title: Expression data from human osteosarcoma bone primaries or lung metastases

status: Public on Aug 13 2016

first: Wu

last: Zhang

address: 197 Rui Jin Er Road

institute: Shanghai Institute of Hematology

summary:
The high concentration of Well5 cells was resuspended into 20μl PBS, the needle along the tibia direction, before reaching in a breakthrough sense, direct injection cells. At 7 days after injection, proximal tibia was able to reach mass production. At 20 days after injection, the proximal tibia mass increased.If prolonging exposure by BLI,this stage displayedthat tumor cell signalsbegan to lung metastasis. Osteosarcoma orthotopic lung metastasis model was successfully constructed. Total RNA was extracted from sorted osteosarcoma cells of the primary site and lung metastases using Trizol (Invitrogen).
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during osteosarcoma lung metastasis. In support of the notion that fibrosis marks the lung metastasis, the expression of numerous fibrosis-related genes such as FN1, COLs, and MMPs were upregulated from the primary site to lung metastasis in Well5-luc orthotopic inoculation model.

overall_design: Total RNA was extracted from sorted osteosarcoma cells using Trizol (Invitrogen). Gene expression profiling was conducted by Shanghai Biotechnology Corporation using Affymetrix U133 plus 2.0 arrays (Affymetrix, Santa Clara, CA). All data were analyzed according to the manufacturer’s protocol. Raw data generated from Affymetrix CEL files were normalized by RMA background correction; values were log2 transformed. For the enrichment of P values of each GO term, we used Fisher’s exact test to calculate P values and R package stats to calculate FDR (q value) by BH method (www.r-project.org).

first: Jiang

last: Zhu


title: ZIP7 is indispensable for proliferation of intestinal epithelial cells and maintenance of intestinal stem cells

status: Public on Aug 19 2016

city: Yokohama, Kanagawa

first: Yoshiki

last: Mochizuki

address: 1-7-22 Suehiro-cho

country: Japan

institute: RIKEN

summary: Intestinal epithelium are generated by intestinal stem cells, which are recognized morphologically as slender columnar cells at the base of the crypt. Stem cells produce transit-amplifying (TA) cells, which divide a number of times and the daughter cells differentiate into absorptive enterocytes as well as secretory-lineages. Intestinal stem cells highly express Lgr5 which is decreased in TA cells. Here, we show that the zinc transported SLC39A7/ZIP7 is essential for the proliferation of TA cells and maintenance of intestinal stem cells. Lgr5Med TA cells derived from Zip7-deficient mice upregulated the expression of unfold protein responses-related genes including pro-apoptotic genes, indicating of induction of ER stress in these cells. The same effect was seen in Lgr5Hi stem cells derived from Zip7-deficient mice. We conclude that ZIP7 is fundamental to the maintenance of crypt homeostasis by resolving ER stress.

overall_design: Small intestinal crypts were isolated form tamoxifen-treated control (Zip7flox/+, Villin-CreERT2, Lgr5-EGFP-ires-CreERT2) and tamoxifen-treated Zip7∆IEC (Zip7flox/flox, Villin-CreERT2, Lgr5-EGFP-ires-CreERT2) mice. We FACS purified intestinal crypt cells according to their Lgr5 expression levels. RNA was isolated from four FACS sorted cell populations: Lgr5Hi cells and Lgr5Med cells derived from control mice, Lgr5Hi cells and Lgr5Med cells derived from Zip7∆IEC mice. Isolated RNA was analyzed using the Affymetrix platform.

first: W

last: Ohashi

first: K

last: Hase

first: T

last: Fukada


title: The gene regulation of SPANXA in lung cancer

status: Public on Aug 12 2016

city: Taipei

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

summary:
SPANXA is identified as a cancer-testis antigens expressed in normal testis but dysregulated in various tumors. It plays unknown roles. This study sought to investigate the effects of the nuclear protein, SPANXA, on the biological behavior and global gene expression profiles of lung cancer cells. Expression microarray and bioinformatics analyses indicated that SPANXA mainly regulated genes involved EMT pathways in CL1-5 cells, a pattern that correlated with the altered behavior of CL1-5 cells observed after overexpressed SPANXA.
We used microarrays to identify the global gene alterations in lung cancer cells CL1-5 after ectopic expressing SPANXA.

overall_design: Ectopic expressing SPANXA-V5 and vector in low-expressed SPANXA lung cancer cell line, CL1-5

first: Yi-Jing

last: Hsiao

first: Shih-Chun

last: Hsu

first: Kang-Yi

last: Su


title: ZBP1 is a cytosolic RNA virus sensor driving activation of the NLRP3 inflammasome, pyroptosis, necroptosis and apoptosis

status: Public on Aug 11 2016

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

country: USA

institute: St Jude Childrens Research Hospital

summary: The innate immune system recognizes nucleic acids as a signature of microbial infection and initiates host-protective responses, including the production of type I IFN and proinflammatory cytokines. Z-DNA binding protein 1 (ZBP1, also known as DLM-1 or DAI) was previously identified as a dsDNA binding protein, triggering DNA-mediated activation of innate immune responses. However, mice or cells lacking ZBP1 produce normal levels of type I IFN in response to dsDNA. Therefore, the classification of ZBP1 as a true DNA sensor remains to be resolved. Here, we report that the single stranded RNA virus, influenza A virus (IAV) is a trigger of the cytosolic sensor ZBP1. Sensing of IAV infection by ZBP1 engages a novel NLRP3 inflammasome pathway that is not defined by the conventions of the canonical and non-canonical NLRP3 inflammasome pathways. Surprisingly, IAV-induced cell death was not prevented by the absence of the NLRP3 inflammasome. Instead, we identified parallel contributions from pyroptosis, necroptosis and apoptosis in the execution of ZBP1-dependent cell death, mediated by the kinase RIPK3. Overall, the ability of ZBP1 to sense IAV infection signifies a point of divergence for IAV-induced programmed cell death pathways and inflammasome activation.

overall_design: We used microarrays to explore the gene expression profiles differentially expressed in influenza-infected bone marrow derived macrophages (BMDM) isolated from Ifnar1-/- and wild-type mice.

first: Teneema

last: Kuriakose

first: Si

middle: M

last: Man

first: Thirumala-Devi

last: Kanneganti


title: Transcriptomic evaluation of bovine embryo quality on blastocysts obtained from peri-pubertal oocyte donors

city: Quebec

first: Léonie

last: Morin-Doré

state: Quebec

address: 2440, boulevard Hochelaga

department: Animal Sciences

country: Canada

institute: Laval University

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

overall_design: Refer to individual Series


title: Transcriptomic evaluation of bovine embryo quality on blastocysts obtained from peri-pubertal oocyte donors [11 mo vs 14 mo]

summary: Assisted reproduction technologies (ART) and high selection pressure observed in the dairy industry are leading towards the use of younger females for reproduction purpose, reducing the interval between generations. This situation might have an impact on

overall_design: 10 young Holstein cows were used 3 times each at different ages for ovarian stimulation protocols and oocyte collections (at 8, 11 and 14 months). These oocytes were then fertilized in vitro with adult bull semen, generating 3 lots of embryos per animal.

first: Patrick

last: Blondin

first: Christian

last: Vigneault

first: François-Xavier

last: Grand

first: Rémi

last: Labrecque

first: Marc-André

last: Sirard


title: Transcriptomic evaluation of bovine embryo quality on blastocysts obtained from peri-pubertal oocyte donors [8 mo vs 14 mo]

summary: Assisted reproduction technologies (ART) and high selection pressure observed in the dairy industry are leading towards the use of younger females for reproduction purpose, reducing the interval between generations. This situation might have an impact on embryo quality, which can affect the success rate of the procedures. This study aims to document the effect of donor age on embryo quality, on transcriptomic level, in order to caracterize the effect of using young animals for reproduction purpose.

overall_design: 10 young Holstein cows were used 3 times each at different ages for ovarian stimulation protocols and oocyte collections (at 8, 11 and 14 months). These oocytes were then fertilized in vitro with adult bull semen, generating 3 lots of embryos per animal. Semen from the same bull was used for all females, at all times. Each animal was used as its own control for age-effect evaluation. EmbryoGENE plateform allowed whole genome assessment of gene expression patterns at the blastocyst stage. Embryos from animals at 8 vs 14 months and at 11 vs 14 months were used for microarray hybridization. Validation was done performing RT-qPCR tests on 7 candidate genes.


title: Atrial fibrillation is associated with altered left-to-right atria gene expression ratio: implications for arrhythmogenesis and thrombogenesis

status: Public on Aug 09 2016

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

institute: Ming Chuan Univ

summary:
Background: Atrial fibrillation (AF) causes atrial remodeling, and the left atrium (LA) is the favored substrate for maintaining AF. However, it remains unclear if AF remodels both atria differently and contributes to LA arrhythmogenesis and thrombogenesis.
Results: AF was associated with differential LA-to-RA gene expression related to specific ion channels and pathways as well as upregulation of thrombogenesis-related genes in the LA appendage. Targeting the molecular mechanisms underlying the LA-to-RA difference and AF-related remodeling in the LA appendage may help provide new therapeutic options in treating AF and preventing thromboembolism in AF.

overall_design: Paired left atrial and right atrial specimens were obtained from 13 patients with persistent AF receiving valvular surgery. The Paired specimens were sent for microarray comparison. Selected results were validated by quantitative real time-PCR (q-PCR) and Western blotting. Ultrastructural changes in the atria were evaluated by immunohistochemistry.

first: Feng-Chun

last: Tsai

first: Yen-Chen

last: Li

first: Shang-Hung

last: Chang

first: Gwo-Jyh

first: Yu-Juei

first: Yuan-Min

last: Lin

first: Chun-Li

last: Wang

first: Yung-Hsin

last: Yeh


title: Expression microarray analysis of HaCaT epidermal keratinocyte treated with AdcaRAS/dnRAS, p53 siRNA, and/or TGF-beta

city: Tokyo

first: Daizo

last: Koinuma

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

department: Pathology

institute: University of Tokyo

summary:
We demonstrate that activation of Ras and TGF-β pathways strengthens the binding of p63 to its genomic sites and modulates the expression of p63 target genes.
Our findings support a model of mutual inhibition between ΔNp63α, DUSP6 and mutant p53 downstream of oncogenic Ras and TGF-β.

overall_design: We used expression microarrays to evaluate the effect of caRAS/dnRAS, p53 siRNA, and/or TGF-beta in HaCaT epidermal keratinocyte.

first: Eleftheria

last: Vasilaki

first: Masato

last: Morikawa

first: Anna

last: Mizutani

first: Yudai

last: Hirano

first: Shogo

last: Ehata

first: Anders

last: Sundqvist

first: Hiroyuki

last: Aburatani

first: Aristidis

last: Moustakas

first: Carl-Henrik

last: Heldin

first: Kohei

last: Miyazono


title: A comprehensively characterized cell line panel highly representative of clinical ovarian high-grade serous carcinomas

city: Vancouver

first: Kelsie

middle: L

last: Thu

state: British Columbia

address: 675 West 10th Avenue

institute: BC Cancer Research Centre

type: Methylation profiling by genome tiling array


title: Gene expression profiling of supporting, interstitial/stromal, and germ cells in the differentiating mouse gonads

city: Krakow

first: Michal

last: Kolasa

address: Gronostajowa 9

country: Poland

institute: Jagiellonian University

summary: The aim of this study was to analyze the gene expression profile for three main cell lines (supporting, interstitial/stromal, and germ cells) isolated from developing gonads at the critical period of sexual differentiation (between 11.5, and 13.5 dpc).

