title: EFFECTS OF IDURSULFASE® TREATMENT ON EXTRACELLULAR MATRIX COMPONENTS, INTRACELLULAR SIGNALING AND PROLIFERATION/DIFFERENTIATION REGULATION IN CALVARIA-DERIVED BONE TISSUE OF APERT SYNDROME PATIENTS

city: Bogota

first: Diana

last: Ramirez

state: Bogota

address: Calle 53 Cra 37 Ed. 426

department: Medicine Faculty

country: Colombia

institute: Universidad Nacional de Colombia

summary: Experimental in vtiro approach to molecular pathways implicated in Apert Syndrome’s craniosynostosis through transcriptomics techniques. FGFR2 activation requires a tridimensional configuration between ligand, receptor and heparan sulfate(HS). Mutations in the extracellular region of this receptor affect the balance between proliferation and differentiation of osteoprogenitor cells, leading to craniosynostosis as Apert Syndrome (AS). We postulate that the degradation of HS in periosteal tissue in patients with AS can modify the gene expression profile and modulate cell behavior. Based on previous evidence we propose that the treatment with an enzyme that degrades HS, as Idursulfase, in periosteal tissue of patients with AS, could be affect the formation of the ternary complex (FGF / FGFR / HS), triggering changes in gene profiles expression in several molecular pathways, regarding their basal state with the mutated receptor.

overall_design:
To delineate this, fibroblasts were obtained from three patients, these were cultivated and stimulated with FGF2 for 24 hours and with Idursulfase®( Elaprase-Shire) (0.025mg / ml) for 48 hours in triplicate in biological replicas for treatment conditions (E) y untreatment conditions (ST). Total RNA (> 50 ng / uL) was obtained to validate gene expression using GeneChip Human Gene 2.0 ST Array (Affymetrix).                                                                                The Array GeneChip Human Gene 2.0 ST (Whole transcriptome,Affymetrix®) was chosen for this study. The methodological process was carried out according to manufacturer's instructions (GeneChip Whole Transcript PLUS reagent kit).  The cDNA sense was fragmented and biotinylated using TdT (terminal deoxynucleotidyl transferase) and using the GeneChip WT Terminal labeling kit.  Approximately 5.5μg of target DNA marked was hybridized to the GeneChip at 45° C for 16 hours.  The hybridized arrays were washed and stained in the fluidics station for GeneChip450 and scanned with the Scanner GCS3000 (Affymetrix).  Signal values were computed using the GeneChip™ Comand Console® software.     Raw data were extracted automatically using the data extraction protocol included in the software.  After importing the CEL files, the data were summarized and normalized using the RMA method implemented in the Affymetrix® Expression Console™.  The results were exported using the RMA analysis and then the gene level protocol was performed for determining differentially expressed genes (DEG). The statistical significance of the expression data was determined using fold change.  For each SDR set, hierarchical cluster analysis was performed using complete linkage and Euclidean distance as similarity measures.  Enrichment analysis of genes and functional annotation was performed using DAVID (http://david.abcc.ncifcrf.gov/home.jsp). Each term was assigned a score (EASA), which consists of the p-value modified by the Fisher Exact Test. If the value was less than 0.05 it was classified as enrichment.  All data analysis and visualization of differentially expressed genes were performed using R 3.1.2 (www.r-project.org). The genes obtained in functional annotations were grouped into clusters and those that had a fold change of2and significant p value were selected. Corrections of p value for the statistical significance of the findings were performed by using Bonferroni, Benjamini, and FDR tests.
To delineate this, fibroblasts were obtained from three patients, these were cultivated and stimulated with FGF2 for 24 hours and with Idursulfase®( Elaprase-Shire) (0.025mg / ml) for 48 hours in triplicate in biological replicas for treatment conditions (E) y untreatment conditions (ST). Total RNA (> 50 ng / uL) was obtained to validate gene expression using GeneChip Human Gene 2.0 ST Array (Affymetrix). The Array GeneChip Human Gene 2.0 ST (Whole transcriptome,Affymetrix®) was chosen for this study. The methodological process was carried out according to manufacturer's instructions (GeneChip Whole Transcript PLUS reagent kit).

middle: A

first: Angela

last: Muñoz

first: Lilian

last: Torres-Tobar

first: Luz

last: Gutierrez

first: Harvy

last: Velasco

first: Rolando

last: Prada

first: Angel

last: Carracedo


title: Expression data from 12 BPDCN samples, 35 T-ALL samples, and 65 AML samples

status: Public on Feb 10 2017

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

summary: Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is an aggressive hematological. We used transcriptomic analysis to investigate LXR pathway, and cholesterol metabolism in leukemic cells. Malignancy with a poor prognosis that derives from plasmacytoid dendritic cells (PDC). No consensus for optimal treatment modalities is available today and the full characterization of this leukemia is still emerging. We identified here a BPDCN-specific transcriptomic profile when compared to those of acute myeloid leukemia (AML) and T-acute lymphoblastic leukemia (T-ALL), as well as the transcriptomic signature of primary PDC. This BPDCN gene signature identified a dysregulation of genes involved in cholesterol homeostasis, some of them being liver X receptor (LXR) target genes. LXR agonist treatment of primary BPDCN cells and BPDCN cell lines restored LXR target gene expression and increased cholesterol efflux via the upregulation of ATP Binding Cassette (ABC) transporters, ABCA1 and ABCG1. LXR agonist treatment was responsible for limiting BPDCN cell proliferation and inducing intrinsic apoptotic cell death. LXR activation in BPDCN cells was shown to interfere with three signaling pathways associated with leukemic cell survival, namely: NF-κB activation, as well as Akt and STAT5 phosphorylation in response to the BPDCN growth/survival factor IL-3. These effects were increased by the stimulation of cholesterol efflux through a lipid acceptor, the apolipoprotein A1. In vivo experiments using a mouse model of BPDCN cell xenograft revealed a decrease of leukemic cell infiltration and BPDCN-induced cytopenia associated with an increased survival after LXR agonist treatment. This demonstrates that cholesterol homeostasis is modified in BPDCN and can be normalized by treatment with LXR agonists which can be proposed as a new therapeutic approach.

overall_design: Leukemic samples were obtained from patients at diagnosis, with acute leukemia through bone marrow aspirates or blood collection, for RNA extraction and hybridization on Affymetrix microarrays. Acute leukemia were classified according to the standard morphological and immunophenotypic and/or immunohistochemical World Health Organization (WHO) criteria. AML samples were sub-categorised following French-American-British (FAB) classification. T-ALL were sub-categorised as described (Asnafi et al., Blood 2003). The 12 BPDCN were obtained from our national network (authorization number DC-2008-713). Diagnosis was established BPDCN based on histopathology and immunostaining of cutaneous lesions, as described previously (Garnach-Ottou et al., Br J Haematol., 2009; Angelot-Delettre et al., Cytometry A., 2012; Riaz et al., Cancer Control., 2014).

first: Christophe

last: Roumier

first: Anne

last: Roggy


title: Expression data from adult and neonatal human platelets

status: Public on Feb 03 2017

city: MURCIA

first: Raul

last: Teruel-Montoya

address: Ronda Garay s/n

department: Hematology and Medical Oncology Deparment

country: Spain

institute: Centro Regional de Hemodonación, Morales Meseguer University Hospital, IMIB-Arrixaca

summary:
Understanding the underlying mechanisms of the well-established platelet hyporeactivity in neonates, would be of great relevance for both improving the clinical management of neonates, a population with a higher bleeding risk than adults (especially among sick and preterm infants), and getting new insights onto the regulatory mechanisms of platelet biology. Transcriptome analysis is a useful tool to identify mRNA signature affecting platelet function. However, human fetal/neonatal platelet transcriptome analysis has never been reported. Here, we used, for the first time, mRNA expression array to compare the platelet transcriptome changes during development. Microarray analysis was performed in pure platelet RNA obtained from adult and cord blood, using the same platform in two independent laboratories.
A high correlation was obtained between arrays results for both adult and neonate platelet samples. There was also a good agreement between our adult results and those previously reported in three different studies. Gene enrichment analysis demonstrated that immunity- and platelet function-related genes are highly expressed in either developmental stage. Remarkably, 201 genes were found to be differentially expressed along development. In particular, neonatal platelets contain higher levels of mRNA that are associated with protein synthesis and processing, while they carry significantly lower levels of genes related with calcium transport/metabolism and cell signaling (including GNAZ). Overall, our results highlight that variations in platelet transcriptome may underline the hypo-functional phenotype of neonatal platelets, and further support the role of platelets in cellular immune response. A better characterization of the platelet transcriptome across development may help to elucidate the implications of transcriptome changes in different pathological conditions.

overall_design: Two pools (platelet RNA from 4 newborns or 4 adults) were sent to LC Sciences laboratories (Houston, TX) (referred to as array A). Another pair of pooled platelet RNA, from 2 newborns- or 2 adults was sent to the central Molecular Biology Service of the University of Murcia (Murcia, Spain) (referred to as array B). Both arrays were performed with GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA) containing 54,675 probes covering 38,500 genes

first: Francisca

last: Ferrer-Marín

first: Raúl


title: Novel ABCG2 antagonists to reverse topotecan-mediated chemotherapeutic resistance in ovarian carcinoma xenografts.

city: Albuquerque

first: Richard

last: Larson

state: New Mexico

address: 915 Camino de Salud NE

department: Office of Research

country: USA

institute: University of New Mexico

summary:
In order to address the treatment difficulties associated with chemotherapetic resistance in ovarian cancer, we combined our compounds with topotecan and admininstered the mixture to chemoresistant Igrov1/T8 ovarian cancer
cells in vitro and Igrov1/T8 xenografts in CB-17 SCID mice.

overall_design: We ran 2 Parental Igrov1 ovarian cancer cells and 2 Igrov1 derived cell line overexpressing ABCG2, Igrov1/T8.

first: Jerec

middle: W

last: Ricci

first: Debbie

middle: M

last: Lovato

first: Virginia

last: Severns

first: Larry

last: Sklar

middle: S


title: Gene expression response to Pax7 in murine myoblasts

status: Public on Feb 01 2017

city: London

first: Matthew

last: Arno

state: LONDON

address: 150 Stamford Street

department: Genomics Centre

country: United Kingdom

institute: King's College London

summary:
Pax7 is a paired box transcription factor that is central to skeletal muscle satellite cell function
Microarrays were used to examine gene expression after primary murine satellite cell-derived myoblasts were retrovirally infected with constructs encoding Pax7, PAX7-FOXO1A, dominant negative Pax7-ERD and retroviral control.

overall_design: Primary murine satellite cell-derived myoblasts were expanded and then divided and each infected with a different construct. After a further 48 hours in culture, RNA was isolated.

