title: Gene expression analysis of hESC-derived-MESP1 expressing progenitors

city: Leiden

first: Sabine

last: Den Hartogh

state: Zuid-Holland

address: Einthovenweg 20

department: Anatomy and Embryology

institute: LUMC

summary:
A hESC MESP1-MCHERRY reporter line was used to isolate and study the molecular character of MESP1 expressing pre-cardiac progenitors, derived from hESC. MESP1 is a key-transcription factor for pre-cardiac mesoderm and is marking the progenitor for almost all cells of the heart.
This reporter line was used to study cardiac differentiation and the derivation of early cardiac progenitors in vitro.

overall_design: hESCs were differentiated towards the cardiac lineage, expressing MESP1-mCherry at day 3 of differentiation. Total RNA obtained from isolated MESP1-mCherry expressing progenitors was compared to that of non-MESP1-expressing progenitors and undifferentiated hESCs in order to characterize MESP1-specific transcription factors and proteins.

first: Robert

last: Passier


title: The role of cancer exosomes in non-tumorigenic cells

status: Public on Aug 27 2014

city: Houston

first: RAGHU

last: KALLURI

address: 1881 East Rd.

department: CANCER BIOLOGY

country: USA

institute: MDACC

summary: The goal of this study is to report that breast cancer associated exosomes contain microRNAs (miRNAs) associated with the RISC Loading Complex  (RLC) and display cell-independent capacity to process precursor microRNAs (pre-miRNAs) into mature miRNAs. Pre-miRNAs, along with Dicer, AGO2, and TRBP, are present in exosomes of cancer cells. CD43 mediates the accumulation of Dicer specifically in cancer exosomes. Cancer exosomes mediate an efficient and rapid silencing of mRNAs to reprogram the target cell transcriptome. Exosomes derived from cells and sera of patients with breast cancer instigate non-tumorigenic epithelial cells to form tumors in a Dicer-dependent manner. These findings offer opportunities for the development of exosomes based biomarkers and therapies.

overall_design: Exosomes from cancer cells were isolated using established ultracentrifugation methods. The global miRNA content of non-tumorigenic cells was investigated before and after exosomes treatment to study the role of microRNA biogenesis in exosomes for cancer progression and the transformation process of normal cells.

first: Sonia

middle: A

last: Melo

first: Raghu

last: Kalluri


title: Reduced gene expression levels after chronic exposure to high concentrations of air pollutants

city: Prague

first: Pavel

last: Rossner

address: Videnska 1083

department: Genetic Ecotoxicology

country: Czech Republic

institute: Institute of Experimental Medicine

summary: We analyzed the ability of particulate matter (PM) and chemicals adsorbed onto it to induce diverse gene expression profiles in subjects living in two regions of the Czech Republic differing in levels and sources of the air pollution.  A total of 312 samples from polluted Ostrava region and 154 control samples from Prague were collected in winter 2009, summer 2009 and winter 2010. The highest concentrations of air pollutants were detected in winter 2010 when the subjects were exposed to: PM of aerodynamic diameter < 2.5 µm (PM2.5) (70 vs. 44.9 µg/m3); benzo[a]pyrene (9.02 vs. 2.56 ng/m3) and benzene (10.2 vs. 5.5 µg/m3) in Ostrava and Prague, respectively. Global gene expression analysis of total RNA extracted from leukocytes was performed using Illumina Expression BeadChips microarrays. The expression of selected genes was verified by quantitative real-time PCR (qRT-PCR). Gene expression profiles differed by locations and seasons. Despite lower concentrations of air pollutants a higher number of differentially expressed genes and affected KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways was found in subjects from Prague. In both locations immune response pathways were affected, in Prague also neurodegenerative diseases-related pathways. Over-representation of the latter pathways was associated with the exposure to PM2.5. The qRT-PCR analysis showed a significant decrease in expression of APEX, ATM, FAS, GSTM1, IL1B and RAD21 in subjects from Ostrava, in a comparison of winter 2010 and summer 2009. In Prague, an increase in gene expression was observed for GADD45A and PTGS2. In conclusion, high concentrations of pollutants in Ostrava were not associated with higher number of differentially expressed genes, affected KEGG pathways and expression levels of selected genes. This observation suggests that chronic exposure to air pollution may result in reduced gene expression response with possible negative health consequences.

overall_design: Total RNA was extracted from leukocytes of total of 154 control subjects and 312 subjects exposed to heavy air pollution. The samples were collected in three seasons (winter 2009, summer 2009, winter 2010) with different levels of air pollution. Most of the subjects were sampled repeatedly; however, some of them joined the study in summer 2009 or winter 2010.


title: Endometriosis: Normal endometrial stromal cells and endometriotic stromal cells

status: Public on Aug 01 2014

city: Chicago

first: Diana

last: Monsivais

address: 750 N Lake Shore Dr

institute: Northwestern University

summary: Gene expression profiling of primary stromal cell cultures isolated from human endometrium and ovarian endometriosis. Samples are derived from the endometrium of 6 healthy patients and the endometriomas of 6 diseased patients. The results indicate the gene expression differences between these two cell populations.

overall_design: Stromal cells were obtained from human normal endometrial tissues and ovarian endometriomas. The tissues were digested enzymatically, and pure stromal cell populations were established.


title: A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequence Quality Control consortium

status: Public on Aug 08 2014

city: Shanghai

first: Leming

last: Shi

address: 2005 Songhu Road

department: School of Life Sciences

country: China

institute: Fudan University

type:
Expression profiling by array
Expression profiling by RT-PCR

summary: We present primary results from the Sequencing Quality Control (SEQC) project, coordinated by the United States Food and Drug Administration. Examining Illumina HiSeq, Life Technologies SOLiD and Roche 454 platforms at multiple laboratory sites using reference RNA samples with built-in controls, we assess RNA sequencing (RNA-seq) performance for sequence discovery and differential expression profiling and compare it to microarray and quantitative PCR (qPCR) data using complementary metrics. At all sequencing depths, we discover unannotated exon-exon junctions, with >80% validated by qPCR. We find that measurements of relative expression are accurate and reproducible across sites and platforms if specific filters are used. In contrast, RNA-seq and microarrays do not provide accurate absolute measurements, and gene-specific biases are observed, for these and qPCR. Measurement performance depends on the platform and data analysis pipeline, and variation is large for transcriptlevel profiling. The complete SEQC data sets, comprising >100 billion reads (10Tb), provide unique resources for evaluating RNA-seq analyses for clinical and regulatory settings.

overall_design: The well-characterized reference RNA samples A (pooled cell lines) and B (human brain) from the MAQC consortium, adding spike-ins of synthetic RNA from the External RNA Control Consortium (ERCC).  Samples C and D were then constructed by combining A and B in known mixing ratios, 3:1 and 1:3, respectively.  All samples were distributed to several independent sites for RNA-Seq library construction and profiling by Illumina HiSeq 2000 and LifeTech SOLiD 5500 platforms.  Also, vendors created their own cDNA libraries that were then distributed to each test site, in order to examine the degree of a “site effect” that was independent of the library preparation process.  To support an assessment of gene models, samples A and B were also sequenced at independent sites by the Roche 454 platform, providing longer reads.  For comparison to other technologies, these data were also compared to the MAQC-I Affymetrix U133 Plus2 microarray, several current microarray platforms, and also assessed by 20,801 PrimePCR reactions.

first: Zhenqiang

last: Su

first: Pawel

middle: P

last: Labaj

first: Sheng

last: Li

first: Jean

last: Thierry-Mieg

first: Danielle

first: Wei

first: Charles

last: Wang

first: Gary

last: Schroth

first: Wendell

middle: D

last: Jones

first: Wenzhong

last: Xiao

first: Weihong

last: Xu

first: Roderick

middle: V

last: Jensen

first: Reagan

last: Kelly

first: Joshua

first: Ana

last: Conesa

first: Hanlin

last: Gao

first: Nadereh

last: Jafari

first: Fei

last: Lu

first: Edward

middle: J

last: Oakeley

first: Craig

last: Praul

first: Javier

last: Santoyo-Lopez

first: Xin-Xing

last: Tan

first: E

last: Thompson

first: Jo

last: Vandesompele

first: Zhiyu

last: Peng

first: Andreas

last: Scherer

first: Jiri

last: Zavadil

first: Huixiao

last: Hong

first: Yang

last: Liao

last: Setterquist

first: Shashi

last: Amur

first: Scott

middle: S

last: Auerbach

first: Desmond

middle: I

last: Bannon

first: Wenjun

last: Bao

first: Hans

last: Binder

first: Thomas

last: Blomquist

first: Cecilie

last: Boysen

first: Kelli

last: Bramlett

first: Murray

middle: H

last: Brilliant

first: Pierre

middle: R

last: Bushel


title: mRNA Expression data from A549 cell line post non-thermal plasma treatment

city: Hefei

first: Wei

last: Han

state: Anhui

address: #155 Shushanghu Road

institute: Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences

summary:
Although accumulated evidence suggests that NTP induces death of various cancer cell types, thus offering a promising alternative treatment, the mechanism of its therapeutic effect is little understood. To understand basic molecular and cellular mechanisms triggered by plasma treatment, we firstly investigated biological effects of helium plasma on human non-small cell lung cancer A549 cell line.
The presented data of the tumor transcriptome help identifying the key players of modulated gene expression following exposure to plasma at the molecular level and interpreting the downstream process.

overall_design: We set several groups including 1 min plasma treatment, 3 min plasma treatment and sham control. In 1 min group, we collected samples at 4 hr postr the stimulation, and in 3 min group, the samples at 1, 2, 4 h after treatment have been collected for analysis.

first: Jue

last: Hou


title: Genome-wide analysis of gene expression in human iPSCs and NSCs engineered by safe-harbor TALEN-mediated gene targeting

status: Public on Sep 01 2014

city: Bethesda

first: Jizhong

last: Zou

state: MD

address: 50 South Drive, Room 1146

institute: NIAMS/NIH

summary: Human iPSCs and NSCs were engineered by AAVS1 and/or C13 safe-harbor TALENs which mediated targeted integration of various reporter genes at single or dual safe-harbor loci. Multiple clones of targeted human iPSCs were used to compare with parental untargeted NCRM5 iPSCs. Polyclonal targeted human NSCs were used to compare with their parental untargeted NCRM1NSCs or H9NSCs.

overall_design: Total RNA obtained from targeted human iPSCs or NSCs compared to untargeted control iPSCs or NSCs.