overall_design: Three cell lines (supporting, interstitial/stromal, and germ cells) were isolated from murine fetal XX and XY gonads at three time points (11.5, 12.5, and 13.5 dpc). Transgenic mouse strains with the expression of cell type specific fluorescent markers were used to isolate the cell lines. Cells were sorted using FACS method and then the RNA was extracted.

first: M

first: A

last: Korzenny


title: Different effects of IL-13 and IL-4 on Mφ in the presence of IL-10

status: Public on Aug 06 2016

city: Penzberg

first: Leon

last: Pradel

address: Nonnenwald 2

country: Germany

institute: Roche Innovation Center Munich

summary: Tumor-associated macrophages (TAM) represent an abundant cell population of the immune infiltrate in solid tumors and have been shown to orchestrate escape from immune surveillance. Macrophages display a very plastic phenotype which is recapitulated in vitro by classifying certain subsets according to exposure with defined, individual cytokines. The tumor-promoting M2 macrophages are polarized in vitro by differentiating human monocyte-derived macrophages with the T helper cell type 2 (Th2) response cytokines interleukin-4 and interleukin-13 or the immunosuppressive cytokine interleukin-10. Notably, only the latter macrophage subset undergoes apoptosis when treated with the colony stimulating factor 1 receptor (CSF1R) blocking antibody emactuzumab. However, under physiologic conditions the phenotype of TAM is shaped by a combination of cytokines. Hence, we evaluated if the addition of IL-10 to IL-4 or IL-13 differentiated macrophages is able to override IL-4/-13 mediated signaling and to restore susceptibility to emactuzumab. Though addition of IL-10 did not restore emactuzumab susceptibility, we surprisingly detected that only IL-4 differentiated macrophages sustained their specific marker expression while IL-10 skewed the IL-13 differentiated macrophage profile towards the IL-10 regulated phenotype. In-depth characterization by gene expression profiling revealed unique signatures of IL-4+IL-10 and IL-13+IL-10 differentiated macrophage subsets characterized by upregulation of the canonical NFκB signaling or Wnt/β-catenin signaling pathways, respectively. In silico-based analysis of a large cohort of cancer patients revealed distinct interleukin-4 or interleukin-13 overexpression patterns in a subset of patients with partial co-expression of IL-10 but almost absent IL-4/IL-13 co-expression. These patients may have less TAM depletion under therapy with CSF1R inhibitors.

overall_design: Five different macrophage subtypes were differentiated for six days with respect to different cytokines and transcriptomically profiled with three biological replicates derived from three different human, healthy volunteer donors

middle: P

first: Andreas

last: Franke

first: Carola

middle: H

last: Ries


title: Molecular, Phenotypic, and Sample-associated Data to Describe Pluripotent Stem Cell Lines and Derivatives

status: Public on Aug 20 2016

city: Seattle

first: Kenneth

last: Daily

state: WA

address: 1100 Fairview Ave N

institute: Sage Bionetworks

summary: The use of induced pluripotent stem cells (iPSC) derived from independent patients and sources holds considerable promise to improve the understanding of development and disease. However, optimized use of iPSC depends on our ability to develop methods to efficiently qualify cell lines and protocols, monitor genetic stability, and evaluate self-renewal and differentiation potential. To accomplish these goals, 57 stem cell lines from 10 laboratories were differentiated to 7 different states, resulting in 248 analyzed samples. Cell lines were differentiated and characterized at a central laboratory using standardized cell culture methodologies, protocols, and metadata descriptors. Stem cell and derived differentiated lines were characterized using RNA-seq, miRNA-seq, copy number arrays, DNA methylation arrays, flow cytometry, and molecular histology. All materials, including raw data, metadata, analysis and processing code, and methodological and provenance documentation are publicly available for re-use and interactive exploration at https://www.synapse.org/pcbc . The goal is to provide data that can improve our ability to robustly and reproducibly use human pluripotent stem cells to understand development and disease.

overall_design:
114 samples
This submission represents DNA methylation component of study.


title: Illumina HumanMethylation450 array data for Ovarian Cancer Samples

summary: This study aimed to generate a new panel of comprehensively, genomically characterized high-grade serous ovarian carcinoma (HGSOC) cell line and xenograft models. Multidimensional genomic data were generated and compared between cell lines/xenografts and the tumours they were derived from, indicating the cell lines/xenografts are highly similar to their patient-matched tumours. Cell line/xenograft data were also compared to TCGA ovarian tumours to show the cell lines are good models of clinical HGSOC.

overall_design: Illumina HumanMethylation450 arrays were performed according to the manufacturer's directions on DNA extracted from i) tumour cells purified from ovarian tumour ascites, and ii) established cell lines. Evaluation of the similarity in copy number/methylation/gene expression/mutational profiles of cell lines/tumours/xenografts was performed.

first: Adi

middle: F

last: Gazdar


title: Stilbenoids remodel the DNA methylation patterns in breast cancer cells and inhibit oncogenic NOTCH signaling through epigenetic regulation of MAML2 transcriptional activity

status: Public on Aug 10 2016

first: Barbara

last: Stefanska

state: BC

address: 2205 East Mall

department: Land and Food Systems

institute: The University of British Columbia

summary: Genome wide DNA methylation profiling of human breast cancer cell lines, lowly invasive MCF10CA1h and highly invasive MCF10CA1a, treated with vehicle control (ethanol) and with RSV (resveratrol). The Illumina Infinium 450K Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 450,000 CpGs in human cell lines exposed to described treatments. Samples included biological triplicate of MCF10CA1h control (ethanol treated), biological triplicate of MCF10CA1h treated with RSV, biological triplicate of MCF10CA1a control (ethanol treated), biological triplicate of MCF10CA1a treated with RSV.

overall_design: Bisulphite converted DNA from the 12 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip v1.2

first: Katarzyna

last: Lubecka

first: Lucinda

last: Kurzava

first: Kirsty

last: Flower

first: Hannah

last: Buvala

first: Hao

last: Zhang

first: Dorothy

last: Teegarden

first: Ignacio

last: Camarillo

first: Matthew

last: Suderman

first: Shihuan

last: Kuang

first: Ourania

last: Andrisani

first: James

last: Flanagan


title: Epigenetic clonality confers por prognosis in colorrectal cancer patients (technical replicates)

status: Public on Aug 16 2016

city: L'Hospitalet del Llobregat

first: Sebastian

last: Moran

state: Barcelona

address: Av. Gran Via de l'Hospitalet, 199-203

department: PEBC

country: Spain

institute: IDIBELL

summary:
In CRC, 1) to identify epigenetic changes at inter-tumor and intra-tumor level, and 2) to relate intra-tumor clonality to clinical, molecular and histopathologic parameters. From 79 FFPE tumors, 3 different regions were macrodissected: invasive front (IF), digestive tract surface (DTS) and central bulk (CB). Clinical, molecular, and histopathologic parameters were stablished. Epigenetic analysis was performed using Infinium 450K beadchip (Illumina) and R statistics. Intra-tumor regions clustered together by patient. The biggest epigenetic changes were in IF vs DTS/CB. By patient, the most often divergent region was IF (49.4%) comparing with DTS and CB (25.3% in both). It did not correlate with histopathologic, molecular and clinical parameters.Epigenetic clonality is higher at intra-tumor level. The highest changes are observed in IF vs DTS/CB. No association with histopathologic, molecular, and clinical characteristics was found.
Technical replicates of 12 samples previously hybridized on the Infinium HumanMethylation450 to demonstrate technique robustness.

overall_design: From 79 FFPE tumors, 3 different regions were macrodissected: invasive front (IF), digestive tract surface (DTS) and central bulk (CB). When available, metastasis and normal tissue were also collected.

first: Anna

last: Martinez-Cardus

first: Manel

last: Esteller


title: Side population phenotype in quiescent human/murine tissue resident memory (TRM) T cells: Role of ABC transporters and NR4A1 in TRM biology

status: Public on Aug 02 2016

city: New Haven

first: Rakesh

last: Verma

state: CT

address: 333 Cedar St.

department: Yale Cancer Center

institute: Yale University

summary: The ability to detect and isolate human CD8 TSP (Side population), Naïve, Effector memory (EM), Central memory (CM) cells allowed us to compare the global gene expression profiles of these cells. Human TSP cells comprise of distinct gene expression profile specifically enriched for genes overexpressed in TRM cells.

overall_design: RNA samples from CD8 TSP (Side population), Naïve, Effector memory (EM), Central memory (CM) cells were amplified, labeled, and hybridized on the Affymetrix Human Genome U133 Plus 2.0 microarray chips. The data were analyzed with GeneSpring GX 12.5 (Agilent Technologies)


title: Functional screening implicates miR-371-3p and peroxiredoxin 6 in reversible tolerance to cancer drugs [SPR899]

status: Public on Aug 01 2016

city: South San Francisco

first: Richard

last: Bourgon

state: CA

address: 1 DNA Way, MS 93

department: Bioinformatics & Computational Biology

institute: Genentech, Inc.

summary: Acquired resistance to cancer drug therapies almost always occurs in advanced-stage patients even following a significant response to treatment. In addition to mutational mechanisms, various non-mutational resistance mechanisms have now been recognized. We previously described a chromatin-mediated subpopulation of reversibly drug-tolerant persisters (DTPs) that is dynamically maintained within a wide variety of tumor cell populations. Here, we explored a potential role for microRNAs in such transient drug tolerance. Functional screening of 879 human microRNAs revealed miR-371-3p as a potent suppressor of drug tolerance. PRDX6 (peroxiredoxin 6) was identified as a key target of miR-371-3p in establishing drug tolerance by regulating PLA2/PKCα activity and reactive oxygen species. PRDX6 expression is associated with poor prognosis in cancers of multiple tissue origins. These findings implicate miR-371-3p as a suppressor of PRDX6 and suggest that co-targeting of PRDX6 or modulating miR-371-3p expression together with targeted cancer therapies may delay or prevent acquired drug resistance.

overall_design: Drug tolerant persisters (DTPs) generated in response to erlotinib treatment were the basis for RNA extraction and hybridization on Affymetrix microarrays. PC9 cells were treated with DMSO or Erlotinib for 9 days to generate DTPs, then RNA was isolated for analyzing the differential gene expression pattern in DTPs compared to parental cells.

first: Nisebita

last: Sahu

first: Jean-Philippe

last: Stephan

first: Darlene

last: Dela Cruz

first: Mark

last: Merchant

first: Benjamin

last: Haley

first: Marie

last: Classon

first: Jeff

last: Settleman


title: Functional screening implicates miR-371-3p and peroxiredoxin 6 in reversible tolerance to cancer drugs [SPR1108]

overall_design: PC9 stable cell lines expressing GFP vector or miR-371-3p were generated to study the effect of miR-371-3p in response to erlotinib treatment for RNA extraction and hybridization on Affymetrix microarrays. Stable cell lines were treated with DMSO or erlotinib for 24hrs and RNA isolated for analyzing the effect of miR-371-3p on gene expression upon erlotinib treatment.


title: Genes regulated by HS3ST2

status: Public on Aug 15 2016

city: Singapore

first: George

middle: W

last: Yip

address: 4 Medical Drive, Block MD10

country: Singapore

institute: National University of Singapore

summary: We used Affymetrix HG U133 Plus 2.0 GeneChips to compare the transcriptome of HS3ST2-transfected and control vector-transfected MDA-MB-231 cells.

overall_design: MDA-MB-231 cells were transfected with HS3ST2- or control-vector. Subsequently, total RNA was collected and processed for analysis using Affymetrix microarrays. Three independent replicates were prepared for each comparison group.

