title: Pi3kcb links Hippo-YAP and PI3K-AKT signaling pathways to promote cardiomyocyte proliferation and survival [microarray]

city: Boston

first: Fei

last: Gu

address: 320 Longwood Ave.

department: Cardiology

institute: Childrens hospital boston, Harvard Medical School

summary: Background—YAP, the nuclear effector of Hippo signaling, regulates cellular growth and survival in multiple organs, including the heart, by interacting with TEAD sequence specific DNA-binding proteins. Recent studies showed that YAP stimulates cardiomyocyte proliferation and survival. However, the direct transcriptional targets through which YAP exerts its effects are poorly defined.   Methods and Results—To identify genes directly regulated by YAP in cardiomyocytes, we combined differential gene expression analysis in YAP gain- and loss-of-function with genome-wide identification of YAP bound loci using chromatin immunoprecipitation and high throughput sequencing. This screen identified Pik3cb, encoding p110β, a catalytic subunit of phosphoinositol-3-kinase (PI3K), as a candidate YAP effector that promotes cardiomyocyte proliferation and survival. We validated YAP and TEAD occupancy of a conserved enhancer within the first intron of Pik3cb, and show that this enhancer drives YAP-dependent reporter gene expression. Yap gain- and loss-of-function studies indicated that YAP is necessary and sufficient to activate the PI3K-Akt pathway. Like Yap, Pik3cb gain-of-function stimulated cardiomyocyte proliferation, and Pik3cb knockdown dampened the YAP mitogenic activity. Reciprocally, Yap loss-of-function impaired heart function and reduced cardiomyocyte proliferation and survival, all of which were significantly rescued by AAV-mediated Pik3cb expression.   Conclusion—Pik3cb is a crucial direct target of YAP, through which the YAP activates PI3K-AKT pathway and regulates cardiomyocyte proliferation and survival.

overall_design: Two groups were involved in this study:TNTcreYapfl_het group and TNTcreYapfl_KO group. Each group contained three biological replicates. Embryo hearts were collected at E12.5 and dissociated.  Cardiomyocytes were collected by FACS. The total RNA of cardiomyocytes were isolated for microarray analysis.

first: Pingzhu

last: Zhou

first: Alexander

last: von Gise

first: Qing

last: Ma

first: Haidong

last: Guo

first: Pim

last: van Gorp

first: William

last: Pu


title: A Myc-dependent role for cohesin in the heterokaryon-mediated reprogramming of somatic nuclei

status: Public on Feb 19 2015

city: London

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

country: United Kingdom

institute: MRC London Institute of Medical Sciences

summary:
Analysis of gene expression changes in mESCs where the cohesin subunit Scc1 has been depleted.
There are 6 samples. 3 Scc1 wt/wt ERT2-Cre biological replicas and 3 Scc1 lox/lox ERT2-Cre biological replicas, all treated with 4'-OHT 80nM final concentration for 24h.

overall_design: Scc1 wt/wt and Scc1 lox/lox ERT2-Cre mES cells where grown in N2B27 +2i+LIF medium (Ying et al. 2008) for 24h in the presence of 80mM 4-OHT to induce cohesin depletion. Three biological replicates were collected and RNA was extracted. Microarray samples were prepared following the manufacturers instructions (Affymetrix) using 200ng of total RNA. Microarry samples were hybridized to Affymetrix GeneChip Mouse Gene 1.0 ST Arrays and the analysis was performed using the Bioconductor Package for R.

first: Thais

last: Lavagnolli

first: Hegias

last: Mira-Bontenbal

first: Matthias

last: Merkenschlager


title: Identification of genes dysregulated with the disruption acRPB1

city: Nashville

first: John

middle: A

last: Capra

state: TN

address: VU Station B, Box 35-1634

country: USA

institute: Vanderbilt University

summary: RPB1, the largest subunit of RNA polymerase II, contains a highly modifiable C-terminal domain (CTD) that consists of variations of a consensus heptad repeat sequence (Y1S2P3T4S5P6S7). The consensus CTD repeat motif and tandem organization represent the ancestral state of eukaryotic RPB1, but across eukaryotes CTDs show considerable diversity in repeat organization and sequence content. These differences may reflect lineage-specific CTD functions mediated by protein interactions. Mammalian CTDs contain eight non-consensus repeats with a lysine in the seventh position (K7). Posttranslational acetylation of these sites was recently shown to be required for proper polymerase pausing and regulation of two growth factor-regulated genes. To investigate the origins and function of RPB1 CTD acetylation (acRPB1), we computationally reconstructed the evolution of the CTD repeat sequence across eukaryotes and analyzed the evolution and function of genes dysregulated when acRPB1 is disrupted. Modeling the evolutionary dynamics of CTD repeat count and sequence content across diverse eukaryotes revealed an expansion of the CTD in the ancestors of Metazoa. The new CTD repeats introduced the potential for acRPB1 due to the appearance of distal repeats with lysine at position seven. This was followed by a further increase in the number of lysine-containing repeats in developmentally complex clades like Deuterostomia. Mouse genes enriched for acRPB1 occupancy at their promoters and genes with significant expression changes when acRPB1 is disrupted are enriched for several functions, such as growth factor response, gene regulation, cellular adhesion, and vascular development. Genes occupied and regulated by acRPB1 show significant enrichment for evolutionary origins in the early history of eukaryotes through early vertebrates. Our combined functional and evolutionary analyses show that RPB1 CTD acetylation was possible in the early history of animals, and that the K7 content of the CTD expanded in specific developmentally complex metazoan lineages. The functional analysis of genes regulated by acRPB1 highlight functions involved in the origin of and diversification of complex Metazoa. This suggests that acRPB1 may have played a role in the success of animals.

overall_design: We used a HA-tagged mouse RPB1 construct in which all K7 residues were substituted with arginines (8KR). This mutation resembles unacetylated lysines by conserving the positive charge at these positions, but preventing acetylation. To examine the potential functions of K7 acetylation in regulating gene expression, we stably expressed wildtype or 8KR HA-RPB1 in murine NIH/3T3 fibroblasts and cultured these cells in media containing α-amanitin. Both were expressed at equivalent levels, but acetylation was present only in wildtype, and not mutant HA-RPB1. We then performed gene expression profiling using the Affymetrix Mouse Gene 1.0 ST microarray with three biological replicates.

first: Sebastian

last: Schroeder

first: Melanie

last: Ott


title: Expression data from WIF1 induced LN-229 (GBM cell line)

status: Public on Feb 23 2015

city: lausanne

first: Irene

last: Vassallo

state: vaud

address: av bugnon 46

country: Switzerland

institute: CHUV

summary: Glioblastoma is the most aggressive primary brain tumor in adults and due to the invasive nature it cannot be completely removed. We have recently shown that the WNT inhibitory factor 1 (WIF1), a secreted inhibitor of WNTs, is downregulated in glioblastoma and acts as strong tumor suppressor. In search of a mediator for this function differential gene expression profiles of WIF1-expressing cells were performed. MALAT1, a long non-coding RNA and key positive regulator of invasion, emerged as the top downregulated gene. Indeed, knock-down of MALAT1 reduced migration in glioblastoma cells, without effect on proliferation.

overall_design: LN-229 cells  induced with Doxocyclin to express WIF1 were compared to the non-induced control (two biological replicates each)

first: Pascal

last: Zinn

first: Marta

last: Lai

first: Premnath

last: Rajakannu

first: Marie-France

last: Hamou

first: Monika

middle: E

last: Hegi


title: A Whole Blood Molecular Signature for the Identification of Acute Myocardial Infarction Without Relying Upon Myonecrosis (microarray)

status: Public on Feb 28 2015

city: La Jolla

first: Eri

last: Kramer

state: CA

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

summary:
Despite the significant reduction in the overall burden of cardiovascular disease (CVD) over the past decade, CVD still accounts for a third of all deaths in the United States and worldwide each year. While efforts to identify and reduce risk factors for atherosclerotic heart disease (i.e. hypertension, dyslipidemia, diabetes mellitus, cigarette smoking, inactivity) remain the focus of primary prevention, the inability to accurately and temporally predict acute myocardial infarction (AMI) impairs our ability to further improve patient outcomes.  Our diagnostic evaluation for the presence of coronary artery disease relies on functional testing, which detects flow-limiting coronary stenosis, but we have known for decades that most lesions underlying AMI are only of mild to moderate luminal narrowings, not obstructing coronary blood flow. Accordingly, there is a dire need of improved diagnostics for underlying arterial plaque dynamics, fissure and rupture. Here we describe the designation of a specific gene expression pattern acting as a molecular signature for acute myocardial infarction present in whole blood of patients that was determined using microarray analysis of enriched circulating endothelial cells (CEC).
We isolated circulating endothelial cells from patients experience acute myocardial infartion and healthy cohorts, and measured gene expression using the HG-133U_PLUS_2 microarray

overall_design: Circulating endothelial cells were isolated from patients experiencing acute myocardial infarction (n=49) and from healthy cohorts (n=50). The patients were separated into a discovery cohort (n=43) for biomarker discovery and model training; and into a validation cohort (n=56) for biomarker validation and model testing.

first: Eric

middle: R


title: Microvascular endothelial heterogeneity

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: The goal of this study was to gain insight into the molecular heterogeneity of capillary endothelial cells derived from different organs by microarray profiling of freshly isolated cells and identify transcription factors that may determine the specific gene expression profile of endothelial cells from different tissues. The study focused on heart endothelial cells and presents a validated signature of 31 genes that are highly enriched in heart endothelial cells. Within this signature 5 transcription factors were identified and the optimal combination of these transcription factors was determined for specification of the heart endothelial fingerprint.

overall_design: From three tissue types (mouse brain, heart and liver), we collected five freshly isolated endothelial cell samples each. For each brain sample we pooled RNA from 6 mice. For each heart sample we pooled RNA from 4 mice. For each liver sample we pooled RNA from 2 mice. The three endothelial subtypes were then compared. For each subtype, specific gene profiles were defined by determining the genes that were highly enriched versus the other two endothelial subtypes.

first: Giulia

last: Coppiello

first: Xabier

middle: L

last: Aranguren

first: Aernout

last: Luttun


title: Expression data from Dicer WT and Dicer KO mouse CD4 T cells.

status: Public on Feb 15 2015

first: Gopuraja

last: Dharmalingam

summary: miRNA regulate gene expression at the post-transcriptionnal level. To gain further insight into this process, we analysed by Affymetrix microarray, the transcriptome of Dicer WT or Dicer deleted mouse CD4 T cells.

overall_design: Mouse CD4 T cells were sorted by flow cytometry from control CD4Cre neg Dicer lox/lox or CD4Cre pos Dicer lox/lox animals, total RNA was extracted using RNA bee and amplified before hybridization onto Mouse Gene arrays. Three biological replicate were analysed for each condition (3 Dicer WT control and 3 Dicer KO).

first: Antoine

last: Marçais


title: DNA methylation patterns in newborns exposed to tobacco in utero

status: Public on Feb 16 2015

city: Oviedo

first: Agustin

middle: F

last: Fernandez

email: affernandez@hca.es, agusff@gmail.com

state: Asturias

address: Avenida de Roma s/n

department: IUOPA

country: Spain

institute: Oviedo University-HUCA

type: Methylation profiling by genome tiling array

summary:
Background: Maternal smoking during pregnancy is a major risk factor for adverse health outcomes. The main objective of the study was to assess the impact of in utero tobacco exposure on DNA methylation in children born at term with appropriate weight at birth.

