title: Trans-effects of chromosome aneuploidies on DNA methylation patterns:  DNA methylation analysis of Down syndrome in human brain tissues and cells

city: hackensack

first: Benjamin

last: Tycko

state: NJ

address: 40 prospect avenue

department: Epigenetics

institute: HUMC

summary: Background: Trisomy 21 causes Down syndrome (DS), but the mechanisms by which the extra chromosome leads to deficient intellectual and immune function are not well understood.  Results: Here, we profile CpG methylation in DS and control cerebral and cerebellar cortex of adults and cerebrum of fetuses. We purify neuronal and non-neuronal nuclei and T-lymphocytes and find biologically relevant genes with DS-specific methylation (DS-DM) in brain cells. Some genes show brain-specific DS-DM, while others show stronger DS-DM in T cells. Both 5-methyl-cytosine and 5-hydroxy-methyl-cytosine contribute to the DS-DM. Thirty percent of genes with DS-DM in adult brain cells also show DS-DM in fetal brains, indicating early onset of these epigenetic changes, and we find early maturation of methylation patterns in DS brain and lymphocytes. Some, but not all, of the DS-DM genes show differential expression. DS-DM preferentially affected CpGs in or near specific transcription factor binding sites, implicating a mechanism involving altered transcription factor binding. Methyl-seq of brain DNA from mouse models with sub-chromosomal duplications mimicking DS reveals partial but significant overlaps with human DS-DM and shows that multiple chromosome 21 genes contribute to the downstream epigenetic effects.  Conclusions: These data point to novel biological mechanisms in DS and have general implications for trans effects of chromosomal duplications and aneuploidies on epigenetic patterning.

overall_design: Bisulfite converted DNA from 119 samples from Down syndrome patients and controls  were hybridised to the Illumina Infinium 450k Human Methylation Beadchip. In addition, we re-analyzed 6 Down syndrome and 6 control cerebellum DNA samples on the 450K BeadChips using an adaptation of the Illumina probe preparation protocol (TrueMethyl kit; Cambridge Epigenetics, CEGX), in which parallel analyses of bisulfite and oxidative bisulfite DNA for each sample allows assessment of the relative contributions of 5mC and 5hmC to net methylation.

first: Maite

last: Mendioroz

first: Catherine

last: Do

first: Xiaoling

last: Jiang

first: Chunhong

last: Liu

first: Huferesh

middle: K

last: Darbary

first: Charles

middle: F

last: Lang

first: John

last: Lin

first: Anna

last: Thomas

first: Sayeda

last: Abu-Amero

first: Philip

last: Stanier

first: Alexis

last: Temkin

first: Alexander

last: Yale

first: Meng-Min

first: Yang

last: Li

first: Martha

last: Salas

first: Kristi

last: Kerkel

first: George

last: Capone

first: Wayne

last: Silverman

first: Eugene

first: Gudrun

last: Moore

first: Jerzy

last: Wegiel


title: Effect of YAP overexpression on HuCCT1 cholangiocarcinoma cell line transcriptome

status: Public on Oct 27 2015

city: Basel

first: Yann

last: Abraham

address: Postfach

department: NIBR/DMP

country: Switzerland

institute: Novartis Pharma AG

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

overall_design: Refer to individual Series


title: Comparison of Nanostring nCounter data on FFPE colon cancer samples and Affymetrix microarray data on matched frozen tissues

city: Nashville

first: Pengcheng

last: Lu

state: TN

address: 2200 Pierce Avenue

country: USA

institute: Vanderbilt University

summary: The prognosis of colorectal cancer (CRC) stage II and III patients is still a challenge due to the difficulties of finding robust biomarkers and assays. The majority of published gene signatures of CRC have been generated on frozen colorectal tissues. Because collection of fresh frozen tissues is not routine and the quantity and quality of RNA derived from formalin-fixed paraffin-embedded (FFPE) tissues is vastly inferior to that derived from fresh frozen tissue, a clinical test for improving staging of colon cancer will need to be designed for FFPE tissues in order to be widely applicable. We have designed a custom Nanostring nCounter assay for quantitative assessment of expression of 414 gene elements consisting of multiple published gene signatures for colon cancer prognosis, and systematically compared the gene expression quantification between nCounter data from FFPE and Affymetrix microarray array data from matched frozen tissues using 414 genes.

overall_design:
For microarray studies, representative sections of fresh tissue specimens were flash frozen in liquid nitrogen and stored at −80°C until RNA isolation. RNA was purified from tissue sections containing >80% epithelial tumor tissue using RNeasy (QIAGEN, Valencia, CA) according to manufacturer’s instructions. Samples were hybridized to Affymetrix arrays Human Genome U133 Plus 2.0 GeneChip Expression Arrays, Santa Clara, CA). The samples included four healthy control patient tissues, 12 stage I, 17 stage II, 20 stage III and 15 stage IV CRC patient tissues.

Please note that only the *matched.csv files containing matched 414 genes' microarray and nanostring data are provided without the nanostring experimental descriptions.
The matching samples between GSE62932 and the Nanostring study are indicated in the matching_samples.txt.

first: R

middle: D

last: Beauchmap

first: Xi

last: Chen


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

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 an empty vector or a vector overexpressing the constitutively active YAP1 S127A; 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

middle: M

last: Terracciano

first: Markus

middle: H

last: Heim

first: Jan

middle: S

last: Tchorz


title: Epigenome analysis of clear cell renal cell carcinoma (ccRCC) tissue versus matched normal kidney tissue

status: Public on Oct 26 2015

city: Guangzhou

first: jinhuan

last: wei

address: No.58 zhongshan 2rd Road

country: China

institute: SYSU

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of clear cell renal cell carcinoma (ccRCC) tissue versus matched normal kidney tissue. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in tumor and adjacent normal kidney tissue samples from ccRCC patients. Samples included 46 paired fresh frozen ccRCC tumor and adjacent normal kidney tissues.

overall_design: Bisulphite converted DNA from the 92 samples were hybridised to the Illumina Infinium 450 Human Methylation Beadchip v1.2

first: Junhang

last: Luo


title: Expression data of mouse NIH3T3 and NIH3T3-k-ras transformed cell lines after Forskolin treatment

status: Public on Oct 24 2015

city: Milan

first: Ferdinando

last: Chiaradonna

address: Piazza della scienza, 2

department: Biotechnology and Biosciences

country: Italy

institute: University of Milano-Bicocca

summary:
Forskolin treatment induces activation of protein kinase A. This activation protects transformed cells from death induced by glucose starvation.
We used microarray to identify the mechanisms involved in such a pro-survival effect.

overall_design: NIH3T3 and NIH3T3-K-ras were plated at 1mM glucose and then daily treated or not with 10uM FSK until 72h of growth. The microarray analysis has been performed at 72h in order to identify specific mechanisms associate with transformed cells survival.

first: Yuri

last: Pirola

first: Roberta

last: Palorini


title: Gene expression data of GBM146 and GBM157 at day0, 7, 30 after serum exposure

city: Ariake, Koto-ku

first: Rie

last: Ouchi

state: Tokyo

country: Japan

institute: Japanese Foundation for Cancer Research

summary: Glioblastoma (GBM) is a lethal brain cancer composed of heterogeneous cellular populations including glioma stem cells (GSCs) and their progeny differentiated non-stem glioma cells (NSGCs). Although accumulating evidence points out the significance of GSCs for tumour initiation and propagation, the roles of NSGCs remain elusive. Here we demonstrate that, when patient-derived GSCs in GBM tumours undergo differentiation with diminished telomerase activity and shortened telomeres, they subsequently become senescent phenotype, thereby secreting angiogenesis-related proteins, including vascular endothelial growth factors. Interestingly, these secreted factors from senescent NSGCs promote proliferation of human umbilical vein endothelial cells and tumorigenic potentials of GSCs in immunocompromised mice. These experimental data are likely clinically-relevant, since immunohistochemistry of both patient tumours of GBM and the patient GSC-derived mouse xenografted tumours detected tumour cells that express a set of markers for the senescence phenotype. Collectively, our data suggest that the inter-cellular signals from senescent NSGCs promote GBM tumour angiogenesis thereby increasing malignant progression of GBM.

overall_design: We monitored gene expression profiling in GSC, differentiated NSGC (GSC at day7 after serum exposure), and senescent NSGC (GSC at day30 after serum exposure) of GBM146 and GBM157.

first: Sachiko

last: Okabe

first: Hiroyuki

last: Seimiya


title: Sputum gene expression profiling in asthmatics

status: Public on Oct 23 2015

city: Nutley

first: Donavan

last: Cheng

address: 340 Kingsland Ave

department: Translational Research Sciences

institute: Hoffmann-LaRoche

summary: Gene expression profiling was performed on sputum samples obtained from asthmatics and matched healthy controls, to identify markers associated with various asthma subtypes.

overall_design: Sputum samples were collected from asthmatics and healthy controls and subjected to expression profiling using Affymetrix HG-U133Plus2.0 microarrays.

first: Radhika

last: Kajekar

first: Christopher

middle: E

last: Brightling


title: Nasal scrape gene expression profiling in asthmatics

summary: Gene expression profiling was performed on nasal scrape samples obtained from asthmatics and matched healthy controls, to identify markers associated with various asthma subtypes.

overall_design: Nasal scrape samples were collected from asthmatics and healthy controls and subjected to expression profiling using Affymetrix HG-U133Plus2.0 microarrays.


title: Bruton's Tyrosine Kinase Regulates TLR9 but not TLR7 Signaling in Human pDCs

first: Kai

last: Lau

address: 340 Kingsland St

institute: Hoffmann-La Roche

summary: Plasmacytoid dendritic cells (pDCs) can be activated by the endosomal TLRs, and contribute to the pathogenesis of systemic lupus erythematosus (SLE) by producing type I IFNs. Thus, blocking TLR-mediated pDC activation may represent a useful approach for the treatment of SLE. In an attempt to identify a therapeutic target for blocking TLR signaling in pDCs, we investigated the contribution of Bruton's tyrosine kinase (Btk) to the activation of pDCs by TLR7 and TLR9 stimulation by using a selective Btk inhibitor RN486. Stimulation of TLR7 and 9 with their respective agonist, namely, gardiquimod and type A CpG ODN2216, resulted in the activation of human pDCs, as demonstrated by the expression of activation markers (CD69, CD40, and CD86), elevated production of IFN-alpha and other inflammatory cytokines, as well as up-regulation of numerous genes including IFN-alpha-inducible genes and activation of interferon regulatory factor 7 (IRF7) and NF-kB. RN486 inhibited all of these events induced by TLR9, but not TLR7 stimulation, with a nanomolar potency for inhibiting type A CpG ODN2216-mediated production of cytokines (e.g., IC50=386 nM for inhibiting IFN-alpha). Our data reveal Btk as an important regulatory enzyme in the TLR9 pathway, and a potential therapeutic target for SLE and other TLR-driven diseases.

overall_design: pDCs from healthy donors (n=4) were treated with gardiquimod (TLR7 agonist) or ODN 2216 (TLR9 agonist) with or without BTK inhibitor for 3 hours.

