title: Epigenome analysis of female identical twins

city: Beijing

first: Bingbing

last: Xie

address: Beicheng west road

institute: Beijing Istitute of Genomics

summary: Genome wide DNA methylation profiling of blood samples from eight female identical twins of Han Chinese for forensic age prediction, age 21 to 32. The Illumina Infinium HumanMethylation450 BeadChip was used to obtain DNA methylation profiles across approximately 485,000 CpGs at a single-nucleotide resolution. Samples included 8 pairs of identical female twins of Han Chinese.

overall_design: Bisulphite converted DNA isolated from blood of identical twin pairs were hybridised to the Illumina Infinium HumanMethylation450 BeadChip.

first: Cheng

last: Xu

first: Hongzhu

last: Qu

first: Guangyu

last: Wang

first: Jiangwei

last: Yan

first: Lei

last: Feng


title: DNA methylation analysis in idiopathic and LRRK2-associated Parkinson's disease (PD)

status: Public on Dec 01 2015

city: Barcelona

first: Mario

last: Ezquerra

state: Catalonia

address: Villarroel 170

department: Neurology

country: Spain

institute: Fundacio Clinic/IDIBAPS

summary: We performed a genome-wide DNA methylation study in induced pluripotent stem cells (IPSC)-derived dopaminergic neurons (DAn) generated from keratinocytes of monogenic and sporadic Parkinson disease (PD) patients as well as of healthy subjects. We observed extensive DNA methylation changes in DAn from PD patients. These changes were neither present in the original keratinocytes nor in the undifferentiated IPSCs, suggesting latent molecular defects in PD keratinocytes that are manifested only upon differentiation into DAn. We also found that enhancers showing abnormal DNA hypermethylation in PD were enriched for binding sites of transcription factors such as FOXA1, NR3C1, HNF4A and FOSL2 which are involved in the survival of DAn and showed reduced expression. These data suggest that aberrant epigenomic remodeling of IPSC-derived DAn in PD is mediated by the down-regulation of key transcription factors. Our study suggests that future cell replacement strategies should pay careful attention to the correct epigenomic status of the reprogrammed cells, especially when using patient own skin cells.

overall_design: Number of samples analyzed: 14 iPSC-derived dopaminergic neurons, 7 fibroblasts and 7 IPSCs. Control (C) samples, no pathological changes: SP-09,   SP-11   SP-15  SP-17. Samples from idiopathic Parkinson's Disease (IPD) patients: SP-01,  SP-02, SP-04,  SP-08, SP-10, SP-16. Samples from Parkinson's disease patients carriers of G2019S LRRK2 mutation (MPD): SP-05,  SP-06, SP-12, SP-13. No replicates. iPSC: induced pluripotent stem cells. FIB: fibroblasts. HumanMethylation 450K BeadChip Kit (Illumina Inc., CA, USA) were used to analyse DNA methylation.

first: Ruben

last: Fernandez-Santiago

first: Eduardo

last: Tolosa

first: Àlex

last: Sànchez-Pla

first: Jose

middle: L

last: Mosquera


title: Variation in 5-hydroxymethylcytosine (5hmC) across human cortex and cerebellum

status: Public on Nov 30 2015

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

type: Methylation profiling by genome tiling array

summary:
The most widely utilized approaches for quantifying DNA methylation involve the treatment of genomic DNA with sodium bisulfite, although this method cannot distinguish between DNA methylation (5mC) and DNA hydroxymethylation (5hmC). Previous studies have shown that 5hmC is enriched in the brain, although little is known about its genomic distribution and how it differs between anatomical regions and individuals. In this study, we combined oxidative bisulfite (oxBS) treatment with the Illumina Infinium 450K BeadArray to quantify genome-wide patterns of 5hmC in two distinct anatomical regions of the brain (prefrontal cortex and cerebellum) dissected from multiple individuals. We identified 37,145 and 65,563 sites passing our threshold for detectable 5hmC in the prefrontal cortex and cerebellumm, respectively, with 23,445 loci common across both brain regions. Distinct patterns of 5hmC were identified in each brain region, with notable differences in the genomic location of the most hydroxymethylated loci between these brain regions. Tissue-specific patterns of 5hmC were subsequently confirmed in an independent set of prefrontal cortex and cerebellum samples. Our data are available as downloadable UCSC genome browser tracks (http://epigenetics.iop.kcl.ac.uk/HMC/) as a resource to the community.
Our study represents the first systematic analysis of 5hmC in the human brain, identifying tissue-specific hydroxymethylated positions and genomic regions characterized by inter-individual variation in DNA hydroxymethylation. This study demonstrates the utility of combining oxBS-treatment with the Illumina 450k methylation array to systematically quantify 5hmC across the genome and the potential utility of this approach for epigenomic studies of brain disorders.

overall_design: Prefrontal cortex and cerebellum brain tissue from six control donors, with no evidence of neurological impairment, was bisulfite treated and oxidative bisulfite treated. DNA modifications for these samples were quantified using the Illumina Infinium Human 450K Methylation Array. The level of 5-hmC within each sample was identified by subtracting the oxBS (CEGX) beta-value from the BS (CEGX) beta value at each probe on the 450K array (ΔβBS-oxBS) in each sample. A threshold for detection of 5hmC was established by determining the lowest fifth percentile in the data (i.e., -0.09158275 in this study). We then applied this value as a threshold for the positive data. Sites with an average 5hmC level in either the prefrontal cortex or cerebellum above this level (i.e., +0.09158275) were classified as having "detectable" levels of 5hmC. CEGX control samples are from a Cambridge Epigenetix conversion kit.

first: Katie

last: Lunnon

first: Eilis

last: Hannon

middle: G

first: Emma

last: Dempster

first: Chloe

last: Wong

first: Joe

last: Burrage

first: Claire

last: Troakes

first: Safa

last: Al-Sarraj

first: Leonard

last: Schalkwyk

first: Jonathan

last: Mill


title: TLR2/6 agonists and IFNgamma induce CXCL10 from melanoma

status: Public on Nov 22 2015

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

summary: Clinical approaches to treat advanced melanoma include immune therapies, whose benefits depend on tumor-reactive T-cells to infiltrate metastases. However, most tumors lack significant immune infiltration prior to therapy, and some immune therapies are hindered by a persistent lack of immune cell infiltration. CXCL10 has been implicated as a critical chemokine supporting T-cell migration into tumors; thus agents that induce CXCL10 in tumors may improve patient responses to systemic immune therapy. We find that melanoma cells treated with TLR2/6 agonists (MALP-2 or FSL-1) and interferon-gamma (IFNgamma) upregulate CXCL10 production, when compared to IFNgamma treatment alone or no treatment. Gene profiling of melanoma cells lines treated with TLR2/6 agonists and IFNgamma demonstrate that a selective profile of genes are induced which may be favorable for promoting immune cell infiltration of tumors. TLR2 and TLR6 are widely expressed on human melanoma cells, and treatment of melanoma cells with TLR2/6 agonists and IFNgamma does not hinder melanoma cell apoptosis or promote proliferation. Furthermore, melanoma cells from surgically resected patient tumors upregulate CXCL10 production after treatment with TLR2/6 agonists and IFNgamma when compared to treatment with either agent alone. Collectively, these data identify TLR2/6 agonists and IFNgamma as a novel target for promoting CXCL10 production directly from melanoma cells.

overall_design: Samples from four human melanoma cell lines, VMM1 (n=6), DM13 (n=6), DM93 (n=6) and VMM39 (n=6), were treated with media alone, MALP-2 (TLR2/6 agonist), FSL-1 (TLR2/6 agonist), IFNgamma alone, MALP-2 and IFNgamma, or FSL-1 and IFNgamma.


title: Expression Data form parental vs. TAE684 resistant SH-SY5Y neuroblastoma cells

status: Public on Nov 21 2015

city: Boston

first: David

last: Debruyne

address: 450 Brookline avenue

country: USA

institute: Dana-Farber Cancer Institute

summary:
The crizotinib–resistant ALKF1174L mutation arises de novo in neuroblastoma (NB) and is acquired in ALK translocation-driven cancers, lending impetus to the development of novel ALK inhibitors with different modes of action. The diaminopyrimidine TAE684 and its derivative ceritinib (LDK378), which are structurally distinct from crizotinib, are active against NB cells expressing ALKF1174L. Here we demonstrate acquired resistance to TAE684 and LDK378 in ALKF1174L-driven human NB cells that is linked to overexpression and activation of the AXL tyrosine kinase and epithelial-to-mesenchymal transition (EMT). AXL phosphorylation conferred TAE684 resistance to NB cells through upregulated ERK signaling. Inhibition of AXL partly rescued TAE684 resistance, resensitizing these cells to this compound. AXL activation in resistant cells was mediated through increased expression of the active form of its ligand, GAS6, which also served to stabilize the AXL protein. Although ectopic expression of AXL and TWIST2 individually in TAE684-sensitive parental cells led to the elevated expression of mesenchymal markers and invasive capacity, only AXL overexpression induced resistance to TAE684 as well. TAE684-resistant cells showed greater sensitivity to HSP90 inhibition than did their parental counterparts, with downregulation of AXL and AXL-mediated ERK signaling. Our studies indicate that aberrant AXL signaling and development of an EMT phenotype underlie resistance of ALKF1174L-driven NB cells to TAE684 and its derivatives. We suggest that the combination of ALK and AXL or HSP90 inhibitors be considered to delay the emergence of such resistance.
In order to understand the molecular mechanisms driving resistance to ALK inhibition in ALK-mutated neuroblatoma, we established cell line models of resistance to TAE684, an ALK inhibitor, by treating SH-SY5Y cells (bearing the ALKF1174L mutation) with increasing concentration of this compound over time. We then performed an analysis of gene expression changes genome wide using Affymetrix U133 Plus 2 arrays, by comparing the TAE684-sensitive parental SH-SY5Y cells to the TAE684-resistant SH-SY5Y cells (named SY5Y-TR1).

overall_design: For that experiment, we analyzed gene expression variations by comparing the parental SH-SY5Y (control sample) to the resistant SY5Y-TR1 cells. So 2 samples were analyzed, with 3 replicates run for each.

first: Rani

middle: E

last: George

first: Namrata

last: Bhatnagar

middle: N


title: Expression data from Aortic Macrophages

status: Public on Dec 07 2015

city: Toronto

first: Clint

last: Robbins

state: Ontario

address: 100 College St

country: Canada

institute: University Health Network

summary: Normal arteries contain a large population of tissue resident macrophages (MΦ). Their origins, as well as the mechanisms that sustain them during homeostasis and disease, however, are poorly understood. Gene expression profiling, we show, identifies arterial MΦ as a distinct population among tissue MΦ. Ontologically, arterial MΦ arise before birth, though CX3CR1-, Csf1r-, and Flt3-driven fate mapping approaches demonstrate MΦ colonization occurs through successive contributions of yolk sac (YS) and conventional hematopoiesis. In adulthood, arterial MΦ renewal is driven by local proliferation rather than monocyte recruitment from the blood. Proliferation sustains MΦ not only during steady state conditions, but mediates their rebound after severe depletion following sepsis. Importantly, the return of arterial MΦ to functional homeostasis after infection is rapid; repopulated MΦ exhibit a transcriptional program similar to resting MΦ and efficiently phagocytose bacteria. Collectively, our data provide a detailed framework for future studies of arterial MΦ function in health and disease.

