title: The differences between CD166+ pancreatic cancer cells and CD166- cells

summary: Microarray analyses using CD166+ and CD166- pancreatic cancer cell lines from both Panc-1 and SW1990 cells.

overall_design: We carried out microarray analyses using the CD166+ and CD166- separated cells from both Panc-1 and SW1990. The quality of the RNA samples was evaluated using a 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany). We used a Human HT-12v4 Expression BeadChip (Illumina, San Diego, CA) for these analyses. The data were analyzed using BeadStudio software version 3.2.3 (Illumina).

first: Masafumi

last: Sada

first: Kohei

last: Horioka

first: Charles

middle: D

last: Ulrich III

first: Shunichi

last: Takahata


title: Identification of mechano- and/or 5Aza-sensitive genes in mouse carotid artery endothelium in vivo exposed to disturbed blood flow for 7 days

status: Public on Mar 25 2014

city: Atlanta

first: Jessilyn

last: Dunn

state: GA

address: 1760 Haygood Drive HSRB E197

department: Biomedical Engineering

country: USA

institute: Georgia Tech & Emory University

summary: Atherosclerosis preferentially occurs in arterial regions of disturbed blood flow (d-flow), which alters gene expression, endothelial function, and atherosclerosis. Here, we show that d-flow regulates genome-wide DNA methylation patterns in a DNA methyltransferase (DNMT)-dependent manner. D-flow induced expression of DNMT1 in mouse arterial endothelium in vivo and in cultured endothelial cells by oscillatory shear (OS) in vitro. The DNMT inhibitor 5-Aza-2’deoxycytidine (5Aza) or DNMT1 siRNA significantly reduced OS-induced endothelial inflammation. Moreover, 5Aza reduced lesion formation in two ApoE-/- mouse atherosclerosis models. To identify the 5Aza mechanisms, we conducted two genome-wide studies: reduced representation bisulfite sequencing (RRBS) and microarray using endothelial-enriched gDNA and RNA, respectively, from the partially-ligated left carotid artery (LCA exposed to d-flow) and the right contralateral control (RCA) of mice treated with 5Aza or vehicle. Systems biological analyses using RRBS and transcriptome data revealed 11 mechanosensitive genes whose promoters were hypermethylated under d-flow conditions, but rescued by 5Aza treatment. Of those, the two transcription factors HoxA5 and Klf3 contain cAMP- response-elements, and their methylation status could serve as a mechanosensitive master switch in gene expression. Our results demonstrate that d-flow controls epigenomic DNA methylation patterns in a DNMT-dependent manner, which in turn alters endothelial gene expression and induces atherosclerosis.

overall_design: We used 6- to 8-week-old male C57Bl/6 mice (The Jackson Laboratory) according to the approved Institutional Animal Care and Use Committee protocol by Emory University. Mice were subjected to partial carotid ligation surgery under anesthesia. Brieﬂy, 3 of 4 caudal branches of LCA (left external carotid, internal carotid, and occipital artery) were ligated with 6-0 silk suture, although the superior thyroid artery was left intact. Development of low and oscillatory blood flow in the Left Carotid Artery of each mouse was determined by ultrasound measurements. Each sample contained total RNA from 3 pooled RCAs or LCAs. We ran 3 samples of LCA, RCA, AzaLCA, and AzaRCA on 2 microarrays.

middle: P

first: Hanjoong

last: Jo

first: Chanwoo

last: Kim


title: Targeting Csnk1a1 induces selective p53-dependant killing of leukemia stem cells

status: Public on Feb 23 2014

city: Cambridge

first: Fatima

last: Al-Shahrour

state: MA

address: 7 Cambridge Center

department: Cancer program

institute: Broad Institute of MIT and Harvard

summary: We found found that casein kinase 1 alpha (Csnk1a1), a serine threonine kinase and negative regulator of beta catenin, is essential for leukemia cells in vivo.

overall_design: We examined the effect of Csnk1a1 knowckdown by gene expression profiling in primary leukemia cells.

first: Marcus

last: Järås

first: Peter

middle: G

last: Miller

first: Lisa

last: Chu

first: Rebekka

middle: K

last: Schneider

first: Rishi

middle: V

last: Puram

first: Jordan

last: Breyfogle

first: Emma

last: Fink

first: Kimberly

middle: A

last: Hartwell

first: Marie

middle: E

last: McConkey

first: Glenn

middle: S

last: Cowley

first: David

last: Root

first: Michael

last: Kharas

first: Ann

last: Mullally

first: Benjamin

middle: L

last: Ebert


title: Genome-wide characterization of a novel necrotic granuloma model of latent tuberculosis infection and reactivation in mice

status: Public on Feb 20 2014

city: Baltimore

first: Noton

last: Dutta

state: MD

address: 1550 Orleans Street, Room 110

department: Medicine

institute: Johns Hopkins University

summary:
We sought to develop and characterize a novel paucibacillary model in mice, which develop necrotic lung granulomas following infection with Mycobacterium tuberculosis.
Paucibacillary infection was established, recapitulating the sterilizing activities of human LTBI regimens. TNF neutralization led to increased lung bacillary load, disrupted granuloma architecture with expanded necrotic foci and reduced tissue hypoxia, and accelerated animal mortality. TNF-neutralized mouse lungs and sera showed significant upregulation of IFNγ, IL-1β, IL-6, IL-10, CCL2, CCL3, and matrix metalloproteinase genes

overall_design: Six weeks after aerosol-immunization with recombinant M. bovis BCG overexpressing the 30-kilodalton antigen, C3HeB/FeJ mice were aerosol-infected with M. tuberculosis H37Rv. Six weeks later, mice were treated with one of three standard regimens for latent TB infection (LTBI) or TNF-neutralizing antibody. Mouse lungs were analyzed by histology, positron emission tomography/computed tomography, whole-genome microarrays, and RT-PCR. Lungs and sera were studied by multiplex enzyme-linked immunosorbent assays

first: Petros

middle: C

last: Karakousis


title: Gene expression comparison of microRNA-181d Transgenic and microRNA-181d Knock-in thymocytes

city: Dallas

first: Nicolai S.C.

last: van Oers

state: Texas

address: 6000 Harry Hines Blvd

department: Immunology

institute: University of Texas Southwestern Medical Center

summary: T cell-specific over-expression of microRNA-181d reduced number of immature CD4+CD8+ thymocytes.

overall_design: Whole thymus tissues were isolated from the miR-181d transgenic (Tg-8) and miR-181d knockin (KI) mice, followed by total RNA isolation.

first: Serkan

last: Belkaya

first: Nicolai


title: Different gene expression profile in acute coronary sindrome (ACS) patients compared to stable angina(SA) patients.

status: Public on Feb 14 2014

city: Napoli

first: Liberato

middle: Pia

last: Berrino

address: via costantinopoli

department: Medicina Sperimentale

country: Italy

institute: Seconda Università degli Studi di Napoli

summary: We have employed whole genome microarray expression profiling as a discovery platform to identify genes involved in plaque rupture. Human coronary artery endothelial cells (ECs) were stimulated in vitro for 12 hours with plasma obtained from the coronary sinus (CS) and the aorta (Ao) of patients with ACS (n=8), or patients with stable angina (SA, n=4). For each patient, gene expression profile was evaluated by microarray technology in ECs exposed to plasma obtained from CS and compared to that of ECs exposed to plasma sampled from Ao. In patient with ACS we found 684 genes up-regulated and 283 down-regulated was observed as compared to patients with SA. Functional and network analyses of statistically significant gene showed that the up regulated genes were associated to pathways IL17 Signaling. To validate the microarray data the RNAs were used for Real Time PCR experiment.


title: Breast Brain Metastasis, Non-Neoplastic Brain, and Non-Neoplastic Breast Gene Expression

status: Public on Mar 13 2014

city: Phoenix

first: Bodour

last: Salhia

state: AZ

address: 445 N Fifth Street

department: Integrated Cancer Genomics Division

institute: Translational Genomics Research Institute

summary: The central nervous system (CNS) is a common site of metastatic disease in patients with breast cancer and has few therapeutic options with dismal outcomes. The purpose of our study was to identify common and rare events that underlie breast cancer CNS metastasis. We performed deep genomic profiling, which integrated gene copy number, gene expression and DNA methylation datasets on a collection of  breast brain metastases. We identified frequent large chromosomal gains in 1q, 5p, 8q, 11q, and 20q and frequent broad level deletions involving 8p, 17p, 21p and Xq.  Frequently amplified and overexpressed genes included ATAD2, BRAF, DERL1, DNMTRB and NEK2A. The ATM, CRYAB and HSPB2 genes were commonly deleted and underexpressed. Knowledge mining revealed enrichment in cell cycle and G2/M transition pathways, which contained AURKA, AURKB and FOXM1. Using the PAM50 breast cancer intrinsic classifier, Luminal B, Her2+/ER negative, and basal-like tumors were identified as the most commonly represented breast cancer subtypes in our CNS metastasis cohort. While overall methylation levels were increased in breast cancer CNS metastasis, basal-like CNS metastases were associated with significantly lower levels of methylation. Integrating DNA methylation data with gene expression revealed defects in cell migration and adhesion due to hypermethylation and downregulation of PENK, EDN3, and ITGAM. Hypomethylation and upregulation of KRT8 likely affects adhesion and permeability. Genomic and epigenomic profiling of breast CNS metastasis has provided insight into the somatic events underlying this disease, which have potential in forming the basis of future therapeutic strategies.

overall_design: Three sample-types: 35 Breast Brain Metastasis samples, 10 Non-Neoplastic Brain samples, and 10 Non-Neoplastic Breast samples.

first: B

first: J

last: Ross


title: Genome-wide analysis of gene expression changes accompanied with up-regulation of GATA1 in murine hematopoietic stem/progenitors

status: Public on Feb 18 2014

city: Fukuoka

first: Kohta

last: Miyawaki

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

country: Japan

institute: Kyushu University

summary: Analysis of hematopoietic stem/progenitors from GATA-1-GFP transgenic mouse bone marrow at gene expression level. Results provide changes in gene expression pattern accompanied with up-regulation of GATA-1 transcription factor at early stage of murine adult hematopoiesis.

overall_design: RNA samples obtained from isolated GATA1+LSK and other hemaopoietic stem/progenitor populations including GATA1-LSK, LMPP, CMP and LT-HSC were subjected to mRNA amplification and cDNA microarray analysis.


title: Argonaute2 mediates compensatory expansion of the pancreatic ß-cell

status: Public on Feb 06 2014

city: Rehovot

first: Jean

last: Hausser

address: Herzl St.

country: Israel

institute: Weizmann Institute of Science

summary: Pancreatic ß-cells adapt to compensate for the increased metabolic demand during insulin resistance. While the microRNA pathway has an essential role in the expansion of ß-cell mass, the extent of its contribution is unclear. Here we show that miR-184 is silenced in the pancreatic islets of several insulin-resistant mouse models and in the islets of type-2 diabetic human subjects. Reduction of miR-184 promotes the expression of its target Argonaute2 (Ago2), a component of the microRNA-induced silencing complex. While over-expression of Ago2 increased ß-cell proliferation, conditional deletion decreased ß-cell number. Moreover, restored expression of miR-184 in leptin-deficient ob/ob mice decreased Ago2 and prevented compensatory ß-cell expansion. Loss of Ago2 expression during insulin resistance blocked ß-cell growth and relieved the regulation of miR-375-targeted genes including the growth suppressor Cadm1. This study identifies the regulation of Ago2 by miR-184 as an essential component of the compensatory response to promote proliferation during insulin resistance.