first: Jingming

last: Wang

middle: Y

first: Jimmy

last: Jung

first: Palanikumar

last: Ravindran

first: Julie

last: Hang

first: Valerie

last: Carvajal

first: Rupal

last: Majmudar

first: John

last: Allard

first: Hans

last: Bitter

first: Satwant

last: Narula

first: Larry

last: Peterson


title: DNA methylation profiling for BGC823 cells stably transfected with an artificial P16 DNA methyltransferase (P16-Dnmt)

status: Public on Oct 22 2015

city: Beijing

first: Dajun

last: Deng

state: Beijing

address: Fu-Cheng-Lu No.52

department: Dept Aetiology

institute: Peking University Cancer Hospital and Institute

summary:
Differential methylation between human gastric cancer cell BGC823 transfected with P16-Dnmt or pTRIPZ control vector was identified using Illumina HumanMethylation450K array.
The genome-wide methylation detection experiment was carried out by Shanghai Oebiotech Company.

overall_design: Bisulphite converted DNA from the 4 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip.

first: Baozhen

last: Zhang


title: Differential expression and prognostic significant of SOX genes in pediatric medulloblastoma and ependymoma identified by microarray analysis

status: Public on Oct 21 2015

city: Utrecht

first: Judith

middle: M.

last: Boer

address: Heidelberglaan 25

country: Netherlands

institute: Prinses Maxima Centrum

summary: This file contains the expression data for pediatric medulloblastomas and ependymomas

overall_design: See J.M. de Bont et al. [Neuro Oncol. 2008 Dec;10(6):1040-60]

last: de Bont

first: Monique

middle: L

last: den Boer


title: Using human genetic variation to improve red blood cell production from stem cells

city: Cambridge

first: Vijay

middle: G

last: Sankaran

state: MA

address: 7 Cambridge Center

institute: Broad Institute

summary: Multipotent and pluripotent stem cells have significant potential as sources for cell replacement therapies. However, the low yield and quality of in vitro differentiated cells produced from various stem cell sources presents a significant limitation for therapeutic applications. The most mature use of these stem cell products is in the field of transfusion medicine, where stem cell-derived red blood cells (RBCs) have clinically-proven potential as alternative transfusion products. To improve upon current approaches for RBC production, we used insight from both common and rare human genetic variation of blood counts to focus on the SH2B3 gene. By producing loss of function of SH2B3 using targeted knockdown and genome editing approaches in human hematopoietic stem and progenitor cells, as well as human pluripotent stem cells, we are able to significantly improve both the quality and yield of in vitro derived RBCs. We illustrate how insight from human genetic variation can assist in the development of broadly applicable approaches that have tremendous value for regenerative medicine.

overall_design: CD34+ cells from G-CSF mobilized peripheral blood was purified by positive magnetic selection using an Ultrapure Microbead Kit (Miltenyi Biotech) according to the manufacturer's protocol following mononuclear cell purification on a Ficoll Density Gradient. At least 95% purity was reached as assessed by post-purification flow cytometry with a PE conjugated anti-human CD34 antibody (8012-0349, eBioscience). shRNA constructs targeting SH2B3 were used with the following sequences: sh83 (CCGGCCTGACAACCTTTACACCTTTCTCGAGAAAGGTGTAAAGGTTGTCAGGTTTTTG) and sh84 (CCGGGCCTGACAACCTTTACACCTTCTCGAGAAGGTGTAAAGGTTGTCAGGCTTTTTG). Both constructs were in the pLKO.1-puro lentiviral vector. The lentiviral vectors pLKO-GFP and pLKO.1-puro Luciferase served as controls (the RNAi consortium of the Broad Institute of MIT and Harvard). At day 7 post infection, cells were isolated and Human Gene 2.0 ST microarrays were performed on RNA.

first: Jacob

middle: C

last: Ulirsch


title: Upper airway gene expression is an effective surrogate biomarker for Th2-driven inflammation in the lower airway

first: Donavan

last: Cheng

summary: Molecular profiling studies in asthma cohorts have identified a Th2-driven asthma subtype, characterized by elevated lower airway expression of POSTN, CLCA1 and SERPINB2. To assess upper airway gene expression as a potential biomarker for lower airway Th2 inflammation, we assayed upper airway (nasal) and lower airway (bronchial) epithelial gene expression, serum total IgE, blood eosinophils and serum periostin in a cohort of 54 allergic asthmatics and 30 matched healthy controls. 23 of 51 asthmatics in our cohort were classified as ‘Th2 high’ based on lower airway Th2 gene signature expression. Consistent with this classification, ‘Th2 high’ subjects displayed elevated total IgE and blood eosinophil levels relative to ‘Th2 low’ subjects. Upper airway Th2 signature expression was significantly correlated with lower airway Th2 signature expression (r=0.44), with similar strength of association as serum total IgE and blood eosinophils, known biomarkers of Th2 inflammation. In an unbiased genome-wide scan, we identified 8 upper airway genes more strongly correlated with lower airway Th2 gene signature expression (r=0.58), including Eotaxin-3 (CCL26), Galectin-10 (CLC) and Cathepsin-C (CTSC). Asthmatics classified as ‘Th2 high’ using this 8-gene signature show similar serum total IgE and blood eosinophil levels as ‘Th2 high’ asthmatics classified using lower airway Th2 gene signature expression. We have identified an 8-gene upper airway signature correlated with lower airway Th2 inflammation, which may be used as a diagnostic biomarker for Th2-driven asthma.

overall_design: Upper airway (nasal) and lower airway (bronchial) epithelial brushings obtained from a cohort of 54 allergic asthmatics and 30 matched healthy controls were profiled by gene expression by microarray.   Subjects were assayed for gene expression, serum total IgE, blood eosinophils and serum periostin.

first: Michelle

last: Staudt

first: Catherine

last: Tribouley

first: Chunsheng

last: He

first: Melissa

last: Buckland

first: Christopher

last: Stevenson

first: Radhika

last: Kajekar

first: Gerhard

last: Wolff

first: Sudha

last: Viswanathan

first: Harsukh

last: Parmar

first: Sreekumar

last: Pillai

first: Ronald

last: Crystal


title: Effects of Salidroside on gene expression in ischemic brain of rats

status: Public on Oct 30 2015

city: Fuzhou,

first: guizhu

last: HONG

state: Fujian

address: No. 1 Huatou Road, Minhou Shangjie

department: Centre of Biomedical Research & Development

institute: Fujian University of Traditional Chinese Medicine

summary: We employed DNA microarray to identify genes differentially regulated by salidroside in ischemic brain of MCAO rats. With a cut of p < .01 and 2-fold change, we found that 121 genes were upregulated and 142 genes were down-regulated in the MCAO group, compared to the sham group. Administration of salidroside (1 h after reperfusion, daily for 6 d) enhanced 28 transcripts and suppressed 16 transcripts. The genes involved in neuroplasticity and oxygen carrier were further confirmed by qRT-PCR. Our data suggest that salidroside could regulate neuroplasticity in post-ischemic stroke, in addition to its neuroportective function.

overall_design: MCAO rats were injected intraperitoneally with salidroside (50 mg/kg body weight) or vehicle (saline) once a day for 6 d, commencing 1 h after reperfusion (n=3  /group). Ischemic brain was dissected for RNA extraction. Differential gene expression regulated by salidroside were analysed by microarray and subsequently confirmed by qRT-PCR.

first: Guizhu

last: Hong

first: Wenfang

last: Lai

first: Xiaoqin

last: Zhang


title: Expression data from the human nasopharyngeal carcinoma cell line CNE2Z transfected with AGO2 shRNAs or control shRNA

status: Public on Oct 20 2015

first: jinfeng

last: meng

address: No. 27, Taiping Road, Haidian District

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College

summary:
Nasopharyngeal carcinoma (NPC) is an epithelial malignancy with striking racial and geographic distribution differences. Furthermore, numerous genetic linkage and association studies have reported a few genes contributing to the risk of this malignancy. The identification of susceptibility genes contributing to NPC would assist in predicting individual and population risk of NPC development and would help to clarify the pathogenesis relevant to this disorder. Argonaute 2 (AGO2), a central component of RNA-induced silencing complex, plays critical roles in cancer. We examined whether the single nucleotide polymorphisms (SNPs) of AGO2 were related to the risk of nasopharyngeal carcinoma (NPC).
Twenty-five tag SNPs within AGO2 were genotyped in Guangxi population consisting of 855 NPC patients and 1036 controls. The SNPs significantly associated with NPC were further replicated in Guangdong population consisting of 996 NPC patients and 972 controls. Functional experiments were conducted to examine the biologic roles of AGO2 in NPC.
A significantly increased risk of advanced lymph node metastasis of NPC was identified for the AGO2 rs3928672 GA + AA genotype compared with GG genotype in both the Guangxi and Guangdong populations. In addition, AGO2 knockdown reduced cell proliferation, induced apoptosis, and inhibited migration of NPC cells. Furthermore, gene expression microarray showed that genes altered following AGO2 knockdown were clustered in tumorigenesis and metastasis relevant pathways. Our findings suggest that the genetic polymorphism in AGO2 may be a risk factor for the advanced lymph node metastasis of NPC in Chinese populations, and AGO2 acts as an oncogene in the development of NPC.

overall_design: The human nasopharyngeal carcinoma cell line CNE2Z was transfected with AGO2 shRNAs or control shRNA. Three biological replicates each.

first: Jinfeng

last: Meng

first: Peiyao

last: Li

first: Pengbo

last: Cao


title: Transcriptomic Comparison of Neuronal Development Stages using Induced Pluripotent Stem Cells from Bipolar Disorder Patients

city: Indianapolis

first: Jiangang

last: Liu

state: IN

address: 893 S Delaware St

department: Tailored Therapeutics

institute: Eli Lilly and Company

summary: Fibroblasts from patients with Type I bipolar disorder (BPD) and their unaffected siblings were obtained from an Old Order Amish pedigree with a high incidence of BPD and reprogrammed to induced pluripotent stem cells (iPSCs). Established iPSCs were subsequently differentiated into neuroprogenitors (NPs) and then to neurons. Transcriptomic microarray analysis was conducted on RNA samples from iPSCs, NPs and neurons matured in culture for either 2 weeks (termed early neurons, E) or 4 weeks (termed late neurons, L). Global RNA profiling indicated that BPD and control iPSCs differentiated into NPs and neurons at a similar rate, enabling studies of differentially expressed genes in neurons from controls and BPD cases. Significant disease-associated differences in gene expression were observed only in L neurons. Specifically, 328 genes were differentially expressed between BPD and control L neurons including GAD1, glutamate decarboxylase 1 (2.5 fold) and SCN4B, the voltage gated type IV sodium channel beta subunit (-14.6 fold). Quantitative RT-PCR confirmed the up-regulation of GAD1 in BPD compared to control L neurons. Gene Ontology, GeneGo and Ingenuity Pathway Analysis of differentially regulated genes in L neurons suggest that alterations in RNA biosynthesis and metabolism, protein trafficking as well as receptor signaling pathways GSK3β signaling may play an important role in the pathophysiology of BPD.

overall_design: Samples for each of four iPSCs, NPs and neurons matured in culture for either 2 weeks (termed early neurons, E) or 4 weeks (termed late neurons, L) were analyzed

first: Kwi

last: Kim

first: Rachelle

middle: J

last: Sells Galvin

first: Jeffrey

last: Dage

first: Janice

middle: A

last: Egeland

first: Rosamund

last: Smith

first: Kalpana

last: Merchant

first: Steven

last: Paul


title: Integrated bioinformatic and wet-lab approach to identify potential oncogenic networks in neuroblastoma: MYCN