Methods: Twenty mother-newborn dyads, after uncomplicated pregnancies, in the absence of perinatal illness were included. All mothers were healthy with no cardiovascular risk factors, except for the associated risks among those mothers who smoked. Umbilical cord blood (for methylation arrays) and maternal peripheral venous blood (for cotine level measurement) were collected and an epigenome-wide association study was performed using a 450K epigenome-wide scan (Illumina Infinium HumanMethylation 450BeadChip) with adjustment to normalize the DNA methylation for data cell variability in whole blood.

Results: The maternal plasmatic cotinine levels ranged from 10.70-115.40 ng/ml in the exposed group to 0-0.59 ng/ml in the non-exposed group. After adjusting for multiple comparisons in 427102 probes, statistically significant differences for 31 CpG sites, associated to 25 genes were observed.  There was a greater than expected proportion of statistically-significant loci located in CpG islands (Fisher’s exact test, p=0.029) and of those CpG islands, 90.3% exhibit higher methylation levels in the exposed group. The most striking and significant CpG site, cg05727225, is located in the chromosome 11p15.4, within the adrenomedullin gene.

Conclusions: In utero tobacco exposure, even in the absence of fetal growth restriction, may alter the epigenome, contributing to global DNA hypomethylation. Therefore, DNA status can be used as a biomarker of prenatal insults. Considering the possibility to reverse epigenetic modifications, a window of opportunity exists to change the programmed chronic disease.

overall_design: Twenty mother-newborn dyads, after uncomplicated pregnancies, in the absence of perinatal illness were included. All mothers were healthy with no cardiovascular risk factors, except for the associated risks among those mothers who smoked. Umbilical cord blood were collected and an epigenome-wide association study was performed using a 450K epigenome-wide scan (Illumina Infinium HumanMethylation 450BeadChip) with adjustment to normalize the DNA methylation for data cell variability in whole blood.

first: Carmen

last: Ivorra

first: Mario

last: Fraga

first: Gustavo

last: Bayón

first: Agustín

last: Fernández

first: Consuelo

last: García-Vicent

first: F

middle: J

last: Chaves

first: Josep

last: Redon

first: Empar

last: Lurbe


title: Gene expression profiles of RPMI8226 cells after knockdown of KDM3A and KLF2

status: Public on Feb 18 2015

first: Manoj

last: Bhasin

state: MA

address: 330 Brookline Avenue  RN 380E

institute: Beth Israel Deaconess Medical Center

summary:
Recent studies have implicated KDM3A, which catalyzes removal of H3K9 methylation, is associated with tumorigenesis. However, the biological role of KDM3A in multiple myeloma, has not been delineated. Here we identify KDM3A-KLF2-IRF4 axis dependence in multiple myeloma. We demonstrate that knockdown of KDM3A leads to apoptosis and significant growth inhibition in myeloma cells. Mechanistically, KDM3A directly regulates myeloma cell survival factor IRF4 expression through H3K9 demethylation at its promoter. We further show that KDM3A directly regulates KLF2 expression and that knockdown of KLF2 leads to growth inhibition in myeloma cells.
The goal of this analysis is to identify genes whose expression changes after shRNA-mediated knockdown of KDM3A and KLF2 using the human U133 plus 2.0 Affymetrix GeneChip in myeloma cell line (RPMI8226).

overall_design:
Two independent experiments were performed:
1. Myeloma cell line (RPMI8226) was transduced with either shRNAs targeting KDM3A (duplicate hairpins) or luciferase (control) in duplicate. The gene expression profiles of KDM3A knockdown cells were compared with that of control cells. A total of 6 RNA samples (4 KDM3A knockdown and 2 control) were analyzed.
2. Myeloma cell line (RPMI8226) was transduced with either shRNAs targeting KLF2 (duplicate hairpins) or luciferase (control) in duplicate. The gene expression profiles of KLF2 knockdown cells were compared with that of control cells.  A total of 6 RNA samples (4 KLF2 knockdown and 2 control) were analyzed.

first: Hiroto

last: Ohguchi

first: Kenneth

middle: C

last: Anderson


title: Expression data from isolated E17.5 mouse skin with or without Ovol2 overexpression

status: Public on Feb 14 2015

city: Irvine

first: Xing

last: Dai

state: Ca

address: Med Sci I D288

institute: UC Irvine

summary: During epithelial tissue morphogenesis, developmental progenitor cells undergo dynamic adhesive and cytoskeletal remodeling to trigger proliferation and migration. Transcriptional mechanisms that restrict such mild form of epithelial plasticity to maintain lineage-restricted differentiation in committed epithelial tissues are poorly understood. Here we report that simultaneous ablation of transcriptional repressor-encoding Ovol1 and Ovol2 results in expansion and blocked terminal differentiation of embryonic epidermal progenitor cells. Conversely, mice overexpressing Ovol2 in their skin epithelia exhibit precocious differentiation accompanied by smaller progenitor cell compartments. We show that Ovol1/2-deficient epidermal cells fail to undertake alpha-catenin–driven actin cytoskeletal reorganization and adhesive maturation, and exhibit changes that resemble epithelial-to-mesenchymal transition (EMT). Remarkably, these alterations as well as defective terminal differentiation are reversed upon depletion of EMT-promoting transcriptional factor Zeb1. Collectively, our findings reveal Ovol-Zeb1-a-catenin sequential repression and highlight novel functions of Ovol as gatekeepers of epithelial adhesion and differentiation by inhibiting progenitor-like traits and epithelial plasticity.

overall_design: Skin from control and Ovol2 overexpression (Ovol2 BT) were physically isolated for RNA extraction and hybridization on Affymetrix microarrays. In order to identify changes in differentiation of the epidermis, we analyzed skin from E17.5 mice, when differentiation of the epidermis was more advanced.

first: Briana

last: Lee


title: Expression data from isolated keratinocytes from mouse skin with or without Ovol1 and Ovol2 expression

overall_design: Isolated keratinocytes from control, Ovol1 knockout and Ovol1/2 double knockout were physically isolated for RNA extraction and hybridization on Affymetrix microarrays. In order to identify primary changes, we isolated the keratinocytes from mouse skin and allowed them to grow in culture for 2-5 days.


title: Gene expression data from Wilms tumor samples

city: Heidelberg

first: Marcel

last: Kool

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

country: Germany

institute: German Cancer Research Center DKFZ

summary: Wilms tumor (nephroblastoma) is a pediatric kidney tumor that arises from renal progenitor cells. Since the blastemal type is associated with adverse prognosis, we characterized such Wilms tumors by exome and transcriptome analysis. We detected novel, recurrent somatic mutations affecting the SIX1/2 – SALL1 pathway implicated in kidney development, the DROSHA/DGCR8 microprocessor genes as well as alterations in MYCN and TP53, the latter being strongly associated with dismal outcome. The DROSHA mutations impair the RNase III domains, while DGCR8 exhibits stereotypic E518K mutations in the RNA binding domain - both may skew miRNA representation. SIX1 and SIX2 mutations affect a single hotspot (Q177R) in the homeodomain indicative of a dominant effect. In larger cohorts, these mutations cluster in blastemal and chemotherapy-induced regressive tumors that likely derive from blastemal cells and these are characterized by generally higher SIX1/2 expression. These findings broaden the spectrum of human cancer genes and may open new avenues for stratification and therapeutic leads for Wilms tumors.

overall_design: 53 Wilms tumor samples were selected for RNA extraction and hybridization on Affymetrix Affymetrix Human Genome U133 Plus 2.0 Arrays.

first: Manfred

last: Gessler

first: Stefan

last: Pfister


title: Expression data from isolated E16.5 mouse skin with or without Ovol2 overexpression

overall_design: Skin from control and Ovol2 overexpression (Ovol2 BT) were physically isolated for RNA extraction and hybridization on Affymetrix microarrays. In order to identify primary changes, we analyzed skin from E16.5 mice, when morphological differences between control and Ovol2 overexpression were still minimal.


title: Expression data from calcium-induced isolated keratinocytes from mouse skin with or without Ovol1 and Ovol2 expression

overall_design: Isolated keratinocytes from control, Ovol1 knockout and Ovol1/2 double knockout were physically isolated for RNA extraction and hybridization on Affymetrix microarrays. In order to identify differentiation changes, we isolated the keratinocytes from mouse skin and allowed them to grow in culture for 2-5 days, then added calcium and allowed them to grow another 3-5 days.


title: Gene expression profile analysis of PLS-123 in OCI-Ly7 cells

status: Public on Feb 11 2015

city: Beijing

first: Jun

last: Zhu

address: No.52 Fucheng Road, Haidian District

country: China

institute: Peking University Cancer Hospital & Institute

summary: To exploit targets or signaling pathways affected by PLS-123 during anti-tumor process, gene expression profiling was carried out in representative OCI-Ly7 cells treated for 24 hours.

overall_design: OCI-Ly7 cells were treated with ibrutinib, PLS-123 or vehicle for 24 hours.

first: Ning

last: Ding


title: Ovol as gatekeepers of epithelial adhesion and differentiation

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

overall_design: Refer to individual Series


title: Gene expression profile analysis of PLS-123 in xenograft model.

summary: To exploit targets or signaling pathways affected by PLS-123 during anti-tumor process, gene expression profiling was carried out in OCI-Ly7 inoculated xenograft model.

overall_design: Six- to eight-week-old male SCID mice were inoculated subcutaneously with OCI-Ly7 tumor cells in 0.1 ml PBS for tumor development


title: A Methylation-Based Signature Predicts Survival In Hepatocellular Carcinoma Patient

status: Public on Feb 13 2015

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

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

department: PEBC

institute: IDIBELL

summary: Epigenetic deregulation is a critical event in human malignancies. A number of DNA methylation markers are currently under evaluation as diagnostic and prognostic biomarkers for many cancers. However, its potential role in hepatocellular carcinoma (HCC) is under-explored. Aims: To develop a DNA methylation-based prognostic signature in surgically resected HCC

overall_design: Tumors from 224 HCC resected patients, 10 normal Liver individuals and 9 Cirrhotic patients were analyzed. Methylome profiling was done with Illumina HumanMethylation450 (485,000 CpG, 96% of known CpG islands). We selected probes in CpG islands located in promoters, hypermethylated (B value higher than 50%) in at least 5% of the tumors and hypomethylated (B value lower than 33%) in more than 90% of normal liver.

first: Anna

last: Portela

first: Augusto

last: Villanueva

last: Llovet


title: Gene expression in DCIS.COM and SUM225 MIND xenografts during transition from 2 to 6 to 10 weeks

status: Public on Feb 12 2015

city: Kansas City

first: Hanan

last: Elsarraj

state: KS

address: 3901 Rainbow Blvd.

department: Pathology and Laboratory Medicine

institute: University of Kansas Medical Center

summary: We utilized DCIS mouse intraductal (MIND) models with both SUM225 and DCIS.COM cell lines to characterize the sequential and temporal changes in mRNA expression over a time course of 2, 6, and 10 weeks during in vivo progression in the epithelial cells from DCIS to invasive cancer.

