title: 7q11.23 dosage-dependent dysregulation in the human pluripotent state primes aberrant transcriptional programs in disease-relevant lineages (aCGH)

status: Public on Dec 15 2014

city: Milano

first: Giuseppe

last: Testa

address: Via Adamello, 16

institute: European Institute of Oncology & University of Milano, Italy

summary: We apply the cellular reprogramming experimental paradigm to two disorders caused by symmetrical copy number variations (CNV) of 7q11.23 and displaying a striking combination of shared as well as symmetrically opposite phenotypes: Williams Beuren syndrome (WBS) and 7q microduplication syndrome (7dupASD). Through a uniquely large and informative cohort of transgene-free patient-derived induced pluripotent stem cells (iPSC), along with their differentiated derivatives, we find that 7q11.23 CNV disrupt transcriptional circuits in disease-relevant pathways already at the pluripotent state. These alterations are then selectively amplified upon differentiation into disease-relevant lineages, thereby establishing the value of large iPSC cohorts in the elucidation of disease-relevant developmental pathways. In addition, we functionally define the quota of transcriptional dysregulation specifically caused by dosage imbalances in GTF2I (also known as TFII-I), a transcription factor in 7q11.23 thought to play a critical role in the two conditions, which we found associated to key repressive chromatin modifiers. Finally, we created an open-access web-based platform (accessible at http://bio.ieo.eu/wbs/ ) to make accessible our multi-layered datasets and integrate contributions by the entire community working on the molecular dissection of the 7q11.23 syndromes.

overall_design: We reprogrammed skin fibroblasts from patients harbouring a 7q11.23 hemi-deletion (WBS, 4 patients; +1 atypical deletion, AtWBS) or microduplication (7dupASD; 2 patients), as well as from one unaffected relative and two unrelated controls, using integration-free mRNA-reprogramming, leading to the establishment of a total of 27 characterized iPSC clones. We profiled by aCGH each established iPSC clone as well as the original fibroblasts (for all patients and the unaffected relative).

first: Antonio

last: Adamo

first: Sina

last: Atashpaz

first: Pierre-Luc

last: Germain

first: Matteo

last: Zanella

last: D'Agostino

first: Veronica

last: Albertin

first: Josh

last: Chenoweth

first: Lucia

last: Micale

first: Carmela

last: Fusco

first: Christian

last: Unger

first: Bartolomeo

last: Augello

first: Orazio

last: Palumbo

first: Brad

last: Hamilton

first: Massimo

last: Carella

first: Emilio

last: Donti

first: Giancarlo

last: Pruneri

first: Angelo

last: Selicorni

first: Elisa

last: Biamino

first: Paolo

last: Prontera

first: Ronald

last: McKay

last: Merla


title: Pit-1 overexpression in the human breast adenocarcinoma MCF-7 cell line

status: Public on Dec 12 2014

city: Santiago de compostela

first: Samuel

last: Seoane

state: A Coruña

address: Avd de Barcelona sn

department: CIMUS-Endocrine

country: Spain

institute: University of Santiago de Compostela

summary:
The aim of the study is to evaluate Pit-1-induced genes in the MCF-7 cell line
The Pit-1 transcription factor (also known as POU1F1) plays a critical role in cell differentiation during organogenesis of the anterior pituitary in mammals and is a transcriptional activator for pituitary gene transcription. Increased expression of Pit-1 has been reported in human tumorigenic breast cells. Here, we found that Pit-1 overexpression or knockdown in human breast cancer cell lines induced profound phenotypic changes in the expression of proteins involved in cell proliferation, apoptosis, and invasion. In immunodeficient mice, Pit-1 overexpression induced tumoral growth and promoted metastasis in lung. In patients with invasive ductal carcinoma of the breast and node-positive tumors elevated expression of Pit-1 was significantly and independently associated with the occurrence of distant metastasis. These findings suggest that Pit-1 could help to make a more accurate prognosis in patients with node positive breast cancer and may represent a new therapeutic target (Journal of Clinical Investigation 2010, 120:4289-4302)

overall_design: MCF-7 cells were transfected with the pcDNA3 (control, two samples as condition, named C1 and C2) or the pcDNA3-Pit-1 overexpression vector (two samples as condition, named 1+ and 2+) for 48 hours.