overall_design: MIN6 cells were transfected with Doxycyline responsive plasmids including the tetO-184 construct in biological triplicates for every time point. The conditions included untransfected control (CTR, induced), Transfected Control (TC, uninduced) along the time points of miR-184 overexpression in 16, 24, 48, and 72 hours of doxycycline treatment.

first: Sudhir

last: Tattikota

first: Thomas

last: Rathjen

first: Sarah

middle: J

last: McAnulty

first: Hans-Hermann

last: Wessels

first: Ildem

last: Akerman

first: Jonathan

last: Esguerra

first: Martijn

last: van de Bunt

first: Anne

last: Musahl

first: Amit

last: Pandey

first: Xintian

last: You

first: Wei

last: Chen

first: Pedro

last: Herrera

first: Louise

last: van der Weyden

first: Allan

last: Bradley

first: Donal

last: O’Carroll

first: Mihaela

last: Zavolan

first: Mark

middle: I

last: McCarthy

first: Anna

last: Gloyn

first: Lena

last: Eliasson

first: Jorge

last: Ferrer

first: Matthew

middle: N

last: Poy


title: The gene expression change of RNF31 depletion in MCF-7 cells

city: Stockholm

first: Chunyan

last: Zhao

address: Hälsovägen 7-9

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

summary: RNF31 is atypical E3 ligase, which is highly expressed in human breast cancers. In order to understand the effect of RNF31 depletion effect in breast cancers, we knocked down the expression of RNF31 in MCF-7 cells. We aim to find the significantly changed pathways and cell biology behavior.

overall_design: 100uM RNF31 siRNA was applied to transfect the MCF-7 cells, while 100uM siControl was used as the control. Cells were cultured in DMEM red medium with 10% of FBS. Seventy two hours of post transfection, the total RNA was extracted to perform RNA expression analysis.

first: Jian

last: Zhu

first: Karin

last: Dahlman-Wright


title: A specific CBP/p300-dependent gene expression program drives the metabolic remodelling in late stages of spermatogenesis.

status: Public on Mar 12 2014

city: La Tronche

first: Sophie

last: Rousseaux

address: Bd de la Chantourne

department: IAB

country: France

institute: INSERM-UGA

summary: Histone hyperacetylation is thought to drive the replacement of histones by transition proteins that occurs in elongating spermatids after a general shut-down of transcription. The molecular machineries underlying this histone hyperacetylation remain still undefined. Here we focused our attention on the role of Cbp and p300 in histone hyperacetylation and in the preceding late gene transcriptional activity in elongating spermatids. A strategy was designed to partially deplete Cbp and p300 in elongating spermatids. These cells progressed normally through spermiogenesis and showed normal histone hyperacetylation and removal. However, a genome-wide transcriptomic analysis, performed in the round and elongating spermatids, revealed the existence of a gene regulatory circuit encompassing genes presenting high expression levels in pre-meiotic cells, undergoing a repressed state in spermatocytes and early post-meiotic cells, but becoming reactivated in elongating spermatids, just prior to the global shut-down of transcription. Interestingly, this group of genes was over-represented within the genes affected by Cbp/p300 knock-down and were all involved in metabolic remodelling. This study revealed the occurrence of a tightly regulated Cbp/p300-dependent gene expression program that drives a specific metabolic state both in progenitor spermatogenic cells and in late transcriptionally active spermatids and confirmed a special link between Cpb/p300 and cell metabolism programming previously shown in somatic cells.

overall_design: Total RNA were obtained from post meiotic male germ cells (round spermatids and condensing spermatids) of adult mice either wild-type or with a double knock down of Cbp/P300 in post-meiotic cells. In each experiments, 6 replicates of each genotype and cell type were used.

first: Saadi

last: Khochbin

first: Alexandra

last: Debernardi

first: Faycal

last: Boussouar

first: Afsaneh

last: Goudarzi

first: Philippe

last: Guardiola


title: Sequential combination of decitabine and idarubicin synergistically enhances anti-leukemia effect by demethylating Wnt pathway inhibitor promoters and downregulating Wnt pathway nuclear target

status: Public on Feb 13 2014

city: Ningbo

first: Kongfei

last: Li

state: Zhejiang

address: Baizhang East Road 251#

department: the Department of Hematology

country: China

institute: Ningbo Yinzhou Hospital

summary: Purpose: We aimed to investigate the effect of several anti-leukemia drugs in combination with decitabine (DAC) on the proliferation of myeloid leukemia cells in vitro and in vivo, to select the most efficient combination group and explore associated mechanisms of these combination therapies.   Experimental Design: After comparing with five anti-leukemia drugs in several different kinds of cell lines, the combination effect of idarubicin (IDA) with DAC was best. In vivo, by using microPET, TUNEL, and transmission electron microscopy, the inhibitory effects obtained by sequentially combining DAC with IDA, evidenced by evaluating tumor cell proliferation and cell apoptosis. Molecular studies were conducted using gene chip, which was used to explore associated pathways, and real-time quantitative reverse transcription-PCR, western blot and immunohistochemistry (IHC), used to assess regulation of Wnt/β-catenin pathway.   Results: The sequential combination of DAC and IDA showed synergistic induction of cell death in U937, HEL, SKM-1 and cells isolated from AML patients. Importantly, the inhibition of tumor growth in the sequential combination group was found to be significantly higher than that of single drug group or control group in vivo. Moreover, sequential treatment with DAC and IDA induced apoptosis and depression of the Wnt/β-catenin pathway in both culture and animal studies.   Conclusions: Our findings showed that sequentially combining decitabine with idarubicin had a synergistic anti-leukemia effect. These findings were attributed to demethylation of Wnt pathway inhibitors and downregulation of Wnt pathway nuclear targets observed in vitro and in vivo.

first: Hongyan

last: Tong


title: Comparison of Zfp706GT and ZfpGT REV ES cells in 2i

status: Public on Feb 05 2014

city: Vienna

first: Martin

last: Leeb

address: Dr.-Bohr-Gasse 9/3

department: Max Perutz Labs

country: Austria

institute: University of Vienna

summary: Self-renewal circuitry in embryonic stem (ES) cells is increasingly defined. How the robust pluripotency programme is dissolved to enable fate transition is less appreciated. We developed a forward genetic approach using haploid ES cells. We created libraries of transposon integrations and screened for persistent self-renewal in differentiation permissive culture. This yielded multiple mutants in the FGF/Erk and GSK3/Tcf3 modules known to drive differentiation, and in epigenetic modifiers implicated in lineage commitment. We also identified and validated factors not previously considered. These include the conserved small zinc finger protein Zfp706. Loss of Zfp706 function severely delays the exit from self-renewal. To asses a potential function of Zfp706 in regulation of gene expression we compared transcription profiles between Zfp706 gene trap mutant ES cells and genetic revertants.

overall_design: Assessment of differentially expressed genes in Zfp706 gene trap mutants obtained in a haploid ES cell screen for effectors of ES cell differentiation vs. genetic revertants generated by Flp-e mediated excision of the gene trap cassette

first: Austin

last: Smith


title: Identification of novel metastases-suppressor genes involved in breast cancer brain metastases (BCBM) formation

status: Public on Mar 04 2014

city: Ibbenbüren

first: Dirk

last: Kemming

address: Roggenkampstr.

country: Germany

institute: ELA

summary: Initial screening for potential metastases suppressors down regulated by methylation was performed using breast cancer cell line models specific for site-specific metastasation. Gene expression profiling and qRT-PCR validations were conducted on tumor tissues from primary breast cancer (BC) and BCBM. CADM1 and RECK were further characterized for their methylation patterns and finally the protein expression of CADM1 was validated in a large number of BC and BCBM samples and correlated with clinico-pathologic parameters.

overall_design: A subclone of MDA-MB-231, which has a high metastatic potential for the brain (MDA-MB-231 BR), was compared to the parental MDA-MB-231 WT and to a bone-seeking subclone (MDA-MB-231 SA) in order to find genes, which might be specifically involved in brain metastasis formation. The cell lines were treated with 5-Aza-2'-deoxycytidine in order to find genes potentially down regulated by methylation. The non-tumorigenic epithelial cell line MCF 10A was used to control for stress response after the treatment with 5-Aza-2'-deoxycytidine.

first: Harriet

last: Wikman


title: Leukemia Cell Lines Induce Changes in Bone Marrow Stromal Cells

status: Public on Feb 04 2014

city: BETHESDA

first: PING

last: JIN

address: 9000 ROCKVILLE PIKE

department: DTM

institute: CC/DTM/NIH

summary: Bone marrow derived stromal cells (BMSCs) are a multipotent population that supports angiogenesis, wound healing, immunomodulation and plays an active role in the hematopoietic niche. On the other hand, they are also involved in the nurturing of bone marrow tumors and metastasis, showing a pro-tumorigenic behavior. BMSCs secrete a wide range of cytokines, growth factors and matrix proteins that are likely responsible for many of these effects. However, it is not clear whether this pro-tumorigenic behavior of BMSCs is induced by the tumor cells, neither in what extent the tumor cells affect the type and quantity of factors produced by BMSCs. To determine how tumor cells that arise from bone marrow affect the BMSCs, we selected three myeloid leukemia cell lines (TF-1, TF-1alpha and K562) and co-cultured them with BMSCs from healthy donors. We found that, under co-culture condition, the gene expression profiling of BMSCs revealed up-regulation of many pro-inflammatory signaling related genes, mainly IL-17 signaling-related genes. Moreover, IL-17 signaling-related cytokines CCL2 and IL8, were increased in co-culture supernatants. We conclude that BMSCs react to the presence of leukemia cells undergoing changes in the cytokine and chemokine secretion profile. Thus, BMSCs and leukemia cells both contribute to the creation of a competitive niche more favorable to leukemia stem cells.

overall_design: BMSCs from healthy donors were transwell co-cultured with three different myeloid leukemia cell lines: TF-1 (n=3), TF-1alpha (n=3) and K562 (n=3). A 1-um Transwell system (BDBiosciences, San Jose, CA USA) was used to maintain the cultured BMSC and leukemia cell populations separate from each other. As a control BMSCs were also transwell co-cultured under the same conditions with CD34+ cells (n=9) isolated from G-CSF-mobilized peripheral blood stem cells from healthy donors. An alternative co-culture method was used to analyze BMSCs and leukemia cells in direct contact: TF-1 (n=3), TF-alpha (n=3) and K562 (n=3). The two populations were cultured together in the same well without any membrane separation. BMSCs (n=18), TF-1 (n=3), TF-1alpha (n=3), K562 (n=3) and CD34+ (n=9) cells cultured alone (mono-cultures) were used as controls. Cells from both mono- and co-culture conditions were harvested at 4h, 10h, and 24h.


title: CCL2/CCR2-dependent recruitment of functional antigen-presenting cells into tumors post-chemotherapy

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: Analysis of MCA205 tumors developed in C57bl/6 mice on day 2, 7 and 10 after intratumoral treatment with doxorubicin (DX) or PBS solvent. DX triggers the immunogenicity of dying tumor cell and activates anti-tumor immunity. Results provided insight into molecular basis of DX induced immune response.

overall_design: C57bl/6 mice bearing palpable MCA205 fibrosarcoma tumors (25-45mm2) were treated with DX or PBS intratumorally and tumors were recovered 2, 7 or 10 days post treatment. DX treated samples on day 7 were also divided into responder and non responder groups according to tumor shrinkage.