overall_design: DCIS cell lines: DCIS.COM and SUM225 were injected intraductally into the MIND model as triplicates. At 2, 6, and 10 weeks post-injection, the mammary glands were collected and magnetically sorted for the epithelial cells. Affymetrix microarray was utilized to analyze gene expression profiles from RNA isolated from these cells.

first: Yan

last: Hong

first: Kelli

last: Valdez

first: Whitney

last: Michaels

first: Markus

last: Hooks

first: Jason

last: Herschkowitz

first: Melissa

last: Troester

first: Fariba

last: Behbod


title: Increased CLL Proliferation upon IgM stimulation is Sustained by the Up-regulation of miR-132 and miR-212: a Combined miRNA and Gene Expression Profiling Analysis and Correlation with Disease Progression [gene expression]

status: Public on Feb 10 2015

city: Rome

first: Teresa

last: Colombo

address: p.le A. Moro 7

department: Institute of Molecular Biology and Pathology (IBPM)

country: Italy

institute: Consiglio Nazionale delle Ricerche (CNR)

summary: In order to investigate a potential involvement of miRNAs in BCR stimulation, in the present work we first evaluated their expression following IgM cross-linking in CLL cells, as well as in healthy B lymphocytes. Next, to infer putative miRNA targeting networks, we combined miRNA profiling results with gene expression and functional analyses

overall_design: Gene expression profiling analysis by microarray analysis of CLL samples.

first: S

last: Tavolaro

first: T


title: Effect of over-expression of AR-V7 in MDA-MB-453 breast cancer cells

city: Bedford Park

first: Luke

last: Selth

state: SA

address: Flinders Drive

department: College of Medicine and Public Health

country: Australia

institute: Flinders University

summary: The effect of transient transfection of a construct designed to over-express the androgen receptor (AR) variant AR-V7 on gene expression in MDA-MB-453 cells was assessed using Affymetrix Gene 2.0 ST arrays. Transfection of an AR-expressing construct or an empty construct served as controls.

overall_design: AR-V7, AR or empty vector was transfected into MDA-MB-453 cells. Cells were treated with vehicle control or DHT.

first: Wayne

middle: D

last: Tilley


title: Expression data by telomere elongation in xenograft.

status: Public on Feb 05 2015

city: Koto-ku

first: kyotaro

last: HIRASHIMA

state: Tokyo

address: 3-8-31 Ariake

department: Cancer Chemotherapy Center

country: Japan

institute: The JFCR-Cancer Inst.

summary: Telomere erosion causes cell mortality, suggesting that longer telomeres allow greater number of cell division. In telomerase-positive human cancer cells, however, telomeres are often kept shorter than the surrounding normal tissues. Recently, we have shown that telomere elongation in cancer cells represses innate immune genes and promotes their differentiation in vivo. This implies that short telomeres contribute to cancer malignancy, but it is unclear how such genetic repression is caused by long telomeres. Here we report that telomeric repeat-containing RNA (TERRA) induces genome-wide alteration of gene expression in telomere-elongated cancer cells in vivo. Using three different cell lines, we found that telomere elongation upregulates TERRA and downregulates innate immune genes in vivo xenograft tumors. Most of the suppressed genes belonged to innate immune system categories and were upregulated in various cancers. We propose that TERRA G4 counteracts cancer malignancy through suppression of innate immune genes.

overall_design: Four samples are telomere-elongated cells (PC3/LhTERTL, PC3/LhTERTL/cre, HBC4/hTERT and MKN74/hTERT), and the other four samples are control cell lines.

first: Kyotaro

last: Hirashima

first: Hiroyuki

last: Seimiya


title: Expression data by G-quadruplex (G4) forming oligonucleotides transfection in 3D culture.

summary: Telomere erosion causes cell mortality, suggesting that longer telomeres allow greater number of cell division. In telomerase-positive human cancer cells, however, telomeres are often kept shorter than the surrounding normal tissues. Recently, we have shown that telomere elongation in cancer cells represses innate immune genes and promotes their differentiation in vivo. This implies that short telomeres contribute to cancer malignancy, but it is unclear how such genetic repression is caused by long telomeres. Here we report that telomeric repeat-containing RNA (TERRA) induces genome-wide alteration of gene expression in telomere-elongated cancer cells in vivo. Using three different cell lines, we found that G4 forming oligonucleotide repressed innate immune genes in vivo 3D culture conditions. Most of the suppressed genes belonged to innate immune system categories and were upregulated in various cancers. We propose that TERRA G4 counteracts cancer malignancy through suppression of innate immune genes.

overall_design: Six samples are G4 oligo-transfected cells (PC-3/(uuaggg)^4, PC-3/AS1411, HBC4/(uuaggg)^4, HBC4/AS1411, MKN74/(uuaggg)^4 and MKN74/AS1411), and the other six samples are control oligo-transfected cells.


title: LncRNA Expression Discriminates Karyotype and Predicts Survival in B-lymphoblastic Leukemia (Affymetrix)

city: LOS ANGELES

first: Dinesh

middle: S

last: Rao

address: 750 CHARLES E YOUNG DRIVE, 12-272 FACTOR

department: PATHOLOGY AND LABORATORY MEDICINE

institute: UCLA

summary: Long non-coding RNAs (lncRNAs) have been found to play a role in gene regulation with dysregulated expression in various cancers. The precise role that lncRNA expression plays in the pathogenesis of B-acute lymphoblastic leukemia (B-ALL) is unknown. Therefore, unbiased microarray profiling was performed on human B-ALL specimens and it was determined that lncRNA expression correlates with cytogenetic abnormalities, which was confirmed by RT-qPCR in a large set of B-ALL cases. Importantly, high expression of BALR-2 correlated with poor overall survival and diminished response to prednisone treatment. In line with a function for this lncRNA in regulating cell survival, BALR-2 knockdown led to reduced proliferation, increased apoptosis, and increased sensitivity to prednisolone treatment. Conversely, overexpression of BALR-2 led to increased cell growth and resistance to prednisone treatment. Interestingly, BALR-2 expression was repressed by prednisolone treatment and its knockdown led to upregulation of the glucocorticoid response pathway in both human and mouse B-cells. Together, these findings indicate that BALR-2 plays a functional role in the pathogenesis and/or clinical responsiveness of B-ALL and that altering the levels of particular lncRNAs may provide a future direction for therapeutic development.

overall_design: To define gene expression changes attributable to expression of lncRNAs, we transduced RS4;11 cells with a siRNA against BALR-2 or control vector.  These cells were left untreated or treated with prednisolone.

first: Thilini

last: Fernando

first: Norma

last: Rodriguez-Malave

first: Ella

middle: V

last: Waters

first: Weihong

last: Yan

first: David

last: Casero

first: Giuseppe

last: Basso

first: Martina

last: Pigazzi


title: Mechanisms of Chorioamnionitis-associated Preterm Birth: Interleukin 1 β inhibits Progesterone Receptor Expression in Decidual Cells

city: Columbus

first: S.

middle: Joseph

last: Huang

state: Ohio

department: Ob/Gyn

institute: The Ohio State University

summary: In chorioamnionitis (CAM), a major cause of preterm birth (PTB), maternal-fetal inflammatory responses in the decidua and amnio-chorion cause the release of cytokines that elicit cervical ripening, fetal membrane rupture and myometrial activation. We posited that this inflammatory milieu can trigger PTB via inhibited progesterone receptor (PR) expression and increased decidual prostaglandin (PG) production. We found significantly lower decidual cell PR levels in CAM-complicated PTB using immunohistochemistry. Decidual cells (DCs) treated with IL-1β displayed decreased PR expression and significantly increased PGE2 and PGF2α production and COX2 expression.  While addition of PGF2α to DC cultures was also found to suppress PR expression, the COX inhibitor, indomethacin, did not reverse IL-1β suppression of PR expression in DC cultures. Although IL-1β treatment activated NF-B, ERK1/2 and p38 MAPK signaling cascades in DCs, only inhibition of ERK1/2 MAPK signaling completely reversed IL-1β suppressed PR levels. These findings suggest that CAM-associated PTB is induced at least in part by IL-1β-mediated functional progesterone withdrawal.

overall_design: Total RNA (n=3) obtained from cultured TDCs incubated 6h with estradiol or estradio + medroxyprogesterone acetate with or without 1 ng/ml IL-1β for 6h.

first: Fredrick

last: Schatz

first: Charles

last: Lockwood

first: Felice

last: Arcuri

first: Catalin

last: Buhimschi

first: Irina

first: Murat

last: Basar

first: Umit

last: Kayisli

first: Ozlem

last: Guzeloglu-Kayisli

first: Nihan

last: Semerci

first: Lynn

last: Buchwalder


title: LncRNA Expression Discriminates Karyotype and Predicts Survival in B-lymphoblastic Leukemia

first: Dinesh

last: Rao


title: Increased chronic lymphocytic leukemia proliferation upon IgM stimulation is sustained by the upregulation of miR-132 and miR-212

first: Teresa

last: Colombo

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

platform_organism:
Homo sapiens
synthetic construct


title: Expression data from B220+ Hspa9+/+ and Hspa9+/- CFU-PreB colonies isolated on Day 7 of culture

status: Public on Feb 04 2015

first: Matt

last: Walter

address: 4940 parkview

department: oncology

institute: washington university in st.louis school of medicine

summary:
CFU-PreB colonies are reduced in number and size in Hspa9+/- mice compared to wildtype littermates. We compared the expression profiles of these colonies to gain insight into the mechanism driving this difference.
HSPA9 is located on chromosome 5q31.2 in humans, a region that is commonly deleted in patients with myeloid malignancies [del(5q)], including myelodysplastic syndromes (MDS).  HSPA9 expression is reduced by 50% in patients with del(5q)-associated MDS, consistent with haploinsufficient levels. Zebrafish mutants and knockdown studies in human and mouse cells have implicated a role for HSPA9 in hematopoiesis. To comprehensively evaluate the effects of Hspa9 haploinsufficiency on hematopoiesis, we generated an Hspa9 knockout mouse model. While homozygous knockout of Hspa9 is embryonic lethal, mice with heterozygous deletion of Hspa9 (Hspa9+/-) are viable and have a 50% reduction in Hspa9 expression. Hspa9+/- mice have normal basal hematopoiesis and do not develop MDS. However, Hspa9+/- mice have a cell-intrinsic reduction in bone marrow CFU-PreB colony formation without alterations in the number of B-cell progenitors in vivo, consistent with a functional defect in Hspa9+/- B-cell progenitors. We further reduced Hspa9 expression (<50%) using RNAi and observe reduced B-cell progenitors in vivo, indicating that appropriate levels (≥50%) of Hspa9 are required for normal B-lymphopoiesis in vivo. Knockdown of Hspa9 in an IL-7 dependent mouse B-cell line reduced Stat5 phosphorylation following IL-7 receptor stimulation, supporting a role for Hspa9 in Stat5 signaling in B-cells. Collectively, these data implicate a role for Hspa9 in B-lymphopoiesis and Stat5 activation downstream of IL-7 signaling.