first: Roman

last: Perez-Fernandez


title: Anti-BRAF mutation drug resistance enhances EGFR expression in melanomas [expression profiling]

status: Public on Dec 17 2014

city: Santa Monica

first: Dave

last: Hoon

state: CA

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

country: USA

institute: Saint John's Cancer Institute

summary: We treated melanoma cells with BRAF mutation with BRAF inhibitor and screened for BRAF inhibitor resistant cells. We extracted total mRNA from parental cells and resistant cell lines.  We compared their expression by carried out Affymetrix Huex 1.0 ST expression array.

overall_design: Two paired parental/derived cell lines were screened as per the summary above. BRAF inhibitory resistant cells had gene expression compared to the parental cell lines.

first: Jinhua

last: Wang


title: Transcriptome analysis in preimplantation kidney biopsies

status: Public on Dec 01 2014

city: Sao Paulo

first: Karina

middle: Lumi

last: Mine

address: Rua Loefgreen, 1235

department: Instituto de Imunogenetica

country: Brazil

institute: AFIP

summary: To identify early markers to predict post-transplantation outcomes we performed a transcriptome analysis in pre-implantation kidney biopsies from deceased donors searching for genes associated with DGF and graft function one year post-transplantation.

overall_design: We studied 54 pre-implantation kidney biopsies from deceased donors. Twenty seven recipients with and 27 without DGF. Within DGF group 13 had prolonged DGF (pDGF, DGF lasting > 14 days). Renal function at one year post-transplantation was evaluated using the estimated glomerular filtration rate (eGFR), calculated using abbreviated MDRD formula. The group with poor renal function at one year post-transplantation, low eGFR (<45 mL/min/1.73 m2), was composed by 18 patients and the high eGFR group (≥ 45 mL/min/1.73 m2) by 35 recipients.

middle: L

first: Tuíla

middle: B

last: Mourão

first: Erika

middle: F

last: Campos

first: Vinicius

last: Andrade

first: Jose

middle: O

last: Medina-Pestana

first: Helio

last: Tedesco-Silva

first: Maria

last: Gerbase-DeLima


title: Late stage ovarian cancer gene expression profiles

status: Public on Dec 04 2014

city: Philadelphia

first: Hongzhe

last: Li

state: Pennsylvania

address: 415  Curie Blvd

department: Biostatistics and Epidemiology

institute: University of Pennsylvania

summary:
Gene expression profiling on 63 stage III-IV papillary serous ovarian cancer samples resected during primary debulking at the University of Turin, Italy.  Only the primary ovarian mass and no metastases were included in this analysis.
The study focused on ovarian cancer chemokine expressions

first: George

last: Coukos


title: Gene expression profiling of 13 primary and established human ovarian cancer cell lines

status: Public on Nov 22 2014

summary: Gene expression analysis was also performed on 13 primary and established human ovarian cancer cell lines (A2008, OAW42, OVCAR2, OVCAR3, OVCAR4, OVCAR5, OVCAR8, OVCAR10, OV7M, OV95, PE01, PE04, SKOV3) using Affymetrix Human Gene 1.0 ST Arrays

overall_design: The study focused on ovarian cancer chemokine expressions


title: TOX3 is Expressed in Mammary ER Positive Epithelial Cells and Regulates a Subset of ER Target Genes in a Ligand-Independent Manner in Luminal Breast Cancer

city: Los Angeles

first: Wolf

last: Wiedemeyer

state: California

address: 8700 Beverly Blvd.

department: BMS

institute: Cedars-Sinai

summary: To assess how the TOX3 nuclear protein can modulate gene expression in luminal epithelial cells, MCF7 cells were transfected with a TOX3 expression vector or vector control. In both instances, GFP was coexpressed, allowing isolation of transfected cells by flow cytometry before transcriptome analysis. Experiments were carried out under estrogen depleted conditions, and cells isolated 48 hours after transfection.