overall_design: Aortic macrophages (CD11bhighF4/80highCD45+MerTK+CD64+) were isolated from C57/B6 wild-type male mice aged 6-8 weeks before and 7 days after induction of sepsis by cecal puncture. 18-20 aortas were pooled per sample. Each condition contained three biological replicates.

middle: S


title: Expression data from chronic lymphocytic leukemia (CLL) tumors and sorted CD19pos B cells from healthy donors

first: Jennifer

middle: R.

last: Brown

state: MA

address: 450 Brookline Avenue

department: Department of Medical Oncology

summary: As part of a large study regarding the epigenetics of CLL we also acquired 3UTR expression arrays.

overall_design: We have analysed the data to evaluate whether downregulated genes have higher entropy in DNA methylation

first: Dan

last: Landau

first: Bethany

last: Tesar

middle: R

first: Catherine

last: Wu


title: Genome-wide DNA methylation signature in lung adenocarcinomas has prognostic impact

status: Public on Nov 27 2015

city: Oslo

first: Thomas

last: Fleischer

address: Ullernchausséen 70

department: Department of Cancer Genetics, Institute for Cancer Research

country: Norway

institute: Oslo University Hospital

summary:
Purpose: DNA methylation alterations are early events in tumorigenesis and important in the regulation of gene expression in cancer cells. Lung cancer has in general a poor prognosis, and a deeper insight into the epigenetic landscape in lung adenocarcinoma tumors and its prognostic implications is needed.
Experimental Design: We determined whole-genome DNA methylation profiles of 164 lung adenocarcinoma samples and 19 samples of matched normal lung tissue samples using the Illumina Infinium 450K array. The methylation levels were correlated with gene expression levels analyzed by the Agilent 60K mRNA expression array. Methylation changes were studied specifically in tumors from never-smoking patients, and in tumors with mutations in the EGFR-, KRAS- or TP53 genes, and survival analyses were performed.
Results: We identified a large number of differentially methylated CpGs in lung adenocarcinoma tissue, and different methylation profiles in tumors from smokers and never-smokers. Specific methylation profiles were observed in tumors with mutations in the EGFR-, KRAS- or TP53 gene. Both positive and negeative correlations between DNA methylation levels and mRNA expression levels were seen. Methylation profiles of the tumor samples identified clusters of patients with distinct prognosis. A prognostic index based on the methylation levels of 33 CpGs was established, and validated in an independent cohort of lung adenocarcinoma patients from the TCGA project. Among the CpGs in the prognostic signature, some were localized in the HOX B and HOX C gene clusters.
Conclusions: Methylation differences mirror biological important features the etiology of lung adenocarcinomas and influence prognosis.

overall_design: Bisulphite converted DNA from the 183 samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip

first: Maria

middle: M

last: Bjaanæs

first: Ann

last: Halvorsen

first: Antoine

last: Daunay

first: Florence

last: Busato

first: Steinar

last: Solberg

first: Lars

last: Jørgensen

first: Elin

last: Kure

first: Hege

last: Edvardsen

first: Anne-Lise

last: Børresen-Dale

first: Odd

middle: T

last: Brustugun

first: Jörg

last: Tost

first: Vessela

last: Kristensen

first: Åslaug

last: Helland


title: IFNa dose response in primary murine B cells

status: Public on Nov 20 2015

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: B cells respond robustly to IFNa. Here we analyze gene expression profiles of primary murine splenic B cells treated with 10 fold serially diluted IFNa in vitro. We explore sensitivity to ISGs to IFNa as they relate to dose. Generally ISGs do not cluster significantly in a dose dependent manner. However there are notable spreads in sensitivity to IFNa.

overall_design: Splenic B cells were isolated by negative selection from 6wk old male C57BL/6 mice. These were cultured with IFNa (0U/ml-10 000U/ml) for 2hrs 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 in triplicate for each concentration of IFNa.

first: Sara

last: Mostafavi

first: Hideyuki

last: Yoshida

first: Devapregasan

last: Moodley

first: Andrew

last: Rhoads

first: Adriana

last: Ortiz-Lopez

first: Liang

last: Yang

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Increased Longevity in the Insulin-sensitive Syntaxin 4 Transgenic Mouse

city: Indianapolis

first: Debbie

middle: Carolyn

last: Thurmond

state: IN

address: 635 Barnhill Drive, MS 2031

department: Pediatrics

institute: Indiana University

summary: There is a good deal of indirect evidence that improved insulin sensitivity may contribute to improved lifespan of mice in which aging has been slowed by mutations, drugs, or dietary means, even in stocks of mice that do not show signs of late-life diabetes.  Peripheral responses to insulin can be augmented by over-expression of Syntaxin 4 (Syn4), a membrane SNARE protein.  We show here that Syn4 transgenic (Tg) mice live approximately 33% longer than controls, and show increased peripheral insulin sensitivity, even at ages where controls show age-related insulin resistance.  Hence, presumably Syn4 Tg mice spend more hours of each day under normoglycemic conditions, which may slow multiple aspects of aging and thereby extend lifespan, even in non-diabetic mice.

overall_design: control vs. Syn4 transgenic (overexpression) mice

first: Eujin

last: Oh

first: Richard

middle: A

last: Miller

middle: C


title: Medulloblastoma Methylation Profiling

status: Public on Nov 19 2015

first: Vijay

last: Ramaswamy

state: ON

address: 555 University Avenue

institute: Hospital for Sick Children

summary:
Genome wide DNA methylation profiling of human medulloblastoma. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 450,000 CpGs.
Preprocessed data performed using Illumina normalization in the minfi package as described in Sturm et al, Cancer Cell, 2012.

overall_design: Bisulphite converted DNA from the 91 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip v1.2

first: Michael

middle: D

last: Taylor


title: Identification of genes involved in enhancement of hyperthermia sensitivity by knockdown of BAG3 in human oral squamous cell carcinoma cells

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

country: Japan

institute: University of Toyama

summary:
Hyperthermia (HT) treatments in combination with either chemotherapy, radiotherapy or both are used for patients with cancer in various organs. However, the acquisition of thermotolerance in cancer cells due to the increase in cytoprotective proteins attenuates the therapeutic effects of HT. BAG3 (BCL2-associated athanogene 3) is a cytoprotective protein that acts against various stresses including heat stress. Recently, we demonstrated that the inhibition of BAG3 improves cell death sensitivity to HT in cancer cells. However, a detailed molecular mechanism involved in the enhancement of HT sensitivity by BAG3-knockdown (KD) in cancer cells is unclear.
In this study, to identify genes involved in the enhancement of HT sensitivity by BAG3-knockdown (KD) in cancer cells, global-scale gene expression analysis was carried out using a GeneChip® system.

overall_design: Human oral squamous carcinoma cell HSC-3 cells were treated with a combination of HT (at 44°C for 90 min) and siRNA for BAG3 or luciferase. Total RNA samples were prepared from the cells, and quality of the RNA was analyzed using a Bioanalyzer 2100. Gene expression was analyzed by an Affymetrix GeneChip® system with a Human Genome U133-plus 2.0 array. Sample preparation for array hybridization was carried out as described in the manufacturer’s instructions.

first: Tatsuya

last: Yunoki


title: In vivo effect of OOS on AML models

city: Salamanca

first: Elena

last: Diaz-Rodriguez

state: Salamanca

address: Campus Miguel de Unamuno, s/n

institute: Centro de Investigación del Cáncer

summary: The in vivo effects of Ocoxin Oral solution (OOS) were evaluated on acute myeloid leukemia mice models. With that purpose RNA from 3 control untreated animals and 3 daily-OOS treated animals was purified and their gene expression profiles compared using the Affimetrix Transcriptome Analysis console.

overall_design: Gene expression profiles of 3 untreated control tumors were compared to 3 OOS treated tumors

first: E


title: Kinetics of IFNa response

first: CBDM

last: Lab

summary: We describe finely resolved kinetics of the transcriptional response to IFNa in B cells in vivo.  Temporal changes in expression of the most robustly induced ISGs were analyzed across 23 (15min - 15hrs) timepoints. Most ISGs reach peak induction at approximately 2hrs and generally in a synchronus manner. These analses provide insight into the regulatory network structure of IFN responses.

overall_design: Male C57BL/6 mice were injected subcutaneously with 10,000U IFNa according to time course profile. Splenic B cells were sorted by FACS directly into TriZol and gene expression profiling was performed on Affymetrix Mouse Gene 1.0 ST Arrays.

first: Sara


title: Resveratrol ameliorates Imiquimod-induced psoriasis-like skin inflammation in mice

status: Public on Nov 17 2015

city: Aarhus

first: Kasper

last: Thorsen

address: Brendstrupgaardsvej

country: Denmark

institute: Aarhus University Hospital

summary: The polyphenol resveratrol has anti-inflammatory effects in various cells, tissues, animals and human settings of low-grade inflammation. Psoriasis is a disease of both localized and systemic low-grade inflammation. The Sirtuin1 enzyme thought to mediate the effects of resveratrol is present in skin and resveratrol is known to downregulate NF-κB; a major contributor in the development of psoriasis. Consequently we investigated whether resveratrol has an effect on an Imiquimod induced psoriasis-like skin inflammation in mice and sought to identify candidate genes, pathways and interleukins mediating the observed effects. The study consisted of three treatment groups: A control group, an Imiquimod group and an Imiquimod+resveratrol group. Psoriasis severity was assessed using elements of the Psoriasis Area Severity Index, actual skin thickness measurements, and histological examination. We performed an RNA microarray from lesional skin and afterwards Ingenuity pathway analysis to identify affected signalling pathways. Our microarray was compared to a previously deposited microarray to determine if gene changes were psoriasis-like, and to a human microarray to determine if findings could be relevant in a human setting.        Imiquimod treatment induced a psoriasis-like skin inflammation. Resveratrol significantly diminished the severity of the psoriasis-like skin inflammation. The RNA microarray revealed a psoriasis-like gene expression-profile in the Imiquimod treated group, and highlighted several resveratrol dependent changes in relevant genes, such as increased expression of genes associated with retinoic acid stimulation and reduced expression of genes involved in IL-17 dependent pathways (e.g.IL-17A, IL-17F,IL-23p19 ). Quantitative PCR confirmed a resveratrol dependent decrease in mRNA levels of IL-17A and IL-19; both central in developing psoriasis.   In conclusion, resveratrol ameliorates psoriasis, and changes in expression of retinoic acid stimulated genes, IL-17 signalling pathways, IL-17A and IL-19 mRNA levels in a beneficial manner suggests it might have a role in the treatment of psoriasis and should be explored further in a human setting.

overall_design:
Three control mice, two mice with Imiquimod-induced psoriasis and two mice with Imiquimod-induced psoriasis treated with Resveratrol were used.
The mice were distributed into 3 groups; a control group, an IMQ group and an IMQ-RSV (8, 10 and 10 mice per group). The mice in groups IMQ and IMQ-RSV received a daily dose of 62.5 mg of 5% IMQ cream (Aldara; MEDA AS) applied on their backs and right ear folds. The mice in the control group received a similar daily dose of vehicle cream (Vaseline Lanette cream; Fagron). The feed was pulverized (standard chow with protein, carbohydrate and fat accounting for 20%/70%/10% of caloric intake, respectively). Trans-RSV was added to the pulverized feed given to the IMQ-RSV group in an amount of 400 mg/kg animal/day based on average food intake. All animals were assessed for the severity of the psoriasis-like skin condition on days 0, 2, 4 and 7, using 2 elements of the Psoriasis Area Severity Index (PASI), to assign a score of 0-4 (0, none; 1, mild; 2, moderate; 3, severe; 4, very severe) for each of the parameters erythema and scaling. Omitting evaluation of induration by PASI, we used thickness of a skinfold on the back (day 7) and thickness of the right ear fold (day 0 and 7) measured by using a calliper (accuracy:   0,02mm, Mitsutomo, Japan).  On day 7, the animals were euthanized and the shaved area of skin on their backs was immediately excised. A 4 mm punch biopsy of lesional skin was fixed in formalin and paraffin embedded for histological analysis. The remaining lesional skin was snap frozen in liquid nitrogen and stored at -80 C .