first: Nasir

last: Malik


title: Systems Analysis of a RIG-I Agonist Inducing Broad Spectrum Inhibition of Virus Infectivity [Kinetic]

status: Public on Aug 21 2014

city: Port Saint Lucie

first: John

last: Hiscott

state: Florida

address: 9801 SW Discovery Way

department: Infectious Diseases

institute: Vaccine and Gene Institute-Florida

summary: The RIG-I like receptor pathway is stimulated during RNA virus infection by interaction between cytosolic RIG-I and viral RNA structures that contain short hairpin dsRNA and 5’ triphosphate (5’ppp) terminal structure. In the present study, an RNA agonist of RIG-I was synthesized in vitro and shown to stimulate RIG-I-dependent antiviral responses at concentrations in the picomolar range. In human lung epithelial A549 cells, 5’pppRNA specifically stimulated multiple parameters of the innate antiviral response, including IRF3, IRF7 and STAT1 activation, andinduction of inflammatory and interferon stimulated genes - hallmarks of a fully functional antiviral response. Evaluation of the magnitude and duration of gene expression by transcriptional profiling identified a robust, sustained and diversified antiviral and inflammatory response characterized by enhanced pathogen recognition and interferon (IFN)signaling. Bioinformatics analysis further identified a transcriptional signature uniquely induced by 5’pppRNA, and not by IFNα-2bthat included a constellation of IRF7 and NF-kB target genes capable of mobilizing multiple arms of the innate and adaptive immune response. Treatment of primary PBMCs or lung epithelial A549 cells with 5’pppRNA provided significant protection against a spectrum of RNA and DNA viruses. In C57Bl/6 mice, intravenous administration of 5’pppRNA protected animals from a lethal challenge with H1N1 Influenza, reduced virus titers in mouse lungs and protected animals from virus-induced pneumonia. Strikingly, the RIG-I-specific transcriptional response afforded partial protection from influenza challenge, even in the absence of type I interferon signaling. This systems approach providestranscriptional, biochemical, and in vivo analysis of the antiviral efficacy of 5’pppRNA and highlights the therapeutic potential associated with the use of RIG-I agonists as broad spectrum antiviral agents.

overall_design: Kinetic analysis of A549 cells treated with 5'pppRNA and analyzed at 1h, 2h, 4h, 6h, 8h, 12h, 24h or 48h.

first: Marie-Line

last: Goulet

first: David

last: Olagnier

first: Zhengyun

last: Xu

first: Suzanne

last: Paz

first: S

middle: M

last: Belgnaoui

first: Erin

last: Lafferty

first: Valérie

last: Janelle

first: Meztli

last: Arguello

first: Marilene

last: Paquet

first: Khader

last: Ghneim

first: Stephanie

last: Richards

first: Andrew

last: Smith

first: Peter

last: Wilkinson

first: Mark

last: Cameron

first: Ulrich

last: Kalinke

first: Salman

last: Qureshi

first: Alain

last: Lamarre

first: Elias

middle: K

last: Haddad

first: Rafick

last: Sekaly

first: Suraj

last: Peri

first: Siddharth

last: Balachandran

first: Rongtuan

last: Lin


title: Receptor-independent ectopic activity of PROLACTIN predicts aggressive lung tumors and indicates HDACi-based therapeutic strategies.

status: Public on Aug 05 2014

city: La Tronche

first: Sophie

last: Rousseaux

address: Bd de la Chantourne

department: IAB

country: France

institute: INSERM-UGA

summary: Aim: PROLACTIN (PRL), normally produced by the pituitary gland, acts through its receptor (PRL-R) to initiate a signalling cascade to the genome. PRL can also be produced by cancer cells and become oncogenic by stimulating its receptor following an autocrine or paracrine route. Here we investigated the oncogenic activities of PRL in lung cancer. Results: PRL is ectopically activated in a subset of very aggressive lung tumours, associated with a rapid fatal outcome, in our cohort of 293 lung tumour patients as well as in an external independent series of patients. An investigation of the molecular basis of PRL adverse effects surprisingly showed an absence of PRL-R expression in the vast majority of PRL-expressing lung tumours. Additionally, a detailed analysis of the ectopically expressed PRL transcripts in lung tumours and cell lines revealed systematic alterations of its first exons encoding the signal peptide. Finally, the transcriptomes of two PRL expressing lung cancer cell lines, with or without silencing of PRL, showed that PRL directly or indirectly sustains the expression of a group of genes that are frequently up-regulated in a variety of unrelated cancers. Interestingly, the gene signature repressed by PRL ectopic expression in lung tumour cells is also specifically up-regulated by HDAC inhibitor treatment or HDAC1/2/3 knock-down. Innovation and conclusion: Altogether, this work sheds lights on the poorly understood impact of the recently-shown large-scale out-of-context gene activity in cancer and also suggests that PRL-expressing aggressive lung cancers could be particularly responsive to a HDAC inhibitor-based treatment.

overall_design: Total RNA was extracted from two small cell lung carcinoma (SCLC) cell lines expressing PRL (H146 and h524: si control) or not (siPRL) and the differentially expressed genes. Five replicates were analysed for each of the four conditions.

first: Saadi

last: Khochbin

first: Aurore

last: Lebescont

first: Philippe

last: Guardiola

first: Alexandra

last: Debernardi

first: Anne-Laure

last: Vitte


title: All-trans retinoic acid effect on the squamous cell carcinoma cell line ME180: time course

city: Washington

first: Tabari

last: Baker

state: District of Columbia

address: 3970 Reservoir Rd. NW

department: Oncology

institute: Georgetown University

summary: All-trans retinoic acid (ATRA) has been shown to have anti-proliferative effects, particularly in the context of cancer.  However, the effects of ATRA on gene and microRNA expression in solid tumors have not been investigated.  In this study, we performed gene expression and microRNA analysis of the squamous cell carcinoma cell line, ME180, following treatment with 10 micromolar all-trans retinoic acid (ATRA) for 1, 3, and 6 hours.  Results provide insight into the temporal regulation of genes and microRNAs by retinoids.

overall_design: 16 samples (4 DMSO-Treated, 4-1 hour 10μM ATRA, 4-3 hours 10μM ATRA, 4-6 hours 10μM ATRA)

first: Anton

last: Wellstein


title: Role of Ubc13 in Breast Cancer Metastasis

status: Public on Aug 18 2014

city: Singapore

first: Michael

last: Poidinger

address: #04-06, 8A Biomedical Grove

department: Bioinformatics

country: Singapore

institute: Singapore Immunology Network

summary: We recently found that Ubc13 controls breast cancer metastasis. However, the underlying molecular mechanisms remain elusive. In order to gain a better understanding of the signaling pathways controlled by Ubc13 in metastasis, we performed a gene array analysis on xenografts derived from orthotopically implanted MDA-MB-231 LM2 cells, which preferentially metastazize to lung in NOD/SCID mice.

overall_design: MDA-MB-231 LM2 cells were infected with lentivial shRNA constructs targeting either GFP (Control) or Ubc13 (ubc13). The resulting Control or Ubc13-silenced cells were implanted into fat pads of six weeks old female virgin NOD/SCID mice.  After eight weeks, tumors were excised, followed by collagenase/hyaluronidase digestion to establish single cell suspension, from which epithelial cells were enriched by depleting mouse cells of hematopoietic, endothelial, and fibroblast origin (CD45, TER119, CD31 and BP-1). The enrihced epithelial cells (three Control and three Ubc13-KD cells) were lysed in TRIZOL to extract RNA, which were then used to run microarray.

first: Subhra

last: Biswas

first: Xuefeng

last: Wu

last: Karin


title: Gene expression profiles of two lung squamous cell carcinoma cell lines treated with SOX2 siRNA

status: Public on Jul 30 2014

city: Miaoli County

first: Shih Sheng

last: Jiang

address: No. 35 Keyan Road, Zhunan County

department: National Institute of Cancer Research

country: Taiwan

institute: National Health Research Institutes

summary: SOX2 is a transcription factor essential for self-renewal and pluripotency of embryonic stem cells. Recently SOX2 was found overexpressed in the majority of the lung squamous cell carcinoma (SQC), in which it acts as a lineage-survival oncogene. However, downstream targets/pathways of SOX2 in lung SQC cells remain to be identified. In order to identify genes/pathways likely to be downstream of SOX2, we conducted SOX2 silencing experiments in LK2 and NCI-H520 (H520 thereafter), two SOX2-abundant lung SQC cell lines and analyzed global gene transcription changes by gene expression microarray assay.

overall_design: Each of H520 and LK2 cell lines was treated with either pooled siRNAs of SOX2 or non-silencing (control) siRNAs. After 48 h, cells were harvested and totoal RNA extracted for gene expression microarray analysis using Illumina HumanHT12 v3 BeadChip.

first: S

first: I

last: Chang


title: Gene expression profiles from joint-matched macroscopically intact and OA affected cartilage of patients undergoing joint replacement surgery due to end-stage OA

status: Public on Jul 28 2014

first: Yolande

middle: F. M.

last: Ramos

department: Molecular Epidemiology

country: Netherlands

institute: Leiden University Medical Center

summary: Genome wide gene expression was determined in paired samples of OA affected and preserved cartilage of the same joint using microarray analysis for 33 patients of the RAAK-study. Among the 1717 genes that were significantly different expressed between OA affected and preserved cartilage we found significant enrichment for genes involved in skeletal development (e.g. TNFRSF11B and FRZB). Also several inflammatory genes such as CD55, PTGES and TNFAIP6, previously identified in within-joint analyses as well as in analyses comparing preserved cartilage from OA affected joints versus healthy cartilage were among the top genes. A notable new gene was NGF, highly up-regulated in OA cartilage.

overall_design: To identify gene expression profiles associated with OA processes in articular cartilage and determine pathways responsive to the disease process gene expression profiles of paired preserved and OA affected cartilage samples of the same joint were determined.

middle: F

first: Wouter

last: den Hollander

first: Judith

last: Bovée

first: Nils

last: Bomer

first: Ruud

last: van der Breggen

first: Nico

last: Lakenberg

first: J

middle: C

last: Keurentjes

first: Jelle

last: Goeman

first: P

middle: E

last: Slagboom

first: Rob

middle: G

last: Nelissen

first: Steffan

last: Bos

first: Ingrid

last: Meulenbelt


status: Public on Aug 07 2014

city: Urbana

first: Zeynep

last: Madak Erdogan

state: IL

address: 1201 S Goodwin Ave

department: FSHN

institute: UIUC

summary:
The transcription factor FOXM1 coordinates the expression of cell cycle-related genes and plays a pivotal role in tumorigenesis and cancer progression. We have previously shown that FOXM1 acts downstream of 14-3-3ζ signaling, which correlates with a more aggressive tumor phenotype. However, the role that FOXM1 might play in engendering the resistance to endocrine treatments in estrogen receptor-positive (ER+) patients when tumor FOXM1 is high, has not been clearly defined.
To understand the role of FOXM1 in endocrine resistance and cancer aggressiveness, we analyzed FOXM1 protein expression by IHC in 501 ER-positive breast cancers; this revealed high FOXM1 expression in 20% of the tumors and a significantly reduced survival in these patients (p=0.003, log rank Mantel-Cox). We also mapped genome-wide FOXM1 binding events by chromatin immunoprecipitation, followed by high-throughput sequencing (ChIP-seq), in hormone-sensitive and resistant breast cancer cells after tamoxifen treatment. FOXM1 binding sites were enriched at the transcription start site of genes involved in cell cycle progression, maintenance of stem cell properties, and invasion and metastasis, all of which are correlated with the worst prognosis in ERα-positive patients treated with tamoxifen. Binding profiles were also integrated with gene expression data from cells before and after FOXM1 knockdown to highlight specific FOXM1 transcriptional networks. By modulating the levels of FOXM1 and newly discovered FOXM1-regulated genes [in breast cancer cells], we demonstrate that increased expression of FOXM1 was associated with an expansion of the cancer stem-like cell population and with increased cell invasiveness and resistance to endocrine treatments. Use of a selective FOXM1 inhibitor proved very effective in restoring endocrine therapy sensitivity and decreasing breast cancer aggressiveness.
Collectively, our findings uncover novel roles for FOXM1 and FOXM1-regulated genes in promoting cancer stem-like cell properties and therapy resistance, and highlight the relevance of FOXM1 as a therapeutic target to be considered for reducing invasiveness and enhancing breast cancer response to endocrine treatments.