first: G

first: M

last: Götte


title: Effect of LANA deletion on the host gene expression during de novo KSHV infection of SLK cells.

city: Gainesville

first: Zsolt

last: Toth

state: FL

institute: University of Florida

summary: Human SLK cells were infected with wildtype (wt) and LANA knockout (KO) Kaposi's sarcoma-associated herpesvirus (KSHV), separately for 3 days. Cellular gene expression changes were identified upon the wild type and LANA KO KSHV virus infection compared to the uninfected SLK cells using the human gene expression microarray U133plus2.0.

overall_design: 2 independent biological replicates from uninfected SLK cells, wild type KSHV infected SLK cells at 72hrs post-infection (hpi) , and LANA KO infected SLK cells at 72 hrs post-infection were collected and RNA was prepared for microarray analysis.

first: Bernadett

last: Papp

first: J

middle: U

last: Jung


title: Cortical hypermethylation across an extended region spanning the HOXA gene cluster on chromosome 7 is robustly associated with Alzheimer's disease neuropathology

city: Exeter

first: Rebecca

middle: Georgina

last: Smith

state: Devon

address: RILD, RD and E

department: Medical School

country: United Kingdom

institute: University of Exeter

summary: Alzheimer's disease is a progressive neurodegenerative disorder that is hypothesized to involve epigenetic dysfunction. We undertook an epigenome-wide association study across three independent brain tissue cohorts (total n = 999) to identify differential DNA methylation associated with neuropathology in the superior temporal gyrus and prefrontal cortex. We present robust evidence for elevated DNA methylation associated with AD neuropathology across an extended region spanning the HOXA gene cluster on chromosome 7.

overall_design: Prefrontal cortex and superior temporal gyrus tissue from 147 individuals with varying levels of AD pathology. DNA modifications for these samples were quantified using the Illumina Infinium Human 450K Methylation Array.

first: Eilis

last: Hannon

first: Philip

last: De Jager

first: Lori

last: Chibnik

first: Simon

last: Lott

first: Daniel

last: Condliffe

first: Adam

first: Vahram

last: Haroutunian

first: Claire

last: Troakes

first: David

last: Bennett

first: John

last: Powell

last: Lovestone

first: Leonard

last: Schalkwyk

first: Jonathan

last: Mill

first: Katie

last: Lunnon


title: Epigenetic clonality confers por prognosis in colorrectal cancer patients (first study)

first: Sebastian

last: Moran

summary: In CRC, 1) to identify epigenetic changes at inter-tumor and intra-tumor level, and 2) to relate intra-tumor clonality to clinical, molecular and histopathologic parameters. From 79 FFPE tumors, 3 different regions were macrodissected: invasive front (IF), digestive tract surface (DTS) and central bulk (CB). Clinical, molecular, and histopathologic parameters were stablished. Epigenetic analysis was performed using Infinium 450K beadchip (Illumina) and R statistics. Intra-tumor regions clustered together by patient. The biggest epigenetic changes were in IF vs DTS/CB. By patient, the most often divergent region was IF (49.4%) comparing with DTS and CB (25.3% in both). It did not correlate with histopathologic, molecular and clinical parameters.Epigenetic clonality is higher at intra-tumor level. The highest changes are observed in IF vs DTS/CB. No association with histopathologic, molecular, and clinical characteristics was found.

first: Anna

last: Martinez-Cardus

first: Manel

last: Esteller


title: CDK4/6 inhibitors in ER positive breast cancers

city: Dallas

first: Erik

last: Knudsen

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: Gene expression levels were determined with control or PD-0332991 treatment

overall_design: MCF7, T47D cells were subject to DMSO/ PD-0332991 treatment .   RNA was harvested at 120 hours post treatment and analyzed on Illumina microarrays

middle: S


title: Neural differentiated mouse embryonic stem cells (mESCs) under exposure to sodium valproate and sodium arsenite

city: Baltimore

first: Lena

last: Smirnova PhD

state: MD

address: 615 North Wolfe St

department: School of Public Health

institute: The Johns Hopkins University

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

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

platform_organism:
Mus musculus
synthetic construct

overall_design: Refer to individual Series


title: HBV Infection and DNA Stimulation Induce a Unique Innate Immune Response in Hepatocytes

city: Miami

first: Emmanuel

last: Thomas

address: 1550 NW 12th Ave, Papanicolaou Bldg., RM. PAP 514

department: Schiff Center for LIver Diseases

institute: University Of Miami School of Medicine

summary:
Background and Aims: Recent identification of intracellular DNA sensing pathways and involvement in numerous diverse disease processes including viral pathogenesis and autoimmunity suggests a role for these processes in liver pathology. The presence of these pathways in the liver and their role in HBV infection is unknown.  Methods: In order to characterize the role of DNA sensing pathways in the liver, we utilized in vitro models. Microarray was performed on DNA treated and HBV infected hepatoma primary human hepatocytes.  Results: Here we show that HBV infection and foreign DNA results in a significant innate immune response characterized by the production of inflammatory chemokines.
The goal of this study is to characterize the changes in gene expression triggered by HBV and foreign DNA in primary human hepatocytes.

overall_design: PHHs were infected with HBV (MO.I = 50) for 40 hours. PHHs were transfected with 1μg/mL of ISD/dsDNA90 for 12 or 24 hours.  Three replicates were performed for each condition.

first: M

last: Yoneda

first: J

last: Hyun

first: E

middle: R

last: Schiff


title: Functional screening implicates miR-371-3p and peroxiredoxin 6 in reversible tolerance to cancer drugs

first: Richard

last: Bourgon


title: The epigenetic signature of systemic insulin resistance in obese women [BL]

city: Huddinge

first: Ingrid

last: Dahlman

address: Hälsovägen 7

department: Department of Medicine

country: Sweden

institute: Karolinska Institute

summary: Impaired ability of insulin to stimulate cellular glucose uptake and regulate metabolism, that is insulin resistance (IR), links adiposity to metabolic disorders such as type 2 diabetes (T2D), dyslipidemia and cardiovascular disease (Langenberg, 2012). Both genetic and epigenetic factors are implicated in development of systemic IR (Vaag, 2001). IR is characterized by elevated levels of fasting insulin in the general circulation. The aim of this study is to explore whether white adipose tissue (WAT) epigenetic dysregulation is associated with systemic IR by global CpG methylation and gene expression profiling in subcutaneous and visceral adipose tissue. A secondary aim is to determine whether the DNA methylation signature in peripheral blood mononuclear cells reflect WAT methylation, and can be used as marker for systemic IR.

overall_design:
DNA methylation was analyzed in DNA extracted from SAT (subcutaneous adipose tissue) and VAT (visceral adipose tissue) pieces, as well as PBMCs (peripheral blood mononuclear cells), using the Infinium Human Methylation 450 BeadChip assay.
This data is from PBMCs.

first: Peter

last: Arner

last: Sahlqvist

first: Indranil

last: Sinha

first: Hua

last: Xu

first: Xiang

last: Yao

first: Dawn

last: Waterworth

first: Katrina

last: Loomis

first: Anders

last: Thorell

last: Näslund

first: Mikael

last: Ryden


title: Transcriptional Alterations in Bone Marrow Mesenchymal Stromal Cells derived from Acute Myeloid Leukemia patients (AML BM-MSC)

status: Public on Jul 27 2016

city: Berlin

first: Eva

middle: Kristin

last: von der Heide

address: Hindenburgdamm 30

department: Hematology

institute: Charite Berlin

summary:
The aim of the study was to get insights into transcriptional alterations in bone marrow mesenchymal stromal cells derived from acute myeloid leukemia patients
We compared the global gene expression profile from AML BM-MSC (n=19) to healthy donor (HD) controls (HD BM-MSC n=4)

overall_design: AML BM-MSC and HD BM-MSC were isolated from bone marrow aspirates (see below) and hybridized on an Affymetrix HG-U133 Plus 2.0 GeneChip

middle: K

first: Martin

last: Neumann

first: Sebastian

last: Vosberg

first: Jutta

middle: O

last: Tanchez

first: Konstandina

last: Isaakidis

first: Cornelia

last: Schlee

first: Korinna

last: Jöhrens

first: Ioannis

last: Anagnostopoulos

first: Liliana

last: Mochmann

first: Daniel

last: Nowak

first: Wolf-Karsten

last: Hofmann

first: Philipp

middle: A

last: Greif

first: Claudia

middle: D

last: Baldus


title: Immuno-genomic effects of JAK blockade in vivo

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: Small molecule inhibitors of JAK kinases have shown clinical effcacy in the treatment of certain autoimmune diseases. While these are known to block upstream JAK signalling events, their broader impact on the transcriptional footprint in immunocytes are unknown. Here we explore the effects of pan- and isoform-specific JAK blockade on the immuno-genomic network by genomic profiling.

overall_design: 6week old male C57BL/6 mice were gavaged with JAK inhibitor or vehicle for indicated treatment periods. Spleens were harvested and mechanically disrupted to prepare single cell suspensions. These were then stained in multiple surface marker panels to differentiate distinct immunocyte populations.  Cells were sorted directly into TriZol. RNA was prepared in Trizol for gene expression profiling by  Affymetrix Mouse Gene 1.0 ST Arrays.

first: Devapregasan

last: Moodley

first: Hideyuki

last: Yoshida

first: Sara

last: Mostafavi

first: Natasha

last: Asinovski

first: Adriana

last: Ortiz-Lopez

first: Peter

last: Symanowicz

first: Jean-Baptiste

last: Telliez

last: Hegen

first: James

last: Clark

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Transcriptomics changes in neural differentiated mouse embryonic stem cells (mESCs) under exposure to sodium valproate

first: Lena

last: Smirnova PhD

summary:
Studying chemical disturbances during neural differentiation of mES cells has been established as an alternative in vitro testing approach for the identification of developmental toxicants. miRNAs represent a class of small regulatory RNA molecules, which bind to target mRNAs thereby repressing their translation. Many studies have shown an essential role of miRNAs in regulation of gene expression during development and ESC differentiation. Thus, neural differentiation of ESC in vitro allows investigating the role of miRNAs in chemical-mediated developmental toxicity. We analyzed the expression of miRNAs and transcriptomics changes during neural differentiation of mESC exposed to the developmental neurotoxicant sodium valproate (VPA).  A total of 110 miRNAs and 377 mRNAs were identified differently expressed in neural differentiating mES cells under VPA treatment (300µM) compared to solvent control on day 16 of differentiation. Analysis of miRNA expression revealed that valproate switches the lineage specification from neural to myogenic differentiation (upregulation of muscle-enriched miRNAs mir-206, mir-133a and mir-10a and downregulation of neuro-specific miRNAs mir-124a, mir-128 and mir-137). The findings on the miRNA level could be confirmed on mRNA level (induction of expression of myogenic regulatory factors (MRFs) as well as muscle specific genes (Actc1, calponin, myosin light chain, asporin, decorin) and repression of genes involved in neurogenesis (Otx1 and 2, Zic3, 4, 5)) as well as morphologically by immunocytochemistry. The observed results were VPA specific and most probably due to inhibition of histone deacetylase (HDAC) activity of VPA for two reasons: (i) we did not observe any induction of muscle specific miRNAs in neural differentiating ES cells exposed to the unrelated developmental neurotoxicant sodium arsenite; (ii) expression of muscle specific mir-206 and muscle enriched mir-10a was similarly increased in cells exposed to a structurally different HDAC inhibitor, trichostatin A (TSA). Furthermore, using our in vitro cell system we could confirm an aberrant expression of known VPA target genes and genes involved in neural tube closure. We conclude that miRNA expression profiling is a suitable molecular endpoint for developmental neurotoxicity. Observed lineage shift into myogenesis, where miRNAs play a significant role, could be a major developmental neurotoxical mechanism of VPA.
We used microarray approach to identify altered miRNA expression in neural differentiated mES cells exposed to two known developmental neurotxicants and epigenetic active substances, sodium valproate (VPA) and sodium arsenite (As)

overall_design: mES cells line W4 were induced to differnetiate into neurons under exposure to VPA for 16 days. RNA for microarrays was collected on day 16 of differentiation from three biological replicates of solvent control (PBS) and VPA treated cells.