overall_design: Bone marrow cells from 5 Hspa9+/+ and 5 Hspa9+/- mice were independently cultured in CFU-PreB methylcellulose medium for 7 days. PreB colonies were isolated and B220+ cells were flow sorted for RNA isolation.

first: Kilannin

last: Krysiak

first: Justin

last: Tibbitts

first: Jin

last: Shao

first: Tuoen

last: Liu

first: Matthew

last: Ndonwi


title: Expression data from renal dendritic cells under homeostatic conditions and from donor and host dendritic cells from renal allografts (3 days post-transplantation), isolated from cortex and medulla.

first: Thomas

last: Hielscher

address: INF 280

department: Biostatistics

institute: German Cancer Research Center

summary: Renal dendritic cells play key roles in renal homeostasis and during kidney allograft rejection. Microarray analysis aims to evaluate whether dendritic cells modulate their gene expression profile in relation to their distribution in the different renal compartments (with varying biophysical characteristics), under homeostatic conditions and during acute renal allograft rejection (3 days post-transplantation).

overall_design: Renal dendritic cells from homeostatic (healthy) kidneys and donor/host dendritic cells from renal allografts (3 days post-kidney transplantation) were isolated from cortex and medulla, through fluorescence-activated cell sorting (FACS). Total RNA was isolated from FACS-sorted cells and amplified. The cDNA product was fragmented, biotin-labeled and hybridized on Affimetrix arrays.

first: Federica

last: Chessa


title: Human bone and marrow niche formation by mesenchymal progenitors in vivo is predefined by an organotypic epigenetic signature

city: Graz

first: Andreas

last: Reinisch

address: Auenbruggerplatz 38

department: Dept. of Internal Medicine, Division of Hematology, Stem Cell Research Unit

country: Austria

institute: Medical University of Graz

summary: In this study, we have analyzed DNA methylation characteristics of human mesenchymal stem and progenitor cells (MSPCs) form different tissue sources including bone marrow (BM), white adipose tissue (WAT ), umbilical cord (UC) as well as dermal fibroblasts by using the HumanMethylation450K array. Cells able to form bone through endochondral ossification and attract bone marrow in an innovative in vivo model were compared to cells lacking these capacities. Interestingly only BM-derived MSPCs were capable of bone formation and marrow attraction. These features correlated with unique epigenetic characteristics potentially enabling BM-derived cells to undergo endochondral ossification.

overall_design: 12 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Nathalie

last: Etchart

first: Nicole

last: Hofmann

first: Margareta

last: Fruehwirth

first: Anna

last: Ortner

first: Daniela

last: Thaler

first: Birgit

last: Feilhauer

first: Udo

last: Hartwig

first: Christine

last: Beham-Schmid

first: Slave

last: Trajanoski

first: Wolfgang

last: Wagner

first: Qiong

last: Lin

first: Christian

last: Dullin

first: Frauke

last: Alves

first: Katharina

last: Schallmoser

first: Michael

last: Andreeff

first: Dirk

last: Strunk


title: Disruption of STAT3 signaling promotes KRAS induced lung tumorigenesis

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

institute: Medical University Vienna

summary: Oncogenic STAT3 functions are known in various malignancies. We found that STAT3 plays an unexpected tumor suppressive role in KRAS-mutant non-small-cell-lung cancer (NSCLC). In mice, tissue-specific inactivation of Stat3 resulted in increased Kras (G12D)-driven NSCLC initiation and malignant progression leading to markedly reduced survival. Clinically, low STAT3 expression levels correlate with poor survival in human lung adenocarcinoma patients with smoking history. Consistently, KRAS-mutant lung tumors showed reduced STAT3 levels. Mechanistically, we show that STAT3 controls NFκB-induced IL-8-expression by sequestering NFκB in the cytoplasm while IL-8 in turn regulates myeloid tumor infiltration and tumor vascularization thereby promoting tumor progression. These results identify a novel STAT3-NFκB-IL-8 axis in KRAS-mutant NSCLC with therapeutic and prognostic relevance

overall_design: WT: Control lung; KRAS: Lung tumors expressing KRAS G12D; KRAS STAT3 KO: Lung tumors expressing KRAS G12D- STAT3 deficient; tumors of four mice pooled per sample

first: Emilio

last: Casanova

first: Beatrice

last: Grabner


title: A DNA methylation definition of biologically distinct breast cancer subtypes

first: Manel

last: Esteller

summary: Genome wide DNA methylation profiling of normal and tumoral tissues of the breast. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450 thousand CpGs in fresh frozen tissue samples (40 primary breast tumours and 17 normal breast tissues). Samples included morphologically normal samples of each tissue and tumor samples.

overall_design: Bisulphite converted DNA from the 57 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip.

first: Olafur

last: Stefansson


title: Tenascin-C Protects Cancer Stem-Like Cells from Immune Surveillance

status: Public on Feb 03 2015

city: Pula

first: Ignazio

middle: Stefano

last: Piras

address: Loc. Piscinamanna

summary: Precociously disseminated cancer cells may seed quiescent sites of future metastasis if they can protect themselves from immune surveillance. However, there is little knowledge about how such sites might be achieved. Here we present evidence that prostate cancer stem-like cells (CSC) can be found in histopathologically negative prostate draining lymph nodes (PDLN) in mice harboring oncogene-driven prostate intraepithelial neoplasia (mPIN). PDLN-derived CSC were phenotypically and functionally identical to CSC obtained from mPIN lesions, but distinct from CSCs obtained from frank prostate tumors. CSC derived from either PDLN or mPIN used the extracellular matrix protein Tenascin-C (TNC) to inhibit T cell receptor-dependent T cell activation, proliferation and cytokine production. Mechanistically, TNC interacted with α5β1 integrin on the cell surface of T cells, inhibiting reorganization of the actin-based cytoskeleton therein required for proper T cell activation. CSC from both PDLN and mPIN lesions also expressed CXCR4 and migrated in response to its ligand CXCL12, which was overexpressed in PDLN upon mPIN development. CXCR4 was critical for the development of PDLN-derived CSC, as in vivo administration of CXCR4 inhibitors prevented establishment in PDLN of an immunosuppressive microenvironment. Taken together, our work establishes a pivotal role for TNC in tuning the local immune response to establish equilibrium between disseminated nodal CSC and the immune system.

overall_design: A total of six sample of TPIN (N = 3) and TNE (N = 3) cultured cells from TRAMP mouse model were analyzed

first: E

last: Jacchetti

first: S

last: Caputo

last: Mazzoleni

first: C

last: Brambillasca

first: M

last: Grioni

first: I

first: U

last: Restuccia

first: A

last: Calcinotto

last: Freschi

last: Bachi

first: R

last: Galli

last: Bellone


title: Gene expression data from Peyer's patch mononuclear phagocyte system

city: MARSEILLE

first: Hugues

last: Lelouard

address: Centre d’Immunologie de Marseille-Luminy  Parc Scientifique & Technologique de Luminy, 163 avenue de luminy

country: France

institute: CIML

summary:
Peyer’s patches (PP) are primary inductive sites of mucosal immunity. Defining PP mononuclear phagocyte system (MPS) is thus crucial to understand the initiation of mucosal immune response. We provide a comprehensive analysis of the phenotype, distribution,
ontogeny, lifespan, function and transcriptional profile of PP MPS. We show that monocytes give rise to macrophages and to lysozyme-expressing DC (LysoDC) which are both involved in particulate antigen uptake, display strong innate antiviral and antibacterial gene
signatures and, upon TLR7 stimulation, secrete IL-6 and TNF but no IL-10. However, unlike macrophages, LysoDC display a rapid renewal rate, strongly express genes of the MHCII presentation pathway and prime naïve helper T cells for IFNg production. Our results show
that in PP,  at steady state, monocytes generate both LysoDC and macrophages which display distinct features from their adjacent villus counterparts.

overall_design:
3 replicates of 3 different mononuclear phagocyte subsets have been extracted from Peyer's Patches of WT C57Bl/6 mice: CD11b+ DC, lysoDC and lysoMac. The total RNA of PP-sorted cells from the 3 independent experiments was extracted with a Qiagen  micro RNAeasy
PLUS kit. Quantity, quality and absence of genomic DNA contamination were assessed with a Bioanalyser (Agilent). Microarray experiments were performed by the Plateforme Biopuces of Strasbourg (France) using the GeneChip® Mouse Gene 1.0 ST array.

first: Johnny

last: Bonnardel

first: Clément

last: Da Silva

first: Sandrine

last: Henri

first: Samira

last: Tamoutounour

first: Lionel

last: Chasson

first: Frederic

last: Montañana-Sanchis

first: Jean-Pierre

last: Gorvel


title: Gene expression profiling of dectin-1 and NFAT responsive genes in dendritic cells

city: Farmington

first: Marina

last: Yurieva

state: Connecticut

address: 10 Discovery dr

department: Computational Sciences

institute: Jackson Laboratory

summary:
This study provides the dectin-1 and NFAT responsive genes for 2h and 4h of curdlan treatment.
Affymetrix Mouse Gene 1.0ST Arrays were used to profile gene expression in curdlan-stimulated D1 cells (2h or 4h exposure) that had been treated or not with FK506 for the duration of culture.

overall_design: Dendritic cell line D1 was treated with curdlan for 2h and 4h, and curdlan + Fk506 for 2h and 4h in three replicate.

first: Hong-Bing

last: Yu


status: Public on Feb 02 2015

city: Kumamoto

first: Shinjiro

last: Hino

address: 2-2-1 Honjo

institute: Kumamoto University

summary: Transcriptome analysis of LSD2-depleted HepG2 cells revealed that many of the target genes were related to lipid metabolism. We found that LSD2 is an important epigenetic regulator of hepatic lipid metabolism.

overall_design: We depleted LSD2 in HepG2 human hepatic cells using three different siRNAs, and then carried out an expression microarray experiment.

first: Katsuya

last: Nagaoka

first: Mitsuyoshi

last: Nakao


title: Microarray analysis of Adipose tissue of Short-term HFD-fed mice

city: Seoul

first: Jae Bum

last: Kim

address: Bldg 105-Rm. 333, Seoul National University, San 56-1, Sillim Dong, Kwanak-Gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

summary: Tissue inflammation is a key factor underlying insulin resistance in established obesity. Several models of immuno-compromised mice are protected from obesity-induced insulin resistance. However, it is unanswered whether inflammation triggers systemic insulin resistance or vice versa in obesity. The purpose of this study was to assess these questions.

overall_design: 8-week-old C57BL/6J male mice was treated with 60% HFD for 0 day (NCD), 3 days, and 7 days. Eipididymal fat was fractionated. Each groups have three replicates.

first: Jae-Bum

first: Yun-Sok

last: Lee

first: Jin-Young

last: Huh

first: Mira

last: Ham

first: In-Jae

last: Hwang

first: Jong-In


title: Whole gene expression data from osteocyte-like cell line MLO-Y4 under large gradient high magnetic field (LG-HMF)

city: Xi'an

first: Yang

last: Wang

state: Shaanxi

address: 127 Youyi Xilu

department: Biology

institute: Northwestern Polytechnical University

summary:
osteocyte is the mechanosensor in bone, taking up pivotal position in mediating the mechano-induced bone remodeling. Dimagnetic levitation has been used to stimulating a reduced gravity environment for studing the effects of changed gravity to different organisms.we constructed a superconducting magnet based platform with a large gradient high magnetic field(LG-HMF),which can provide three apparent gravity levels (μ-g,1-g and 2-g).
osteocytes are sensetive to gravitational changes, our aim is to explore what  responses do osteocytes exists under different gravitational environments in gene level, together with filtering the up-  and down-regulated genes.

