title: Identification of novel markers in rheumatoid arthritis through integrated analysis of DNA methylation and microRNA expression

status: Public on May 07 2013

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

institute: Josep Carreras Research Institute (IJC)

summary: Autoimmune rheumatic diseases are complex disorders, whose etiopathology is attributed to a crosstalk between genetic predisposition and environmental factors. Both variants of autoimmune susceptibility genes and environment are involved in the generation of aberrant epigenetic profiles in a cell-specific manner, which ultimately result in dysregulation of expression. Furthermore, changes in miRNA expression profiles also cause gene dysregulation associated with aberrant phenotypes. In rheumatoid arthritis, several cell types are involved in the destruction of the joints, synovial fibroblasts being among the most important. In this study we performed DNA methylation and miRNA expression screening of a set of rheumatoid arthritis synovial fibroblasts and compared the results with those obtained from osteoarthritis patients with a normal phenotype. DNA methylation screening allowed us to identify changes in novel key target genes like IL6R, CAPN8 and DPP4, as well as several HOX genes. A significant proportion of genes undergoing DNA methylation changes were inversely correlated with expression. miRNA screening revealed the existence of subsets of miRNAs that underwent changes in expression. Integrated analysis highlighted sets of miRNAs that are controlled by DNA methylation, and genes that are regulated by DNA methylation and are targeted by miRNAs with a potential use as clinical markers. Our study enabled the identification of novel dysregulated targets in rheumatoid arthritis synovial fibroblasts and generated a new workflow for the integrated analysis of miRNA and epigenetic control.

overall_design: Comparison between the DNA methylation levels of synovial fibroblasts isolated from 6 Osteoarthritis and  6 Rheumatoid arthritis patients isolated from synovial tissues at the time of joint replacement.  Bisulphite converted DNA from the 12 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Lorenzo

last: de la Rica

first: José

last: Urquiza

last: Gómez-Cabrero

first: Abul

last: Islam

first: Nuria

last: López-Bigas

first: Jesper

last: Tegnér

first: René

last: Toes


title: Bcl11a controls Flt3 expression in early hematopoietic progenitors and is required for pDC development in vivo

status: Public on May 06 2013

city: St. Louis

first: Xiaodi

last: Wu

state: Missouri

address: 4940 Parkview Pl

country: USA

institute: Washington University/HHMI

summary:
Bcl11a is a transcription factor known to regulate lymphoid and erythroid development. Recent bioinformatic analysis of global gene expression patterns has suggested a role for Bcl11a in the development of dendritic cell (DC) lineages. We tested this hypothesis by analyzing the development of DC and other lineages in Bcl11a(-/-) mice. We show that Bcl11a is required for expression of IL-7 receptor (IL-7R) and Flt3 in early hematopoietic progenitor cells. The loss of IL-7R(+) common lymphoid progenitors accounts for previously described lymphoid defects in Bcl11a(-/-) mice. In addition, we found severely decreased numbers of plasmacytoid dendritic cells (pDCs) in Bcl11a(-/-) fetal livers and in the bone marrow of Bcl11a(-/-) fetal liver chimeras. Moreover, Bcl11a(-/-) cells show severely impaired in vitro development of Flt3L-derived pDCs and classical DCs (cDCs). In contrast, we found normal in vitro development of DCs from Bcl11a(-/-) fetal liver cells treated with GM-CSF. These results suggest that the persistent cDC development observed in Bcl11a(-/-) fetal liver chimeras reflects derivation from a Bcl11a- and Flt3-independent pathway in vivo.
We compared global gene expression by microarray for donor-derived wild-type and Bcl11a(-/-) populations isolated from chimeric bone marrow to identify Bcl11a target genes that explain its role in hematopoietic progenitors.

overall_design: GMP and MPP populations were sorted from fetal liver chimeras and pooled by donor genotype. RNA was isolated using an RNAqueous-Micro Kit (Ambion) and submitted for amplification, labeling and hybridization. Expression values were analyzed after RMA quantile normalization using ArrayStar software (DNASTAR).

first: Ansuman

middle: T

last: Satpathy

first: Wumesh

last: KC

first: Kenneth

middle: M

last: Murphy


title: KDM4A regulated genes in human squamous carcinoma cells

status: Public on May 03 2013

city: Los angeles

first: Xiangming

last: Ding

state: CA

address: 650 Charles E Young Dr S, Los Angeles, CA 90095

institute: UCLA

summary:
To establish a robust cellular model system for screening genes associated with cell invasion, we over-expressed the oncogenic translocated promoter region (Tpr)-MET proteins in SCC23 cells (SCC23/MET). Using a functional siRNA screen, we identified that the histone demethylase KDM4A played a critical role in the invasive growth and metastasis of SCC mediated by the Oncogenic MET.
To investigate the molecular mechanism through which KDM4A inhibit the tumor cell invasion, we knock-down KDM4A in SCC23/MET cell and performed a gene microarray to examine which genes may be regulaged by kDM4A.

overall_design: We generated two stable cell lines. one was infected with virus containing scramble and another infected with virus infected with virus containing KDM4A shRNA. Total RNA were extracted from these two cell lines and subject to microarray.

first: Cun-yu

last: Wang


title: Dietary heme induces instantaneous oxidative stress but delayed cytotoxicity and compensatory hyperproliferation in mouse colon

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary:
Red meat consumption is associated with an increased colon cancer risk. Heme, present in red meat, injures the colon surface epithelium by luminal cytotoxicity and reactive oxygen species. This surface injury is compensated by hyperproliferation and hyperplasia of crypt cells, which was induced by a changed surface to crypt signalling as recently described. It is unknown whether the change in signaling is caused by cytotoxic stress and/or by oxidative stress, as these processes were never studied separately. Therefore, the aim of this study was to determine the possible differential effects of dietary heme on these luminal stressors and their impact on the colonic mucosa after 2, 4, 7 and 14 days of heme feeding. Mice received a purified humanized control diet or this diet supplemented with 0.2 µmol heme/g. Oxidative stress was measured as Thiobarbituric Acid Reactive Substances (TBARS) in fecal water. Cytotoxicity of fecal water was quantified with a bioassay. Epithelial cell proliferation was determined by Ki67 immunohistochemistry and mucosal responses were further studied in detail by whole genome transcriptomics. Dietary heme caused instantaneous and delayed changes in the luminal contents which were reflected in the mucosa. Instantaneous, there was an increase in reactive oxygen species leading to increased levels of lipid peroxidation products. Mucosal gene expression showed an instantaneous antioxidant response and PPAR target gene activation. After day 4 cytotoxicity of the colonic contents was increased and hyperproliferation was initiated, indicating that cytotoxicity was causal for the initiation of hyperproliferation. Several oncogenes were activated and tumor protein 53 was inhibited. In conclusion, dietary heme caused an instantaneous production of reactive oxygen species in mouse colon. A lag time was observed in the formation of cytotoxicity which coincided with the initiation hyperproliferation.

Keywords: expression profiling by array

overall_design: Mice were fed a Westernized high fat control diet, or the same diet supplemented with 0.2 µmol heme/g diet. After different days of intervention, mice were killed and gene expression was profiled in colon.

first: Noortje

last: IJssennagger

first: Anneke

last: Rijnierse

first: Nicole

last: de Wit

first: Mark

last: Boekschoten

first: Jan

last: Dekker

first: Arjan

last: Schonewille

first: Michael

last: Müller

first: Roelof

last: van der Meer


title: DNA Methylation Profiling of Human Saliva

status: Public on May 13 2013

city: Saarbruecken

first: Pavlo

last: Lutsik

country: Germany

institute: Saarland University

summary:
Background: Low birth weight is associated with an increased adult metabolic disease risk. It is widely discussed that poor intrauterine conditions could induce long-lasting epigenetic modifications, leading to systemic changes in regulation of metabolic genes. In a unique cohort of 17 monozygotic (MZ) monochorionic female twins very discordant for birth weight (relative differences ranging from 21.3-35.7%), we examined if adverse prenatal growth conditions experienced by the smaller co-twins lead to systemic long-lasting DNA methylation changes. Genome-wide DNA methylation profiles were acquired from saliva DNA using the Infinium HumanMethylation450 BeadChip, targeting ~2% of all CpGs in the genome.
Results: Overall, co-twins showed very similar genome-wide DNA methylation profiles. Since observed differences were almost exclusively caused by variable cellular composition, an original marker-based adjustment strategy was developed to eliminate such variation at affected CpGs. Among adjusted and unchanged CpGs 3153 were differentially methylated between the heavy and light co-twins at nominal significance (p<0.01), of which 45 showed absolute mean β-value differences >0.05 (max=0.08). Deep bisulfite sequencing of eight such loci revealed that differences remained in the range of technical variation, arguing against a reproducible biological effect. Analysis of methylation in repetitive elements using methylation-dependent primer extension assays also indicated no significant intra-pair differences.
Conclusions: Severe intrauterine growth differences observed within these MZ twins are not associated with long-lasting DNA methylation differences in cells composing saliva, detectable with up-to-date technologies. Additionally, our results indicate that uneven cell type composition can lead to spurious results and should be addressed in epigenomic studies.

overall_design: DNA methylation profiles of saliva from 17 Adult Female MZ MC Twins discordant for birth weight.

middle: Y

last: Souren

first: Gilles

last: Gasparoni

first: Sascha

last: Tierling

first: Jasmin

last: Gries

first: Matthias

last: Riemenschneider

first: Jean-Pierre

last: Fryns

first: Catherin

last: Derom

first: Maurice

last: Zeegers

first: Joern

last: Walter


title: Expression data from mouse embryonic stem cells

city: Vancouver

first: Annaick

last: Carles

state: BC

address: 2125 East Mall

country: Canada

institute: University of British Columbia

summary:
Analysis of the transcriptome of ß-catenin flox/- mES cells in comparison with ß-catenin null mES cells or ß-catenin null mES cells stably transfected with an E-cadherin-α-catenin fusion protein.
Expression assay was performed using the Affymetrix GeneChip Mouse Gene 1.0 ST array.

overall_design: The experiment includes ß-catenin flox/-, ß-catenin null and ß-catenin null Eα mouse embryonic stem cells with three biological replicates for each sample.

first: Yong

last: Li

first: Ignacio

last: del Valle

first: Stefan

last: Rudloff

first: Rolf

last: Kemler


title: A transcriptionally induced antioxidant program is elicited in thyroid cells after exposure to hydrogen peroxide

city: Anderlecht

first: Maxime

last: Tarabichi

state: Bruxelles

address: Route de Lennik 808

country: Belgium

institute: IRIBHM

summary: Radiation is an established cause of thyroid cancer and growing evidence supports a role for H2O2 in spontaneous thyroid carcinogenesis. Little is known about the molecular programs activated by these agents in thyroid cells. We profiled the DNA damage response and cell death induced by γ-radiation (0.1–5Gy) and H2O2 (0.0025–0.3mM) in primary human thyroid cells and T-cells. While the two cell types had more comparable radiation responses, 3- to 10-fold more H2O2 was needed to induce detectable DNA damage in thyrocytes. At H2O2 and radiation doses incurring double-strand breaks (DSB), cell death occurred after 24hrs in T-cells, but not in thyrocytes. We next prepared thyroid and T-cells primary cultures from 8 donors operated for non-cancerous pathologies and profiled their genome-wide transcriptional response 4hr after: 1) exposure to 1 Gy radiation, 2) treatment with H2O2, or 3) no treatment. Two H2O2 doses were investigated, calibrated in each cell type as to elicit levels of single- and double-strand breaks equivalent to 1 Gy γ-radiation. The transcriptional responses of thyrocyte and T-cells to radiation were similar, involving DNA repair and cell death genes. In addition to this transcriptional program, H2O2 also upregulated antioxidant genes in thyrocytes, including glutathione peroxidases (GPx) at the DSB-inducing dose. By contrast, a transcriptional storm involving thousands of genes was raised in T-cells. Finally, we showed that GPx inhibition reduced the DNA damaging effect of H2O2 in thyrocytes. We conjecture that defects of anti- H2O2 protection could promote spontaneous thyroid cancers.