overall_design: MCF-7 human breast adenocarcinoma cells were tranfected with control, and FOXM1 siRNA for 72 hours and treated with 0.1% EtOH (Vehicle) or 1 uM TOT for 24 hours, and cDNA microarray analyses were carried out using Affymetrix [HG-U133A_2] Affymetrix Human Genome U133A 2.0 Array.

last: Erdogan

first: Benita

last: Katzenellenbogen


title: Molecular changes in lobular breast cancers in response to endocrine therapy

status: Public on Aug 11 2014

city: Carrington Crescent

first: Andrew

last: Sims

state: Edinburgh

address: Systems Medicine Building

department: Institute of Genetics and Molecular Medicine

country: United Kingdom

institute: University of Edinburgh

summary: Invasive lobular cancer (ILC) accounts for approximately 10-15% of breast carcinomas and although it responds poorly to neoadjuvant chemotherapy, it appears to respond well to endocrine therapy.   Pre- and on-treatment (after 2 weeks and 3 months) biopsies and surgical samples were obtained from 14 post-menopausal women with ER+ histologically confirmed ILC who responded to 3 months of neoadjuvant letrozole and were compared with a cohort of 14 responding infiltrating ductal carcinomas (IDCs) matched on clinicopathological features by gene expression profiling. Dynamic clinical response was assessed using periodic 3D ultrasound measurements performed during treatment and defined as a reduction of >70% in tumour volume by 3 months.  The changes in gene expression in response to letrozole were highly consistent between responding ILC and IDC tumours, genes involved in proliferation were down-regulated and those involved with immune function and ECM remodelling were up-regulated. However, molecular differences between the histological subtypes were maintained upon treatment.  This is the first study of molecular changes in ILC in response to endocrine therapy to date. The genes which change on letrozole are highly consistent between ILC and IDC. Differences in gene expression between ILC and IDC at diagnosis and are maintained at each time point on treatment.

overall_design:
14 Pre treatment, 10 two week and 14 three month on-treatment ILC and 14 Pre treatment, 14 two week and 14 three month on-treatment IDC samples from the same patients.
Pre- and on-treatment samples from 7ILC & 6IDC patients were profiled on Illumina HT-12v4 (GPL10558) and samples from 7ILC and 8 IDC patients were profiled previously on Affymetrix U133A (GPL96) see GSE20181


title: Regulatory consequences of TARBP2 over-expression in MDA-231 cell-line

status: Public on Jul 24 2014

city: San Francisco

first: Hani

last: Goodarzi

state: CA

department: Biochemistry and Biophysics

institute: UCSF

summary: Transient transfection of TARBP2 expression vectors (along with GFP controls) followed by transcriptomic profiling revealed that over-expression of TARBP2 resulted in a significant enrichment of sRSE-carrying transcripts among the down-regulated transcripts.

overall_design: Transient transfection of CMV-driven TARBP2 was used to over-express this protein in MDA-231 cells. The cells were then subjected to transcripome profiling in comparison to mock-transfected cells.

first: H

first: S

last: Zhang

first: C

last: Buss

first: L

last: Fish

last: Tavazoie


title: Epigenetic and molecular signatures of cord blood CD34(+) cells treated with histone deacetylase inhibitors

status: Public on Jul 29 2014

city: New York,

first: Pratima

last: Chaurasia

state: New York

address: One Gustave  L Levy Place

department: Medicine

institute: Icahn School of Medicine at Mount Sinai

summary: Gene expression profiling of primary cord blood hematopoietic stem cell (day 0, CD34+ cells), enriched control  (untreated), Scriptaid and Valproic acid expanded CD34+ cells after a week in culture. Cord blood CD34+ cells were processed individually and equal number of  PC and reisolated CD34+ cells from 3-4 samples were pooled after expansion to avoid sample variations.

overall_design: Gene expression profiles of primary  human cord blood  CD34+ cells (day0), primary cells (PC)  expanded in the presence or absence of histone deacetylase inhibitors (HDACIs) in serum containing cultures supplemented with a combination of cytokines (SCF, FLT3, IL3 and TPO) for 7 days.

first: Weijia

first: Ronald

last: Hoffman


title: Expression profile of lung adenocarcinoma, A549 cells following induction of non metastatic 2 (NME2/NM23 H2)

status: Public on Aug 04 2014

city: Delhi

first: Vinod

middle: Kumar

last: Yadav

state: Delhi

address: Mall Road

country: India

institute: IGIB

summary: It is widely believed that reorganization of nucleosomes result in availability of binding sites that engage transcription factors during eukaryotic gene regulation. Recent findings, on the other hand, suggest that transcription factors induced as a result of physiological perturbations directly (or in association with chromatin modifiers) may alter nucleosome occupancy to facilitate DNA binding. Although, together these suggest a close relationship between transcription factor binding and nucleosome reorganization, the nature of the inter-dependency, or to what extent it influences regulatory transcription is not clear. Moreover, since most studies used physiolgical pertubations that induced multiple transcription factor chromatin modifiers, the relatively local (or direct) effect of transcription factor binding on nucleosome occupancy remains unclear. With these in mind, we used a single transcription factor to induce physiological changes, representing metastatic (aggressive cancer) and the corresponding non-metastatic state, in human cancer cells. Following characterization of the two states (before and after induction of the transcription factor) we determined: (a) genome wide binding sites of the transcription factor, (b) promoter nucleosome occupancy and (c) transcriptome profiles, independently in both conditions. Interestingly, we find only ~20% of TF binding results from nucleosome reorganization - however, almost all corresponding genes were transcriptionally altered. Whereas, in cases where TF-occupancy was independent of nucleosome repositioning (in close vicinity), or co-occurred with nucleosomes, only a small fraction of the corresponding genes were expressed/repressed. Together, these indicate a model where TF occupancy only when coupled with nucleosome repositioning in close proximity is transcriptionally active. This, to our knowledge, for the first time also helps explain why genome wide TF occupancy (e.g., from ChIP-seq) is typically associated with only a small fraction of genes that change expression.

overall_design: For expression profiling of cells in NME2-induced conditions, A549 cells were transfected with pcDNA-NME2-MYC or pcDNA-MYC (control). RNA was isolated from the cells 48h after transfection using the trizol method (Sigma) as per manufacturer’s protocol. Total RNA was processed to hybridize to Illumina Human HT-12 v4 Expression BeadChip as per manufacturer’s instructions. Three biological replicates were averaged and data was analyzed using BeadStudio (P <0.05 of fold change).

first: Akinchan

last: Kumar

first: Shantanu

last: Chowdhury


title: Regulatory consequences of TARBP2 knock-down in CN-LM1a cell-line

summary: siRNA-mediated knock-down followed by transcriptomic profiling revealed that silencing of TARBP2 resulted in a significant up-regulation of sRSE-carrying transcripts.

overall_design: Two independent siRNAs were used to knock down TARBP2 in metastatic CN-LM1a cells. The cells were then subjected to transcripome profiling in comparison to mock-transfected cells.


title: Regulatory consequences of TARBP2 knock-down in MDA-LM2-shDicer cell-line

overall_design: Two independent siRNAs were used to knock down TARBP2 in metastatic MDA-LM2 shDicer cells. The cells were then subjected to transcripome profiling in comparison to mock-transfected cells.


title: Regulatory consequences of TARBP2 knock-down in293T cell-line

overall_design: Two independent siRNAs were used to knock down TARBP2 in metastatic 293T cells. The cells were then subjected to transcripome profiling in comparison to mock-transfected cells.


title: Regulatory consequences of TARBP2 knock-down in MDA-LM2 cell-line [stability experiment]

summary: siRNA-mediated knock-down followed by transcriptomic profiling revealed that silencing of TARBP2 resulted in a significant increase in the stability of sRSE-carrying transcripts.

overall_design: Two independent siRNAs were used to knock down TARBP2 in metastatic MDA-LM2 cells. The cells were then subjected to whole-genome transcript stabiliy measurements in comparison to mock-transfected cells.


title: In-culture titration experiment for sRSE

summary: In order to test the transcriptome-wide functionality of the identified sRSE instances, we performed an in vivo titration experiment in which synthetic RNA oligonucleotides harboring tandem sRSE1 repeats were used as intracellular decoys that would bind the putative trans factor, preventing it from targeting endogenous transcripts.

overall_design: Capped and poly-adenylated RNAs carrying tandem sRSE elements were transfected along with scrambled RNA molecules as control. 48 hours post-transfection, samples were subjected to transcriptome profiling to measure the regulatory consequences of the in-vivo titration of the sRSE-binding trans factor.


title: Effect of CHADL knockdown in ATDC cells

status: Public on Jul 31 2014

city: Lund

first: James

middle: Chin Shing

last: Ho

address: Sölvegatan 23

country: Sweden

institute: Lund University

summary:
The human genome contains several homologous Small Leucine-Rich Protein (SLRP)-encoding genes, many of which orchestrate collagen fibril assembly. All SLRP gene products have not been identified or characterized. In this report, we describe a novel class IV SLRP - Chondroadherin-like (CHADL).
Microarray analysis of CHADL knockdown in ATDC5 cells suggests collagen receptor-related changes, a pro-proliferative and pro-differentiation profile.

overall_design: Two samples in duplicates are analyzed. The two control samples are transfected with scrambled negative control shRNA.The two knockdown samples are transfected with shRNA specific for CHADL.


title: Gene Body Methylation Directly Increases Gene Expression and is a Therapeutic Target for Genes Upregulated in Cancer (gene expression)

city: Los Angeles

first: Xiaojing

last: Yang

address: 1441 Eastlake Ave, Room 7336

institute: USC/Norris Comprehensive Cancer Center

summary: Demethylation treatment reduce gene body methylation as well as gene expression

overall_design: Total RNA obtained from untreated and treated cell lines were hybridised to the HumanHT12_V4 Human Expression Beadchip

first: Han

last: Han


title: Gene expression profiling of the response to interferon beta in EBV-transformed and primary B cells of patients with multiple sclerosis

city: Haifa

first: Tamar

last: Paperna

address: Efron St. 1

department: Faculty of Medicine

country: Israel

institute: Technion

summary: To identify gene expression changes and pathways induced by interferon-β (IFN-β) in B cells, we studied the in vitro response of EBV-transformed B cells (lymphoblast cell lines-LCLs). LCLs were derived from an MS patient repository. Whole genome expression analysis identified 115 genes that were more than two-fold differentially up-regulated following IFN-β exposure, with over 50 novel IFN-β response genes. Pathways analysis demonstrated that IFN-β affected LCLs in a similar manner to other cell types by activating known IFN-β canonical pathways. Additionally, IFN-β increased the expression of innate immune response genes, while down-regulating many B cell receptor pathway genes and genes involved in adaptive immune responses. Several of the novel response genes  were tested and validated as IFN-β response genes in human primary B cells.

overall_design: Total RNA from LCL samples treated for four hours with interferon beta (100u/ml) was compared to RNA from untreated LCLs (paired analysis). LCL samples were from patients with MS.

first: Rana

last: Khsheibun

first: Nili

last: Avidan

first: Ariel

last: Miller


title: Expression data of WT and Attim17-1 Arabidopsis seeds during stratification and germination

city: Umeå

first: Simon

middle: R.