overall_design: Treatment vs. Control

first: Akop

last: Seksenyan

first: Jonathan

last: Kaye

first: Asha

last: Kadavallore

first: Ann

middle: E

last: Walts

first: Brian

last: de la Torre

first: Dror

last: Berel

middle: P

last: Strom

first: Parinaz

last: Aliahmad

first: Vincent

last: Funari


title: Upregulation of Dicer expression by calcitriol induces microRNAs with potential tumor-suppressive effects in cancer cervical cells

status: Public on Nov 30 2014

city: Mexico

first: Sandra

middle: Lorena

last: Romero-Cordoba

state: Mexico

address: Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan. México, D.F.

department: Cancer Genomics

country: Mexico

institute: National Instute of Genomic Medicine

summary: Dicer is a key endoribonuclease of the microRNA biogenetic machinery. Downregulation of Dicer has been associated with aberrant expression of microRNAs and the promotion of tumorigenesis. Calcitriol, the hormonal form of vitamin D3, increases microRNA expression in tumor cells, but the mechanism is not yet understood. Given the essential role of Dicer in microRNAs biogenesis, the purpose of this study was to evaluate whether this gene is a target for calcitriol and to explore the effects of this hormone on microRNA expression. Our findings demonstrate that calcitriol increased Dicer mRNA and protein in SiHa and HeLa cervical cancer cells, which expressed the vitamin D receptor. The inductive effect of calcitriol on Dicer mRNA was not observed in C33-A cells lacking this nuclear receptor. To explore the potential effect of Dicer upregulation by calcitriol on microRNA processing, we performed a microRNA profiling study in SiHa cells treated with calcitriol. The analysis of microRNA expression revealed that this hormone promotes the maturation of a subset of microRNAs with potential regulatory function in cancer pathways. Among these, miR-22 and miR-296-3p have already been associated with tumor-supressive effects. Our results suggest that Dicer upregulation by calcitriol could be associated, at least in part, with an increase in the maturation of a subset of tumor-suppressor microRNAs in cervical cancer cells.

overall_design: SiHa cell lines were treated with calcitriol or ethanol as vehicle for 24 or 48 h in medium supplemented with charcoal-treated serum.

first: Ramiro

middle: J

last: González-Duarte

first: Verna

last: Cázares-Ordoñez

last: Romero-Córdoba

first: Víctor

last: Ortíz

first: Julio

middle: A

last: Freyre-González

first: Lorenza

last: Díaz

first: Alfredo

last: Hidalgo-Miranda

first: Fernando

last: Larrea

first: Euclides

last: Avila


title: Comparative study of transcriptome from human breast cancer cell lines MCF7 treated with trichodermin

city: Salamanca

first: Enrique

last: Monte

state: Salamanca

address: Rio Duero

department: Spanish-Portuguese Centre for Agricultural Research

institute: University of Salamanca

summary: Trichodermin is a member of a group of closely related compounds-the 12,13-epoxytrichothecenes that form a medically and economically important class of mycotoxins. This sesquiterpene was purified by HPLC from cultures of the fungi Trichoderma brevicompactum. We report the antitumoral activity of trichodermin and here we show that trichodermin had inhibitory effects against tumoral cell lines (A-549, MCF-7, Hep-G2, Hep-G3). In addition, trichodermin was found to increase the expression level of apoptotic genes such as jun, fos, egr, egr2, casp9, ankd1, socs3 anddkk1 that induce cell death mechanisms, being the nuclear receptor subfamily 4, group A, member 1(NR4A1) one of the central molecule in the network.

overall_design:
Human Gene 1.0 ST expression chips (Affymetrix, Inc., Santa Clara, CA, USA) containing 28,869 genes probes were used.
Trichodermin was found to increase the expression level of apoptotic genes such as jun, fos, egr, egr2, casp9, ankd1, socs3 and dkk1 that induce cell death mechanisms.
MCF-7 cells were grown for 8 h in the absence (C) or presence of 10 µM trichodermin (T). Trichodermin was purified by HPLC from fermentation broth of 14-days-old potato dextrose broth (PDB) (Difco Becton Dickinson, Sparks, MD) cultures of T. brevicompactum strain IBT 40841 as previously described (Tijerino et al., 2011). Three replicates for each condition were performed.