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

institute: msterdam UMC and University of Amsterdam

summary: mRNA profiles of thousands of human tumors are available, but methods to deduce oncogenic signaling networks from these data lag behind. It is especially challenging to identify main-regulatory routes, and to generalize conclusions obtained from experimental models. We designed the bioinformatic platform R2  (http://r2.amc.nl) in parallel with a wet-lab approach of neuroblastoma. Here we demonstrate how R2 facilitates an integrated analysis of our neuroblastoma data. Analysis of the MYCN pathway suggested important regulatory connections to the polyamine synthesis route, the Notch pathway and the BMP/TGFβ pathway. A network of genes emerged connecting major oncogenes in neuroblastoma. Genes in the network carried strong prognostic values and were essential for tumor cell survival.

overall_design: Time-course experiments in triplicate of MYCN induction after doxycycline addition, with 7 timepoints.

first: Linda

last: Valentijn

first: Jan

last: Koster

first: Rogier

last: Versteeg


title: Expression data from Huh7.5 hepatoma cells transfected with 100 nM miR-185 mimic

status: Public on Oct 19 2015

city: Ottawa

first: John

middle: Paul

last: Pezacki

state: ON

address: 150 Louis-Pasteur Pvt

department: Chemistry and Biomolecular Sciences

country: Canada

institute: University of Ottawa

summary:
Our work demonstrated that 25-hydroxycholesterol induces the expression of miR-185, a microRNA which reinforces the oxysterol's antiviral effects on hepatic metabolism.
We used microarrays to detail the effect of miR-185 on hepatic gene expression, and, within repressed genes, identified an enrichment for genes associated with cholesterol biosynthesis.

overall_design: Huh7.5 cells were transfected with miR-185 or control mimics (100 nM), and total RNA was isolated 72 hours post-transfection.

first: Ragunath

last: Singaravelu

middle: P


title: MALT1 protease activity controls the expression of inflammatory genes in keratinocytes upon Zymosan stimulation

city: Tübingen

first: Günter

last: Jäger

address: Calwerstr. 7

country: Germany

institute: Institute of Medical Genetics Tübingen

type: Expression profiling by high throughput sequencing

summary:
The protease activity of the paracaspase MALT1 plays an important role in antigen receptor-mediated lymphocyte activation by controlling the activity of the transcription factor NF-kB and is thus essential for the expression of inflammatory target genes.
MALT1 is not only present in cells of the hematopoietic lineage, but is ubiquitously expressed. Here we report that Zymosan or S. aureus stimulation induced MALT1 protease activity in human primary keratinocytes.

overall_design: Human primary keratinocytes were treated for 8 h with solvent control (DMSO), PMA/Ionomycin (P/I) or P/I with MALT1-inhibitor LVSR-fmk. Three biological replicates of each stimualtion were analyzed for gene expression profiles.

first: Anja

last: Schmitt

first: Paula

last: Grondona

first: Tabea

last: Maier

first: Marc

last: Brändle

first: Caroline

last: Schönfeld

first: Franziska

last: Eberle

first: Margot

last: Thome

first: Klaus

last: Schulze-Osthoff

first: Amir

last: Yazdi

first: Stephan

last: Hailfinger


title: Mapping DNA methylation across development, genotype, and schizophrenia in the human frontal cortex

city: Baltimore

first: Andrew

last: Jaffe

state: MD

address: 855 N Wolfe St, Ste 300

department: Clinical Sciences

institute: Lieber Institute for Brain Development

summary: DNA methylation (DNAm) is important in brain development, and potentially in schizophrenia. We characterized DNAm in prefrontal cortex from 335 non-psychiatric controls across the lifespan and 191 patients with schizophrenia, and identified widespread changes in the transition from prenatal to postnatal life. These DNAm changes manifest in the transcriptome, correlate strongly with a shifting cellular landscape, and overlap regions of genetic risk for schizophrenia. A quarter of published GWAS-suggestive loci (4,208/15,930, p<10-20) manifest as significant methylation quantitative trait loci (meQTLs), including 59.6% of GWAS-positive schizophrenia loci. We identified 2,104 CpGs that differ between schizophrenia patients and controls, enriched for genes related to development and neurodifferentiation. The schizophrenia-associated CpGs strongly correlate with changes related to the prenatal-postnatal transition and show slight enrichment for GWAS risk loci, while not corresponding to CpGs differentiating adolescence from later adult life.  These data implicate an epigenetic component to the developmental origins of this disorder.

overall_design: DNA methylation data from the dorsolateral prefrontal cortex from 335 controls and 191 patients with schizophrenia. Some samples were run multiple times. The `BrNum` column delineates individual subjects and the `bestQC` column below indicates which samples to use to result in one array per subject.

first: Thomas

last: Hyde

first: Joel

last: Kleinman

first: Daniel

middle: R

last: Weinberger


title: Expression data from A2780 cell line and wild type ovarian cancer cell line (with resistant sublines)

status: Public on Oct 14 2015

city: Poznań

first: Radosław

last: Januchowski

address: 6 Święcickiego St.

department: Histology and Embryology

country: Poland

institute: University of Medical Sciences

summary:
The development of cytostatic-drug resistance renders chemotherapy ineffective in treating ovarian cancer, the most lethal gynaecological malignancy. In many cases, it is difficult to explain the development of drug resistance based on the expression patterns of genes known to be involved in this process. Microarray-based assays can provide information about new genes that are involved in the resistance to cytostatic drugs. This report describes alterations in the level of expression of genes in cisplatin- (CisPt), doxorubicin- (Dox), topotecan- (Top), and paclitaxel- (Pac) resistant variants of W1 and A2780 ovarian cancer cell lines. These drug-resistant variants of the W1 and A2780 cell lines were generated through the stepwise selection of cells tolerant of exposure to the indicated drugs at incrementally increased concentrations. Affymetrix GeneChip Human Genome Array Strips were used for hybridization assays. The genes with significantly altered expression levels (upregulated by more than fivefold or downregulated by less than fivefold relative to the level in the parental line) in the drug-resistant sublines were selected and were filtered using volcano plotting.
We observed alterations in the expression of 22 genes that were common to all three cell lines that were resistant to the same cytostatic drug. The level of expression of 13 genes was upregulated and that of nine genes was downregulated. In the CisPt-resistant cell line, we observed downregulated expression of ABCC6, BST2, ERAP2 and MCTP1; in the Pac-resistant cell line, we observe upregulated expression of ABCB1, EPHA7 and RUNDC3B and downregulated expression of LIPG, MCTP1, NSBP1, PCDH9, PTPRK and SEMA3A. The expression levels of three genes, ABCB1, ABCB4 and IFI16, were upregulated in the Dox-resistant cell lines. In the Top-resistant cell lines, we observed increased expression levels of ABCG2, HERC5, IFIH1, MYOT, S100A3, SAMD4A, SPP1 and TGFBI and decreased expression levels of MCTP1 and PTPRK

overall_design: In this study, we used two ovarian cancer cell lines, the established ovarian cancer A2780 cell line and the primary ovarian cancer W1 cell line. The human ovarian carcinoma A2780 cell line was purchased from ATCC. A2780 sublines that were resistant to CisPt [A2780CR1 and A2780CR2 (A2780 cisplatin resistant)], Pac [A2780PR1 and A2780PR2 (A2780 paclitaxel resistant)], Dox [A2780DR1 and A2780DR2 (A2780 doxorubicin resistant)] and Top [A2780TR1 and A2780TR2 (A2780 topotecan resistant)] were generated by exposing A2780 cells to the relevant drugs at incrementally increased concentrations. The human ovarian cancer W1 cell line was established using ovarian cancer tissue obtained from an untreated patient. W1 sublines resistant to CisPt  [W1CR (W1 cisplatin resistant)], Dox [W1DR (W1 doxorubicin resistant)], Top  [W1TR (W1 topotecan resistant)], Met [W1MR (W1 methotrexate resisntant)], Vin [W1VR (W1 vincristine resistant)] and Pac [W1PR (W1 paclitaxel resistant)] were obtained by exposing W1 cells to the drugs at incrementally increased concentrations.

first: Piotr

last: Zawierucha

first: Marcin

last: Ruciński

first: Michał

last: Nowicki

first: Maciej

last: Zabel


title: Epigenetic analysis of normal prostate tissue and prostate adenocarcinoma

status: Public on Oct 15 2015

city: Moscow

first: Elizaveta

last: Babikova

address: Malaya Pirogovskaya 1a

department: Molecular Biology

country: Russia

institute: Research Institute of Physico-Chemical Medicine

summary: Genome-wide DNA methylation profiles were obtained from prostate adenocarcinoma samples (20) and corresponding cancer-unrelated normal prostate tissue (28) using Illumina HumanMethylation450 BeadChips. Approximately 485000 CpG sites were measured in every sample.

overall_design: Bisulphite-converted DNA from the 48 samples were hybridised to the Illumina HumanMethylation450 BeadChip.

first: Edward

middle: V

last: Generozov


title: Analysis of gene expression levels between CCl4 induced mouse fibrotic liver tissues and vehicle treated mouse control liver tissues.

city: Shanghai

first: Jun

last: Li

state: Shanghai

address: 800 Dongchuan Road

department: Shanghai Cancer Institute

institute: State Key Laboratory for Oncogenes and Related Genes

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

summary: To investigate the altered gene expression levels in mouse fibrotic liver tissues, C57BL6/J mice were intraperitoneally injected with CCl4 or vehicle twice every week. After 8 weeks, livers were harvested and RNA was extracted by Trizol. The gene expression levels were analyzed and compared between CCl4 treated group and vehicle treated (control) group.

overall_design: Three CCl4 induced mouse fibrotic liver tissues, three vehicle treated mouse control liver tissues.

first: Zhi-Gang

last: Zhang

first: Ya-Hui

last: Wang


title: Aging-associated inflammation promotes selection for adaptive oncogenic events in B cell progenitors

city: Cleveland

first: Jihye

last: Kim

state: Ohio

address: 9500 Euclid Ave.

department: Quantitative Health Sciences

institute: Cleveland Clinic

summary:
Cancer incidence increases in the elderly, although the underlying reasons for this association are unknown. We show that B-progenitors in old mice exhibit profound signaling and metabolic defects, and that expression of BCR-ABL, NRASV12 and MYC reverses these fitness defects, leading to selection of oncogenically-initiated cells and leukemogenesis in old hematopoietic backgrounds. Aging is associated with increased inflammation in the BM microenvironment, and inducing inflammation in young mice phenocopies aging B-lymphopoiesis. Importantly, reducing inflammation in aged mice preserves the function of B-progenitors and prevents NRasV12-mediated oncogenesis. We conclude that chronic microenvironments in old age lead to reductions in the fitness of hematopoietic stem and progenitor cell populations. This reduced progenitor pool fitness leads to selection for cells harboring oncogenic mutations in part due to their ability to correct aging-associated functional defects.
Aging B-lymphopoiesis is accompanied by significant reductions in purine and pyrimidine metabolism. Microarray experiment results also indicated that mitochondrial dysfunction accompanied aging B-lymphopoiesis.

overall_design: Microarray on combined pro- and pre-B cell populations isolated from young (2 month old) and old (24 month old) mice.