last: Smirnova

first: Michael

last: Bonin


title: The epigenetic signature of systemic insulin resistance in obese women [OM]

first: Ingrid

last: Dahlman

overall_design:
DNA methylation was analyzed in DNA extracted from SAT (subcutaneous adipose tissue) and VAT (visceral adipose tissue) pieces, as well as PBMCs (peripheral blood mononuclear cells), using the Infinium Human Methylation 450 BeadChip assay.
This data is from VAT (omental).

last: Arner

first: Anna

last: Sahlqvist

first: Indranil

last: Sinha

first: Hua

last: Xu

first: Xiang

last: Yao

first: Dawn

last: Waterworth

first: Katrina

last: Loomis

first: Anders

last: Thorell

first: Erik

last: Näslund

first: Mikael

last: Ryden


title: The epigenetic signature of systemic insulin resistance in obese women


title: Expression data of the acrR mutant E.coli compared to wild-type

city: Seoul

first: Ok Bin

last: Kim

address: Ewhayeodae-gil 52

department: Department of Life Science

country: South Korea

institute: Ewha University

summary:
AcrR is a known transcriptional repressor for AcrAB-TolC multidrug efflux system and mar-sox regulators. We used microarrays to investigate genome-wide target genes for AcrR.
In the acrR deletion mutant, the transcription of genes for flagella and motility are significantly increased, indicating that AcrR plays a role in motility of E. coli.

overall_design: Two E. coli strains, acrR deletion mutant and wild-type, grew on LB medium. At exponential phase (OD600=0.8), RNA was extracted and hybridized on Affymetrix microarrays. We sought to find the genes that the transcription is significantly increased in the acrR deletion mutant.

first: Ye-Jin

first: Ok-Bin


title: KDM4A regulated gene expression in human prostate cancer LNCaP cell

status: Public on Jul 26 2016

city: Sacramento

first: Ling-Yu

last: Wang

department: Biochemistry and Molecular Medicine

institute: University of California, Davis

summary: Histone lysine demethylase KDM4A is overexpressed in prostate cancer and plays a crucial role in tumor growth and survival. To understand the mechanisms underlying KDM4A-depedent cell growth and survival, microarray analysis was performed in LNCaP cells transduced with control or KDM4A specific-knockdown construct. The role of KDM4A in prostate carcinogenesis involves activation of E2F1 and androgen receptor transcriptional profiles.

overall_design: LNCaP cells were transduced by lentivirus carrying control pLKO.1 (empty vector) or shKDM4A construct (KDM4A-specific shRNA) for three days, followed by RNA extraction. Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays were used for microarray analysis.

first: Clifford

last: Tepper

first: Hsing-Jien

last: Kung


title: Expression data from mouse liver tissue from SKH:QS mice treated with commercially available sunscreens containing ZnO or TiO2 nanoparticles, or no nanoparticles

city: North Ryde

first: Megan

last: Osmond-McLeod

address: 11 Julius Avenue

country: Australia

institute: CSIRO

summary: ZnO and TiO2 nanoparticles can elicit a range of perturbed cell responses in vitro. Exposure to topically applied sunscreens containing ZnO or TiO2 particles may or may not elicit a biological effect in mice. We aimed to compare the biological responses of immune-competent hairless mice receiving topical applications of commercially available sunscreens with or without metal oxide nanoparticles, with the responses of mice receiving no sunscreen.

overall_design: Commercially available sunscreens containing ZnO nanoparticles, a mixture of TiO2 nanoparticles and organic UVR filters, or only organic UVR filters were applied to the backs of SKH:QS mice weekly over 36 weeks, with or without subsequent exposure to 29 kJ/m2 UVR. After 36 weeks and 30 treatments, mice were sacrificed and liver tissue was harvested for RNA isolation and whole genome transcriptional profiling, comparing the expression profiles of treated mice with untreated mice.

last: Osmond

first: Yalchin

last: Oytam

first: Fariborz

last: Sobhanmanesh


title: Genome-wide analysis of RARβ transcriptional targets in mouse striatum links retinoic acid signaling with Huntington’s disease and other neurodegenerative disorders

city: Illkirch

first: Doulaye

last: Dembele

address: 1 rue Laurent Fries

department: Biopuces

country: France

institute: IGBMC

summary:
Transcriptome analysis of  nucleus accumbens shell samples from RARβ-null mutant mice and their wild type littermates
The active vitamin A derivative retinoic acid (RA) is an important regulator of adult brain functions. How these regulations are achieved is poorly known, partly due to the paucity of information on RA molecular targets. The striatum, the region involved in control of motor, cognitive and affective functions, may be particularly prone to such regulation as it displays the highest levels of RA and its receptors (RARs). We report the first genome-wide analysis of RAR-binding sites in the brain. Using chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq), as well as transcriptomic analysis of RARβ-null mutant mice, we identified genomic transcriptional targets of RARβ in the striatum. Our data point to a strong contribution of RARβ in controlling neurotransmission, energy metabolism, and transcription, with a particular involvement of G-protein, cAMP and calcium signaling. Quantitative PCR analysis of striatal subregions revealed a higher sensitivity of ventral structures (nucleus accumbens) to lack of RARβ signaling. There is a high overlap of transcriptional targets of RARβ and genes affected in expression in Huntington’s disease (HD), and we observed a decrease of RARβ expression in the striatum of R6/2 transgenic mice, a murine model of HD. A large number of genes bearing RARβ binding sites have also been implicated in Alzheimer’s and Parkinson’s diseases, raising the possibility that compromised RA signaling in striatum may be a mechanistic link explaining the similar affective and cognitive symptoms of these diseases. Globally, our data point to a possibility of a neuroprotective function of RARβ in the striatum.

overall_design: We analyzed nucleus accumbens from 11 mice (6 WT, 5 RARβ-null mutant mice) using the Affymetrix GeneChip Mouse Gene 1.0 ST arrays.

first: Anna

last: Niewiadomska-Cimicka

first: Agnieszka

last: Krzyzosiak

first: Tao

last: Ye

last: Podlesny-Drabiniok

first: Pascal

last: Dolle

first: Wojciech

last: Krezel


title: Expression data from Prkch-/-Apoe-/- mouse

status: Public on Jul 31 2016

city: Fukuoka

first: Yusaku

last: Nakabeppu

state: Fukuoka

address: 3-1-1 Maidashi Higashi-ku

department: Department of Immunobiology and Neuroscience

institute: Medical Institute of Bioregulation, Kyushu University

summary:
To examine function of PKCh for atherosclerosis, we compared the gene expression profiles of control Apoe-/- and Prkch-/-Apoe-/- mice by microarray analysis.
In peritoneal macrophages, higher expression of Arginase, type II gene were found in Prkch-/-Apoe-/- cells. Expression of genes involved in cholesterol biosynthesis were upregulated in Prkch-/-Apoe-/- liver.

overall_design: Mice used in this study were backcrossed onto C57BL/6J for more than 12 generations. Total RNA from pritoneal macrophages, aorta and liver of Apoe-/- and Prkch-/-Apoe-/- mice mice was prepared using ISOGEN and RNeasy Mini kits.  For cDNA synthesis from samples prepared from macrophages and liver, total RNA was added to poly-A control and treated with WT Expression Kit. cDNA was labeled using WT terminal labeling kit and hybridized with Affymetrix GeneChip Mouse Gene 1.0 ST platform (GPL6246). For cDNA synthesis from samples prepared from aorta, total RNA pooled from 4 independent mice was used for biotin-labeled cRNA synthesis using one-cycle target labeling and control reagents (Affymetrix), and the labeled cRNA was subjected to hybridization with Affymetrix GeneChip Mouse Genome 430A 2.0 platform (GPL8321).

first: Kumiko

last: Torisu

first: Takahide

last: Kaji


title: Analysis of epigenetic changes in F-36P leukemic cells by arsenic disulfide treatment

city: Hachioji

first: Kenji

last: Onda

state: Tokyo

department: Clinical Pharmacology

institute: Tokyo University of Pharmacy and Life Sciences

summary: Genome wide DNA methylation profiling of F-36P leukemic cells treated by arsenic disulfide,  The Illumina HumanMethylation450 BeadChip was used to obtain DNA methylation profiles

overall_design: Bisulphite converted DNA from the 3 samples were hybridised to the Illumina  HumanMethylation450 BeadChip

first: Qing-bing

last: Zhou


title: A comparison of GS-5759, a bifunctional β2-adrenoceptor agonist and PDE4 inhibitor, and indacaterol and GSK 256066 in combination on gene expression changes in the BEAS-2B human airway epithelial cell line

city: Calgary

first: Mark

last: Giembycz

state: Alberta

address: 3280 Hospital Drive NW

department: Physiology & Pharmacology

institute: University of Calgary

summary:
GS-5759 is a bifunctional ligand composed of a quinolinone-containing pharmacophore found in several β2-adrenoceptor agonists linked covalently to a phosphodiesterase 4 inhibitor (PDE4) related to GSK 256066 by a pent-1-yn-1-ylbenzene spacer. The object of the study was to detemine if gene expression changes induced by GS-5759 were replicated by a β2-adrenoceptor agonist (indacaterol; Ind) and a PDE4 inhibitor (GSK 256066; GSK) in combination.
Microarray analysis was performed on RNA from BEAS-2B cells treated with GS-5759 and a combination of indacaterol and GSK 256066 to identify differentialy expressed genes.

overall_design: Confluent BEAS-2B cells were treated with vehicle, Ind/GSK or GS-5759 for 1h, 2h, 6h or 18h. Total RNA was extracted, quantified (NanoDrop 2000) and the quality of each sample determined by using the Agilent 2100 Lab-on-a-Chip system before being processed for gene expression chnages by Expression Analysis Inc (Dunham, NC, USA).


title: Epigenetic Dysregulation in the Developing Down Syndrome Brain

status: Public on Aug 03 2016

city: Würzburg

first: Marcus

last: Dittrich

address: Biozentrum, Am Hubland

department: Biozentrum

institute: University of Würzburg

summary: Using Illumina 450K arrays, 1.85% of analyzed CpG sites were hypermethylated and 0.31%  hypomethylated in fetal Down syndrome (DS) cortex throughout the genome. The vast  majority of differentially methylated promoters and genes was hypermethylated in DS and  located outside chromosome 21, including the γ-protocadherin (PCDHG) cluster on  chromosome 5q31, which is crucial for neural circuit formation in the developing brain.  Bisulfite pyrosequencing and targeted RNA sequencing showed that several genes of PCDHG  subfamilies A and B are hypermethylated and transcriptionally downregulated in fetal DS  cortex. Decreased PCDHG expression is expected to reduce dendrite arborization and growth  in cortical neurons. Dysregulation of CPT1B and NOX5 may be associated with mitochondrial  dysfunction and increased cell damage in the developing DS brain. Since constitutive  hypermethylation of PCDHG and other genes affects multiple tissues, including blood, it may  provide useful biomarkers for DS brain development and pharmacologic targets for  therapeutic interventions.