first: Thomas

last: Kjær

first: Steen

middle: B

last: Pedersen


title: Density variation of MCF10A human breast epithelial cells

city: Jacksonville

first: Derek

middle: Charles

last: Radisky

state: Florida

address: 4500 San Pablo Road

department: Cancer Biology

institute: Mayo Clinic

summary: Response of mammary epithelial cells to different cell densities

overall_design: Cells were plated in 35 mm dishes at 50K, 100K, 200K, 400K, 600K, and 800K, cultured for 24h, then isolated for RNA.


title: Idiopathic and LRRK2-associated Parkinson's disease

first: Mario

last: Ezquerra

type:
Expression profiling by array
Methylation profiling by array

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

overall_design: Refer to individual Series


title: Regulation of Epithelial-Mesenchymal Transition in Breast Cancer Cells by Cell Contact and Adhesion

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Identification of global regulators of T-helper cell lineage specification (microarray)

city: Turku

first: Kartiek

last: Kanduri

address: Tykistokatu 6

country: Finland

institute: Turku Centre for Biotechnology

summary: The aim of the dataset was to identify genome-wide regulators of gene expression in early differentiation of human cord blood derived CD4+ T cells cultured under Th1 (Act+IL12) and Th2 (Act+IL4) polarizing conditions.

overall_design:
Total RNA from naive CD4+ T cells was compared to total RNA from cells cultured in the following three conditions:
activating (antiCD3+antiCD28)+antiIL4+antiIFNG;
activating (antiCD3+antiCD28)+IL12+antiIL4;
activating (antiCD3+antiCD28) +IL4+antiIFNG.
Samples from 3 biological replicates were analysed.

first: Subhash

last: Tripathi

first: Antti

last: Larjo

first: Henrik

last: Mannerström

first: Ubaid

last: Ullah

first: Riikka

last: Lund

first: David

last: Hawkins

first: Bing

last: Ren

first: Harri

last: Lähdesmäki

first: Riitta

last: Lahesmaa


title: Expression data from odontogenic epithelial cells

status: Public on Nov 18 2015

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 odontogenic epithelial cells from epithelial cell rests of Malassez in comparison with gingival epithelial cells by carrying out a geome-wide expression analysis.

overall_design: Total RNA from human odontogenic epithelial cell line, OdE and human immortalized gingival epithelial cell line, OBA-9 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: Microarray profiling shows distinct differences between primary tumors and commonly used preclinical models in hepatocellular carcinoma

city: Singapore

first: Yonghui

last: Wu

address: 11 Hospital Drive

country: Singapore

institute: NCCS

summary:
Background: Despite advances in therapeutics, outcomes for hepatocellular carcinoma (HCC) remain poor and there is an urgent need for efficacious systemic therapy. Unfortunately, drugs that are successful in preclinical studies often fail in the clinical setting, and we hypothesize that this is due to functional differences between primary tumors and commonly used preclinical models. In this study, we attempt to answer this question by comparing tumor morphology and gene expression profiles between primary tumors, xenografts and HCC cell lines.
Methods: Hep G2 cell lines and tumor cells from patient tumor explants were subcutaneously (ectopically) injected into the flank and orthotopically into liver parenchyma of Mus Musculus SCID mice.  The mice were euthanized after two weeks. RNA was extracted from the tumors, and gene expression profiling was performed using the Gene Chip Human Genome U133 Plus 2.0. Principal component analyses (PCA) and construction of dendrograms were conducted using Partek genomics suite.
Results: PCA showed that the commonly used HepG2 cell line model and its xenograft counterparts were vastly different from all fresh, primary tumors. Expression profiles of primary tumors were also significantly divergent from their counterpart patient-derived xenograft (PDX) models, regardless of the site of implantation. Xenografts from the same primary tumors were more likely to cluster together regardless of site of implantation, although heat maps showed distinct differences in gene expression profiles between orthotopic and ectopic models.
Conclusions: The data presented here challenges the utility of routinely used preclinical models. Models using HepG2 were vastly different from primary tumors and PDXs, suggesting that this is not clinically representative.  Surprisingly, site of implantation (orthotopic versus ectopic) resulted in limited impact on gene expression profiles, and in both scenarios xenografts differed significantly from the original primary tumors, challenging the long-held notion that orthotopic PDX model is the gold standard preclinical model for HCC.

overall_design: In this study, we investigate and compare the effects of two factors (cell lines vs. patient explants; ectopic vs. orthotopic) on gene expression profiles of HCC tumors. We hypothesized that differences would be observed in gene expression between ectopically and orthotopically transplanted tumors, and also between fresh patient-explanted tumors and established commercial cell lines.  The similarities or differences between the sites and tumor types could potentially direct areas for future study.

first: Weining

last: Wang

first: N

last: Iyer

first: Hsien

last: Ts'ung Tay

first: Tony

middle: K

last: Lim

first: Lin

last: Zheng

first: In

last: Song

first: Chee

last: Kwoh

first: Hung

last: Huynh

first: Patrick

middle: O

last: Tan

first: Pierce

last: Chow


title: The effects of long-term daily folic acid and vitamin B12 supplementation on genome-wide DNA methylation in elderly subjects

status: Public on Nov 16 2015

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: Folate, and its synthetic form folic acid, function as donor of one-carbon units and have been, together with other B-vitamins, implicated in programming of epigenetic processes such as DNA methylation during early development. To what extent regulation of DNA methylation can be altered via B-vitamins later in life, and how this relates to health and disease, is not exactly known. The aim of this study was to identify effects of long-term supplementation with folic acid and vitamin B12 on genome-wide DNA methylation in elderly subjects. This project was part of a randomized, placebo-controlled trial on effects of supplemental intake of folic acid and vitamin B12 on bone fracture incidence (B-PROOF study). Participants with mildly elevated homocysteine levels, aged 65-75 years, were randomly assigned to take 400 µg folic acid and 500 µg vitamin B12 per day or a placebo during an intervention period of two years. DNA was isolated from buffy coats, collected before and after intervention, and genome-wide DNA methylation was determined in 87 participants (n=44 folic acid/vitamin B12, n=43 placebo) using the Infinium HumanMethylation450 BeadChip. After intervention with folic acid and vitamin B12, 162 (versus 14 in the placebo group) of the 431,312 positions were differentially methylated as compared to baseline. Comparisons of the DNA methylation changes in the participants receiving folic acid and vitamin B12 versus placebo, revealed one single differentially methylated position (cg19380919) with a borderline statistical significance. However, based on the analyses of differentially methylated regions (DMRs) consisting of multiple positions, we identified 6 regions that differed statistically significantly between the intervention and placebo group. Pronounced changes were found for regions in the DIRAS3, ARMC8 and NODAL genes, implicated in carcinogenesis and early embryonic development. Furthermore, serum levels of folate and vitamin B12 or plasma homocysteine were related to DNA methylation of 173, 425 and 11 regions, respectively. Interestingly, for several members of the developmental HOX genes, DNA methylation was related to serum levels of folate. Long-term supplementation with folic acid and vitamin B12 in elderly subjects resulted in effects on DNA methylation of several genes, among which genes implicated in developmental processes.

overall_design: A randomized, placebo-controlled intervention trial was used to study the effects of long-term supplementation (2 year) with folic acid (400 µg/day) and vitamin B12 (500 µg/day) on DNA methylation in elderly subjects. This entry contains the DNA methylation data of DNA isolated from buffy coats collected before and after the intervention with folic acid / vitamin B12 or placebo.

first: Dieuwertje

last: Kok

first: Rosalie

last: Dhonukshe-Rutten

first: Carolien

last: Lute

first: Sandra

middle: G

last: Heil

first: Andre

last: Uitterlinden

first: Nathalie

last: van der Velde

first: Joyce

last: van Meurs

first: Natasja

last: van Schoor

middle: J

first: Lisette

last: de Groot

first: Ellen

last: Kampman

first: Wilma

last: Steegenga


title: Cell specific response to IFNa

first: CBDM

last: Lab

summary: We report cell specific responses to IFNa in 11 different peripheral immunocyte populations in the mouse. These cells represent the core ImmGen immunocyte lineage panel. Profiles from these were used to analyze cell specific responses to IFNa. In general a core set of ISG transcripts are induced in all cells. Smaller sets of ISGs were induced in a cell specific manner. In particular, splenic granulocytes and dendritic cells show restriced indcution of sets of ISGs.

overall_design: Male C57BL/6 mice were injected subcutaneously with 10,000U IFNa according to time course profile. Splenocytes/Peritoneal lavage suspensions were stained in multicolor antibody panels that were used to distinguish 11 different immunocyte populations (Immgen 11 cell set). These cells were sorted by FACS directly into TriZo and gene expression profiling was performed on Affymetrix Mouse Gene 1.0 ST Arrays.

first: Sara

last: Mostafavi

first: Hideyuki

last: Yoshida

first: Devapregasan

last: Moodley

first: Andrew

last: Rhoads

first: Adriana

last: Ortiz-Lopez

first: Liang

last: Yang

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Gene expression analysis of BE(2)C cells treated with MYCN siRNA (MYCN1 #SI03087518)

city: Randwick

first: Daniel

last: Carter

address: Lowy Cancer Research Centre

country: Australia

institute: Children's Cancer Institute

summary: Amplification of the MYCN oncogene predicts treatment resistance in childhood neuroblastoma. Using a MYC target gene signature that predicts poor neuroblastoma prognosis we identified the histone chaperone, FAcilitates Chromatin Transcription (FACT), as a crucial mediator of the MYC signal and a therapeutic target in the disease. FACT and MYCN expression created a forward feedback loop in neuroblastoma cells that was essential for maintaining mutual high expression. FACT inhibition by the small molecule Curaxin compound, CBL0137, markedly reduced tumor initiation and progression in vivo. CBL0137 exhibited strong synergy with chemotherapy in standard use by blocking repair of DNA damage caused by genotoxic drugs, thus creating a synthetic lethal environment in MYCN amplified neuroblastoma cells and a treatment strategy for MYCN-driven neuroblastoma

overall_design: BE(2)C neuroblastoma cells were transfected with either control non-targeting siRNA's or siRNA's directed against MYCN. 36 hours post-transfection, RNA was isolated for hybridisation on Affymetrix Human Gene 2.0 ST arrays.