overall_design:
Here we characterize the response of thyrocytes to H2O2 from the perspective of DNA damage (SSB and DSB), cell death and genome-wide transcription. We adopted a dual comparative set up. First, in order to gain preliminary insights about which effects are specific to thyrocytes, all experiments were run in parallel in T-cells. Second, all experiments were replicated with radiation, providing a comparison with a proven etiological agent of PTCs. Hence, we investigated all 4 combinations of two factors: thyrocytes vs. T-cells and H2O2 vs. radiation.
Cell lines divide indefinitively owning to basic dysfunctions of cell cycle controls. These have the potential to distort the stress response, DNA repair and cell death in particular. Hence, we worked exclusively on human primary cultures. The radiation and presumably also the H2O2 responses vary among individuals. We seek to average out individual effects by replicating the microarray experiments across the matched T-cells and thyrocytes of 8 donors.

first: Soetkin

last: Versteyhe

first: Natacha

last: Driessens

first: Chiraz

last: Ghaddhab

first: Candice

last: Hoste

first: Xavier

last: De Deken

first: Jacques

middle: E

last: Dumont

first: Françoise

last: Miot

first: Bernard

last: Corvilain

first: Vincent

last: Detours


title: Elk1 Directs a Critical Component of Growth Signaling by the Androgen Receptor in Prostate Cancer

status: Public on May 02 2013

city: Toledo

first: Robert

middle: J

last: Trumbly

state: OH

address: 3000 Arlington Avenue

department: Biochemistry and Cancer Biology

institute: University of Toledo

summary: Elk1 directs selective gene induction that is a substantial and critical component of growth signaling by AR in PC cells.

overall_design: Gene expression in  LNCaP cells was determined in androgen-depleted medium in response to R1881 in  ELK1 knock down (via AR shRNA) or in  cells treated with control shRNA.

first: Suneethi

last: Sivakumaran

first: Mugdha

last: Patki

first: Mesfin

last: Gonit

first: Venkatesh

last: Chari

first: Manoha

last: Ratnam


title: Gene expression in murine stromal cells with MEK inhibition

status: Public on May 01 2013

city: 91400 Orsay

first: Florent

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

summary: comparative expression between stromal MS5 cells treated with (MS5_PD18) or without (MS5_DMSO) MEKi

overall_design: Stromal MS5 cells were treated during 7 days with MEKi (1µM) or diluent

first: Benjamin

last: Uzan


city: Kanazawa

first: Yuji

last: Hodo

address: 13-1 Takara-Machi

country: Japan

institute: Kanazawa University Graduate School of Medical Sciences

summary: IL28B genotype was shown to be associated with treatment outcome of antiviral thearpy for HCV infection. We tried to clarify the molecular feature that was asocciated with IL2B genotype by comparing Hepatic gene expression of HCV related Hepatocellular carcinoma and non-cancerous tissue with Il28B rs8099917 TT genotype and TG/GG genotype.

overall_design: We tried to clarify the molecular feature that was asocciated with IL2B genotype by comparing Hepatic gene expression of HCV related Hepatocellular carcinoma and non-cancerous tissue with Il28B rs8099917 TT genotype and TG/GG genotype. We analyzed ten HCC patients were selected from each IL28B genotype, and their gene expression was determined using Affymetrix genechip analysis.

first: Y

first: M

last: Honda

first: A

last: Tanaka

last: Nomura

first: K

last: Arai

first: T

last: Yamashita

last: Sakai

first: E

last: Mizukoshi

first: S

last: Kaneko


title: Buccals are likely to be a more informative surrogate tissue than blood for epigenome-wide association studies [Illumina tiling]

city: London

last: Lowe

address: 4 Newark Street

department: Blizard Institute

country: United Kingdom

institute: QMUL

type: Methylation profiling by genome tiling array

summary: There is increasing evidence that interindividual epigenetic variation is an etiological factor in common human diseases. Such epigenetic variation could be genetic or non-genetic in origin, and epigenome-wide association studies (EWASs) are underway for a wide variety of diseases/phenotypes. However, performing an EWAS is associated with a range of issues not typically encountered in genome-wide association studies (GWASs), such as the tissue to be analyzed. In many EWASs, it is not possible to analyze the target tissue in large numbers of live humans, and consequently surrogate tissues are employed, most commonly blood. But there is as yet no evidence demonstrating that blood is more informative than buccal cells, the other easily accessible tissue. To assess the potential of buccal cells for use in EWASs, we performed a comprehensive analysis of a buccal cell methylome using whole-genome bisulfite sequencing. Strikingly, a buccal vs. blood comparison reveals >6X as many hypomethylated regions in buccal. These tissue-specific differentially methylated regions (tDMRs) are strongly enriched for DNaseI hotspots. Almost 75% of these tDMRs are not captured by commonly used DNA methylome profiling platforms such as Reduced Representational Bisulfite Sequencing and the Illumina Infinium HumanMethylation450 BeadChip, and they also display distinct genomic properties. Buccal hypo-tDMRs show a statistically significant enrichment near SNPs associated to disease identified through GWASs. Finally, we find that, compared with blood, buccal hypo-tDMRs show significantly greater overlap with hypomethylated regions in other tissues. We propose that for non-blood based diseases/phenotypes, buccal will be a more informative tissue for EWASs.

overall_design: Bisulphite converted DNA from the 22 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip


title: Potential capacity of aptamers to trigger immune activation in human blood

city: Tübingen

first: Meltem

last: Avci-Adali

address: Calwerstr. 7/1

institute: UKT

summary: Target specific short single-stranded DNA (ssDNA) molecules, called aptamers, are auspicious ligands for numerous in vivo applications. However, aptamers are synthetic molecules, which might be recognized by the immune cells in vivo and induce an activation of the innate immune system. Thus, immune activation potential of synthetic ssDNA oligonucleotides (ODNs) was determined using a well established closed-loop circulation model. Fresh human blood was incubated at 37°C for 2 or 4 hours with ssDNA ODNs (SB_ODN) or CpG ODN as positive control. Transcriptional changes were determined by microarray analyses. Blood samples containing SB_ODN demonstrated after 4 hours a significant regulation of 295 transcripts. Amongst others, CCL8, CXCL10, CCL7 and CXCL11 were highest regulated genes. Gene Ontology terms and KEGG pathway analyses exhibited that the differentially expressed genes belong to the transcripts that are regulated during an immune and inflammatory response, and were overrepresented in TLR signaling pathway. This study shows for the first time the potential of aptamers to activate immune system after systemic application into the human blood. Thus, we highly recommend performing of these preclinical tests with potential aptamer-based therapeutics.

overall_design: To evaluate the influence of synthetic ssDNA oligonucleotides (SB_ODN, CpG_ODN) on the cells of circulating peripheral blood (n=3), the samples were divided into 7 groups, 0h_without ssDNA, 2h_without ssDNA, 2h_with SB_ODN, 2h_with CpG_ODN, 4h_without ssDNA, 4h_with SB_ODN, 4h_with CpG_ODN. Baseline value samples (0h_without ssDNA) were obtained after blood collection without rotating in the closed-loop model. Negative control samples (2h_without ssDNA and 4h_without ssDNA) did not include oligonucleotides but rotated in the closed-loop model.

first: Heidrun

last: Steinle

first: Tatjana

last: Michel

first: Christian

last: Schlensak

first: Hans

middle: P

last: Wendel


title: FOXO3a Is A Major Target Of Inactivation By PI3K/AKT Signaling In Aggressive Neuroblastoma

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: Neuroblastoma is a pediatric tumor of the peripheral sympathetic nervous system with a highly variable prognosis. Activation of the PI3K/AKT pathway in neuroblastoma is correlated with poor patient prognosis, but the precise downstream effectors mediating this effect have not been determined. Here, we identify the forkhead transcription factor FOXO3a as a key target of the PI3K/AKT pathway in neuroblastoma. FOXO3a expression was elevated in low stage neuroblastoma tumors and normal embryonal neuroblasts, but reduced in late stage neuroblastoma. Inactivation of FOXO3a by AKT was essential for neuroblastoma cell survival. Treatment of neuroblastoma cells with the dual PI3K/mTOR inhibitor PI-103 activated FOXO3a and triggered apoptosis. This effect was rescued by FOXO3a silencing. Conversely, apoptosis induced by PI-103 or the AKT inhibitor MK-2206 was potentiated by FOXO3a overexpression. Further, levels of total or phosphorylated FOXO3a correlated closely with apoptotic sensitivity to MK-2206. In clinical specimens, there was an inverse relationship between gene expression signatures regulated by PI3K signaling and FOXO3a transcriptional activity. Moreover, high PI3K activity and low FOXO3a activity were each associated with an extremely poor prognosis. Our work indicates that expression of FOXO3a and its targets offer useful prognostic markers as well as biomarkers for PI3K/AKT inhibitor efficacy in neuroblastoma.

overall_design: Affymetrix U133 Plus 2.0 profiling of SY5Y-TetR-FOXO3A cells treated with doxycycline and/or the PI3K/mTOR inhibitor PI-103. Each condition profiled in triplicate.

first: Evan

last: Santo

first: Peter

last: Stroeken

last: v Sluis

first: Jan

last: Koster

first: Rogier

last: Versteeg

first: Ellen

last: Westerhout


city: Tampa

first: Amer

last: Beg

state: FL

address: 12902 Magnolia Drive

institute: Moffitt Cancer Center

summary:
Effect of NF-kB inhibition and activation on gene expression in mouse and human lung cancer cell-lines.