first: Robert

middle: B

last: White

first: Peter

last: Zammit


title: Genes differentially expressed in long-term hematopoietic stem cells with latexin deletion [multipotent progenitor cells, MPPs]

status: Public on Feb 09 2017

city: Lexington

first: Ying

last: Liang

state: KY

address: Health Sciences Research Bldg. Rm. 340, 1095 V.A. Drive

department: Toxicology and Cancer Biology

institute: University of Kentucky

summary:
Latexin is a hematopoietic stem cells (HSCs) and progenitor cells (HPCs) regulatory gene. Its deletion leads to the expansion of HSC and HPC population. The underlying mechanims are largely unknown.
We therefore perfored microarrary analysis in HPCs with (Lxn-/-) and without (wild-type, WT) latexin deletion, and determined genes that were altered by latexin deletion. This led us to identify the molecular mechanims by which latexin regulates HSC function.

overall_design: HPCs were immunophenotypically-defined as Lin-Sca1+c-Kit+Flt2+CD34+ (specifically named as multipotent progenitor cells, MPP) and sorted from bone marrow of WT and Lxn-/- mice. Total RNA was extracted and probed onto Affymetrix Gene Chip MoGene-1-0-st-v1 arrays. Three biological samples were obtained from each strain. Each sample contained nearly 100,000 LT-HSCs that were pooled from 10-20 mice. Microarray data were normalized by RMA method. The limma package(Smyth 2004) in R/Bioconductor was used to determine the differentially expressed genes.

first: Yi

last: Liu


title: Expression data from ovarian cancer cells grown in different culture condtions

status: Public on Feb 02 2017

city: Bethesda

first: Christina

last: Annunziata

address: 10 Center Drive, Room 4B54

department: Women's Malignancies Branch

institute: National Cancer Institute

summary:
Cells grown in culture conditions that enrich for cancer stem cells are more tumoigenic and have higher resistance to chemotherapy.
We used Affymetric microarrays to understand the global gene expression patterns that are suppressed or enhanced to understand the mechanisms of drug resistance and tumorigenecity

overall_design: Ovarian cancer cells were grown in various conditions for three days before collection of cells for RNA extraction, purification and hybridization on Affymetrix arrays. The experiment was performed three for each condition leading to three independent biological replicates.


title: Genes differentially expressed in long-term hematopoietic stem cells with latexin deletion [Long-term hematopoietic stem cells, LT-HSCs]

summary:
Latexin is a hematopoietic stem cell (HSC) regulatory gene. Its deletion leads to the expansion of HSC population. The underlying mechanims are largely unknown.
We therefore perfored microarrary analysis in HSCs with (Lxn-/-) and without (wild-type, WT) latexin deletion, and determined genes that were altered by latexin deletion. This led us to identify the molecular mechanims by which latexin regulates HSC function.

overall_design: Long-term HSCs were immunophenotypically-defined as Lin-Sca1+c-Kit+Flt2-CD34- and sorted from bone marrow of WT and Lxn-/- mice. Total RNA was extracted and probed onto Affymetrix Gene Chip MoGene-1-0-st-v1 arrays. Three biological samples were obtained from each strain. Each sample contained nearly 100,000 LT-HSCs that were pooled from 10-20 mice. Microarray data were normalized by RMA method. The limma package(Smyth 2004) in R/Bioconductor was used to determine the differentially expressed genes.


title: DNA methylation profile of triple negative breast cancer specific genes (validation)

city: New Lambton Heights

first: Kelly

last: Avery-Kiejda

state: NSW

address: Kookaburra Circuit

department: Medical Genetics

country: Australia

institute: Hunter Medical Research Institute

summary:
Purpose Triple negative breast cancer (TNBC) is the most aggressive breast cancer subtype with no targeted treatment available. Our previous study identified 38 TNBC-specific genes with altered expression in tumour samples compared to normal samples. This study aimed to identify whether DNA methylation contributed to these gene expression changes in the same breast cancer cohort. Additionally, we aimed to identify a whole genome methylation profile that contributes to the progression from primary breast tumour to lymph node metastasis.  Methods We used the DNA of 23 primary TNBC samples, 12 matched lymph node metastases, and 11 matched normal adjacent tissues to perform 450K Illumina methylation arrays. The results were validated in an independent cohort of 70 primary TNBC samples.  Results The gene expression of 16/38 TNBC-specific genes was associated with significantly altered methylation. Furthermore, altered methylation of 18 genes associated with lymph node metastasis was identified and validated in an independent cohort. Additionally, novel methylation changes between primary tumours and lymph node metastases, as well as those associated with survival were identified.  Conclusion This study has shown that DNA methylation plays an important role in altered gene expression patterns of TNBC-specific genes and is the first study to perform whole genome DNA methylation analysis that includes matched lymph node metastases in this breast cancer subtype. This novel insight into the progression of TNBC to secondary cancers may provide potential prognostic indicators for this hard-to-treat breast cancer subtype.
Validation cohort (70 IDC TNBC samples)

overall_design: Methods We used the DNA of 23 primary TNBC samples, 12 matched lymph node metastases, and 11 matched normal adjacent tissues (3 pools and one single) to perform 450K Illumina methylation arrays. The results were validated in an independent cohort of 70 primary TNBC samples

first: Andrea

last: Mathe

first: Michelle

last: Wong-Brown

first: Warwick

middle: J

last: Locke

first: Clare

last: Stirzaker

first: Stephen

middle: G

last: Braye

first: John

middle: F

last: Forbe

first: Susan

last: Clar

last: Avery-Kiejd

first: Rodney

last: Scott


title: Expression data from mouse brain cortex

city: Boston

first: Erming

last: Wang

state: MA

address: 72 E Concord street

department: Pharmacology

institute: Boston University

summary: Recent research has shown that peripheral treatment with amylin reduces Alzheimer’s disease (AD) pathology in the brain and improves learning and memory in AD mouse models. To understand the mechanism underlying this novel treatment for AD, we interrogated the transcriptome for changes in cortical gene expression in amyloid precursor protein (APP) transgenic mice treated with amylin compared to a vehicle treated group and wild type (WT) mice. Using weighted gene co-expression network analysis, we discovered that amylin treatment influenced two gene modules linked to AD pathology: 1) a module related to proinflammation and transport/vesicle process that included a hub gene of Cd68, and 2) a module related to mitochondria function that included a hub gene of Atp5b. Amylin treatment restored the expression of most genes in the APP cortex toward levels observed in the WT cortex including 23 key hub genes in these two modules. In cultured activated microglia cell line BV-2, we validated that Cd68 expression was attenuated by amylin through binding to the amylin receptor. Using publically-available transcriptomic human data, we found that the expression levels of the orthologues of these hub genes, including Cd68 and Atp5b, strongly correlated with the neurofibrillary tangle burden in the AD brain and with Mini-Mental Status Exam scores. Our study is the first to show the transcriptome-wide targets of amylin treatment, and further supports the potential use of amylin-type peptides to treat AD.

overall_design: Cortical transcriptomic changes in gene expression were investigated on 5xFAD transgenic mice treated with amylin compared to a vehicle treated group and wild type (WT) mice.

first: E

first: H

last: Zhu

first: X

first: A

middle: C

last: Gower

first: M

last: Wallack

first: J

middle: K

last: Blusztajn

first: N

last: Kowall

first: W

middle: Q

last: Qiu


title: Monocyte-derived dendritic cells response to mycobacterial glycolipid, phosphatidyl-inositol mannosides (PIM)

status: Public on Jan 31 2017

city: Kagoshima

first: Kenji

last: TOYONAGA

address: 8-35-1 Sakuragaoka

department: Department of Immunology

country: Japan

institute: Graduate School of Medical and Dental Sciences, Kagoshima University

summary:
Phosphatidyl-inositol mannosides (PIM) are unique mycobacterial glycolipids. However, the PIM-induced immunostimulatory activities remain controversial.
Here we report on gene expression analysis of monocyte-derived dendritic cells stimulated with tri-acylated PIM2 (AcPIM2) or tetra-acylated PIM2 (Ac2PIM2). Results provide evidence for the adjuvant activity of PIM.

overall_design: Total RNA isolated from monocyte-derived dendritic cells stimulated with tri-acylated PIM2 (AcPIM2) or tetra-acylated PIM2 (Ac2PIM2) for 8 hours.

last: Toyonaga

first: Sho

last: Yamasaki


title: Gene expression in microvascular endothelial cells co-cultured with dorsal root ganglion cells

city: Kahoku-gun

first: Yasuo

last: Yoshitomi

state: Ishikawa

address: 1-1 Daigaku, Uchinada-machi

department: Biochemistry

institute: Kanazawa Medical University

summary: Analysis of gene expressions in human microvascular endothelial cells (HMVEC)s following co-cultured with mouse dorsal root ganglion cells. Results provide insight into a role for responses of neurovascular interaction in endothelial cell in angiogenesis and vascular remodeling.

overall_design: Gene expression analysis of primary human microvascular endothelial cells (HMVECs) co-cultured with primary mouse dorsal root ganglion cells (DRGs) in comparison with separately cultured HMVECs and DRGs.


title: E-cadherin re-expression shows in vivo evidence for mesenchymal to epithelial transition in clonal metastatic breast tumor cells

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

summary:
Substantial experimental evidence has shown that dedifferentiation from an epithelial state to a mesenchymal-like state (EMT) drives tumor cell metastasis. This transition facilitates tumor cells to acquire motility and invasive features. Intriguingly, tumor cells at the metastatic site are primarily epithelial, and it is believed that they re-differentiate back to an epithelial state by a process called mesenchymal to epithelial transition (MET). However, there is little in vivo evidence to support the MET process.
In this study we show that clonal epithelial tumor cells undergo EMT (including loss of E-cadherin expression) in the primary tumor over time. At the metastatic site the cells show evidence of MET by re-expression of E-cadherin.

overall_design: To investigate EMT and MET in vivo, we generated two epithelial (E) and two mesenchymal (M) primary clonal cell lines from a spontaneous mouse mammary tumor (Tg MMTV/neu). These cells were labeled with reporters (GFP and luciferase), and tracked in vivo during primary tumor growth and subsequent metastasis. Once E cells were implanted into the mammary fat pad, E-cadherin expression progressively decreased and continued to decrease as the primary tumor enlarged over time. A greater percentage of E tumor cells expressed E-cadherin at the secondary metastatic site as compared to the corresponding primary tumor. Collectively, these data provide direct in vivo evidence that epithelial tumor cells have metastatic potential, undergo EMT at the primary tumor site, and MET at the metastatic site.

first: Katie

last: Palen

first: James

last: Weber

first: Michael

last: Dwinell

first: Bryon

middle: D

last: Johnson

first: Ramani

last: Ramchandran

first: Jill

last: Gershan


title: Aberrant methylation-mediated silencing of microRNAs contributes to HPV-induced anchorage independence