last: Law

state: Västerbotten

address: Umeå University

institute: Umeå Plant Science Centre

summary:
The translocase of the inner membrane 17-1 (Tim17-1) plays a defined role in germination in Arabidopsis thaliana
A transcriptomic analysis of Attim17-1 during seed germination

overall_design: Total RNA extraction was carried out on 80 mg of  WT Arabidopsis seeds and  Attim17-1 seeds at 4 time points during germination in triplicate. The time points selected were:seeds following 15 days of ripening (0 h), 48 h of stratification (48 h S), followed by seed collected 6 hours into the light (6 h SL) and 24 hours into the light (24 h SL).

first: Yan

last: Wang

first: Reena

last: Narsai

first: Olivier

last: Van Aken

first: Vindya

last: Uggalla

first: Marna

last: van Der Merwe

first: Owen

last: Duncan

last: Whelan

first: Monika

middle: W

last: Murcha


title: Sox2 promotes malignancy in glioblastoma by regulating plasticity and astrocytic differentiation

status: Public on Jul 22 2014

city: Grand Rapids

first: David

last: Cherba

state: MI

address: 333 Bostwick Ave

department: Bioinformatics and Biostatistic Core

institute: Van Andel Institute

summary:
Making use of a previously described isogenic cancer stem cells and serum differentiated cultures we show that Sox2 controls developmental stated specific programs in glioblastoma. Glioblastoma cells were cultured as control and with SOX2 knockdown to identify the scope of SOX2 interactions. The SOX2 knockdown were accomplished using two knockdown technologies.  The knockdown cells were compared to controls, early passage, and scrambled controls.
For Sox2 knockdown in low passage 10% FBS cells, the following oligonucleotides targeting human SOX2 coding sequence, or non-silencing control sequence, were cloned into BLOCK-iT Pol II miR RNAi expression vectors (Invitrogen), before cell transfection into GBM monolayer cells using Lipofectamine-2000 (Invitrogen):
Sox2miRNA1R:5’CCTGTGCATGGGCTGTCTGCGCTGTCAGTCAGTGGCCAAAACAGCGCAGATGCAGCCCATGCAC
Sox2miRNA1F:5’TGCTGTGCATGGGCTGCATCTGCGCTGTTTTGGCCACTGACTGACAGCGCAGACAGCC
Sox2miRNA2R:5’CCTGAACCCATGGAGAAGAGCCAGTCAGTCAGTGGCCAAAACTGGCTCTTGGCTCCATGGGTTC
Sox2miRNA2F:5’TGCTGAACCCATGGAGCCAAGAGCCAGTTTTGGCCACTGACTGACTGGCTCTTCTCCATGGGTT
miRNAnegative:5’GAAATGTACTGCGCGTGGAGACGTTTTGGCCACTGACTGACGTCTCCACGCAGTACATTT
Sox2 knockdown in neurospheres: GIPZ Lentiviral shRNAmir constructs targeting human Sox2 (clones V3LHS_404430 and V3LHS_404432) and non-silencing control (RHS4346) were obtained (Thermo Scientific Open Biosystems) and lentivirus were prepared according to the manufacturer’s instructions.
Sox2 ectopic expression: Sox2 cDNA was subcloned from pCMV6-XL5-NM_002106.2 (Origene) into pcDNA 3.1 mammalian expression vector (Invitrogen), under control of constitutive CMV promoter.  Plasmid DNA constructs were stably transfected into GBM monolayer cells using Lipofectamine-2000 (Invitrogen).

overall_design: Control Glioblastoma cells cultured as neurospheres and monolayer early passage are compared to multiple shRNA SOX2 knockdown and multiple miR knockdown cell cultures. A total of 8 samples are analyzed for significant fold change genes identifying gene-gene interactions associated with the SOX2 knockdown. High fold change genes are grouped in lists to be analyzed for network-pathway enrichment.  Overlap of significant gene list for each method were analyzed.

first: Ana

last: deCarvalho

first: Laila

last: Poisson

first: Artem

middle: D

last: Berezovsky

first: Craig

last: Webb

first: Andrea

last: Transou

first: Xin

last: Hong

first: Laura A

last: Hasselbach

first: Susan

last: Irtenkauf

first: Tom

last: Mikkelsen


title: Merlin/NF2-loss Driven Tumorigenesis Linked to CRL4(DCAF1)-Mediated Inhibition of the Hippo Pathway Components Lats1 and 2

status: Public on Jul 15 2014

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

summary: Studies in drosophila have suggested that Merlin/NF2 suppresses tumorigenesis by activating upstream components of the Hippo pathway at or near the plasma membrane.  In contrast, studies of Merlin-deficient tumor cells have indicated that Merlin suppresses tumorigenesis by entering into the nucleus where it inhibits the E3 ubiquitin ligase CRL4DCAF1. We found that CRL4DCAF1 promotes YAP and TEAD-dependent transcription by ubiquitylating and thereby inhibiting Lats1 and 2 in the nucleus. Genetic epistasis experiments and analysis of tumor-derived missense mutations indicate that this signaling connection sustains the oncogenicity of Merlin-deficient tumor cells. Analysis of clinical samples confirms that this pathway operates in NF2 mutant mesotheliomas, schwannomas and meningiomas. We conclude that de-repressed CRL4DCAF1 controls the output of the Hippo pathway by inhibiting Lats1 and 2 in the nucleus.

overall_design: To generate a gene expression signature reflective of CRL4(DCAF1)-dependent YAP activity, we used DNA microarray analysis to compare the effect of inactivation of CRL4(DCAF1) and simultaneous inactivation of YAP and TAZ on gene expression in Meso-33 human mesothelioma cells

first: Wei

last: Li

first: Jonathan

last: Cooper

first: Lu

last: Zhou

first: Chenyi

last: Yang

first: Hediye

last: Erdjument-Bromage

last: Zagzag

first: Matija

last: Snuderl

first: Marc

last: Ladanyi

first: C

middle: O

last: Hanemann

first: Pengbo

first: Matthias

middle: A

last: Karajannis

first: Filippo

last: Giancotti


title: Trasncriptional response of human whole blood following TLR2 or TLR4 ligation in vitro

status: Public on Jul 11 2014

city: London

first: Simon

last: Blankley

address: The Ridgeway

department: Division of Immunoregulation

institute: MRC - National Insititute for Medical Research

summary: Use of human whole blood for transcriptomic analysis has potential advantages over the use of isolated immune cells for studying the transcriptional response to pathogens and their products. Whole blood stimulation can be carried out in a laboratory without the expertise or equipment to isolate immune cells from blood, with the added advantage of being able to undertake experiments using very small volumes of blood.   Toll like receptors (TLRs) are a family of pattern recognition receptors which recognise highly conserved microbial products. Using the TLR2 ligand (Pam3CSK4) and the TLR4 ligand (LPS) human whole blood was stimulated for 0, 1, 3, 6, 12 or 24 hours at which times mRNA was isolated and a comparative microarray was undertaken. A common NFκB transcriptional programme was identified following both TLR2 and TLR4 ligation which peaked at between 3 to 6 hours including upregulation of many of the NFκB family members. In contrast an interferon transcriptional response was observed following TLR4 but not TLR2 ligation as early as 1 hour post stimulation and peaking at 6 hours. These results recapitulate the findings observed in previously published studies using isolated murine and human myeloid cells indicating that in vitro stimulated human whole blood can be used to interrogate the transcriptional kinetics response of innate cells to TLR ligands.   Our study demonstrates that with a systems biology approach analysis of mRNA isolated from human whole blood can delineate both the temporal response and the key transcriptional differences following TLR2 and TLR4 ligation.

overall_design: 6 healthy human volunteers. 1ml whole blood stimulated in vitro with either LPS (1ng/ml), Pam3CSK4 (200ng/ml) or media for 0, 1, 3, 6 12 or 24 hours.

first: Anne

last: O'Garra


title: T cell responses to H1N1v and a longitudinal study of seasonal influenza vaccination - 2009

status: Public on Jul 20 2014

city: Stanford

first: David

last: Furman

address: 279 Campus Dr, B226

department: Microbiology and Immunolgy

institute: Stanford University

summary: Systems biology approach to examine effects of seasonal flu vaccination in adults of different ages on gene expression, cytokine stimulation and serum cytokines with parameters such as immune senescence to uncover new markers and mechanisms behind failure of immune function in many older people.

overall_design: Total RNA was extracted from whole-blood lysates obtained from individuals immediately prior to vaccination against seasonal influenza, followed by depletion of globin messenger RNA. The goal was to evaluate potential gene expression signatures at Day 0 associated with immune senescence.

first: Mark

last: Davis


title: T cell responses to H1N1v and a longitudinal study of seasonal influenza vaccination - 2010


title: T cell responses to H1N1v and a longitudinal study of seasonal influenza vaccination

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

overall_design: Refer to individual Series


title: Regulatory consequences of TARBP2 knock-down in MDA-LM2 cell-line

first: Hani

last: Goodarzi

overall_design: Two independent siRNAs were used to knock down TARBP2 in metastatic MDA-LM2 cells. The cells were then subjected to transcripome profiling in comparison to mock-transfected cells.

first: H

first: S

last: Zhang

last: Buss

first: L

last: Fish

last: Tavazoie


title: Gene expression analysis of ectopic cyclin D1-expressing myeloma cells compared to their non expressing counterparts

status: Public on Jul 23 2014

city: Caen Cedex

first: Brigitte

last: Sola

address: CHU Côte de Nacre

department: UFR de médecine

institute: Université de Caen

summary: We analyzed gene expression profiles of myeloma cells belonging to the group of bas prognosis RPMI 8226 and LP1 expressing either the GFP protein or a cyclin D1-GFP fusion protein

overall_design: Two cell lines RPMI 8226 and LP1. Two clones from each cell line GFP and cyclin D1-GFP. Four biological replicates independently grown and harvested. One replicate per array.


title: Regulatory consequences of ZNF395 knock-down in MDA-LM2-shTARBP2 cell-line

summary: shRNA-mediated knock-down followed by transcriptomic profiling revealed that silencing of ZNF395 resulted in a significant up-regulation in several key oncogenes.

overall_design: ZNF395 was knocked-down, via expression of short-hairpin RNAs targeting its transcript. The cells were then subjected to transcripome profiling in comparison to mock-transfected cells.


title: Analysis of ALK TKI sensitive and ALK TKI resistant isogenic pairs of H3122 (EML4-ALK E13;A20) cells

status: Public on Jul 14 2014

city: Nashville

first: Pengcheng

last: Lu

state: TN

address: 2200 Pierce Avenue

institute: Vanderbilt University

summary: Starting with H3122 cells, which harbor the EML4-ALK E13;A20 fusion and are known to be sensitive to ALK tyrosine kinase inhibitors, we generated isogenic pairs of ALK TKI sensitive and ALK TKI resistant cell lines using established methods (see Chmeliecki, J et al Science Trans Med 2011). We modeled resistance against the currently FDA approved ALK TKI, crizotinib (also called PF-1066). We also modeled resistance against a novel more potent ALK inhibitor, X-376 (ref: Lovly, CM et al Cancer Research 2011). We compared gene expression profiles between the 'parental' (ALK TKI sensitive) H3122 cells and the drug resistant cells (H3122 CR for Crizotinib resistant cells and H3122 XR for X-376 resistant cells).

overall_design: Total RNA was obtained from H3122 Parental, H3122 PF1066R, and H3122 X376R cells. The experiment was performed in triplicate.

first: Christine

last: Lovly

first: William

last: Pao

first: Xi

last: Chen


title: Genome-wide analysis of androgen receptor (AR) SUMOylation effects on gene expression (HEK293).