title: Gene expression analysis of BE(2)C cells treated with MYCN siRNA (MYCN2 #SI03113670)


title: Epigenetic Inactivation of the Putative DNA/RNA Helicase SLFN11 in Human Cancer Confers Resistance to Platinum-derived Drugs

city: L'Hospitalet del Llobregat

first: Sebastian

last: Moran

state: Barcelona

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

department: PEBC

institute: IDIBELL

summary: Platinum-derived drugs such as cisplatin and carboplatin are among the most commonly used cancer chemotherapy drugs, but very few specific molecular and cellular markers to predict different sentivity to these agents in a given tumor type have been clearly identified. Because epigenetic gene silencing is increasingly being recognized as a factor in conferring distinct tumoral drug sensitivity, we have used a comprehensive DNA methylation microarray platform to interrogate the widely characterized NCI60 panel of human cancer cell lines according to CpG methylation status and cisplatin/carboplatin sensitivity. Using this approach, we have identified that promoter CpG island hypermethylation-associated silencing of the putative DNA/RNA helicase Schlafen-11 (SLFN11) is associated with increased resistance to platinum-derived compounds. We have also experimentally validated these findings in vitro. In this setting, we were also able to identify the BRCA1 interacting DHX9 RNA helicase (also known as RHA) as a protein partner for SLFN11, suggesting a mechanistic pathway for the observed chemoresistance effect. Most importantly, we were able to extend these findings to the clinical setting where we observed that those patients with ovarian and non-small cell lung cancer carrying SLFN11 hypermethylation showed poor response to cisplatin and carboplatin treatments. Overall, these results identify SLFN11 epigenetic inactivation as a predictor of resistance to platin-derived drugs in human cancer.

overall_design: DNA was quantified by Quant-iT PicoGreen dsDNA Reagent (Invitrogen) and the integrity was analyzed in a 1.3% agarose gel. Bisulfite conversion of 600 ng of each sample was perform according to the manufacturer's recommendation for Illumina Infinium Assay. Effective bisulphite conversion was checked for three controls that were converted simultaneously with the samples. 4 ul of bisulfite converted DNA were used to hybridize on Infinium HumanMethylation 450 BeadChip, following Illumina Infinium HD Methylation protocol. Chip analysis was performed using Illumina HiScan SQ fluorescent scanner. The intensities of the images are extracted using GenomeStudio (2011.2) Methylation module (1.8.5) software. Methylation score of each CpG is represented as beta value.

first: Manel

last: Esteller

first: Vanesa

last: Nogales

first: Sebastián

last: Morán


title: Gene expression analysis of BE(2)C cells treated with SSRP1 siRNA

overall_design: BE(2)C neuroblastoma cells were transfected with either control non-targeting siRNA's or siRNA's directed against SSRP1. 72 hours post-transfection, RNA was isolated for hybridisation on Affymetrix Human Gene 2.0 ST arrays. Each sample has two replicates


title: Molecular mechanism of silver nanoparticles in human intestinal cell line Caco-2

status: Public on Nov 13 2015

city: Berlin

first: Linda

last: Böhmert

address: Max-Dohrn-Straße 8-10

country: Germany

institute: Federal Institute for risk assessment

summary: Silver nanoparticles are used in consumer products like food contact materials, drinking water technologies and supplements, due to their antimicrobial properties. This leads to an oral uptake and exposure of intestinal cells. In contrast to other studies we found no apoptosis induction by surfactant coated silver nanoparticles in the intestinal cell model Caco-2 in a previous study, although the particles induced oxidative stress, morphological changes and cell death. Therefore, this study aimed to analyze the molecular mechanism of silver nanoparticles in Caco-2 cells. We used global gene expression profiling in differentiated Caco-2 cells, supported by verification of the microarray data by quantitative real time RT-PCR and microscopic analysis, impedance measurements and assays for apoptosis and oxidative stress. Our results revealed that the majority of surfactant coated silver nanoparticles are not taken up into differentiated Caco-2 cells. and probably affect the cells by outside-in signaling. They induce oxidative stress and have an influence on canonical pathways related to FAK, ILK, ERK, MAPK, integrins and adherence and tight junctions, thereby inducing transcription factors like AP1, NFĸB and NRF2, which mediate cellular reactions in response to oxidative stress and metal ions and induce changes in the cytoskeleton and cell-cell and cell-matrix contacts. The present data confirm the absence of apoptotic cell death. Non-apoptotic, necrotic cell death, especially in the intestine, can cause inflammation and influence the mucosal immune response.

overall_design: differentiated (21 days post-confluence) Caco-2 cells (p22) in 75 cm² cell culture flask were incubated in 20 mL DMEM with 1 % ITS (Insulin, Transferin, Selen) and 1 % Penecillin/Streptomycin for 24 h with surfactant coated silver nanoparticles or silver ions

first: Birgit

last: Niemann

first: Dajana

last: Lichtenstein

first: Sabine

last: Juling

first: Alfonso

last: Lampen


title: Expression data from MSC-treated monocytes

status: Public on Nov 10 2015

city: St. Lucia

first: Othmar

last: Korn

state: Queensland

address: University of Queensland

institute: Australian Institute for Bioengineering and Nanotechnology

summary:
Chronic inflammation leading to pro-inflammatory macrophage infiltration contributes to the pathogenesis of type 2 diabetes and subsequently the development of diabetic nephropathy. Mesenchymal stem cells (MSCs) possess unique immunomodulatory and cytoprotective properties making them an ideal candidate for therapeutic intervention
We used microarrays to detail changes in the gene expression profile of monocytes isolated from type 2 diabetic patients with end-stage renal disease and non-diabetic control subjects following co-culture with MSCs.

overall_design: Control blood samples were obtained from 4 donors from the Australian Red Cross Blood Service. Blood was also obtained from 5 diabetic patients with end-stage renal disease receiving haemodialysis at the Monash Medial Centre. CD14+ monocytes were isolated from blood using microbeads and co-cultured for 48 hours with and without human bone marrow-derived MSCs using an in vitro transwell system. An Affymetrix GeneChip Human Gene 2.0 ST array was used.

first: Andrea

middle: F

last: Wise

first: Timothy

last: Williams

first: Stephen

last: Rudd

first: Christine

last: Wells

first: Peter

last: Kerr

first: Sharon

last: Ricardo


status: Public on Nov 12 2015

city: Jerusalem

first: Uri

last: Ben-David

address: Givat-Ram

department: Genetics

country: Israel

institute: Hebrew University

summary: Human pluripotent stem cells (hPSCs) tend to acquire chromosomal aberrations in culture, which may increase their tumorigenicity. However, the cellular mechanism(s) underlying these aberrations are largely unknown. Here we show that the DNA replication in aneuploid hPSCs is perturbed, resulting in high prevalence of defects in chromosome condensation and segregation. Global gene expression analyses in aneuploid hPSCs revealed decreased levels of actin cytoskeleton genes and their common transcription factor SRF. Down-regulation of SRF or chemical perturbation of actin cytoskeleton organization in diploid hPSCs resulted in increased replication stress and perturbation of chromosome condensation, recapitulating the findings in aneuploid hPSCs. Altogether, our results revealed that in hPSCs DNA replication stress results in a distinctive defect in chromosome condensation, underlying their ongoing chromosomal instability. Our results shed a new light on the mechanisms leading to ongoing chromosomal instability in hPSCs, and may be relevant to tumor development as well.

overall_design:
Expression data from diploid human pluripotent stem cells
Total RNA was isolated from undifferentiated human pluripotent stem cells grown under standard human ES conditions or under condition media

first: Juan

last: Biancotti


title: Expression data from mouse calvarial suture mesenchymal cells

status: Public on Nov 11 2015

city: Cambridge

first: Wei

last: Hsu

address: 245 First St

department: Mineralized TIssue Biology

institute: Forsyth Institute

summary:
Axin2-expressing calvarial suture stem cells can contribute to calvarial development, homeostatic maintenance, repair, and regeneration.
We used microarray to examine the gene expression profiles of Axin2-expressing suture stem cells and Axin2-negative cells in suture mesenchyme.

overall_design: Three of Axin2+/GFP+ and three of Axin2-/GFP- cell samples were collected from mice carrying Axin2rtTA and TREH2BGFP transgenes. Each samples were isolated from 6-8 Axin2rtTA; TRE-H2BGFP mice and sorted by the GFP intensity.

first: Takamitsu

last: Maruyama


title: Whole-genome effects of elaidic and oleic acids

city: Leon

first: Silvio

last: Zaina

state: Gto

address: 20 de Enero no. 929

department: Department of Medical Sciences

country: Mexico

institute: University of Guanajuato

summary: Trans fatty acids (tFAs) may have deleterious, long-term transcriptional effects. To explore that issue, we assessed the effects of the tFA elaidic acid and its cis isomer oleic acid on transcription and, in parallel, on DNA methylation.

overall_design: Human THP-1 monocytes were stimulated with 50 microM of either fatty acid for 24 h, in triplicate.

first: Gertrud

last: Lund


title: MLL5 orchestrates a cancer self-renewal state by repressing the histone variant H3.3 and globally reorganizing chromatin [methylation]

status: Public on Nov 15 2015

city: Toronto

last: Dirks

department: Developmental and Stem Cell Biology

institute: The Hospital for Sick Children

summary: Genome wide DNA methylation profiling of fourteen adult GBM primary cultures and their comparison to pediatric GBMs [GSE36278; GSE55712]

overall_design: Bisulphite converted DNA from fourteen adult GBM primary cultures were hybridised to the Illumina 450k Human Methylation Beadchip

first: Marco

last: Gallo

first: Robert

last: Vanner

first: Fiona

last: Coutinho

first: Tenzin

last: Gayden

first: Marc

last: Remke

first: Ren

last: Li

last: Mack

first: Kinjal

last: Desai

first: Lilian

last: Lee

first: Xiaoyang

last: Lan

first: Nicole

last: Park

first: Dominik

last: Sturm

first: Dalia

last: Barsyte

first: David

last: Smil

first: Michelle

last: Kushida

first: Renee

last: Head

first: Ian

last: Clarke

first: Cheryl

last: Arrowsmith

first: Stefan

last: Pfister

first: Michael

last: Taylor

first: Nada

last: Jabado

middle: P

last: Bazett-Jones

first: Mathieu

last: Lupien


title: Differential gene expression in human THP-1 cell line undifferentiated, 3 days or 8 days differentiated with phorbol myristate acetate (PMA)

status: Public on Nov 09 2015

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

institute: Institut fuer Zellbiologie

summary:
We analysed the capacity of THP-1 cells (differentiated to macrophagoid cells) to recognize  RNA sequences via pattern recognition receptors in vitro. Gene expression was analysed by RNA-Microarray. Cytokine production was analysed by ELISA assays.
We used microarrays to investigate differential gene expression in THP-1 cell line undifferentiated in comparison with 3 days or 8 days differentiated with phorbol myristate acetate (PMA). Microarray analysis revealed differential gene expression patterns of THP-1 when differentiated.

overall_design: THP-1 cells, undifferentiated, 3 days PMA-differentiated and 8 days PMA-differentiated

first: L

first: A

last: Krüger

first: C

last: Kirschning


title: Treatment effects of trastuzumab and TDM-1 in a murine model of breast cancer brain metastasis

city: Charlestown

first: Kamila

last: Naxerova

address: 149 13th Street

department: Center For Systems Biology

institute: Massachusetts General Hospital / Harvard Medical School

summary:
Background: Central nervous system (CNS) metastases represent a major problem in the treatment of HER2-positive breast cancer due to the disappointing efficacy of HER2-targeted therapies in the brain microenvironment. The antibody-drug conjugate ado-trastuzumab emtansine (T-DM1) has shown efficacy in trastuzumab-resistant systemic breast cancer. Here, we tested the hypothesis that T-DM1 could overcome trastuzumab resistance in preclinical models of brain metastases.