first: Anamariela

last: Tijerino

first: Rosa

last: Hermosa


title: Human skeletal muscle transcriptome responses to differentiated exercise

status: Public on Nov 19 2014

city: Copenhagen

first: Peter

last: Schjerling

address: Bispebjerg Bakke 23, M81

department: Institute of Sports Medicine Copenhagen, ISMC

country: Denmark

institute: Bispebjerg Hospital

summary: The few investigations on exercise-induced global gene expression responses in human skeletal muscle haves typically focused at one specific mode of exercise and few such studies have implemented control measures. However, interpretation on distinct phenotype regulation necessitate comparison between essentially different modes of exercise and the ability to identify true exercise effects, necessitate implementation of independent non-exercise control subjects. Furthermore, muscle transkriptometranscriptome data made available through previous exercise studies can be difficult to extract and interpret by individuals that are inexperienced with bioinformatic procedures. In a comparative study, we; (1) investigated the human skeletal muscle transcriptome response to differentiated exercise and non-exercise control intervention, and; (2) aimed to develop a straightforward search tool to allow for easy extraction and interpretation of our data. We provide a simple spreadsheet containing transcriptome data allowing other investigators to see how mRNA of their interest behave in skeletal muscle following exercise, both endurance, strength and non-exercise.   Our approach, allow investigators easy access to information on genuine transcriptome effects of differentiated exercise, to better aid hyporthesis-driven question in this particular field of research.

overall_design: 18 subjects were divided into 3 groups, performing 12 weeks of Endurance or Strength training or no training. Biopsies for microarray were take before (Pre) and 2½ and 5 hours after the last training session. Isolated RNA from these biopsies were then measured with the Affymetrix Human Gene 1.0 ST arrays.

first: Kristian

last: Vissing


title: Biological and molecular characterization of CMA03/06, a newly established interleukin-6 independent variant of the CMA03 human myeloma cell line.

status: Public on Nov 21 2014

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

summary: We performed a biological and molecular characterization of the novel human multiple myeloma cell line CMA03/06, an IL-6-independent variant of CMA03 cell line  previously established in our Institution. We showed that the CMA03/06 cells grows in the absence of IL-6 with a doubling time comparable to CMA03; the addition of IL-6 to the culture medium or co-culture with multipotent mesenchymal stromal cells does not induce an increase in proliferation rate. Interestingly, we provided evidence that IL-6 independence of CMA03/06 cells is not a consequence of the development of an autocrine IL-6 loop, even though the cells maintain the IL-6 signaling pathway responsiveness as demonstrated by STAT1 and STAT3 induction by IL-6. A slight constitutive activation of STAT3 has been observed in CMA03/06 cell line; however STAT3 silencing in CMA03/06 cells did not affect their viability and proliferation suggesting that this pathway is not the only responsible for the IL-6 independency of CMA03/06 cell line. The new cell line showed a lower susceptibility to camptothecin-induced apoptosis compared to CMA03 cells, whereas an increased induction of apoptosis was observed in CMA03/06 cell line after Bortezomib treatment which may suggest the involvement NF-kB pathway in the IL-6 independent growth and survival of CMA03/06 cells. Finally, global gene expression profiling analysis allowed the identification of a list of 308 modulated genes in CMA03/06 versus CMA03 cells, many of which particularly relevant for MM biology. Overall, the novel CMA03/06 cell line may represent a suitable model for studies investigating molecular mechanisms involved in clonal evolution towards IL-6 and/or stroma-independent growth and survival of myeloma cells.

overall_design: This series of microarray experiments contains the gene expression profiles of 3 independent replicas of CMA03 grown in  in normal culture conditions and in absence of IL-6, respectively, and 3 independent replicas of CMA03/06 in normal culture conditions. Cell pellets were resuspended in TRIzol Reagent (Life Technologies, Inc., Rockville, MD, USA), total RNA was then purified using the RNeasy® total RNA Isolation Kit (Qiagen, Valencia, CA).5.5 micrograms of single-stranded DNA target obtained from 100 ng of purified total RNA was fragmented and then labeled using the WT Terminal Labeling Kit according to the standard Affymetrix protocol (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual).The fragmented labeled single-stranded DNA target was hybridized for 16 hr 30 minutes at 45°C on GeneChip® Gene 1.0 ST array according to the standard Affymetrix protocol. The arrays were washed and stained in the Affymetrix Fluidics Station 450.