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

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

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

overall_design: Refer to individual Series


title: Microarray of CHD1 Knockdown in PC3 cells and CHD1 knockout in LNCaP cells

city: Houston

first: Guocan

last: Wang

state: TX

address: 1515 Holcombe Blvd, T7.3900

institute: MD Anderson Cancer Center

summary: We used microarrays to study the global gene expression and identified differentially expressed genes in CHD1 knockdown PC-3 cells and CHD1 KO LNCaP cells, aiming to identify genes and pathways that are regulated by CHD1

overall_design: 2 independent shRNAs for CHD1 and 1 control shRNA were used in PC3 cells. In addtion, CHD1 knockout cells were generated by CRISPR genome editing using sgRNAs. The samples used in the microarray analysis were in triplicates.

first: G

first: D

last: Zhao

first: R

last: DePinho

first: Y


title: A common promoter hypomethylation signature in invasive breast, liver and prostate cancer cell lines reveals novel targets involved in cancer invasiveness (methylation)

city: Montreal

first: David

last: Cheishvili

state: Quebec

address: 3655 Sir William Osler

country: Canada

institute: McGill

summary:
Cancer invasion and metastasis is the most morbid aspect of cancer and is governed by different cellular mechanisms than those driving the deregulated growth of tumors. We addressed here the question of whether a common DNA methylation signature of invasion exists in cancer cells from different origins that differentiates invasive from noninvasive cells. We identified a common DNA methylation signature consisting of hyper- and hypomethylation and determined the overlap of differences in DNA methylation with differences in mRNA expression using expression array analyses. A pathway analysis reveals that the hypomethylation signature includes some of the major pathways that were previously implicated in cancer migration and invasion such as TGF beta and ERBB2 triggered pathways. The relevance of these hypomethylation events in human tumors was validated by identification of the signature in several publicly available databases of human tumor transcriptomes. We shortlisted novel invasion promoting candidates and tested the role of four genes from the list C11orf68, G0S2, SHISA2 and TMEM156 in invasiveness using siRNA depletion.  Importantly these genes are upregulated in human cancer specimens as determined by immunostaining of human normal and cancer breast, liver and prostate tissue arrays. Since these genes are activated in cancer they constitute a group of targets for specific pharmacological inhibitors of cancer invasiveness.
Our study provides evidence that common DNA hypomethylation signature exists between cancer cells derived from different tissues, pointing to a common mechanism of cancer invasiveness in cancer cells from different origins.

overall_design: Genomic DNA obtained from MCF7, MDA-MB-231, HepG2, SKHep1, LNCaP and PC3 cancer cell lines.  IDAT files were not submitted for GSM1841870 and GSM1841871

first: Moshe

last: Szyf


title: The expression of hematopoietic progenitor cell antigen CD34 is regulated by DNA methylation in a site-dependent manner in gastrointestinal stromal tumours (GISTs)

status: Public on Jan 24 2017

city: Erlangen

first: Evgeny

middle: A.

last: Moskalev

address: Ktankenhausstr. 8-10

department: Institute of Pathology

country: Germany

institute: University of Erlangen-Nuremberg

type: Methylation profiling by genome tiling array

summary: The anatomic site-dependent expression of hematopoietic progenitor cell antigen CD34 is a feature of gastrointestinal stromal tumours (GISTs). The basis for the differential CD34 expression is only incompletely understood. This study aimed at understanding the regulation of CD34 in GISTs and clarification of its site-dependent expression. Two sample sets of primary GISTs were interrogated including 52 fresh-frozen and 134 paraffin-embedded and formalin-fixed specimens. DNA methylation analysis was first performed by HumanMethylation450 BeadChip array in three cell lines, namely GIST-T1, GIST882 and GIST48b, that were derived from gastric and intestinal GISTs, and differentially methylated CpG sites were identified upstream of CD34. The methylation degree was further quantified by pyrosequencing and inversely correlated with CD34 mRNA and protein abundance. The gene's expression could be activated upon induction of DNA hypomethylation with 5-aza-2'-deoxycytidine in GIST-T1 and GIST882 cells. In patient samples, a strong inverse correlation of DNA methylation degree with immunohistochemically evaluated CD34 expression was documented. Both CD34 expression and DNA methylation levels were specific to the tumours' anatomic location and mutation status. A constant decrease in methylation levels was observed ranging from almost 100% hypermethylation in intestinal GISTs from duodenum to hypomethylation in rectum. CD34 was heavily methylated in gastric PDGFRA-mutant GISTs in comparison to hypomethylated KIT-mutant counterparts. Our results strongly suggest an epigenetic control of CD34 expression in GISTs by DNA methylation. Differential methylation and expression of CD34 in GISTs along the gastrointestinal tract axis and in tumours that harbour different gain-of-function mutations suggest the origin from different cell populations in the gastrointestinal tract.

overall_design: Bisulphite-converted DNA from three biological samples was hybridised to the Infinium HumanMethylation450 BeadChip. Three replicates were included for each biological specimen. Differentially methylated CpG sites upstream of CD34 that were identified in GIST cell lines were further interrogated in two independent patient GIST sample sets by using bisulfite pyrosequencing.

first: Florian

last: Haller


title: EED226, an allosteric PRC2 inhibitor, modulates gene transcription in EZH2 mutant lymphoma cell Karpas422 through PRC2 inhibition

status: Public on Jan 30 2017

city: Shanghai

first: Vicky

last: Qi

address: No. 4218 Jinke Road

country: China

institute: China Novartis Institutes for BioMedical Research Co., Ltd

summary: Polycomb repressive complex (PRC) 2, containing minimally EZH2, EED and Suz12, is the H3 lysine 27 methyltransferase playing pivotal roles in transcriptional regulation. EZH2 is the catalytic subunit, and H3K27me3 activates PRC2 through binding EED to propagate the repressive mark. Cofactor SAM-competitive (SAM-C) PRC2 inhibitors (PRC2is) have been discovered to treat lymphoma and rhabdoid tumors. Here we report the discovery of EED226, a potent and selective PRC2i directly binding to the H3K27me3 pocket of EED. Upon binding, EED226 induces conformational change in EED protein. Interestingly, it inhibits both the basal and the H3K27me3-stimulated PRC2 activities. Furthermore, EED226 selectively pulled down the endogenous PRC2 complex from human cell lysates, specifically modulates H3K27 methylation and target genes similarly as SAM-C PRC2 inhibitors, and effectively regresses human lymphoma xenograft tumor in mouse. More importantly, EED226 potently inhibits the SAM-C inhibitor-resistant PRC2 and synergizes with SAM-C PRC2i in cell proliferation blocking. Together, EED226 is an inhibitor of PRC2 with a novel mechanism and represent a potential complementary strategy for PRC2-targeted cancer therapy.

overall_design: The dataset includes gene expression profiling of DLBCL cell line Karpas422 at 1 day, 2 days, 3 days, and 6 days after DMSO or EZH2 inhibitor (5 uM) treatment with biological triplicates.

first: Lin

last: Teng

first: Yue

last: Fan

first: Shannon

last: Chuai

first: Hui

last: Ge

first: Wei


title: Mouse expression data from Glioblastoma cell malignancy and drug sensitivity are affected by the cell of origin.

status: Public on Jan 23 2017

city: Uppsala

first: Sven

last: Nelander

address: Dag Hammarskjölds v. 20

department: Department of Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

summary:
The cell of origin in glioblastoma is not formally proven but generally accepted to be a neural stem cell or glial precursor cell. In addition, there is also limited knowledge about the functional consequences of the cell of origin for glioblastoma development and response to therapy.
We have investigated the role of cell of origin in glioblastoma by inducing glioblastomas of defined cell of origin using PDGFB in the brains of adult mice. Gene expression was analysed from cultured mouse glioblastoma cells and a mouse cell origin gene signature was extracted that we used in a cluster analysis on gene expression data from patient-derived glioblastoma cell lines.

overall_design: Gene expression was analysed in mouse glioblastoma cell cultures of three different origins using G/tv-a;Arf-/-, N/tv-a;Arf-/- and C/tv-a;Arf-/- mouse lines (three independent cultures from each mouse line) and in mouse NSC cultures (one from each transgenic mouse line).  All cells were cultured adherently under stem cell conditions.

first: L

last: Uhrbom

last: Jiang


title: 5-aza treatment of breast cancer and non-tumorigenic breast cells

city: Ankara

first: Isik

last: Yulug

state: Bilkent

address: Bilkent University

department: Molecular Biology and Genetics

country: Turkey

institute: Bilkent University

summary:
CpG hypermethylation in gene promoters is a frequent mechanism of tumor suppressor gene silencing in various types of cancers. 5-aza-2'-deoxycytidine (AZA) is a DNA demethylating and anti-cancer agent resulting in induction of genes suppressed via DNA hypermethylation.
Using microarray expression profiling of AZA or DMSO treated and untreated breast cancer (MCF7 and MDA-MB-231) and non-tumorigenic breast (NTB) cells, we aim to identify candidate genes that are downregulated via promoter hypermethylation in breast cancer.

overall_design: MCF7, MDA-MB-231 and MCF12A cell lines were treated with 5µM of 5-aza-2'-deoxycytidine, for 4 days, with everyday drug refreshments. AT the end of 96th hour, cells were harvested, RNA isolation was performed and standard protocol was followed for hybridization to Affymetrix Hgu-133 Plus 2.0 arrays.

first: Nilufer

last: Sayar

first: Gurbet

last: Karahan


title: Sharpin promotes hepatocellular carcinoma progression via transactivation of versican expression

city: Bunkyo-ku, Tokyo

first: Yasuo

last: Tanaka

address: 7-3-1 Hongo

department: Gastroenterology

institute: The University of Tokyo

summary: Sharpin (Shank-associated RH domain-interacting protein, also known as SIPL1) is a multifunctional molecule that participates in various biological settings, including nuclear factor-κB signaling activation and tumor suppressor gene inhibition. Sharpin is upregulated in various types of cancers, including hepatocellular carcinoma (HCC), and is implicated in tumor progression. However, the exact roles of Sharpin in tumorigenesis and tumor progression remain largely unknown. Here, we report novel mechanisms of HCC progression through Sharpin overexpression.  Sharpin was upregulated in human HCC tissues. Increased Sharpin expression enhanced hepatoma cell invasion, whereas decrease in Sharpin expression by RNA interference inhibited invasion. Microarray analysis identified that versican, a chondroitin sulfate proteoglycan that plays crucial roles in tumor progression and invasion, was also upregulated in stably Sharpin-expressing cells. Versican expression increased in the majority of HCC tissues and knocking down of versican greatly attenuated hepatoma cell invasion. Sharpin expression resulted in a significant induction of versican transcription synergistically with Wnt/-catenin pathway activation. Furthermore, Sharpin overexpressing cells had high tumorigenic properties in vivo.   These results demonstrate that Sharpin promotes versican expression synergistically with the Wnt/-catenin pathway, potentially contributing to HCC development. A Sharpin/versican axis could be an attractive therapeutic target for this currently untreatable cancer.

overall_design: To identify genes regulated by Sharpin in hepatocellular carcinoma, transcriptional profiling of Huh7 cells infected with either control or Sharpin-expressing lentivirus was performed using whole human genome microarrays.