Publication reference: Hopewell, E.L., Zhao, W., Fulp, W.J., Bronk, C.C., Lopez, A.S., Massengill, M., Antonia, S., Celis, E., Haura, E.B., Enkemann, S.A., Chen, D.T., and Beg, A.A. 2013. Lung tumor NF-kappaB signaling promotes T cell-mediated immune surveillance. The Journal of clinical investigation 123:2509-2522.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Cells were transduced with control retrovirus (MiG) or MiG retrovirus expressing IkB alpha super-repressor (SR) mutant (S32, S36 to A mutations) or activated IKK beta (S177, S181 to E mutations). Cells were FACS sorted by GFP expression. RNA isolated from these cells was used for microarray studies.

middle: A

first: Emily

middle: L

last: Hopewell

first: Steven

last: Enkemann


title: Expression data from PDE1C knockdown glioblastoma short-term cultures

city: Wolverhampton

first: Farjana

middle: B

last: Rowther

address: Wulfruna Street

department: BRAIN TUMOUR RESEARCH LAB

institute: University of Wolverhampton

summary: In our lab we detected focal genomic amplification of PDE1C in 90% of short term GBM cultures. Knocking down of PDE1C was associated with compromised capacity opf these cultures to proliferate, migrate and invade. Therefore we carried out affymetric whole genome expression analysis to identify the down stream gene effectors of this function effects.

overall_design: IN1472 and IN1760 - 2 GBM short term cultures were transfected with siRNA either for PDE1C (siPD) or non-targeting (siNT) and its down gene effectors were studied.


title: Peripheral blood mononuclear cell (PBMC) gene expression in healthy adults rapidly transported to high altitude

status: Public on Apr 30 2013

city: Rochester

first: Nicole

last: Herman

state: MN - Minnesota

address: 200 1st St SW

institute: Mayo Clinic

summary: Differential expression analysis comparing healthy volunteers at sea level and after acute exposure to altitude

overall_design:
PBMCs were isolated from healthy volunteers participating in the United States Antarctic Program.  Array data was processed
using the Affymetrix HG U133 Plus 2 array

first: N

first: D

last: Grill

first: P

last: Anderson

first: A

middle: D

last: Miller

first: J

last: Johnson

first: K

last: O'Malley

first: M

last: Ceridon Richert

first: B


title: Continuous analysis captures cellular states that reflect dominant effects of the HTT CAG repeat in human lymphoblastoid cell lines.

city: Boston

first: Jong-Min

last: Lee

state: MA

department: CHGR

institute: MGH

summary: In Huntington’s disease (HD), expanded HTT CAG repeat length correlates strongly with age at motor onset, indicating that it determines the rate of the disease process leading to diagnostic clinical manifestations. Similarly, in normal individuals, HTT CAG repeat length is correlated with biochemical differences that reveal it as a functional polymorphism.  Here, we tested the hypothesis that gene expression signatures can capture continuous, length-dependent effects of the HTT CAG repeat.  Using gene expression datasets for 107 HD and control lymphoblastoid cell lines, we constructed mathematical models in an iterative manner, based upon CAG correlated gene expression patterns in randomly chosen training samples, and tested their predictive power in test samples.  Predicted CAG repeat lengths were significantly correlated with experimentally determined CAG repeat lengths, whereas models based upon randomly permuted CAGs were not at all predictive.  Predictions from different batches of mRNA for the same cell lines were significantly correlated, implying that CAG length-correlated gene expression is reproducible.  Notably, HTT expression was not itself correlated with HTT CAG repeat length. Taken together, these findings confirm the concept of a gene expression signature representing the continuous effect of HTT CAG length and not primarily dependent on the level of huntingtin expression.  Such global and unbiased approaches, applied to additional cell types and tissues, may facilitate the discovery of therapies for HD by providing a comprehensive view of molecular changes triggered by HTT CAG repeat length for use in screening for and testing compounds that reverse effects of the HTT CAG expansion.

overall_design: To evaluate the continuous analytical approach as a strategy to discover the molecular consequences of the HTT CAG repeat, genome-wide gene expression datasets were generated from a panel of 107 human lymphoblastoid cell lines with HTT CAGs spanning the entire spectrum of allele sizes.


title: Transgene-free iPSCs generated from small volume peripheral blood nonmobilized CD34+ cells

status: Public on Apr 26 2013

city: Bethesda

first: Timothy

middle: G

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

summary: A variety of somatic cells can be reprogrammed to induced pluripotent stem cells (iPSCs), but the small number of CD34+ hematopoietic stem cells (HSCs) present in non-mobilized peripheral blood (PB) would be a convenient and desirable starting target. We report here a simple method for targeting derivation of iPSC from non-mobilized PB CD34+ HSCs using immunobead purification and 2-4 day culture to achieve enrichment of CD34+ HSCs to 80±9%, followed by reprogramming transduction with loxP-flanked polycistronic (Oct4, Klf4, Sox2, and c-Myc) STEMCCA-loxP lentivector at an MOI of 2. Our yield was 4.7±2.2 iPSC colonies (n=12) per 20 mL non-mobilized peripheral blood, where most colonies had single copy STEMCCA-loxP that was easily excised by transient transfection expression of Cre. Resultant iPSC clones expressed pluripotent cell markers, had genomic methylation pattern closely matching embryonic stem cells, and generated teratomas containing tissues of all three germ lineages in immunodeficient mice. Furthermore, we conclude that these iPSC are derived from the non-mobilized CD34+ HSCs enriched from PB rather than from any lymphocyte or monocyte contaminants because they lacked somatic rearrangements typical of T or B lymphocytes, and because we demonstrated that purified CD14+ monocytes do not yield iPSC colonies under these reprogramming conditions.

overall_design: Comparison of pluripipotent, induced pluripotent, and differentiated cell types

first: Randall

middle: K

last: Merling

first: Colin

last: Sweeney

first: Uimook

last: Choi

first: Suk

middle: S

last: DeRavin

first: Francisco

last: Otaizo-Carrasquero

first: Jason

last: Pan

first: Gilda

last: Linton

first: Lifeng

last: Chen

first: Sherry

last: Koontz

first: Narda

last: Theobald

first: Harry

last: Malech


title: Gene expression analysis of primitive neuroectodermal tumors

city: Nottingham

first: Hazel

middle: Anne

last: Rogers

address: Medical School

department: Clinical Sciences

institute: University of Nottingham

summary:
Central nervous system primitive neuroectodermal tumors (CNS PNET) and medulloblastomas are both embryonal tumors that predominantly occur in children.
We used microarrays to analyse a cohort of CNS PNETs and medulloblastomas to identify gene expression related to tumor subgroups.

overall_design: RNA extracted from 23 frozen tumor samples, plus a commercial fetal brain sample, was analysed using Affymetrix U133 plus 2.0 arrays. Tumour subgroups, based on gene expression, were identified using clustering methods.

first: Suzanne

last: Miller

first: James

last: Lowe

first: Graham

last: Ball

first: Beth

last: Coyle

first: Richard

last: Grundy


title: Targeting proximal tubule mitochondrial dysfunction attenuates the renal disease of methylmalonic acidemia

city: bethesda

first: abdel

last: elkahloun

address: 50 south dr

institute: nih

summary: Isolated methylmalonic acidemia (MMA) is a pleiotropic enzymatic defect of branched-chain amino acid oxidation most commonly caused by deficiency of methylmalonyl-CoA mutase (MUT). End stage renal disease (ESRD) is emerging as an inevitable disease-related complication, recalcitrant to conventional therapies and liver transplantation. To establish a viable model of MMA-associated renal disease, methylmalonyl-CoA mutase (Mut) was expressed in the liver of Mut -/- mice as a stable transgene under the control of an albumin (INS-Alb-Mut) promoter. Mut -/- ;TgINS-Alb-Mut  mice were rescued from the neonatal lethality displayed by Mut -/- mice and manifested a decreased glomerular filtration rate (GFR), chronic tubulointerstital nephritis (CTIN) and prominent ultrastructural changes in the proximal tubular mitochondria, replicating precisely the renal manifestations seen in a large MMA patient cohort.

overall_design: To explore the pathophysiological changes that underlie the renal disease of MMA, we compared gene expression profiles of whole kidney mRNA samples between 4 female Mut +/+, Mut +/- and Mut -/- ;TgINS-Alb-Mut mice after they ingested a HP diet for 2 months. Females were used because more survived the dietary challenge, whereas the histology, ultrastructure and GFR effects were identical between sexes

first: Irini

last: Manoli

first: Justin

middle: R

last: Sysol

first: Abdel

last: Elkahloun

first: Charles

last: Venditti


title: Gene expression profiling of murine innate lymphoid cells

city: Philadelphia

first: Laurel

last: Monticelli

state: PA

address: 344 BRB II/III, 421 Curie Blvd

department: Microbiology

institute: University of Pennsylvania

summary:
Innate lymphoid cells (ILCs) are a recently recognized heterogenous group of immune cells that are critical in orchestrating immunity and inflammation in the intestine, but whether ILCs influence immune responses or tissue homeostasis at other mucosal sites remains poorly characterized. Here we identify a population of lung-resident ILCs in mice and humans that expressed the alloantigen Thy-1 (CD90), interleukin 2 (IL-2) receptor a-chain (CD25), IL-7 receptor a-chain (CD127) and the IL-33 receptor subunit T1-ST2. Notably, mouse ILCs accumulated in the lung after infection with influenza virus, and depletion of ILCs resulted in loss of airway epithelial integrity, diminished lung function and impaired airway remodeling. These defects were restored by administration of the lung ILC product amphiregulin. Collectively, our results demonstrate a critical role for lung ILCs in restoring airway epithelial integrity and tissue homeostasis after infection with influenza virus.

As part of this study, we performed gene expression profiling to examine how the transcriptional signatures compared between murine naïve group 2 lung ILC and group 3 splenic LTi cell populations.

overall_design: Group 2 ILCs from the lung (Lin- CD90+ CD25+ T1/ST2+) and Group 3 LTi cells from the spleen (Lin- CD90+ CD25+ CD4+) were sort-purified from naive wildtype C57BL/6 mice using BD FACS Aria. Four biological replicates were collected, each replicate containing 1.5 x 104 to 2 x104 cells sorted to a purity >97% from six pooled lungs (ILCs) or 10 pooled spleens (LTi cells). Cells were sorted directly into TRIzol LS (Invitrogen), then mRNA was isolated, amplified, labeled, and hybridized to Affymetrix GeneChip (Mouse Gene 1.0 ST).

first: David

last: Artis


title: Microarray Analysis of differential gene expression in peripheral blood cells of patients with human essential hypertension

city: Beijing,China

first: MELVIN

last: KORKOR

address: 18 Life Science Parkway, Changping District, Beijing,China

department: INTERNAL MEDICINE

country: China

institute: JILIN UNIVERSITY

summary:
The polygenic nature of essential hypertension and its dependence on environmental factors pose a challenge for biomedical research. We hypothesized that microarray analysis of differential gene expression in peripheral blood cells would distinguish patients with hypertension from normotensive controls.
We utilized microaaray analysis of differential gene expression in peripheral blood cells to identify differences in transcription profile of human essential hypertension compared with normotensive volunteers.

overall_design: Samples were pooled from participants who met with our recruitment criteria for RNA extraction and hybridization on Affymetrix Gene Chips Human Genome U133 Plus 2.0 Array. Experiments were performed at CapitalBio Corporation (Beijing, China)

first: Melvin

last: Korkor

first: Zhi

middle: H

last: Zhao

first: Ping

last: Yang


title: Expression data from GBM and normal neural CD133+ and CD133- cells

city: Stanford

first: Hadi

last: Zarkoob

state: California

address: 450 Serra Mall  Stanford

institute: Stanford University

summary: We use gene expression data to provide a three-faceted analysis on the links between molecular subclasses of glioblastima, epithelial-to mesenchymal transition (EMT) and CD133 cell surface protein. The contribution of this paper is three-folded: First, we used a newly identified signature for epithelial-to-mesenchymal transition in human mammary epithelial cells, and demonstrated that genes in this signature have significant overlap with genes differentially expressed in all known GBM subtypes. However, the overlap between the genes up-regulated in the mesenchymal subtype of GBM and in the EMT signature was more significant than other GBM subtypes. Second, we provided evidence that there is a negative correlation between the genetic signature of EMT and that of CD133 cell surface protein, a putative marker for neural stem cells. Third, we studied the correlation between GBM molecular subtypes and the genetic signature of CD133 cell surface protein. We demonstrated that the mesenchymal and neural subtypes of GBM have the strongest correlations with the CD133 genetic signature. While the mesenchymal subtype of GBM demonstrates similarity with the signatures of both EMT and CD133, it also demonstrates some differences with each of these signatures that is partly due to the fact that the signatures of EMT and CD133 are inversely related to each other. Taken together this data sheds light on role of the mesenchymal transition and neural stem cells, and their mutual interaction, in molecular subtypes of glioblastoma multiforme.