overall_design: Bisulphite converted DNA from the 72 samples were hybridised to the Illumina HumanMethylation450 BeadChip

first: Thomas

last: Haaf


title: Placental DNA methylation difference in spontaneous preterm delivery

status: Public on Jul 25 2016

city: Honolulu

first: Dongmei

last: Li

state: HI

address: 1960 East-West Road

institute: University of Hawaii at Manoa

summary: Genome wide placental DNA methylation profiling of full term and preterm deliveries sampled from 5 full term deliveries and 4 preterm deliveries. The Illumina HumanMethylation450 Beadchip was used to obtain DNA methylation profiles across approximately 485,577 CpGs in formalin fixed samples. Samples included 4 placental tissues from 4 women with preterm delivery and 5 placental tissues from 5 women with full term delivery.

overall_design: 9 women's placental DNA (4 women had perterm deliveries and 5 women had full term deliveries) were hybridised to the Illumina HumanMethylation450 Beadchip

first: Marc

last: Le Pape

first: Nisha

last: Parikh

first: Will

middle: X

last: Chen

first: Timothy

last: Dye


title: Effects of vitamin A on ventricular myocardium gene expression [left ventricle]

city: Scarborough

first: Douglas

last: Sawyer

state: ME

address: 81 Research Dr

department: Cardiovascular Institute

institute: Maine Medical Center

summary: LRAT knockout mice on vitamin A sufficient or deficient diets were compared to age and gender matched wildtype mice on a vitamin A sufficient diet

overall_design: RNA was isolated  from the left ventricle of the heart and one array was run for each sample.

first: Mary-Ann

last: Asson-Batres

middle: B

first: Cristi

last: Galindo

first: Duarte

last: Christine


title: The epigenetic signature of systemic insulin resistance in obese women [SC]

first: Ingrid

last: Dahlman

overall_design:
DNA methylation was analyzed in DNA extracted from SAT (subcutaneous adipose tissue) and VAT (visceral adipose tissue) pieces, as well as PBMCs (peripheral blood mononuclear cells), using the Infinium Human Methylation 450 BeadChip assay.
This data is from SAT.

first: Peter

last: Arner

first: Anna

last: Sahlqvist

first: Indranil

last: Sinha

first: Hua

last: Xu

first: Xiang

last: Yao

first: Dawn

last: Waterworth

first: Katrina

last: Loomis

first: Anders

last: Thorell

first: Erik

last: Näslund

first: Mikael

last: Ryden


title: CHIP knockdown effect on breast cancer cell line

city: Kyotanabe

first: Tsuyoshi

last: Waku

address: 1-3 Tatara Miyakodani

institute: Doshisha University

summary:
Analysis of MCF-7 cell clones lacking the E3 ubiquitin liganse CHIP.
We used microarrays to detail the global gene expression profiles effected by CHIP in human brest cancer.

overall_design: Total RNA was extracted from CHIP or LacZ knockdown MCF7 and hybridized on Affymetrix microarrays.

first: Mai

last: Tsuchiya

first: Junn

last: Yanagisawa


title: Expression analysis of ovarian cancer cell line

status: Public on Jul 23 2016

first: Satoshi

last: Fukagawa

address: 7-45-1 Nanakuma, Jonan-ku

department: Fuculty of Medicine

institute: Fukuoka University

summary:
The aim of this analysis is  searching the target gene of miR-135a-3p in ovarian cancer cell line.
The gene expression of cell line with overexpressed miR-blank or miR-135a-3p was compared.

overall_design: Three ovarian cancer cell lines were enrolled this study. Those cells were transfected with miR-blank as control or miR-135a-3p.

first: Kohei

last: Miyata

first: Fusanori

last: Yotsumoto

first: Shingo

last: Miyamoto


title: The mdx mutation in the 129/Sv background results in a milder phenotype: Transcriptome comparative analysis searching for the protective factors

status: Public on Jul 24 2016

city: Sao Paulo

first: Mariz

last: Vainzof

state: Sao Paulo

address: Rua do Matao, 106

department: Genetics and Evolutionary Biology

country: Brazil

institute: University of Sao Paulo

summary:
Transcriptome analysis of hindlimb muscles from dystrophic mice.
The mdx mouse is a good genetic and molecular murine model for Duchenne Muscular Dystrophy (DMD), a progressive and devastating muscle disease. However, this model is inappropriate for testing new therapies due to its mild phenotype. Here, we transferred the mdx mutation to the 129/Sv strain with the aim to create a more severe model for DMD. Unexpectedly, functional analysis of the first three generations of mdx129 showed a progressive amelioration of the phenotype, associated to less connective tissue replacement, and more regeneration than the original mdxC57BL. Transcriptome comparative analysis was performed to identify what is protecting this new model from the dystrophic characteristics. The mdxC57BL presents three times more differentially expressed genes (DEGs) than the mdx129 (371 and 137 DEGs, respectively). However, both models present more overexpressed genes than underexpressed, indicating that the dystrophic and regenerative alterations are associated with the activation rather than repression of genes. As to functional categories, the DEGs of both mdx models showed a predominance of immune system genes. Excluding this category, the mdx129 model showed a decreased participation of the endo/exocytic pathway and homeostasis categories, and an increased participation of the extracellular matrix and enzymatic activity categories. Spp1 gene overexpression was the most significant DEG exclusively expressed in the mdx129 strain. This was confirmed through relative mRNA analysis and osteopontin protein quantification. The amount of the 66 kDa band of the protein, representing the post-translational product of the gene, was about 4.8 times higher on Western blotting. Spp1 is a known DMD prognostic biomarker, and our data indicate that its upregulation can benefit phenotype. Modeling the expression of the DEGs involved in the mdx mutation with a benign course should be tested as a possible therapeutic target for the dystrophic process.

overall_design: We analyzed calf muscles from five Dmdmdx, three hybrids of Dmdmdx with 129/Sv in generations F1, F2 and F3; five C57BL/6 and three 129/Sv as normal controls. All animals were six months old. We used the Affymetrix Mouse Gene 1.0 ST platform. Array data was processed by Expression Console. No technical replicates were performed.


title: Interferon-stimulated gene expression in STAT1 knockout cells

status: Public on Jul 22 2016

city: Eiheiji

first: Shota

last: Yamauchi

state: Fukui

address: 23-3 Matsuokashimoaizuki

department: Faculty of Medical Sciences

institute: University of Fukui

summary:
STAT1 plays a cental role in the induction of interferon-stimulated genes, but interferon alpha can activate a STAT1-independent pathway that leads to gene expression.
We performed microarray analysis to examine whether like interferon alpha, interferon lambda, a newly discovered interferon, can induce the expression of interferon-stimulated genes in the absence of STAT1.

overall_design: Control and STAT1 knockout Huh-7.5 hepatoma cells were left untreated or treated with 1000 U/ml of human interferon alpha 2a or interferon lambda 1 (PBL) for 24 h, and total RNA was extracted. Sense-strand DNA was generated from 200 ng of total RNA, fragmented, and labeled using a GeneChip WT Plus Reagent Kit (Affymetrix). Six samples were obtained and each sample was anlyzed using one GeneChip.

first: Kiyonao

last: Sada


title: Annexin 2A sustains glioblastoma cell dissemination and proliferation affecting patient prognosis

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

country: Italy

institute: università di padova

summary:
Glioblastoma (GBM) is the most devastating tumour of the brain, endowed with a fatal prognosis. Indeed, the complete eradication of cancer cell disseminated outside the GBM mass still remains a crucial issue. Given the reported strong association existing between Annexin 2A (ANXA2) expression and cell dissemination in many cancers, we evaluated the effects exerted by the modulation of ANXA2 levels in GBM cells and assessed its potential in predicting patient outcome. Here, we show that expression of ANXA2 positively correlates with metastatic gene signatures and demonstrates to be prognostic by itself. Indeed, we prove that ANXA2 is involved in cell migration, invasion, cytoskeletal remodeling and proliferation in GBM cells. Moreover, we were able to construct a gene signature representative of ANXA2 inhibition, which showed a significant prognostic potential in different GBM patient cohorts.
In this study, we demonstrate that ANXA2 acts at multiple levels in determining the disseminating and aggressive behaviour of GBM tumours. In particular, we clearly show that ANXA2 is involved in determining a migrating and disseminating phenotype of GBM cells, in controlling specific cell cycle checkpoints and a cytoskeletal remodeling associated to cell movement. These data sustain the potential of ANXA2 as a possible target and strong prognostic factor in the future management of GBM patients.

overall_design: Gene expression was measured on Affymetrix in 4 independent experiments of primary GBM cells treated with an ANXA2 neutralizing antibody

first: Silvia

last: Bresolin

first: Luca

last: Persano


title: Prognostic significance of overexpression of Traf2- and Nck- interacting kinase (TNIK) in colorectal cancer [152 samples]

city: Bunkyo-ku

first: Kaoru

last: Mogushi

address: 2-1-1 Hongo

department: Intractable Disease Research Center

institute: Juntendo University

summary: Background: The potential of expression profiling using microarray analysis as a tool to predict the prognosis for different types of cancer has been realized. This study aimed to identify a novel biomarker for colorectal cancer (CRC).   Methods: The expression profiles of cancer cells in 152 patients with stage I-III CRC were examined using microarray analysis. High expression in CRC cells, especially in patients with distant recurrences, was a prerequisite to select candidate genes. Thus, we identified eleven candidate genes, and selected Traf2- and Nck-interacting kinase (TNIK), which was known to be associated with progression in CRC through Wnt signaling pathways. We analyzed the protein expression of TNIK using immunohistochemistry (IHC) and investigated the relationship between protein expression and patient characteristics in 220 stage I-III CRC patients.   Results: Relapse-free survival was significantly worse in the TNIK high expression group than in the TNIK low expression group in stage II (p = 0.028) and stage III (p = 0.006) patients. In multivariate analysis, high TNIK expression was identified as a significant independent risk factor of distant recurrence in stage III patients.   Conclusion: This study is the first to demonstrate the prognostic significance of intratumoral TNIK protein expression in clinical tissue samples of CRC, in that high expression of TNIK protein in primary tumors was associated with distant recurrence in stage II and III CRC patients. This TNIK IHC study might contribute to practical decision-making in the treatment of these patients.

overall_design: Gene expression profiles for 152 cancer tissues from colorectal cancer patients were measured by Affymetrix HG-U133 Plus 2.0 arrays. Normalization was performed by robust multi-array average (RMA) method under R 2.12.1 statistical software with affy package from BioConductor. The normalized gene expression levels were presented as log2-transformed values by RMA.

first: Hidenori

last: Takahashi

first: Toshiaki

last: Ishikawa

first: Megumi

last: Ishiguro

last: Okazaki

first: Hirotoshi

last: Kobayashi

first: Satoru

last: Iida

first: Hiroshi

last: Mizushima

last: Tanaka

first: Hiroyuki

last: Uetake

first: Kenichi

last: Sugihara


title: Gene expression after 24h Urolithin A incubation in LNCaP cells

city: Barcelona

first: Carlos

middle: J

last: Ciudad

address: Av. Juan XXIII-27

department: Biochemistry and Molecular Biology

institute: University of Barcelona

summary: The identification of new agents that may modulate the progression of cancer cell growth is of great interest. In this regard, dietary agents can be utilized to identify molecular targets to be used as part of a chemopreventive strategy. Walnuts contain several bioactive compounds, including pedunculagin, a polyphenol metabolized by microbiota to form urolithins, namely urolithin A (UA).  We performed a genomic analysis to study the effect of UA on androgen-dependent LNCaP prostate adenocarcinoma cells. Cells were incubated with 40µM UA for 24 hours, then, RNA was extracted.  RNA samples were processed in the automated  Biomek FX System (Beckman Coulter), where  aRNA was produced, and labeled with Biotin, purified , fragmented and hybridized onto HG U219-24 Array, using the GeneChip HT 3’IVT Express Kit . Afterwards, the GeneTitan® Multi-Channel (MC) Instrument (Affymetrix) was used to hybridize, wash , stain , and scan the arrays. Microarray results were analyzed using the GeneSpring GX v13.0 software.