first: Keisuke

last: Tateishi


title: Genomic, epigenomic, and transcriptomic profiling towards identifying omics-features and specific biomarkers that distinguish uterine leiomyosarcoma and leiomyoma at molecular levels (methylation)

city: Fukuoka

first: Tomoko

last: Miyata

state: Fukuoka

address: 3-1-1 Maedashi, Higashi-ku

department: Gynecology and Obstetrics

institute: Kyushu University

summary: Uterine leiomyosarcoma (LMS) is the worst malignancy among the gynecologic cancers. Uterine leiomyoma (LM) is a benign tumor of myometrial origin and is the most common among women of childbearing age. Because the symptoms of women with LMS such as abnormal vaginal bleeding, palpable pelvic mass, and pelvic pain resemble with those of women with LM, it is difficult to preoperatively distinguish LMS and LM only by ultrasound and pelvic MRI. While histopathological diagnosis after hysterectomy is the current major means to distinguish them postoperatively, unusual histologic variants of LM tend to be misdiagnosed as LMS. Furthermore, the low incidence of LMS has been preventing elucidating its causal mechanisms and developing effective diagnoses and treatments. Therefore, development of molecular diagnosis as an alternative or confirmatory means helps diagnosing LMS more accurately. We adopted omics-based technologies to identify genome-wide features to distinguish LMS from LM, and revealed that copy-number, gene expression, and DNA methylation profiles successfully distinguished between these tumors. LMS was found to possess features typically observed in malignant solid tumors, such as extensive chromosomal abnormalities, overexpression of cell cycle –related genes, and hypomethylation spreading through large genomic regions as well as frequent hypermethylation at polycomb group target gene and cadherin gene loci. We also identified candidate expression and DNA methylation markers, which will help establishing diagnostic tests using conventional quantitative assays. While the identified omics-signatures and certain markers specific to LMS need to be further validated in larger numbers of LM and LMS samples, our results demonstrate the practical feasibility of establishing a postoperative diagnostic test to distinguish LMS from LM with high accuracy, and also suggest the future possibility of developing preoperative and non-invasive diagnostic methods.

overall_design: DNA methylation profiles of human normal uterine myometrium (3 samples), human uterine leiomyoma (3 samples), human uterine leiomyosarcoma (3 samples), and three cell lines of human uterine leiomyosarcoma (SKN, SK-UT-1, SK-UT-1B) were generated using with Infinium HumanMethylation450 BeadChips (Illumina).

first: Kazuhiko

last: Nakabayashi


title: Single cell RNA-seq analysis of IDH-mutant astrocytoma

status: Public on Mar 31 2017

city: Rehovot

first: Itay

last: Tirosh

address: Herzl 234

country: Israel

institute: WEIZMANN INSTITUTE OF SCIENCE

type: Expression profiling by high throughput sequencing

summary: To understand the diversity of expression states within IDH-mutant astrocytoma tumors, we profiled 6341 cells from 10 tumors by single cell RNA-seq

overall_design:
Tumors were disaggregated, sorted into single cells, and profiled by Smart-seq2.
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**Submitter declares reads will be made available through controlled access SRA and/or dbGaP.**

first: Andy

last: Venteicher

first: Mario

last: Suva

first: Aviv

last: Regev


title: Gene expression profiling of esophageal squamous cell carcinomas

city: Chuo-ku

first: Hiroki

last: Sasaki

state: Tokyo

institute: National Cancer Center Reseach Institute

summary: To identify the specific genes for subtyping.

overall_design: We performed comprehensive gene expression profiling of pretreatment 274 biopsy specimens in esophageal squamous cell carcinomas by Affymetrix Gene Chip HG-U133Plus2.0.

last: Aoyagi

first: Manabu

last: Muto

first: Keiko

last: Minashi

first: Yasuhide

last: Yamada


title: Transient Dicer deletion in ESCs

status: Public on Jan 18 2017

city: London

first: Tristan

last: Rodriguez

address: Du Cane Road, Hammersmith Hospital Campus

department: National Heart and Lung Institute

institute: NHLI Imperial College London

summary: Deletion of Dicer by tamoxifen addition to Dicerflox/flox cells and sample collection 5 days post-deletion

overall_design: Comparison of the gene expression levels in Dicer Fx/Fx before and after Dicer deletion by tamoxifen addition

first: Juan

last: Sanchez


title: Liver gene expression profiles of  interferon therapy in chronic hepatitis B Patients (mRNA)

city: Taichung

first: Tzu-Hung

last: Hsiao

address: 1650 Taiwan Boulevard Sect. 4

department: Department of Medical Research

country: Taiwan

institute: Taichung Veterans General Hospital

summary: With 350 million carriers worldwide who may suffer from serious sequelae, including hepatocellular carcinoma, chronic hepatitis B virus (CHB) infection remains an important health issue. Current antiviral therapies hardly eradicate the virus. Therefore, there are still imperative need to develop new therapeutic strategies and predictors for treatment response to cure the disease and avoid futile treatment. By taking the advantage of having the paired liver biopsy samples of IFNalpha responders before/after treatment and pretreatment samples from responders and non-responders, we could characterize the intrahepatic expression profiles associated with necroinflammatory activity and the profiles/signature potentially predictive of response to IFNalpha therapy for CHB in this study.

overall_design: RNA was extracted from pairedliver tissues for gene expression analysis.  The gene expression profiles of seven paired liver biopsy samples of IFNalpha responders before/after treatment and other 3 pre- treatment samples were obtained by Affymatrix U133plus2 microarray. We also pooled samples of 11 responders  and 11 non-responders to perform affymatrix EXON ST 1.0 array.

first: Hui-Lin

last: Wu

first: Chun-Jen

last: Liu


title: Liver gene expression profiles of interferon therapy in chronic hepatitis B Patients


title: Identification of a Novel SYK/c-MYC/MALAT1 Signaling Pathway and Its Potential Therapeutic Value in Ewing Sarcoma

status: Public on Jan 17 2017

city: Singapore

first: Phillip

middle: H

last: Koeffler

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute

summary: Ewing Sarcoma (EWS) is a devastating soft tissue sarcoma affecting predominantly young individuals. Tyrosine kinases (TKs) and associated pathways are continuously activated in many malignancies including EWS; these enzymes provide candidate therapeutic targets. Using two high-throughput screens with EWS cell lines (a siRNA library and a small-molecule inhibitor library of that predominantly target the TK family), we identified spleen tyrosine kinase (SYK) as a candidate actionable target. SYK is highly phosphorylated in the majority of EWS cells, and SYK inhibition by a variety of genetic and pharmacological approaches markedly inhibited EWS cells both in vitro and in vivo. Ectopic expression of SYK rescued the cytotoxicity triggered by SYK-depletion associated with the reactivation of AKT and c-MYC. Transcriptome analysis identified that a Long non-coding RNA, metastasis associated lung adenocarcinoma transcript 1 (MALAT1), was dependent on by SYK-mediated signaling. Moreover, c-MYC, a SYK up-regulated gene, bound to the promoter region of MALAT1 and transcriptional activated MALAT1, which further promoted the proliferation of EWS cells. Taken together, the present study identifies a novel signaling involving SYK/c-MYC/MALAT1 as a promising therapeutic target for the treatment of EWS.

overall_design: TC71 cells after SYK inhibition through either stable shRNA knockdown vectors or GS-9973 exposure (2 µmol/L, 24 h), and compared the results to control cells.

first: Haibo

last: Sun

first: De-Chen

last: Lin

first: Qi

last: Cao

first: Brenden

last: Pang

first: David-Hayon

last: Gae

first: Victor

last: Lee

first: Huey

last: Lim

first: Ngan

last: Doan

first: Jonathan

last: Said

first: Sigal

last: Gery

first: Anand

last: Mayakonda

first: Charles

last: Forscher

first: Jeffery

last: Tyner


title: Enhancer Remodeling During Adaptive Bypass to MEK Inhibition Is Attenuated by Pharmacological Targeting of the P-TEFb Complex (DNA methylation)

status: Public on Jan 20 2017

city: Chapel Hill

first: Gary

middle: L

last: Johnson

state: NC

address: 4009 Genetic Medicine Building, 120 Mason Farm Road

institute: University of North Carolina School of Medicine

summary: Targeting the dysregulated BRaf-MEK-ERK pathway in cancer has increasingly emerged in clinical trial design. Despite clinical responses in specific cancers using inhibitors targeting BRaf and MEK, resistance develops often involving non-genomic adaptive bypass mechanisms.   Inhibition of MEK1/2 by trametinib in triple negative breast cancer (TNBC) patients induced dramatic transcriptional responses, including upregulation of receptor tyrosine kinases (RTKs) comparing tumor samples before and after one week of treatment.  In preclinical models MEK inhibition induced genome-wide enhancer formation involving the seeding of BRD4, MED1, H3K27 acetylation and p300 that drives transcriptional adaptation.  Inhibition of P-TEFb associated proteins BRD4 and CBP/p300 arrested enhancer seeding and RTK upregulation. BRD4 bromodomain inhibitors overcame trametinib resistance, producing sustained growth inhibition in cells, xenografts and syngeneic mouse TNBC models.  Pharmacological targeting of P-TEFb members in conjunction with MEK inhibition by trametinib is an effective strategy to durably inhibit epigenomic remodeling required for adaptive resistance.

overall_design: 10 experimental Illumina Infinium 450k samples treated with DMSO or trametinib, 2 controls: Human WGA Methylated DNA & Non-methylated DNA, Zymo Research

first: Jon

last: Zawistowski


title: The effects of adenine-midiated purinergic signaling in 3T3 fibroblasts and adipocytes

status: Public on Feb 07 2017

city: Taipei

first: Guang-Huar

last: Young

state: Taiwan (TWN)

address: 6F.-3, No.21, Ln. 583, Ruiguang Rd., Neihu Dist., Taipei City 114, Taiwan (R.O.C.)

department: Scientific Research

summary: In previous study, we demonstrated that adenine could activate AMPK signaling in 3T3 fibroblast. To investigate the changes of transcriptome in differential 3T3 cells by adenine stimulation, we used microarrays to analyze undifferentited annd differentiated 3T3-L1 adipocytes in mRNA levels.

overall_design: A chip study using total RNA recovered from undifferentiated and differentiated 3T3-L1 adipocytes incubated with/without adenine or AICAR.

first: Han-Min

last: Chen


title: Expression data from patients with Essential Thrombocythemia (ET), Polycythemia Vera (PV), Primary Myelofibrosis (PMF) (untreated)

city: Roskilde

first: Vibe

last: Skov

address: Koegevej 7-13

department: Hematology

country: Denmark

institute: Roskilde Hospital

summary: Microarrays were used to assess gene expression in patients with ET, PV, and PMF before treatment with IFNalpha2.

overall_design: Total RNA was purified from whole blood and amplified to biotin-labeled aRNA and hybridized to microarray chips. Background correction, normalization, and gene expression index calculation were performed with the robust multi-array (rma) method. The regularized t-test limma was used to calculate differences in gene expression between patients and control subjects.