first: Curtis

last: Henry

first: Matias

last: Casas-Selves

first: Vadym

last: Zaberezhnyy

first: Leila

last: Aghili

first: Ashley

last: Daniel

first: Tania

last: Azam

first: Eoin

last: N. McNamee

first: Eric

last: Clambey

first: Jelena

last: Klawitter

first: Natalie

last: Serkova

first: Aik

last: Tan

first: Charles

last: Dinarello

first: James

last: DeGregori


title: Aberrant DNA methylation in Non Small Cell Lung Cancer associated fibroblasts

status: Public on Oct 13 2015

city: L'Hospitalet del Llobregat

first: Sebastian

last: Moran

state: Barcelona

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

department: PEBC

country: Spain

institute: IDIBELL

summary: Epigenetic changes through altered DNA methylation have been implicated with critical aspects of tumor progression, and have been extensively studied in cancer cells and tumor tissue samples. In contrast, our current knowledge of the aberrant genomic methylation in tumor-associated fibroblasts (TAFs), which are critical co-conspirators of tumor progression, is very scarce. To address this gap of knowledge, we conducted genome-wide DNA methylation profiling on lung TAFs and paired control fibroblasts (CFs) from surgical non-small cell lung cancer patients. We found widespread DNA hypomethylation concomitant with focal gains of DNA methylation in TAFs compared to CFs. The aberrant DNA methylation landscape of TAFs had a global impact on gene expression and a selective impact on the TGF-β pathway. The latter included hypermethylation-associated SMAD3 silencing, which was associated with a hyperresponsiveness to exogenous TGF-β1 in terms of contractility and extracellular matrix expression. In turn, activation of CFs with exogenous TGF-β1 partially mimicked the epigenetic alterations observed in TAFs, suggesting that TGF-β1 may be necessary but not sufficient to elicit such alterations. In addition, pathway enrichment analysis of the DNA methylation alterations revealed that a fraction of TAFs may be bone marrow-derived fibrocytes. Finally, survival analyses using DNA methylation and gene expression datasets identified aberrant DNA methylation on the EDARADD promoter sequence as a prognostic factor in NSCLC patients. Our findings shed light on the unique origin and molecular alterations underlying the aberrant phenotype of lung TAFs, and identify a stromal biomarker with potential clinical relevance.

overall_design: 28 samples

first: Miguel

last: Vizoso

first: Manel

last: Esteller


title: Poly I:C Induced Gene Expression Changes in Non-Human Primates III

status: Public on Oct 11 2015

first: Donavan

last: Cheng

address: 340 Kingsland Ave

institute: Hoffmann-LaRoche

summary: The respiratory epithelium is the body’s first line of defense to pathogens, pollutants, and other potentially injurious agents that can be inhaled.  Sampling the upper respiratory tract is becoming a widely used technique in the clinic to examine the molecular changes in the diseased airway;  however, it is unclear as to whether the responses in the upper respiratory tract (i.e. the nasal turbinates) reflect the changes that occur in the lower  respiratory tract (i.e. trachea and lungs). Here, we assessed the responses to poly I:C, a synthetic double-stranded RNA molecule that is meant to  mimic the acute effects of a viral infection, in both the upper and lower respiratory tracts of cynomolgus macaques. To do this, we compared the in  vivo response after a nasal poly I:C challenge in a nasal scrape samples (performed using a nasal curette) to responses that occurred after ex vivo  poly I:C stimulation in nasal scrapes, tracheal epithelial brushings, and lung tissue explants in non-human primates.

overall_design: Nasal scrapes, tracheal brushings, and lung tissue were collected from NHPs during a necropsy, plated in 24 well plates in Clonetics SABM media.  Samples were stimulated with poly I:C (100 mg) or a mock control and collected at time points indicated. There were 2-3 technical replicates for the tracheal brushings and the lung explants

first: Javad

last: Golji

first: Palanikumar

last: Ravindran

first: Hans

last: Bitter

first: Mario

last: Giron

first: Holly

last: Hilton

first: Paul

last: Harris

first: Gaurav

last: Tyagi

first: Heather

last: Martin

first: Laura

last: Singer

first: Carla

last: Bauer

first: Christopher

last: Stevenson


title: TERT  rearrangements are frequent in neuroblastoma and identify aggressive tumors

first: Richard

last: Volckmann

summary: Whole genome sequencing detected structural rearrangements of TERT in 17/75 high stage neuroblastoma with 5 cases resulting from chromothripsis. Rearrangements were associated with increased TERT expression and targeted immediate up- and down-stream regions of TERT, placing in 7 cases a super-enhancer close to the breakpoints. TERT rearrangements (23%), ATRX deletions (11%) and MYCN amplifications (37%) identify three almost non-overlapping groups of high stage neuroblastoma, each associated with very poor prognosis

overall_design: 34 human Neuroblastoma samples were analyzed

first: R

last: volckmann

last: Versteeg


title: Optimizing microarray gene expression profiling workflow for formalin-fixed paraffin-embedded  tissues

status: Public on Oct 10 2015

city: Ankara

first: Nevin

last: Belder

state: Tandogan

address: De gol

department: Biotechnology

country: Turkey

institute: Ankara University

summary: The use of nucleic acids from formalin-fixed paraffin-embedded (FFPE) tissues for high-throughput molecular techniques, such as microarray gene expression profiling has become widespread in molecular research area. However, working with FFPE tissues is challenging because of  degradation, cross-linking with proteins, and RNA chemical modifications. Also, there is no generally accepted procedure for RNA extraction to microarray analysis. Thus, there is a need for a standardized workflow for FFPE samples to study microarray transcriptome profiling. Therefore, the main purpose of this study was to conduct a standardized process from deparaffinization to RNA extraction and microarray gene expression analysis. Firstly, deparaffinization procedure was optimized for FFPE samples and then Trizol, PicoPure RNA isolation kit, and Qiagen RNeasy FFPE kit performances were compared in terms of yield and purity. Finally, two different cRNA/cDNA preparation and labeling protocols with two different array platforms (Affymetrix Human Genome U133 Plus 2.0 and U133_X3P) were also evaluated to determine which combination gives the best percentage of present call. Our optimization study shows that the Qiagen RNeasy FFPE kit with modified deparaffinization step gives better results (RNA quantity and quality) than the other two isolation kits. The Ribo-SPIA protocol and U133_X3P array combination gave a significantly higher percentage of present calls than the 3’ IVT cDNA amplification and labeling system. However, no significant differences were found between the two array platforms.  These results present a workflow for microarray gene expression profiling of FFPE tissues. The findings also indicate that sufficient quality gene expression data can be obtained from FFPE-derived RNA.

overall_design: Four FFPE colon cancer tissue sections were used for this study. 4 sections (each 8 μm thick) were cut from each sample and used for RNA extractions. RNA amplifications were performed using the Affymetrix 3’ IVT Kit and the NuGEN Ovation FFPE WTA system. Four different hybridization combinations were performed on four labeled samples which were amplified by two different kits. Human Genome U133 Plus 2.0 and U133_X3P arrays were used for these four combinations. Three of these four samples have matched control samples. In this study gene expression data analysis was also performed to detect differentially expressed genes for these three matched samples. These three matched normal controls were  independently isolated, amplified, fragmented and labeled for another larger microarray gene expression study using our optimized workflow. These samples were hybridized to same microarray platform (U133_X3P Array) as the matched tumor samples.

first: Öznur

last: Coşkun

first: Beyza

middle: D

last: Erdoğan

first: Özlem

middle: i

last: Dağ

first: Berna

last: Savaş

first: Arzu

last: Ensari

first: Hilal

last: Özdağ


title: Proliferating Langerhans cells dampen inflammation in established mouse psoriatic lesions

status: Public on Oct 12 2015

city: MARSEILLE

first: Marc

last: DALOD

address: Parc Scientifique et Technologique de Luminy, 163 avenue de Luminy, Case 906, 13288 Marseille cedex 9

country: France

institute: CIML

summary: Psoriasis is a chronic inflammatory skin disease of unknown etiology. Although macrophages and dendritic cells (DCs) have been proposed to drive the psoriatic cascade, their largely overlapping phenotype hampered studying their respective role. Topical application of Imiquimod, a Toll-like receptor 7 agonist, induces psoriasis in patients and psoriasiform inflammation in mice. We showed that daily application of Imiquimod for 14 days recapitulated both the initiation and the maintenance phase of psoriasis. Based on our ability to discriminate Langerhans cells (LCs), conventional DCs, monocytes, monocyte-derived DCs and macrophages in the skin, we characterized their dynamics during both phases of psoriasis. During the initiation phase, neutrophils infiltrated the epidermis whereas monocytes and monocyte-derived DCs were predominant in the dermis. During the maintenance phase, LCs and macrophage numbers increased in the epidermis and dermis, respectively. LC expansion resulted from local proliferation, a conclusion supported by transcriptional analysis. Continuous depletion of LCs during the course of Imiquimod treatment aggravated chronic psoriatic symptoms as documented by an increased influx of neutrophils and a stronger inflammation. Therefore, by developing a mouse model that mimics the human disease more accurately, we established that LCs play a negative regulatory role during the maintenance phase of psoriasis.

overall_design: DCs and other myeloid cell types were isolated from lymphoid organs as previously described (Henri et al. 2010). Briefly, LNs were cut into small pieces and digested for 20 min at room temperature with a mixture of type II collagenase (Worthington Biochemical) and DNase I (Sigma-Aldrich). The resulting cell suspension was treated with 5 mM EDTA to disrupt DC-T cell conjugates. After eliminating undigested material, light-density cells were enriched by centrifugation on an Optiprep solution (d = 1.32 g/mL, Abcys). To extract skin mononuclear phagocytic cells, ears were splitted into dorsal and ventral parts and incubated with a solution of PBS containing 1 mg/mL dispase (Roche) for 2 h at 37° C or overnight at 4° C, as specified. The dorsal and ventral parts were then cut into small pieces and incubated for 90 min at 37° C with RPMI containing 1 mg/mL DNase and 1 mg/mL Collagenase IV (Worthington Biochemical). The resulting single cell suspension was subjected to centrifugation on a Percoll gradient (Amersham-Pharmacia).

first: D

last: Terhorst

first: C

last: Malosse

first: S

last: Tamoutounour

last: Chelbi

first: A

last: Jorquera

first: M

last: Bajenoff

last: Dalod

first: B

last: Malissen

last: Henri


title: Track normalization and averaging of H3K4me3 ChIP-seq data across various cell and tissue types from Mouse ENCODE.

status: Public on Oct 09 2015

city: Bethesda

first: Ian

last: Fingerman

address: 45 Center Dr.

department: NCBI Epigenomics

institute: National Institutes of Health

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Data tracks from chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq) experiments were processed using an in-house algorithm that provides normalization functionality followed by generation of a track average.

overall_design: Re-analysis of Mouse ENCODE H3K4me3 ChIP-seq datasets using an in-house algorithm to create an average data track.


title: Integrated ordination of miRNA and mRNA expression profiles [mRNA]

status: Public on Oct 08 2015

city: Cagliari

first: Giacomo

last: Diaz

address: Via Porcell 4

department: Dept Biomedical Sciences

institute: University of Cagliari

summary: Several studies have shown that negative and positive miRNA-mRNA correlations are symmetrically distributed. While negative correlations are consistent with a faster degradation of miRNA targets, the presence of positive correlations suggests bidirectional interactions between the two classes of molecules. However, a comprehensive study of miRNA and mRNA correlations is lacking. A homogeneous map of miRNA and mRNA relationships was obtained by multidimensional scaling (MDS) applied to a single matrix including both heterologous (miRNA-mRNA) and homologous (miRNA-miRNA and mRNA-mRNA) correlations.