overall_design: mouse osteocyte-like cell line MLO-Y4 were cultured under three different apparent gravity levels  (μ-g,1-g and 2-g) and normal gravity environment (control) for 48 hours, after which total RNA was extracted . And then RNA samples  hybridized  on affymetrix microarrays to obtain the whole genome expression profiles. the aim that we selected 48 hours as the cell culture time was to make a comparison with our previous researches of osteocytes.

first: Airong

last: Qian

first: Zhihao

last: Chen

first: Chun

last: Yin

first: Jianhua

last: Ma

first: Dijie

last: Li

first: Fan

last: Zhao

first: Yulong

last: Sun

first: Lifang

last: Hu

first: Peng

last: Shang


title: 5-hydroxymethylcytosine marks promoters in colon that resist hypermethylation in cancer [Methylation450 Array]

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

summary: The discovery of cytosine hydroxymethylation (5-hmC) as a mechanism that potentially controls DNA methylation changes typical of neoplasia prompted us to investigate its behavior in colon cancer. 5-hmC is globally reduced in proliferating cells such as colon tumors and the gut crypt progenitors, from which tumors can arise. Here, we show that colorectal tumors and cancer cells express Ten-Eleven Translocation (TET) transcripts at levels similar to normal tissues. Genome-wide analyses show that promoters marked by 5-hmC in normal tissue, and those identified as TET2 targets in colorectal cancer cells, are resistant to methylation gain in cancer. In vitro studies of TET2 in cancer cells confirm that these promoters are resistant to methylation gain independently of sustained TET2 expression. We also find that a considerable number of the methylation gain-resistant promoters marked by 5-hmC in normal colon overlap with those that are marked with poised bivalent histone modifications in embryonic stem cells. Together our results indicate that promoters that acquire 5-hmC upon normal colon differentiation are innately resistant to neoplastic hypermethylation by mechanisms that do not require high levels of 5-hmC in tumors. Our study highlights the potential of cytosine modifications as biomarkers of cancerous cell proliferation.

overall_design: Six samples were analyzed. 2 biological replicates each of HCT116 cells stably transfected with an empty vector control (TET_KD_Plk), with shRNA to TET2 (TET_KD_2C) and with shRNA to TET2 and TET3 (TET_KD_2.3)

first: Santago

last: Uribe-Lewis

first: Silvia

last: Halim

first: Matthieu

last: Defrance


title: Enhancing the Functional Maturity of iPSC-Derived Human Hepatocytes Via Controlled Presentation of Cell-Cell Interactions In Vitro

status: Public on Feb 01 2015

city: Fort Collins

first: Salman

last: Khetani

state: Colorado

address: 1301 Campus Delivery, 200 West Lake Street

department: Department of Mechanical Engineering, School of Biomedical Engineering

institute: Colorado State University

summary:
Induced pluripotent stem cell-derived human hepatocyte-like cells (iHeps) could provide a powerful tool for studying the mechanisms underlying human liver development and disease, testing the efficacy and safety of pharmaceuticals across different patients (i.e. personalized medicine), and enabling cell-based therapies in the clinic. However, current in vitro protocols that rely upon growth factors and extracellular matrices (ECM) alone yield iHeps with low levels of liver functions relative to adult primary human hepatocytes (PHHs). Moreover, these low hepatic functions in iHeps are difficult to maintain for prolonged times (weeks to months) in culture. Here, we engineered a micropatterned co-culture (iMPCC) platform in a multi-well format that, in contrast to conventional confluent cultures, significantly enhanced the functional maturation and longevity of iHeps in culture for 4 weeks in vitro when benchmarked against multiple donors of PHHs. In particular, iHeps were micropatterned onto collagen-coated domains of empirically optimized dimensions, surrounded by 3T3-J2 murine embryonic fibroblasts, and then sandwiched with a thin layer of ECM gel (Matrigel™). We assessed iHep maturity via global gene expression profiles, hepatic polarity, secretion of albumin and urea, basal CYP450 activities, phase-II conjugation, drug-mediated CYP450 induction, and drug-induced hepatotoxicity. Conclusion:  Controlling both homotypic interactions between iHeps and heterotypic interactions with stromal fibroblasts significantly matures iHep functions and maintains them for several weeks in culture. In the future, iMPCCs could prove useful for drug screening, studying molecular mechanisms underlying iHep differentiation, modeling liver diseases, and integration into human-on-a-chip systems being designed to assess multi-organ responses to compounds.
We used Affymetrix microarrays to profile the global gene expression of co-culture stabilized iHeps (iMPCCs) relative to freshly isolated and co-culture stabilized primary human hepatocytes (2 donors).

overall_design: To assess the transcriptomic stability of iHeps in iMPCCs, RNA was extracted following 9 and 21 days of culture for hybridization to Affymetrix microarrays. The hepatic maturation state of iHeps was assessed by comparing gene expression against microarrays containing data from two primary human hepatocyte donors, both following hepatocyte isolation (day 0) and after stabilization in the micropatterened co-culture platform (day 6 and day 42 MPCCs), as previously described.

first: Dustin

last: Berger


title: Enterohemorrhagic Escherichia coli (EHEC) deletions of glmY and glmZ

city: Dallas

first: Charley

last: Gruber

state: TX

address: 6000 Harry Hines

department: Microbiology

institute: UTSW

summary: Transcriptional analysis of the effects of the deletion of the sRNAs glmY and glmZ in EHEC

overall_design: Wt, ΔglmY, and ΔglmZ strains were grown for 6 hours in low glucose DMEM under static conditions and then processed according to the manufacters instructions.

first: Vanessa

last: Sperandio


title: Inhibition of Interleukin-6 (IL-6) Signaling and Tumor Growth by a Human Neutralizing Anti-IL-6 Antibody with a Prolonged Half-Life

city: Gaithersburg

first: Zheng

last: Liu

address: One Medimmune Way

institute: Medimmune LLC

summary: Interleukin-6 (IL-6) is a pleiotropic cytokine that plays a major role in responding to injury or infection as well as immune response, inflammation, and hematopoiesis.  High levels of circulating IL-6 are observed in many tumor types and are associated with poor outcomes.  We show that knockdown of IL-6 or IL-6 receptor (IL-6R) inhibits IL-6 signaling and cell viability.  In contrast, over-expression of IL-6 enhances tumor growth in vitro and in vivo, thereby supporting the role of IL-6 in tumorigenesis.  We developed a human monoclonal antibody against human IL-6 (MEDI5117) that bears Fc mutations (YTE) to extend its half-life.  We tested this antibody in several cancer cell lines that secrete high levels of IL-6, soluble IL-6R, and express gp130.  High constitutive pSTAT3 (phosphorylated signal transducer and activator of transcription 3) activation is seen in several of these cell lines, suggesting autocrine growth stimulation by IL-6. Treating these cell lines with MEDI5117 effectively blocked phosphorylation of STAT3 and inhibited IL-6-induced cell proliferation.  In vivo, MEDI5117 suppressed the growth of multiple cancer xenograft models and specifically modulated IL-6 signaling and downstream gene expression.  Combining MEDI5117 with chemotherapy or gefitinib demonstrated significantly enhanced anti-tumor activities in vivo.  Taken together, our data suggest that IL-6 signaling contributes to tumor growth, thereby supporting the development of MEDI5117 as a therapy to treat solid tumors.

overall_design: Xenograft tumors from DU145, KPL4, and NCI-H1650 were treated with 30 mg/kg of MEDI5117 or IgG isotype control IgG1 for a total of two doses.  Differentially expressed genes were identified and canonical pathway enrichment analysis was performed

first: Haihong

last: Zhong

first: Rosa

last: Carrasco

first: Cui

first: Shannon

last: Breen

first: Yong

last: Chang

first: Jiaqi

last: Huang

first: Yihong

last: Yao

first: David

last: Tice

first: Ronald

last: Herbst

first: Zhan

last: Xiao

first: Robert

last: Hollingsworth


title: DNA Methylation Changes and Childhood Asthma in the Inner City [methylation]

city: Aurora

last: Schwartz

state: CO

address: Anschutz Medical Campus

department: Medicine

institute: University of Colorado, Anschutz Medical Campus

summary: Background:  Epigenetic marks, like asthma, are heritable. They are influenced by the environment, direct the maturation of T cellslymphocytes, and have been shown to enhance the development of allergic airways disease in mice.  Thus, we hypothesized that epigenetic marks are associated with allergic asthma in inner-city children.  Methods:  We compared methylation patterns and gene expression in inner-city children with persistent atopic asthma versus healthy controls, using DNA and RNA from peripheral blood mononuclear cells (PBMCs) from inner city children aged 6-12 years with persistent atopic asthma children and healthy controls.     Results were externally validated with the GABRIELA study population.    Results:  Comparing asthmatics (N=97) to controls (N=97), we identified 81 regions that were differentially methylated.  Several immune genes were hypomethylated in asthmatics, including IL-13, RUNX3, and a number of specific genes relevant to natural killer cells (KIR2DL4, KIR2DL3, KIR3DL1, and KLRD1) and T cells lymphocytes (TIGIT).   14 differentially methylated regions (DMRs) were associated with the serum IgE concentration of IgE, including RUNX3.  These results were internally and externally validated with a global methylation assessment using a different methodology in our inner-city cohort and an independent European cohort (GABRIELA).  Hypo- and hypermethylated genes tended to be associated with increased and decreased gene expression, respectively (P<0.6x10-11 for asthma and ; P<0.01 for IgE).  To further explore the relationship between methylation and gene expression, we created a matrix of genomic changes in methylation versus transcriptional changes (methyl eQTL) for asthma, and identified cis- and trans-regulated genes whose expression was related to asthma asthma-associated methylation marks.

overall_design: peripheral blood mononuclear cells (PBMCs) from 97 atopic asthmatic and 97 nonatopic nonasthmatic children

first: Ivana

last: Yang

first: Brent

last: Pedersen

first: Andrew


title: mRNA Profiling of cytoplasmic and polysome fractions from #483 T-ALL treated with 4EGI-1 or DMSO

city: Hannover

first: Adrian

last: Schwarzer

address: Carl-Neuberg-Str. 1

department: Experimental Hematology

institute: Hannover Medical School

type:
Expression profiling by array
Third-party reanalysis

summary: High activation of the PI3K-AKT-mTOR pathway is characteristic for T-cell acute lymphoblastic leukemia (T-ALL). Here we investigated how 4EGI-1, a small inhibitor of cap-dependent translation, induces apoptosis in T-ALL clones displaying hyperactive PI3K-AKT-mTOR signaling.  4EGI-1 treatment  reduced the ribosomal occupancy of transcripts that define the molecular difference between T-ALL blasts and normal thymocytes. These transcripts encoded proteins for the translational machinery, for mitochondrial metabolism as well as oncoproteins such as Cyclin D1, Bcl-2 and c-myc. Therefore, targeting translation initiation proves valuable in situations where mTOR is activated by multiple events.