status: Public on Jul 03 2014

city: Kuopio

first: Päivi

last: Sutinen

address: Yliopistonranta 1 E

department: School of Medicine

country: Finland

institute: University of Eastern Finland

summary: Androgen receptor (AR) plays an important regulatory role during prostate cancer development. AR’s transcriptional activity is regulated by androgenic ligands, but also by post-translational modifications. To study the role of the AR SUMOylation in genuine chromatin environment, we compared androgen-regulated gene expression and AR chromatin occupancy in PC-3 prostate cancer and HEK293 cell lines stably expressing wild-type (wt) or SUMOylation site-mutated AR (AR-K386R,K520R). Our genome-wide gene expression analyses reveal that the SUMOylation modulates the AR function in a target gene and pathway selective manner. The transcripts that are differentially regulated by androgen and SUMOylation are linked to cellular movement, cell death, cellular proliferation, cellular development and cell cycle. In line with these data, SUMOylation mutant AR cells proliferate faster and are more sensitive to apoptosis. Moreover, ChIP-seq analyses show that the SUMOylation modulates the chromatin occupancy of AR on many loci in a fashion that parallels with their differential androgen-regulated expression. De novo motif analyses show that other transcription factor-binding motifs are differentially enriched at the wtAR- and the AR-K386R,K520R-preferred genomic binding positions. Taken together, our data indicate that SUMOylation does not simply repress the AR activity, but it regulates AR’s interaction with the chromatin and the receptor’s target gene selection.

overall_design: Isogenic HEK293 cells stably expressing wild-type AR (wtAR) or SUMOylation-defective AR (AR-K2R) were treated 24 h with 10 nM R1881 or vehicle (EtOH). All conditions were performed in triplicate. The effect on gene expression was assessed by microarray.

first: Marjo

last: Malinen

first: Sami

last: Heikkinen

first: Jorma

middle: J

last: Palvimo


title: Genome-wide analysis of androgen receptor (AR) SUMOylation effects on gene expression (PC-3).

overall_design: PC-3 cells stably expressing wild-type AR (wtAR) or SUMOylation-defective AR (AR-K2R) were treated 16 h with 10 nM R1881 or vehicle (EtOH). All conditions were performed in triplicate. The effect on gene expression was assessed by microarray.


title: Gene expression profiles at the day 5 blastocyst implantation and interimplantation sites of the hamster [human array]

status: Public on Jul 17 2014

first: Bibhash

last: Paria

address: 2215 B. Garland Avenue

institute: Vanderbilt

summary:
Current knowledge of the molecular regulation of the blastocyst implantation event has been largely derived from studies in the mouse that requires ovarian estrogen for initiation of the implantation event. However, there are species such as the hamster, guinea pig, pig, horse, rhesus monkey and perhaps the human where the blastocyst implantation event initiates only in the progesterone-primed uterus. Despite this fundamental difference in the requirement of ovarian hormones in initiating blastocyst implantation among species, efforts to identify gene networks relevant for the blastocyst implantation event in progesterone–dependent species are limited. In this study, cDNA prepared from RNAs of day 5 blastocyst implantation and interimplantation sites were hybridized with mouse and human oligonucleotide microarray platforms to discern the transcriptional networks underlying the regulation of blastocyst implantation in hamsters. Compared with the inter-implantation site, blastocyst implantation sites showed upregulation and downregulation of a sizable number of genes by both cross-species arrays.The merit of the cross-species hybridization and reliability of the identified up- and down-regulated genes at the implantation sites were validated by detecting differential expression of a few randomly selected genes from both arrays by real-time PCR. Function gene ontology and pathway analysis revealed that differentially expressed genes are associated with several biological events and molecular pathways that are likely to be taking place at the blastocyst implantation site. This is the first study that identified the differential gene expression profile at the blastocyst implantation site of the hamsters, and revealed molecular pathways that are possibly associated with the progesterone-dependent blastocyst implantation process.
We used microarrays to detail the expression differences in hamster implantation and interimplantation sites.

overall_design: Total RNAs were prepared from the hamster day 5 blastocyst implantation and interimplantation sites. Three sets of RNAs were isolated from three different animals and were subjected to microarray analysis using Affymetrix mouse and human array platforms.


title: The impact of miR-542-3p on gene expression profile in U2OS cells

status: Public on Jul 02 2014

city: Seattle

first: Yemin

last: Wang

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Centre

summary: Analysis of gene expression change in U2OS cells expression synthetic miR-542-3p mimics.

overall_design: Forty-eight hours after transfection with negative miRNA mimics or miR-542-3p mimics, U2OS cells were subjected to RNA isolation.


title: The genomic architecture of sickle cell disease in children from West Africa

status: Public on Jul 01 2014

city: Montreal

first: Jacklyn

last: Quinlan

state: Qc

address: 3175 Cote Ste-Catherine

department: Pediatrics

country: Canada

institute: CHU Ste-Justine Hospital

summary: Sickle cell disease (SCD) is caused by a pathogenic hemoglobin (Hb) mutation, yet patients can have dramatically variable clinical manifestations. Here we address the genetic basis of this clinical heterogeneity. Using a systems genetics approach, we performed whole blood gene expression analysis and eQTL analysis on different clinical phenotypes in SCD patients.

overall_design:
We generated whole blood gene expression profiles for 311 West-African children recruited from the National Sickle Cell Disease Centre in Cotonou, Benin which included 250 patients with varying degrees of SCD severities and 61 age-matched controls. SCD is caused by a point-mutation in the beta-hemoglobin gene that changes the normal HbAA protein into, most often, an abnormal HbSS or HbSC protein. The SCD patients recruited in the study either had HbSS or HbSC phenotypes and were categorized into different 3 clinical states based on follow-up status (Rahimy, MC, et al. Effect of a comprehensive clinical care program on disease course in severely ill children with sickle cell anemia in sub-Saharan African setting. Bood 102, 834-838. 2002). When patients are refered to the clinic, they are enrolled when they are in steady-state condition, and are labeled as entry (E). Patients followed at the SCD clinic are labeled as FU. Control patients were recruited and are labeled as C. Patients were also assigned a severity score (Sebastiani, P. et al. A network model to predict the risk of death in sickle cell disease. Blood 110, 2727-2735, 2007). Hemoglobin protein status (Hb phenotype) was confirmed for each patient using standard electrophoretic techniques. We generated genotypes for 263 of these individuals and performed principal component analysis (PCA) which identified 2 signigicant genotypic principal components (gPC1 and gPC2). Using the gene expression and genotyping data, we performed an eSNP analysis.
.
Gene expression data presented in this study.

first: Philip

last: Awadalla


title: Electrophilic lipid mediator 15-deoxy-Δ12,14-prostaglandin J2 modifies glucocorticoid signaling via receptor SUMOylation

status: Public on Jun 30 2014

first: Ville

last: Paakinaho

address: Yliopistonranta 8

summary: Cortisol, the central stress hormone in humans, activates the glucocorticoid receptor (GR). Anti-inflammatory effects are the most important pharmaceutical effects mediated by the GR. Inasmuch as electrophilic cyclopentenone prostaglandin 15-deoxy-Δ12,14-prostaglandin J2 (15d-PGJ2) has potent anti-inflammatory properties and activates the SUMOylation pathway, we have investigated the effect of 15d-PGJ2 on glucocorticoid signaling and receptor SUMOylation. To this end, we studied isogenic HEK293 cells expressing either wild-type GR or SUMOylation-defective GR. Interestingly, 15d-PGJ2 triggered SUMO-2/3 modification in the primary SUMOylation sites of the GR. Gene expression profiling and pathway analyses indicate that 15d-PGJ2 inhibits GR signaling in a genome-wide fashion that is significantly dependent on the GR SUMOylation sites. Chromatin immunoprecipitation assays showed that the repressive effect of 15d-PGJ2 on GR target gene expression occurs in parallel with the inhibition of receptor binding to the target gene chromatin. Furthermore, depletion of the sole SUMO E2 conjugase UBC9 from HEK293 cells confirmed the involvement of active SUMOylation in the regulatory process. Taken together, our data indicate that GR SUMOylation modulates the glucocorticoid signaling during acute cell stress. Our data also suggest that GR SUMOylation modulates crosstalk of the glucocorticoid signaling with other transcription factors that are responsive to cell stress.

overall_design: Total RNA isolated from isogenic HEK293 cell lines stably expressing either wild-type GR (wtGR) or SUMOylation-defective GR (GR3KR) treated with 100 nM of dexamethasone (dex) in the presence or absence of 5 µM 15d-PGJ2 for 6h. All conditions are performed in triplicate


title: Genome-wide analysis of MEF2-dependent gene expression in human NSCs

city: San Diego

first: xiayu

last: huang

address: 3010 Science Park Road

institute: Sanford|Burnham Medical Research Institute

summary: Redox-mediated posttranslational modifications represent a molecular switch that controls major mechanisms of cell function. Nitric oxide (NO) can mediate redox reactions via S-nitrosylation, representing transfer of an NO group to a critical protein thiol. NO is known to modulate neurogenesis and neuronal survival in various brain regions in disparate neurodegenerative conditions. However, a unifying molecular mechanism linking these phenomena remains unknown. Here we report that S-nitrosylation of myocyte enhancer factor 2 (MEF2) transcription factors acts as a redox switch to inhibit both neurogenesis and neuronal survival. Structure-based analysis reveals that MEF2 dimerization creates a pocket, facilitating S-nitrosylation at an evolutionally conserved cysteine residue in the DNA binding domain. S-Nitrosylation disrupts MEF2-DNA binding and transcriptional activity, leading to impaired neurogenesis and survival in vitro and in vivo. Our data define a novel molecular switch whereby redox-mediated posttranslational modification controls both neurogenesis and neurodegeneration via a single transcriptional signaling cascade.

overall_design: Total RNA obtained from human NSCs transfected with constitutively-active MEF2 (MEF2CA) compared to vector control (ptd-Tomato)

first: Shing

last: Chan

first: Shu-ichi

last: Okamoto

first: Stuart

last: Lipton


title: RABL6A promotes G1-S phase progression and pancreatic neuroendocrine tumor cell proliferation in an Rb1-dependent manner

city: Iowa City

first: Benjamin

last: Darbro

state: IA

address: 200 Hawkins Drive

institute: University of Iowa

summary: Mechanisms of neuroendocrine tumor (NET) proliferation are poorly understood and therapies that effectively control NET progression and metastatic disease are limited. We found amplification of a putative oncogene, RABL6A, in primary human pancreatic NETs (PNETs) that correlated with high level RABL6A protein expression. Consistent with those results, stable silencing of RABL6A in cultured BON-1 PNET cells revealed that it is essential for their proliferation and survival. Cells lacking RABL6A predominantly arrested in G1 phase with a moderate mitotic block. Pathway analysis of microarray data suggested activation of the p53 and retinoblastoma (Rb1) tumor suppressor pathways in the arrested cells. Specific inactivation of p53 had no effect on the RABL6A knockdown phenotype, indicating RABL6A functions independent of p53 in this setting. By comparison, Rb1 inactivation restored G1 to S phase progression in RABL6A knockdown cells although it was insufficient to override the mitotic arrest and cell death caused by RABL6A loss. Thus, RABL6A promotes G1 progression in PNET cells by inactivating Rb1, an established suppressor of PNET proliferation and development. This work identifies RABL6A as a new negative regulator of Rb1 that is essential for PNET proliferation and survival. We suggest RABL6A is a new potential biomarker and target for anticancer therapy in PNET patients.