first: Yuting

last: Ma

first: Stephen

middle: R

last: Mattarollo

first: Sandy

last: Adjemian

first: Heng

last: Yang

first: Laetitia

last: Aymeric

first: Dalil

last: Hannani

first: João-Paulo

last: Catani

first: Helene

last: Duret

first: Kim

last: Steegh

first: Oliver

last: Kepp

first: Gautier

last: Stoll

first: Yidan

last: Wang

first: Antonella

last: Sistigu

first: Lorenzo

last: Galluzzi

first: Laurence

last: Zitvogel

first: Mark

last: Smyth

first: Guido

last: Kroemer


title: Beneficial Metabolic Effects of Rapamycin are Associated with Enhanced Regulatory Cells in Diet-Induced Obese Mice.

status: Public on Feb 01 2014

city: Lille

first: kassem

last: makki

address: 1, rue du Pr Calmette

institute: CNRS UMR8199

summary: Analysis of rapamycin effects on white adipose tissue at gene expression level. The hypothesis tested in the present study was that rapamycin could modify immune cell composition and inflammatory state of the adipose tissue of obese mice.

overall_design: Total RNA prepared from the adipose tissue of obese mice treated with rapamycin or its excipient solution (referred as vehicle), compared to adipose tissue of lean mice.

first: Kassem

last: MAKKI

first: Isabelle

last: WOLOWCZUK

first: Philippe

last: FROGUEL


title: Microarray analysis of B16 cells in pigmentation oscillator

status: Public on Feb 03 2014

city: Delhi

first: Vivek

middle: T

last: Natarajan

state: Delhi

address: Mathura Road

country: India

institute: CSIR-IGIB

summary: Cellular homeostasis is an outcome of complex interacting processes with nonlinear feedbacks that span spatiotemporal scales. Skin tanning is one such dynamic response that maintains genome integrity of epidermal cells. While pathways underlying hyperpigmentation cascade are recognized, negative feedback regulatory loops that can dampen the activated melanogenesis process are not completely understood. By designing a pigmentation oscillator, in this study we delineate the role of interferon gamma (IFN-γ) signaling in skin pigmentation homeostasis. IFN-γ signaling reversibly controls maturation of the key organelle melanosome by concerted regulation of several pigmentation genes. We show that this temporal effect is mediated through interferon regulatory factor-1 (IRF-1) independent of the central regulator microphthalmia-associated transcription factor (MITF). Chronic expression of IFN-γ in mouse and human skin shows hypopigmentation phenotype, further providing a strong support to the under-appreciated function of IFN-γ in skin pigmentation. Our studies thus reveal the hitherto missing link between immune system and pigmentation, which may have implications in depigmentary and malignant cutaneous disorders.

overall_design: there are 12 samples from two consecutive cycles of pigmentation oscillator, termed set 1 and set 2 analysis is performed wrt to day 0 of first cycle

first: Parul

last: Ganju

first: Vinaya

last: Vijayan

first: Chetan

last: Gadgil

first: Rajni

last: Rani

first: K

first: Rajesh

last: Gokhale


title: Cyclin D1 Transgenic Mice with Bim-deficient B-cells

city: New Haven

first: Hailong

last: Meng

state: CT

address: 300 George Str

institute: Yale University

summary: Expression analysis from a genetically engineered mouse model of mantle cell lymphoma (MCL)

overall_design: Gene expression was measured in fourteen mice that overexpress cyclin D1 and delete Bim in their B cells and that were stimulated with sheep red blood cells (SRBC) and irradiation (I), pristane (P) or only SRBC weekly (A).  Mice that developed disease based on histopathologic criteria were compared to ones that did not.  An additional seven stimulated mice that only overexpressed cyclin D1 were used to estimate the data set variance.

first: Samuel

last: Katz

first: Loren

last: Walensky

first: Steven

middle: H

last: Kleinstein


title: Characterization of Gene Expression in liver cell

status: Public on Jan 31 2014

city: ShangHai

first: Yang

last: Bu

address: 180 Fenglin Road

institute: Liver Cancer Institute, Zhongshan Hospital, Fudan University

summary:
The Human Agilent 60-mer, oligonucleotide microarray consists of a total of  probes covering 41,096 genes of human. Through a validation study, total RNA isolated from liver cells were used for comparison of gene expression profiles via microarray examination. A list of significantly differentially expressed genes was generated;
267 genes were  up-regulated genes, and 65 genes were  down-regulated genes.

overall_design:
The Agilent microarray platform is based upon the hybridization of a single labeled sample (derived from RNA), followed by one-channel detection. The intensity of the hybridization signal is used to determine target concentration. In order to validate the technical quality of each probe in our arrays, we carried out 6 independent hybridizations on samples   To examine the gene expression profiles between rice root and shoot development, total RNA extracted from cell lines were processed on the Agilent microarray following the standard protocol using five arrays for each tissue type. Raw expression data from 6 microarrays  were normalized and Pearson’s correlation coefficients were calculated for the data sets of hybridization signal intensities.
Oxaliplatin-resistant MHCC97H liver cell line treated with Oxaliplatin or control.

first: Qing

last: Jia


title: Comparison of gene expression in cardiac macrophages from P1 or P14 mice 3 days following MI

first: Arin

middle: B

last: Aurora

state: TX

department: Molecular Biology

institute: UT Southwestern Medical Center

summary: Myocardial infarction (MI) leads to cardiomyocyte death, which triggers an immune response that clears  debris and restores tissue integrity. In the adult heart, the immune system facilitates scar formation, which  repairs the damaged myocardium but compromises cardiac function. In neonatal mice, the heart can regenerate  fully without scarring following MI; however, this regenerative capacity is lost by P7. The signals that  govern neonatal heart regeneration are unknown. By comparing the immune response to MI in mice at P1  and P14, we identified differences in the magnitude and kinetics of monocyte and macrophage responses to  injury. Using a cell-depletion model, we determined that heart regeneration and neoangiogenesis following MI  depends on neonatal macrophages. Neonates depleted of macrophages were unable to regenerate myocardia  and formed fibrotic scars, resulting in reduced cardiac function and angiogenesis. Immunophenotyping and  gene expression profiling of cardiac macrophages from regenerating and nonregenerating hearts indicated  that regenerative macrophages have a unique polarization phenotype and secrete numerous soluble factors  that may facilitate the formation of new myocardium. Our findings suggest that macrophages provide necessary  signals to drive angiogenesis and regeneration of the neonatal mouse heart. Modulating inflammation  may provide a key therapeutic strategy to support heart regeneration.

overall_design: Total RNA was isolated from CD11b+Ly6G- cells sorted from hearts 3 days following ligation of LAD.  6 samples total: Triplicates of cells from P1 mice and from P14 mice


title: Critical roles of Rictor/Sin1complexes in IFN-dependent Stat activation and generation of antiproliferative responses

status: Public on Jan 28 2014

city: Torino

first: Raffaele

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

institute: University of Torino

summary: We provide evidence that IFN-induced Stat-activation is defective in cells with targeted disruption of the Rictor gene, whose protein product is a key element of mTOR complex 2 (mTORC2).   Our studies show that transient or stable knockdown of Rictor leads to decreased expression of several IFN-inducible genes that mediate important biological functions, including antiproliferative and pro-apoptotic responses.

overall_design: Rictor+/+ and Rictor-/- MEFs were treated with 2500 U/ml of mouse IFNα for 24 hours

first: Surinder

last: Kaur

first: Barbara

last: Kroczynska

first: Bhumika

last: Sharma

first: Antonella

last: Sassano

first: Beata

last: Majchrzak

first: Brady

last: Stein

first: Brandon

last: McMahon

first: Altman

last: Su

first: Eleanor

last: Fish

first: Leonidas

last: Platanias


title: Identification of heavily translated mRNAs in PRR16/Largen-overexpressing cells.

city: Nagasaki

first: Kazuo

last: Yamamoto

state: Nagasaki

address: 1-12-4 Sakamoto

department: Biomedical Research Support Center

institute: Nagasaki University School of Medical Sciences

summary: The hypothesis tested in the present study was that PRR16/Largen influences mRNA translation to control mammalian cell size. Results provide important information of the effects of PRR16/Largen on translation of particular sets of mRNAs encoding histones, mitochondrial, and vascular transport proteins.

overall_design: mRNAs obtained from heavy and light polysomes in PRR16/Largen-overexpressing cells subjected to the identification of mRNAs enriched in heavy polysomes compared to control cells.

first: Tak

middle: W

last: Mak


title: DNA methylation status of myelinating Schwann cells during development and in diabetic neuropathy [Gene Expression Array: GNMT mice]

status: Public on Jan 27 2014

city: Derio

first: Jose

middle: Luis

last: Lavin

state: Bizkaia

address: Parque Tecnológico de Bizkaia Building 502, Floor 0

country: Spain

institute: CIC bioGUNE

summary:
DNA methylation is a key epigenetic regulator of mammalian embryogenesis and somatic cell differentiation. Using high-resolution genome-scale maps of methylation patterns, we show that the formation of myelin in the peripheral nervous system, proceeds with progressive DNA demethylation, which coincides with an upregulation of critical genes of the myelination process. More importantly, we found that, in addition to expression of DNA methyltransferases and demethylases, the levels of S-adenosylmethionine (SAMe), the principal biological methyl donor, could also play a critical role in regulating DNA methylation during myelination and in the pathogenesis of diabetic neuropathy. In summary, this study provides compelling evidence that SAMe levels need to be tightly controlled to prevent aberrant DNA methylation patterns, and together with recently published studies on the influence of SAMe on histone methylation in cancer and embryonic stem cell differentiation show that in diverse biological processes, the methylome, and consequently gene expression patterns, are critically dependent on levels of SAMe.
Axonal myelination by Schwann cells in the peripheral nervous system is essential for rapid saltatory impulse conduction, and malformation or destruction of myelin sheaths can lead to severe motor and sensory disabilities (peripheral neuropathies). Using high-resolution genome-scale methylome maps, we found that DNA methylation could play a critical role in the generation of myelinated Schwann cells. This process was accompanied by a global DNA demethylation at most genomic elements. Notably, demethylation at gene-regulatory regions was associated with activation of critical myelination-specific genes. Furthermore, we found an aberrant DNA methylation pattern in a mouse model of diabetic neuropathy, which could be involved in the pathogenesis of the disease. Importantly, we found that these methylation patterns in both situations could be regulated by levels of S-adenosylmethionine (SAMe), the principal biological methyl donor. Together with recent studies on the influence of SAMe on histone methylation in diverse biological processes, we conclude that the methylation landscape of cells could be critically dependent on levels of SAMe. These provide a mechanistic link between metabolism and gene regulatory networks in normal and pathological situations.

overall_design: Sciatic nerves from post natal day 90 GNMT (wt and KO)  mice of either sex were dissected and pooled together, 2 replicates per sample group.

first: Ashwin

last: Woodhoo


title: DNA methylation status of myelinating Schwann cells during development and in diabetic neuropathy [Gene Expression Array: C57Bl6J mice]

overall_design: Sciatic nerves from C57Bl6J mice of either sex, were dissected and pooled together at different developmental stages, 3 replicates per sample group.