overall_design: For each biological replicate 5 x 107 #483 T-ALL cells were treated with 100 μM 4EGI-1 or DMSO. After 2 h incubation at 37°C cells were washed in ice-cold PBS containing cycloheximide (0.1 mg/ml), pelleted and resuspended in extraction buffer (20 mM Tris-HCl, pH 8.0, 140 mM KCl, 0.5 mM DTT, 5 mM MgCl2, 0.5 % nonidet-P40, 0.1 mg/ml cycloheximide, 10000 IU/ml dalteparin sodium) and incubated for 5 min on ice. All subsequent steps were carried out in the cold. After centrifugation for 10 min at 12000 x g, 0.4 ml supernatant was layered onto a 12 ml linear sucrose gradient (10 – 50% sucrose [w/v] in extraction buffer without nonidet-P40) and centrifuged at 4 °C in an SW40Ti rotor (Beckman) at 35000 rpm without brake for 120 min. The gradients were harvested and absorbance profiles at 254 nm recorded (type 11 optical unit/UA-6 detector, ISCO). 1 ml fractions were collected and supplied with 0.1 volume of 3 M sodium acetate (pH 5.2) and 1 volume of isopropanol for overnight precipitation at -20 °C. RNA was purified using Nucleospin RNAII tubes (Macherey & Nagel) following the manufacturer´s protocol. For microarray analysis RNA from polysome fractions were pooled, precipitated by adding LiCl to a final concentration of 2 M and resolubilized in 15 µl of RNase-free water. RNA concentrations were determined and the samples were stored at -80 °C. The cytosolic/total- RNA sample for normalization was obtained from the same samples (106 treated/non-treated cells) using the standard Trizol protocol.


title: DNA Methylation Changes and Childhood Asthma in the Inner City

type:
Methylation profiling by array
Expression profiling by array

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

overall_design: Refer to individual Series


title: MiR-30e in Aortic Smooth Muscle Cells and Bone Marrow Mesenchymal Stem Cells [Experiment 1]

status: Public on Jan 30 2015

city: Miami

first: Lina

last: Shehadeh

state: FL

institute: University of Miami

summary: MiR-30e represses the osteogenic program in mesenchymal stem cells (MSCs) and smooth muscle cells (SMCs) by targeting IGF2, and drives their differentiation into adipogenic or smooth muscle lineage, respectively.

overall_design:
In Experiment 1, SMCs were cultured from mouse aortas and transduced with miR-30e or control lentivirus.
In Experiment 2, MSCs were extracted from mouse bone marrow and transduced with miR-30e or control lentivirus.
In Experiment 3, the MSCs were transfected with a scrambled oligo or anti-miR-30e oligo.
In all 3 experiments, N=3 per group. RNA was extracted from each experiment and run on Affymetrix arrays.


title: MiR-30e in Aortic Smooth Muscle Cells and Bone Marrow Mesenchymal Stem Cells [Experiment 2]


title: Expression data of colony-stimulating factor (CSF) grown bone marrow derived cells

first: Yi Rang

address: 101, daehak-ro Jongro-gu

department: Microbiology and Immunology

institute: Seoul National University College of Medicine

summary:
Granulocyte-Macrophage colony stimulating factor (GM-CSF) devlops heterogenous myeloid cell populations from bone marrow progenitor cells. In vitro generated bone marrow derived cells are excellent sources for obtaining dendritic cells or macrophages, but it is still not clear about the exact mixed population characteristics of GM-CSF grown cells. We revealed here that GM-CSF grown bone marrow cell derived attaching cells were composed of dendritic cells (GM-BMDC) as well as macrophages (GM-BMM). We compared the transcriptome profiles of these cell populations as well as M-CSF grown bone marrow derived macrophages (M-BMM).
We used microarrays to detail the global profile of gene expressions between three populations of CSF-grown bone marrow derived cells: GM-CSF derived dendritic cells (GM-BMDC), GM-CSF derived macrophages (GM-BMM) and M-CSF derived macrophages (M-BMM).

overall_design: Bone marrow cells were differentiated for 7 days with 25 ng/ml GM-CSF or 20% L cell conditioned media as a M-CSF supplier. GM-BMDCs were sorted from MHCIIhighF4/80low population and GM-BMMs were sorted in the MHCIIlowF4/80high population. M-BMMs were sorted from CD11b+F4/80+ population.

first: Yi-Rang

first: Seung-Hyeok

last: Seok


title: MiR-30e in Aortic Smooth Muscle Cells and Bone Marrow Mesenchymal Stem Cells [Experiment 3]


title: Distinct mechanisms of inadequate erythropoiesis induced by tumor necrosis factor alpha or malarial pigment

city: Oxford

first: Alison

middle: T

last: Merryweather-Clarke

address: John Radcliffe Hospital, Headley Way, Headington

institute: NHSBT Oxford

summary:
The role of infection in erythropoietic dysfunction is poorly understood. In children with P. falciparum malaria, the by-product of hemoglobin digestion in infected red cells (hemozoin) is associated with the severity of anemia which is independent of circulating levels of the inflammatory cytokine tumor necrosis alpha (TNF-alpha). To gain insight into the common and specific effects of TNF-alpha and hemozoin on erythropoiesis, we studied the gene expression profile of purified primary erythroid cultures exposed to either TNF-alpha (10ng/ml) or to hemozoin (12.5microgram/ml heme units) for 24 hours. Perturbed gene function was assessed using co-annotation of associated gene ontologies and expression of selected genes representative of the profile observed was confirmed by real time PCR (rtPCR). The changes in gene expression induced by each agent were largely distinct; many of the genes significantly modulated by TNF-alpha were not affected by hemozoin.
The genes modulated by TNF-alpha were significantly enriched for those encoding proteins involved in the control of type 1 interferon signalling and the immune response to viral infection. In contrast, genes induced by hemozoin were significantly enriched for functional roles in regulation of transcription and apoptosis. Further analyses by rtPCR revealed that hemozoin increases expression of transcription factors that form part of the integrated stress response which is accompanied by reduced expression of genes involved in DNA repair. This study confirms that hemozoin induces cellular stress on erythroblasts that is additional to and distinct from responses to inflammatory cytokines and identifies new genes that may be involved in the pathogenesis of severe malarial anemia. More generally the respective transcription profiles highlight the varied mechanisms through which erythropoiesis may be disrupted during infectious disease.

overall_design: Erythroblasts derived from PBMCs were enriched to 97% purity for proerythroblast and intermediate/normoblast phases of differentiation using magnetic bead isolation. There were three treatment groups: media, P.falciparum hemozoin (12.5 microgram /ml hematin units) and tumour necrosis factor alpha(10ng/ml). Total RNA using 7.5 x105 cells per treatment from one donor was extracted using Trizol. Highly significant gene ontological findings (where  p> x10^-17 but < x10^-7) were confirmed by quantitative PCR.

first: Abigail

last: Lamikanra

first: Alex

last: Tipping

last: Roberts


title: MiR-30e in Aortic Smooth Muscle Cells and Bone Marrow Mesenchymal Stem Cells


title: In vitro assessment of drug-induced liver steatosis based on human dermal stem cell-derived hepatic cells.

city: Brussels

first: Robim

middle: M

last: Rodrigues

address: Laarbeeklaan 103

department: IVTD

institute: Vrije Universiteit Brussel

summary:
Human skin-derived precursor cells (hSKP) are a post natal stem cell population isolated from the dermis. These cells acquire hepatic characteristics upon differentiation with hepatogenic factors. Differentiated hSKP show characteristics of hepatocyte precursor cells and respond to hepatotoxic compounds in a comparable way as human hepatocyte cultures.
We used microarray analyses to evaluate the modulation of gene expression due to exposure to a steatosis-inducing compound.

overall_design: hSKP obtained from 3 different donors were firstly differentiated and cultivated in the presence or absence of sodium valproate (Na-VPA). Control and Na-VPA samples were collected after 24h exposure.

first: Steven

last: Branson

first: Agapios

last: Sachinidis

first: Veerle

last: De Boe

first: Vera

last: Rogiers

first: Joery

last: De Kock

first: Tamara

last: Vanhaecke


title: Selective Loss of RB in Resistant EGFR Mutant Lung Adenocarcinomas that Transform to SCLC

city: Boston

first: Kenneth

middle: N

last: Ross

address: 450 Brookline Ave., Rm M640

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

type:
Expression profiling by array
Genome variation profiling by SNP array


title: Intra-sample heterogeneity of sperm DNA methylation

status: Public on Jan 31 2015

city: Salt Lake City

first: Douglas

last: Carrell

state: UT

address: 675 Arapeen Dr. Suite 201

institute: University of Utah

summary: Genome wide DNA methylation profiling of 2 distinct subpopulations of sperm within a single ejaculate. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs. Samples were provided by 20 normozoospermic individuals. A density gradient centrifugation was performed on each samples to yeild two distict populations for each ejaculate (one from the 90% isolate layer high quality sperm and one from the 35% isolate layer low quality sperm of the column).

overall_design: Bisulphite converted DNA from the 40 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Timothy

middle: G

last: Jenkins


title: Selective Loss of RB in Resistant EGFR Mutant Lung Adenocarcinomas that Transform to SCLC [gene expression]

summary:
The study was designed to identify the molecular changes that occur in EGFR mutant NSCLCs that become resistant to TKI by transforming to SCLC.
Tyrosine kinase inhibitors (TKIs) are effective treatments for non-small cell lung cancers (NSCLCs) with epidermal growth factor receptor (EGFR) mutations.  However, they do not lead to cures, and, on average, relapse occurs after one year of continuous treatment.  In a subset of patients, a fundamental histological transformation from NSCLC to small cell lung cancer (SCLC) is observed in the resistant cancers, but the molecular changes associated with this transformation remain unknown. Analysis of a cohort of tumor samples and cell lines derived from resistant EGFR mutant patients with SCLC transformation revealed that RB is lost in 100% of these cases, but rarely in those that remain NSCLC.  Global changes in gene expression, including increased neuroendocrine marker expression and absence of EGFR expression, are observed in cancers that transformed to SCLC.  Consistent with their genetic and epigenetic similarities to classical SCLC, cell lines derived from resistant EGFR mutant SCLC biopsies are substantially more sensitive to ABT-263 treatment compared to those derived from resistant EGFR mutant NSCLCs.  Together, these findings suggest that despite developing initially as EGFR mutant adenocarcinomas, this subset of resistant cancers ultimately take on many of the molecular and phenotypic characteristics of classical SCLC.

overall_design: The patient-derived cell line models MGH119, MGH121, MGH125, MGH126, MGH131-1, MGH131-2, MGH134 and MGH156 were developed on collagen coated plates in ACL4 medium and transferred to RPMI. MGH157 was developed initially in RPMI.  The cell line MGH141 was derived using the feeder system with irradiated fibroblasts (5000 rad) from normal patient tissue.  When a tumor cell majority was observed it was passaged off of the feeder layer and later transferred to RPMI medium for experiments.  The development of a model was considered complete when it was independent of the feeder system, free of stromal cells, and determined to maintain known patient tumor mutations. MGH119-R was derived in vitro from the treatment naive model, MGH119, through in vitro exposure to gefitinib, escalating from 10nM to a final concentration of 1μM.

