 expression can be regulated by the different concentrations of doxycycline. Tumor cell lines were exposed to different concentrations of doxycycline, and total RNAs were isolated at 3 and 48 hours after the doxycycline exposure.

first: Kazunari


title: MicroRNA-155 confers encephalogenic potential to Th17 cells by promoting IL-23 responsiveness and effector gene expression

status: Public on May 01 2013

city: Salt Lake City

first: Brett

last: Milash

state: UT

department: Center for High Performance Computing

institute: University of Utah

summary: We examined the role of miR-155 in differentiated Th17 cells during their induction of Experimental Autoimmune Encephalomyelitis (EAE). Using adoptive transfer experiments, we found that highly purified, MOG antigen specific Th17 cells lacking miR-155 are defective in their capacity to cause EAE. Gene expression profiling of purified miR-155-/- IL-17F+ Th17 cells identified a subset of effector genes that are dependent upon miR-155 for their proper expression through a mechanism involving repression of the transcription factor Ets1. Among the genes reduced in the absence of miR-155 was IL-23R, resulting in miR-155-/- Th17 cells being hypo-responsive to IL-23. Taken together, our study demonstrates a critical role for miR-155 in Th17 cells as they unleash autoimmune inflammation, and finds that this occurs through a signaling network involving miR-155, Ets1 and the clinically relevant IL-23-IL-23R pathway.

overall_design: two biological replicates of miR-155-/- CD4+ IL-17F RFP+ T cells compared to two biological replicates of miR-155+/+CD4+IL-17F RFP+ T cells (as a control).

first: Ruozhen

last: Hu

first: Thomas

last: Huffaker

first: Dominique

last: Kagele

first: Marah

middle: C

last: Runtsch

first: Erin

last: Bake

first: June

last: Round

first: Ryan

last: O'Connell


title: Expression data from mouse insulinoma cells

status: Public on Apr 22 2013

city: Suita

first: Eiji

last: Yamato

address: 2-2 Yamadaoka

institute: Osaka University

summary: We previously isolated a subclone, MIN6 clone 4, from the parental MIN6 cells, that shows well-regulated insulin secretion in response to glucose, glybenclamide, and KCl, even after prolonged culture. To investigate the molecular mechanisms responsible for preserving GSIS in this subclone, we compared four groups of MIN6 cells: Pr-LP (parental MIN6, low passage number), Pr-HP (parental MIN6, high passage number), C4-LP (MIN6 clone 4, low passage number), and C4-HP (MIN6 clone 4, high passage number). Based on their capacity for GSIS, we designated the Pr-LP, C4-LP, and C4-HP cells as “responder cells.” In a DNA microarray analysis, we identified a group of genes with high expression in responder cells (“responder genes”), but extremely low expression in the Pr-HP cells.

overall_design: MIN6 clone 4 cells are a subclone isolated from low-passage-number parental MIN6 cells by the limiting dilution method (JM, unpublished). This subclone was maintained in the same culture conditions as the parental cells, and retained good GSIS even after 6 months of continuous culture. For the low-passage-number parental MIN6 cells (Pr-LP), we used cells passaged 17-20 times; for the high-passage-number MIN6 cells (Pr-HP), we used cells passaged 35-40 times. Seventeen to 20 passages were also used for the low-passage-number MIN6 clone 4 cells (C4-LP), and the high-passage ones (C4-HP) were used after 40 to 50 passages.


title: Host response in the lung to influenza infection with PR8, VN or X31 strains at 12, 16 and 24 hours

status: Public on Mar 31 2013

city: Seattle

first: Aderem

last: Lab

state: WA

address: 307 Westlake Avenue North, Suite 500

institute: Seattle Children's Research Institute

summary: Array analysis of total lung RNA obtained from mice 12,16,24 h post infection with influenza. Strains used were Mock, PR8, X31, VN62 (1x10^5pfu)

overall_design: Time Point: 12, 16, 24 h post infection (Mock, PR8, X31, VN62); Mock group has three biological replicates, virally infected groups have nine replicates.