Methods: We treated mice bearing BT474 or MDA-MB-361 tumors in the CNS (N=9-11 per group), or cancer cells grown in organotypic brain slice cultures with trastuzumab or T-DM1 at equivalent or equipotent doses. Using intravital imaging, molecular techniques and histological analysis we determined tumor growth, mouse survival, cancer cell apoptosis and proliferation, tumor drug distribution, and HER2 signaling. All statistical tests were two-sided.

Results: T-DM1 significantly delayed the growth of HER2-positive breast cancer brain metastases compared to trastuzumab. These findings were consistent between HER2-driven and PI3K-driven tumors. The activity of T-DM1 resulted in a striking survival benefit (median survival for BT474 tumors: 28d for trastuzumab vs 112d for T-DM1, HR=6.2, 95% CI=6.1 to 85.84; P<.001). No difference in drug distribution and HER2-signaling was revealed between the two groups. However, T-DM1 led to a significant increase in tumor cell apoptosis (One-way ANOVA for ApopTag, p<.001), which was associated  with mitotic catastrophe.

Conclusions: T-DM1 can overcome resistance to trastuzumab therapy in HER2-driven and PI3K-driven breast cancer brain lesions due to the cytotoxicity of the DM1 component. Clinical investigation of T-DM1 for patients with CNS metastases from HER2-positive breast cancer is warranted.

overall_design: Comparison of trastuzumab (n=4) and TDM-1 (n=4) treated BT-474 human breast carcinoma cells growing in murine brain

first: Vasileios

last: Askoxylakis


title: Differential gene expression in human THP-1 monocytes expressing the RdRP∆cat mutant transgene compared to THP-1 empty vector control cells

status: Public on Nov 08 2015

city: Rochester

first: Meghan

last: Painter

state: MN

address: 200 1st St SW

department: Mayo Graduate School of Medicine

summary: Previously, we reported that mice made transgenic for a picornaviral RdRP – the 3Dpol protein of Theiler’s murine encephalomyelitis virus (TMEV) – suppress infection by diverse viruses. Using mouse genetic studies, we determined that uninfected RdRP transgenic mice inherently induce an arsenel of prominent antiviral effectors and that this phenotype is MDA5-, MAVS- and IFNαβR-dependent. To determine the mechanism underlying MDA5 activation and induction of constitutive antiviral signaling by the picornaviral RdRP, we constructed mutant RdRP transgenes. First, we introduced pervasive, coding-neutral point mutations into the RdRP cDNA to maximally disrupt primary and secondary RNA structure (RdRP∆rna). Another mutant, RdRP∆cat, lacks catalytic activity due to alanine substitution of the key catalytic center triad aspartate residues (D233, D328, and D329), but is otherwise intact at the nucleotide and amino acid levels. The WT,  RdRP∆rna, and RdRP∆cat versions of the RdRP transgenes were transduced with lentiviral vectors into human THP-1 monocytes, with RdRP mRNA transcription controlled by the Spleen Focus Forming Virus (SFFV) promoter. In parallel a control cell line transduced with a vector lacking any RdRP transgene (null THP-1) was generated.

overall_design: RdRP cDNAs and a GFP-puromycin fusion protein selection marker were cloned into transfer constructs containing HIV LTRs, a small portion of gag, an RRE, and a cPPT. Transfer constructs were transfected into HEK 293T cells along with packaging construct R∆8.9 and envelope pseudotyping construct expressing VSV-G. RT-normalized amounts of vector were used to transduce THP-1 cells. After selection in puromycin, whole-genome expression profiling was performed on total RNA extracted from the different THP-1 lines.

first: Eric

last: Poeschla

first: Moses

last: Rodriguez


title: Differential gene expression in human THP-1 monocytes expressing the RdRP∆rna mutant transgene compared to THP-1 empty vector control cells


title: ST3GAL1-Associated Transcriptomic Program in Glioblastoma Tumor Growth, Invasion, and Prognosis

first: Edwin

last: Sandanaraj

address: 11 Jalan Tan Tock Seng

department: Research

institute: NNI

summary: Cell surface sialylation confers many roles in cancer biology including cell proliferation, invasiveness, metastasis and angiogenesis. We show here that ST3Gal1 sialyltransferase marks a self-renewing cellular fraction. Depletion of ST3GAL1 abrogates glioma cell growth and tumorigenicity. In contrast, TGFb induces ST3GAL1 expression and correlates with the pattern of ST3Gal1 activation in patient tumors of the mesenchymal molecular subtype. To delineate the downstream events of ST3Gal1 signaling, we utilized a bioinformatical approach that leveraged on the greater statistical power of large patient databases, and subsequently verified our predictions in patient-derived glioma cells. We identify FoxM1, a major stem cell regulatory gene, as a downstream effector, and show that ST3Gal1 mediates the glioma phenotype through control of FoxM1 protein degradation

overall_design: Total RNA from primary neurosphere culture of brain tumor specimens non-treated and ST3GAL1 KD clones. The mRNAs of 5 unique glioma propagating cells (GPCs) were hybridized on Affymetrix HG-U133 Plus2 chips to study the transcriptomic impact of ST3GAL1 knock-down.  Specimens were obtained from 5 glioma patients and replicate arrays were performed for all 5 neurosphere cultures.

first: Yuk

last: Chong

first: Tan

last: Toh

first: Moogaambikai

last: Thangaveloo

first: Melanie

middle: S

last: Tan

first: Lynnette

middle: W

last: Koh

first: Grace

last: Lim

first: Joanna

last: Holbrook

first: Oi

middle: L

last: Kon

first: Mahendran

last: Nadarajah

first: Ivan

last: Ng

first: Wai

middle: H

first: Kah

first: Carol

last: Tang

first: Beng

last: Ang


title: Differential gene expression in human THP-1 monocytes expressing the RdRP transgene (WT version) compared to THP-1 empty vector control cells

first: Meghan

middle: M

first: Eric


title: Antiviral Protection via RdRP-Mediated Stable Activation of Innate Immunity

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

overall_design: Refer to individual Series


title: Gene expression profiling of macrophages from conventional or antibiotic-treated mice

status: Public on Nov 05 2015

city: New York

first: Michael

last: Abt

state: NY

institute: Memorial Sloan Kettering Cancer Center

summary:
Antibiotic-treated (ABX) mice exhibit an impaired innate and adaptive antiviral immune response and substantially delayed viral clearance following exposure to systemic LCMV or mucosal influenza virus.  Genome-wide transcriptional profiling of macrophages isolated from ABX mice revealed decreased expression of genes associated with antiviral immunity. Moreover, macrophages from ABX mice exhibited defective responses to type I and type II IFNs and impaired capacity to limit viral replication. Collectively, these data indicate that commensal-derived signals provide tonic immune stimulation that establishes the activation threshold of the innate immune system required for optimal antiviral immunity.
In this study, we performed gene expression profiling to compare the transcriptional signatures of macrophages isolated from mice exposed to commensal bacteria-derived signals to macrophages isolated from mice depleted of commensal bacteria.

overall_design: Peritoneal macrophages (CD3ε-, CD5-, CD19-, CD11b+, F4/80+)  from naïve CNV or ABX mice were sorted directly into TRIzol (Invitrogen) on a BD Aria (Beckson Dickson). Test sorts were ≥95% pure. For microarray analysis, RNA was extracted from 3 sorted biological replicates of peritoneal macrophages from naïve CNV or ABX mice. cDNA was amplified using NuGen WT Ovation Pico kit and hybridized to Affymetrix GeneChip Mouse Gene 1.0 ST microarrays

first: David

last: Artis

first: E

last: Wherry


title: Expression data from WT and Klrc1-/- CD8+ T cells

status: Public on Nov 07 2015

city: Saint Louis

first: Aaron

last: Rapaport

state: Missouri

address: 660 South Euclid Avenue, Box 8118, BJCIH 8107, Colonna Lab

department: Pathology and Immunology

institute: Washington University in St. Louis

summary:
CD8+ T cells and NK cells protect from viral infections by killing virally-infected cells and secreting interferon-g.  Several inhibitory receptors limit the magnitude and duration of these anti-viral responses.
We used microarrays to assess the transcriptome of ectromelia virus (ECTV) specific CD8+ T cells that genetically lack one such receptor, NKG2A, which is encoded by Klrc1.

overall_design: Naïve or ECTV-specific CD8+ T cells were sorted directly into RLT buffer.  RNA was then extracted, processed, and hybridized to Affymetrix arrays.

first: Marco

last: Colonna


title: Astrocytes are reprogrammed into iPS cells through a neural stem cell-like state

status: Public on Nov 06 2015

city: Kyoto

first: Eisuke

last: Nishida

address: Kitashirakawa, Sakyo-ku

department: Department of Cell and Developmental Biology

institute: Graduate School of Biostudies, Kyoto University

summary:
It remains controversial whether the routes from differentiated cells to iPSCs are related to the reverse order of normal developmental processes or independent of them. Here, we generated iPSCs from mouse astrocytes by three (Oct3/4, Klf4 and Sox2 (OKS)), two (OK), or four (OKS plus c-Myc) factors. Sox1, a neural stem cell (NSC)-specific transcription factor, is transiently upregulated during reprogramming and Sox1-positive cells become iPSCs. The upregulation of Sox1 is essential for OK-induced reprogramming. Genome-wide analysis revealed that the gene expression profile of Sox1-expressing intermediate-state cells resembles that of NSCs. Furthermore, the intermediate-state cells are able to generate neurospheres, which can differentiate into both neurons and glial cells. Remarkably, during MEF reprogramming, neither Sox1 upregulation nor an increase in neurogenic potential occurs. Thus, astrocytes are reprogrammed through an NSC-like state, suggesting that reprogramming partially follows the retrograde pathway of normal developmental processes.
To investigate the gene expression profile of intermediate-state cells during astrocyte reprogramming, we performed genome-wide gene expression analysis in  five samples; starting astrocytes, intermediate-state cells expressing Sox1-GFP, NSCs, iPSCs established from astrocytes, and iPSCs established from MEFs (iPS-MEF-Ng-20D-17) that had previously been reported (Okita, K. et al. Nature 448: 313-317 (2007)).

overall_design: Two (NSCs, iPSCs from astrocytes and MEFs) or three (astrocytes, intermediate-state cells) biological replicates were prepared for microarray samples. Total RNA was extracted with an RNeasy kit (Qiagen). cDNA synthesis and transcriptional amplification were performed using 50-100 ng of total RNA with the GeneChip WT PLUS Reagent Kit (Affymetrix). Fragmented and biotin-labeled cDNA targets were hybridized to GeneChip Mouse Gene 1.0 ST arrays (Affymetrix) according to the manufacturer’s protocol. Hybridized arrays were scanned using an Affymetrix GeneChip Scanner.