overall_design: LNCaP cells were plated in 35mm wells, the following day they were treated with 40µM urolithin A (UA) for  24 hours, after incubation Total RNA was extracted using Qiagen RNAeasy minikit. The Affymetrix Human Genome U219 array plate was used, which measures gene expression of more than 36 000 transcripts and variants per sample, which represent more than 20 000 genes.

first: Maria

last: Izquierdo-Pulido

first: Veronica

middle: N

last: Mata

first: Claudia

last: Sanchez-Gonzalez


title: Colonic gene expression data of TIMP1 knock out colitis mice

city: Leuven

first: Ingrid

last: Arijs

address: Herestraat 49

department: Clinical and Experimental Medicine

country: Belgium

institute: KULeuven

summary: Increased levels of tissue inhibitor of metalloproteinase-1 (TIMP-1) have been detected in fibrotic strictures in Crohn’s disease. In a murine model of chronic inflammation, fibrosis was associated with an increase in TIMP-1 and inhibition of matrix metalloproteinase (MMP)-mediated degradation. We investigated the effect of TIMP-1 deficiency on the colonic gene expression in acute and chronic murine models of colitis, using whole genome gene expression arrays.

overall_design: Colitis was induced via oral administration of dextran sodium sulphate (DSS) to B6.129S4-Timp1tm1Pds/J knock-out (KO) and C57BL/6J wild-type (WT) mice. Total RNA extracted from snap frozen colon was used to analyze mRNA expression via Affymetrix Mouse Gene 1.0 ST Arrays

first: Christine

last: Breynaert

first: Magali

last: de Bruyn

first: Jonathan

last: Cremer

first: Erik

last: Martens

first: Leentje

last: Van Lommel

first: Karel

last: Geboes

first: Gert

last: De Hertogh

first: Frans

last: Schuit

first: Marc

last: Ferrante

first: Séverine

last: Vermeire

first: Jan

last: Ceuppens

first: Ghislain

last: Opdenakker

last: Van Assche


title: Expression data from Human Ishikawa cells treated with Genistein

city: MASON

first: Jay

middle: Patrick

last: Tiesman

state: OH

address: PO BOX 8006

department: Global Biotechnology

institute: Procter & Gamble

summary:
This study provides a comprehensive evaluation of changes in gene expression during treatment with Genistein in vitro.
Ishikawa cells were maintained and grown (to confluency or at a desired cell density between 500,000 - 1 million cells/mL) in DMEM/F-12 Medium (supplemented with 10% Fetal Bovine Serum + 1X penicillin/streptomycin) in xenoestrogen-free Corning plasticware.  Cells were gently washed in warm PBS and transferred to phenol red-free DMEM/F-12 Medium (supplemented with 10% Charcoal-Stripped Fetal Bovine Serum + 1X penicillin/streptomycin) in Corning Cell Culture Cluster wells overnight and then challenged with 10pM (very low, vL), 1 nM (low, L), 10nM (high, H), and 1uM (very high, vH) levels of Genistein.  Prior to collection, cells were washed in warm PBS, resuspended & briefly incubated in TRI-Reagent, & finally collected (in quintuplicate replicates) at time each specific time point: 8 hours, 24 hours, and 48 hours.  Following RNA isolation, the best RNA yields for each quadruplicate set was selected for target preparation and GeneChip processing.

overall_design: 60 total samples:  5 Doses [Vehicle Control, Very Low (1 pM), Low (100 pM), High (1 nM), Very High (1 uM)]; 3 Timepoints [8 hour, 24 hour, 48 hour]; 4 Replicates each

middle: P


title: Effect of GDF11 on RANKL-induced osteoclastogenesis

status: Public on Jul 21 2016

city: Chengdu

first: Quan

last: Yuan

state: Sichuan

address: 14 Third section, Renmin Nan Road

country: China

institute: West China Hospital of Stomatology, Sichuan University

summary:
GDF11 treatment leads to  bone loss in mice and strongly stimulates RANKL-induced osteoclastogenesis of bone marrow–derived macrophages (BMMs) in vitro.
We used microarrays to identified distinct classes of up-regulated genes in BMMs after GDF11 treatment.

overall_design: Mouse BMMs were treated with or without GDF11 for RNA extraction and and hybridization on Affymetrix microarrays

first: Weiqing

last: Liu


title: Effect of JAK blockade on IFNa response in B cells in vitro

status: Public on Jul 20 2016

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: B cells respond robustly to type 1 interferons which signal through JAK1 and TYK2. Here we analyzed the effects of a panel of JAK inhibitors on the IFNa transcriptional response in activated B cells in vitro.

overall_design: Splenic B cells were isolated by negative selection from 6wk old male C57BL/6 mice. These were activated with LPS(10ug/ml) for 48hrs and thereafter cultured with IFNa (100U/ml) in the presence or absence of JAK inhibitors at IC80 for 2hrs or 8hrs in vitro. Cells were then transferred directly into TriZol. RNA was prepared in Trizol for gene expression profiling by  Affymetrix Mouse Gene 1.0 ST Arrays.

first: Devapregasan

last: Moodley

first: Hideyuki

last: Yoshida

first: Sara

last: Mostafavi

first: Natasha

last: Asinovski

first: Adriana

last: Ortiz-Lopez

first: Peter

last: Symanowicz

first: Jean-Baptiste

last: Telliez

first: Martin

last: Hegen

first: James

last: Clark

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Effect of JAK1/3 blockade on IL2 response in NK cells

summary: IL2 signals are transmitted through JAK1 and JAK3, but the transcriptomic consequences of each to the overall response is unclear. Here we analyzed the relative contribution of JAK1 and JAK3 to the NK cell IL2 response in vitro using titrated doses of isoform specific JAK inhibitors. Blockade of JAK1 and JAK3 have unequal effects on IL2-induced transcripts at pharmacologically relevant doses.

overall_design: Splenic NK cells were isolated by negative selection from 6wk old male C57BL/6 mice. These were cultured with IL2 (250U/ml) in the presence or absence of JAK1/3 inhibitors for 8hrs in vitro. Cells were then transferred directly into TriZol. RNA was prepared in Trizol for gene expression profiling by  Affymetrix Mouse Gene 1.0 ST Arrays.


title: The Nuclear Receptor Rev-erb alpha Regulates Adipose Tissue-Specific FGF21 Signaling (Microarray)

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

summary: To investigate the role of the transcriptional repressor Rev-erb alpha in epididymal white adipose tissue, we performed a microarray analysis of gene expression in the epididymal white adipose tissue of wildtype and Rev-erb alpha knock-out mice.

overall_design: Examination of the transcriptome in epididymal white adipose tissue of Rev-erb alpha kockout mice compared to wildtype mice.

first: Jennifer

last: Jager

first: Fenfen

last: Wang

first: Bin

last: Fang

first: David

last: Steger

first: Kyoung-Jae

last: Won

first: Mitchell

last: Lazar


title: B cell response to IFNa in vitro

first: CBDM

last: Lab

summary: Here we analyzed thetranscriptional response to IFNa in activated B cells in vitro. We found robust induction of ISGs as early as 2hrs.

overall_design: Splenic B cells were isolated by negative selection from 6wk old male C57BL/6 mice. These were activated with LPS(10ug/ml) for 48hrs and thereafter cultured with IFNa (100U/ml) for 2hrs or 8hrs in vitro. Cells were then transferred directly into TriZol. RNA was prepared in Trizol for gene expression profiling by  Affymetrix Mouse Gene 1.0 ST Arrays.

first: Devapregasan

last: Moodley

first: Hideyuki

last: Yoshida


title: Effects of vitamin A on Ventricular myocardium gene expression [right ventricle]

first: Douglas

last: Sawyer

summary: LRAT knockout mice on vitamin A sufficient or deficient diets were compared to age-matched wildtype mice on a vitamin A sufficient diet

overall_design: RNA was isolated from right ventricle of the heart and one array was run for each sample.

first: Mary-Ann

last: Asson-Batres

first: Cristi

last: Galindo

first: Duarte

last: Christine


title: Expression data comparing murine AE9a high and AE9a low expressing hematopoietic cells

status: Public on Jul 19 2016

first: Kevin

last: Link

address: 3333 Burnet Ave

summary: Microarray analysis was performed to examine potential differences in target gene expression of AE9a expressing low cells compared to AE9a expressing high cells. Potential contributing factors to AE9a induced leukemia were investigated.

overall_design: Embryonic day 13.5 to 14.5 fetal liver cells were harvested from C57Bl6 females. Cells were cultured in StemSpan media with 50ng/ml rat recombinant SCF, 10ng/ml human IL-6, and 10ng/ml murine IL-3. After overnight stimulation, cells were collected and transduced with two rounds of retrovirus (MIG-AE9a). Post transduction, cells were collected, counted and transplanted into lethally irradiated BoyJ recipient mice. Cells were expanded two to three weeks in vivo, mice were sacrificed, and bone marrow (BM) harvested. c-Kit+ cells were sorted (BD FACS Aria) for 30% low and 30% high GFP-expressing populations. Six AE9a low and six AE9a high samples were compared. RNA was isolated via the Qiagen RNeasy RNA isolation kit and submitted to the CCHMC Microarray Core. Samples were hybridized to an Affymetrix Mouse Gene 1.0 ST chip. Data was normalized using Expression Console and was analyzed using Qlucore Omics Explorer software.

first: Shan

last: Lin

first: James

middle: C

last: Mulloy


title: Effects of vitamin A on ventricular myocardium gene expression

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

overall_design: Refer to individual Series


title: Aging reduces the pro-tumorigenic potential of bone marrow cells and influences triple-negative breast cancer progression

city: Lund

first: Björn

last: Nilsson

address: BMC

department: Hematology and Transfusion Medicine

institute: Lund University

summary: To examine the effects of recombinant granulin on human mammary stromal fibroblasts, we cultured immortalized GFP+ normal human mammary fibroblasts in the presence of recombinant human granulin (1ug/ml) or PBS every 24h for 6 days. To generate GRN-independent CAFs, we injected immortalized GFP+ human mammary fibroblasts, MCF7Ras human breast carcinoma cells, and 20% Matrigel subcutaneously into nude mice. Tumors were allowed to form for a period of 45 days.  GFP+ fibroblasts were isolated from tumors by mincing the tumors, dissociating, and culturing in the presence of 1 ug/ml puromycin for ~3-4 weeks.  CAF purity was confirmed by ensuring that 100% of the population was GFP-positive.

overall_design: We cultured normal human mammary fibroblasts in the presence human granulin (1ug/ml) or PBS control every 24h for 6 days.  The analysis showen are for 3 control (control) and 3 granulin-treated (PGRN) fibrobast cultures.

first: Sandra

last: McAllister

first: Bjorn


title: Expression analysis of transgenic mice with a cardiac specific overexpression of DSC2.

first: Andreas

last: Brodehl

address: 3280 Hospital Drive NW

department: Libin Institute for Cardiovascular Research

institute: University of Calgary

summary:
Gene expression data indicate an early up-regulation of inflammatory and fibrotic remodeling pathways in DSC2 transgenic mice vs. non-transgenic control mice. The mice were analyzed at the age of 3.5 and 13 weeks.
The mice were analyzed at the age of 3.5 and 13 weeks.