first: Alan

last: Aderem


title: Gene expression profile of gliadin effects on intestinal epithelial cells suggests novel non-enzymatic functions of pepsin and trypsin

status: Public on Mar 21 2013

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

summary: Gliadin triggers T-cell mediated immunity in celiac disease, and has cytotoxic effects on enterocytes mediated through obscure mechanisms. In addition, gliadin transport mechanisms, potential cell surface receptors and gliadin-activated downstream signaling pathways are not completely understood. In order to screen for novel downstream gliadin target genes we performed a systematic whole genome expression study on intestinal epithelial cells. Undifferentiated Caco-2 cells were exposed to pepsin- and trypsin- digested gliadin (PT-G), a blank pepsin-trypsin control (PT) and to a synthetic peptide corresponding to gliadin p31-43 peptide for six hours. RNA from four different experiments was used for hybridization on Agilent one color human whole genome DNA microarray chips. The microarray data were analyzed using the Bioconductor package LIMMA. Genes with nominal p < 0.01 were considered statistically significant. Compared to the untreated cells 1705, 1755 and 211 probes were affected by PT-G, PT and p31-43 respectively. 46 probes were significantly different between PT and PT-G treated cells. Among the p31-43 peptide affected probes, 10 and 21 probes were affected by PT-G and PT respectively. Only PT-G affected genes could be validated by quantitative real-time polymerase chain reaction. All the genes were, nonetheless, also affected to a comparable level by PT treated negative controls. In conclusion, we could not replicate previously reported direct effects of gliadin peptides on enterocytes. The PT-G affected genes in the microarray analysis were validated by qRT-PCR, however these genes were also affected by PT treated negative controls suggesting that certain epitopes derived from pepsin and trypsin may also affect epithelial cell gene transcription. Our study demonstrates novel non-enzymatic effects of pepsin and trypsin on cells and calls for proper controls in pepsin and trypsin digested gliadin experiments. It is conceivable that gliadin effects on enterocytes are secondary mediated through oxidative stress, NFkB activation and IL-15 up-regulation.

overall_design: In total, 16 samples were analyzed of which 4 were control (MED) samples, 4 samples of p31-43 treatment, 4 samples of PT treatmetn and 4 samples of PT-G treatment

first: Amarjit

last: Parmar

first: Jarkko

last: Venäläinen

first: Massimiliano

last: Gentile

first: Emma

last: Dukes

first: Päivi

last: Saavalainen


title: Brain microvessel: Alzheimer disease vs normal

status: Public on Mar 29 2013

city: Lubbock

first: Uzma

last: Qaisar

state: TX

institute: Texas Tech University

summary: The enigma that is Alzheimer's disease (AD) continues to present daunting challenges for effective therapeutic intervention. The lack of disease-modifying therapies may, in part, be attributable to the narrow research focus employed to understand this complex disease. Most studies into disease pathogenesis are based on a priori assumptions about the role of AD lesion-associated proteins such as amyloid-β and tau. However, the complex disease processes at work may not be amenable to single-target therapeutic approaches. Genome-wide expression studies provide an unbiased approach for investigating the pathogenesis of complex diseases like AD. A growing literature suggests a role for cerebrovascular contributions to the pathogenesis of AD. The objective of the current study is to examine human brain microvessels isolated from AD patients and controls by microarray analysis. Differentially expressed genes with more than 2-fold change are used for further data analysis. Gene ontology analysis and pathway analysis algorithms within GeneSpringGX are employed to understand the regulatory networks of differentially expressed genes. Twelve matched pairs of AD and control brain microvessel samples are hybridized to Agilent Human 4 × 44 K arrays in replication. We document that more than 2,000 genes are differentially altered in AD microvessels and that a large number of these genes map to pathways associated with immune and inflammatory response, signal transduction, and nervous system development and function categories. These data may help elucidate heretofore unknown molecular alterations in the AD cerebromicrovasculature.