overall_design: Two GBM samples (BT1 and BT2) and two normal samples (N1 and N2) were sorted for CD133 expression (overall eight samples, four positive and four negative).

first: Joseph

last: Taube

first: Sheila

last: Singh

first: Sendurai

last: Mani

first: Mohammad

last: Kohandel


title: Genome-scale methylome profiling of pheochromocytomas and paragangliomas with Illumina HumanMethylation450 arrays

city: Paris

first: Eric

last: Letouzé

address: 15 rue de l'école de médecine

institute: Ligue Contre Le Cancer

summary: Genome-scale DNA methylation was analyzed in a cohort of paragangliomas to identify DNA methylation changes.

overall_design: Bisulfite converted DNA from 22 fresh frozen paragangliomas and 2 normal adrenal medulla samples were hybridized to Illumina HumanMethylation450 BeadChips.

first: Anne-Paule

last: Gimenez-Roqueplo

first: Judith

last: Favier


title: Expression data from mouse cecum

status: Public on Apr 25 2013

city: Davis

first: Michael

last: George

address: 451 Health Sciences Drive

department: Medical Microbiology and Immunology

institute: University of California, Davis

summary:
To adapt the lives of organisms to the day-night cycle, evolution has built a complex machinery, whose molecular components are able to anticipate and drive changes in organism behavior and metabolism. A mutual bidirectional interaction exists between circadian abnormalities and development of diseases.
Microarrays were used to determine whether circadian regulation occurs at the transcriptional level in response to Salmonella Typhimurium infection.

overall_design: Cecal tissues from wild type mice and Clock mutant mice infected with S. Typhimurium or mock control at two circadian times (10am and 10pm) were used for RNA extraction and hybridization on Affymetrix microarrays.

first: Marina

last: Bellet


title: Global Gene Expression Analysis of Term Amniotic Fluid Cell-Free Fetal RNA

status: Public on Apr 23 2013

city: Medford

first: Heather

middle: C

last: Wick

address: 161 College Ave

department: Department of Computer Science

institute: Tufts University

summary:
The objective of this study was to identify the tissue expression patterns and biological pathways enriched in term amniotic fluid cell-free fetal RNA by comparing functional genomic analyses of term and second-trimester amniotic fluid supernatants.
There were 2,871 significantly differentially regulated genes. In term amniotic fluid, tissue expression analysis showed enrichment of salivary gland, tracheal, and renal transcripts as compared with brain and embryonic neural cells in the second trimester. Functional analysis of genes upregulated at term revealed pathways that were highly specific for postnatal adaptation such as immune function, digestion, respiration, carbohydrate metabolism, and adipogenesis. Inflammation and prostaglandin synthesis, two key processes involved in normal labor, were also activated in term amniotic fluid.

overall_design: This was a prospective whole genome microarray study comparing eight amniotic fluid samples collected from eight women at term who underwent prelabor cesarean delivery and eight second-trimester amniotic fluid samples from routine amniocenteses. A functional annotation tool was used to compare tissue expression patterns in term and second-trimester samples. Pathways analysis software identified physiologic systems, molecular and cellular functions, and upstream regulators that were significantly overrepresented in term amniotic fluid.

first: Lisa

last: Hui

first: Andrea

last: Edlow

first: Janet

last: Cowan

first: Diana

middle: W

last: Bianchi


title: TRNP1 regulates expansion and folding of the mammalian cerebral cortex by control of radial glial fate

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

summary: Evolution of the mammalian brain encompassed a remarkable increase in size of cerebral cortex, including tangential and radial expansion, but the mechanisms underlying these key parameters are still largely unknown. Here, we identified the novel DNA associated protein TRNP1 as a regulator of cerebral cortical expansion in both these dimensions. Gain and loss of function experiments in the mouse cerebral cortex in vivo demonstrate that high Trnp1 levels promote neural stem cell self-renewal and tangential expansion, while lower levels promote radial expansion resulting in a potent increase in the generation of intermediate progenitors and outer radial glial cells resulting in folding of the otherwise smooth murine cerebral cortex. Remarkably, TRNP1 expression levels exhibit regional differences also in the cerebral cortex of human fetuses anticipating radial or tangential expansion respectively. Thus, the dynamic regulation of TRNP1 is critical to regulate tangential and radial expansion of the cerebral cortex  in mammals.

overall_design: We performed gene expression microarray analysis on embryonic mouse cerebral cortex derived from Trnp1 knockdown and control animals.

first: Ronny

last: Stahl

first: Tessa

last: Walcher

first: Camino

last: de Juan Romero

first: Martin

last: Irmler

first: Victor

last: Borrell

first: Robert

last: Blum

first: Magdalena

last: Goetz


title: The histone demethylase Jarid1b ensures faithful mouse development by protecting developmental genes from aberrant H3K4me3 [Affymetrix]

city: Copenhagen

first: Sandra

middle: Ursula

last: Schmitz

address: Ole Maaløes Vej 5

country: Denmark

institute: Biotech Research and Innovation Centre

summary:
Embryonic development is tightly regulated by transcription factors and chromatin-associated proteins. H3K4me3 is associated with active transcription and H3K27me3 with gene repression, while the combination of both keeps genes required for development in a plastic state. Here we show that deletion of the H3K4me2/3 histone demethylase Jarid1b (Kdm5b/Plu1) results in major neonatal lethality due to respiratory failure. Jarid1b knockout embryos have several neural defects including disorganized cranial nerves, defects in eye development and increased incidences of exencephaly. Moreover, in line with an overlap of Jarid1b and Polycomb targets genes, Jarid1b knockout embryos display homeotic skeletal transformations typical for Polycomb mutants. Genome-wide analysis demonstrated that normally inactive genes encoding developmental regulators acquire aberrant H3K4me3 in early Jarid1b knockout embryos. H3K4me3 accumulates as embryonic development proceeds, leading to increased expression of neural master regulators in knockouts. Taken together, these results suggest that Jarid1b contributes to mouse development by protecting developmental genes from inappropriate acquisition of active histone modifications.
* Lack of Jarid1b leads to major neonatal lethality and defects in neural systems
* Jarid1b mutants display homeotic skeletal transformations
* H3K4me3 is increased at inactive transcriptional regulators in Jarid1b-/- embryos
* Chromatin changes are accompanied by elevated levels of key neural transcription factors

overall_design: RNA was extracted from heads of E8.5 embryos, three pools of 4 heads each were used per genotype

first: Mareike

last: Albert


title: HeLa cells consist of two cell types, as evidenced by cytochemical staining for alkaline phosphatase activity: A possible model for cancer stem cell study

city: Kagoshima

first: Masahiro

last: Sato

state: Kagoshima

address: 8-35-1 Sakuragaoka

department: Frontier Science Research Center

institute: Kagoshima University

summary: Alkaline phosphatase (ALP) is known to be a marker for several somatic stem cells and cancer cells. We found that human squamous cell carcinoma HeLa cells are comprised by ALP-positive and negative cells. Single cell-derived colony assay revealed that the former cells are labile with respect to ALP activity, but the latter are stable. We cloned ALP-negative cells from the HeLa cells, and named H-1 clone. DNA microarray analysis revealed that gene expression pattern of H-1 cells is almost the same with that of their parental HeLa cells, but several genes for glycoprotein hormone alpha chain, ras-related and estrogen-regulated growth inhibitor, ALP, and Frizzled-10 was respectively 18.2, 9.6, 9.2 and 10.5–fold are upregulated in the HeLa cells. Although there is no evidence that the ALP-positive cells are cancer stem cells (CSCs) at present, HeLa cells comprised by ALP-positive and -negative cells may be a good model for CSC study in future.

overall_design: HeLa cells consist of two cell types, namely alkaline phosphatase (ALP)-positive and negative cells. To distinguish gene expression pattern between these two types of cells, microarray analysis was performed using HeLa cells (parental cell line; a mixture of ALP-positive and negative cells) and H-1 cells, ALP-negative cells derived from HeLa cells

first: Naoko

last: Kubota

first: Emi

last: Inada

first: Issei

last: Saitoh

first: Masato

last: Ohtsuka

first: Shingo

last: Nakamura

first: Takayuki

last: Sakurai

first: Satoshi

last: Watanabe


title: Inactive or moderately active human promoters are enriched for inter-individual epialleles [Methylation BeadChip]

status: Public on Apr 22 2013

city: Cambridge

first: Thomas

last: Down

address: Tennis Court Road

department: WT/CRUK Gurdon Institute

institute: University of Cambridge

summary: We first demonstrate that non-genetically determined inter-individual differentially methylated regions (iiDMRs) can be temporally stable for at least two years. Then, we show that iiDMRS are associated with concomitant changes in chromatin state as measured by inter-individual differences in the levels of the histone variant H2A.Z. However, the correlation of promoter iiDMRs with gene expression is negligible and this correlation is not improved even by integrating H2A.Z information. We find that most promoter epialleles, whether genetically or non-genetically determined, are associated with low levels of transcriptional activity, depleted for house keeping genes, and either depleted for H3K4me3/enriched for H3K27me3, or lacking both these marks in human embryonic stem cells. These findings validate in an independent cohort. Interestingly, the key features of iiDMRs are reminiscent of those previously observed for promoters that undergo hyper-methylation in various cancers, in vitro cell culture, and human chronological ageing.