first: May

last: Nakajima-Koyama

first: Joonseong

last: Lee

first: Sho

last: Ohta

first: Takuya

last: Yamamoto


title: Acutely isolated murine cortical astrocytes and microglia: Alzheimer's disease vs wildtype

status: Public on Nov 04 2015

city: Utrecht

first: Elly

last: Hol

address: Universiteitsweg 100

department: Department of Translational Neuroscience

institute: University Medical Center Utrecht

summary:
Isolation of glia from Alzheimer's mice reveals inflammation and dysfunction.
Reactive astrocytes and microglia are associated with amyloid plaques in Alzheimer's disease (AD). Yet, not much is known about the molecular alterations underlying this reactive phenotype. To get an insight into the molecular changes underlying AD induced astrocyte and microglia reactivity, we performed a transcriptional analysis on acutely isolated astrocytes and microglia from the cortex of aged controls and APPswe/PS1dE9 AD mice. As expected, both cell types acquired a proinflammatory phenotype, which confirms the validity of our approach. Interestingly, we observed that the immune alteration in astrocytes was relatively more pronounced than in microglia. Concurrently, our data reveal that astrocytes display a reduced expression of neuronal support genes and genes involved in neuronal communication. The microglia showed a reduced expression of phagocytosis and/or endocytosis genes. Co-expression analysis of a human AD expression data set and the astrocyte and microglia data sets revealed that the inflammatory changes in astrocytes were remarkably comparable in mouse and human AD, whereas the microglia changes showed less similarity. Based on these findings we argue that chronically proinflammatory astrocyte and microglia phenotypes, showing a reduction of genes involved in neuronal support and neuronal signaling, are likely to contribute to the neuronal dysfunction and cognitive decline in AD.

overall_design: 2 cell types from 2 conditions: cortical microglia and cortical astrocytes from 15-18 month old APPswe/PS1dE9 mice compared to wildtype littermates. Biological replicates: microglia from APPswe/PS1dE9, N=7, microglia from WT, N=7, astrocytes from APPswe/PS1dE9, N=4, astrocytes from WT, N=4

first: Marie

last: Orre

first: Willem

last: Kamphuis

first: Koen

last: Bossers


title: Mechanosensitive proteins are sensitized in myelinated afferents following in vivo inflammation

city: Milwaukee

first: Andy

last: Weyer

state: WI

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

summary: Here we identified two populations of myelinated sensory neurons that display markedly different phenotypes in terms of their action potential characteristics and responses to mechanical stimuli based on their expression of Calcitonin Gene-Related Peptide (CGRP). Myelinated neurons that did not express CGRP responded to mechanical stimuli with significantly larger currents during whole-cell voltage clamp recordings than their CGRP-positive counterparts, regardless of whether these neurons projected to the dorsal hindpaw skin or the gastrocnemius muscle. Importantly, this discrepancy could not be explained by a differential expression of mechanosensitive or mechanically-gated proteins like Stoml3 or Piezo2. Following inflammation of the skin or muscle, myelinated neurons demonstrated a sensitization to mechanical stimuli characterized by increased current amplitudes. Interestingly, myelinated neurons expressing CGRP are sensitized to mechanical stimuli following cutaneous inflammation of the paw, while myelinated neurons that do not express CGRP are sensitized to mechanical stimuli following inflammation of the gastrocnemius muscle. Microarray data was obtained from these populations by first using Fluorescence-Activated Cell Sorting (FACS) to separate the populations of interest.

overall_design: 15 different samples were analyzed, 3 biological replicates for each group (5 groups: saline paw-injected, CFA paw-injected, saline muscle-injected, acid muscle-injected, and CFA muscle-injected). The saline injected groups (paw and muscle) are considered controls.

first: Cheryl

last: Stucky


city: Singapore

first: Edwin

last: Sandanaraj


title: Assessing transcriptionally functional CpGs in articular cartilage

city: Leiden

first: Wouter

middle: den

last: Hollander

address: Einthovenweg 20

department: Molecular Epidemiology

institute: LUMC

summary: Preserved and affected cartilage from 17 knees and 14 hip joints were sampled from patients undergoing joint replacement surgery, due to primary OA.

overall_design: 17 knees and 14 hip joints

last: den Hollander


title: Epigenetic profiling in CD4 and CD8 T cells from Graves’ disease patients reveals changes in genes associated with T cell receptor signaling [methylation]

city: Tartu

first: Pärt

last: Peterson

address: Ravila 19

department: Department of Biomedicine

country: Estonia

institute: University of Tartu

summary: In Graves’ disease (GD), a combination of genetic, epigenetic and environmental factors causes an autoimmune response to the thyroid gland, characterized by lymphocytic infiltrations and autoantibodies targeting the thyroid stimulating hormone receptor (TSHR) and other thyroid antigens. To identify the epigenetic changes involved in GD, we performed a genome-wide analysis of DNA methylation and enrichment of H3K4me3 and H3K27ac histone marks in sorted CD4+ and CD8+ T cells. We found 365 and 3322 differentially methylated CpG sites in CD4+ and CD8+ T cells, respectively. Among the hypermethylated CpG sites, we specifically found enrichment of genes involved in T cell signaling (CD247, LCK, ZAP70, CD3D, CD3E, CD3G, CTLA4 and CD8A) and decreased expression of CD3 gene family members. The hypermethylation was accompanied with the active chromatin histone modifications as we found decreased signals of H3K4me3 and H3K27ac marks at several T cell signaling genes in ChIP-seq analysis. In addition, we found hypermethylation of the TSHR gene first intron, where several GD-associated polymorphisms are located. Our results demonstrate an involvement of dysregulated DNA methylation and histone modifications at T cell signaling genes in GD patients.

overall_design: Individuals were recruited from the Estonian Genome Center of the University of Tartu. Genomic DNA was extracted from sorted CD4+ (31 controls and 36 GD patients) and CD8+ (31 controls and 37 GD patients) T cells. The data collection was performed at the SNP&SEQ Technology Platform in Uppsala University, and data analysis was done at the Institute of Biomedicine and Translational Medicine in the University of Tartu.

first: Lili

last: Milani


title: IRE1alpha is an endogenous substrate of endoplasmic reticulum-associated degradation

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

institute: Wageningen University

summary: Endoplasmic reticulum-associated degradation (ERAD) represents a principle quality control (QC) mechanism to clear misfolded proteins in the ER; however, its physiological significance and the nature of endogenous ERAD substrates remain largely unknown. Here we discover that IRE1alpha, the sensor of unfolded protein response (UPR), is a bona fide substrate of the Sel1L-Hrd1 ERAD complex. Mechanistically, ERAD-mediated IRE1alpha degradation occurs in a Bip-dependent manner under basal conditions and is attenuated in response to ER stress. Both intramembrane hydrophilic residues of IRE1alpha and lectin protein OS9 are required for IRE1alpha degradation. ERAD deficiency causes IRE1alpha protein stabilization, accumulation and mild activation both in vitro and in vivo, leading to cellular hypersensitivity to ER stress and inflammation. Furthermore, though enterocyte-specific Sel1L-knockout mice (Sel1LΔIEC) are viable and appear normal, they are more susceptible to experimental colitis in an IRE1alpha-dependent but CHOP-independent manner. Collectively, these results demonstrate that Sel1L-Hrd1 ERAD serves a distinct, essential function in restraint of IRE1alpha signaling in vivo by managing its protein turnover.

overall_design: Colon epithelium of wild type and enterocyte-specific Sel1L knockout mice were subjected to gene expression analysis.

first: Shengyi

last: Sun

first: Guojun

last: Shi

first: Haibo

last: Sha

first: Yewei

last: Ji

first: Xuemei

last: Han

first: Xin

last: Shu

first: Hongming

last: Ma

first: Inoue

last: Takamasa

first: Beixue

last: Gao

first: Pengcheng

last: Bu

first: Robert

last: Guber

first: Xiling

last: Shen

first: Ann

first: Takao

last: Iwawaki

first: Adrienne

last: Paton

first: James

first: Deyu

last: Fang

first: Billy

last: Tsai

first: John

middle: R

last: Yates III

first: Haoquan

last: Wu

first: Sander

last: Kersten

first: Qiaoming

last: Long

first: Gerald

middle: E

last: Duhamel

first: Kenneth

last: Simpson

first: Ling

last: Qi


title: Genome-wide screen reveals rhythmic regulation of genes involved in odor processing in the olfactory epithelium

city: Berlin

first: Karsten

last: Jürchott

address: Luisenstraße

department: Rahel Hirsch Center

institute: BIH at Charité

summary:
Odor discrimination behavior displays circadian fluctuations in mice indicating that mammalian olfactory function is under control of the circadian system. This is further supported by the facts that odor discrimination rhythms depend on the presence of clock genes and that olfactory tissues contain autonomous circadian clocks. However, the molecular link between circadian function and olfactory processing is still unknown. In order to elucidate the molecular mechanisms underlying this link, we focused on the olfactory epithelium (OE), the primary target of odors and the site of the initial events in olfactory processing. We asked whether olfactory sensory neurons (OSNs) within the OE possess an autonomous circadian clock and whether olfactory pathways are under circadian control. Employing clock gene-driven bioluminescence reporter assays, immunohistochemistry and a time-dependent microarray-based transcriptome analysis on OE samples, we found robust circadian rhythms of core clock genes and their proteins in OSNs, suggesting that the OE indeed contains an autonomous circadian clock.
Furthermore, we identified several OSN-specific components of the olfactory pathway that are under circadian control, including several candidates with putative roles in circadian olfactory processing, such as KIRREL2 -- an established factor involved in short-term OSN activation. The spatiotemporal expression patterns of our candidate proteins suggest that they are involved in short-term anabolic processes to rhythmically prepare the cell for peak performances and to promote circadian function of OSNs.

overall_design: We performed a genome-wide expression study with RNA from OE tissue extracted at 4-h intervals in constant darkness from previously entrained mice. Total RNA of four mice per sampling time was pooled in equal amounts.

first: Manjana

last: Saleh

first: Achim

last: Kramer

first: Ute

last: Abraham


title: Eed conditional knockout in chondrocytes

status: Public on Nov 01 2015

city: Boston

first: Tatsuya

last: Kobayashi

address: 50 Blossom Street, Thier 1101

department: Endocrine Unit

institute: Massachusetts General Hospital

overall_design: Primary rib chondrocyte  were isoloated from P0.5-day old wildtype and Col2-Cre:floxed EED conditional knockout mouse pups,and cultured overnight in 10%FCS containing DMEM.  RNA was isolated and subjected to Affymetrix Mouse Gene ST 1.0 array.  Biological duplicate.  Mice were in a mixed genetic background of C57/B6 and 129sv.


title: Microarray Analysis of Cohesin Mutant HSPC

status: Public on Nov 03 2015

city: Stanford

first: Ravi

last: Majeti

state: California

address: 235 Campus Drive

institute: Stanford University

summary: Transciptome analysis of CD34+ enriched human HSPC lentivirally transduced with cohesin WT or mutant

overall_design: CD34+ enriched HSPCs from cord blood were transduced with a constitutive lentiviral vector expressing cohesin WT or mutant tagged to GFP. After 72hrs cells were GFP+ sorted and subjected to downstream microarray protocol.

first: Claire

last: Mazumdar


title: Gene expression profiling of sensitive skin

city: Seoul

first: Eun Ju

last: Kim

address: 101 Daehakro Jongnogu

department: Department of Dermatology

country: South Korea

institute: Seoul National University College of Medicine

summary: Sensitive skin is a hyperactive skin condtion, characterized by prickling, burning, itching, stinging, pain, or tingling sensation, which develops in response to various internal and external stimulants that can be tolerated by most people. The pathophysiology involved in the development of sensitive skin remains largely elusive. To characterize differential gene expression profiles in sensitive skin, we investigated the genome-wide patterns of gene expression from skin samples from subjects with sensitive or non-sensitive skin, following lactic acid challenge or normal saline application using cDNA microarrays.