title: Expression data of Brti1 shRNA knockdown and control shRNA in MCF-10A cells

status: Public on Jan 24 2014

city: Houston

first: Chun-Jen

middle: Curtis

last: Lin

address: 7345 Fannin Street

department: Systems Biology

institute: University of Texas MD Anderson Cancer Center

summary: Homologous recombination-mediated DNA repair deficiency (HRD) predisposes to cancer development, but also provides therapeutic opportunities Here, we identified an HRD gene signature that robustly predicted HRD status Unexpectedly, concurrent loss of PTEN in BRCA1-deficient cells might extensively rewire the HR repair network and confer resistance to PARP inhibitor, partially through over-expression of TTK We used the HRD gene signature as a drug discovery tool and found several PARP-inhibitor-synergizing agents through the connectivity map Thus gene expression profiling can be used to define the functional status of the HR repair network providing prognostic and therapeutic information

overall_design:
Various shRNAs that target genes involved in homologous recombination (HR) were transfected in MCF-10A non-transformed breast cells lines Stable HR gene knockdown MCF-10A cells were seeded 200000 at 10 cm plate Cells were harvested after 48 hours culturing and used for gene expression profiling

The shRNA that target Brit1 genes was transfected in MCF-10A non-transformed breast cell line by lentiviral particles and selected stable Brit1 knockdown MCF-10A cells. Scrambled control shRNA-transfected MCF-10A cells were applying as control.  Both stable Brit1 knockdown and control MCF-10A cells were seeded with 2 x 10^5 cells at 10 cm culture plate. Cells were cultured in MCF-10A medium and harvested after 48 hours culturing.  mRNA was extracted from collected cells and performing gene expression profiling. Three or four biological replicates were applied.

first: Guang

last: Peng

first: Curtis

first: Wei

last: Mo

first: Hui

last: Dai

first: Yun-Yong

last: Park

first: Soo-Mi

last: Kim

first: Qianxing

first: Yang

first: Stefan

last: Siwko

first: Ruozhen

last: Hu

first: Ju-Seog

last: Lee

first: Bryan

last: Hennessy

first: Samir

last: Hanash

first: Gordon

last: Mills

first: Shiaw-Yih


title: Myotonic dystrophy type 1 (DM1) leads to altered mRNA expression in heart tissue

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: Myotonic dystrophy type 1 (DM1) is a dominantly inherited disease that affects multiple organ systems. Cardiac dysfunction is the second leading cause of death in DM1. We quantified gene expression in heart tissue from a heart-specific DM1 mouse model (EpA960/MCM) which inducibly expresses human DMPK exon 15 containing 960 CUG expanded repeats and that reproduced Celf1 up regulation. To assess if, in addition to splicing and miRNA defects, CUGexp RNA also perturbed the steady state mRNA levels of genes, we carried out a microarray study on wildtype E14, adult, MCM controls and DM1 mouse hearts. As anticipated we noted a large number of genes to be developmentally regulated in wildtype hearts, however, within 72h of induction of CUGexp RNA there appeared to be a coordinate adult-to-embryonic shift in steady state levels of many genes.

overall_design:
We identified transcripts over-expressed or under-expressed in hearts of wildtype adult mice, wildtype embryonic day 14 (E14), and DM1 mice induced to express CUGexp RNA for 72h and 1wk, when compared to MCM controls.
Multiple group comparison.

first: Auinash

last: Kalsotra

first: Thomas

last: Wheeler

first: Yiqun

last: Zhang


title: Maternal western diet primes susceptibility to hepatic inflamation in adult male mouse offspring

status: Public on Jan 21 2014

city: Groningen

first: vincent

last: bloks

department: Pediatrics

country: Netherlands

institute: UMCG

summary:
Background & Aims: The influences of the maternal diet during gestation has been suggested to be involved in the development of different aspects of the metabolic syndrome. In our mouse model we characterised the role of maternal western diet in the development of non-alcoholic fatty liver disease (NAFLD) in the offspring.
Methods: Female mice were fed either a western (W) or low-fat control (L) semi-synthetic diet before and during gestation and lactation. At weaning, male offspring were assigned either the W or the L diet, generating four experimental groups: WW, WL, LW and LL offspring. Biochemical, histological and epigenetic indicators were investigated at 29 weeks of age.
Results: Male offspring exposed to prenatal western style diet  and to a post-weaning W diet (WW) showed hepatomegaly combined with increased hepatic cholesterol and triglycerides accumulation, compared to LW offspring. This was associated with up-regulation of de novo lipid synthesis and dysregulation of beta oxidation and lipid storage. Elevated hepatic transaminases and increased expression of Tnfa, Cd11, Mcp1 and Tgfb underpin the severity of liver injury. Histological analysis supported the presence of steatohepatitis in the WW offspring. In addition alterations in DNA methylation in key metabolic genes (Ppara, Insig, Fasn)  were detected.
Conclusion: Maternal dietary fat intake during critical developmental phases programs susceptibility to liver disease in mouse offspring. This was mediated by shifts in lipid metabolism and inflammatory response. Long lasting epigenetic changes may underlie this dysregulation

overall_design: 4 groups of 6 male mouse were analysed , 1 experimental and 1 biological outlier was excluded , so n=6,5,5,6 in the 4 groups (LL,LW,WL,WW)

first: M

middle: G

last: Pruis

first: A

last: Lendvai

first: V

last: Bloks

middle: V

last: Zwier

first: J

middle: F

last: Baller

last: Bruin de

middle: K

last: Groen

first: T

last: Plosch


title: aCGH analysis was performed in the spleen of βcat(ex3)osb mice

city: New York

first: Stavroula

last: Kousteni

state: NY

address: 650 West 168th Street

department: Physiology and Cellular Biophysics

institute: Columnia University

summary: Cells of the osteoblast lineage affect homing, number of long term repopulating hematopoietic stem cells (HSCs) HSC mobilization and lineage determination and Blymphopoiesis . More recently osteoblasts were implicated in pre-leukemic conditions in mice. Yet, it has not been shown that a single genetic event taking place in osteoblastscan induce leukemogenesis. We show here that in mice, an activating mutation of β-catenin leading to development of acute myeloid leukemia (AML) with common chromosomal aberrationsand cell autonomous progression. Activated β-catenin stimulates expression of the Notch ligand Jagged-1 in osteoblasts. Subsequent activation of Notch signaling in HSCprogenitors induces the malignant changes. Demonstrating the pathogenetic role of theNotch pathway, genetic or pharmacological inhibition of Notch signaling ameliorates AML. Nuclear accumulation and increased β-catenin signaling in osteoblasts was also identified in 38% ofpatients with MDS/AML. These patients showed increased Notch signaling in hematopoietic cells. These findings demonstrate that genetic alterations in osteoblasts can induce AML, identify molecular signals leading to this transformation and suggest a potential novel pharmacotherapeuticapproach to AML. The present entry describes a comparison of copy numbers of DNA from βcat(ex3)osb mice from the mouse spleen with that of WT (C57BL/J Mice) mice.

overall_design:
DNA from spleen myeloid cells from βcat(ex3)osb mice and WT mice were hybridized to Agilent CGH 244A arrays.
DNA from spleen myeloid cells from βcat(ex3)osb mice in C57BL/J background was labeled with red dye.
DNA from spleen myeloid cells from WT (C57BL/J) mice were labeled with green  dye.
There were five arrays with DNA from 1 mouse of each genotype per array.

first: Aruna

last: Kode

first: John

middle: S

last: Manavalan

first: Ioanna

last: Mosialou

first: Govind

last: Bhagat

first: Chozha

last: Rathinam

last: Luo

first: Hossein

last: Khiabanian

first: Albert

last: Lee

first: Murty

last: Vundavalli

first: Richard

middle: A

last: Friedman

first: Andrea

last: Brum

first: David

last: Park

first: Siddhartha

last: Mukherjee

first: Julie

last: Teruya-Feldstein

first: Azra

last: Raza

first: Raul

last: Rabadan

first: Ellin

last: Berman


title: Sex differences in neonatal mouse cortex/hippocampus gene expression

status: Public on Jan 23 2014

city: Los Angeles

first: Christopher

last: Armoskus

state: CA

department: Biological Sciences

institute: California State University - Long Beach

summary: Analysis of mouse genes showing a sex difference in gene expression in the cortex and hippocampus on the day of birth

overall_design: 17 samples, all collected on the afternoon of birth (1pm-3pm local), including 9 male and 8 female samples. All samples include both cortex and hippocampus dissected out from other brain.

first: Houng-Wei

last: Tsai


title: Tissue-specific pioneer factors associate with androgen receptor cistromes and transcription programs.  [microarray]

city: Helsinki

first: Olli

middle: A.

last: Jänne

department: Inst. of Biomedicine/Physiology

country: Finland

institute: University of Helsinki

summary: We report the in vivo androgen receptor (AR) binding sites in murine prostate, epididymis and kidney in response to physiological androgen testosterone using ChIP-sequencing and gene expression profiling by microarray. From AR cistrome analysis, we identified tissue-specific collaborating factors i.e. FoxA1 in prostate, Hnf4a in kidney and AP2a in epididymis and validated by ChIP-seq. The ChIP experiments have been performed using antibodies specific to AR, FoxA1, Hnf4a, AP-2a and IgG non-specific antibody as a negative control.

overall_design: Expression profiling by microarray of mouse androgen responsive tissues, prostate, kidney and epididymis castrated and treated with vehicle or testosterone for 3 days or 12 or 24 hours after single testosterone-injection.

first: Päivi

last: Pihlajamaa

first: Biswajyoti

last: Sahu

first: Lauri

last: Lyly

first: Viljami

last: Aittomäki

first: Sampsa

last: Hautaniemi


title: Polymicrobial periodontal pathogens transcriptomes in calvarial bone and soft tissue

status: Public on Jan 10 2014

city: Gainesville

first: Kesavalu

middle: Naidu

last: Lakshmyya

state: FL

address: 1600 SW Archer road, D11-24

department: Periodontology

institute: University of Florida, College of Dentistry

summary:
The objectives of this investigation were to examine changes in the host transcriptional profiles during a polymicrobial periodontal pathogens Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia infection using a murine calvarial model of inflammation and bone resorption.  P. gingivalis FDC 381, T. denticola ATCC 35404, and T. forsythia ATCC 43037 was injected into the subcutaneous soft tissue over the calvaria of BALB/c mice for 3 days, after which the soft tissues and calvarial bones were excised.  RNA was isolated from infected soft tissues and calvarial bones and analyzed for transcript profiles using Murine GeneChip® MG-MOE430A Affymetrix arrays to provide a molecular profile of the events that occur following infection of these tissues.
We used mouse microarrays to detail the molecular profile of the events that occur following infection of calvarial and bone tissues and identified distinct classes of up- and down-regulated genes during this process.

overall_design: P. gingivalis/T. denticola/T. forsythia was injected at 5 x 108 each (N = 10) into the soft tissues overlying the calvaria of the mice for 3 days. A control group (N = 9) was injected with vehicle once daily for 3 days. Mice were euthanized 8 h after the last injection.  The calvarial bones and overlying soft tissues from 5 mice in each group were excised, snap frozen in liquid nitrogen, and stored at –80°C until RNA isolation. Total RNA was isolated from the frozen calvarial tissue and calvarial bone from each mouse (Polymicrobial bacteria infected and control animals, N = 5 in each group) with Trizol reagent (Invitrogen, CA).  Equal amounts of RNA from samples were labeled and hybridized on a mouse GeneChip following the protocol described in the GeneChip Expression Analysis Technical manual (Affymetrix, Santa Clara, CA). After hybridization, the GeneChip arrays were stained and scanned in an Affymetrix GCS 3000 7G Scanner.