overall_design:
DNA Methylation, H2A.z ChIP-seq, RNA-seq (submitted) separately were collected for five normal individuals (samples with "T" prefixes).   T21/T22 and T31/T32 are monozygotic twins.  Further DNA methylation data was collected from and additional two pairs of MZ twins with technical replication (samples with "C" prefixes - the three digits are pair number, individual number, and replicate number).
Bisulphite converted DNA was hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: C

last: Gemma

first: S

middle: V

last: Ramagopalan

first: T

first: H

last: Beyan

first: M

middle: I

last: Hawa

last: Holland

first: P

last: Hurd

first: G

last: Giovannoni

first: R

last: Leslie

last: Ebers

first: V

last: Rakyan


title: Optimization of Direct Fibroblast Reprogramming to Cardiomyocytes Using Calcium Activity as a Functional Measure of Success

first: Russell

last: Addis

address: 3400 Civic Center Blvd, Bldg 421, SCTR 9-196

department: Cell and Developmental Biology

summary: Direct conversion of fibroblasts to induced cardiomyocytes (iCMs) has great potential for regenerative medicine. Recent publications have reported significant progress, but the evaluation of reprogramming has relied upon non-functional measures such as flow cytometry for cardiomyocyte markers or GFP expression driven by a cardiomyocyte-specific promoter. The issue is one of practicality: the most stringent measures - electrophysiology to detect cell excitation and the presence of spontaneously contracting myocytes - are not readily quantifiable in the large numbers of cells screened in reprogramming experiments. However, excitation and contraction are linked by a third functional characteristic of cardiomyocytes:  the rhythmic oscillation of intracellular calcium levels.  We set out to optimize direct conversion of fibroblasts to iCMs with a quantifiable calcium reporter to rapidly assess functional transdifferentiation.  We constructed a reporter system in which the calcium indicator GCaMP is driven by the cardiomyocyte-specific Troponin T promoter. Using calcium activity as our primary outcome measure, we compared several published combinations of transcription factors along with novel combinations in mouse embryonic fibroblasts. The most effective combination consisted of Hand2, Nkx2.5, Gata4, Mef2c, and Tbx5 (HNGMT). This combination is >50-fold more efficient than GMT alone and produces iCMs with cardiomyocyte marker expression, robust calcium oscillation, and spontaneous beating that persists for weeks following inactivation of reprogramming factors.  HNGMT is also significantly more effective than previously published factor combinations for the transdifferentiation of adult mouse cardiac fibroblasts to iCMs.  Quantification of calcium function is a convenient and effective means for the identification and evaluation of cardiomyocytes generated by direct reprogramming.  Using this stringent outcome measure, we conclude that HNGMT produces iCMs more efficiently than previously published methods.

overall_design: Mouse embryonic fibroblasts were treated with different combinations of transcription factors to drive transdifferentiation to induced cardiomyocytes (iCMs). Putative iCMs were enriched by zeocin selection. Zeocin resistance was conferred to iCMs via the TroponinT-GCaMP5-Zeo lentiviral reporter.

first: Jamie

last: Ifkovits

first: Filipa

last: Pinto

first: Lori

last: Kellam

first: Paul

last: Esteso

first: Stacey

last: Rentschler

first: Nicolas

last: Christoforou

first: Jonathan

last: Epstein

first: John

last: Gearhart


title: Doxycycline alters metabolism and proliferation of human cell lines

city: Los Angeles

first: William

middle: Juster

last: Sullivan

address: 354-06 BSRB, 615 Charles E. Young Drive S

department: Biological Chemistry

institute: University of California, Los Angeles

summary: The tetracycline antibiotics are widely used in biomedical research as mediators of inducible gene expression systems. Despite many known effects of tetracyclines on mammalian cells -- including inhibition of the mitochondrial ribosome -- there have been few reports on potential off-target effects at concentrations commonly used in inducible systems. Here, we report that in human cell lines, commonly used concentrations of doxycycline change gene expression patterns and concomitantly shift metabolism towards a more glycolytic phenotype, evidenced by increased lactate secretion and reduced oxygen consumption. We also show that these concentrations are sufficient to slow proliferation and alter cell cycle progression in vitro. These findings suggest that researchers using doxycycline in inducible expression systems should design appropriate controls to account for potential confounding effects of the drug on cellular metabolism.

overall_design: Total RNA was extracted from MCF12A cells treated with either vehicle control or Dox at 1 ug/mL. The experiment was performed in biological triplicate. Microarray results were processed using the RMA method.

first: Ethan

last: Ahler

middle: J

first: Ashley

last: Cass

first: Daniel

last: Braas

first: Autumn

last: York

first: Steven

last: Bensinger

first: Thomas

last: Graeber

first: Heather

last: Christofk


title: Genes regulated by miR-203 in breast cancer cell line MDA-MB-231

city: Los angeles

first: Xiangming

last: Ding

address: 650 Charles E Young Dr S, Los Angeles, CA 90095

institute: UCLA

summary: To investigate the mechanism through which miR-203 inhibited the breast cancer cell invasion, we overpression miR-203 in MDA-MB-231 cell line and performed a microarray to examine the genes which maybe targeted and down-regulated by miR-203.

overall_design: We made a stable cell line(MB231/miR-203) which overexpressing miR-203 and a control cell line (MB231/EV) which expressing a contrlol vector. Total RNA were extracted from these two cell lines and subject to microarray.

first: Cun-yu

last: Wang


title: HDAC Inhibitors induce tumor cell-selective pro-apoptotic transcriptional responses.

city: Clayton

first: Wei

last: Shi

state: Victoria

address: Wellington Rd

country: Australia

institute: Monash University

summary:
The identification of recurrent somatic mutations in genes encoding epigenetic enzymes, coupled with biochemical studies demonstrating aberrant recruitment of epigenetic enzymes such as histone deacetylases (HDACs) and histone methyltransferases (HMTs) to promoter regions through association with oncogenic fusion proteins such as PML-RARα and AML1-ETO has provided a strong rationale for the development compounds that target the epigenome for the treatment of cancer.  HDAC inhibitors (HDACi) are potent inducers of tumor cell apoptosis but it remains unclear why tumor cells are selectively sensitive to HDACi-induced cell death.
Herein we assessed the biological and molecular responses of normal and transformed cells to the FDA-approved HDACi vorinostat.  Both HDACi selectively killed cells of diverse tissue origin that had been transformed through the serial introduction of different oncogenes. Time course microarray expression profiling revealed that normal and transformed cells transcriptionally responded to vorinostat treatment. Over 4200 genes responded differently to vorinostat in normal and transformed cells and gene ontology and pathway analyses identified a tumor-cell-selective pro-apoptotic gene-expression signature that consisted of BCL2 family genes.  In particular, HDACi induced tumor cell-selective upregulation of the pro-apoptotic gene BMF and downregulation of the pro-survival gene BCL2A1 encoding BFL-1.  Maintenance of BFL-1 levels in transformed cells through forced expression conferred vorinostat resistance indicating that specific and selective engagement of the intrinsic apoptosis pathways underlies the tumor cell-selective apoptotic activities of these agents. The ability of HDACi to affect the growth and survival of tumor cells whilst leaving normal cells relatively unharmed is fundamental to their successful clinical application. This study provides new insight into the transcriptional effects of HDACi in human donor-matched normal and transformed cells, and identifies molecules and pathways that could underpin the tumor-selective cytotoxic activity of these compounds.

overall_design: Whole genome expression profiling was performed for vorinostat-treated samples and control samples (DMSO vehicle control). Fourteen samples were included in this study. Each sample has three biological replicates, making forty-two arrays in total.

first: Jessica

middle: E

last: Bolden

first: Kacper

last: Jankowski

first: Flora

last: Kahn

first: Leonie

last: Cluse

first: Karen

last: MacKenzie

first: Gordon

last: Smyth

first: Ricky

last: Johnstone


title: Expression data from uncastrasion and castration tumor from LNCAP Orhotopic xenograft models of prostate cancer

status: Public on Apr 20 2013

city: tianjin

first: ning

last: jiang

address: hexi district pingjiang road 23

department: urology institute

institute: tianjin medical university

summary:
To identify molecular singnal alterations between androgen dependent prostate cancer and castration resistant prostate cancer, we performed interspecies comparative microarray analyses using RNAs prepared from uncastrasion and castration tumor from LNCAP Orhotopic xenograft models of prostate cancer.
microarray data from uncastrasion and castration tumor revealed that the gene expression profile is most significantly altered in between androgen dependent prostate cancer and castration resistant prostate cancer. Comparative analyses of LNCAP Orhotopic xenograft models of prostate cancer showed that genes involved in androgen dependent and androgen independent tumor were significantly altered.

overall_design: We prepared RNA samples from 4 samples uncastrasion and 4 samples castration tumors from LNCAP Orhotopic xenograft models of prostate cancer . High-quality RNA samples were subjected to microarray analysis using the Affymetrix Human Gene 2.0 ST platform, and only those results that passed examinations for quality assurance and quality control of the Human Gene 2.0 ST arrays were retrieved. In total, we obtained gene expression profiles from the following samples: 4 samples uncastrasion and 4 samples castration tumors

first: Ning

last: Jiang

first: Yuanjie

last: Niu

first: Amilcar

last: Flores-Morales


title: Large Granular Lymphocyte Leukemia Mesenchymal Stem Cells

city: Tampa

first: Adam

last: Mailloux

address: 12902 Magnolia Drive

department: Immunology

institute: Moffitt Cancer Center & Research Institute

summary:
The bone marrow microenvironment in Large Granular Lymphocyte Leukemia (LGLL) patients has been unexplored for it’s role in the development of cytopenias, which lead to complications resulting in the most prominent causes of morbidity and mortality.
We used microarrays on primary mesenchymal stem cell (MSC) cultures isolated from bone marrow aspirates from LGLL patients to identify genetic programs that may lead to the observed profibrotic and extrinsically senescent phenotype.

overall_design: Isolated primary MSC cultures were maintained under reduced oxygen conditions (2%).  All cultures displayed trilineage pluripotency (adipogenesis, osteogenesis, and chondrogenesis).  For comparison, normal MSC cultures in early passage (p2-3; same number of population doublings as the LGLL MSCs) and later passage (p7-9; same time spent in culture as the LGLL MSCs) are included.

first: Ling

last: Zhang

first: Cody

last: Wei

first: Steven

last: Enkemann

first: Sean

last: Yoder

first: Gregory

last: Bloom

first: Lubomir

last: Sokol

first: Lynn

last: Moscinski

first: John

middle: M

last: Bennett

middle: P

last: Loughran

first: Pearlie-K

last: Epling-Burnette


title: Acute myeloid leukemia with CEBPA double-mutations harbors in 76.8% of cases concomitant molecular mutations with TET2 and GATA2 alterations demonstrating strong prognostic impact

city: Munich

first: Andreas

last: Roller

address: Max-Lebsche-Platz 31

institute: Munich Leukemia Laboratory

summary: Acute myeloid leukemia (AML) with CEBPA mutations is determined as provisional entity in the current WHO. A difference in clinical outcome between single- (sm) and double-mutated (dm) cases has been reported, whereupon dm cases were shown to be associated with longer overall survival (OS). The occurrence and prognostic impact of concomitant molecular mutations in addition to CEBPAdm has not been assessed until now. Here, we investigated a cohort of 95 AML CEBPAdm cases for concomitant mutations. TET2 was found to be the most frequent mutation (32/94, 34.0%), followed by GATA2 (20/95, 21.0%), WT1 (13/95, 13.7%), DNMT3A (9/94, 9.6%), ASXL1 (9/95, 9.5%), NRAS (8/95, 8.4%), KRAS (3/94, 3.2%), IDH1/2 (6/95, 6.3%), FLT3-ITD (6/95, 6.3%), FLT3-TKD (2/95, 2.1%), NPM1 (2/95, 2.1%), and RUNX1 (1/94). No mutation was detected in MLL-PTD and TP53. With respect to prognostic impact, we observed that those cases harboring additional mutations in TET2 showed significant worse survival than wild-type cases (P=0.035), whereas GATA2 mutated cases showed improved survival (P=0.032). Further, using gene expression microarray analysis we identified no clear different clustering within the CEBPAdm cases with the distinct concomitant mutated genes. In conclusion, we demonstrated that 76.8% of CEBPAdm cases harbored additional alterations in other molecular markers and that CEBPA is a suitable MRD marker to control therapy.