overall_design: Seven DSC2 transgenic and seven non-transgenic control mice were analyzed at the age of 3.5 and 13 weeks.

first: Paul

middle: M

last: Gordon

first: Brenda

last: Gerull


title: Expression data from mouse spleens after experimental stroke

city: Edinburgh

first: Barry

middle: W

last: McColl

address: 49 Little France Crescent

department: Centre for Discovery Brain Sciences

institute: University of Edinburgh

summary:
Infection is a major complication and cause of mortality and morbidity after acute stroke however the mechanisms are poorly understood.   After experimental stroke the microarchitecture and cellular composition of the spleen are extensively disrupted resulting in deficits to immune function.
We used microarray to determine differentially expressed genes in the spleens of mice after experimental stroke to determine contributers to immunosuppression after stroke.

overall_design: We extracted RNA from spleens from 3 mice 5 d after experimental stroke when we have shown peak disruption to cellular composition and also from spleens from 2 sham-operated control mice for comparison.

first: Laura

last: McCulloch


title: Immuno-genomic effects of JAK blockade

first: CBDM

last: Lab


title: CD4+ T cell response to IL12 in vitro

summary: Here we analyzed the transcriptional response to IL12 in activated CD4+ T cells in vitro.

overall_design: Splenic CD4+ T cells were isolated by negative selection from 6wk old male C57BL/6 mice. These were activated with CD3/28 beads for 48hrs and thereafter cultured with IL12 (100U/ml) for 2hrs or 8hrs in vitro. Cells were then transferred directly into TriZol. RNA was prepared in Trizol for gene expression profiling by  Affymetrix Mouse Gene 1.0 ST Arrays.

first: Devapregasan

last: Moodley

first: Hideyuki

first: Sara

last: Mostafavi

first: Natasha

last: Asinovski

first: Adriana

last: Ortiz-Lopez

first: Peter

last: Symanowicz

first: Jean-Baptiste

last: Telliez

first: Martin

last: Hegen

last: Clark

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: CD4+ T cell response to IFNa in vitro

summary: Here we analyzed the transcriptional response to IFNa in activated CD4+ T cells in vitro. We found robust induction of ISGs as early as 2hrs.

overall_design: Splenic CD4+ T cells were isolated by negative selection from 6wk old male C57BL/6 mice. These were activated with CD3/28 beads for 48hrs and thereafter cultured with IFNa (100U/ml) for 2hrs or 8hrs in vitro. Cells were then transferred directly into TriZol. RNA was prepared in Trizol for gene expression profiling by  Affymetrix Mouse Gene 1.0 ST Arrays.

last: Yoshida

first: James


title: NK cell response to IL2 in vitro

summary: Here we analyzed the transcriptional response to IL2 in NK cells in vitro.

overall_design:
Splenic NK cells were isolated by negative selection from 6wk old male C57BL/6 mice. These were directly cultured with IL2 (250U/ml) for 8hrs in vitro. Cells were then transferred directly into TriZol. RNA was prepared in Trizol for gene expression profiling by  Affymetrix Mouse Gene 1.0 ST Arrays.

The samples in this series are re-analyzed samples from GSE84562.


title: Demonstration of a day-night rhythm in human skeletal muscle oxidative capacity.

city: Lille

first: Lefebvre

last: Philippe

state: Nord

address: Blvd Pr. J.Leclerc

institute: Inserm

summary: Five consecutive skeletal muscle biopsies were taken from a young healthy male research volunteer under controlled living conditions consisting of 3 meals and normal sleeping time. Samples were obtained with five hour-intervals, always at least 4 hours after the last meal at 8AM, 1PM, 6PM, 11PM and 4AM the next day. Biopsies were taken according to the Bergström method under local anesthesia from the m. vastus lateralis. The first biopsy was taken from the left leg and each consecutive biopsie was taken from the other leg.

overall_design: RNAs were extracted from SKM biopsies.  RNA integrity was assessed using a Bioanalyzer 2100 (Agilent) and RIN were above 9.0.  RNAs were then processed to generate labeled ssDNA using the Whole Transcript cDNA synthesis and amplification and the Terminal Labeling kit as suggested by the manufacturer (Affymetrix). Samples were hybridized to HuGene 2.0 arrays and native .CEL files imported into GeneSpring (v13,1,1, Agilent) after quality controls using the Affymetrix Expression Console.

first: Philippe

last: Lefebvre

first: Dirk

last: Van Moorsel

first: Bart

last: Staels

first: Patrick

last: Schrauwen


title: Voluntary exercise suppresses tumor growth through exercise-directed recruitment and intratumoral infiltration of NK cells

city: Little Rock

first: Intawat

last: Nookaew

address: 4301 W Markham St

department: Department of Biomedical Informatics

institute: University of Arkansas for Medical Sciences

summary: Voluntary exercise reduces the risk of cancer and lowers the risk of disease recurrence. Yet the mechanisms for this protection remain to be elucidated. Here we demonstrate that exercise halves tumor growth through an exercise-dependent mobilization and intratumoral infiltration of NK cells in malignant melanoma. Using voluntary wheel running, we show that exercise prior to and during B16 tumor challenge reduced tumor growth by 67%, and this reduction was associated with increased inflammation and immune cell infiltrates, especially NK cells, in the tumors from exercising mice. Depletion of NK cells blunted the exercise-dependent reduction in tumor growth. Moreover, during exercise, NK cells were engaged through an epinephrine-dependent mobilization to the circulation and redistributed to peripheral tissues through an IL-6 dependent mechanism. This study highlights the importance of exercise-dependent immune regulation in the control of malignant melanoma

overall_design: Gene expression profile of melanoma tumor tissue from two groups of exercise and non-exercise mice

first: Line

last: Pedersen

first: Pernille

last: Højman


title: Gene expression profiles of Lhcgr-deficient testes

status: Public on Jul 15 2016

city: Kyoto

first: Takashi

last: Tanaka

address: 53 Kawahara-cho, Shogolin, Sakyo-ku

department: Molecular Genetics

country: Japan

institute: Kyoto University

summary: Spermatogonial stem cells (SSCs) provide foundation for spermatogenesis by undergoing continuous self-renewal division. Previous studies have reported conflicting results on the role of the pituitary gland activity in SSC self-renewal. In this study, we analyzed the role of hormonal regulation of SSCs using Lhcgr (luteinizing hormone/choriogonadotropin receptor) knockout mice. Analysis of gene expression profiles showed that testes of Lhcgr-deficient mice exhibit significantly enhanced Wnt5a expression in Sertoli cells.

overall_design: Lhcgr KO and control WT mice were treated with busulfan in order to eliminate germ cells. The total RNA samples from their testes were subjected to microarray analysis to compare their gene expression profiles.

first: T

first: M

last: Kanatsu-Shinohara

first: C

middle: V

last: Rao

first: Z

last: Lei

last: Shinohara


title: Direct in vivo evidence for B-cell receptor and NF-KB activation in mantle cell lymphoma: role of the lymph node microenvironment and activating mutations. [Affymetrix]

city: Bethesda

first: Delong

last: Liu

address: 10 Center Drive

institute: NHLBI/NIH

summary:
We provide direct in vivo evidence for activation of the BCR and canonical NF-KB pathways in MCL that, in the absence of activating mutations, is dependent on the lymph node microenvironment.
This finding provides a mechanistic explanation for the surprising efficacy of ibrutinib for the treatment of this type of lymphoma. Mutations in components of the BCR and NF-KB pathways are associated with cell-autonomous signaling and resistance to ibrutinib.

overall_design: Lymph node biopsies and peripheral blood samples were obtained from 55 patients with previously untreated MCL.  The samples are distributed into 3 groups: peripheral blood (purified CD19, N=17), unpurified lymph node biopsy (mixed tissue biopsy, N=34), and purified lymph node (purified CD19 Tumor, N=4).

first: Nakhle

last: Saba


title: Identification of megakaryoblastic leukemia-1 (Mkl1) target genes in 4T1 mammary carcinoma cells

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

summary: The present study was designed to identify Mkl1 target genes whose expression requires either the B1 site of Mkl1 and serum response factor (SRF), respectively, or the SAP domain of Mkl1. For this purpose, we obtained the transcriptomes of four stable 4T1 cell lines that either overexpress full length Mkl1-RFP (4T1-FL), Mkl1-RFP with a mutated SRF-interaction site (4T1-mutB1), Mkl1-RFP with a deletion of the SAP domain (4T1-ΔSAP) or an empty vector encoding RFP alone (4T1 control).

overall_design: Stable 4T1 cell lines were grown in triplicates in 0.03% FCS/DMEM medium for 48 h before total RNA was extracted. RNA was converted into labeled cDNA and hybridized to Affymetrix GeneChip Mouse Gene 1.0 ST arrays. RMA normalized expression values were calculated with the affy package from the Bioconductor 2.4 release (1) and differentially expressed genes were identified using moderated t-statistics calculated with the empirical Bayes method as implemented in the Bioconductor limma package (2). To be considered as differentially expressed between 4T1-FL and 4T1-mutB1 or 4T1-∆SAP cells, genes had to pass the filters: adjusted P-value ≤ 0.01 (with Benjamin-Hochberg false discovery correction), a minimum absolute linear fold change difference of 2.0 and a minimum average expression value of 4.0 (log2).  References:  (1) Gentleman, R., Carey, V., Bates, D., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J., Hornik, K., Hothorn, T., Huber, W., Iacus, S., Irizarry, R., Leisch, F., Li, C., Maechler, M., Rossini, A., Sawitzki, G., Smith, C., Smyth, G., Tierney, L., Yang, J., Zhang, J. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biology 5, R80  (2) Smyth, G. K., Speed, T. (2003) Normalization of cDNA microarray data. Methods 31, 265-273

first: Maria

last: Asparuhova

first: Stephane

last: Thiry

first: Ruth

last: Chiquet


title: DNA methylation data from human parthenogenetic haploid ESCs (hPGES), normal human ESCs(H9) and human forskin fibroblast

status: Public on Jul 13 2016

city: shanghai

first: cuiqing

last: zhong

address: yueyang road 320

institute: institute of biochemistry and cell biology

summary: Here we report the derivation of human parthenogenetic haploid ESCs which contain only one set of chromosome. These two cell lines, which we designated hPGES1 and hPGES2, show conventional ESCs and parthenogenetic-derived DNA methylation state.

overall_design: we use normal human ESCs and human fibroblast as control and analyse the DNA methylation status of hPGES. DNA methylation profile of these cell lines were performed on Infinium Human Methylation450 BeadArray

first: Jinsong

last: Li


title: Total and MicroRNA from transgenic mice

city: Taipei

first: Kung-Hao

last: Liang

address: Tung Hwa North Road

country: Taiwan

institute: Chang Gung Memorial Hospital


title: Genome-wide shRNA screen to identify cellular regulators of the maintenance of HIV-1 latency

status: Public on Jul 14 2016

city: Piscataway

first: Joseph

last: Dougherty

state: NJ

address: 675 Hoes Lane West

department: Department of Pharmacology

country: USA

institute: Rutgers University - Robert Wood Johnson Medical School

summary: Latent HIV-1 infection represents a barrier to virus eradication as latent HIV-1 is impervious to the effects of antiretroviral drugs and can avoid detection by the host immune system. Strategies to clear latent HIV-1 infection in patients have so far failed in clinical trials to increase the decay rate of the latent reservoir underscoring the need for continued study of HIV-1 latency. In this study, a genome-wide RNAi screen was performed to probe cellular factors involved in maintaining HIV-1 latency in HeLa cells latently infected with an HIV-1 reporter virus.