overall_design: Liver samples were obtained from 4 patients with HBV-associated acute liver failure (ALF), 10 liver donors and 7 subjects who underwent hepatic resection for liver angioma.

first: Fausto

last: Zamboni

first: Ashley

last: Tice

first: Patrizia

last: Farci


title: Poly I:C Induced Gene Expression Changes in Non-Human Primates IV

city: Nutley

first: Donavan

last: Cheng

overall_design: Animals were sedated with ketamine (10-15 mg/kg) delivered i.m. For nasal scrapes, a nasal curette was used to take a sample from the  nasal cavity (blind, but likely to be from the inferior/maxilloturbinate). After sedation, the left nasal cavity was sampled at T = 0. Saline or poly I:C (100 mg) was subsequently administered to the right nasal cavity using a Penn-Century microspray device. At T = 6h post-poly I:C administration animals were sedated once more and a nasal scrape was collected from the nasal turbinates in the right nasal cavity. For these studies, each treatment group had n = 12 non-human primates and within each treatment group there were n = 6 that were sensitized and n = 6 that were not sensitized to A.suum. 2 samples were removed as outliers (detected by PCA).

first: Javad

last: Golji

first: Palanikumar

last: Ravindran

middle: T

first: Hans

last: Bitter

first: Mario

last: Giron

first: Holly

last: Hilton

first: Paul

last: Harris

first: Gaurav

last: Tyagi

first: Heather

last: Martin

first: Laura

last: Singer

first: Carla

last: Bauer

first: Christopher

last: Stevenson


title: Poly I:C Induced Gene Expression Changes in Non-Human Primates I

overall_design: Nasal scrapes were collected from NHPs during a necropsy, plated in 24 well plates in Clonetics SABM media.  Samples were stimulated with poly I:C (100 mg) or a mock control and collected at time points indicated. There were 2-3 technical replicates for the tracheal brushings and the lung explants


title: Vitamin D stimulation of primary skeletal muscle myoblasts

status: Public on Oct 18 2015

city: Stockholm

first: Eric

last: Rullman

address: C1:82 Karolinska University Hospital, Huddinge

department: Laboratory Medicine

country: Sweden

institute: Karolinska Institutet

summary: Expression profiling of proliferating primary myoblasts obtained from vastus lateralis muscle biopsises from healthy individuals and stimulated with Vitamin D (100 nM 1,25(OH)2D3) or vehicle for 24h.

overall_design: Myoblasts isolated from 6 healthy donors were either sitmuleted with Vitamin D (n=6) or vehcicle (n=6) for 24 h


title: Genome-scale profiling of the DNA methylation landscape in human AML patients

status: Public on Oct 07 2015

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

summary: Genome-scale DNA methylation profiling using the Infinium DNA methylation BeadChip platform and samples from acute myeloid leukemia patients screened for their mutation status of DNMT3a, a frequent aberration in AML.

overall_design: DNA methylation analysis of blood samples from patients suffering from acute myeloid leukemia using the Infinium DNA methylation BeadChip platform .

first: Holger

last: Heyn


title: Poly I:C Induced Gene Expression Changes in Non-Human Primates V

overall_design: Lung tissue were collected from NHPs during a necropsy, plated in 24 well plates in Clonetics SABM media.  Samples were stimulated with poly I:C (100 mg) or a mock control and collected at time points indicated. There were 2-3 technical replicates for the tracheal brushings and the lung explants


title: Poly I:C Induced Gene Expression Changes in Non-Human Primates II

overall_design: Animals were sedated with ketamine (10-15 mg/kg) delivered i.m. For nasal scrapes, a nasal curette was used to take a sample from the  nasal cavity (blind, but likely to be from the inferior/maxilloturbinate). Repeated sampling in NHPs sensitized (n = 4) and not sensitized (n =3) to Ascaris suum occurred at baseline (0h), 6h, 24h and 72h time points.


title: Integrated ordination of miRNA and mRNA expression profiles

first: Giacomo

last: Diaz

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

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: Transcriptomic effects of TNFa in primary fibroblast-like synovial cell cultures

city: Brussels

first: Bernard

middle: Robert

last: Lauwerys

address: Avenue Hippocrate 10

department: Institut de Recherches Expérimentales et Cliniques

country: Belgium

institute: Université catholique de Louvain

summary:
Gene expression profiles in synovial biopsies from patients with rheumatoid arthritis (RA) display a high level of plasticity related to disease activity and response to therapy.
In order to identify TNFa-dependent genes in ex vivo RA or other synovial biopsies, we generated the present set of data using primary fibroblast-like synovial cell (FLS) cultures incubated overnight in the presence or the absence of TNFa.

overall_design: FLS were purified from knee synovial biopsies obtained in one patient with RA, and one patient with osteoarthritis. For this experiment, cells between passage 7 and 9 were cultured in the presence or the absence of 10 ng/ml human recombinant TNFa. After overnight incubation, cells were detached, total RNA was extracted, amplified and labeled using a standard Affymetrix procedure, and hybridized on HGU133 Plus2.0 slides.

first: Aurélie

last: De Groof

first: Patrick

last: Durez


title: Transcriptional response to interferon beta-1a treatment in patients with secondary progressive multiple sclerosis

status: Public on Oct 06 2015

city: Ramat-Gan

first: Michael

last: Gurevich

address: Tel-Hashomer

department: Multiple Sclerosis Center

country: Israel

institute: Sheba Medical Center

summary:
Interferon (IFN) beta-1a is an approved treatment for relapsing remitting multiple sclerosis (RRMS) and has been examined for use in secondary progressive multiple sclerosis (SPMS). However, no information regarding blood transcriptional changes induced by IFN treatment in SPMS patients is available.
Our aim was to identify a subgroup of SPMS patients presenting a gene expression signature similar to that of RRMS patients who are clinical responders to IFN treatment.

overall_design: SPMS patients (n=50, 20 IFN treated and 30 untreated) were classified using unsupervised hierarchical clustering according to IFN inducible gene expression profile identified in RRMS clinical responders to treatment. IFN inducible gene expression profile was determined by finding differentially expressed genes (DEGs) between IFN treated (n=10) and untreated (n=25) RRMS patients.

first: Gadi

last: Miron

first: Rina

last: Falb

first: David

last: Magalashvili

first: Mark

last: Dolev

first: Yael

last: Stern

first: Anat

last: Achiron


title: Phenotypic comparison of common mouse strains developing high-fat diet-induced hepatosteatosis

city: Munich

first: Barbara

last: Fridrich

address: Ingolstädter Landstraße 1

institute: Hemholtz Center Munich

summary:
Genetic predisposition and environmental components contribute to an individuals’ non-alcoholic fatty liver disease (NAFLD) susceptibility. Therefore, we compared phenotypic variations of mouse strains extensively used in biomedical research during induction of high-fat diet (HFD)-mediated NAFLD and assessed transcriptional alterations in livers. In a time-resolved fashion we determined a wide spectrum of physiological parameters in C3HeB/FeJ (C3H), C57BL/6NTac, C57BL/6J, and 129P2/OlaHsd (129) males during a 7, 14, or 21 days HFD challenge and performed gene transcription analyses in steatotic livers.
HFD exposure for 21 days progressively increased liver triacylglycerol concentrations (TAG) in 129. Strain-specific liver transcription profiles in this model suggest a transition from benign fatty liver to inflammation-associated NAFLD. No comparable changes were observed in C3H males where after an initial increase, hepatic TAG declined. In all genetic backgrounds hepatosteatosis was paralleled by a concerted repression of genes potentially increasing the liver’s vulnerability to oxidative stress damage thereby contributing to the progression of benign hepatosteatosis to NASH later on. The products of further identified strain-independent gene candidates might represent putative molecular links between the pathogenesis of NAFLD and cancer, insulin resistance, type 2 diabetes, and neurodegenerative disorders. Phenotypic characteristics and strain-dependent and -independent transcriptional changes in liver in different murine genetic backgrounds in this work can be exploited in the search for molecular mechanisms implicated in the development of HFD-mediated NAFLD, the investigation of potential therapeutic targets and in selecting a suitable murine genetic background for studies and mouse mutant engineering.

overall_design: We performed gene expression microarray analysis on liver from C3HeB/FeJ (C3H), C57BL/6NTac, C57BL/6J, and 129P2/OlaHsd (129) males during 21 days HFD challenge.

first: Melanie

last: Kahle

first: Marion

last: Horsch

first: Anett

last: Seelig

first: Jürgen

last: Schultheiß

first: Jörn

last: Leonhardt

first: Martin

last: Irmler

first: Johannes

last: Beckers

first: Birgit

last: Rathkolb

first: Eckhard

last: Wolf

first: Nicole

last: Franke

first: Valerie

last: Durner

first: Helmut

last: Fuchs

last: Hrabe de Angelis

first: Susanne

last: Neschen


title: A subset of metastatic pancreatic ductal adenocarcinomas depends quantitatively on oncogenic Kras/Mek/Erk-induced hyperactive mTOR signalling

status: Public on Oct 05 2015

city: Neuherberg

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

summary:
Objective
Oncogenic Kras-activated robust Mek/Erk signals phosphorylate to the tuberous sclerosis complex (Tsc) and deactivates mammalian target of rapamycin (mTOR) suppression in pancreatic ductal adenocarcinoma (PDAC); however, Mek and mTOR inhibitors alone have demonstrated minimal clinical antitumor activity.
Design
We generated transgenic mouse models in which mTOR was hyperactivated either through the Kras/Mek/Erk cascade, by loss of Pten or through Tsc1 haploinsufficiency. Primary cancer cells were isolated from mouse tumours. Oncogenic signalling was assessed in vitro and in vivo, with and without single or multiple targeted molecule inhibition. Transcriptional profiling was used to identify biomarkers predictive of the underlying pathway alterations and of therapeutic
response. Results from the preclinical models were confirmed on human material.
Results
Reduction of Tsc1 function facilitated activation of Kras/Mek/Erk-mediated mTOR signalling, which promoted the development of metastatic PDACs. Single inhibition of mTOR or Mek elicited strong feedback activation of Erk or Akt, respectively. Only dual inhibition of Mek and PI3K reduced mTOR activity and effectively induced cancer cell apoptosis. Analysis of downstream targets demonstrated that oncogenic activity of the Mek/Erk/Tsc/mTOR axis relied on Aldh1a3 function. Moreover,
in clinical PDAC samples, ALDH1A3 specifically labelled an aggressive subtype.
Conclusions
These results advance our understanding of Mek/Erk-driven mTOR activation and its downstream targets in PDAC, and provide a mechanistic rationale for effective therapeutic matching for Aldh1a3-positive PDACs.

overall_design: We performed gene expression microarray analysis in duplicates on 11 cell lines representing three experimental models

first: Bo

last: Kong

first: Weiwei

last: Wu

first: Tao

last: Cheng

first: Anna

middle: M

last: Schlitter

first: Philipp

last: Bruns

first: Carsten

last: Jäger

first: Ivonne

last: Regel

last: Raulefs

first: Nora

last: Behler

first: Mert

last: Erkan

first: Fabian

last: Theis

first: Irene

last: Esposito

first: Jörg

last: Kleeff

first: Christoph

middle: W

last: Michalski


title: Human Stem Cells from Single Blastomeres Reveal Pathways of Embryonic or  Trophoblast Fate Specification.