overall_design: Two condition experiment, diseased vs normal, our study included 12 pairs of biological replicates and each pair was repeated with dye swap making total of 24 double channel hybridizations. we excluded 4 samples for not passing QC. So 20 samples were included in the data analysis.

first: Shu

last: Wang


title: Upregulation of ERBB3 by FOXD3, an adaptive response to RAF and MEK inhibitors

city: PHILADELPHIA

first: Adam

last: Ertel

address: 233 S 10TH ST

department: Cancer Biology

institute: Thomas Jefferson University

summary: To understand the transcriptional impact of FOXD3 in melanoma cells, we utilized a microarray approach. We collected RNA from three unrelated mutant B-RAF melanoma cell lines (WM115, WM793, and A375) that were engineered to inducibly express FOXD3 or the control gene, β-galactosidase (LacZ), after 5 days of transgene induction. This time point was chosen based on maximal phenotypic changes previously observed. Comparison of gene signatures between the 3 cell lines produced approximately 2,600 common genes differentially regulated by FOXD3-expressing cells compared to the LacZ controls.

overall_design: Three unrelated mutant B-RAF melanoma cell lines (WM115, WM793, and A375) were induced to express FOXD3 and compared against the same cell lines expressing the control gene, β-galactosidase (LacZ).

first: Ethan

last: Abel

first: Paolo

last: Fortina

first: Andrew

last: Aplin


title: Gene expression in tolerogenic TGFb-treated macrophages

status: Public on Mar 22 2013

city: Louisville

first: Michele

last: Kosiewicz

state: KY

address: 319 Abraham Flexner Way, Rm 405

department: Microbiology & Immunology

institute: University of Louisville

summary:
F4/80+ macrophages treated with TGFb2 are potently tolerogenic.  Our understanding of the molecular mechanisms mediating the development of these tolerogenic properties is incomplete.
We used microarray analysis to identify molecules that are involved in the tolerogenic mechanisms in murine TGFb-treated macrophages.

overall_design: Thioglycolate-elicited peritoneal exudate cells (F4/80+ macrophages) were treated with either PBS or TGFb2 overnight then total RNA extracted and subjected to microarray analysis.


title: Systems-wide RNAi analysis of different chr13 genes in colorectal cancer cell line (SW480)

status: Public on Apr 05 2013

city: Göttingen

first: Tim

last: Beissbarth

address: Humboldtallee 32

department: Medical Statistics

institute: University Medical Center Göttingen

summary: Expression profiles were generated for eight genes located on chromosome 13 following RNAi to enable the determination of gene specific LOF RNAi signatures in the colorectal cancer cell line SW480.

overall_design: Triplicate transfections of SW480 cells were performed using two different siRNA duplexes corresponding to each gene target in 6-well plates using the same protocol scaled 30-fold. RNA was purified 72 hrs after transfection. RNA was also purified from negative control siRNA-transfected cells (AllStar siNegative (siNEG), Qiagen). Reduction in target mRNA levels was confirmed by real-time PCR prior to the array analysis.

first: Jordi

last: Camps

first: Jason

middle: J

last: Pitt

first: Georg

last: Emons

first: Amanda

last: Hummons

first: Chanelle

last: Case

first: Marian

last: Grade

first: Tamara

last: Jones

first: Quang

middle: T

last: Nguyen

first: B

last: Ghadimi

first: Michael

last: Difilippantonio

first: Natasha

last: Caplen

first: Thomas

last: Ried


title: Combination of celecoxib and sorafenib provides synergistic antiproliferative and proapoptotic effects in human liver cancer cells