overall_design: Total RNA obtained from human BON-1 PNET cells with RABL6A shRNA knockdown compared to BON-1 cells expressing control vector.

first: Dawn

last: Quelle


title: Early lineage restriction and regional segregation during mammalian heart development

status: Public on Jul 10 2014

city: Bruxelles

first: Samira

last: Chabab

address: 808, Route de Lennik

country: Belgium

institute: Université Libre de Bruxelles

summary:
Cardiac development arises from two sources of mesoderm progenitors, the first (FHF) and the second heart field (SHF). Mesp1 has been proposed to mark the most primitive multipotent cardiac progenitors common for both heart fields. Here, using clonal analysis of the earliest prospective cardiovascular progenitors in a temporally controlled manner during the early gastrulation, we found that Mesp1 progenitors consist of two temporally distinct pools of progenitors restricted to either the FHF or the SHF. FHF progenitors were unipotent, while SHF progenitors, were either uni- or bipotent. Microarray and single cell RT-PCR analysis of Mesp1 progenitors revealed the existence of molecularly distinct populations of Mesp1 progenitors, consistent with their lineage and regional contribution. Altogether, these results provide evidence that heart development arises from distinct populations of unipotent and bipotent cardiac progenitors that independently express Mesp1 at different time points during their specification, revealing that the regional segregation and lineage restriction of cardiac progenitors occurs very early during gastrulation.
We used microarrays to characterize the molecular mechanisms that control Mesp1 progenitor specification and lineage segregation during the early stage of cardiac mesoderm formation,

overall_design: 50 Mesp1 H2B-GFP+ or Mesp1 H2B-GFP- cells at E6.5 or E7.5 from mouse embryos were sorted for RNA extraction, amplification and hybridization on Affimetrix microarrays. Microaarrays were performed on Mouse Genome 430 PM strip Affymetrix array. The overall design was repeated in two different biological samples.

first: Fabienne

last: Lescroart

first: Cédric

last: Blanpain


title: Comparative RNA-sequencing analysis of myocardial and circulating small RNAs in human heart failure and their utility as biomarkers [array]

first: Kemal

middle: Marc

last: Akat

address: 1230 York Avenue

institute: The Rockefeller University

summary: Heart failure is associated with high morbidity and mortality and its incidence increases worldwide. MicroRNAs (miRNAs) are potential markers and targets for diagnostic and therapeutic applications, respectively. We determined myocardial and circulating miRNA abundance and its changes in patients with stable and end-stage heart failure before and at different time points after mechanical unloading by a left ventricular assist device (LVAD) by small-RNA-sequencing. MiRNA changes in failing heart tissues partially resembled that of fetal myocardium. Consistent with prototypical miRNA–target-mRNA interactions, target mRNA levels were negatively correlated to changes in abundance for highly expressed miRNAs in heart failure and fetal hearts. The circulating small RNA profile was dominated by miRNAs, and fragments of tRNAs and small cytoplasmic RNAs. Heart- and muscle-specific circulating miRNAs (myomirs) increased up to 140-fold in advanced heart failure, which coincided with a similar increase in cardiac troponin I protein, the established marker for heart injury. These extracellular changes nearly completely reversed 3 months following initiation of LVAD support. In stable heart failure, circulating miRNAs showed less than 5-fold differences compared to normal, and myomir and cardiac troponin I levels were only captured near the detection limit. These findings provide the underpinning for miRNA-based therapies and emphasize the usefulness of circulating miRNAs as biomarkers for heart injury performing similar to established diagnostic protein biomarkers.

overall_design: Total RNA isolated from human left ventricular myocardium of failing hearts due to dilated or ischemic cardiomyopathy before and after mechanical unloading by a left ventricular assist device (LVAD), and fetal myocardium compared to non-failing postnatal myocardium.

first: Thomas

last: Tuschl

first: Paul

last: Schulze


title: Gene expression profile of Hodgkin’s lymphoma cells after knock-down of DUSP5

city: Halle (Saale)

first: Martin

middle: Sebastian

last: Staege

state: Sachsen-Anhalt

address: Ernst-Grube-Str. 40

department: Universitätsklinik u. Poliklinik für Kinder- u. Jugendmedizin

country: Germany

summary: By using high-density DNA microarrays, we analyzed the gene-expression profile of Hodgkin's lymphoma cell line L-428 after knock-down of DUSP5 (dual specificity phosphatase 5)

overall_design: RNA was extracted from established Hodgkin's lymphoma cell line L-428 and hybridized with Affymetrix HG_U133A microarrays.

first: Katja

last: Müller

middle: S


title: Identification of MIR196B (or MIR375 or MIR429) target genes in Colon cancer cell lines

status: Public on Jun 27 2014

city: Iksan

first: Soo-Cheon

last: Chae

state: Cheonbuk

address: Iksandaero

department: Department of Patholgy

country: South Korea

institute: Wonkwang University School of Medicine

summary: MIR196B  (or MIR375 or MIR429) target genes were identified by comparing the mRNAs downregulated in MIR196B  (or MIR375 or MIR429) -overexpressing cells (determined by mRNA microarray analysis) with target genes predicted by public bioinformatics tools.

overall_design: Total RNA obtained from non-trancfected or transfected SW480 or Caco2 cells by MIR196B  (or MIR375 or MIR429)


title: Genome-wide analysis of serum starved prelamin A-accumulating hMSCs gene expression.

status: Public on Jun 23 2014

city: Barakaldo

first: Clara

middle: Isabel

last: Rodriguez

state: Bizkaia

address: Edificio de Anatomía Patológica, planta 2, Hospital Universitario Cruces

country: Spain

institute: BioCruces Research Health Institute

summary: Analysis of serum starved prelamin A-accumulating hMSCs at gene expression level. The hypothesis tested in the present study was that prelamin A accumulation induces the dysregulation of genes that are essensial for cell survival under a stress condition such as serum starvation. The results provide important information about these genes and the functional categories that are dysregulated due to prelamin A accumulation in serum starved hMSCs.

overall_design: Two samples are analyzed in this microarray experiment: human mesenchymal stem cell cultured under serum starvation conditions (during 24 hours) which accumulate prelamin A (pre-hMSCs) and control mesenchymal stem cells (ctrl-hMSCs). 2 biological replicates (hMSCs derived from 2 different bone marrow donors) and 1 technical replicate are included in this analysis.

first: Arantza

last: Infante

first: Andrea

last: Gago

first: Garbiñe

last: Ruiz de Eguino

middle: I

last: Rodríguez


title: Peripheral blood gene-expression in heavy vs. moderate drinkers exposed to three types of personalized imagery

status: Public on Jul 09 2014

city: New Haven

first: Robert

last: Beech

state: CT

address: 34 Park St

department: Psychiatry

country: USA

institute: Yale University

summary: Alterations in stress-related gene-expression may play a role in stress-related drinking and the risk for alcohol dependence.  Microarrays were used to measure changes in gene-expression in peripheral blood in non-smoking, social drinking subjects exposed to three types of personalized imagery: neutral, stressful (but not alcohol- related), and alcohol-related cues. Gene-expression was measured at baseline, immediately after, and 1 hour after stimulus presentation. Subjects were allowed to drink up to 750cc of beer in a “taste-test” following stimulus presentation in each imagery condition, and the amount of beer consumed was recorded. Gene-expression levels were compared in 2 groups of non-smoking subjects (n=11/group): heavy drinkers (HD, defined as regular alcohol use over the past year of at least 8 standard drinks/week for women and at least 15 standard drinks/week for men), and moderate drinkers (MD, defined as up to 7 standard drinks/week for women and 14 standard drinks/week for men).

overall_design: 198 samples total. Total RNA isolated from PAXgene blood RNA tubes from heavy drinkers (n=11) and moderate drinkers (n=11) exposed to 3 different types of personalized imagery (stress, neutral, or alcohol-cue) at three time-points per condition (baseline, immediately after cue presentation,and 1 hour after cue presentation)(9 samples per subject).


title: Gene expression sensitivity at detecting cancer in prostate core biopsies [Expression Profiles]

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

summary: The aim of this study was to analyze critically the potential usefulness of selected RNA biomarkers in supporting conventional histological diagnostic tests for PCa. The selection of potential biomarkers was conducted by microarray profiling of gene expression on prostate tissues extracted from the gland after total radical prostatectomy.

overall_design: Gene expression profiles of 16 prostate samples without carcinoma and 16 matched pairs of samples with and without cancer cells isolated from prostates containing prostate carcinoma

first: Agnieszka

last: Paziewska

first: Michalina

last: Dabrowska

first: Artur

last: Antoniewicz

first: Jakub

last: Dobruch

first: Michal

last: Mikula

first: Dorota

last: Jarosz

first: Lukasz

last: Zapala

first: Andrzej

last: Borowka

first: Jerzy

last: Ostrowski


title: Loss of Oncogenic Notch1 Contributes to PI3 Kinase Inhibitor Resistance in T Lineage Leukemia

status: Public on Jun 24 2014

city: Memphis

first: Shann-Ching

last: Chen

address: 262 Danny Thomas Place

department: Pathology

institute: St. Jude Children's Research Hospital

summary: Somatic NOTCH1 mutations are found in ~60% of T lineage acute lymphoblastic leukemias (T-ALLs). Notch1 is cleaved by γ secretase to generate activated Notch intracellular domain (NICD) proteins. The NOTCH1 mutations found in T-ALL constitutively activate Notch1 signaling by increasing NICD levels. Genetic alterations in components of the Ras/PI3 kinase (PI3K)/Akt pathway are also highly prevalent in T-ALL, and often coexist with NOTCH1 mutations. Exposing a T-ALL cell line to the PI3 kinase (PI3K) inhibitor GDC-0941 generated drug resistant clones that down-regulated NICD expression. To address the in vivo relevance of this unexpected observation, we transplanted primary wild-type (WT) and KrasG12D mutant T-ALLs into recipient mice, and treated them with GDC-0941 alone and in combination with the MEK inhibitor PD0325901 (PD901). Although many leukemias responded dramatically to these targeted agents in vivo, drug-resistant clones invariably emerged. Multiple resistant T-ALLs lost NICD expression through mechanisms that included loss of Notch1 mutations found in the parental T-ALL. These GDC-0941-resistant leukemias exhibited reduced expression of many Notch1 target genes, elevated levels of phosphorylated Akt (pAkt), and displayed cross-resistance to γ secretase inhibitors (GSIs). Consistent with these data, inhibiting Notch1 activity in T-ALL cells enhanced PI3K signaling, providing a likely mechanism for in vivo selection against clones with Notch1 pathway activation. Thus, oncogenic Notch1 mutations that promote clonal outgrowth during malignant transformation unexpectedly “switch” to become deleterious during treatment with a PI3K inhibitor. These data advance our understanding of T-ALL pathogenesis and have implications for implementing new therapeutic regimens.

overall_design: We analyzed 28 mouse T-ALL samples obtained after in vivo treatment with GDC-0941 alone or GDC-0941 + PD0325901.  These T-ALL samples are either Kras wild type or harbor a KrasG12D mutations.

first: Monique

last: Dail

first: Jason

last: Wong

first: Jessica

last: Lawrence

first: Daniel

last: O’Connor

first: Joy

last: Nakitandwe

first: Keiko

last: Akagi

first: Jon

last: Aster

first: Warren

last: Pear

first: James

middle: R

last: Downing

first: Deepak

last: Sampath

first: Kevin

last: Shannon


title: CD4+ T cells treated with TNFalpha blocking agents during activation.