city: La Jolla

first: Kristopher

middle: L.

last: Nazor

state: CA

address: 10550 North Torrey Pines Road

department: Regenerative Medicine

institute: The Scripps Research Institute

summary: Mechanisms of initial cell fate decisions differ among species. To gain insights into lineage allocation in humans, we derived ten human embryonic stem cell lines from single blastomeres of four 8-cell embryos and one 12-cell embryo from a single couple (UCSFB1-10). Versus numerous conventional lines from blastocysts, they had unique gene expression and DNA methylation patterns, in part, indicative of trophoblast competence. At a transcriptional level, UCSFB lines from different embryos were often more closely related than those from the same embryo. As predicted by the transcriptomic data, immunolocalization of EOMES, BRACHYURY, GDF15 and active β-catenin revealed differential expression among blastomeres of 8-10-cell human embryos. The UCSFB lines formed derivatives of the three germ layers and CDX2-positive progeny, from which we derived the first human trophoblast stem cell line. Our data suggest heterogeneity among early-stage blastomeres and that the UCSFB lines have unique properties, indicative of a more immature state than conventional lines.

overall_design: This study was designed to determine whether human embryonic stem cells (hESCs) derived from early-stage embryos had unique transcriptional and epigentic properties as compared to conventional lines that are typically derived from later-stage blastocysts.


title: Inhibition of de novo Palmitate Synthesis by Fatty Acid Synthase Induces Apoptosis in Tumor Cells by Remodeling Cell Membranes, Inhibiting Signaling Pathways, and Reprogramming Gene Expression

status: Public on Oct 02 2015

city: Menlo Park

first: Timothy

middle: S.

last: Heuer

address: 1050 Hamilton Court

department: Biology

institute: 3-V Biosciences

summary:
TVB-3166, an orally available, reversible, potent, and selective FASN inhibitors, was used to investigate FASN as a cancer therapeutic target. FASN inhibition with TVB-3166 induces apoptosis, inhibits anchorage-independent cell growth under lipid-rich conditions, and inhibits in vivo xenograft tumor growth.
The effects are dose dependent between 20-200 nM TVB-3166, which agrees with the IC50 value in biochemical FASN and cellular palmitate synthesis assays. Studies to understand the mechanism of action show that FASN inhibition disrupts lipid raft architecture, inhibits biological pathways such as lipid biosynthesis, PI3K-AKT-mTOR and β-catenin signal transduction, and inhibits expression of downstream oncogenic effectors such as c-Myc. These effects are observed in tumor cells but not fibroblast or endothelial cell types. Our results show that FASN inhibition has anti-tumor activities in biologically diverse preclinical tumor models, including those expressing mutant K-Ras, ErbB2, c-Met, and PTEN. The reported findings inform ongoing studies to link specific mechanisms of action with defined tumor types and advance the discovery of biomarkers to support development of FASN inhibitors as novel cancer therapeutics.

overall_design: PANC-1 cells were seeded in growth media. The following day, treatment media with DMSO alone or with TVB-3166 (0.1 or 1.0 µM) was added and cells were incubated for an additional 48 (22Rv1) or 72 hours (PANC-1). All treatments were performed in triplicate. For Panc-1 Affymetrix microarray studies (HG-U133 Plus 2.0), cells were lysed using Qiazol (Qiagen, 79306) and processed using the RNeasy microarray kit (Qiagen, 73304). Microarray analysis was performed at Expression Analysis (Durham, NC). Data analysis was performed at 3-V Biosciences using Partek Genomics Suite software (St. Louis, MO).

middle: S

first: Richard

last: Ventura


title: Role of Gata5 in vascular endothelial cells

status: Public on Oct 01 2015

city: Ottawa

first: Smail

last: Messaoudi

state: Ontario

address: 451 smyth road

department: BMI

institute: University of Ottawa

summary: Despite its high prevalence and economic burden, the etiology of human hypertension remains incompletely understood. Here we identify the transcription factor Gata5, as a new gene involved in regulation of blood pressure (BP). GATA5 is expressed in microvascular endothelial cells (mEC) and its genetic inactivation in mice leads to hypertension, vascular endothelial dysfunction and renal inflammation. Aged Gata5-Null mice develop salt-sensitivity and target-organ damage reminiscent of the progression of human hypertension. Endothelial-specific inactivation of Gata5 increases BP and leads to vascular endothelial dysfunction, confirming the endothelial component of Gata5 inactivation-related hypertension. To directly assess the effect of loss of GATA5 on endothelial cells, we generated a stable GATA5 knockdown cell line (HDMEC-Gata5KO) by infecting human dermal microvascular endothelial cells with a lentiviral vector containing an anti-Gata5 shRNA  followed by a transcriptomic analysis. The control cells were infected with a lentivirus containing an empty vector pLKO2.

overall_design:
GATA5 MISSION® TRC2 pLKO.shRNA (TRCN0000431556) and MISSION® TRC2 pLKO-puro Non-Mammalian shRNA Control (SHC202) plasmids were purchased from Sigma-Aldrich. Viral particles were generated by co-transfection of phoenix cells with the lentiviral vector (GATA5 TRC2 shRNA or the shRNA control plasmids), the packaging vector psPAX2 and the envelope vector pMD2G. Co-transfection was performed using the Qiagen’s Effectene transfection reagent (301425). Twenty-four hours after transfection, medium was discarded and replaced by Endothelial Growth Medium 2 (Promocell, C-22021). Forty-eight hours later, the medium (EGM2) was collected, filtered, and used for infection of Human Dermal Microvascular Endothelial Cells (HDMEC; Promocell, C-14016). Infected cells were selected with addition of puromycin (Sigma-Aldrich, P8833) to culture medium at the concentration of 2.5 μg/ml for 15 days. Control (HDMEC-pLKO-Ctrl) and HDMEC-GATA5-KD cells were then grown and maintained in EGM2 containing puromycin at the concentration of 0.25 μg/ml.
RNA was extracted and hybridized on Affymetrix microarray


title: Validated prediction of pro-invasive growth factors using a transcriptome-wide invasion signature derived from a complex 3-D invasion assay

first: Johannes

last: Beckers

summary: The invasion of activated fibroblasts represents a key pathomechanism in fibrotic diseases, carcinogenesis and metastasis. Here, invading fibroblasts contribute to fibrotic extracellular matrix (ECM) formation and the initiation, progression, or resistance of cancer, respectively. To construct a transcriptome-wide signature of fibroblast invasion, we used a multiplex phenotypic 3D invasion assay using murine lung fibroblasts. Microarray-based gene expression profiles of invading and non-invading fibroblasts were highly distinct: 1049 genes were differentially regulated (>1.5-fold). An unbiased pathway analysis (Ingenuity) identified a significant enrichment for the functional clusters ‘invasion of cells’, ‘idiopathic pulmonary fibrosis (IPF)’ and ‘metastasis’. Particularly, matrix metalloprotease13 (MMP13), transforming growth factor (TGF)β1, Caveolin1 (Cav1), Phosphatase and Tensin Homolog (Pten), and secreted frizzled-related protein1 (Sfrp1) were among the highest regulated genes. In silico analysis by Ingenuity predicted TGFβ1, epidermal growth factor (EGF), fibroblast growth factor2 (FGF2), and platelet-derived growth factor (PDGF)-BB to induce invasion. As such, these growth factors were tested in the 3D invasion assay and displayed a significant induction of invasion, thus validating the transcriptome profile. Accordingly, our transcriptomic invasion signature describes the invading fibroblast phenotype in unprecedented detail and provides a tool for future functional studies of cell invasion and therapeutic modulation thereof.

overall_design: We performed gene expression microarray analysis on the mouse lung fibroblast line MLg 2908. In a 3D collagen invasion assay we analysed invading and non-invading cells at different time points

first: Bettina

last: Oehrle

first: Gerald

last: Burgstaller

first: Martin

last: Irmler

first: Stefan

last: Dehmel

first: Tiffany

last: Hwang

first: Susanne

last: Krauss-Etschmann

first: Silke

last: Meiners

first: Oliver

last: Eickelberg


title: Influence of ascorbic acid depletion on gene expression in liver and lipid metabolism

status: Public on Oct 04 2015

city: Akita

first: Tomokazu

last: Konishi

state: Akita

address: Shimoshinjyo Nishi

department: Bioresource Sciences

institute: Akita Prefectural University

summary: Ascorbic acid (AA) is a powerful antioxidant and play as a cofactor for various enzymes in vivo. In this study, we investigated the effect of AA depletion on gene expression in the liver and lipid metabolism by using SMP30/GNL knockout (KO) mice which are unable to biosynthesis AA. First, we performed microarray analysis. Briefly, SMP30/GNL KO mice were weaned and divided into two groups; AA-depleted and supplemented groups, which mice were free access to water containing 1.5 g/L AA. After 4 weeks, mRNA was isolated and purified from the liver. In this study, Affymetrix® GeneChip® was used for microarray analysis. Actually, AA-depletion altered many gene expressions related to lipid metabolism. Especially, Cytochrome P450 7a1 (Cyp7a1), a late-limiting enzyme of bile acid biosynthesis, gene expression was significantly up-regulated. We also confirmed Cyp7a1 protein levels by Western blotting. Next, we investigated the influence of AA depletion on lipid metabolism. We examined the lipid and bile acid levels in the liver, plasma, and gallbladder from SMP30/GNL KO mice. Amount of total bile acid (TBA), free fatty acid (FA), total cholesterol (TC), triglyceride (TG), and phospholipids (PL) were measured by colorimetric method. AA depletion reduced TBA levels in the liver and gallbladder. However, FA, TC, TG, and PL in the plasma and liver were not changed by AA depletion. Although Cyp7a1 gene expression and protein levels were increased by AA depletion, amount of bile acid were reduced. Conclusively, we have shown that AA depletion reduced bile acid biosynthesis and elevated Cyp7a1 gene expression and protein levels. Thus, AA is an essential for bile acid biosynthesis pathway.

overall_design: To investigate SMP30 gene in metabolism of ascorbic acid, liver transcriptome were compared between SMP30/GNL KO mice fed with AA-free diet, AA-supplemented KO mice, and wild type mice.

first: Keita

last: Takahashi

first: Yuki

last: Kishimoto

first: Kentaro

last: Shimokado

first: Naoki

last: Maruyama

first: Akihito

last: Ishigami


title: Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits [Microarray]

city: Cambridge

first: Vijay

middle: G

last: Sankaran

address: 7 Cambridge Center

institute: Broad Institute

summary: Genome-wide association studies (GWAS) have successfully identified thousands of associations between common genetic variants and human disease phenotypes, but the majority of these variants are non-coding, often requiring genetic fine-mapping, extensive epigenomic profiling, and individual reporter assays to delineate potential causal variants. We employ a massively parallel reporter assay to simultaneous screen 2756 variants in strong linkage-disequilibrium with 75 sentinel variants associated with red blood cell traits. We show that this assay identifies elements with erythroid-specific endogenous regulatory activity. Across 23 variants, we conservatively identified 32 putative causal variants (PCVs). We demonstrate endogenous enhancer activity for three PCVs that predominantly affect the transcription of SMIM1, RBM38, and CD164 using targeted genome editing. Functional follow up of RBM38 delineates a key role for this gene in the dramatic alternative splicing program occurring during terminal erythropoiesis. Finally, we provide evidence for how common GWAS-nominated variants can disrupt cell-type specific transcriptional regulatory pathways.