overall_design: We recruited eighteen healthy volunteers with sensitive skin (n=9) or non-sensitive skin (n=9). From each subject, two skin samples were obtained following lactic acid or normal saline application.(18 samples/group) Based on the existence of sensitive skin and lactic acid challenge, samples were pooled into sets of three individuals each. Global transcriptome profiling was conducted using Affymetrix Human Genome U133 Plus 2.0 array.

first: Eun-Ju

first: Jin-Ho

last: Chung


title: Transcriptomic analysis after transfection in murine genetically modified stem cells overexpressing the RAX gene (CCE-Rx cells) of either a siRNA against SOX2 or a scramble siRNA

city: Toulouse

first: Nicolas

last: Chassaing

address: Place du Dr Baylac

department: Service de Génétique Médicale

country: France

institute: CHU Toulouse

summary: SOX2 is the main gene involved in anophthalmia. In order to identify genes regulated by SOX2 transcription factors (genes that could be good candidates to also be involved in ocular development), we studied transcriptomic profiles of murine genetically modified stem cells overexpressing the RAX gene (CCE-Rx cells) after transfection by a siRNA against SOX2 or a scramble siRNA.

first: N


title: Ikaros-induced gene expression chages upon Ikaros re-expression in the ILC87 Ikaros-deficient tumor cell line

city: Illkirch

first: Attila

last: Oravecz

address: 1 rue Laurent Fries

institute: IGBMC

summary: We used microarrays to analyze gene expression changes in the Ikaros null ILC87 T cell tumor line after re-expression of Ikaros.

overall_design: ILC87 cells were transduced to stably express the 4-hydroxytamoxifen-inducible (4OHT) Ikaros1-ER fusion protein. ILC87-Ik1-ER cells were treated with mock (EtOH) or 4OHT for 1 day and the global gene expression changes were assessed by microarray analysis.

first: Philippe

last: Kastner

first: Apostol

last: Apostolov


title: The Nasal Methylome and Childhood Atopic Asthma

city: Aurora

first: David

last: Schwartz

state: CO

address: Anschutz Medical Campus

department: Medicine

institute: University of Colorado, Anschutz Medical Campus

summary: Background:    Nasal epithelia are emerging as a proxy measure of gene expression of the airway epithelium in asthma. We hypothesized that epigenetic marks regulate gene expression of the nasal epithelia and consequently may provide a novel target for allergic asthma.   Methods:    We compared genomic DNA methylation patterns and gene expression in African American children with persistent atopic asthma [N=36] versus healthy controls [N=36].  Results were validated in an independent population of asthmatics [N=30].    Results:    We identified 186 genes with significant methylation changes, either as regions (differentially methylated regions [DMRs]) or single CpGs (differentially methylated probes [DMPs]) after adjustment for age, gender, race/ethnicity, batch effects, inflation, and multiple comparisons (false discovery rate-adjusted q<0.05). Genes differentially methylated include those with established roles in asthma and atopy, components of the extracellular matrix, genes related to immunity, cell adhesion, epigenetic regulation, and airway obstruction. The methylation changes are large (median 9.5%, range: 2.6-29.5% methylation change) and similar in magnitude to those observed in malignancies. Hypo- and hyper-methylated genes were associated with increased and decreased gene expression respectively (P<2.8x10-6 for DMRs and P<7.8x10-10 for DMPs). Quantitative analysis of methylation-expression relationships in 53 differentially expressed genes demonstrated that 32 (60%) have significant (q<0.05) methylation-expression relationships within 5kb of the gene. 10 loci selected based on the relevance to asthma, magnitude of methylation change, and asthma specific methylation-expression relationships were validated in an independent cohort of children with asthma.   Conclusions:    Our findings that epigenetic marks in respiratory epithelia are associated with allergic asthma in inner-city children provide new targets for biomarker development, and novel approaches to understanding disease pathogenesis.

overall_design:
Case control design with nasal epithelial cells from 36 atopic asthmatic and 36 nonatopic nonasthmatic children from the inner city

Note: The Sample data tables are incomplete (truncated at 65535 rows, related to row-limit in older version of Excel).

first: Ivana

middle: V

last: Yang

first: Brent

last: Pedersen

middle: A


title: Gene expression profile of HIF-1α silenced or non-silenced human DCs stimulated with A. fumigatus under normoxic or hypoxic conditions

city: Wuerzburg

first: Mirjam

last: Fliesser

state: Bavaria

address: Josef-Schneider-Str. 2

department: Medical Clinic II

institute: University Hospital Wuerzburg

summary:
DCs play a central role for the immune response against the mold Aspergillus fumigatus. Hypoxic microenvironments occur during infection with A. fumigatus. Hypoxia and signaling via hypoxia inducible factor 1α may modulate the response of DCs; however, the role in fungal infections is unclear.
We used microarrays to determine the influence of hypoxia and HIF-1α signaling on the immune response of human DCs towards A. fumigatus.

overall_design: HIF-1α silenced or non-silenced, human monocyte-derived DCs were cultivated for 6 h in normoxia or hypoxia (1 % O2) without stimulation or stimulated with inactivated germ tubes of A. fumigatus. Three independent experiments with DCs derived from different blood donors were performed. RNA was extracted and hybridized on Affymetrix microarrays.

first: Juergen

last: Loeffler

first: Michael

last: Bonin


title: UV-irradiation of skin enhances glycolytic flux in bone marrow-differentiated dendritic cells

status: Public on Oct 30 2015

city: Perth

first: Kim

middle: Warwick

last: Carter

state: Western Australia

address: 100 Roberts Road, Subiaco

institute: Telethon Kids Institute

summary: Following UV irradiation of skin, dendritic cells (DCs) differentiating from the bone marrow (BM) of mice have a reduced ability to prime new immune responses; their reduced immunogenicity is maintained for at least 16 weeks in UV-chimeric mice. We hypothesized that different metabolic states underpin changes in DC function. Compared with DCs from the BM of non-irradiated mice, DCs from the BM of UV-irradiated mice produced more lactate and utilized greater amounts of glucose, a profile that was supported by greater glycolytic flux when incubated in low-serum-containing medium. Responses to a mitochondrial stress test were similar suggesting that the DCs from the BM of UV-irradiated mice had not switched from a profile of oxidative phosphorylation, but were imprinted for greater glycolytic responses. After microarray profiling, RT-qPCR confirmation and Ingenuity pathway analysis, greater expression of the enzyme, 3-hydroxyanthranilate 3,4-dioxygenase, was identified as a potential contributor to increased glycolysis by BM-differentiated DCs. This enzyme provides the final step of the biosynthetic pathway from tryptophan to quinolinate, the universal de novo precursor to the pyridine ring of nicotinamide adenine dinucleotide (NAD), and may provide a mechanism to ensure sufficient NAD is available to support enhanced glycolysis. Increased lactate production was also measured for DCs from the BM of 16-week engrafted UV-chimeric mice and suggests long-lasting imprinting of progenitor cells for altered immunometabolism in their progeny cells. This study provides evidence of changes to metabolic states that associate with altered DC function.

overall_design:
Female C57BL/6J (CD45.2 alloantigen) and B6.SJL-Ptprca (CD45.1 alloantigen) mice were obtained from the Animal Resources Centre (Murdoch, Western Australia). A bank of TL40W/12RS lamps (Philips, Amsterdam, The Netherlands) emitting broadband UVR with 65% UVB (280-320 nm) and peak emission at 313 nm was used. Twenty-four h prior to irradiation, a uniform area of dorsal skin of mice was shaved (8 cm2). To administer UVR, mice were held in perspex compartments which were covered with 0.2 mm polyvinyl chloride plastic to eliminate wavelengths <290 nm. The compartments were placed 20 cm beneath the UV lamps and up to 8 kJ/m2 UVR was delivered. Eight kJ/m2 UVR is equivalent to 3-4 minimal erythemal doses . The UVB output by the lamps was measured using a UVX radiometer (Ultraviolet Products Inc., Upland, CA). Mice were 6-10 wk old at the time of irradiation unless otherwise stated. Mice were subcutaneously implanted with two PGE2 pellets, each containing 0.1 mg with a constant release of 4.76 µg/day over 21 days (total 9.52 µg/day, Innovative Research of America, Sarasota, FL), three days prior to isolation of BM cells. The pellets were inserted into the loose skin at the top of the back. Freshly-isolated BM cells were cultured for 5 days in RPMI-1640 (HyClone, GE Health Care Life Sciences, Logan, UT) supplemented with 10% FCS (RPMI-10), 10 ng/ml GM-CSF and 10 ng/ml IL-4 (Peprotech Inc, Rocky Hill, NJ) at a density of 8 x 105 cells/ml in 24 well plates to promote CD11c+ cell differentiation (medium replaced on days 2 and 4). Non-adherent cells were enriched to >95% CD11c+ cells (confirmed by flow cytometry) using anti-CD11c magnetic microbeads (Miltenyi Biotec, Bergisch Gladbach, Germany) and autoMACS-Pro (Miltenyi Biotec) separation. Total RNA was extracted from triplicate preparations of BM-differentiated CD11c+ cells.
Two sample groups;
BM-differentiated DC sample from C57BL/6J mice injected with 2 x 10^6 BM cells from a naïve congenic B6.SJL-Ptprca mouse
BM-differentiated DC sample from C57BL/6J mice injected with 2 x 10^6 BM cells from a UV irradiated congenic B6.SJL-Ptprca mouse

first: Terence

last: McGonigle

first: Kevin

middle: N

last: Keane

first: Simon

last: Ghaly

first: Denise

last: Anderson

first: Naomi

last: Scott

first: Helen

last: Goodridge

first: Philip

last: Newsholme

first: Prue

last: Hart


title: Childhood Atopic Asthma

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

overall_design: Refer to individual Series


title: A cross species and multi-omics (including metabolomics) analysis in pancreatic neuroendocrine tumours (tumor stages)

city: Sutton

first: Anguraj

last: Sadanandam

state: Surrey

address: 15 Cotswold Road

department: Molecular Pathology

country: United Kingdom

institute: Institute of Cancer Research (ICR), London

summary:
Pancreatic neuroendocrine tumor (PanNET) is relatively infrequent but is nevertheless metastatic. Seeking to extend a new paradigm of personalized medicine, we performed an integrative analysis of transcriptomic (mRNA and microRNA) and mutational profiles and defined three clinically relevant human PanNET subtypes. Importantly, cross-species analysis revealed two of these three subtypes in a well-characterized, genetically engineered mouse model (RIP1-Tag2) of PanNET and its cell lines. Each subtype share similarities to distinct cell types in pancreatic neuroendocrine development, features are reflected in their metabolic profiles. Subtype-specific molecular signatures metabolites are proposed to identify these subtypes.
Gene expression data from different stages of RIP1-TAG2 genetically engineered PanNET mouse model

overall_design: RT2 mouse PanNET tumors, liver metastases, normal, hyperplastic, and angiogenic islets were dissected out or isolated. RNA was extracted and hybridized on Affymetrix GeneChip Mouse Gene 1.0 ST arrays. The CEL files were processed using aroma.affymetrix.