city: Quebec

first: Dimcho

last: Bachvarov

state: Quebec

address: 9, rue McMahon

department: Medicine

institute: Laval university

summary: Molecular targeted therapy has shown promise as a treatment for advanced hepatocellular carcinoma (HCC). Sorafenib, a multikinase inhibitor, recently received FDA approval for the treatment of advanced HCC. However, although sorafenib is well tolerated, concern for its safety has been expressed. Celecoxib (Celebrex®) is a selective cyclooxygenase-2 (COX-2) inhibitor wich exhibits antitumor effects in human HCC cells. The present study examined the interaction between celecoxib and sorafenib in two human liver tumor cell lines HepG2 and Huh7. Our data showed that each inhibitor reduced cell growth and the combination of celecoxib with sorafenib synergistically inhibited cell growth and increased apoptosis. To better understand the molecular mechanisms underlying the synergistic antitumor activity of combination, we investigated the expression profile of the combination-treated liver cancer cell lines, using microarray analysis. Combination treatment significantly altered expression levels of 1,986 and 2,483 transcripts in HepG2 and Huh7 cells, respectively. Genes, functionally involved in cell death, signal transduction and regulation of transcription were predominantly up-regulated, while genes implicated in metabolism, cell cycle control and DNA replication and repair were mainly down-regulated upon treatment. However, combination-treated HCC cell line displayed specificity in the expression and activity of crucial factors involved in hepatocarcinogenesis. The altered expression of some of these genes was confirmed by semiquantitative and quantitative RT-PCR and by Western blotting. Many novel genes emerged from our transcriptomics analyses, and further functional analyses may determine whether these genes can serve as potential molecular targets for more effective anti-HCC strategies.

overall_design: To identify new potential mechanisms of combined action of celecoxib and sorafenib, their effects on global gene expression in both cell lines were investigated and compared using the DNA microarray technology. Agilent 44K Human Whole Genome Oligonucleotide Microarrays (containing ~44,000 genes) were used to identify global gene expression changes in the HepG2 and Huh7 hepatocellular carcinoma (HCC) cell lines, following simultaneous treatment with 50 µM celecoxib and 7.5 µM sorafenib for 48 hours. All microarray experiments (a total of four) were performed in duplicates applying dye-swaps to avoid labeling bias.


title: RNASET2-silenced and control OVCAR3 cell clones injected into nude mice.

city: Varese (VA)

first: Marco

last: Fabbri

address: via dunant 5

country: Italy

institute: Università dell'Insubria

summary: To investigate the molecular pathways underlying RNASET2-mediated tumor suppression in vivo, we investigated the gene expression profile of tumor samples obtained from control and  RNASET2-silenced OVCAR3  xenografts,  respectively. In order to evaluate the contribution of human cancer cells and the murine host stroma to RNASET2-mediated tumorigenesis responses, total RNA extracted from tumor xenografts derived from six independent OVCAR3 cell clones (three parental and three RNASET2-silenced clones) was fluorescently labeled and hybridized to  human Agilent whole-genome microarrays.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Control and  RNASET2-silenced OVCAR3 were injected subcutaneously into  nude mice. After 39 days mice were sacrified, tumors were extracted and total RNA purified.

first: Laura

last: Monti

first: Maria

last: Sacco

first: Angelo

last: Collotta

last: Gribaldo

first: Francesco

last: Acquati

first: Roberto

last: Taramelli


title: Gene expression signatures in miR-29c overexpressed gastric cancer cells.

status: Public on Mar 27 2013

city: Yufu-city

first: Yoshiyuki

last: Tsukamoto

state: Oita

address: hasamacho idaigaoka 1-1

department: Molecular Pathology

institute: Oita university, Faculty of Medicine

summary: To explain the mechanism that miR-29c affects the cell proliferation, we attempted to identify the miR-29c target genes in gastric carcinoma. The expression profiles in MKN45, MKN7 and MKN74 cells transfected with miR-29c oligo or Negative control oligo were obtained from microarray analysis. Then, the genes differentially expressed (Fold change >= 2.0) in miR-29c-transfected cells compared with negative control-transfected ones were identified in each cell lines, respectively. The differentially expressed genes shared among 3 cell lines were identified as the candidates for miR-29c targets.