first: V

first: H

last: Hasselbalch


title: Gene expression profile in human T-cell acute lymphoblastic leukemia (T-ALL) cell lines

first: Takaomi

last: Sanda

address: 14 Medical Dr 12-01

institute: Cancer Science Institute of Singapore, National University of Singapore

summary: We performed microarray gene expression profiling in 16 T-ALL cell lines

overall_design: Human T-ALL cell lines were cultured at the same density for 24 hours.  RNA samples were used for microarray gene expression analysis.

first: Thomas

last: Look


title: Glioblastoma cell malignancy and drug sensitivity are affected by the cell of origin

first: Sven

last: Nelander

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Targeting of apoptotic pathways by SMAC or BH3 mimetics distinctly sensitizes paclitaxel-resistant triple negative breast cancer cells

status: Public on Jan 26 2017

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

summary: Standard chemotherapy is the only systemic treatment for triple-negative breast cancer (TNBC). Despite the good initial responses, resistance remains a major therapeutic obstacle. Here, we employed a High-Throughput Screen to identify targeted therapies that overcome chemoresistance in TNBC. We applied short-term paclitaxel treatment and screened 320 small-molecule inhibitors of known targets to identify drugs that preferentially and efficiently target paclitaxel-treated TNBC cells. Among these compounds the SMAC mimetics (BV6, Birinapant) and BH3-mimetics (ABT-737/263) were recognized as potent targeted therapy for multiple paclitaxel-residual TNBC cell lines. However, acquired paclitaxel resistance through repeated paclitaxel pulses result in desensitization to BV6, but not to ABT-263, suggesting that short- and long-term paclitaxel resistance are mediated by distinct mechanisms. Gene expression profiling of paclitaxel-residual, -resistant and naïve MDA-MB-231 cells demonstrated that paclitaxel-residual, as opposed to -resistant cells, were characterized by an apoptotic signature, with downregulation of anti-apoptotic genes (BCL2, BIRC5), activation of apoptosis inducers (IL24, PDCD4), and enrichment of TNFα/NF-κB pathway, including upregulation of TNFSF15, coupled with cell-cycle arrest. BIRC5 and FOXM1 downregulation and IL24 induction was also evident in breast cancer patient datasets following taxane treatment. Exposure of naïve and paclitaxel-resistant cells to supernatants of paclitaxel-residual cells sensitized them to BV6, and treatment with TNFα enhanced the potency of BV6, suggesting that sensitization to BV6 is mediated, at least partially, by secreted factor(s). Our results suggest that administration of SMAC or BH3 mimetics following short-term paclitaxel treatment could be an effective therapeutic strategy for TNBC, while only BH3-mimetics could effectively overcome long-term paclitaxel resistance

overall_design: The transcritomes of naive, Paclitaxel residual and resistant MDA-MB-231 breast cancer cell lines were compared in biological triplicates.

first: Melanie

last: Boerries

first: Effrosini

last: Panayotopoulou

first: Sima

last: Lev


title: microarray analysis in SREBP2-knockdown cells under low pH (pH 6,8) culture conditions

status: Public on Jan 25 2017

city: Tokyo

first: Tsuyoshi

last: Osawa

address: 4-6-1 Komaba, Meguro-ku

department: RCAST

summary: The conditions of the tumor microenvironment, such as hypoxia and nutrient starvation, play critical roles in cancer progression. However, the role of acidic extracellular pH in cancer progression is not studied as extensively as that of hypoxia. Here, we show that extracellular acidic pH (pH 6.8) triggered activation of sterol regulatory element-binding protein 2 (SREBP2) by stimulating nuclear translocation and promoter binding to its targets along with intracellular acidification. Interestingly, inhibition of SREBP2, but not SREBP1, suppressed the upregulation of low pH-induced cholesterol biosynthesis-related genes. Moreover, acyl-CoA synthetase short-chain family member 2 (ACSS2), a direct SREBP2 target, provided a growth advantage to cancer cells under acidic pH. Furthermore, acidic pH-responsive SREBP2 target genes were associated with reduced overall survival of cancer patients. Thus, our findings show that SREBP2 is a key transcriptional regulator of metabolic genes and progression of cancer cells, partly in response to extracellular acidification.

overall_design: Gene expression in PANC-1 and AsPC-1 cells under Control (pH 7.4) or low pH (ph 6.8) culture condition by treatment with two different siRNAs targeting SREBP2 was analyzed by Affymetrix U133plus2 array.

first: Ayano

last: Kondo

first: Hiroyuki

last: Aburatani


title: Gene expression response to DUX4 in murine myoblasts

first: Matthew

last: Arno

address: 150 Stamford Street

department: Genomics Centre

institute: King's College London

summary:
DUX4 is generally agreed to underlie pathology in Facioscapulohumeral muscular dystrophy
Microarrays were used to examine gene expression after primary murine satellite cell-derived myoblasts were retrovirally infected with constructs encoding DUX4, DUX4c, constitutively active, dominant negative and truncated DUX4 versions.

overall_design: Primary murine satellite cell-derived myoblasts were expanded and then divided into six sister cultures and each infected with a different construct. After a further 20 hours in culture, RNA was isolated.

first: Paul

last: Knopp

first: Peter

last: Zammit


title: A new syndrome of overgrowth, macrocephaly, hypoglycemia, enlarged ventricles, mild, and moderate intellectual disability and recurrent inflammatory disease is due to mutations in RNF125

status: Public on Jan 22 2017

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: Methylation analysis of individuals with RNF125 mutations

overall_design: Methylation analysis utilizing the Illumina Infinium HumanMethylation450 BeadChip arrays

first: Pablo

last: Lapunzina

first: David

last: Monk


title: Global transcript analysis of livers of Lrh-1 K289R knockin mice under refed conditions

status: Public on Jan 19 2017

city: Lausanne

first: Kristina

last: Schoonjans

address: Station 15

department: SV IBI GR-SCH

country: Switzerland

institute: Ecole Polytechnique Fédérale de Lausanne

summary:
Transcript data from liver receptor homolog-1 (LRH-1) WT and LRH-1 K289R livers from mice fasted for 24h followed by 6h refed.
We used microarrays to detail the global program of gene expression underlying hepatic function under refed conditions.

overall_design: Male mice (n=6) were fasted and then refed, sacrificed at 8 am and livers snap-frozen in liquid nitrogen for RNA extraction and hybridization on Affymetrix microarrays.

first: Sokrates

last: Stein

first: Vera

last: Lemos


title: Genomic pathways modulated by Twist in breast cancer

status: Public on Jan 13 2017

city: Baltimore

first: Venu

last: Raman

state: Maryland

address: 720 Rutland Ave, Traylor 338

department: Radiology

institute: Johns Hopkins University

summary:
Background: The basic helix-loop-helix transcription factor TWIST1 (Twist) is involved in embryonic cell lineage determination and mesodermal differentiation. There is evidence to indicate that Twist expression plays a role in breast tumor formation and metastasis, but the role of Twist in dysregulating pathways that drive the metastatic cascade is unclear. Importantly, the genes and pathways dysregulated by Twist in cell lines and mouse models have not been validated against data obtained from patient samples.

Methods: We over-expressed the human Twist gene in non-metastatic MCF-7 breast cancer cells to generate the estrogen-independent metastatic breast cancer cell line MCF-7/Twist. These cells were then inoculated in the mammary fat pad of female severe compromised immunodeficient mice, which subsequently formed xenograft tumors that metastasized to the lungs. Microarray data was collected from both in vitro (MCF-7 and MCF-7/Twist cell lines) and in vivo (primary tumors and lung metastases) models of Twist expression. Our data was compared to publically available gene signatures of different subtypes, classes, and grades of human breast cancers.

Results: Our data establishes a Twist over-expressing mouse model of breast cancer, which metastasizes to the lung and replicates some of the ontogeny of human breast cancer progression. Gene profiling data, following Twist expression, exhibited novel metastasis driver genes as well as cellular maintenance genes that were synonymous with the metastatic process. We demonstrated that the genes and pathways altered in the transgenic cell line and metastatic animal models generated, parallel many of dysregulated gene pathways observed in human breast cancers.

Conclusions: Analogous gene expression patterns observed in both in vitro and in vivo Twist preclinical models of breast cancer metastasis and public patient data sets supports the functional role of Twist in promoting breast tumor metastasis. Our data indicates that genetic dysregulation of Twist at the cellular level drives alterations in related gene pathways in the Twist metastatic mouse model which are comparable to changes seen in breast cancer patient samples. Lastly, we have identified novel genes and pathways that could be further investigated as targets for drugs to ultimately treat metastatic breast cancer.

overall_design: Samples were selected from all stages of the metastatic cascade in both cell culture and in the resulting metastatic mouse model of breast cancer. RNA was extracted from the MCF-7 cell line (2 replicates), MCF-7/Twist cell line (2 replicates), cells cultured from MCF-7/Twist primary tumors in mice (2 replicates), and cells cultured from MCF-7/Twist lung metastases (4 replicates).

first: Farhad

last: Vesuna


title: Cancer cells with genetic disruption of DNA methyltransferases

first: Stephen

last: Baylin

state: MD

address: 1650 Orleans St. Suite 541


title: NKL homeobox gene activities in hematopoietic stem cells, T-cell development and T-cell leukemia

city: Braunschweig

first: Claudia

last: Pommerenke

address: Inhoffenstraße 7B

institute: Leibniz Institute DSMZ

summary: T-cell acute lymphoblastic leukemia (T-ALL) cells represent developmentally arrested T-cell progenitors, subsets of which aberrantly express homeobox genes of the NKL subclass, including TLX1, TLX3, NKX2-1, NKX2-5, NKX3-1 and MSX1. Here, we analyzed the transcriptional landscape of all 48 members of the NKL homeobox gene subclass in CD34+ hematopoietic stem cells (HSCs) and during lymphopoiesis, identifying activities of 9 particular genes. Four of these were expressed in HSCs (HHEX, HLX1, NKX2-3 and NKX3-1) and three in common lymphoid progenitors (HHEX, HLX1 and MSX1). Interestingly, our data indicated downregulation of NKL homeobox gene transcripts in late progenitors and mature T-cells, a phenomenon which might explain the oncogenic impact of this group of genes in T-ALL. Using MSX1-expressing T-ALL cell lines as models, we showed that HHEX activates while HLX1, NKX2-3 and NKX3-1 repress MSX1 transcription, demonstrating the mutual regulation and differential activities of these homeobox genes. Analysis of a public T-ALL expression profiling data set comprising 117 patient samples identified 20 aberrantly activated members of the NKL subclass, extending the number of known NKL homeobox oncogene candidates. While 7/20 genes were also active during hematopoiesis, the remaining 13 showed ectopic expression. Finally, comparative analyses of T-ALL patient and cell line profiling data of NKL-positive and NKL-negative samples indicated absence of common target genes but instead highlighted deregulation of apoptosis as common oncogenic effect. Taken together, we present a comprehensive survey of NKL homeobox genes in early hematopoiesis, T-cell development and T-ALL, showing that these genes generate an NKL-code for the diverse stages of lymphoid development which might be fundamental for regular differentiation.