overall_design: HeLa cells that were latently infected with an HIV-1 reporter virus (referred to as the experimental sample) and uninfected, parental HeLa cells (referred to as the reference control sample) were transduced with the GeneNet Genome-wide Human 50K Lentiviral shRNA Library (System Biosciences (SBI), Mountain View, CA). The library consists of approximately 200,000 shRNA constructs targeting about 38,000 human transcripts. It includes 1-4 shRNA constructs per gene, each targeting a different sequence within a specific gene. Transduced cells were selected with puromycin and cultured for a total of 17 days, which was experimentally determined to provide ample time for shRNA expression and knockdown of the target gene, as well as viral reactivation and viral protein-mediated cell death in the experimental sample. In other words, a negative selection protocol was used to identify shRNAs that activated latent virus by taking advantage of the cytotoxic effects of the HIV-1 viral protein Vpr. Following the culture period, cells were lysed and total RNA was isolated, reverse transcribed, amplified, and hybridized to an Affymetrix GeneChip Array (HG-U133+ 2.0) for identification. As the functional assay employed in this screen involved viral protein-mediated cell death upon the re-activation of latent HIV-1, signals from the reference control sample microarray that were at least three times greater than the corresponding signals from the experimental sample microarray were scored as “hits” and statistically analyzed further.

first: Leia

last: Miller

first: Yoshifumi

last: Kobayashi

first: Timothy

last: Russnak

first: Chiann-Chyi

last: Chen


title: Gene expression of E13 fetal liver of common lymphoid progenitors Flt3+ a4b7+ compared to  a4b7-HSAint, a4b7-HSAhi or  a4b7-HSAlow

city: Paris

first: Ana

last: Cumano

address: 25 Rue du Dr. Roux

department: Immunology

institute: Pasteur Institute

summary: We used whole genome transcriptome as gene discovery to further understand the rules of lineage restriction in the lymphoid compartment

overall_design: Mouse embryos at days 13 gestation were isolated and the fetal livers were dissected. Single cell suspension was prepared and treated with biotinilated antibodies to CD3, CD4, CD8, TER119, Gr1, CD25, CD19, NK1.1 and CD11c. Cell suspensions were then incubated with streptavidin Miltenyi Macs beads. Lineage negative cells were recovered in Macs collumns. Cell suspensions were then incubated with antibodies against Flt3, c-kit, Sca-1, a4b7, HSA and Streptavidin bound to Pacific Blue. Lin-, c-kit+, Flt3+, Sca-1lo,  a4b7+ or a4b7-HSAlow,or a4b7- HSAint or a4b7- HSAhi cells were then isolated by cell sorting. 3 biological replicates of each sample were isolated with 5x103 cells. These subsets were shown in single cell diferentiation assays to be have differentpotentials because a4b7+ cells lost B cell potential, while HSA low partially lost B cell potential, HSAhi partially lost T cell potential and HSA int are unbiased in their differentiation potential.


title: Expression data from Clear cell odontogenic carcinoma cell line

city: Tokushima

first: Yasusei

last: Kudo

address: 3-18-15 Kuramoto

department: Institute of Biomedical Sciences

institute: Tokushima University Graduate School

summary: The aim to the study was to elucidate the character of Clear cell odontogenic carcinoma cell line in comparison with mucoepidermoid carcinoma cell line by carrying out a geome-wide expression analysis.

overall_design: Total RNA from human clear cell odontogenic carcinomal cell line, CCOC-T and human mucoepidermoid carcinoma cell line, NCI-H292 was hybridized on Affymetrix® GeneChip Human Gene 2.0 ST arrays. The key findings were verified by quantitative real-time PCR (QPCR).

first: Hideaki

last: Horikawa


title: Lymphatic endothelial cells comparison gene array data

city: Baltimore

first: Jonathan

middle: S

last: Bromberg

address: 800 West Baltimore Street

department: Center for Vascular and inflammatory Diseases

institute: University of Maryland School of Medicine

summary:
GeneChip® Mouse Gene 2.0 ST Array for C57BL/6 mouse skin dermal primary lymphatic endothelial cells (Ms LEC) and mouse lymphatic endothelial cell line SVEC4-10
GeneChip® Human Gene 2.0 ST Array for human primary lymphatic endothelial cells (Hu LEC)
Total RNA from lymphatic cell line SVEC4-10 were used for GeneChip® Mouse Gene 2.0 ST Array.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: SVEC4-10 samples, human and mouse LEC samples.

first: Yanbao

last: Xiong

first: C

last: Brinkman

last: S Bromberg


title: DNA methylation profiles of human blood samples from younger Tsimane and Caucasians

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

summary:
Human DNA methylation Beadchip v1.2 was used to profile n=46 whole blood samples.
The main goal of the study was to measure the epigenetic age (also known as DNA methylation age) of different ethnic groups. Here we focus on subjects younger than 35 years old. Groups include Tsimane Indians and Caucasian samples. To measure DNA methylation age, we used the epigenetic clock software described in Horvath S (n=2013) DNA methylation age of human tissues and cell types. Genome Biology.2013, 14:R115. DOI: 10.1186/10.1186/gb-2013-14-10-r115 PMID: 24138928.

overall_design: We analyzed whole blood samples from 24 Caucasians and 22 Tsimane Indians.

first: Michael

last: Gurven


title: Expression data from transgenic mice

summary:
This study aimed to evaluate the change of liver status in the presence of hepatitis B viral proteins
We evaluated the messenger RNA expression profiles of liver tissues of transgenic mices carrying wild type or mutant viral surface proteins

overall_design: We checked the differential RNA expressions in different transgenic mice, each with three biological replicates


title: Effect of JAK blockade on IFNa response in CD4+ T cells in vitro

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

summary: CD4+ T cells respond robustly to type 1 interferons which signal through JAK1 and TYK2. Here we analyzed the effects of a panel of JAK inhibitors on the IFNa transcriptional response in activated CD4+ T cells in vitro.

overall_design: Splenic CD4+  T cells were isolated by negative selection from 6wk old male C57BL/6 mice. These were activated with CD3/28 beads for 48hrs and thereafter cultured with IFNa (100U/ml) in the presence or absence of JAK inhibitors at IC80 for 2hrs or 8hrs in vitro. Cells were then transferred directly into TriZol. RNA was prepared in Trizol for gene expression profiling by  Affymetrix Mouse Gene 1.0 ST Arrays.

first: Devapregasan

last: Moodley

first: Hideyuki

last: Yoshida

first: Sara

last: Mostafavi

first: Natasha

last: Asinovski

first: Adriana

last: Ortiz-Lopez

first: Peter

last: Symanowicz

first: Jean-Baptiste

last: Telliez

first: Martin

last: Hegen

first: James

last: Clark

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Genome-scale methylation assessment did not identify prognostic biomarkers in oral tongue carcinomas

status: Public on Jul 18 2016

city: Clayton

first: Nicholas

last: Wong

state: Victoria

address: Wellington Road

department: Monash Bioinformatics Platform, Central Clinical School

institute: Monash University

summary: DNA methylation profiling of heterogeneous head and neck squamous cell carcinoma (HNSCC) cohorts has been reported to predict patient outcome. We investigated if a prognostic DNA methylation profile could be found in tumour tissue from a single uniform subsite, the oral tongue. The methylation status of 83 comprehensively annotated oral tongue squamous cell carcinoma (OTSCC) formalin-fixed paraffin-embedded (FFPE) samples from a single institution were examined with the Illumina HumanMethylation450K (HM450K) array.

overall_design: 83 FFPE primary OTSCC tumour samples were analysed in one experimental run.

first: Annette

last: Lim

first: Danny

last: Rischin

first: Benjamin

last: Solomon


title: TGFbeta-induced switch from adipogenic to osteogenic differentiation of human mesenchymal stem cells

city: Nijmegen

first: Everardus

last: van Zoelen

address: Heyendaalseweg 135

department: Faculty of Science

country: Netherlands

institute: Radboud University Nijmegen

summary:
Gene Expression analysis of a differentiation timeseries of human Mesenchymal Stem Cells (hMSCs) in the presence of adipogenic/osteogenic factors. hMSCs differentiate into fat cells when treated with dexamethasone (10^-6 M), insulin (10 ug/ml), rosiglitazone (10^-7 M) and IBMX (250 uM).  TGFbeta (5 ng/ml)  inhibits this process and redirects these cells to differentiate into bone cells.
Introduction: Patients suffering from osteoporosis show an increased number of adipocytes in their bone marrow, concomitant with a reduction in the pool of human mesenchymal stem cells (hMSCs) that are able to differentiate into osteoblasts, thus leading to suppressed osteogenesis.
Methods: In order be able to interfere with this process, we have investigated in vitro culture conditions whereby adipogenic differentiation of hMSCs is impaired and osteogenic differentiation is promoted. By means of gene expression microarray analysis, we have investigated genes which are potential targets for prevention of fat cell differentiation.
Results: Our data show that BMP2 promotes both adipogenic and osteogenic differentiation of hMSCs, while TGFβ inhibits differentiation into both lineages. However, when cells are cultured under adipogenic differentiation conditions, which contains cAMP-enhancing agents such as IBMX of PGE2, TGFβ promotes osteogenic differentiation, while at the same time inhibiting adipogenic differentiation. Gene expression and immunoblot analysis indicated that cAMP-induced suppression of HDAC5 levels plays an important role in the inhibitory effect of TGFβ on osteogenic differentiation. By means of gene expression microarray analysis, we have investigated genes which are downregulated by TGFβ under adipogenic differentiation conditions and may therefore be potential targets for prevention of fat cell differentiation. We thus identified 9 genes for which FDA-approved drugs are available. Our results show that drugs directed against the nuclear hormone receptor PPARG, the metalloproteinase ADAMTS5 and the aldo-keto reductase AKR1B10 inhibit adipogenic differentiation in a dose-dependent manner, although in contrast to TGFβ they do not appear to promote osteogenic differentiation.
Conclusions: The approach chosen in this study has resulted in the identification of new targets for inhibition of fat cell differentiation, which may not only be relevant for prevention of osteoporosis, but also of obesity.

overall_design: hMSCs were induced to differentiate in the presence dexamethasone, insulin and rosiglitazone, to which was added either 50 ng/ml BMP2; BMP2 + TGFbeta; BMP2 + IBMX; BMP2 + TGFbeta + IBMX.

first: Isabel

last: Duarte

first: José

last: Hendriks

first: Sebastian

last: van der Woning


title: Transcriptome analysis of innate intestinal intraepithelial lymphocytes

status: Public on Jul 08 2016

city: Ghent

first: Georges

last: Leclercq

address: De Pintelaan 185 (MRB2 building)

department: Department of Clinical chemistry, microbiology and immunology

institute: Ghent University

summary: Characterization of intraepithelial ILC on the basis of CD8α and Ly49E expression

overall_design: CD3- CD45+ CD8αα- Ly49E+, CD3- CD45+ CD8αα+ Ly49E+ and CD3- CD45+ CD8αα+ Ly49E- cells were sorted to high purity (>98%) from the small intestinal intraepithelial lymphocyte fraction of NOD-SCID mice using a BD FACSAria III cell sorter (BD Biosciences). RNA was isolated using the RNeasy Plus Micro Kit (Qiagen, Hilden, Germany). Amplification and hybridization was carried out with the Ovation Pico WTA V2 kit (NuGen Technologies, San Carlos, CA, USA) and the Affymetrix Mouse Gene 1.0ST Array (Affymetrix, Santa Clara, CA, USA).

first: Aline

last: Van Acker