overall_design: Human gastric cancer cell lines, MKN45, MKN74 and MKN7 were transfected with miR-29c oligo or negative control oligo (n=2) (Ambion). At 24h after, total RNA was extracted and microarray analysis was performed. The genes with common expression changes among three cell lines miR-29c-transfected were identified as the candidates for miR-29c targets.

first: Chisato

last: Nakada


title: Gene profiles of pathway interference downstream neurofibromin signaling

status: Public on Mar 15 2013

city: Detroit

last: Tainsky

state: MI

address: 110 E Warren  Room 311

department: Center for Molecular Medicine and Genetics

institute: Wayne State University

summary: Malignant peripheral nerve sheath tumor (MPNST) is a type of soft tissue sarcoma that occurs in carriers of mutations in the neurofibromatosis type I gene (Nf1) as well as sporadically.　Plexiform neurofibromas in NF1 patients have a significant risk of developing into MPNSTs leading to increased morbidity and mortality from this syndrome.　Surgery is the primary intervention but it is not always effective due to the tendency of MPNSTs to infiltrate the surrounding tissue or grow in an inoperable location.  Neurofibromin, the protein coded by the Nf1 gene, functions as a GTPase activating protein (GAP) whose mutation leads to constitutive activation of RAS and mitogen-activated protein kinase (MAPK) signaling in NF1 patients’ tumors.  However, therapeutic targeting of RAS and MAPK have had limited success (Kalamarides, et al., 2012).    　In this study, we modulated NRAS, MEK1/2 and neurofibromin levels in MPNST cell lines and determined the global gene expression changes that were associated with each experimental condition.  Furthermore, gene expression changes due to neurofibromin deficiency but independent of NRAS and MEK1/2 regulation were characterized for the first time in MPNST cell lines.

overall_design: There are total 4 comparison scenarios. Each scenario has two different samples to compare and each sample has three replicates. Comparison 1: ST88-14 cell line versus normal human schwann cell; comparison 2: U0126 treated ST88-14 versus DMSO treat ST88-14 as control; comparison 3: siNRAS treated ST88-14 versus scrambled control treated ST88-14 cell line; comparison 4: siNf1 treated STS26T cell line versus scrambled control RNA treated STS26T cell line.

first: Daochun

last: Sun

first: Ramsi

last: Haddad


title: Human peripheral IL-10-secreting vs non- IL-10-secreting B cells

status: Public on Mar 04 2013

city: Davos Platz

first: Willem

last: van de Veen

address: Oberestrasse 22

country: Switzerland

institute: Swiss Institute of Allergy and Asthma Research

summary: Transcriptional profiling of human peripheral B cell subsets sorted by flow cytometry based on the secretion of IL-10 in response to CpG2006 stimulation. Goal was to identify molecular markers to distinguish IL-10-producing B cells form non-IL-10-producing B cells.

overall_design: Two-condition experiment, non-IL-10-secreting B cells vs. IL-10-secreting B cells. Healthy donors. Biological replicates: 6

first: Mübeccel

last: Akdis


title: A role for the nucleoporin Nup170p in chromatin structure and gene silencing [Agilent ChIP-chip]

status: Public on Feb 28 2013

city: Nanjing

first: Yakun

last: Wan

address: Sipailou #2

institute: Southeast University

type: Genome binding/occupancy profiling by array

summary: Embedded in the nuclear envelope, nuclear pore complexes (NPCs) not only regulate nuclear transport, but also interface with both transcriptionally active euchromatin and largely silenced heterochromatin, as well as the boundaries between these regions. It is unclear what functional role NPCs play in establishing or maintaining these distinct chromatin domains. Here we report that the yeast NPC protein Nup170p interacts with specific regions of the genome containing ribosomal protein and subtelomeric genes. At these locations, Nup170p functions to establish normal nucleosome positioning and as a repressor of transcription. We show that the function of Nup170p in subtelomeric gene silencing is linked to its association with the RSC chromatin-remodeling complex and the silencing factor Sir4p, and that the binding of Nup170p and Sir4p to subtelomeric chromatin is cooperative and necessary for the association of telomeres with the nuclear envelope. Our results establish the NPC as an active participant in the formation of peripheral heterochromatin.