first: A

first: D

last: Hanahan


title: Cell cycle-dependent reconfiguration of the DNA (hydroxy) methylome during terminal differentiation of human B cells into plasma cells [expression array]

city: Rennes

first: Gilles

last: Salbert

address: Avenue du Général Leclerc

department: Biology

institute: University of Rennes 1

summary: Molecular mechanisms underlying terminal differentiation of B-cells into plasma cells are major determinants of adaptive immunity but remain only partially understood. Here, we present the transcriptional and epigenomic landscapes of cell subsets arising from activation of human naive B-cells and differentiation into plasmablasts. Cell proliferation of activated B cells was linked to a slight decrease in DNA methylation levels but followed by a committal step in which an S-phase-synchronized differentiation switch was associated with an extensive DNA demethylation and local acquisition of 5-hydroxymethylcytosine at enhancers and genes related to plasma cell identity.

overall_design: Number of samples analyzed: 16 in vitro-derived human B cells, spanning 5 cell populations. No technical replicates.

first: Thierry

last: Fest

first: Jose

middle: I

last: Martin-Subero

first: Céline

last: Delaloy

first: Delphine

last: Rossille


title: Transcriptional profiles of pilocytic astrocytoma

city: Gliwice

first: Aleksandra

last: Pfeifer

address: Wybrzeze Armii Krajowej 15

country: Poland

institute: MSC Memorial Cancer Center and Institute of Oncology

summary: Pilocytic astrocytoma is the most common type of brain tumor in pediatric population, generally connected with favorable prognosis, although recurrences or dissemination sometimes are also observed. For tumors originating in supra- or infratentorial location different molecular background was suggested but plausible correlations between transcriptional profile and radiological features and/or clinical course are still undefined. The purpose of this study was to identify gene expression profiles related to the most frequent locations of this tumor, subtypes based on various radiological features and clinical pattern of the disease.   According to the radiological features presented on MRI, all cases were divided into four subtypes: solid or mainly solid, cystic with an enhancing cyst wall, cystic with a non-enhancing cyst wall and solid with central necrosis. Bioinformatic analyses showed that gene expression profile of pilocytic astrocytoma highly depends on the tumor location. Most prominent differences were noted for IRX2, PAX3, CXCL14, LHX2, SIX6, CNTN1 and SIX1 genes expression which could distinguish pilocytic astrocytomas of different location even within supratentorial region. Analysis of the genes potentially associated between radiological features showed much weaker transcriptome differences. Single genes showed association with the tendency to progression.   Here we showed that pilocytic astrocytomas of three different locations could be precisely differentiated on the basis of gene expression level but their transcriptional profiles did not strongly reflect the radiological appearance of the tumor or the course of the disease.

overall_design: Gene expression profiling was performed in 47 pilocytic astrocytoma tumours characterized by different localization, radiology and progression.

first: Krzysztof

last: Zakrzewski

first: Michał

last: Jarząb

first: Małgorzata

last: Oczko-Wojciechowska

first: Barbara

first: Paweł

last: Liberski

first: Magdalena

last: Zakrzewska


title: Cell cycle-dependent reconfiguration of the DNA (hydroxy) methylome during terminal differentiation of human B cells into plasma cells [methylation array]

overall_design: Number of samples analyzed: 26 in vitro-derived human B cells, spanning 7 cell populations. No technical replicates.


title: hESC MIXL1+ MIXL1- microarray

city: Los Angeles

first: Rhys

middle: John Powling

last: Skelton

state: CA

address: 675 Charles E Young Dr S, Room 3645

department: Eli and Edythe Broad Stem Cell Research Center

country: USA

institute: UCLA

summary: Microarray analysis of isolated hES cells from day 3 of cardiac differentiation was used to identify differences between MIXL1eGFP+ and MIXL1eGFP- transcriptomes. We identified 6,757 differentially regulated genes, of which 2,520 were upregulated ≥2-fold in the eGFP+ (MIXL1+) mesoderm population

overall_design: A stencil differentiation protocol was used to isolate mesodermal cells based on GFP expression from the MIXL1 locus. Microarray analysis of isolated cells from day 3 of differentiation was used to identify differences between MIXL1eGFP+ and MIXL1eGFP- transcriptomes.

first: Bevin

last: Brady

first: Debashis

last: Sahoo

first: Oscar

last: Abilez


title: Role of Tet1 and Tet3 genes and Chromatin Remodeling in Cerebellar Circuit Formation [gene expression]

status: Public on Oct 31 2015

city: New York

first: Michelle E.

last: Ehrlich

address: 1 Gustave L. Levy Pl, New York, NY 10029

department: Department of Psychiatry

institute: Icahn School of Medicine at Mount Sinai

summary:
Transcriptome analysis of mRNA samples purified from developing cerebellar granule cells and ES cell-derived granule cells using translating ribosome affinity purification (TRAP) method.
Although mechanisms underlying early steps in cerebellar development are known, evidence is lacking on genetic and epigenetic changes during the establishment of the synaptic circuitry. Using metagene analysis, we report pivotal changes in multiple reactomes of epigenetic pathway genes in cerebellar granule cells (GCs) during circuit formation.  During this stage, Tet genes are up-regulated and vitamin C activation of Tet enzymes increases the levels of 5-hydroxymethylcytosine (5hmC) at exon start sites of up-regulated genes, notably axon guidance genes and ion channel genes.  Knockdown of Tet1 and Tet3 by RNA interference in ex vivo cerebellar slice cultures inhibits dendritic arborization of developing GCs, a critical step in circuit formation.  These findings demonstrate a role for Tet genes and chromatin remodeling genes in the formation of cerebellar circuitry.

overall_design: We analyzed gene expression of cerebellar granule cells and ES cell-derived granule cells using the Affymetrix mouse gene 1.0 ST platform. Array data was processed by metagene analysis which was developed by the Broad Institute.

first: Xiaodong

last: Zhu

first: David

last: Girardo

first: Eve-Ellen

last: Govek

first: Keisha

last: John

first: Marian

last: Mellén

first: Pablo

last: Tamayo

first: Jill

last: Mesirov

first: Mary

last: Hatten


title: Altered lipid metabolism in the aging kidney identified by three layered omic analysis

city: Cologne

first: Peter

last: Frommolt

address: Joseph-Stelzmannstr. 26

institute: CECAD

summary:
Aging-related diseases and their comorbidities affect the life quality of a constantly growing proportion of our population. Age-associated changes of kidney structure and function are considerable contributors to the dramatically increased incidence of chronic kidney disease world-wide which has been identified to be a prominent cardiovascular risk factor. In order to detect molecular mechanisms involved in kidney aging we analyzed gene expression profiles of kidneys from adult and aged wild-type mice by a three-layered omics strategy. To this end, transcriptomic, proteomic and targeted lipidomic profiles of young and aged mice were generated and integrated. Transcriptome and proteome analyses revealed differential expression of genes involved primarily in lipid metabolism and immune response. Additional lipidomic analyses uncovered significant age-related differences in the total amount of phosphatidylethanolamines, phosphatidylcholines and sphingomyelins as well as in subspecies of phosphatidylserines and ceramides, while total ceramide levels remained unchanged. By integration of these datasets we identified Aldh1a1, a key enzyme in vitamin A metabolism specifically expressed in the medullary ascending limb, as one of the most prominent upregulated proteins in old kidneys. Moreover, ceramidase Asah1 was highly expressed in aged kidneys, consistent with a decrease in ceramide C16.
In summary, our data suggest that changes in lipid metabolism are involved in the process of kidney aging and in the development of chronic kidney disease.

overall_design: 14 weeks females (4 replicates); 96 weeks females (5 replicates)

first: Fabian

last: Braun

first: Markus

last: Rinschen

first: Valerie

last: Bartels

first: Bianca

last: Habermann

first: Jan

last: Hoeijmakers

first: Björn

last: Schumacher

first: Martijn

last: Dollé

first: Roman-Ulrich

last: Müller

first: Thomas

last: Benzing

first: Bernard

last: Schermer

first: Christine

last: Kurschat


title: Effect of YAP overexpression on HuCCT1 cholangiocarcinoma cell line transcriptome (shRNA targeting YAP)

status: Public on Oct 27 2015

city: Basel

first: Yann

last: Abraham

address: Postfach

department: NIBR/DMP

country: Switzerland

institute: Novartis Pharma AG

summary:
The YAP pathway in regulating organ size by integrating external signals to control the expression of genes involved in cell proliferation. YAP is known to be involved in tumorigenesis in several tissues, yet its role in cholangiocarcinoma is not established
We used microarrays to assess the role of YAP pathway in cholangiocarcinoma either by overexpressing a constitutively active YAP1 mutant, or by downregulating YAP1 expression using shRNA

overall_design: HuCCT1 cells where transfected with either a control scrambled shRNA or a shRNA targeting YAP1; cells were harvested, RNA was collected and analyzed using microarray

first: Patricia

last: Marti

first: Tanja

last: Blumer

first: Michael

middle: T

last: Dill

first: Claudia

last: Stein

first: Philippe

last: Megel

first: Giorgia

last: Jurisic

first: Zuzanna

last: Makowska

first: Monika

last: Pikiolek

first: Vanessa

last: Orsini

last: Agarinis

first: Luigi

last: Tornillo

first: Tewis

last: Bouwmeester

first: Heinz

last: Ruffner

first: Andreas

last: Bauer

first: Tobias

last: Schmelzle

first: Christian

last: Parker

last: Terracciano

last: Heim

last: Tchorz


title: Intestinal epithelial TRE-Msi1

status: Public on Oct 24 2015

city: Philadelphia

first: Christopher

last: Lengner

state: PA

address: 3800 Spruce Street, Room 390EA

department: Biomedical Sciences

institute: University of Pennsylvania

summary: Comparison of gene expression in intestinal epithelial cells in the presence or absence of ectopic induction of Msi1 in vivo

overall_design: Total RNA was isolated from preparations of total intestinal epithelial cells taken from the jejunum from 3 control (R26-M2rtTA +doxycycline for 24 hrs) and 3 experimental (TRE-Msi1::R26-M2rtTA +doxycycline for 24 hrs) animals and subjected to profiling on affymetrix Gene 1.0ST arrays

first: Zhengquan

last: Yu

first: Chris


title: Expression data from E15.5 mouse embryos

city: Tsukuba

first: Ahmed

last: Abdellatif

state: Ibaraki

address: 1.1.1. Tennodai, Tsukuba-shi, Ibaraki-ken

department: Anatomy and Embryology

institute: University of Tsukuba

summary:
The pancreatic beta cells are the only cells that can produce insulin in response to prevailing glycemia. The development of beta cells was found to be depending on the activity of a complex genetic network. Overexpression of transcriptional factor MafK in beta cells have resulted in impairment of thier functions and suppressed insulin secretion and increased the severity of beta cell loss resulting  in an overt diabetes.
We used microarrays to study the changes in islet gene expression profiles in MafK Tg. Mafk overexpression was expected to disrupt functions of genes containing MARE sites in their regulatory regions by bindig to cis-regulatory elements. Exploration of new factors with sunctional MAREs in thier regulatory regions in beta cells will improve our targeting stratigies for treatment of diabetes.

overall_design:
A 0.78 kb full-length cDNA encoding the murine MafK protein including a FLAG peptide at the N-terminus was inserted into the rat insulin I promoter. Then, the construct was injected into BDF1-fertilized eggs to generate transgenic mice. All Tg mice were maintained on an ICR genetic background.
Whole pancreata were collected from MafK transgenic embryos as well as wild type embryos at E15.5 (N=3 per each gentype). Total RNA was extracted and hybridized for Affymetrix microarray analysis.

first: Yunshin

last: Jung

first: Hisashi

last: Oishi

first: Satoru

last: Takahashi