first: Lakshmyya

last: Kesavalu

first: Vasudevan

last: Bakthavatchalu

first: Archana

last: Meka

first: Sabapathi

last: Sathishkumar

first: Cecilia

middle: M

last: Lopez

first: Indraneel

last: Bhattacharyya

first: Brendan

last: Boyce

first: Jeffrey

middle: J

last: Mans

last: Lamont

first: Henry

last: Baker

middle: L

last: Ebersole


title: Regulatory role of multinucleated giant cells derived from placental CD14+ macrophages: Pathophysiological implications

status: Public on Jan 07 2014

city: Lyon

first: Julien

last: Textoris

address: Hôpital Edouard herriot - Pavillon P; 5 place d'Arsonval

department: Medical Diagnostic Discovery Department (MD3)

institute: bioMérieux

summary: The role of placental macrophages is largely ignored in the success of pregnancy. We found that CD14+ macrophages purified from at-term placentas spontaneously matured into multinucleated giant cells (MGCs). MGCs lost the expression of CD14 and co-inhibitory molecules, such as Programmed cell Death-Ligands 1 and 2. Although MGCs kept phagocytosis and property to produce ROS, their inflammatory potential measured by TNF/IL-10 imbalance and activation of p38 MAPK and NF-κB was blunted without being associated with M2 phenotype. The investigation of gene expression revealed the enrichment with categories related to inflammation, apoptosis and canonical functions of macrophages in MGCs. Whereas most of the genes associated with inflammation and immune responses were down-modulated, those such as VEGFC or associated with matrix remodeling were specifically up-regulated in MGCs. Importantly, we found that patients with preeclampsia or chorioamnionitis, two inflammatory and infectious pathologies, respectively, that affect placentas, were unable to generate MGCs. Taken together, these results suggest that MGCs represent a new way to regulate the inflammatory and cytocidal activity of placental macrophages in a context that imposes contradictory constraints, such as semi-allograft acceptance and defense against aggression. The dysregulation of MGC formation may be associated with placental inflammatory and infectious pathologies.

overall_design: Placental macrophages CD14+ were cultured for 9 days to form multinucleated giant cells (MGC). The transcriptome of MGCs was compared to the transcriptome of placental macrophages (CD14+)

first: Amira

last: Ben Amara

first: Laurent

last: Gorvel

first: Christel

last: Verollet

first: Justine

last: Derain-Court

first: Vikram

last: Mehaj

first: Abdoulaye

middle: O

last: Barry

first: Florence

last: Bretelle

first: Eric

last: Ghigo

first: Christian

last: Capo

first: Isabelle

last: Maridonneau-Parini

first: Jean-Louis

last: Mège


title: Gene expression profiling of Activin-like kinase 2 knockout in mice

first: Chad

last: Creighton

summary: Implantation of an embryo in the uterus is a multistep process tightly controlled by an intricate regulatory network of interconnected ovarian, uterine, and embryonic factors. Bone morphogenetic protein (BMP) ligands and receptors are expressed in the pregnant uterus, and BMP2 has been shown to be a key regulator of implantation. In this study, we investigated the roles of the BMP type 1 receptor, activin-like kinase 2 (ALK2), during mouse pregnancy by producing uterine-specific Alk2 conditional knockout (cKO) mice. In the absence of ALK2, embryos can invade the uterine epithelium and stroma, but stromal cells cannot undergo uterine decidualization, resulting in sterility. Mechanistically, microarray analysis revealed that CCAAT/enhancer-binding protein β (Cebpb) expression is suppressed during decidualization in Alk2 cKO females. These findings and the similar phenotypes of Cebpb cKO and Alk2 cKO mice lead to the hypothesis that BMPs act upstream of C/EBPβ to regulate decidualization. To test this hypothesis, we knocked down ALK2 in human uterine stromal cells (HESC) and discovered that ablation of ALK2 alters HESC decidualization and suppresses CEBPB mRNA and protein levels. Chromatin immunoprecipitation (ChIP) analysis of decidualizing HESC confirmed that BMP signaling protein, SMAD1, directly regulates expression of CEBPB by binding a distinct regulatory sequence in the CEBPB promoter; C/EBPβ, in turn, regulates the expression of progesterone receptor (PGR). Our work clarifies the conserved mechanisms through which BMPs regulate embryo implantation in rodents and primates and, for the first time, uncovers a linear pathwayof BMP signaling through ALK2 to regulate CEBPB and, subsequently, PGR during decidualization.

overall_design: gene expression profiling of two groups: control mice and Alk2 cKO mice

first: Marty

last: Matzuk

first: Francesco

last: DeMayo

first: Caterina

last: Clementi


title: Overexpression of cSki in hematopoietic stem and progenitor cells

city: Fitzroy

first: Carl

last: Walkley

state: Victoria

address: 9 Princes St

country: Australia

institute: St. Vincent's Institute of Medical Research

summary:
Human cSki was overexpressed using MIGR1 retrovirus in sorted murine Lin-c-Kit+Sca-1+ cells. Cells were infected and cultured for 2 days after infection prior to isolation of GFP+ve cells and microarray. GFP+ve MIGR1 and cSKI cells were compared.
Each sample represents an independent infection with either cSki or MIGR1

overall_design: Comparison of GFP+ve LKS+ infected with MIGR1 and cSki

first: S

last: Singbrant

first: M

last: Wall

first: J

last: Moody

first: G

last: Karlsson

first: A

last: Chalk

first: B

last: Liddicoat

first: K

last: Olson

middle: R

last: Russel

last: Miyazono

first: C


title: Medial Tibial Plateau articular cartilage changes 2 ,4 and 8 weeks after DMM

status: Public on Jan 08 2014

city: Oxford

first: Anastasios

last: Chanalaris

address: Roosevelt Drive

department: Kennedy Institute of Rheumatology

country: United Kingdom

institute: University of Oxford

summary:
Objective: To Identify gene changes in the medial tibial plateau of articular cartilage at 2, 4 and 8 weeks after destabilisation of the medial meniscus (DMM) in mice and compare our data set with previously published sets to ascertain dysregulated pathways and genes in osteoarthritis.

Materials and methods: RNA was extracted from the ipsilateral and contralateral medial tibial plateaus, amplified, labelled and hybridized on Illumina WG_v2 microarrays. Results were confirmed by RT-PCR for selected genes.

Results: Transcriptional analysis and network reconstruction revealed changes in extracellular matrix (ECM) and cytoskeletal genes induced by DMM. TGFalpha signalling pathway and complement and coagulation cascade genes were regulated at 2 weeks. Fibronectin (FN1) is a hub in a reconstructed network of potential protein-protein interactions at 2 weeks. Regulated genes decrease over time and by eight weeks fibromodulin (FMOD) and tenascin N (TNN) are the only dysregulated genes present in the DMM operated knees. Comparison with human and rodent published gene sets discovered genes overlapping between our array and 6 others.

Conclusions: Cartilage contributes a minute percentage to the RNA extracted from the whole joint (>0.2%), yet is sensitive to changes in gene expression post-DMM. The post-DMM transcriptional reprogramming wanes over time and dissipates by 8 weeks. Common pathways between published gene sets include focal adhesion, regulation of actin cytoskeleton and TGFalpha. Common genes include Jagged 1 (Jag1), Tetraspanin 2 (Tspan2), neuroblastoma, suppression of tumourigenicity 1 (Nbl1) and N-myc downstream regulated gene 2 (Ndrg2). The concomitant genes and pathways we identify are novel and warrant further investigation as biomarkers or modulators of osteoarthritis.

overall_design: In total 18 samples. Each sample was a pool of the medial tibial plateau of 8 mice. Two categories (Treated and untreated) with three biological replicates each and three time points (2, 4 and 8 weeks post-surgery).

first: Matthew

last: Gardiner


title: The RON receptor tyrosine kinase promotes metastasis by triggering epigenetic reprogramming through the thymine glycosylase MBD4 (gene expression array)

status: Public on Jan 02 2014

city: Salt Lake City

first: Stephanie

last: Cunha

state: Utah

address: 2000 Circle of Hope

department: Oncological Science

institute: Huntsman Cancer Institute, University of Utah

summary: Metastasis is the major cause of death in cancer patients, yet the genetic/epigenetic programs that drive metastasis are poorly understood. Here, we report a novel epigenetic reprogramming pathway that is required for breast cancer metastasis. Concerted differential DNA methylation is initiated by activation of the RON receptor tyrosine kinase by its ligand, macrophage stimulating protein (MSP). Through PI3K signaling, RON/MSP promotes expression of the G:T mismatch-specific thymine glycosylase MBD4. RON/MSP and MBD4-dependent aberrant DNA methylation results in misregulation of a specific set of genes. Knockdown of MBD4 reverses methylation at these specific loci, and blocks metastasis. We also show that the MBD4 glycosylase catalytic residue is required for RON/MSP-driven metastasis. Analysis of human breast cancers revealed that this epigenetic program is significantly associated with poor clinical outcome. Furthermore, inhibition of Ron kinase activity with a new pharmacological agent blocks metastasis of patient-derived breast tumor grafts in vivo.

overall_design: To determine the molecular mechanisms by which RON/MSP drives breast cancer metastasis, we performed microarray gene expression profiling of MCF7, MCF7-RON/MSP and MCF7-RON/MSP-shMBD4 cells.

first: Alana

last: Welm


title: gene expression Fulminant type 1 diabetes vs classical type 1A diabetes vs healthy controls

status: Public on Jan 01 2014

city: Suita

first: Shinsuke

last: Nakata

address: 2-2-B5, Yamadaoka

department: Metabolic Medicine

institute: Osaka University, Graduate School of Medicine

summary: We determined the genes that were differentially expressed between fulminant type 1 diabetes and classical type 1A diabetes or healthy control using gene expression microarray in peripheral blood cells.

overall_design: Ten patients with type 1 diabetes (5 fulminant and 5 classical type 1A) and 6 healthy controls were enrolled in this study.  All patients had recovered from ketosis or ketoacidosis at disease onset and had been receiving intensive insulin injection therapy for at least 1 month, which means that all patients and healthy controls were free of metabolic derangements at the time of blood sampling.  To determine the genes that were differentially expressed among   fulminant type 1 diabetes, classical type 1A and healthy controls, a volcano plot analysis (fold change >1.5 and p-value <0.05) was performed.


title: NANOG amplifies STAT3 activation and they synergistically induce the naïve pluripotent program

status: Public on Jan 06 2014

city: Cambridge

first: Hannah

middle: Taylor

last: Stuart

address: Tennis Court Road

department: University of Cambridge

institute: Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute

summary: We generated Nanog-/- iPSCs from both EpiSCs and pre-iPSCs. We wanted to compare the global gene expression profile of these iPSCs to their parental cells lines and to wild-type and Nanog-/- ESCs.

overall_design: We analysed two technical replicates of each cell line.

first: José

last: Silva


title: Study of the effect on indoxyl sulfate on endothelial gene expression

city: MARSEILLE

first: ariane

last: duval-sabatier

address: Faculté Pharmacie 27 bd Jean Moulin

department: Physiopathologie de l'endothélium

institute: Inserm 608-Université Aix-Marseille

summary:
The aim of this study is to determine the molecular mechanism by which indoxyl sulfate acts on endothelial cells. Endothelial cells (HUVECs) were incubated  with medium containing indoxyl sulfate at concentration found in chronic kidney disease patients (1mM).
Since indoxyl sulfate is a potassium salt, control medium contains KCl at 1mM. Cells were incubated during  four hours in presence of indoxyl sulfate or KCl. Seven biological replicates were obtained for these two conditions.