overall_design: The genome-wide localization profiles of Nup170p and Nup157p were determined by chromatin immunoprecipitation and DNA microarray analysis using agilent whole genome Saccharomyces cerevisiae arrays.  In addition, the localization profile of Nup170p was determined in sir4∆ and yku70∆ strains.

first: David

middle: W

last: Van de Vosse

first: Diego

last: Lapetina

first: Wei-Ming

last: Chen

first: Jung-Hsien

last: Chiang

first: John

last: Aitchison

first: Richard

last: Wozniak


title: Gene expression regulation by miR-145 in pancreatic cancer

status: Public on Mar 19 2013

city: Baltimore

first: Tai-Chung

last: Huang

state: MD

address: 733 N Broadway BRB R560

department: Institute of Genetic Medicine

institute: Johns Hopkins University School of Medicine

summary: miR-145 is a tumor suppressor miRNA in various malignancies including pancreatic cancer. Identification of miR-145 targets can lead to more understanding of the development of pancreatic cancer. Therefore, in this project, we aimed to characterize the changes of transcriptomes caused by miR-145 to identify more miR-145 target transcripts.

overall_design: cDNA microarray was used to compare transcriptomes 48 hr after transfection of miR-145 mimics or control scramble RNA in a pancreatic cancer cell line, Mia-PaCa2.

first: Tai

first: Yi

last: Yang

first: Akhilesh

last: Pandey


title: The differentiation stage of p53- and Rb-deficient bone marrow mesenchymal stem cells imposes the phenotype of in vivo sarcoma development (part II)

status: Public on Jan 28 2013

city: Armilla

first: Alberto

last: Labarga

state: Granada

address: Av. Innovacion 1

institute: Experimental Serendipity S.L.

summary: We have previously reported that the deficiency of p53 alone or in combination with Rb (Rb-/- p53-/-) in adipose-derived MSCs (ASCs) promotes leiomyosarcoma-like tumors in vivo. Here, we hypothesized that the source of MSCs and/or the cell differentiation stage could determine the phenotype of sarcoma development. To investigate whether there is a link between the source of MSCs and sarcoma phenotype, we generated p53-/- and Rb-/-p53-/- MSCs from bone marrow (BM-MSCs). Both genotypes of BM-MSCs initiated leiomyosarcoma formation similar to p53-/- and Rb-/-p53-/- ASCs. In addition, gene expression profiling revealed a link between p53- or Rb-p53-deficient BM-MSCs and ASCs and muscle-associated sarcomagenesis. These data suggest that the tissue source of MSC does not seem a crucial factor in the development of a particular sarcoma phenotype. To analyze whether the differentiation stage defines the sarcoma phenotype, BM-MSCs and ASCs were induced to differentiate towards the osteogenic lineage, and both p53 and Rb were excised using Cre-expressing adenovectors at different stages along osteogenic differentiation. Regardless of the level of osteogenic commitment, the inactivation of Rb and p53 in BM-MSC-derived, but not in ASC-derived, osteogenic progenitors gave rise to osteosarcoma-like tumors which could be serially transplanted. This indicates that the osteogenic differentiation stage of BM-MSCs imposes the phenotype of in vivo sarcoma development, and that BM-MSC-derived osteogenic progenitors rather than undifferentiated BM-MSCs, undifferentiated ASCs or ASC-derived osteogenic progenitors, represent the cell of origin for osteosarcoma development.