overall_design: We infected K562 cells with a HMD-GATA1 lentiviral vector that overexpresses GATA1 as described previously and below (Ludwig et al., 2014).  RNA was isolated 48 hours after infection and cDNA was synthesized as described below. Microarrays (GeneChip Human Gene 2.0 ST Arrays, Affymetrix) were performed on K562 for control (HMD) and GATA1 overexpression (HMD+GATA1). Raw files were processed and normalized using the RMA algorithm from the oligo package in R 3.2 (Carvalho and Irizarry, 2010). Differential expression analyses were conducted using limma (Ritchie et al., 2015). Gene set enrichment analysis (GSEA) was performed comparing GATA1 overexpression to control with gene set permutation (Subramanian et al., 2005). The erythroid differentiation signature gene set was derived by identifying the top 200 genes that were expressed significantly higher in intermediate erythroblasts (CD71+/ CD235a+) compared to colony forming unit erythroid cells (CD71+/ CD235a-) (Merryweather-Clarke et al., 2011). The GATA1 target gene set has been previously described (Ludwig et al., 2014).

first: Jacob

last: Ulirsch


title: Expression data from normal breast tissues and invasive primary breast carcinoma tissues

city: Wuhan

first: Juncheng

last: Wei

address: Jiefang Dadao 1095

department: Department of Obstetrics and Gynecology

institute: Huazhong University of Science and Technology

summary:
The role of lymphangiogenesis in tumor metastasis remains unclear. This study addressed this issue in lymphatic endothelial cells (LECs) derived from primary invasive breast cancer specimens.
LECs were isolated by laser capture microdissection and gene expression was profiled by microarray analysis.

overall_design: To analyze global gene expression patterns in LECs derived from primary invasive breast tumors, we compared gene expression profiles between fresh human normal mammary glands (N4 and N5) and primary invasive breast tumors (BL1 and B14). Specimens were dissected, and rapid immunochemical staining of lymphatic-specific markers, FLT-4 and LYVE-1, was used to identify lymphatic endothelium. Homogenous LECs were separated directly in situ by laser capture microdissection. Intact RNA was extracted, and the RNA samples were used for subsequent GeneChip probe microarrays.

first: Ding

last: Ma

first: Qing-Lei

last: Gao


title: Plasma induced signatures reveal an extracellular milieu possessing an immunoregulatory bias in treatment naïve inflammatory bowel disease

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

summary: The complex milieu of inflammatory mediators associated with many diseases is often too dilute to directly measure in the periphery, necessitating development of more sensitive measurements suitable for mechanistic studies, earlier diagnosis, guiding selection of therapy, and monitoring interventions.  Previously, we determined that plasma of recent-onset (RO) Type 1 diabetes (T1D) patients induce a proinflammatory transcriptional signature in fresh peripheral blood mononuclear cells (PBMC) relative to that of unrelated healthy controls (HC). Here, using an optimized cryopreserved PBMC-based protocol, we apply this approach to inflammatory bowel disease by examining groups of Crohn's disease (CD) and ulcerative colitus (UC) patients.  The induced plasma induced signatures are compared to those of Type 1 diabetes patients (RO T1D) as well as unrelated healthy controls (uHC).

overall_design: UPN727 cells were stimulated with CD plasma (n=22), UC plasma (n=15), Unrelated healthy control (n=10). Gene expression analysis was perfromed in order to evaluate the transcriptional signature associated with IBD.

first: Bhaskar

last: Gurram

first: Nita

middle: H

last: Salzman

first: Mary

middle: L

last: Kaldunski

first: Shuang

last: Jia

first: Michael

last: Stephens

first: Manu

last: Sood


title: Glioblastoma stem cells

city: Los Angeles

first: Cho-Lea

last: Tso

address: 10833 Le Conte Avenue

department: Surgery

institute: University of California, Los Angeles


title: Expression profiles of glioblastoma stem cells (GSC) treated with BMP7

summary:
Comparison of untreated and BMP7 treated  GSC
We used microarrays to identify gene profiles of GSC modulated by BMP7 treatment

overall_design: We treated GSC, using BMP7 (100ng/ml)


title: Glioblastoma stem cell (GSC) clones survived 500uM Temozolomide (TMZ) treatment

summary:
Comparison of parental GSC (GSC-parental) with treatment resistant GSC clones survived 500uM TMZ treatment (GSC-500uM TMZ)
We used microarrays to identify defense profiles of GSC-500uM TMZ

overall_design: We used 500uM TMZ to selecte treatment resistant GSC clones (GSC-500uM TMZ)


title: Gene expression of normal and ASCC1-mutant skin fibroblasts after serum starvation and serum challenge

city: Berlin

first: Markus

last: Schuelke

state: Berlin

address: Augustenburger Platz 1

department: Neuropediatrics

institute: Charite

summary:
In order to investigate the genes that might be regulated by the activating signal cointegrator 1 (ASC-1) complex we performed an expression analysis using the GeneChip® Human Gene 2.0 ST Array (Affymetrix)
Since ASC-1 was predicted to have an influence on the transcription regulation by the serum response factor (SRF), we investigated gene expression after serum starvation and subsequent serum challenge.

overall_design:
Investigation of 4 skin fibroblast control lines and of 2 of patient fibroblast lines that carried a mutation in the ASCC1 (activating signal cointegrator 1 complex subunit 1) gene. Semiconfluent skin fibroblast cultures were serum starved for 24 hour and rech-challenged with 15% FBS for 30 and for 60 minutes.

stress: serum starvation: MS_61_Co_1_00W
stress: serum starvation: MS_64_Co_2_00W
stress: serum starvation: MS_67_Co_3_00W
stress: serum starvation: MS_70_Co_4_00W
stress: serum starvation: MS_73_Pat_1_00W
stress: serum starvation: MS_76_Pat_2_00W
stress: serum challenge 30 minutes: MS_62_Co_1_30W
stress: serum challenge 30 minutes: MS_65_Co_2_30W
stress: serum challenge 30 minutes: MS_68_Co_3_30W
stress: serum challenge 30 minutes: MS_71_Co_4_30W
stress: serum challenge 30 minutes: MS_74_Pat_1_30W
stress: serum challenge 30 minutes: MS_77_Pat_2_30W
stress: serum challenge 60 minutes: MS_63_Co_1_60W
stress: serum challenge 60 minutes: MS_66_Co_2_60W
stress: serum challenge 60 minutes: MS_69_Co_3_60W
stress: serum challenge 60 minutes: MS_72_Co_4_60W
stress: serum challenge 60 minutes: MS_75_Pat_1_60W
stress: serum challenge 60 minutes: MS_78_Pat_2_60W
disease state: healthy control: MS_61_Co_1_00W
disease state: healthy control: MS_62_Co_1_30W
disease state: healthy control: MS_63_Co_1_60W
disease state: healthy control: MS_64_Co_2_00W
disease state: healthy control: MS_65_Co_2_30W
disease state: healthy control: MS_66_Co_2_60W
disease state: healthy control: MS_67_Co_3_00W
disease state: healthy control: MS_68_Co_3_30W
disease state: healthy control: MS_69_Co_3_60W
disease state: healthy control: MS_70_Co_4_00W
disease state: healthy control: MS_71_Co_4_30W
disease state: healthy control: MS_72_Co_4_60W
disease state: homozygous ASCC1 mutation carrier: MS_73_Pat_1_00W
disease state: homozygous ASCC1 mutation carrier: MS_74_Pat_1_30W
disease state: homozygous ASCC1 mutation carrier: MS_75_Pat_1_60W
disease state: homozygous ASCC1 mutation carrier: MS_76_Pat_2_00W
disease state: homozygous ASCC1 mutation carrier: MS_77_Pat_2_30W
disease state: homozygous ASCC1 mutation carrier: MS_78_Pat_2_60W

first: Ellen

last: Knierim


title: Transformation of Barrett's esophagus stem cell, gastric cardia stem cells and normal esophagus stem cells

city: Houston

first: Frank

last: McKeon

state: TX

address: 3455 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

summary: Barrett’s esophagus confers significant risk of esophageal adenocarcinoma.  We have established the cloning of patient-matched stem cells of Barrett’s, gastric, and esophageal epithelium.  Transplantation of transformed Barrett’s stem cells yielded tumors with hallmarks of esophageal adenocarcinoma, whereas transformed esophageal stem cells produced squamous cell carcinomas.  These findings define a stem cell target in a precancerous lesion for preemptive therapies.

overall_design: The cloned patient-matched stem cells of Barrett’s, gastric, and esophageal epithelium were transformed with retroviral infection of hTERT, SV40 and c-myc and then subcutaneously transplanted into highly immunocompromised NSG (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ) mice.  Isolated tumors from transformed Barrett’s (3 patients), gastric (1 patient), and esophageal epithelium (1 patient) stem cells were collected and total RNA was isolated. We used Affymetrix chips (HG-U133_Plus_2).

first: Yusuke

last: Yamamoto

first: Xia

last: Wang

first: Florian

last: Kern

first: Ting

last: Zhang

first: Yuanyu

last: Hu


title: Gene expression data of human primary keratinocytes with control or DDX6 knockdown

first: George

last: Sen

address: 9500 GIlman Drive

department: Dermatology/CMM

institute: UCSD

summary:
Stem and progenitor cells maintain the tissue they reside in for life by regulating the balance between proliferation and differentiation. How this is done is not well understood. Here, we report that DDX6 is necessary for maintaining human epidermal progenitor cell self-renewal.
Global gene expression profiling using U133 plus 2.0 arrays were used to deteremine the genes perturbed by knockdown of DDX6.

overall_design: For gene expression profiling, cultured primary human keratinocytes were knocked down for control (CTL) or DDX6. RNA was harvested from the cells 7 days after knockdown. Microarray analysis using Affymetrix HG-U133 2.0 plus arrays was performed on duplicate samples.

first: Ying

first: Yifang

last: Chen


title: White adipose tissue and brain microarray from eIF6 heteroxygotes and wild-type 5 weeks-old mice

city: Milan

first: Daniela

last: Brina

address: Via Sforza 35

institute: INGM

summary:
White adipose tissue is primary involved in the response to insulin after feeding, while brain is not directly sensitive to insulin levels.
We used microarrays to detail the global programme of gene expression in white adipose tissue upon eIF6 haploinsufficiency and compare the gene expression profiles to brain. We identified distinct classes of down-regulated genes and up-regulated genes in the two tissues.

overall_design: White adipose tissue and brain of 5 weeks-old mice were used for RNA extraction and hybridization on Affymetrix microarrays.