overall_design: NKL positive T-ALL cell lines were compared to NKL negative

first: Stefan

last: Nagel


title: Comparison of the transcriptomic profile of P. falciparum reactive polyfunctional and IFNg monofunctional human CD4 T cells

city: La Jolla

first: Bjoern

last: Peters

state: California

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

summary: Pathogen-specific polyfunctional T cell responses have been associated with favorable clinical outcomes but it is not known whether polyfunctional T cells are distinct from monofunctional cytokine producing T cells. In this study we compared the transcriptomic profile of P. falciparum reactive polyfunctional and IFNg monofunctional CD4 T cells by microarray analysis and show that polyfunctional CD4 T cells are associated with a unique transcriptomic signature.

overall_design: Whole blood samples collected from two independent cohorts (n=4 per cohort) of malaria-naïve humans 28 days after experimental infection with P. falciparum blood-stage parasite were in vitro stimulated overnight with P. falciparum parasite extract. Polyfunctional (IFNg/IL2/TNF), IFNg monofunctional CD4 T cells and IFNg negative CD4 T cells were sorted from each sample directly into RLT lysis buffer using a 3-colour polyfunctional cytokine secreting assay (Burel et al., 2016). mRNA was extracted using the RNEasy micro kit (Qiagen) and samples from each cohort were pooled for microarray analysis. Gene expression profiles for the two independent microarray experiments were determined using the low-input Affymetrix human gene 2.0 ST array at the Ramaciotti centre (University of NSW, Sydney, Australia). A polyfunctional gene signature was defined based on differential expression of genes which had an absolute fold change greater than 2 between IFNg triple positive and IFNg single positive cells in both of the independent microarray experiments.

first: Julie

last: Burel

first: Simon

last: Apte

first: Denise

last: Doolan

first: James

last: McCarthy


title: Microarray of Bordetella-infected bone marrow-derived dendritic cells

city: New York

first: Gregory

last: Sonnenberg

state: NY

address: 413 East 69th Street, Belfer Research Building 512

institute: Weill Cornell Medical College

summary:
Bone marrow-derived dendritic cells were infected with live or heat-killed Bordetella and cells were analyzed on day 4 post-infection
cells were >90% CD11c-positive

overall_design: 3 replicates were performed

first: Thomas

last: Fung


title: Global gene expression analysis of gastric cancer by oligonucleotide microarrays

status: Public on Jan 15 2017

city: Shanghai

first: liu

last: BingYa

address: 197 Ruijin ER RD

department: surgery

institute: RuiJin Hospital,SJTU

summary: Gastric cancer is one of the most common causes of cancer-related death worldwide, and the molecular mechanisms involved in gastric carcinogenesis are still not fully understood. To gain molecular understanding of carcinogenesis, progression, and diversity of gastric cancer, 111 human gastric cancer tissues and 21 noncancerous gastric tissues were analyzed by high-density oligonucleotide microarray in this study. These results provide not only a new molecular basis for understanding biological properties of  gastric cancer, but also useful resources for future development of therapeutic targets and diagnostic markers for gastric cancer.

overall_design: Tumor samples from 111 patients with gastric cancer underwent subtotal gastrectomy. Biopsy Normal gastric mucosa got from 21 volunteer who underwent gastroscopy for health examination.

first: Bingya

last: Liu

first: Zhenggang

last: Zhu

first: Min

last: Yan

first: Jian-fang

last: Li

first: Jun

last: Zhang

first: Chen


title: DNA methylation profiling of cancer cells with genetic disruption of DNA methyltransferases

first: Stephen

summary: Maximizing DNA methyltransferase (DNMT’s) inhibition for cancer therapy requires defining the roles and interactions between these enzymes for maintaining the widespread DNA methylation abnormalities in cancer.  Combining genetic  and shRNA depletion  in colon and other cancer cells reveals that DNMT1 is extremely dominant in this maintenance, with DNMT’s 3A and 3B playing minor roles,  at all genomic loci including promoters and enhancers.  Reducing DNMT1 below a deep threshold level, especially at promoters, is required for reversing abnormal DNA methylation and re-expressing key tumor suppressor genes.  Current DNMT inhibitors (DNMTis) are challenged, at tolerable patient doses, for achieving such reductions.  We introduce a new approach in which reducing levels of the DNMT targeting protein, UHRF1, complements low DNMTi doses to DNA demethylate and reactivate expression of such genes.

overall_design: To understand precisely how the three DNMT’s, 1, 3A, and 3B, interact for maintaining DNA methylation abnormalities in cancer. We perfomed genome-wide DNA methylation and gene expression anaylses in colon cancer and other cancer cell lines following  a series of genetic and shRNA depletions of each enzyme. Our data revealed that DNMT1 overwhelmingly plays the essential maintenance role.  Even with combined deletions of the proteins, lowering DNMT1 below a threshold level is required for maximal loss of  DNA methylation at all genomic regions and is required for maximally reversing promoter DNA promoter DNA hypermethylation with associated re-expression of key tumor suppressor genes.

first: Hsing-Chen

last: Tsai

first: Yi

last: Cai


title: Aire, guardian of immunological tolerance, binds to and activates super-enhancers [expression]

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: Microarray profiles of MECs from mice treated with topoisomerase inhibitors

overall_design: DAPI-CD45-Ly51loMHCIIhi MECs were single sorted from treated mice. Total RNA was prepared using Trizol method followed by amplification and cDNA preparation. cDNA was hybridized to Affymetrix ST1.0 microarrays.

first: Kushagra

last: Bansal

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Expression data from primary breast tumors

city: Rotterdam

first: Marcel

last: Smid

address: Dr. Molewaterplein 50

department: Medical Oncology

institute: Erasmus MC

summary: CHEK2 1100delC is a moderate-risk cancer susceptibility allele that confers a high breast cancer risk in a polygenic setting. Gene expression profiling of CHEK2 1100delC breast cancers may reveal clues to the nature of the polygenic CHEK2 model and its genes involved. Here, we report global gene expression profiles of a cohort of 155 familial breast cancers, including 26 CHEK2 1100delC mutant tumors. A 40-gene CHEK2 signature was defined that significantly associated with CHEK2 1100delC breast cancers. The identification of a CHEK2 gene signature implies an unexpected biological homogeneity among the CHEK2 1100delC breast cancers. In addition, all 26 CHEK2 1100delC tumors classified as luminal intrinsic subtype breast cancers, with 8 luminal A and 18 luminal B tumors. This biological make-up of CHEK2 1100delC breast cancers suggests that a relatively limited number of additional susceptibility alleles are involved in the polygenic CHEK2 model. Identification of these as-yet-unknown susceptibility alleles should be aided by clues from the 40-gene CHEK2 signature.

overall_design: 155 primary tumors from breast cancer patients with known mutation status of BRCA1, BRCA2 or CHEK2 or Non (familial case, but wild-type for aforementioned genes). Expression profiles of these subgroups were compared.

first: John

last: Foekens

last: M Martens

first: Mieke

last: Schutte

first: Hanne

last: Meijers-Heijboer


title: The cellular context-dependent consequences of Apc mutations on gene regulation and cellular behavior

status: Public on Jan 05 2017

first: Yasuhiro

last: Yamada

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

department: Department of Molecular Pathology

institute: University of Tokyo

summary: The spectrum of genetic mutations differs among cancers in different organs, implying a cellular context-dependent effect of the genetic aberrations. However, the extent to which the cellular context affects the consequences of oncogenic mutations remains to be fully elucidated. We reprogrammed colon tumor cells in an Apc Min/+ mouse model, in which the loss of the Apc gene plays a critical role in tumor development, and established reprogrammed tumor cells (RTCs) that exhibit pluripotent stem cell (PSC)-like signatures of gene expression. We show that the majority of the genes in the RTCs that were affected by the Apc mutations did not overlap with the genes that were affected in the intestine or those that were affected by the accumulation of beta-catenin in PSCs. The RTCs lacked pluripotency but exhibited the increased expression of Cdx2 and a differentiation propensity that was biased toward the trophectoderm cell lineage. The genetic rescue of the mutated Apc allele conferred pluripotency on the RTCs and enabled their differentiation into various cell types in vivo. The re-disruption of Apc in the RTC-derived differentiated cells resulted in neoplastic growth that was exclusive to the intestine, yet the majority of intestinal lesions remained pre-tumoral microadenomas. These results highlight the significant influence of the cellular context on gene regulation, cellular plasticity, and cellular behavior in response to the loss of the Apc function. Our results also imply that transition from microadenomas to macroscopic tumors is reprogrammable, which underscores the importance of epigenetic regulation on colon tumor promotion.

overall_design: Utilizing reprogrammed colon tumor cells (RTCs) established by iPSC technology, we investigated the impact of the cellular context on the consequence of Apc mutations in various cell types in vivo and in vitro. Transcriptional profiles of 18 samples were examined to evaluate following subjects: 1) Whether RTCs share features with pluripotent stem cells. 2) The effect of Apc mutation on global gene expressions in various cell types. 3) The effect of mutant B-catenin induction on global gene expression in ESCs and MEFs.

first: Kyoichi

last: Hashimoto

first: Yosuke


title: Epigenetic alterations affecting transcription factors and signaling pathways in stromal cells of endometriosis: Genome-wide DNA methylation data (array)

city: hackensack

first: Benjamin

last: Tycko

state: NJ

address: 40 prospect avenue

department: Epigenetics

institute: HUMC

summary: Endometriosis is characterized by growth of endometrial-like tissue outside the uterine cavity. Since its pathogenesis may involve epigenetic changes, we used Illumina 450K Methylation Beadchips to profile CpG methylation in endometriosis stromal cells compared to stromal cells from normal endometrium. We validated and extended the Beadchip data using bisulfite sequencing (bis-seq), and analyzed differential methylation (DM) at the CpG-level and by an element-level classification for groups of CpGs in chromatin domains. Genes found to have DM included examples encoding transporters (SLC22A23), signaling components (BDNF, DAPK1, ROR1, and WNT5A) and transcription factors (GATA family, HAND2, HOXA cluster, NR5A1, OSR2, TBX3). Intriguingly, among the TF genes with DM we also found JAZF1, a proto-oncogene affected by chromosomal translocations in endometrial stromal tumors. Using RNA-Seq we identified a subset of the DM genes showing differential expression (DE), with the likelihood of DE increasing with the extent of the DM and its location in enhancer elements. Supporting functional relevance, treatment of stromal cells with the hypomethylating drug 5aza-dC led to activation of DAPK1 and SLC22A23 and repression of HAND2, JAZF1, OSR2, and ROR1 mRNA expression. We found that global 5hmC is decreased in endometriotic versus normal stroma, and for JAZF1 and BDNF examined by oxidative bis-seq, found that when 5hmC is detected, patterns of 5hmC paralleled those of 5mC. Together with prior studies, these results define a consistent epigenetic signature in endometriosis stromal cells and nominate specific transcriptional and signaling pathways as therapeutic targets.