overall_design: To understand how uremic solutes participate in endothelial dysfunction and cardiovascular complications of chronic kidney disease patients

first: Ariane

last: Duval-Sabatier

first: Bertrand

last: Gondouin

first: Claire

last: Cerini


title: H1299 cells: p53 transcriptional response in hypoxia

first: Katarzyna

last: Leszczynska

address: Old Road Campus Research Building

department: Oncology

summary: Transcriptional profiling of H1299 non-small cell lung carcinoma cells transfected with either wt p53 or mut(175) p53 driven by the 5xHRE promoter (5 repeats of hypoxia-inducible factor response elements) and treated for 16 h with normoxia (21% O2) or hypoxia(<0.1% O2). 5xHRE promoter ensures that p53 expression is induced in hypoxic conditions only. Goal was to determine the transcriptional response of p53 in hypoxia and the 175 p53 mutant was used as a control as it is DNA-binding defective and transcription-incompetent mutant.

overall_design: Four-condition experiment: wt p53-transfected H1299 cells treated with normoxia, mut p53-transfected H1299 cells treated with normoxia, wt p53-transfected H1299 cells treated with hypoxia, mut p53-transfected H1299 cells treated with hypoxia. Biological replicates: 1 normoxic sample with wt p53, 1 normoxic sample with mut p53, 3 hypoxic samples with wt p53, 3 hypoxic samples with mut p53.

middle: B

first: Francesca

last: Buffa


title: Gene expression Fulminant type 1 diabetes vs classical type 1A diabetes

summary: We determined the genes that were differentially expressed between fulminant type 1 diabetes and classical type 1A diabetes using gene expression microarray in peripheral blood cells.

overall_design: Ten patients with type 1 diabetes (5 fulminant and 5 classical type 1A) were enrolled in this study.  All patients had recovered from ketosis or ketoacidosis at disease onset and had been receiving intensive insulin injection therapy for at least 1 month, which means that all patients and healthy controls were free of metabolic derangements at the time of blood sampling.  To determine the genes that were differentially expressed between classical type 1A and fulminant type 1 diabetes, a volcano plot analysis (fold change >1.5 and p-value <0.05) was performed.


title: IMR90 lung fibroblasts treated with IL-4 or IL-13

status: Public on Dec 31 2013

city: South San Francisco

first: Alex

last: Abbas

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

summary: IL-4 and IL-13 are cytokines involved in type 2 immune responses involved in atopic asthma and other diseases. They have a partially overlapping set of cognate receptors whose roles are incompletely understood. Here we explore the effects of these cytokines on lung fibroblasts in order to assess the global similarities and contrasts in the genes whose expression their ligation modulates.

overall_design: IMR-90 lung fibroblast cells were cultured on matrigel or plastic and treated for 24 hours with IL-4 (10 ng/ml), IL-13 (10ng/ml), or TNFa (10 ng/ml) before harvest.

first: Alexander

first: Joseph

last: Arron

first: Sanjay

last: Chandriani


title: Transcriptomic approach to renal toxicity for cisplatin treatment in Nrf2 WT/KO

city: Seoul

first: Sang Geon

last: Kim

state: Seoul

address: San56-1, Sillim-dong, Kwanak-gu

department: College of Pharmacy

country: South Korea

institute: Seoul National University

summary: NF-E2-related factor 2 (Nrf2), a transcription factor activated by oxidative stress, induces phase II conjugating or antioxidant enzymes. In the present study, we examined the effect of Nrf2 knockout (Nrf2 KO) on the kidney injury induced by cisplatin using cDNA microarray analyses. A transcriptomic approach enabled us to extract gene clusters which show significantly different mRNA expression patterns between wild type (WT) and Nrf2 KO mice. In the experimental set, WT vehicle (WT-Veh) and WT cisplatin (WT-Cis) groups were included in our previous GEO database (GSE35257) because the two groups were simultaneously shared with Nrf2 KO vehicle (Nrf2 KO-Veh) and Nrf2 KO cisplatin (Nrf2 KO-Cis) groups in the current report.   Copyright (c) 2012 by Korea Food & Drug Administration.

overall_design: WT and Nrf2 KO C57BL/6 mice (9 weeks old, male) were intraperitoneally injected with vehicle (saline) or a single dose of cisplatin (15 mg/kg body weight). The cDNA microarray experiments were done for the kidney of mice 3 days after treatment. Three animals were used per group. WT-Veh and WT-Cis groups were already deposited in GSE35257.

first: Chan

last: Lee

first: Il

last: Cho

first: Dal

middle: W

last: Choi

first: Min

last: Joo

first: Sang


title: Four subgroups by gene expression profile correlate with biological and clinical features in colorectal cancer.

city: sendai

first: masahiro

last: inoue

state: miyagi

address: 4-1 seiryo-machi, aobaku

department: department of clinical oncology

institute: tohoku university

summary: (Purpose) Biological classification of colorectal cancer (CRC) can help to understand its heterogeneous background. The purpose of this study is to classify CRC based on gene expression profiles using formalin-fixed paraffin-embedded (FFPE) samples and to correlate subgroups of CRC with biological features and clinical outcomes. (Results) CRC was clustered into four subgroups by unsupervised hierarchical clustering method. These subgroups show different biological and clinical features. (Conclusion) Gene expression profiles of CRC using FFPE samples distinguish four subgroups that had different biological features and clinical outcomes. These subgroups may explain heterogeneity of CRC and be useful biomarker for clinical.

overall_design: Patients and Methods: One hundred patients with unresectable and advanced or recurrent CRC who underwent the surgical resection from 1998 to 2010 were enrolled in this study. RNA extracted from FFPE samples was subjected to gene expression microarray. After comprehensive gene expression analysis, CRC were classified by an unsupervised hierarchical clustering and a principle component analysis (PCA). Mutation analysis of KRAS, BRAF, PIK3CA and TP53 genes were performed by direct DNA sequencing. Correlation between the biological information, clinicopathological factors and clinical outcomes were analyzed.


title: Proton irradiation augments the reduction in tumor progression observed with advanced age

city: Boston

first: christine

middle: elaine

last: briggs

state: MA

address: 736 Cambridge Street

department: Center for Cancer Systems Biology

institute: christine briggs

summary: Proton irradiation is touted for its improved tumor targeting due to the physical advantages of ion beams for radiotherapy. Recent studies from our laboratory have shown that, in addition to targeting advantages, proton irradiation can inhibit angiogenic and immune factors and thereby modulate tumor progression. High-energy protons also constitute a principal component of the galactic cosmic rays to which astronauts are exposed. Increased understanding of the biological effects of proton exposure would thus contribute to both improved cancer therapy and carcinogenesis risk assessment for space travel. In addition, age plays a major role in tumor incidence and is a critical consideration for estimating cancer risk. We investigated the effects of host age and proton exposure on tumor progression. Tumor lag time and growth dynamics were tracked following injection of murine Lewis lung carcinoma (LLC) cells into young (68 day) versus old (736 day) mice with or without coincident irradiation. Tumor progression was suppressed in old compared to young mice. Differences in progression were further modulated by proton irradiation (1GeV), with increased inhibition evident in old mice. Through global transcriptome analysis, TGFβ1 and TGFβ2 were determined to be key players that contributed to the tumor dynamics observed. These findings point to older hosts providing decreased systemic tumor support, which can be further inhibited by proton irradiation.

overall_design: For genome-wide expression profiling of tumor tissue, Mouse WG-6 BeadArray chips (Illumina, San Diego, CA) were used. Total RNA was amplified with the Ambion Illumina TotalPrep Amplification Kit (Ambion, Austin, TX) and labeled from all replicate biological samples for each condition. For tumor replicates, thirty tumor samples from adolescent and thirty tumor samples from old mice, for a total of 60 tumor samples, were used. All replicate samples were run individually. For each age group, ten tumor samples had received proton irradiation while twenty tumor samples were from unirradiated mice (as described above). Total RNA was isolated and purified using TRIzol (Invitrogen) and quantified using an Agilent Bioanalyzer. Samples were deemed suitable for amplification and hybridization if they had 28s/18s = 2:1, RIN >7. Total RNA of 500ng per sample was amplified using AmbionTotalPrep, and 1.5ug of the product was loaded onto the chips. Following hybridization at 55C, the chips were washed and then scanned using the Illumina iScan System. The data was checked with GenomeStudio (Illumina) for quality control. In GenomeStudio, data was background subtracted and rank invariant normalization was applied. Data was imported into MultiExperiment Viewer, MeV, for statistical analysis. The statistically significant genes were determined using MeV by applying a one-way ANOVA analysis with standard Bonferroni correction with a FDR <0.05 that resulted in a list of significant genes. Average gene expression signals <10 were filtered out due to signal being

first: Afshin

last: Beheshti

first: Michael

last: Peluso

first: Philip

last: Hahnfeldt

first: Lynn

last: Hlatky


title: Effects of anti-IL13RA mAbs on IL-4 or IL-13 signalling

summary: IL-4 and IL-13 are cytokines involved in type 2 immune responses involved in atopic asthma and other diseases. They have a partially overlapping set of cognate receptors whose roles are incompletely understood. Here we explore the effects of blocking one or both subunits of the IL-13 alpha receptor on the action of these cytokines on IMR-90 lung fibroblast cells.

overall_design: IMR-90 lung fibroblast cells were cultured on matrigel and treated with various combinations of IL-4 (10 ng/ml), IL-13 (10ng/ml), 228 B/C (which blocks signaling from IL13RA1), and 11H4 (which blocks signaling from IL13RA1 and IL13RA2).


title: Gene expression in teratogenic exposures: a new approach to understanding individual risk

city: Baton Rouge

first: Claudia

last: Kappen

state: LA

address: 6400 Perkins Road

department: Developmental Biology

institute: Pennington Biomedical Research Center

summary: The phenomenon of partial or incomplete penetrance is common to many paradigms of exposure to teratogens, where only some of the exposed individuals exhibit developmental defects. We here argue that the most widely used experimental approaches in reproductive toxicology do not take partial penetrance into account, and are thus likely to miss differences between affected and unaffected individuals that contribute to susceptibility for teratogenesis. We propose that focus on the variation between exposed individuals could help to discover factors that may play a causative role for abnormal developmental processes that occur with incomplete penetrance.

overall_design: Total RNA was extracted from individual embryos E10.5 derived from normal and diabetic pregnancies. A total of 8 sample pools were created, 4 resultiing from normal (C1-C4) and 4 from diabetic (E1-E4) pregnancies. Each pool consisted of RNA from 4 embryos obtained from 4 different pregnancies. Samples E5-E8 consisted of individual embryos with NT defects obtained from diabetic pregnancies.

first: J

last: Salbaum

first: Nancy

last: Arbour-DelaHaye


title: Mac-1 cells with SATB1 silencing vs control Mac-1 cells

city: Beijing

first: Yang

last: Wang

address: No.8 Xishiku Street

department: Department of Dermatology and Venerology

institute: Peking University First Hospital

summary: Transcriptional profiling of primary cutaneous anaplastic large cell lymphoma cell line Mac-1 cells transduced with lenti-virus vector harboring shRNA against SATB1 gene comparing control untreated Mac-1 cells and Mac-1 cells transduced with scrambled shRNA, in which SATB1 expression is not affected.

overall_design: Two condition experiment, SATB1 silenced Mac-1 cells vs control Mac-1 cells. Biological replicates: 2 transduced replicates, 2 control replicates

first: Xiaoguang

last: Gu


title: Identification of the molecular targets of microRNA-181d in murine thymocytes.

city: Dallas

first: Nicolai S.C.