status: Public on Jun 25 2014

city: Amsterdam

first: Martine

middle: A.

last: Boks

address: Plesmanlaan 125

department: Immunopathology

institute: Sanquin Blood Supply

summary: Objective. TNFα is a potent pro-inflammatory cytokine playing a pivotal role in several autoimmune diseases. Neutralizing TNFα inhibits T cell proliferation and IFNγ production, and enhances suppressive capacity of regulatory T cells (Treg). Little is known about the mechanism of TNFα blocking agents on naïve T cell differentiation. Methods. Naïve CD4+ T cells were activated by dendritic cells (DC) in presence or absence of anti-TNFα agents. T cell polarization and activation was assessed during T cell differentiation. In addition, whole genome gene expression analysis was performed on anti-TNFα-treated T cells. Results. Neutralizing TNFα during priming of naïve CD4+ T cells by DC favors development of IL-10+ T helper (Th) cells at the expense of IFNγ induction. TNFα inhibits IL-10 via TNFRII, which becomes expressed after naïve T cell activation. While initial CD4+ T cell activation was not affected, neutralization of TNFα negatively affected later stages of T cell priming by counteracting full T cell activation and survival. Whole genome gene expression analysis revealed a regulatory gene profile of anti-TNFα-treated T cells. Indeed, neutralizing TNFα during naïve T cell priming enhanced the suppressive function of anti-TNFα-treated T cells. Conclusion. Inhibition of TNFα–TNFRII interaction affects late stage effector T cell development and shifts the balance of Th cell differentiation towards IL-10 expressing regulatory T cells, which may be one of the beneficial mechanisms in TNFα blocking therapies.

overall_design: Naïve CD4+ T cells were CFSE labeled and co-cultured for 13 days with allogeneic dendritic cells in the presence or absence of anti-TNFα agents. After 13 days, the CFSElow T cells were FACS sorted. Samples were generated from three independent donors.

first: Judith

last: Kager-Groenland

first: Marieke

last: van Ham

first: Anja

last: ten Brinke


title: Transcriptional landscape of aging in humans

status: Public on Jun 15 2014

city: Brisbane

first: Divya

last: Mehta

state: Queensland

country: Australia

institute: The University of Queensland

summary: We carried out blood transcriptome-wide association studies and replicated results to identify genes whose expression differs across the human aging spectrum.

overall_design: The transcriptional landscape of aging in humans


title: Genome-wide analysis of B lymphocytes derived from human pluripotent stem cells, neonatal and adult sources

status: Public on Jun 20 2014

city: Oxford

first: Stephen

last: Taylor

address: Headington

institute: CBRG

summary: The aim of the array was to compare iPS-derived CD19+CD10+ B cells with B cells from umbilical cord blood (UCB) and adult peripheral blood (PB)

overall_design: iPS-CD34+ cells and UCB-CD133+ cells were differentiated to the B cell lineage in vitro. B cells were also isolated directly from UCB and PB. RNA was extracted from CD19+CD10+ FACS isolated cells from all 4 B cell samples as well as from undifferentiated iPS cells.

first: Anna

last: French

first: Lee

last: Carpenter

first: Suzanne

last: Watt


city: Pieve Emanuele

first: Charlotte

middle: K Y

last: Ng

address: Via Rita Montalcini 4

department: Biomedical Sciences

country: Italy

institute: Humanitas University

summary:
Expression profiling of papillary carcinoma of the breast and grade- and ER-matched cases of invasive ductal breast cancer
To identify differential expression between papillary carcinomas of the breast and grade- and ER-matched invasive ductal breast cancers, we performed expression profiling of 16 cases of papillary carcinomas of the breast and 16 cases of grade- and ER-matched invasive ducatal carcinoma of no special subtype. We further reviewed the papillary carcinomas of the breast and classified them into 3 subtypes, namely, invasive papillary carcinoma, encapsulated papillary carcinoma and solid papillary carcinoma. We also performed a hypothesis-generating comparison of differential expression between the 3 subtypes of papillary carcinoma of the breast.

overall_design: Expression profiling of 16 cases of papillary carcinioma of the brest and 16 cases of invasive ducal carcinomas using the Illumina HT-12 v4 arrays

first: Salvatore

last: Piscuoglio

first: Charlott

last: e Ng

first: Jorge

last: Reis-Filho


title: HGU133A expression array data for diffuse large B cell lymphoma samples

status: Public on Jul 22 2014

city: Essen

first: Rene

last: Scholtysik

address: Virchowstrasse 173

department: IFZ

institute: University Hospital Essen

summary: The pathogenesis of diffuse large B cell lymphomas (DLBCL) is only partly understood. We analyzed 148 DLBCL by high resolution single nucleotide polymorphism (SNP)-chips to characterize genomic imbalances. Seventy-nine cases were of the germinal center B-cell like (GCB) type of DLBCL, 49 of the activated B-cell like (ABC) subtype and 20 were type 3 DLBCL. Twenty-four regions of recurrent genomic gains and 38 regions of recurrent genomic losses were identified over the whole cohort, with a median of 25 imbalances per case for ABC-DLBCL and 19 per case for GCB-DLBCL. Several recurrent copy number changes showed differential frequencies in the GCB- and ABC-DLBCL subgroups, including gains of HDAC7A predominantly in GCB-DLBCL (38% of cases) and losses of BACH2 and CASP8AP2 predominantly in ABC-DLBCL (35%), hinting at disparate pathogenetic mechanisms in these entities. Correlating gene expression and copy number revealed a strong gene dosage effect in all tumors, with 34% of probesets showing a concordant expression change in affected regions. Two new potential tumor suppressor genes emerging from the analysis, CASP3 and IL5RA, were sequenced in 10 and 16 candidate cases, respectively. However, no mutations were found, pointing to a potential haploinsufficiency effect of these genes, considering their reduced expression in cases with deletions. This work thus describes differences and similarities in the landscape of genomic aberrations in the DLBCL subgroups in a large collection of cases, confirming already known targets, but also discovering novel copy number changes with possible pathogenetic relevance.

overall_design: Affymetrix HGU133A arrays were performed according to the manufacturer's directions on RNA extracted from cryopreserved lymph node biopsies of tumor samples.

first: René

first: Markus

last: Kreuz


title: PDX1 Binding in human embryonic stem cell derived pancreatic progenitor cells [expression profiling]

status: Public on Jun 21 2014

city: Singapore

first: Shawn

last: Hoon

address: 61 Biopolis Street

country: Singapore

institute: Agency for Science Technology and Research

summary: PDX1 binds and regulates numerous genes involved in human pancreatic development but also binds hepatic genes

overall_design: Total RNA was extracted from day 0, day 10 and day17 of differentiated HES3 cells. Comparisons were made for day 10 and day 17 to day 0.

first: Adrian

middle: K

last: Teo


title: Characterization of genomic imbalances in diffuse large B-cell lymphoma by high resolution SNP-chip analysis

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

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

overall_design: Refer to individual Series


title: Global gene expression analysis for neuron stem cells (NSC) derived from iPSCs with Fanconi Anemia

status: Public on Jun 14 2014

city: La Jolla

first: Fei

last: Yi

address: 10010 North Torrey Pines Road

institute: Salk Institute

summary:
Fanconi Anemia (FA) is a recessive disorder associated with genomic instability
We generated iPSC from FA patient fibroblasts and further corrected the mutated FANCA gene with a homologous recombination-based approach.

overall_design: The NSCs were differentiated from control-iPSCs, FA-iPSCs, and corrected FA-NSCs, and their gene expressions were determined by microarray analysis.

first: G

last: Liu

first: F

first: Y

last: Gu

first: JC

last: Izpisua-Belmonte


title: FOXO4 knockdown in LNCaP prostate cancer cells

status: Public on Jun 12 2014

city: Buffalo

first: Jianmin

last: Wang

address: Elm and Carlton Streets

department: Bioinformatics and Biostatistics

institute: Roswell Park Comprehensive Cancer Center

summary: Compares shFOXO4 vs. Control in LNCaP grown in culture, or in nude mice as primary orthotopic tumors or lymph node metastases

overall_design: RNA isolated from sub-confluent LNCaP (shFOXO4 vs. sh-Control), or orthotopic primary tumors, or lmph node metastases, subjected to Illumina BeadChip microarray analyses

first: Irwin

middle: H

last: Gelman

first: Bing

last: Su


title: Human leukocytes from 6 volunteers before and 2h after pectin capsules consumption (IV)

status: Public on Jun 10 2014

city: Moscow

first: Anastasia

last: Shindyapina

state: Moscow

address: Mosfilmovskaya 76

department: Biengineering

country: Russia

institute: MSU Lomonosov

summary: Methanol (MeOH) is considered to be a poison in humans because of the alcohol dehydrogenase (ADH)-mediated conversion of MeOH into toxic formaldehyde (FA). Our recent genome-wide analysis of the mouse brain demonstrated that an increase in endogenous MeOH after ADH inhibition led to a significant increase in the plasma MeOH concentration and the modification of mRNA synthesis. These findings suggest endogenous MeOH involvement in homeostasis regulation by controlling mRNA levels. Here, we demonstrate directly that study volunteers displayed increasing concentrations of MeOH and FA in their blood plasma when consuming citrus pectin, ethanol and red wine. A microarray analysis of white blood cells (WBC) in volunteers after pectin intake showed various responses for 30 differentially regulated mRNAs. Most of the mRNAs were somehow involved in the pathogenesis of Alzheimer's disease (AD). There was also a decreased synthesis of hemoglobin  mRNA, HBA and HBB, the presence of which in WBC RNA was not a result of red blood cells contamination because erythrocyte-specific marker genes did not show significant change. A qRT-PCR analysis of volunteer WBC after pectin and red wine intake confirmed the complicated dependence between plasma MeOH content and the mRNA accumulation of previously identified genes, namely GAPDH and SNX27, and MME, SORL1, DDIT4, HBA and HBB genes revealed in this study. We hypothesized that human plasma MeOH, which is replenished from endogenous and exogenous sources (diet), has an impact on the WBC mRNA levels of genes involved in AD pathogenesis and signaling.

overall_design: The subjects fasted for 12 hours prior to beginning each experiment and evaluation session. Each volunteer swallowed capsules with PME containing citrus pectin (6 g) (Nittary Pharmaceuticals, VitaLine, Inc., USA). After 120 min blood samples were obtained. Total RNA was isolated from WBCs with TriReagent (MRC, USA) according to the manufacturer’s protocol.