overall_design: Bisulfite converted DNA from 9 primary cell cultures of endometriosis stromal cells from ovarian ectopic sites (OESC) and control endometrial stromal cells (CESC)  were hybridized to the Illumina Infinium 450k Human Methylation Beadchip.

first: Iveta

last: Yotova

first: Emily

last: Hsu

first: Catherine

last: Do

first: Aulona

last: Gaba

first: Matthias

last: Sczabolcs

first: Sabine

last: Dekan

first: Lukas

last: Kenner

first: Rene

last: Wenzl


title: Expression data from the different EMT and stemness status of lung cancer cell lines

status: Public on Jan 14 2017

city: Kaohsiung

first: Chao-Ju

last: Chen

state: Kaohsiung

address: No.100 , Tzyou 1st Road Kaohsiung 807 , Taiwan, 11F department of laboratory medicine

department: Laboratory medicine

institute: Kaohsiung Medical University Hospital

summary:
To study the drug resistant phenotype between stem-like cancer cells at different EMT status, we isolated 4 subpopulations from the non-small-cell lung cancer cell line (PC14) according to the E-cadherin and CD133 expression level. We demonstrated that the epithelial type CD133high stem-like cells (E-cadhighCD133high) significantly exhibited higher drug resistant ability compared to the mesenchymal type CD133high stem-like cells (E-cadlowCD133high), epithelial type CD133low non-stem like cells (E-cadhighCD133low) and mesenchymal type CD133low non-stem like cells (E-cadlowCD133low).
We used microarray to study the global gene expression profiles of these 4 subpopulations and identified distinct classes of up-regulated genes and down-regulated genes in the epithelial type CD133high stem-like cells.

overall_design: A two-step fluorescence-activated cell sorting (FACS) method was used to isolate the epithelial and mesenchymal types of stem-like cancer cells. First, the E-cadhigh and E-cadlow subpopulations were isolated from PC14 cell line. Genotypic characterization confirmed the homology of the subpopulations. Next, the CD133high and CD133low cells were isolated from the E-cadhigh and E-cadlow subpopulations by using the human CD133 P1-promoter-driven GFP reporter lentiviral vector. Finally, we obtained the 4 subpopulations (E-cadhighCD133high, E-cadlowCD133high, E-cadhighCD133low and E-cadlowCD133low cells) for RNA extraction and hybridization on Affymetrix microarrays.

first: YP

last: Liu

first: M

last: Hsiao

first: CJ


title: 809094 Biomarker Identification in Fracture Healing (experiment #5150 Feb 2015)

status: Public on Jan 06 2017

city: Philadelphia

first: Annamarie

last: Horan

state: PA

address: 3737 Market Street, 6th Floor

department: Orthopaedic Surgery

institute: University of Pennsylvania

summary:
The specific genes that distinguish normal fracture healing from abnormal healing or nonunion in humans are unknown.  This study was an exploratory investigation of peripheral blood from  acutely injured fracture patients collected over multiple days to compare normal healers, slow healers, and nonunion outcomes.
We used microarrays to do a global comparison between acutely injured (AI) subjects (AIS) vs age and sex matched healthy volunteers (HV) and chronic Nonunion (NU) patients.

overall_design: AIS and NU were enrolled into the study upon presentation for fracture care.  Blood was collected into Paxgene blood RNA tubes during the inpatient stay and during clinical follow up.  HV were enrolled in parallel with a one-time blood sample collection into Paxgene blood RNA tubes. RNA was extracted from all samples applicable to this experiment.  We explored the data with Partek Genomics suite using all samples at all time points to identify a panel of genes that is differentially expressed across groups to enable additional biomaker vetting.

first: Samir

last: Mehta


title: Gene expression profiles of pre-confluent 3T3-L1 preadipocytes with low or high adipogenic potential

status: Public on Jan 03 2017

city: Québec

first: Mathieu

last: Laplante

state: Qc

address: 2725 Chemin Sainte-Foy

department: Medicine

institute: Université Laval

summary: The objective of this analysis was to identify the genes that are differentially expressed between preadipocytes with low or high adipogenic capability

overall_design: Clones of 3T3-L1 were isolated by serial dilutions. Each well was visually inspected by microscopy to confirm the presence of a single colony per well. Wells with more than one colony were excluded. The clones were amplified and always maintained at sub-confluence. The adipogenic potential of each clonal lines was tested using an adipogenic cocktail containing insulin, dexamethasone and IBMX. After differentiation, triglycerides were extracted and quantified and clones with a low ability to differentiate into adipocytes were classified as a 'Low' lines and clones with a high adipogenic potential were classified as 'High' lines. For the microarray analysis, RNA was extracted from 5 Low lines and 5 High lines. The RNA was extracted prior to differentiation, in proliferating cells.


title: Developmental programming in Idiopathic pulmonary fibrosis (IPF)

status: Public on Jan 10 2017

city: Birmingham

first: Victor

middle: John

last: Thannickal

state: AL

address: 1530 3rd Avenue South, THT 422

institute: University of Alabama at Birmingham

summary: Global mRNA expression was compared between stable and progressive IPF using bronchoalveolar lavage derived mesenchymal stromal cells

overall_design: Stable and progressive IPF patients were identified by a decline in forced vital capacity (FVC) < 5% and FVC ≥ 10% respectively over preceding 6 months

first: Diptiman

last: Chanda


title: DNA methylation patterns in twins discordant for ALS reveal concordant signatures of disease [array]

city: Darlinghurst

first: Paul

middle: E

last: Young

state: NSW

address: 405 Liverpool Street

institute: Victor Chang Cardiac Research Institute

summary: Our data suggest twin pair specific methylation differences exist in blood that reside in genes that are enriched for neuronal pathways.

overall_design: methylation profiling, of 5 monozygotic twin pairs discordant for ALS

first: Michael

last: Buckland

first: Roger

last: Pamphlett

last: Suter


title: Molecular genomic and transcriptomic profiling of familial breast cancer.

first: Marcel

last: Smid

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

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

overall_design: Refer to individual Series


title: Inhibition of adhesion molecule gene expression and cell adhesion by the metabolic regulator PGC-1alpha

first: Neri

last: Minsky

address: 1230 York Avenue

institute: Rockefeller University

summary:
Cell adhesion plays an important role in determining cell shape and function in a variety of physiological and pathophysiological conditions. While links between metabolism and cell adhesion were previously suggested, the exact context and molecular details of such a cross-talk remain incompletely understood.
Our study shows that PGC-1alpha, a pivotal transcriptional co-activator of metabolic gene expression, acts to inhibit expression of cell adhesion genes.  Using cell lines as well as primary cells, we show that both endogenous and exogenous PGC-1a down-regulate expression of a variety of cell adhesion molecules.

overall_design: Cells were grown in 12-well plates and control adenoviruses (Ad-control) or PGC-1alpha (Ad-PGC-1alpha) were directly added to the culture medium where indicated.

first: N

first: R

last: Roeder


title: Global Gene Expression Profiles of Postnatal Myocardium

status: Public on Jan 12 2017

city: Newark

first: Ruoxin

last: Wang

address: 185 south orange avenue

department: Department of Cell Biology and Molecular Medicine

institute: RUTGERS NEW JERSEY MEDICAL SCHOOL

summary: The present study was to investigate the differentially expressed genes in 24-hour-old (containing proliferative cardiomyocytes), 7-day-old (containing the burst of proliferative cardiomyocytes), and 10-week-old (containing growth-arrested cardiomyocytes) C57BL/6 mouse hearts using global gene expression profiles.

overall_design: The transcriptomic profiles of the samples at the three time points (24-hour old, 7-day old , and 10-week old of postnatal stage) were analyzed by direct comparison of the transcriptional level between the three groups of heart on the same custom Affymetrix Mouse Gene 1.0 ST Array. There are three replicates at each timepoint.

first: Jie

last: Yang

first: Minxin

last: Wei


title: YAP and TAZ modulate cell phenotype in a subset of small cell lung cancer.

city: Los Angeles

first: Masafumi

last: Horie

address: 2011 Zonal Ave

institute: University of Southern California

summary: We explored the functional role of YAP in SCLC cells (SBC3 and SBC5) by YAP knockdown.

overall_design: Total RNA was extracted from SBC3 and SBC5 cells 48 h after siNC or siYAP transfection. Microarray analysis was carried out using the Affymetrix GeneChip Human Genome U133 Plus 2.0 array.

first: Akira

last: Saito


title: Subcutaneous adipose tissue gene expression from men that are part of the METSIM study

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

summary: We analyzed samples from 770 male human subjects who are part of the METSIM study. Ethics Committee of the Northern Savo Hospital District approved the study. All participants gave written informed consent. The population-based cross-sectional METSIM study included 10 197 men, aged from 45 to 73 years, who were randomly selected from the population register of the Kuopio town in eastern Finland (population 95000). Every participant had a 1-day outpatient visit to the Clinical Research Unit at the University of Kuopio, including an interview on the history of previous diseases and current drug treatment and an evaluation of glucose tolerance and cardiovascular risk factors. After 12 h of fasting, a 2 h oral 75 g glucose tolerance test was performed and the blood samples were drawn at 0, 30 and 120 min. Plasma glucose was measured by enzymatic hexokinase photometric assay (Konelab Systems reagents; Thermo Fischer Scientific, Vantaa, Finland). Insulin was determined by immunoassay (ADVIA Centaur Insulin IRI no. 02230141; Siemens Medical Solutions Diagnostics, Tarrytown, NY, USA). Height and weight were measured to the nearest 0.5 cm and 0.1 kg, respectively. Waist circumference (at the midpoint between the lateral iliac crest and lowest rib) and hip circumference (at the level of the trochanter major) were measured to the nearest 0.5 cm. Body composition was determined by bioelectrical impedance (RJL Systems) in subjects in the supine position.

overall_design: Total RNA was obtained from subcutaneous fat biopsies from 770 people participating in the METSIM study

first: Mete

last: Civelek

first: Markku

last: Laakso


title: Restoring miR-150-5p to a triple negative breast cancer cell line [BT-549]

status: Public on Jan 01 2017

city: Aurora

first: Jennifer

last: Richer

state: CO

address: Mail Stop 8104, RC1N 5th Floor P18-5127, 12800 E. 19th Ave.

department: Pathology

institute: University of Colorado Anschutz Medical Campus

summary:
The objective of these experiments is to identify novel direct and indirect targets of miR-150-5p in breast cancer cell lines. The goal is that these will give direction as to what targets or pathways may be contributing to the reduced growth observed in these cell lines upon restoration of miR-150-5p. A therapy directed towards one or more critical subtype-specific targets could be developed as a therapeutic for breast cancer patients.
Using has-miR-150-5p mirVana miRNA mimic (Ambion, 4464066), miR-150-5p was restored to a triple negative breast cancer cell line, BT-549.