first: Mathew

last: Niederst

first: Jeffrey

last: Engelman


title: Functional and evolutionary significance of human microRNA seed region mutations [miR-429]

city: Atlanta

first: Neda

last: Jabbari

state: GA

address: 315 Ferst Dr

institute: Georgia Institute of Technology

summary: MicroRNAs (miRNAs) are small non-coding RNAs that play a central role in the regulation of gene expression at the post transcriptional and/or translational level thus impacting various biological processes. Dysregulation of miRNAs could affect processes associated with progression of a variety of diseases including cancer.  Majority of miRNA targeting in animals involves a 7-nt “seed region” mapping to positions 2-8 at the molecule’s 5' end. The importance of this 7 nt sequence to miRNA function is evidenced by the fact that the seed region sequence of many miRNAs is highly conserved within and between species. In this study, we computationally and experimentally explore the functional significance of sequence variation within the seed region of human miRNAs. Our results indicate that change of a single nt within the 7-nt seed region changes the spectrum of targeted mRNAs significantly meanwhile further nt changes have little to no additional effect. This high functional cost of even a single nucleotide change within the seed region of miRNAs explains why the seed sequence is highly conserved among many miRNA families both within and between species and could help clarify the likely mechanisms underlying the evolution of miRNA regulatory control.

overall_design: mRNAs were collected from 3 miR-429 treated and 3 negative control miRNA treated HEY ovarian cancer cell samples. mRNA expression was captured on Affymetrix U133 Plus 2 chips. To compare mRNA expression pattern between the miR-429 treated cells and the negative control treated cells, present/absent calls were generated using MAS5, while signals were calculated using GCRMA and then log2 transformed. Expression of differentially expressed genes or down regulated miRanda-mirSVR predicted miRNA target genes was compared between miRNA treated samples.

first: C

last: Hill

first: N

first: L

last: Matyunina

first: J

last: McDonald


title: Functional and evolutionary significance of human microRNA seed region mutations [M12]

overall_design: mRNAs were collected from 3 M12 miRNA treated and 3 negative control miRNA treated HEY ovarian cancer cell samples. mRNA expression was captured on Affymetrix U133 Plus 2 chips. To compare mRNA expression pattern between the M12 treated cells and the negative control treated cells, present/absent calls were generated using MAS5, while signals were calculated using GCRMA and then log2 transformed. Expression of differentially expressed genes or down regulated miRanda-mirSVR predicted miRNA target genes was compared between miRNA treated samples.


title: Expression data from Em-Myc mouse lymphomas

city: Cold Spring Harbor

first: Claudio

last: Scuoppo

address: 1 Bungtown Rd

institute: Cold Spring Harbor

summary:
Ezh2 encodes for the catalyc unit of the PRC2 complex. RNAi-mediated suppressing of Ezh2 by two independent shRNAs promotes Em-myc lymphomagenesis in vivo.
Microarray were used to explore the trascriptional changes driven by suppression of Ezh2 in Em-myc cells and to identify which programs contribute to promotion of lymphoma formation.

overall_design: RNA was extracted from  purified primary  lymphoma cells  for each shRNAs targeting Ezh2 and  from two independent preparations of premalignant Em-myc cells. Mouse Genome 1.0 ST arrays were processed according to the manifacturer`s instructions.

first: Agustin

last: Chicas


title: Functional and evolutionary significance of human microRNA seed region mutations [M5]

overall_design: mRNAs were collected from 3 M5 miRNA treated and 3 negative control miRNA treated HEY ovarian cancer cell samples. mRNA expression was captured on Affymetrix U133 Plus 2 chips. To compare mRNA expression pattern between the M5 treated cells and the negative control treated cells, present/absent calls were generated using MAS5, while signals were calculated using GCRMA and then log2 transformed. Expression of differentially expressed genes or down regulated miRanda-mirSVR predicted miRNA target genes was compared between miRNA treated samples.


title: Functional and evolutionary significance of human microRNA seed region mutations

overall_design: Data for miR-429, miR-205, miR-200b, and miR-141 were each compared independently to the  same negative control data contained in the raw .CEL files nc-miR-1-1.CEL, nc-miR-1-2.CEL and nc-miR-1-3.CEL.  For each miRNA, the negative control data were re-normalized together with data only from that specific miRNA.  The experiment for M12 was performed at a later date and an independent set of negative control data was collected at that time. Therefore, only M12 data was compared to the negative control data contained in the raw .CEL files nc-miR-2-1.CEL, nc-miR-2-2.CEL, and nc-miR-2-3.CEL.


title: Functional and evolutionary significance of human microRNA seed region mutations [M14]

overall_design: mRNAs were collected from 3 M14 miRNA treated and 3 negative control miRNA treated HEY ovarian cancer cell samples. mRNA expression was captured on Affymetrix U133 Plus 2 chips. To compare mRNA expression pattern between the M14 treated cells and the negative control treated cells, present/absent calls were generated using MAS5, while signals were calculated using GCRMA and then log2 transformed. Expression of differentially expressed genes or down regulated miRanda-mirSVR predicted miRNA target genes was compared between miRNA treated samples.


title: Expression data from U-87 human glioma cells with proficient and deficient NF-кB after treatment with temozolomide

status: Public on Jan 29 2015

city: Chicago

first: Bakhtiar

last: Yamini

state: IL

address: 956 E 57th street

department: Neurosurgery

institute: Univeristy of Chicago

summary: The transcription factor, NF-кB, plays a central role in the response to DNA damage. This ubiquitous family of proteins is made up of five subunits: p50 (NF-κB1, p105), p52 (NF-κB2, p100), p65 (relA), relB, and crel that appear in their mature form as dimers. Following stimulation, NF-κB dimers translocate to the nucleus where they bind specific consensus elements (κB-sites) in the promoter region of genes involved in cell survival, inflammation and the immune system. While there is a general propensity of NF-кB to mediate survival, this is not always the case and several reports note the pro-apoptotic nature of the NF-кB pathway. In examining the NF-кB response to DNA damage, we have found that the p50 subunit plays a central role in modulating cytotoxicity following TMZ treatment in malignant glioma. In the current study, given the importance of p50 to the cytotoxic response to TMZ, we set out to identify NF-кB-dependent factors that modulate the response to TMZ.

overall_design: U-87 glioma cells stably transfected with either control-shRNA or p105-shRNA and subsequently treated with temozolomide (TMZ) were selected for RNA extraction and hybridization on Affymetrix microarrays. Each category contains 3 biologic replicates.

first: David

last: Voce

first: Wei

last: Zhang

first: Shijun

last: Kang

first: Nikolai

last: Khodarev


title: DNA methylation profiling in chondrocyte dedifferentiation in vitro

city: Shenzhen

first: Li

last: Duan

state: Guangdong

address: Futian District, Sungang WestRoad 3002#

department: Department of Orthopedics

institute: Shenzhen Second People's Hospital

summary: Genome wide DNA methylation profiling of different passages of human articular chondrocytes treated with 5-azacytidine. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,578 CpGs.Samples included 6 different passages of human articular chondrocytes with 5-azacytidine treatment, 6 different passages without 5-azacytidine treatment,

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

first: Daping

last: Wang


title: CMV-Specific CD8+ Memory T Cells Re-Emerge After Viral Challenge And Recapitulate CMV Immunity Under Various Adoptive Transfer Conditions

status: Public on Jan 28 2015

city: Philadelphia

first: Christopher

last: Snyder

state: PA

address: 233 South Tenth Street

department: Department of Microbiology and Immunology

institute: Thomas Jefferson University

summary: Reconstitution of cytomegalovirus (CMV)-specific immunity following transplant remains a primary clinical objective to prevent CMV disease, and adoptive immunotherapy of CMV-specific T cells can be an effective therapeutic approach. Due to the persistence of CMV, most CMV-specific CD8+ T cells become terminally differentiated effector cells (TEFF). However, a minor subset retains a memory phenotype (TM). Interestingly, recent studies suggest that CMV-specific CD8+ T cells with different phenotypes may have different abilities to reconstitute sustained immunity following transfer. The immunology of human CMV (HCMV) infections is reflected in the mouse model of MCMV infection. We found that HCMV- and MCMV-specific T cells displayed shared genetic programs, validating the MCMV model for studies of CMV-specific T cells in vivo. After transfer, the proliferative capacity of MCMV-specific TM cells was vastly superior to TEFF cells. Strikingly, TM cells expanded and established sustained and diverse T cell populations even after multiple challenges. Although both TEFF and TM cells could protect Rag-/- mice, only TM cells could consistently survive after transfer into immune replete, latently infected recipients and respond if recipient immunity was lost. These data show that CMV-specific TM cells retain memory function during persistent infection and can re-establish CMV immunity when necessary.

overall_design: C57BL/6 mice were infected intraperitoneally (i.p.) with MCMV strain MW97.01 between 6-16 weeks of age. Splenocytes were isolated from chronically-infected mice and co-stained with three PE-conjugated tetramers loaded with the antigenic peptides from M38, m139 and IE3, all of which promote memory inflation. Cells were then stained with fluorescently conjugated antibodies and sorted on a MoFlo cell sorter. Naïve CD8+ cells were identified as CD44lo. MCMV-specific T cells were identified as CD8+, CD44hi and tetramer binding and then further segregated into memory and effector cells subsets by their expression of KLRG1 and CD127.

first: Michael

last: Quinn

first: Holly

last: Turula

first: Mayank

last: Tandon

first: Berthony

last: Deslouches

first: Toktam

last: Moghbeli


title: Global gene expression analysis of human colorectal cancer tissue

status: Public on Jan 23 2015

city: Kashiwa

first: Shingo

last: Kawano

state: Chiba

institute: National Cancer Center Hospital East

summary:
Generally, cancer tissue is palpated as a hard mass. On the other hand, it is not clear the nature of elasticity in cancer tissue. The aim in this study is to evaluate clinical utility of measuring elastic module in colorectal cancer tissue. Using a tactile sensor, we measured the elastic module of 106 surgically resected colorectal cancer tissues. The data of the elastic module were compared with the clinicopathological findings including stromal features represented by azan and α-SMA positive area ratio in tumor area. Finally cDNA microarray profile of the tumor with high elastic module was compared with that with low elastic module
Higher elastic module in tumor was associated with pathological T-, N- and M-Stage (p < 0.001, p = 0.001 and p = 0.011, respectively). Patients with high elastic module showed shorter disease free survival than patients with low elastic module. The elastic module showed strongly positive correlation with azan positive area ratio (r = 0.908) and α-SMA positive area ratio (r = 0.921). Finally, the cDNA microarray data of the tumor with high elastic module revealed distinct gene expression profile from that with low elastic module. Assessment of elasticity of colorectal cancer tissue can be available for more accurate clinical stage or prognosis estimation. Distinct phenotypical feature of the high elastic module tumor and their strong association with stromal feature seemed to be suggesting the existence of biological mechanism involved in this phenomenon, which may contribute to the future therapy.

overall_design: We selected four samples from the highest and the lowest EM with RIN > 6.0 measured with a 2100 Bioanalyzer (Aligent Tochnologies, Santa Clara, CA, USA) and with stage II (pTNM pathologic classification). We excluded one sample in each group because of high GAPDH.