overall_design: Total cohort contains 95 cases, but expression data available for 38 cases which were analyzed on Affymetrix HG-U133 Plus 2.0 arrays:  8 CEBPAdm and GATA2 mutated cases, 12 CEBPAdm and TET2 mutated cases, 7 CEBPAdm and ASXL1 mutated cases (n=3 showed an additional TET2 mutation) and 11 CEBPAdm without mutations in GATA2, TET2, and ASXL1.

first: Vera

last: Grossmann

first: Claudia

last: Haferlach

first: Niroshan

last: Nadarajah

first: Annette

last: Fasan

first: Sandra

last: Weissmann

first: Christiane

last: Eder

first: Elisa

last: Stopp

first: Wolfgang

last: Kern

first: Torsten

first: Alexander

last: Kohlmann

first: Susanne

last: Schnittger


title: LMP2A mediated gene expression changes in transfected CD10+ GCB cells

status: Public on Apr 19 2013

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

institute: Durham University

summary:
In this study, we have investigated the effect of LMP2A on gene expression in normal human GC B cells using a non-viral vector based system
Keywords: transfection of viral oncogene in normal human B cells

overall_design: Gene expression was compared between LMP2A-transfected and control vector-transfected GC B cells from three patients. RNA from the FACS-sorted transfected GC B cells was amplified. 10ug of fragmented cRNA was hybridized to HG-U133 Plus 2.0 microarrays. Differentially expressed probe sets were identified using limma with a fold change >1.3 and p < 0.01

first: Martina

last: Vockerodt

first: Eszter

last: Nagy

first: Zuzana

last: Prouzova

first: Alexandra

last: Schrader

first: Dieter

last: Kube

first: Martin

last: Rowe

first: Ciaran

middle: B

last: Woodman

first: Paul

last: Murray


title: Expression data from Control and HIRA knockdown cells

status: Public on Apr 18 2013

city: Glasgow

first: Peter

middle: D.

last: Adams

address: Switchback Rd, Bearsden

institute: University of Glasgow, Beatson Institute for Cancer Research

summary:
The HIRA chaperone complex, comprised of HIRA, UBN1 and CABIN1, collaborates with histone-binding protein ASF1a to incorporate histone variant H3.3 into chromatin in a DNA replication-independent manner. To better understand its function and mechanism, we integrated HIRA, UBN1, ASF1a and histone H3.3 ChIP-seq and gene expression analyses. Most HIRA-binding sites co-localize with UBN1, ASF1a and H3.3 at active promoters and active and weak/poised enhancers. At promoters, binding of HIRA/UBN1/ASF1a correlates with the level of gene expression. HIRA is required for deposition of histone H3.3 at its binding sites. There are marked differences in nucleosome and co-regulator composition at different classes of HIRA-bound regulatory site. Underscoring this, we report novel physical interactions between the HIRA complex and transcription factors, a chromatin insulator and an ATP-dependent chromatin-remodelling complex. Our results map the distribution of the HIRA chaperone across the chromatin landscape and point to different interacting partners at functionally distinct regulatory sites.
We used microarrays to detail the global programme of gene expression after knockdown of HIRA

overall_design: HeLa cells were nucleofacted with Dharmacon control siRNA and siRNA to HIRA and RNA was isolated 72 hours after transfection in four biological replicates

first: Taranjit

last: Rai

first: Tony

last: McBryan

middle: D


title: Expression data from Alzheimer's disease model  mouse

status: Public on Apr 17 2013

city: Fukuoka

first: Yusaku

last: Nakabeppu

state: Fukuoka

address: 3-1-1 Maidashi Higashi-ku

department: Department of Immunobiology and Neuroscience

institute: Medical Institute of Bioregulation, Kyushu University

summary:
To identify molecular pathological alterations in AD brains, we performed interspecies comparative microarray analyses using RNAs prepared from postmortem human brain tissues donated for the Hisayama study and hippocampal RNAs from the triple-transgenic mouse model of AD (3xTg-AD)
Three-way ANOVA of microarray data from frontal cortex, temporal cortex and hippocampus with presence/absence of AD and vascular dementia, and sex, as factors revealed that the gene expression profile is most significantly altered in the hippocampi of AD brains. Comparative analyses of the brains of AD patients and a mouse model of AD showed that genes involved in non-insulin dependent DM and obesity were significantly altered in both, as were genes related to psychiatric disorders and Alzheimer’s disease.

overall_design: 3xTg-AD-H mice harboring a homozygous Psen1M146V mutation and homozygous mutant transgenes for APPSwe and tauP301L, 3xTg-AD-h mice harboring hemizygous APPSwe and tauP301L transgenes with a homozygous Psen1M146V mutation, and non-transgenic control mice (non-Tg) were used in this study, (male, n=3 for each group). RNA samples prepared from hippocampi were subjected to microarray analysis using the Affymetrix Mouse Gene 1.0 ST platform (GPL6246).

first: Masaaki

last: Hokama


title: Gene expression in DN4 thymocytes from mice with an inducible deletion of Ikaros

city: Illkirch

first: Susan

last: Chan

address: 1, rue Laurent Fries

institute: IGBMC

summary: The aim of the experiment was to visualize genes under the control of Ikaros during early T cell development. We used mice carrying floxed Ikaros alleles that were crossed with the Rosa26-CreERT2 mice, and which were injected with tamoxifen for 4 days. DN4 thymocytes were sorted from 4 mice (5-6 week-old) which are positive or not for the Rosa26-CreERT2 transgene.

overall_design: DN4 cells were sorted from 2 Ikf/f Rosa26-CreERT2+ mice and 2 Ikf/f mice, which were all treated with tamoxifen for 4 days. Loss of Ikaros was confirmed in sorted cells from the Ikf/f Rosa26-CreERT2+ mice by western blot. Gene expression profiles were determined on total RNA from sorted cells with Affymetrix Mouse Gene arrays.

first: Philippe

last: Kastner


title: Hela SPAG4 siRNA

status: Public on Apr 16 2013

city: Tokyo

first: Imari

last: Mimura

address: 4-6-1 Komaba Meguro-ku

department: Laboratory for Systems Biology and Medicine

institute: Research Center for Advanced Science and Technology

summary: In order to clarify the downstream target genes of SPAG4, we performed knockdown of SPAG4 using siRNA both under normoxia and hypoxia.

overall_design: Hela cells are cultured for 24 hours under normoxia and hypoxia after knocking down of SPAG4 using different sequences of siRNA.

first: Kumi

last: Shoji


title: AMC tubular and serrated adenomas

status: Public on Apr 14 2013

city: Amsterdam

first: Richard

last: Volckmann

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

institute: msterdam UMC and University of Amsterdam

summary: Profiling project of a panel of tubular adenoma and serrated adenoma patient material collected in the Academic Medical Center (AMC) in Amsterdam, The Netherlands. The aim of the study was to compare the expression profiles of different types of colon cancer precursor lesions (tubular versus serrated adenomas) and determine their correspondence with a set of colon cancer patient-derived profiles that have distinct clinical outcomes.

overall_design: 6 serrated adenomas and 7 tubular adenomas are profiled in this study.

first: Jan

last: Medema

first: Felipe

last: de Sousa E Melo

first: Louis

last: Vermeulen

first: Marnix

last: Jansen

first: Evelien

last: Dekker

first: Carel

last: Van Noesel

first: Evelyn

last: Fessler


title: Genome-wide analysis identifies aberrant methylation in Fragile X syndrome is specific to the FMR1 locus

status: Public on Apr 15 2013

city: Atlanta

first: Pankaj

last: Chopra

state: GA

address: 615 Michael St. NE, Ste. 375

department: Human Genetics

institute: Emory University

summary: Fragile X syndrome (FXS) is a common form of inherited intellectual disability and is caused by an expansion of CGG repeats located in the 5Õ untranslated region (UTR) of the FMR1 gene, leading to hypermethylation and silencing of this locus. While the dramatic increase in DNA methylation (DNAm) of the FMR1 full mutation allele is well documented, the extent that these changes affect DNAm throughout the entire gene and the rest of the genome remains unexplored. Here, we examine the genome-wide methylation in peripheral blood (N = 9) as well as induced pluripotent stem cells (iPSCs; N = 10) from FXS individuals and controls (N = 53 and 9, respectively) and find the expected significant DNAm differences in the FMR1 promoter and 5Õ UTR, but also that these changes inversely persist throughout the FMR1 gene body. Importantly, we find there are no additional differential methylated loci (DML) throughout the remainder of the genome, indicating that the aberrant methylation of the FMR1 in FXS is locus-specific and does not change DNAm genome-wide. This study provides a comprehensive methylation profile of FXS and refines mechanistic considerations of FMR1 silencing.

overall_design: A total of 62 blood (53 controls + 9 Fragile X) samples analyzed using a linear regression model.

first: Steve

last: Warren


title: Transcription factor–mediated reprogramming of fibroblasts to expandable, myelinogenic oligodendrocyte progenitor cells

city: Cleveland

first: Paul

last: Tesar

state: Ohio

address: 10900 Euclid Ave.

department: Genetics & Genome Sciences

institute: Case Western Reserve University

summary: Cell-based therapies for myelin disorders, such as multiple sclerosis and leukodystrophies, require technologies to generate functional oligodendrocyte progenitor cells.  Here we describe direct conversion of mouse embryonic and lung fibroblasts to ‘induced’ oligodendrocyte progenitor cells (iOPCs) using sets of either eight or three defined transcription factors.  iOPCs exhibit a bipolar morphologyical and global gene expression profile molecular features consistent with bona fide OPCs.  They can be expanded in vitro for at least five passages while retaining the ability to differentiate into induced multiprocessed oligodendrocytes.  When transplanted to hypomyelinated mice, iOPCs are capable of ensheathing host axons and generating compact myelinmyelinating axons both in vitro and in vivo.  Lineage conversion of somatic cells to expandable iOPCs provides a strategy to study the molecular control of oligodendrocyte lineage identity and may facilitate neurological disease modeling and autologous remyelinating therapies.

overall_design: 6 total samples were analyzed.  MEFs were either untreated or infected with inducible lentiviral vectors containing the open reading frames of transcription factors.  Samples were compared to bona fide OPCs.

first: Fadi

last: Najm

first: Angela

last: Lager


title: Foxo1 knockout vAbl transformed cells

status: Public on Apr 13 2013

city: Berkeley

first: Kwan

last: Chow

state: CA

address: 439 LSA

institute: UC Berkeley

summary: Foxo1 is required for proper developmental progression due to distinct functions at different stages of B cell development, but specific gene targets in pro-B cells are not identified. We performed a microarray analysis in v-Abl transformed pro-B cells to compare the gene expression pattern between wildtype and Foxo1 knockout cells.

overall_design: Foxo1f/f-ERCre vAbl transformed pro-B cells were treated with Tamoxifen to delete floxed alleles for 2 days.

middle: T

first: Mark

middle: S

last: Schlissel


title: Expression data from WT and Foxo1 KO CD8+ KLRG1high or KLRG1low populations after LCMV infection

city: La Jolla

first: Rodrigo

middle: A

last: Hess

address: 9500 Gilman Dr

department: Cellular and Molecular Medicine

institute: University of California San Diego

summary:
The forkhead O transcription factors (FOXO) integrate a range of extracellular signals including growth factor signaling, inflammation, oxidative stress and nutrient availability, to substantially alter the program of gene expression and modulate cell survival, cell cycle progression, and many cell-type specific responses yet to be unraveled. Naive antigen-specific CD8+ T cells undergo a rapid expansion and arming of effector function within days of pathogen exposure, but in addition, by the peak of expansion, they form precursors to memory T cells capable of self-renewal and indefinite survival.
We used microarrays to determine whether FOXO1 broadly affects effector and memory differentiation, and to what extent FOXO1 determines the program of memory T cell gene expression.