overall_design: Cells were transfected in triplicate for 72 hours with either mock, negative control, or mimic, and RNA isolated from each sample was hybridized onto Affymetrix GeneChip® Human Gene Array 2.0 ST ( probesets).

last: Heinz

last: Spoelstra

first: H

last: Gu

first: J


title: Restoring miR-150-5p to breast cancer cell lines


title: Expression data from 17-AAG resistance cell line

status: Public on Jan 11 2017

city: Incheon

first: Seung Hyun

last: Oh

address: 191 Hambakmoero, Yeonsu-gu

department: College of Pharmacy

country: South Korea

institute: Gachon University

summary: Develop the 17-AAG resistance human lung cancer cell line and used microarrays to observe the gene alternnation

overall_design: Compared 17-AAG resistance human ling cancer cell lines versus parent cell

first: Seung

first: Jong

last: Woo


title: Expression data from human embryonic stem cells, progenitors, and differentiated neurons

city: Albuquerque

first: Jason

last: Weick

state: New Mexico

address: 915 Camino de Salud NE

department: Neurosciences

institute: University of New Mexico Health Sciences Center

summary:
Previous studies have reported that human pluripotent stem cells (hPSCs) generate dorsal forebrain, cortical-like neurons under default differentiation in the absence of patterning morphogens. Novel bioinformatic analyses of whole transcriptome data allow us to examine these cells' regional specification more comprehensively. Furthermore, these tools allow us to ask how well hPSNs mimic their endogenous counterparts during various stages of in vivo human brain development.
Here we performed transcriptome profiling of hPSC-derived neurons (hPSNs) at multiple developmental timepoints during default patterning.

overall_design: Default differentiated neural progenitors and neurons were selected at successive stages of early development for RNA extraction and hybridization on Affymetrix microarrays. We sought to characterize the genetic programs involved with generation of default patterned glutamatergic and GABAergic forebrain neurons.

first: Crina

last: Floruta

middle: P


title: Expression data from intestinal crypts and stroma of wild type and late generation (4th generation) telomerase-deficient mice

city: Saint Louis

first: Ting-Lin

state: Missouri

address: 660 S. Euclid Ave., CB 8123

institute: Washington University of St Louis

summary:
Telomeres shorten with each round of cell division, and the expression of telomerase serves to lengthen telomeres. In the absence of telomerase, telomeres shorten to the point of uncapping and causes defects in tissues with high turnover, including the intestinal epithelium. In mice lacking telomerase (e.g. mTR-/-), telomeres critically shorten after several generations of telomerase deficiency, with pronounced defects in their intestine.
Crypt epithelium and underlying stroma were each isolated from wild type (WT) and late generation (4th generation or G4) mice and used for mRNA expression profiling.

overall_design: We sought out to determine the differences in gene expression profile between wild type and late generation (4th generation) mTR-/- mouse small intestinal crypts and stroma. Intestinal crypts and stroma from age-matched and sex-matched mice were isolated for RNA extraction and hybridization on Affymetrix microarrays.

first: F

last: Johnson


title: Germline BRCA2 mutations drive prostate cancers with distinct evolutionary trajectories

city: Toronto

first: Yu-Jia

last: Shiah

state: Ontario

address: MaRS Centre 661 University Avenue Suite 510

department: Informatics and Bio-computing

institute: Ontario Institute for Cancer Research

summary: Germline mutations in the BRCA2 tumour suppressor are associated with both an increased lifetime risk of developing prostate cancer (PCa) and increased risk of aggressive disease. To understand this aggression, here we profile the genomes and methylomes of localized PCa from 14 carriers of deleterious germline BRCA2 mutations (BRCA2-mutant PCa). We show that BRCA2-mutant PCa harbour increased genomic instability and a mutational profile that more closely resembles metastastic than localized disease. BRCA2-mutant PCa shows genomic and epigenomic dysregulation of the MED12L/MED12 axis, which is frequently dysregulated in metastatic castration-resistant prostate cancer (mCRPC). This dysregulation is enriched in BRCA2-mutant PCa harbouring intraductal carcinoma (IDC). Microdissection and sequencing of IDC and juxtaposed adjacent non-IDC invasive carcinoma in 10 patients demonstrates a common ancestor to both histopathologies. Overall we show that localized castration-sensitive BRCA2-mutant tumours are uniquely aggressive, due to de novo aberration in genes usually associated with metastatic disease, justifying aggressive initial treatment.

overall_design: In total, we have methylation profiles for 172 samples, of which 12 samples (corresponding to 10 unique samples) carry the BRCA2 mutation and the remaining 160 samples (corresponding to 104 unique samples) were sporadic samples. Out of the 10 unique BRCA samples, 2 samples were repeated twice; out of the 104 unique samples, 34 samples were repeated twice, 8 samples repeated three times, 2 samples repeated four times.

first: Paul

last: Boutros

first: Robert

last: Bristow

first: Michael

last: Fraser


title: DNA methylation profiling of first trimester villous cytotrophoblasts

status: Public on Jan 07 2017

city: Paris

first: Akpeli

middle: V.

last: Nordor

address: 26, rue d'Ulm

department: Département de Recherche Translationnelle

country: France

institute: Institut Curie - PSL Research University

summary: Using the Illumina HumanMethylation450 BeadChip platform, we profiled the genome-wide DNA methylation of villous cytotrophoblasts samples isolated ex vivo from placental chorionic villi before they first come into contact with maternal blood (8-10 weeks of gestation, n = 9) and after (12-14 weeks of gestation, n = 10).

overall_design: Bisulphite converted DNA was hybridized to Illumina HumanMethylation450 BeadChip arrays

middle: V

first: Sophie

last: Richon

first: Dominique

last: Bellet

first: Thierry

last: Fournier

first: Martin

last: Aryee


title: Altered epithelial gene expression in peripheral airways of severe asthma

status: Public on Jan 04 2017

city: London

first: Akul

last: Singhania

address: 1 Midland Road

institute: The Francis Crick Institute

summary: Management of severe asthma remains a challenge despite treatment with glucocorticosteroid therapy. The majority of studies investigating disease mechanisms in treatment-resistant severe asthma have previously focused on the large central airways, with very few utilizing transcriptomic approaches. The small peripheral airways, which comprise the majority of the airway surface area, remain an unexplored area in severe asthma and were targeted for global epithelial gene expression profiling in this study.

overall_design: Differences between central and peripheral airways were evaluated using transcriptomic analysis (Affymetrix HG U133 plus 2.0 GeneChips) of epithelial brushings obtained from severe asthma patients (N = 17) and healthy volunteers (N = 23). Results were validated in an independent cohort (N = 10) by real-time quantitative PCR.

first: Christopher

last: Woelk

first: Peter

last: Howarth


title: Mesenchymal Stromal Cells Induce Ex Vivo Proliferation and Erythroid Commitment of Cord Blood Haematopoietic Stem Cells

city: Brescia

first: Simone

last: Perucca

address: Viale Europa

department: Department of Clinical and experimental sciences

country: Italy

institute: University of Brescia

summary: A human bone marrow-derived mesenchymal stromal cell (MSCs) and cord blood-derived CD34+ stem cell co-culture system was set up in order to evaluate the proliferative and differentiative effects induced by MSCs on CD34+ stem cells, and the reciprocal influences on gene expression profiles

overall_design: Bone marrow-derived mesenchymal stromal cells (BM-MSCs) were seeded on a plastic support. Upon reaching 80% of confluence, previously isolated CD34+ cord blood-derived hematopoietic stem cells (CB-CD34+) were plated onto a MSCs layer. After 10 days of culture, cells grown in suspension were collected in plastic tubes, while adherent cells were harvested by trypsinization. Two different fractions of HSCs were obtained: the SN-fraction, representing the HSCs grown in the supernatant of the co-cultures, and the AD-fraction, representing the HSCs grown directly in contact with the stromal layer (co-coltured MSCs). Single cultures of BM-MSCs and CB-CD34+ cells served as controls, namely MSCs-alone and CB-alone

first: Domenico

last: Russo


title: Microenvironment-dependent proliferation and mitochondrial priming loss   in mantle cell lymphoma is overcome by anti-CD20

status: Public on Jan 02 2017

city: Nantes

first: David

last: CHIRON

address: 8 quai Moncousu

institute: CRCNA

summary: Mantle cell lymphoma (MCL) accumulates in lymphoid organs but disseminates early on in extranodal tissues. Although proliferation remains located in lymphoid organs only, suggesting a major role of the tumor ecosystem, few studies have assessed MCL microenvironment. We therefore cocultured primary circulating MCL cells from 21 patients several weeks ex vivo with stromal or lymphoid-like (CD40L) cells to determine which interactions could support proliferation of MCL cells. We showed that coculture with lymphoid-like cells, but not stromal cells, induced cell-cycle progression, which was amplified by MCL-specific cytokines (IGF-1, BAFF, IL-6, IL-10). Of interest, we showed that our model recapitulated the MCL in situ molecular signatures i.e., proliferation, NFkB and survival signatures. We further demonstrated that proliferating MCL harbored an imbalance in Bcl-2 family expression leading to a consequent loss of mitochondrial priming. Interestingly, this loss of priming was overcome by the Type II anti-CD20 antibody obinutuzumab, which counteracted Bcl-xL induction through NFkB inhibition. Finally, we showed that the mitochondrial priming directly correlated with the sensitivity toward venetoclax and alkylating drugs. By identifying the microenvironment as the major support for proliferation and drug resistance in MCL, our results highlight a selective approach to target the lymphoma niche.

overall_design: MCL cells were amplified and RNA were prepared from exponentially growing cells. RNA was extracted using the RNeasy Kit (Qiagen, Hilden, Germany). Biotinylated cRNA was amplified with a double in vitro transcription and hybridized to the human U133 2.0 plus GeneChips, according to the manu- facturer’s instructions (Affymetrix, Santa Clara, CA, USA). Fluorescence intensities were quantified and analyzed using the GECOS software (Affymetrix).

last: Chiron

first: Steven

last: Le Gouill

first: Martine

last: Amiot

first: Catherine

last: Pellat-Deceunynck


title: Clonal isolates of PC3 cells overexpressing CENPU

city: Bethesda

first: Jean

last: Winter

address: 50 South Driver

department: NHGRI

country: USA

institute: NIH

summary:
We identified CENPU as prostate cancer metastases genes by analyzing QTL, transcript profiles and SNP associations with aggressive disease phenotypic traits in transgenic mice and human cohorts
CENPU was futher validated as a metastases genes in vitro and in vivo utilizing prostate cancer cell lines overexpressing the gene, and we used microarray to analyze the changes in transcripts

overall_design: Human prostate cancer cell line PC-3 were cloned with etither a control (empty) p-Lenti vector, or a p-Lenti vector containing the CENPU gene. Cells were selected using blastocydin followed by propagation of 5 clonal isolates for RNA extraction and hybridization onto Affymetrix array

first: Nigel

last: Crawford