middle: V

first: Tatiana

last: Komarova

first: Igor

last: Petrunia


title: Human leukocytes from 6 volunteers before and 2h after pectin capsules consumption (II)


title: Human leukocytes from 6 volunteers before and 2h after pectin capsules consumption (I)


title: Banking Placental Tissue: An Optimized Collection Procedure for Genome-Wide Analysis of Nucleic Acids [gene expression]

status: Public on Jun 09 2014

first: Rathi

last: Thiagarajan

address: 2880 Torrey Pines Scenic Drive

department: Reproductive Medicine

institute: UCSD

summary:
Banking of high-quality placental tissue specimens will enable biomarker discovery and molecular studies on diseases involving placental dysfunction. Systematic studies aimed at developing feasible standardized methodology for placental collection for genomic analyses are lacking. To determine the acceptable timeframe for placental collection, we collected multiple samples from first and third trimester placentas at serial time points 0-120 minutes after delivery, simultaneously comparing the traditional snap-freeze technique to collection in commercial solutions designed to preserve RNA (RNAlaterTM, Ambion), and DNA (DNAgard®, Biomatrica). The performance of RNAlater for preserving DNA was also tested. Nucleic acid quality was assessed by determining the RNA integrity number (RIN) and genome-wide expression and DNA methylation microarray profiling. We found that samples collected in RNAlater had higher and more consistent RINs compared to snap frozen tissue, with similar RINs obtained for tissue collected in RNAlater as large (1 cm3) and small (~0.1 cm3) tissue pieces.  RNAlater appeared to better stabilize the time zero gene expression pattern compared to snap freezing for first trimester placenta.  Microarray DNA methylation analysis showed that overall the DNA methylation profiles remained quite stable over a two hour time period after removal of the placenta from the uterus, with the DNAgard condition being superior to both snap freezing and RNAlater. The collection of placental samples in RNAlater and DNAgard is simple, and eliminates the need for liquid nitrogen or a freezer on-site. Moreover, the quality of the nucleic acids and the resulting data from samples collected in these preservation solutions is actually higher than that from samples collected using the traditional snap-freeze method. Thus, this new approach to placental sample collection is both easier to implement in busy clinical environments and yields higher quality data.
72 samples

overall_design: In this study, our objective was to identify the optimal timing and mode of collection for nucleic acids of sufficient quality to perform genome-wide RNA gene expression and DNA methylation studies for downstream molecular and functional enrichment analysis. To do this, we evaluated three different placenta collection methods: snap freezing in liquid nitrogen, RNAlaterTM, and DNAgard, over a two-hour window upon removal from the uterus, to determine: 1) the optimal collection method(s) for evaluation of mRNA expression and DNA methylation; and 2) the time period after delivery during which such optimal samples should be collected.

first: Lynlee

middle: M

last: Wolfe

last: Thagarajan

first: Francesca

last: Boscolo

first: Veronique

last: Tache

first: Ron

last: Coleman

first: Jessica

last: Kim

first: Wai

last: Kwan

first: Jeanne

middle: F

last: Loring

first: Mana

last: Parast

first: Louise

middle: C

last: Laurent


title: Human leukocytes from 6 volunteers before and 2h after pectin capsules consumption


title: Gene expression profiles associated with acute myocardial infarction and risk of cardiovascular death

city: Chicago

first: Jinhee

state: IL

address: 676 North St. Clair Street Arkes Suite 2330

department: Infectious Disease

institute: Northwestern University

summary: Whole peripheral blood samples collected into Paxgene tubes from 338 adult participants in the Emory University Cardiovascular Biobank, in Midtown Atlanta.  The sample is of mixed cardiovascular function diversity, and is part of a survey of the impact of status of cardiovascular disease on gene expression and clinical attributes. Sample annotations only include gender and proofed ethnicity for purposes of IRB, as well as technical features of the study (plate, phase of study, and RNA quality RIN score).

overall_design: 338 individuals in the Emory Cardiovascular Biobank in Midtown Atlanta., 219 men and 119 women. The age of individulas were between 26 and 85 (mean 62). 333 Caucasian (CAU), 4 African American (AFA), 1 South Asian (SAS).

first: Nima

last: Ghasemzadeh

first: Danny

last: Eapen

first: Neo

last: Chung

first: John

middle: D

last: Storey

first: Arshed

last: Quyyumi

first: Greg

last: Gibson


title: Novel Roles for ERK5 and Cofiin as Critical Mediators Linking Estrogen Receptor α-Driven Transcription, Actin Reorganization and Invasiveness in Breast cancer

status: Public on Jun 03 2014

city: Urbana

first: Zeynep

last: Madak Erdogan

address: 1201 S Goodwin Ave

department: FSHN

institute: UIUC

summary:
Cancer cell motility and invasiveness are fundamental characteristics of the malignant phenotype and are regulated through diverse signaling networks involving kinases and transcription factors. In this study, we identify a nuclear hormone receptor (ERα)-protein kinase (ERK5)-cofilin (CFL1) network that specifies the degree of breast cancer cell aggressiveness through coupling of actin reorganization and hormone receptor-mediated transcription. Using dominant negative and constitutively active forms, as well as small molecule inhibitors of ERK5 and MEK5, we show that hormone activation of estrogen receptor-α determines the nuclear versus cytoplasmic localization of the MAPK family member ERK5, which functions as a coregulator of ERα-gene transcription.
Notably, ERK5 works with the actin remodeling protein, CFL1, and upon hormone exposure both became localized to transcription factories in the nucleus, verified by immunofluorescence and proximity ligation assays. Both factors facilitated PAF1 recruitment to the RNA Pol II complex and both ERK5 and CFL1 were required for regulation of gene transcription. By contrast, in cells lacking ERα, ERK5 and CFL1 localized to cytoplasmic membrane regions of high actin remodeling, promoting cell motility and invasion, thereby revealing a mechanism likely to contribute to the generally poorer prognosis of ERα-negative breast cancers. Our study uncovers the dynamic interplay of nuclear receptor-mediated transcription and actin reorganization in phenotypes of breast cancer aggressiveness, and highlights new prognostic biomarkers and suggests novel approaches for developing targeted therapies to moderate cancer aggressiveness.

overall_design:
MCF-7 human breast adenocarcinoma cells were tranfected with control, and ERK5 siRNA for 72 hours and treated with 0.1% EtOH (Vehicle) or 10 nM E2 for 24 hours, and cDNA microarray analyses were carried out using Affymetrix [HG-U133A_2] Affymetrix Human Genome U133A 2.0 Array.
siRNA knock-down, ligand treatment

last: Erdogan

first: Benita

last: Katzenellenbogen


title: Effects of preoperative fasting on renal ischemia-reperfusion injury in young-lean and aged overweight mice

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

country: Netherlands

institute: Natl. Inst. Public Health & Environment

summary: To study the protective effects of preoperative fasting against renal ischemia-reperfusion injury, young-lean as well as aged overweight mice were subjected to three days of fasting or ad libitum food consumption, and gene expressions in kidneys of male mice were analyzed

overall_design: 19 samples (5 young control, 4 young fasted, 5 aged control, 5 aged fasted), each from individual mice

first: Franny

last: Jongbloed


title: Physiologic Hypoxia Promotes Maintenance of CML Stem Cells Despite Effective BCR−ABL1 Inhibition

first: Kian Leong

last: LEE

state: Singapore

address: #07-21, 8 College Road

department: Duke-NUS Medical School

institute: National University of Singapore (NUS)

summary: ABL1 kinase inhibitors such as imatinib mesylate (IM) are effective in managing chronic myelogenous leukemia (CML) but incapable of eliminating leukemia stem cells (LSCs), suggesting that kinase−independent pathways support LSC survival. Given that the bone marrow hypoxic microenvironment supports hematopoietic stem cells, we investigated if hypoxia similarly contributes to LSC persistence. Importantly, we found that while BCR−ABL1 kinase remained effectively inhibited by IM under hypoxia, apoptosis became partially suppressed. Furthermore, hypoxia enhanced the clonogenicity of CML cells, as well as their efficiency in repopulating immunodeficient mice, both in the presence and absence of IM. HIF1−α, which is the master regulator of the hypoxia transcriptional response is expressed in the bone marrow specimens of CML individuals. In vitro, HIF1−α is stabilized during hypoxia and its expression and transcriptional activity can be partially attenuated by concurrent IM treatment. Expression analysis demonstrates at the whole transcriptome level that hypoxia and IM regulate distinct subsets of genes. Functionally, knockdown of HIF1−α abolished the enhanced clonogenicity during hypoxia. Taken together, our results suggest that in the hypoxic microenvironment, HIF1−α signaling supports LSC persistence independently of BCR−ABL1 kinase activity. Thus targeting HIF1−α and its pathway components may be therapeutically important for the complete eradication of LSCs.

overall_design: 24 samples consisting CD34+ bone marrow aspirates of 3 chronic phase patients that were subjected to 24h or 96h of DMSO/Normoxia (21% oxygen, 5% carbon dioxide) control, 2 µM Imatinib, hypoxia (0.5% oxygen, 5% carbon dioxide) or combined Imatinib/hypoxia treatments in triplicate cultures.

first: King Pan

last: Ng

first: Aditi

last: Manjeri

last: Lee

first: Weijie

last: Huang

first: Soo Yong

last: Tan

first: Charles

middle: T

last: Chuah

first: Lorenz

last: Poellinger

first: Sin Tiong

last: Ong


title: Cooperativity and Equilibrium with FOXA1 Define Androgen Receptor Transcriptional Program [array]

status: Public on Jun 02 2014

first: Hong-Jian

last: Jin

state: IL - Illinois

address: 303 E Superior St

department: Medicine

summary: Previous studies have shown that FOXA1 defines prostatic AR binding events, the underlying mechanisms of which, however, are incompletely understood.

overall_design: To test whether ectopic AR and FOXA1 can activate AR target genes, we performed adenoviral  of LacZ, AR, FOXA1 or AR+FOXA1 proteins in DU145 cells, followed by microarray analysis of these cells.

first: Jindan

last: Yu


title: The transcription factor GATA6 allows self-renewal of colon adenoma stem cells by repressing BMP gene expression.

status: Public on Jun 19 2014

city: Barcelona

first: Evarist

middle: Planet

last: Letschert

state: Spain

address: C/ Baldiri Reixac 10

department: Biostatistics

institute: IRB Barcelona

summary: Aberrant activation of WNT signaling and loss of BMP signals represent the two main alterations leading to the initiation of colorectal cancer (CRC). Here we screen for genes required for maintaining the tumor stem cell phenotype and identify the zinc-finger transcription factor GATA6 as key regulator of the WNT and BMP pathways in CRC. GATA6 directly drives the expression of LGR5 in adenoma stem cells while it restricts BMP signaling to differentiated tumor cells. Genetic deletion of Gata6 in mouse colon adenomas increases the levels of BMP factors, which signal to block self-renewal of tumor stem cells. In human tumors, GATA6 represses BMP4 gene expression through binding to a regulatory region that has been previously linked to increased susceptibility to develop CRC. Thus, GATA6 creates a permissive environment for tumor stem cell expansion by controlling the major signaling pathways that influence CRC initiation.

overall_design: Total RNA from biological replicates of VillinCreERT2Gata6+/+Apcfl/fl and VillinCreERT2Gata6fl/flApcfl/fl  colon adenoma tumor organoids grown for one week in control media (see growth protocol).Total RNA was extracted using the TRIzol® Plus RNA Purification Kit (Life Technologies).

first: Gavin

last: Whissell


title: Inhibition of Hedgehog Signaling Pathway Impairs Cancer Cell Growth via Promotion of Autophagy

city: NANCAHNG

first: Shiwen

last: Luo

state: JiangXi

address: 17 Yong Wai street

department: Center for experimental medicine

country: China

institute: The Frist Affiliated Hospital of Nanchang University

summary: Analysis of gene expression levels in response to inhibition of Hh signaling in ovarian and glioma cancer cells using a cDNA microarray technique. Microarray analyses revealed that differentially expressed genes (DEGs) in human cancer cells are enriched in the senescence and autophagy pathways in response to the inhibition of Hh signaling. Further investigations showed that inhibition of Hh signaling induced autophagy..

overall_design: ES2 and H4 cells were treated with GANT61 (20 μM for 32hr and 48hr) and control vehicle DMSO, respectively.

first: Libin

last: Deng