overall_design:
To obtain an unbiased analysis of genes differentially expressed in antigen-specific Foxo1-/- CD8+ T cells responding to infection, we obtained RNA and performed Affymetrix microarray analysis from KLRG1low and KLRG1high FACS-sorted congenically-marked WT and Foxo1-/- P14 cells obtained from mixed transfers, eight days post-infection with LCMV-Armstrong.  We carried out gene deletion in Rosa26Cre-ERT2 Foxo1f/f (Foxo1-/-) P14 mice just prior to adoptive transfer (Kerdiles et al., 2009), and transfer equal numbers of P14 cells from the spleens of KO (Foxo1-/- P14) and WT P14 mice.
Day8 post infection

last: Michelini

first: Andrew

middle: L

last: Doedens

first: Ananda

last: Goldrath

first: Stephen

last: Hedrick


title: Gene expression of CD19+ b cells

city: Oslo

first: Nicole

last: Bethge

address: Montebello veien

country: Norway

institute: Institute for Cancer Research

summary: We used DNA microarray technology to assess changes in gene expression after treatment of 11 lymphoma cell lines with epigenetic drugs. We identified genes with upregulated expression in treated cell lines and with downregulated expression in B-cell lymphoma patient samples when compared to normal B cells.

overall_design: CD19+ b cells were isolated from buffy coats from diffrent healthy donors. Gene expression of healthy controls (CD19+ b cells) was used as a normal counterpart for lymphoma samples (GSE4732, GSE10846).

first: Guro

last: Lind


title: Extracellular purines promote the differentiation capacity of human bone marrow-derived mesenchymal stem cells

status: Public on Apr 11 2013

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

country: Italy

institute: Centre for Regenerative Medicine

summary:
Extracellular nucleotides are potent signaling molecules mediating cell-specific biological functions. We previously demonstrated that adenosine 5'-triphosphate (ATP) inhibits the proliferation while stimulating the migration, in vitro and in vivo, of human bone marrow-derived mesenchymal stem cells (BM-hMSC). Here, we investigated the effects of ATP on BM-hMSC differentiation capacity.
Molecular analysis showed that ATP treatment modulated the expression of several genes (e.g. wnt-pathway-related genes) governing osteoblastic and adipogenic differentiation of MSCs. Functional studies demonstrated that ATP, under specific culture conditions, stimulated adipogenic and osteogenic differentiation by significantly increasing the lipid accumulation and the expression levels of the adipogenic master gene PPARγ (peroxisome proliferator activated receptor-gamma) and by promoting the mineralization and the expression of the osteoblast-related gene RUNX2 (Runt-related transcription factor 2), respectively.

overall_design: BM-hMSCs cells were transiently exposed to ATP 1mM for 24 hours (ATP pre-treatment) before starting differentiation induction. Then, BM-hMSCs were cultured under adipogenic/osteogenic conditions. Gene Expression Profile was performed on differentiate cells after 3 weeks of induction culture.

first: Ciciarello

last: Marilena

first: Roberta

last: Zini

first: Lara

last: Rossi

first: Valentina

last: Salvestrini

first: Davide

last: Ferrari

first: Roberto

last: Lemoli


title: Gene expression profiling in skeletal muscle before and after GBP surgery

city: Copenhagen N

first: Morten

last: Rasmussen

address: Panum Building 6.6 Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

institute: University of Copenhagen

summary: Profiling of gene expression in Vastus Lateralis from female patients before and after GBP surgery and from lean Control

overall_design: Skeletal muscle samples were obtained from 5 subjects immediately before and 6 months after Gastric Bypass surgery as well as from 6 lean control subjects

first: Romain

last: Barres

first: Henriette

last: Kirchner

first: Jie

last: Yan

first: Fransisc

middle: R

last: Kantor

first: Anna

last: Krook

first: Erik

last: Näslund

first: Juleen

last: Zierath


title: hMSC ATP treatment

summary: Nucleotides triphosphates are extracellular messengers binding to specific plasma membrane receptors (P2Rs) that modulate responses as different as proliferation, differentiation, migration or cell death on several cell types including hematopoietic stem cells. Little and controversial information is available on the role of extracellular nucleotides in human mesenchimal stem cells (hMSCs). In this study, we assessed whether P2Rs are expressed and functional in bone marrow-derived hMSCs. Our results demonstrated, at the mRNA and protein level, the expression of all P2X and P2Y receptor subtypes identified so far. P2R activation by their natural ligands adenosine triphosphate (ATP) and uridine triphosphate (UTP) induced in hMSCs, intracellular Ca2+ concentration changes, plasma membrane depolarization and permeabilization. hMSCs were resistant to the cytotoxic effects of high dose ATP despite the expression of permeabilizing P2Rs as demonstrated by the lack of morphological changes, significant release of intracellular markers of cell death or modification of the mitochondrial network. Gene expression profiling revealed the down-regulation of cell proliferation genes whereas genes involved in cell migration and cytokine production were strongly up-regulated by ATP. Functional studies confirmed the inhibitory activity of ATP on proliferation of hMSCs and clonogenic progenitors. Moreover, ATP exerted a chemotactic effect on hMSCs and increased their migration in response to the chemokine CXCL12. Finally, whereas ATP did not affect T-cell inhibitory activity of hMSCs, the nucleotide increased the production of pro-inflammatory cytokines by hMSCs. Thus, our data show that purinergic signaling modulates hMSC functions and point to a role for extracellular nucleotides on hMSCs biology.

overall_design: hMSCs from 6 healthy donors were seeded at a density of 2.5 x 103 cells/cm2 for 24 hours with or without 1mM ATP. We then assessed the transcriptome profile of ATP–treated and untreated cells using Affymetrix HG-U133 Plus 2 GeneChip array.

first: Sara

last: Gulinelli

first: Giovanna

last: Lucchetti

first: Sergio

first: Francesco

last: Di Virgilio


title: Expression data from human glioma tissues

status: Public on Apr 10 2013

city: Shanghai

first: juxiang

last: chen

address: 415#,Fengyang Road

institute: Changzheng Hospital

summary:
Gliomas are aggressive lethal solid brain tumors arising from support cells in the central nervous system. Despite intense efforts to optimize the treatment of gliomas, the outcomes of high grade glioma patients are still frustrating. The causes and progress of gliomas have been investigated extensively; however, the genetic factors involved in the development of this disease remain poorly understood.
We used microarrays to detail the global program of gene expression in different grade glioma tissues and try to find out some genes associated with the tumorigenesis of gliomas.

overall_design: Grade I to grade IV glioma tissues were selected in surgical operations for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain gene expression profiles. To that end, we hand-selected several genes that were differentially expressed in different grade glioma tissues and then performed a further study to identify the role of these genes in the process of the development of gliomas.

first: Yicheng

last: Lu

first: Juxiang

last: Chen

first: Tao

last: Xu

first: Rong

last: Qin


title: Expression data comparing EBF1 versus Pax5 induced genes

status: Public on Apr 12 2013

city: Philadelphia

first: David

last: Allman

address: 36th & Hamilton Walk, 230 John Morgan Building

institute: University of Pennsylvania

summary: We used microarrays to establish whether EBF1 and Pax5 repress similar or unique genes. We found that EBF1 uniquely represses the expression of the T-lineage transcription factor Gata3.

overall_design: Ebf1-/- pre-pro-B cells were transduced with either control MigR1, MigY-EBF1 or MigR-Pax5 viruses. 24 hours later, RNA was isolated and processed for Affymetrix microarray analysis. Cells expressing EBF1, Pax5, or neither were sorted and processed. Scale represents log2 value of normalized signal level.

first: Anupam

last: Banerjee


title: TGF-beta1-Induced Gene Expression Changes in Primary Murine Hepatocytes

city: Aachen

first: Ralf

last: Weiskirchen

state: NRW

address: Pauwelsstr. 30

department: Institute of Clinical Chemistry and Pathobiochemistry

institute: RWTH University Hospital Aachen

summary: We here compared gene expression profiles of primary murine hepatocytes (mPC) upon stimulation with 1 ng/ml TGF-beta1 for 20 min, 2 hours and 4 hours with untreated cells. Experiments were done in three independent replicates. The goal of this study was to determine genes regulated by TGF-beta1.

overall_design: 12 samples were hybridized to Affymetrix Mouse Gene 1.0 ST Array

first: Steffen

middle: K

last: Meurer

first: Gudrun

last: Walenda

first: Khalid

last: Abnaof

first: Sylvia

last: Joussen

first: Qiong

last: Lin

first: Martin

last: Zenke

first: Kurt

last: Hoffmann

first: Wolfgang

last: Wagner

first: Holger

last: Fröhlich


title: Bleomycin induces molecular changes directly relevant to idiopathic pulmonary fibrosis:  A model for “active” disease

city: Gaithersburg

first: Sriram

last: Sridhar

address: 1 MedImmune Way

department: Translational Medicine

institute: MedImmune

summary: Genomic profiling of RNA from cultured human fibroblasts of donor samples in the 10-14th passage was carried out to determine expression changes in the fibroblasts of individual with different degrees of pulmonary fibrosis. Donors consisted of individuals with rapid progressing pulmonary fibrosis, slow progressing pulmonary fibrosis, or no fibrosis.

overall_design: Genomic characterization of cultured human fibroblasts from donor samples was carried out in samples from donors with from 3 groups: rapid progressing pulmonary fibrosis, slow progressing pulmonary fibrosis, and non-fibrotic individuals. Large RNA (> ~ 200bp) was isolated from fibroblast cultures. Purified total RNA was amplified and labeled using NuGen Ovation kits (NuGEN Technologies, Inc., San Carlos, CA) and RNA from samples was hybridized to Affymetrix HG-U133 plus 2.0 arrays.

first: Christopher

last: Stevenson


title: GEP of the murine cell line BAL17 (BALB/c)

city: Cologne

first: Manuel

last: Montesinos-Rongen

address: Kerpenerstr. 62

department: Institute for Neuropathology

institute: University Hospital Cologne

overall_design: BAL17- / BAL17VII-induced primary CNS lymphoma analysis. 5x10^5 cells were implanted into the brain of BALB/c wt mice and analyzed 21 and 28 days post implantation. The cell lines were also analyzed.


title: Expression data from mouse intestine: C57Bl/6 MTHFR+/- vs BALB/c MTHFR+/-

status: Public on Apr 09 2013

city: Montreal

first: Daniel

last: Leclerc

state: Quebec

address: 4060 Ste-Catherine West

department: Medical Genetics, Room 242

institute: Montreal Children's Hospital

summary:
Previous studies in our laboratory have shown that low folate diet (control diet with 2mg folate/kg, low folate diet with 0.3mg folate/kg) can induce intestinal tumors in BALB/c mice. In addition, we reported that C57Bl/6J mice did not form tumors under the same conditions.
We used microarrays to identify the genetic differences between BALB/c and C57Bl/6J mice that promote tumorigenesis in BALB/c mice.