first: Yuichi

last: Higuchi

first: Motohiro

last: Kojima

first: Atsushi

last: Ochiai


title: Mertk negatively regulates adaptive immunity

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

institute: CIBEREHD

summary: Tolerogenic dendritic cells (tol-DCs) offer a promising therapeutic potential for autoimmune diseases. Tol-DCs have been reported to inhibit immunogenic responses, yet little is known about the mechanisms controlling their tolerogenic status, as well as associated specific markers. Here we show that the anti-inflammatory TAM receptor tyrosine kinase MERTK, is highly expressed on clinical grade dexamethasone-induced human tol-DCs and mediates their tolerogenic effect. Neutralization of MERTK in allogenic mixed lymphocyte reactions as well as autologous DC-T cell cultures leads to increased T cell proliferation and IFN-g production. Additionally, we identify a previously unrecognized non-cell autonomous regulatory function of MERTK expressed on DCs. Recombinant Mer-Fc protein, used to mimic MERTK on DCs, suppresses naïve and antigen-specific memory T cell activation. This mechanism is mediated by the neutralization of the MERTK agonist Protein S (PROS1) expressed by T cells. We find that MERTK and PROS1 are expressed in human T cells upon TCR activation and drive an autocrine pro-proliferative mechanism. Collectively, these results suggest that MERTK on tol-DCs directly inhibits T cell activation through the competition for PROS1 interaction with MERTK in the T cells. Targeting MERTK may provide an interesting approach to effectively increase or suppress tolerance for the purpose of immunotherapy.

overall_design: The complete database comprised the expression measurements of 54,675 genes for: immature (n=9), mature (n=7) and tolerogenic (n=8). Influence of treatment with dexamethasone (n=3) and LPS (n=2)  are included.

first: J

first: D

last: Benitez

first: R

last: Cabezón

first: E

last: Silva


title: Identification of genes regulated by HSF1 and SSBP1 in control and heat-shocked MEF cells

status: Public on Jan 27 2015

city: Ube

first: Eiichi

last: Takaki

state: Yamaguchi

address: minami-kogushi, 1-1-1

institute: Yamaguchi university

summary: To examine the expressions of HSF1 and SSBP1-mediated gene in control and heat shock conditions, we performed DNA microarray analysis.

overall_design: mRNA levels in control and heat-shocked MEF cells, which were infected with adenovirus expressing scramble RNA, or shRNA against HSF1 and SSBP1, were analyzed by DNA microarray analysis using GeneChip Mouse Gene 1.0 ST Array (Affymetrix).

first: K

last: Tan

first: A

last: Nakai


title: Expression data from SMMC-7721 cells

city: Shanghai

first: Boshi

last: Wang

address: No.800 Dongchuan Road

institute: Shanghai Cancer Institute

summary: We performed a genome wide transcription profile analysis to determine the expression alterations between control and the POH1 siRNAs transfected SMMC-7721 cells

overall_design: The liver cancer cell line SMMC-7721  transfected with either the control or POH1 siRNAs were subjected to a genome wide transcription profile analysis through Human U133 Puls 2.0 (Affymetrix) microarray

first: Yongzhong

last: Liu


title: Expression analysis of wild-type and Tfam heterozygous knockout (Tfam+/-) murine embryonic fibroblasts (MEFs).

status: Public on Jan 26 2015

city: Bar Harbor

first: Phillip

last: West

state: ME

address: 600 Main St

institute: The Jackson Laboratory

summary:
The goal of this analysis was to utilize microarray profiling to identify basal alterations in gene expression in response to TFAM depletion and mtDNA stress.
Mitochondrial DNA (mtDNA) is normally present at thousands of copies per cell and is packaged into several hundred higher-order structures termed nucleoids. The abundant mtDNA-binding protein, TFAM (transcription factor A,mitochondrial), regulates nucleoid architecture, abundance and segregation. Complete mtDNA depletion profoundly impairs oxidative phosphorylation, triggering calcium-dependent stress signalling and adaptive metabolic responses. However, the cellular responses to mtDNA instability, a physiologically relevant stress observed in many human diseases and ageing, remain poorly defined. Here we show that moderate mtDNA stress elicited by TFAM deficiency engages cytosolic antiviral signalling to enhance the expression of a subset of interferon-stimulated genes. Mechanistically, we find that aberrant mtDNA packaging promotes escape of mtDNA into the cytosol, where it engages the DNA sensor cGAS (also known as MB21D1) and promotes STING (also known as TMEM173)–IRF3-dependent signalling to elevate interferon-stimulated gene expression, potentiate type I interferon responses and confer broad viral resistance. Furthermore, we demonstrate that herpesviruses induce mtDNA stress, which enhances antiviral signalling and type I interferon responses during infection. Our results further demonstrate that mitochondria are central participants in innate immunity, identify mtDNA stress as a cell-intrinsic trigger of antiviral signaling and suggest that cellular monitoring of mtDNA homeostasis cooperates with canonical virus sensing mechanisms to fully engage antiviral innate immunity.

overall_design: Murine embryonic fibroblasts were isolated from wild-type or Tfam+/- E13.5 littermate embryos.  RNA from passage-matched wild-type and Tfam+/- MEF lines was extracted in duplicate and hybridized onto Affymetrix microarrays. Four arrays were performed in total with two technical replicates per genotype.

first: Gerald

last: Shadel


title: Gene expression analysis of in vivo-grown tumors treated with compounds that either de-bulk the tumor or target cancer stem cells

city: San Diego

first: John

last: Walker

state: CA

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

summary:
A large body of evidence has demonstrated that many human tumors are maintained by a small cell population called cancer stem cells (CSCs) or tumor progenitors, which are responsible for tumor formation, therapy resistance and metastasis. We found that ionizing radiation treatment enriches for the CSC phenotype and properties by preferential survival and expansion of tumor progenitor cells. Our studies revealed that aldehyde dehydrogenase (ALDH) activity is indicative of prostate tumor progenitor cells with increased chemo- and radioresistance, enhanced migratory potential, improved DNA- double strand break repair and activation of the signaling pathways, which promote self-renewal and epithelial-mesenchymal transition. We found that X-ray irradiation can convert the bulk tumor cells to more clonogenic and radioresistant population positive for expression of CSC markers. For the first time we showed that irradiation increases histone H3K4 and H3K36 methylation in prostate cancer cells, thereby reactivating transcription of epigenetically silenced target genes. We showed that radioresistant tumor progenitor population undergoes a phenotypical switching during the course of irradiation, suggesting that controlling the phenotypical and functional properties of CSCs during radiation therapy is ultimative for the optimization of treatment strategies. Our studies have shown that CSC markers may be beneficial in prediction of tumor radiocurability, and combination of irradiation with therapies directed against CSCs can be a useful strategy to improve cancer treatment.
To identify potential biomarkers associated with CSC population in these xenograft tumors, we performed whole genome gene expression profiling of the xenograft tumors treated with NVP-BEZ235, which eliminates prostate cancer progenitor populations or with Taxotere, which targets the bulk tumor cells as compared with vehicle-treated control mice.

overall_design: Treatment with either vehicle, Taxotere, NVP-BEZ235, or a combination of these two.  There are no replicates

first: Monica

last: Cojoc

first: Claudia

last: Peitzsch

first: Ina

last: Kurth

first: Franziska

last: Trautmann

first: Leoni

last: Kunz-Schughart

first: Gennady

last: Telegeev

first: Eduard

last: Stakhovsky

first: Karl

last: Simin

first: Stephen

last: Lyle

first: Mechthild

last: Krause

first: Michael

last: Baumann

first: Anna

last: Dubrovska


title: Gene expression study of developing mammalian vestibular organ of wild type and Insulin-Like Growth Factor I deficient mice using Affymetrix whole transcript arrays

city: Sheffield

first: Marta

last: Milo

state: South Yorkshire

address: Western Bank

department: Biomedical Science

institute: University of Sheffield

summary:
Insulin like growth factor 1 (IGF-1) has a central role in mammalian hearing and hearing loss. The auditory and vestibular systems form the inner ear and have a common developmental origin. During chicken early development IGF-1 modulates neurogenesis of the cochleovestibular ganglion but no further studies have been conducted to explore the potential role of IGF-1 in the vestibular system.
In this study we have compared the whole transcriptome of the vestibular organ from wild type and Igf1-/- mice at different developmental times.

overall_design: RNA was prepared from E18.5, P15 and P90 vestibular organs of Igf1-/- and Igf1+/+ mice and the transcriptome analyzed in triplicates using Affymetrix® Mouse Gene 1.1 ST Array Plates.

first: Lourdes

last: Rodríguez-de la Rosa


title: In vivo investigations of the effect of short- and long-term recombinant growth hormone treatment on DNA-methylation in humans

city: Kiel

first: Susanne

last: Bens

address: Arnold-Heller-Str.3 (Haus 10)

department: Institute of Human Genetics

institute: Christian-Albrechts-University Kiel & University Hospital Schleswig-Holstein

summary: Treatment with recombinant human growth hormone (rhGH) has been consistently reported to induce transcriptional changes in various human tissues including peripheral blood. For other hormones it has been shown that the induction of such transcriptional effects is conferred or at least accompanied by DNA-methylation changes. To analyse effects of short term rhGH treatment on the DNA-methylome we investigated a total of 24 patients at baseline and after 4-day rhGH stimulation. We performed array-based DNA-methylation profiling of paired peripheral blood mononuclear cell samples followed by targeted validation using bisulfite pyrosequencing. Unsupervised analysis of DNA-methylation in this short-term treated cohort revealed clustering according to individuals rather than treatment. Supervised analysis identified 239 CpGs as significantly differentially methylated between baseline and rhGH-stimulated samples (p<0.0001, unadjusted paired t-test), which nevertheless did not retain significance after adjustment for multiple testing. An individualised evaluation strategy led to the identification of 2350 CpG and 3 CpH sites showing methylation differences of at least 10% in more than 2 of the 24 analysed sample pairs. To investigate the long term effects of rhGH treatment on the DNA-methylome, we analysed peripheral blood cells from an independent cohort of 36 rhGH treated children born small for gestational age (SGA) as compared to 18 untreated controls. Median treatment interval was 33 months. In line with the groupwise comparison in the short-term treated cohort no differentially methylated targets reached the level of significance in the long-term treated cohort. We identified marked intra-individual responses of DNA-methylation to short-term rhGH treatment. These responses seem to be predominately associated with immunologic functions and show considerable inter-individual heterogeneity. The latter is likely the cause for the lack of a rhGH induced homogeneous DNA-methylation signature after short- and long-term treatment, which nevertheless is well in line with generally assumed safety of rhGH treatment.

overall_design: Bisulfite converted DNA of PB from 36 SGA born children treated long-term with rhGH and 18 SGA born children with no rhGH treatment (controls) were hybridized to the Illumina Infinium HumanMethylation 450k Bead Chip.

first: Julia

last: Kolarova

first: Ole

last: Ammerpohl

first: Jana

last: Gutwein

first: Maik

last: Welzel

first: Inka

last: Baus

first: Felix

last: Riepe

first: Thomas

last: Eggermann

first: Almuth

last: Caliebe

first: Paul-Martin

last: Holterhus

first: Reiner

last: Siebert