first: Nina

last: Offenhauser


title: Canakinumab treatment for recent-onset type 1 diabeties mellitus: a multicenter randomized, placebo-controlled trial

first: Martin

last: Hessner

summary: Background: Blocking the action of the pro-inflammatory cytokine interleukin-1 (IL-1) reduces beta-cell secretory dysfunction and apoptosis in vitro, diabetes incidence in animal models of Type 1 diabetes mellitus (T1D), and glycaemia via improved beta-cell function in patients with T2D. We hypothesised that canakinumab, a monoclonal antibody to IL-1B, improves beta-cell function in patients with new-onset T1D.   Methods: In an individually randomised, two-group parallel trial involving 12 sites in US, 69 patients aged 6-45 with T1D, < 12 weeks of symptoms, and assigned by centralised computer-generated blocked randomisation with locked computer-file concealment to treatment with 2 mg/kg (maximum 300 mg) canakinumab (n=45) or placebo (n=22) monthly for 12 months as add-on to conventional therapy. Participants and care-givers, but not data monitoring unit, were masked to group assignment. The primary end-point was change in the two-hour area-under-the-curve C-peptide response to MMT 12 months.

overall_design: Transcriptional signatures were induced in healthy cryopreserved human donor peripheral blood mononuclear cells (UPN727) through exposure to 40% subject serum in a 9 hour co-culture. Sixty-Three randomly selected subjects (43 Canakinumab treatment; 20 placebo treatment) were analysed blindedly to treatment assignment. The statistical significance of differential gene expression was determined through ANalysis Of VAriation (ANOVA) and false discovery rates (FDR) using Partek Genomics Suite 6.5.

first: Carla

middle: J

last: Greenbaum

first: Susanne

last: Cabrera

first: Xujing

first: Yi-Guang

first: Shuang

first: Mary

last: Kaldunski

first: Thomas

last: Mandrup-Poulsen


title: Liver microarray from eIF6 heterozygotes or wild-type 3 weeks-old mice

summary:
Liver is primary involved in the response to insulin after feeding. Hepatocytes activates a tightly controlled genetic programme where specific sets of genes are modulates in response to insulin, for activation of the anabolic pathways.
We used microarrays analysis to detail the global programme of gene expression in liver upon eIF6 haploinsufficiency and identified distinct classes of down-regulated genes and up-regulated genes during this process, that globally defines reprogramming of metabolism

overall_design: Liver of 3 weeks-old mice were used for RNA extraction and hybridization on Affymetrix microarrays.

first: Annarita

last: Miluzio


title: Gene expression data of regenerated human epidermis overexpressing control LACZ or SOX2

status: Public on Sep 30 2015

summary:
SOX2 is not expressed in normal human epidermis but its expression is elevated in pre-neoplastic epidermis suggesting that it may have a role in the tumorigenesis process. The goal of this study is to determine the impacts of SOX2 overexpression in regenerated human epidermis.
Global gene expression profiling using U133 plus 2.0 arrays were used to deteremine the genes perturbed by overexpression of SOX2.

overall_design: For gene expression profiling, cultured primary human keratinocytes were transduced to overexpress LACZ or SOX2. These genetically modified keratinocytes were used to regenerate human epidermis.RNA was harvested from regenerated human epidermis 6 days post-seeding of the cells. Microarray analysis using Affymetrix HG-U133 2.0 plus arrays was performed on duplicate samples.

first: Y

first: G


title: Comparative Gene expression analysis of 2fTGH cells expressing Wild type STAT2 vs S734A-STAT2 in response to IFN-α or TNF-α

city: Philadelphia

first: Ana

middle: Maria

last: Gamero

state: PA

address: 3440 N. Broad St.

department: Biochemistry

institute: Temple University

summary:
STAT2 is an essential transcription factor in type I interferon (IFN) signaling. STAT2 is activated following exposure to IFN stimulation by phosphorylation at tyrosine-690. This post-translational modification permits the assembly and nuclear retention of the ISGF3 complex (consisting of STAT1/STAT2/IRF9) to drive gene transcription. We recently identified  STAT2 to be serine phosphorylated in an IFN-dependent manner. The biological significance of these novel phosphorylation events in STAT2 remain to be elucidated. Thus far our data show that serine phosphorylation of STAT2 negatively regulates the biological effects of IFN.
In an effort to understand the scope of STAT2 serine phosphorylation in IFN signaling, we conducted comparative microarray analysis to identify a collection of genes that are regulated by  phosphorylated Ser734-STAT2 vs. unphosphorylated S734-STAT2 after IFN treatment.

overall_design: STAT2 null 2fTGH cells referred thereafter as U6A cells were used to stably restore expression of either mutant STAT2 with Serine 734 changed to Alanine (S734A, S7) or wild type (WT) STAT2.  Cells were stimulated with medium, IFN-α or TNF-α for 4 hours. RNA was extracted and microarrray analysis performed.

first: Hakan

last: Steen


title: Genome-wide profiling of early and late CD8 memory T cells expressing CD62L

city: Iowa City

first: Ramakrishna

last: Sompallae

state: IA

address: 285 Newton Road, 5292 CBRB

department: Iowa Institute of Human Genetics

institute: University of Iowa

summary:
Memory CD8+ P14 cells were generarted through adoptive transfer and infection with LCMV armstrong. Then, early memory (after 30 - 45 days) and late memory (after 8 months) cells were sort purified based on CD62L expression.
Genome-wide expression profiles were captured for early and late memory cells with high and low levels on CD62L using Affymetrics arrays to show their molecular and functional differences.

overall_design: Replicates of early memory P14 cells that are CD62L-, early memory P14 cells that are CD62L+, late memory P14 cells that are CD62L-, and late memory P14 cells that are CD62L+ were analysed for differentially regulated genes and networks.

first: Matthew

last: Martin

first: Vladimir

middle: P

last: Badovinac


title: Expression data from prostate cancer and osteoblast co-cultures

city: Livermore

first: Aimy

last: Sebastian

address: 7000 East Ave

institute: Lawrence Livermore National Laboratory

summary: Dynamic interaction between prostate cancer and the bone microenvironment is a major contributor to metastasis of prostate cancer to bone. In this study we utilized an in-vitro co-culture model of PC3 prostate cancer cells and osteoblasts followed by microarray based gene expression profiling to identify previously unrecognized prostate cancer-bone microenvironment interactions. Factors secreted by PC3 cells resulted in the up-regulation of many genes in osteoblasts associated with bone metabolism and cancer metastasis, including Mmp13, Il-6 and Tgfb2, and down-regulation of Wnt inhibitor Sost. To determine whether altered Sost expression in the bone microenvironment has an effect on prostate cancer metastasis, we co-cultured PC3 cells with Sost knockout (SostKO) osteoblasts and wildtype (WT) osteoblasts and identified several genes differentially regulated between PC3-SostKO osteoblast co-cultures and PC3-WT osteoblast co-cultures. Co-culturing PC3 cells with WT osteoblasts up-regulated cancer-associated long noncoding RNA (lncRNA) MALAT1 in PC3 cells. MALAT1 expression was further enhanced when PC3 cells were co-cultured with SostKO osteoblasts and treatment with recombinant Sost down-regulated MALAT1 expression in these cells. Our results suggest that reduced Sost expression in the tumor microenvironment may promote bone metastasis by up-regulating MALAT1 in prostate cancer.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: We co-cultured highly invasive PC3 cells with UMR osteoblasts and primary osteoblasts isolated from wildtype (WT) or Sost knockout (SostKO) mice  in transwells and profiled gene expression changes in both osteoblasts and PC3 cells

first: Nicholas

middle: R

last: Hum

first: Bryan

last: Hudson

first: Gabriela

last: Loots


title: Comparison of Escherichia coli K-12 tynA- with wild type Escherichia coli K-12

city: Turku

first: Heli

last: Elovaara

address: Tykistokatu 6A

department: Medicity research laboratory

country: Finland

institute: University of Turku

summary:
Escherichia coli (E. coli) amine oxidase (ECAO) encoded by tynA gene has been one of the model enzymes to study the mechanism of oxidative deamination of
amines to the corresponding aldehydes by amine oxidases. The biological roles of ECAO have been less addressed. Therefore we have constructed a gene
deletion Escherichia coli K-12 strain, E. coli tynA-, and used the microarray technique to address its function by comparing the total RNA gene expression to
the one of the wt. Our results suggest that tynA is a reserve gene for stringent environmental conditions and its gene product ECAO a growth advantage compared to other bacteria due to H2O2 production.

overall_design: The effect of deleting the expression of E. Coli amine oxidase by deleting tynA gene to the expression of other genes was done by comparing the knock out strain to wild type strain in different time points.

first: Teija

last: Huusko

first: Mikael

last: Maksimow

first: Kati

last: Elima

first: Gennady

last: Yegutkin

first: Marko

last: Salmi

first: Sirpa

last: Jalkanen


title: Expression data of human aortic valve cusps

city: Oulu

first: Jaana

last: Rysa

address: Aapistie 5B

department: Pharmacology and toxicology

institute: University of Oulu

summary:
Calcific aortic valve disease is the most common form of valvular heart disease in the Western World. Milder degrees of aortic valve calcification is called aortic sclerosis and severe calcification with impaired leaflet motion is called aortic stenosis.
We used microarrays to detail the global programme of gene expression underlying cdevelopment of calcified aortic valve disease in humans.

overall_design: Human aortic valves from during different stages of develoment of calcified aortic valve disease (normal, sclerotic, calcified) was selected for RNA extraction and hybridization on Affymetrix microarrays. All the patients were male.

last: Rysä


title: Interleukin-1 receptor antagonist for recent-onset type 1 diabeties mellitus: a multicenter randomized, placebo-controlled trial

first: Martin

last: Hessner

summary: Background: Blocking the action of the pro-inflammatory cytokine interleukin-1 (IL-1) reduces beta-cell secretory dysfunction and apoptosis in vitro, diabetes incidence in animal models of Type 1 diabetes mellitus (T1D), and glycaemia via improved beta-cell function in patients with T2D. We hypothesised that anakinra, a recombinant human IL-1 receptor antagonist, improves beta-cell function in patients with new-onset T1D.   Methods: In an individually randomised, two-group parallel trial involving 14 European tertiary referral centers, 69 patients aged 18-35 with T1D, < 12 weeks of symptoms, and standard mixed meal test (MMT) stimulated C-peptide ≥ 200 pM were enrolled between January, 2009 and July, 2011 and assigned by centralised computer-generated blocked randomisation with locked computer-file concealment to treatment with 100 mg anakinra (n=35) subcutaneously once daily or placebo (n=34) for 9 months as add-on to conventional therapy. Participants and care-givers, but not data monitoring unit, were masked to group assignment. The primary end-point was change in the two-hour area-under-the-curve C-peptide response to MMT, and secondary end-points changes in insulin requirements, glycaemia, and inflammatory markers at one, three, six, and nine months.  Findings: The study was prematurely terminated due to slow accrual and is closed to follow-up. No interim analysis was performed. Ten patients withdrew in the anakinra and eight in the placebo arm, leaving 25 and 26 patients to be analysed, respectively. There was no statistical difference in adverse event category reporting between arms. Interpretation: Anakinra-treatment in T1D was safe, but the trial failed to meet primary and secondary outcome measures.

overall_design:
Transcriptional signatures were induced in healthy cryopreserved human donor peripheral blood mononuclear cells (UPN727) through exposure to 40% subject serum in a 9 hour co-culture. Twenty-four randomly selected subjects (13 anakinra treatment; 11 placebo treatment) were analysed blindedly to treatment assignment. The statistical significance of differential gene expression was determined through ANalysis Of VAriation (ANOVA) and false discovery rates (FDR) using Partek Genomics Suite 6.5.

Contributor: The Anti-Interleukin-1 in Diabetes Action (AIDA) study group

first: Shuang

last: Jia