overall_design: Two groups of mice will be used in the micro-array experiment. One group will consist of four BALB/c mice and the second group will consist of four C57Bl/6 mice. Both groups have mild MTHFR deficiency (Mthfr+/-) and will receive low folate diet (0.3 mg folate/kg) for one year. RNA samples will be extracted from duodenum, the first section of the small intestine where tumors were observed in BALB/c mice. Eight Affymetrix GeneChip Mouse Gene 1.0 ST Array Chips will be used in this experiment.

first: YuanHang

last: Cao


title: Genome-wide analysis reveals TET- and TDG-mediated 5-methylcytosine oxidation dynamics [Expression]

city: Boston

first: Li

last: Shen

address: 200 Longwood Ave

institute: HHMI/Boston Children's Hospital/Harvard Medical School

summary: Ten-eleven translocation (Tet) family of DNA dioxygenases converts 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5- carboxylcytosine (5caC) through iterative oxidation reactions. While 5mC and 5hmC are relatively abundant, 5fC and 5caC are at very low levels in the mammalian genome. Thymine DNA glycosylase (TDG) and base excision repair (BER) pathways can actively remove 5fC/5caC to regenerate unmethylated cytosine, but it is unclear to what extent and at which part of the genome such active demethylation processes take place. Here, we have performed high-throughput sequencing analysis of 5mC/5hmC/5fC/5caC- enriched DNA using modification-specific antibodies and generated genome-wide distribution maps of these cytosine modifications in wild-type and Tdg-deficient mouse embryonic stem cells (ESCs). We observe that the steady state 5fC and 5caC are preferentially detected at repetitive sequences in wild-type mouse ESCs. Depletion of TDG causes marked accumulation of 5fC and 5caC at a large number of distal gene regulatory elements and transcriptionally repressed/poised gene promoters, suggesting that Tet/TDG-dependent dynamic cycling of 5mC oxidation states may be involved in regulating the function of these regions. Thus, comprehensive mapping of 5mC oxidation and BER pathway activity in the mammalian genome provides a promising approach for better understanding of biological roles of DNA methylation and demethylation dynamics in development and diseases.

overall_design: Gene expression comparison of control and Tdg knockdown mouse embryonic stem cells.

first: Hao

last: Wu

first: Dinh

last: Diep

first: Shinpei

last: Yamaguchi

first: Ana

middle: C

last: D'Alessio

first: Alan

last: Fung

first: Kun

last: Zhang

first: Yi


title: Inhibitor of NFκB ζ (IκBζ) is a transcriptional key regulator of   monocyte chemoattractant protein-1 (MCP-1/CCL2)

city: Münster

first: Niels-Arne

last: Münck

address: Roentgenstraße 21

department: Insitute of Immunology

institute: University of Münster

summary: Monocyte chemoattractant protein 1 (MCP-1/CCL2) is critically involved in directing the migration of blood monocytes to sites of inflammation. Consequently, excessive MCP-1 secretion has been linked to many (auto)inflammatory diseases, whereas a lack of expression severely impairs immune responsiveness. We demonstrate that the atypical inhibitor of NF-κB ζ (IκBζ), a transcriptional co-activator required for the selective expression of a subset of NF-κB target genes, is a key activator of the Ccl2 gene. IκBζ-deficient macrophages exhibited impaired secretion of MCP-1 when challenged with diverse inflammatory stimuli, such as lipopolysaccharide or peptidoglycan. These findings were reflected at the level of Ccl2 gene expression, which was tightly coupled to the presence of IκBζ. Moreover, mechanistic insights acquired by chromatin immunoprecipitation demonstrate that IκBζ is directly recruited to the proximal promoter region of the Ccl2 gene and required for histone H3K9 trimethylation. Finally, IκBζ-deficient mice showed significantly impaired MCP-1 secretion and monocyte infiltration in an experimental model of peritonitis. Together, these findings suggest a distinguished role of IκBζ in mediating the targeted recruitment of monocytes in response to local inflammatory events.

overall_design: Peritoneal macrophages from Wildtype and IκBζ-Knockout mice were either stimulated with 1µg/ml LPS for 4h or left untreated (triplicates each)

first: Dominic

middle: G

last: Hildebrand

first: Eva

last: Alexander

first: Sebastian

last: Hörber

first: Simon

last: Lehle

first: Kerstin

last: Obermayer

first: Oliver

last: Rothfuss

first: Julia-Stefanie

last: Frick

first: Ingo

last: Schmitz

first: Johannes

last: Roth

first: Jan

last: Ehrchen

first: Frank

last: Essmann

first: Klaus

last: Schulze-Osthoff


title: Gpr116 regulates pulmonary surfactant pool size

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary: The amount of pulmonary surfactant within type II cells and in the alveolar space, referred to as surfactant pool sizes, are tightly regulated. The molecular pathways that sense and regulate surfactant pool size within the alveolus have not been identified and constitute a fundamental knowledge gap in the field. Our data show that mice with a germline mutation in the orphan G-protein-coupled receptor, GPR116, have a 30-fold accumulation of surfactant phospholipids that causes respiratory distress in adult animals. This phenotype is associated with increased surfactant secretion and induction of the purinergic receptor P2RY2 in young animals, and lipid-laden macrophages and alveolar destruction in older animals. We further demonstrate that GPR116 mRNA expression is developmentally regulated in the murine lung with peak expression at birth when surfactant pool sizes are maximal. Within the lung, GPR116 protein expression is restricted to the apical plasma membrane of alveolar type I and type II epithelial cells.

overall_design: To better understand the roles and molecular mechanisms by which Gpr116 influences gene expression in lung, the effect of cell-selective deletion of Gpr116 (Gpr116D/D) on genome-wide mRNA expression profiles was determined in murine type II alveolar epithelial cells. Differentially expressed genes were identified from Affymetrix Murine GeneChips analysis and subjected to gene ontology classification promoter analysis, pathway mapping and literature mining.

first: James

last: Bridges

first: Machiko

last: Ikegami


title: Ubiquinol-induced gene expression signatures are translated into reduced erythropoiesis and LDL cholesterol levels in humans

status: Public on Apr 08 2013

city: Kiel

last: Döring

address: Heinrich-Hecht-Platz 10

department: Human Nutrition and Food Science

institute: Christian-Albrechts-University Kiel

summary: Studies in vitro and in mice indicate a role for Coenzyme Q10 (CoQ10) in gene expression. To determine this function in relationship to physiological readouts, a 2-week supplementation study with the reduced form of CoQ10 (ubiquinol, Q10H2, 150 mg/d) was performed in 53 healthy males. Mean CoQ10 plasma levels increased 4.8-fold after supplementation. Transcriptomic and bioinformatic approaches identified a gene-gene interaction network in CD14-positive monocytes, which functions in inflammation, cell differentiation and PPAR-signaling. These Q10H2-induced gene expression signatures were also described previously in liver tissues of SAMP1 mice. Biochemical as well as NMR-based analyses showed a reduction of LDL cholesterol plasma levels after Q10H2 supplementation. This effect was especially pronounced in atherogenic small dense LDL particles (19-21 nm, 1.045 g/l). In agreement with gene expression signatures, Q10H2 reduces the number of erythrocytes but increases the concentration of reticulocytes. In conclusion, Q10H2 induces characteristic gene expression patterns, which are translated into reduced LDL cholesterol levels and erythropoiesis in humans.

overall_design: Whole genome expression profiles were analyzed in isolated monocytes of 3 Q10H2 supplemented subjects at the indicated time points (before (T0) and after (T14) Q10H2 supplementation. This results in a total of 6 microarrays.

first: Constance

last: Schmelzer


title: GFI deficiency in plasmacytoid dendritic cells

status: Public on Apr 07 2013

first: Kwan

last: Chow

summary: Growth factor independence genes (Gfi1 and Gfi1b) repress recombination activating genes (Rag) transcription in developing B lymphocytes. Because all blood lineages originate from hematopoietic stem cells (HSCs) and different lineage progenitors have been shown to share transcription factor networks prior to cell fate commitment, we hypothesized that GFI family proteins may also play a role in repressing Rag transcription or a global lymphoid transcriptional program in other blood lineages. We tested the level of Rag transcription in various blood cells when Gfi1 and Gfi1b were deleted, and observed an upregulation of Rag expression in plasmacytoid dendritic cells (pDCs). Using microarray analysis, we observed that Gfi1 and Gfi1b regulate a broad spectrum of cellular processes in pDCs, but not a lymphoid specific transcriptional program. This study establishes a role for Gfi1 and Gfi1b in Rag regulation in a non-B lineage cell type

overall_design: Gfi1f/f; Gfi1bf/f; ERCre bone marrow progenitors were untreated and treated with tamoxifen (4OHT) to delete floxed alleles during pDC differentiation in culture. Cells from three individual mouse constitute triplicates of untreated (-4OHT) and treated (+4OHT) conditions, corresponding to wildtype or knockout genotypes.

first: Danae

last: Schulz

first: Mark

last: Schlissel


title: Analysis of differentially expressed genes in murine Satb1-deficient hematopoietic stem cells (HSCs) compared to wild-type HSCs

city: Bronx

first: Boris

last: Bartholdy

state: NY

address: 1300 Morris Park Ave

department: Cell Biology

institute: Albert Einstein College of Medicine

summary: Gene expression analysis on purified murine hematopoietic stem cells (HSCs) deficient for Special AT-rich sequence-binding protein 1 (Satb1) compared to wild-type HSCs.

overall_design: Analysis of gene expression of bone marrow-derived CD45.2+ CD150+cKit+Sca-1+CD4-CD8a-CD19-B220-Gr-1- HSCs from congenic recipient animals transplanted >20 weeks with either wild-type or Satb1-deficient hematopoeitic cells.

first: Ulrich

last: Steidl

first: Britta

last: Will


title: RiboTag analysis of actively translated mRNAs in Sertoli and Leydig cells in vivo

status: Public on Apr 06 2013

city: Pullman

first: Ryan

last: Evanoff

state: WA

department: School of Molecular Biosciences

institute: Washington State University

summary: Analysis of Sertoli and Leydig cell “translatome” utilizing an in vivo ribosome tagging strategy (RiboTag) that allows a detailed and physiologically relevant characterization of the polysome-associated mRNAs in vivo.  Although progress has been made in the identification of specific  transcripts that are translated in Sertoli and Leydig cells and their response to hormones, efforts  to expand these studies have been restricted by technical hurdles.  Our analysis identified all previously characterized Leydig and Sertoli cell-specific markers and identified in a comprehensive manner novel markers of Leydig and Sertoli cells; the translational response of these two cell types to gonadotropins or testosterone was also investigated.

overall_design: Leydig cell-specific (Cyp17iCre: RiboTag) and Sertoli cell-specific (AMH-Cre: RiboTag)  RiboTag mice were obtained by crossing RiboTag homozygous mice with Cyp17iCre  or AMH-Cre mice.  For in vivo LH treatment experiments, mice were  injected with the GnRH antagonist acyline for 4 days before a single injection of purified  human LH.  After treatment, testes were homogenized and polysomes were immunoprecipitated by utilizing an anti-HA antibody.  RNA was extracted, labelled, and hybridized to Mouse Gene ST 1.0 arrays.

first: Elisenda

last: Sanz

first: G.

last: McKnight