last: van Oers

state: Texas

address: 6000 Harry Hines Blvd

department: Immunology

institute: University of Texas Southwestern Medical Center

summary:
T cell-specific transgenic expression of microRNA-181d reduced number of immature CD4+CD8+ thymocytes.
Microarray analysis was performed to reveal differentially expressed genes between the wild type and microRNA-181d transgenic thymocytes.

overall_design: Whole thymus tissues were isolated from the wild type (C57BL/6) and microRNA-181d transgenic mice (Tg-38 line), followed by total RNA isolation.

first: Serkan

last: Belkaya

first: Nicolai


title: Capturing the biological impact of the melanoma susceptibility genes CDKN2A and MC1R in  cocultured keratinocytes and melanocytes

city: Valencia

first: Francisco

middle: García

last: García

address: Eduardo Primo Yúfera, 3

department: Bionformatics & Biostatistics Unit

institute: CIPF

summary: Germline mutations in CDKN2A and/or red hair colour variants in MC1R genes are associated with an increased susceptibility to develop  cutaneous melanoma. To investigate the impact of germinal p.G101W CDKN2A mutation and MC1R variants on gene expression and transcription profiles associated to skin cancer and melanoma in particular, we set-up primary skin cultures from twins belonging to the melanoma prone-families with and without these genomic features. were analyzed using expression array methodology.  Overall, 1535 transcripts were deregulated in CDKN2A mutated cells, finding overexpression of immunity-related genes (HLA-DPB1, CLEC2B, IFI44, IFI44L, IFI27, IFIT1, IFIT2, SP110 and IFNK) and downregulation of genes playing a role in the Notch signaling pathway. 3570 transcripts were deregulated in carriers of MC1R variants. In this case, upregulated genes were involved in oxidative stress and DNA damage pathways as well as in neurodegenerative diseases such as Parkinson’s, Alzheimer and Huntington. In contrast, downregulated genes were associated with pigmentation synthesis/transport and angiogenesis. By using a coculture system, this study identified key molecular functions and/or pathways that are deregulated due to alterations in melanoma susceptibility genes which in turn, could be involved in initiation/progression of the disease.

overall_design: 12 samples total.  Several experimental groups: with and without genomic features (CDKN2A, MC1R).

first: Joan

last: Puig-Butille

first: Maria

last: Escamez

last: Garcia-Garcia

first: Gemma

last: Tell

first: Angels

last: Fabra

first: Lucia

last: Martinez-Santamaria

first: Celia

last: Badena

first: Paula

last: Aguilera

first: Marta

last: Pevida

first: Joaquín

last: Dopazo

first: Marcela

last: del Río

first: Susana

last: Puig


title: Expression data from primary CB erythroblasts, immortalized/induced erythroblasts, Fetal liver CD34+ blood stem cells, adult CD34+ blood stem cells, erythroleukemia cell line (TF-1) and human ESC and iPSCs

city: Baltimore

first: Xiaosong

last: Huang

state: Maryland

address: 733 North Broadway, Rm780

department: Medicine/Hematology

institute: Johns Hopkins University

summary: The supply of red blood cells (RBCs) is not sufficient in many developing countries or in developed countries for patients who need chronic transfusion from best-matched donors. Ex vivo expansion and maturation of human erythroid precursor cells (erythroblasts) could represent a potential solution. Proliferating erythroblasts can be expanded from human umbilical cord blood mononuclear cells (CB MNCs) ex vivo for 10^6-10^7 fold (in ~50 days) before undergoing senescence. Here, we report that ectopic expression of three to four genetic factors that have been used for iPS cell derivation enables CB-derived erythroblasts to undergo extended ex vivo expansion (≥10^51 fold in ~9 months) in a defined suspension culture condition without change of cell identity or function. These vastly expanding erythroblasts maintain homogeneously immature erythroblast phenotypes, a normal diploid karyotype and dependence on specific combination of cytokines and hormone for survival and proliferation throughout the continuous expansion period. When switched to a culture condition for terminal maturation, these immortalized erythroblasts gradually exit cell cycle, decrease cell size, accumulate hemoglobin, condense nuclei and eventually give rise to enucleated hemoglobin-containing erythrocytes. Our result may ultimately lead to the development of unlimited sources of cultured RBCs for optimally-matched or personalized transfusion medicine.

overall_design: We compared the global gene expression profiles of different human cell types: iE: immortalized erythroblasts generated by genetic reprogramming from pCBE; pCBE: primary cord blood-derived erythroblasts; CD34+: CD34+ purified hematopoietic stem/progenitor cells from adult blood or fetal liver; TF-1: a human erythroleukemia cell line; ESC: human embryonic stem cells; iPSCs: human induced pluripotent stem cells. We want to see the relationship among these cell types. We included multiple samples (biological replicates) for most cell types.

first: Conover

last: Talbot Jr.

first: Kitman

last: Tsang


title: Differentiation resistant HPV16-immortalized keratinocytes: Six1 transfected vs. Control.

status: Public on Dec 24 2013

city: Columbia

first: Diego

last: Altomare

state: SC

address: 715 Sumter Street, Room 617

department: Department of Drug Discovery and Biomedical Sciences

institute: University of South Carolina

summary: The overexpression of Six1, a member of the Six family of homeodomain transcription factors, has been found in various human cancers, and is associated with tumor progression and metastasis. We previously determined that the expression of Six1 mRNA increased during in vitro progression of human papillomavirus type 16 (HPV16)-immortalized human keratinocytes (HKc/HPV16) toward a differentiation-resistant (HKc/DR) phenotype. However, if Six1 promotes HPV16-mediated transformation or not remains unknown. HKc/DR were transfected with a Six1 or control vector and RNA isolated from these cells were used in an Agilent two-color gene expression profiling experiment. The goal was to determine the effects of Six1 on global gene expression.

overall_design: Two-condition experiment, Six1 vs. Control HKc/DR cells. Biological replicates: 4 Six1-transfected replicates and 4 control-transfected replicates.

first: Hanwen

last: Xu

first: Yu

last: Zhang

first: Fang

last: Wan

last: Pirisi

last: Peña

first: Kim

middle: E

last: Creek


title: Tie-2 expressing monocytes (TEM) expression data

city: Epalinges

first: Marie-Agnès

last: Doucey

address: Biopôle 3; Ch. des Boveresses 155

country: Switzerland

summary: TEM differentiated in vitro were exposed to treatments  increasing or decreasing their proangiogenic activity. We used microarrays to identify the genes differentially expressed among the treatments and associated to changes in TEM proangiogenic and protumoral functions.

overall_design: TEM were exposed  2 hours to the treatments, washed, kept for 30h in culture and used for RNA extraction.

first: Ioannis

last: Xenarios


title: Toll-like receptor 2 and 4 agonists prolong triglyceride retention in macrophages

status: Public on Dec 17 2013

city: Bethesda

first: Timothy

middle: G

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

country: USA

institute: National Institute of Allergy and Infectious Diseases

summary: When macrophages are activated by sensing bacterial lipopolysaccharides (LPS), they greatly increase their motility, mRNA synthesis and protein production.   Most of the ATP needed for these responses is derived from the uptake and catabolism of glucose, a relatively inefficient ATP source.  Although the stimulated cells also increase their uptake of free fatty acids, they store a large fraction as triglycerides (TAG).   We report here that both Toll-like receptor 4 (TLR4) and TLR2 agonists stimulate prolonged TAG retention by primary murine and human macrophages.   Agonist-induced TAG storage lasted at least 72-96 hrs in vitro and was associated with increases in fatty acid (FA) uptake, FA esterification, and FA incorporation into TAG; FA oxidation decreased.  The results of expression and inhibitor studies support a prominent role for increases in long chain acyl CoA synthase 1 (ACSL1) and diacylglycerol acyltransferase-2 (DGAT2) during the sustained response to TLR2/4 activation; decreases in adipose triglyceride lipase (ATGL, Pnpla2) and monoacylglycerol lipase (MgII) may also contribute.   Stimulated murine macrophages that retained TAG carried out phagocytosis more effectively and were protected from saturated fatty acid-induced cell death (lipotoxicity).   TLR agonist-induced TAG retention in macrophages is thus an active, sustained process that may have important adaptive functions.  It may also contribute to the persistence of lipid-laden macrophages in infected tissues, host susceptibility to some microbial pathogens, and the pathogenesis of atherosclerosis.

overall_design: RNA from macrophage loaded with Fatty Acids, stimulated with bacterial lipopolysaccharides (LPS), or both  compared to untreated controls (FA, LPS, FA+LPS, untreated). Replicates from 4 independent experiments.

first: Ying-ling

first: Joel

last: Morales-Rosado

first: Jessica

last: Ray

first: Mingfang

last: Lu

first: Robert

last: Munford


title: Altered mucosal homeostasis in mice lacking secretory antibodies

status: Public on Dec 28 2013

city: Oslo

first: Leonardo

last: Meza-Zepeda

address: Ullernchausseen 70

department: Dept. of Tumor Biology

country: Norway

institute: The Norwegian Radium Hospital

summary: The mammalian gut is inhabited by a large and complex microbial community that lives in a mutualistic relationship with its host. Innate and adaptive mucosal defense mechanisms ensure a homeostatic relationship with this commensal microbiota. Secretory antibodies are generated from the active polymeric Ig receptor (pIgR)-mediated transport of IgA and IgM antibodies to the gut lumen and form the first line of adaptive immune defense of the intestinal mucosa. We probed mucosal homeostasis in pIgR knockout (KO) mice, which lack secretory antibodies. We found that in pIgR KO mice, colonic epithelial cells, the cell type most closely in contact with intestinal microbes, differentially expressed (>2-fold change) more than 200 genes compared with wild type mice, and upregulated the expression of anti-microbial peptides in a commensal-dependent manner. Detailed profiling of microbial communities based on 16S rRNA genes revealed differences in the commensal microbiota between pIgR KO and wild type mice. Furthermore, we found that pIgR KO mice showed increased susceptibility to dextran sulfate sodium (DSS)-induced colitis, and that this was driven by their conventional intestinal microbiota. In conclusion, secretory antibodies or the pIgR itself are required to maintain a stable commensal microbiota. In the absence of these humoral effector components, gut homeostasis is disturbed and the outcome of colitis significantly worsened.

overall_design: 4 groups: wild type mice treated with antibiotic (5 replicates), wild type mice left untreated (5 replicates), pIgR KO mice treated with antibiotic (6 replicates), and pIgR KO mice left untreated (6 replicates).

first: Dag

middle: H

last: Reikvam

first: Alexander

last: Erofeev

first: Rejoanoul

last: Islam

first: Muriel

last: Derrien

first: Vedrana

last: Grcic

first: Anders

last: Sandvik

first: Peter

last: Gaustad

first: Frode

last: Jahnsen

first: Hauke

last: Smidt

first: F

last: Johansen


title: Impact of 5-Aza-2`-deoxycytidine and Epigallocatechin-3-gallate for induction of human regulatory T cells

status: Public on Dec 19 2013

city: Braunschweig

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary: The epigenetic regulation of transcription factor genes is critical for T cell lineage specification. A specific methylation pattern within a conserved region of the lineage specifying transcription factor gene FOXP3, the Treg-specific demethylated region (TSDR), is restricted to regulatory T (Treg) cells and required for stable expression of FOXP3 and suppressive function. We analyzed the impact of hypomethylating agents 5-Aza-2`-deoxycytidine and Epigallocatechin-3-gallate (EGCG) on human CD4+CD25- T for generating Treg cell specific DNA methylation pattern within FOXP3-TSDR and inducing functional Treg cells. Gene expression, including lineage specifying transcription factors of the major T cell lineages and their leading cytokines, functional properties and global transcriptome changes were analyzed.   5-Aza-2`-deoxycytidine induced FOXP3-TSDR methylation and expression of Treg cell specific genes FOXP3 and LRRC32. Proliferation of 5-Aza-2´deoxycytidine treated cells was reduced, but they did not show suppressive function. Hypomethylation was not restricted to FOXP3-TSDR and expression of master transcription factors and leading cytokines of Th1 and Th17 cells were induced. EGCG induced global DNA hypomethylation to a lower degree than 5-Aza-2´deoxycitidine, but no relevant hypomethylation within FOXP3-TSDR or expression of Treg cell specific genes.   Both DNMT inhibitors did not induce full functional human Treg cells. Although 5-Aza-2`-deoxycytidine treated cells phenotypically appeared to be Treg cells, they did not suppress proliferation of responder cells, which is an essential capability to be used in Treg cell transfer therapy.