overall_design: To analyse whether the BM-MSC and Fat-MSC (ASC) differentiation stage may define the sarcoma phenotype, RbloxP/loxPp53loxP/loxP BM-MSCs and ASCs were induced to differentiate towards the osteogenic lineage and both Rb and p53 were excised with adenoviral vectors expressing the Cre-recombinase gene (Ad-CMV-Cre) at different stages (day 0 and 10) along osteogenic differentiation. NSG mice were inoculated subcutaneously with 5×10^6 mutant cells. Animals were killed when tumors reached 1 cm3 or 150 days after infusion. Some of the obtained tumors were mechanically disaggregated to establish ex vivo MSC-transformed cell lines. Gene expression analysis was performed using: WT BM-MSCs and ASCs, Rb-/-p53-/- BM-MSCs and ASCs previously differentiated to the osteogenic lineage for 10 days and a tumor cell line derived from p53-/-Rb-/- BM-MSC differentiated to the osteogenic lineage for 10 days.

first: Ruth

last: Rubio

first: Pablo

last: Menendez

first: Rene

last: Rodriguez


title: Gene expression profiling of human NK cells

status: Public on Feb 10 2013

city: He fei

first: yan

middle: fu

last: Wang

address: 443 huangshan road

institute: University of Science and Technology of China

summary: To investigate novel molecular signatures and transcriptional regulators of immature and mature human NK cells, we performed whole-genome microarray analysis on dNK cells (CD3−CD56+), cNK cells (CD3−CD56+), pNK cells (CD3−CD56+), CD56+ T cells (CD3+CD56+) and T cells (CD3+CD56−). dNK cells were purified from first-trimester deciduas. cNK  cells were puriﬁed from cord-blood mononuclear cells. pNK, CD56+ T and T cells were purified from adult peripheral blood mononuclear cells. Samples were collected from healthy adult donors after obtaining informed consent according to the Ethics Committee of the University of Science & Technology of China.

overall_design: We performed human whole-genome microarray analysis on purified NK cells from normal human decidua during the first trimester of pregnancy, cord blood, and adult peripheral blood; peripheral CD56+ T cells and T cells were used as controls.

first: Fuyan

last: wang

first: Yonggang

last: Zhou

first: Binqing

last: Fu

first: Ruya

last: Zhang

first: Rui

last: Sun

first: Zhigang

last: Tian

first: Haiming

last: Wei


title: Gene expression profile in spleens of congenic mice 24 hours after total body irradiation.

status: Public on Feb 21 2013

city: Salt Lake City

first: Thai

last: Cao

address: 30 North 1900 East, SOM5C402

institute: University of Utah

summary: The Gvh1 gene loci was identified by linkage analysis in a segregating mouse backcross.  Congenic mapping has refined the linked loci to a 1.3 Mb interval on mouse Chr16 (39.41 - 40.71Mb) that constitutes the congenic interval in the B10.BALB-16.C2A mouse line.  Gene expression microarray was performed to characterize downstream transcripitional regulation by risk variants in the congenic interval;.

overall_design: Each individual sample was pooled from 3 mice and performed in triplicate for each experimental group (TBI 900 cGy versus 0 cGy) for statistical analysis.

middle: M


title: Microarray analysis of wildtype, Klf3 H275R homozygous and heterozygous, Klf3 CH gene trap homozygous and heterozygous E12.5 embryos

status: Public on Jan 31 2013

city: University of NSW

first: Alister

last: Funnell

address: School of Biotechnology and Biomolecular Sciences

institute: University of NSW

summary:
The aim of this experiment was to investigate the dysregulation of gene expression in whole E12.5 embryos containing a gene trap (CH) or point mutation (H275R) within the Klf3 gene
Affymetrix microarrays were performed on RNA from wildtype, Klf3 H275R/H275R, Klf3 H275R/+, Klf3 CH homozygous and Klf3 CH heterozygous E12.5 embryos

overall_design: Four wildtype replicates, three Klf3 H275R/H275R replicates, four Klf3 H275R/+ replicates, four Klf3 CH homozygous replicates and two Klf3 CH heterozygous replicates of whole E12.5 embryos, litter-matched where possible.

middle: P

first: Merlin

last: Crossley

first: S

last: Adamson