overall_design: In this study we analyze the potency of the two hypomethylating agents 5-Aza-2`-deoxycytidine (5-Aza-dC) and Epigallocatechin-3-gallate (EGCG) for in vitro induction of functional Treg cell cells through generation of a specific methylation pattern within FOXP3-TSDR. We analyzed the expression of Treg cell specific genes and for their functional properties from CD4+CD25- T cells. 5-Aza-dC is a derivative of 5-Azacytidine. Both substances are inhibitors of DNA methyltransferases (DNMTs) and used for therapy of patients with myelodysplastic syndrome and acute myeloid leukaemia. In these patients, 5-Azacytidine has been reported to augment regulatory T cell expansion in blood. EGCG is the most abundant catechin of green tea and has been reported to have cardio protective, anti-cancer, anti-infective properties and protective effects on autoimmune diseases. EGCG has also been described as a potent inhibitor of DNMTs and to induce Foxp3 in Jurkat T cell line.

first: Jan

last: Kehrmann

last: Buer


title: Microarray analysis of Crx Knock-IN mice E168d2 and R90W

status: Public on Dec 01 2013

city: SAINT LOUIS

first: Nicholas

last: Tran

state: Missouri (MO)

address: 660 S Euclid Ave

department: Ophthalmology

institute: Washington University

summary:
P10 retinal gene expression analysis of the homozygous Crx Knock-OUT or Knock-IN mice carrying the mutation E168d2 or R90W.
Results provide important information about the retinal genes affected by mutations in the transcription factor Crx, which have been implicated in human retinopathies.

overall_design: PolyA RNA isolated from 3 Sex-matched (1M,1F) pairs of P10 mouse retinas from each genotype (WT, E168d2neo/d2neo, R90Wneo/Wneo, and Crx -/-)

first: Shiming

last: Chen


title: Changes in gene expression during acinar morphogenesis of normal-like human mammary epithelial cells in a 3D basement membrane cultures

city: Chiba

first: Kazuhiro

last: DAINO

address: 4-9-1 Anagawa, Inage-ku

country: Japan

institute: National Institutes for Quantum and Radiological Science and Technology

summary: In this study, we examined temporal changes in gene expression during acinar morphogenesis of normal-like human mammary epithelial cells (MCF-10A) in a three-dimensional (3D) basement membrane cultures.

overall_design: Changes in gene expression in 3D culture of MCF-10A cells were measured at 4, 8, and 12 days.

last: Daino

first: Yoshiya

last: Shimada


title: The anti-inflammatory nature of HDL in macrophages is mediated by ATF3

status: Public on Dec 08 2013

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: Elevated plasma levels of High Density Lipoprotein (HDL) are associated with decreased risk of cardiovascular disease (CVD). The protective role of HDL in atherosclerosis has been attributed primarily to its ability to remove excess cholesterol from lipid-laden macrophages (foam cells) within the arterial walls. However, clinical trials that raise HDL cholesterol levels have failed to show a benefit casting doubts on our basic understanding of HDL function. Atherosclerosis is a chronic inflammatory condition underlying CVD and driven in part by the recognition of metabolic danger signals by innate immune receptors on macrophages. A potential feature that could contribute to HDL’s protective effects in CVD could be HDL's anti-inflammatory nature, such as its ability to reduce endothelial cell activation. However, the molecular mechanisms by which HDL reduces inflammatory macrophage responses remain poorly understood and difficult to separate from its cholesterol depleting activity. Here we show that HDL protects against Toll like receptor (TLR)-induced inflammation both in vivo and in vitro under normocholesteremic conditions by suppressing the transcription of inflammatory cytokines in a manner independent of its ability to remove cellular cholesterol. We identify Activating Transcription Factor 3 (ATF3), a transcriptional repressor of the CREB family of basic leucine zipper transcription factors, as a HDL-inducible regulator of macrophage activation. HDL’s ability to down modulate TLR responses was severely compromised in ATF3-deficient cells demonstrating that ATF3 mediates HDL's anti-inflammatory effects and may explain the broad anti-inflammatory functions of HDL.

overall_design: Bone marrow-derived macrophages (BMDMs) were obtained by culturing bone marrow cells from 6 to 8 week old wildtype C57BL/6 mice in DMEM supplemented with 10% FCS, 10 mg ml-1 Ciprobay-500 and 40 ng ml-1 M-CSF (R & D Systems). BMDMs of wt mice were pretreated for 6 h with HDL (2 mg ml-1 ) then stimulated with CpG (100 nM) for 4 h. Further wild type or Atf3-deficient BMDMs were pretreated with 2 mg ml-1 HDL for 6 h and subsequently stimulated with CpG (100 nM) or P3C (50 ng ml-1) for 4 h. For carotid artery injury approximately 12-week old male WT and Atf3-deficient mice were anesthetized with i.p. injection of 150 mg/kg ketaminehydrochloride (Ketanest, Pharmacia) and 0.1 mg/kg xylazinehydrochloride (Rompun 2%, Bayer). A small incision from the cranial apex of the sternum to just below the mandible was made. After careful preparation of an approximately 6 mm long segment proximal of the bifurcation, the common carotid artery was electrically denuded. A 4 mm long lesion was made by applying two serial 5 second bursts of 2 Watt using 2 mm wide forceps. The skin was then sutured and the mice allowed to recover in individual cages before returning to their littermates. Three hours later the mice received a single 200 ?l i.v. injection of 20 mg/kg HDL or PBS.

first: Dominic

last: De Nardo

first: Larisa

last: Labzin

first: Hajime

last: Kono

first: Reiko

last: Seki

first: Susanne

middle: V

last: Schmidt

first: Michael

last: Kraut

first: Anja

last: Kerkseik

first: Niklas

last: Bode

first: Sebastian

last: Zimmer

first: Manfred

last: Kneilling

first: Martin

last: Röcken

first: Dieter

last: Lütjohann

first: Sam

last: Wright

first: Eicke

last: Latz


title: Genome-wide analysis of gene expression within vitiligo mouse skin

status: Public on Dec 12 2013

city: Worcester

first: John

last: Harris

state: MA - Massachusetts

address: 364 Plantation St

department: Medicine - Dermatology

institute: UMass Medical School

summary: Skin samples from mice in a model of vitiligo were selected for gene expression profiling in order to identify active inflammatory pathways.

overall_design: Total RNA isolated from 6 mouse samples from fresh skin, 3 from vitiligo mice and 3 from control mice.


title: Transcriptional consequences of Zfy1 and Zfy2 expression in GV oocytes

status: Public on Nov 27 2013

city: Canterbury

first: Peter

middle: James

last: Ellis

state: Kent

address: Stacey Building

department: School of Biosciences

institute: University of Kent

summary: Sex-reversed ‘XYSry-’ female mice that lack Sry due to the 11 kb deletion Srydl1Rlb have very limited fertility, partly due to the effects of posessing only a single X chromosome. However, the fertility deficit is even worse in sex-reversed XY females than in XO females, implicating Y-linked genes in the further loss of fertility. Transgenic addition of Yp-linked genes to XO females and also to normal XX females implicated Zfy2 (but not the related Zfy1) as the cause of this effect.  This study examines the transcriptional effects of Zfy2 and Zfy1 in GV oocytes from normal XX females.

overall_design: 18 samples representing 3 biological replicates from each of 6 genotypes. Genotypes are XX (normal control); XX,Zfy2-nf (control with non-functional Zfy2 transgene); XX,Zfy2 (with Zfy2 transgene); XX,Zfy2+Eif2s3y (contaminated sample, XX with Zfy2 transgene and also an Eif2s3y transgene in proportion of the cells), XX,Zfy1-lo (with single-copy Zfy1 transgene); XX-Zfy1-hi (with multi-copy Zfy1 transgene).

first: Nadège

last: Vernet

first: Maria

last: Szot

first: Shantha

middle: K

last: Mahadevaiah

first: Fanny

last: Decarpentrie

first: Obah

middle: A

last: Ojarikre

first: Áine

last: Rattigan

first: Teruko

last: Taketo

first: Paul

middle: S

last: Burgoyne


title: Comparison of gene expression profiles of anaplastic glioma with or without the mutated IDH1/2 gene

status: Public on Dec 04 2013

city: Sendai

first: Masayuki

last: Kanamori

state: Miyagi

address: 1-1 Seiryo-cho

department: Neurosurgery

institute: Tohoku University, Graduate School of Medicine

summary: To examine the NRF2 activity in anaplastic glioma with mutated IDH1/2, we conducted the microarray analysis to measure the expression levels of representative NRF2 target genes, including NQO1, HMOX1, GCLM, TXNRD1, and PRDX1.

overall_design: 12 anaplastic gliomas with or without mutated IDH1/2.

first: M

first: K

last: Taguchi

last: Yamamoto

first: H

last: Motohashi


title: Identifying functional CpG island methylation markers in clear cell renal cell cancer cell lines

status: Public on Nov 22 2013

city: Ghent

first: Leander

last: Van Neste

address: Coupure Links 653

department: Molecular Biotechnology

country: Belgium

institute: Ghent University

summary: Clear cell renal cell carcinoma (ccRCC) is the most common adult renal cancer. Although the molecular characteristics of ccRCC are currently being studied, the biologically and clinically relevant ccRCC methylome remains to be elucidated. To explore the RCC hypermethylome we employed massive sequencing of methyl-binding protein enriched DNA and validated the biological relevance of the identified hypermethylated sites by pharmacological inhibition of DNA methylation. We identified four candidate tumor suppressor genes (GREM1, LAD1, NEFH, and NEURL) of which promoter CpG island hypermethylation was strongly predictive for ccRCC survival in two independent series (n=150 and n=185) of ccRCC primary samples. The four markers combined are strongly associated with risk for cancer-related death in the test series (HR 3.64, 95% CI 1.02-13.01) as well as, independently of other clinicopathological characteristics, in the validation series (HR 7.54, 95% CI 2.68-21.19) using Cox proportional hazard models. According to Harrell’s C statistics and the Akaike Information Criterion (AIC) the four marker panel provides the best predictive capacity with the best fit of the model as assessed for the tested markers. These results provide novel insights into the ccRCC hypermethylome and identify a strong methylation marker panel to potentially guide personalized ccRCC patient management. Preliminary to implementation of this marker panel into clinical practice, enrollment of these patients in a Phase-III trial to study adjuvant treatment efficacy is essential.

overall_design: 4 independant clear cell renal cancer cell lines were used before and after treatment with the DNA methylation inhibitor AZA or the HAZA inhibitor TSA.

first: Iris

last: Vlodrop

first: Tim

last: De Meyer

first: Manon

last: van Engeland

first: Stephen

last: Baylin

first: Wim

last: Van Criekinge