first: D

last: Verdelli

first: L

last: Nobili

first: K

last: Todoerti

last: Mosca

first: S

last: Fabris

first: E

last: Pellegrino

first: R

last: Piva

first: G

last: Inghirami

first: A

last: Cortelezzi

last: Baldini

last: Lombardi

last: Neri


title: Genome-wide identification of HIF-1 and HIF-2 binding sites in hypoxic human macrophages alternatively activated by IL-10

city: Frankfurt

first: Nathalie

last: Dehne

address: Theodor-Stern-Kai 7

department: Faculty of Medicine, Institute of Biochemestry I

country: Germany

institute: Goethe-University Frankfurt

summary: Primary human macrophages with a HIF-1alpha or HIF-2alpha knockdown were pretreated with IL-10 for 16h and afterwards for 4h additionaly under hypoxi (1% O2), RNA was isolated usind the Qiagen RNAeasy Kit and cDNA synthesis wos done using  Ambion WT Expression Kit. Expression was compared to si control under control conditions.

overall_design: Samples from 3 donors treated with si control, si HIF-1α or si HIF-2α were compared with each other

first: Claudia

last: Döring


title: Exosome Transfer from Stromal to Breast Cancer Cells Regulates Therapy Resistance Pathways [set 2]

status: Public on Oct 24 2014

first: Andy

last: Minn

state: PA

address: 421 Curie Blvd

summary: Stromal communication with cancer cells can influence treatment response. We show that stromal and breast cancer (BrCa) cells utilize paracrine and juxtacrine signaling to drive chemotherapy and radiation resistance. Upon heterotypic interaction, exosomes are transferred from stromal to BrCa cells. RNA within exosomes, which are largely non-coding transcripts and transposable elements, stimulates the pattern recognition receptor RIG-I to activate STAT1-dependent anti-viral signaling. In parallel, stromal cells also activate NOTCH3 on BrCa cells. The paracrine anti-viral and juxtacrine NOTCH3 pathways converge as STAT1 facilitates transcriptional responses to NOTCH3 and expands therapy resistant tumor-initiating cells. Primary human and/or mouse BrCa analysis support the role of anti-viral/NOTCH3 pathways in NOTCH signaling and stroma-mediated resistance, which is abrogated by combination therapy with gamma secretase inhibitors. Thus, stromal cells orchestrate an intricate cross-talk with BrCa cells by utilizing exosomes to instigate anti-viral signaling. This expands BrCa subpopulations adept at resisting therapy and re-initiating tumor growth.

overall_design: Breast cancer cells lines and MRC5 fibroblasts were mono-cultured or co-cultured together. Cell types were separated by FACS and gene expression changes were examined using the Affymetrix Human Gene 1.0ST arrays. The effect of tumor-stromal cell interaction on different breast cancer cell types was analyzed using biological replicates. Gene expression changes resulting from knockdown of STAT1 was also investigated.


title: Genexpression profiling of wild type, HIF-1α knockdown, or HIF-2α knockdown HepG2 tumor spheroids

summary: 10 days old tumor spheroids were processed for RNA isolation using the Quiagen RNeasy Micro Kit and cDNA synthesis was done using the Ambion WT Expression Kit. Wt, HIF-1α k/d and HIF-2α k/d samples were compared to each other.

overall_design: Samples from 4 different spheroid experiments of wt, HIF-1α knockdown and HIF-2α knockdown HepG2 cells, respectively, were compared with each other

first: Theresa

last: Geis


title: Progestin-containing Contraceptives Alter Expression of Host Defense-related Genes of the Endometrium and Cervix

city: San Francisco

first: Linda

last: Giudice

address: 513 Parnassus Ave. HSE 1619

department: OBGYN and RS

institute: University of California, San Francisco

summary: Epidemiological studies indicate that progestin-containing contraceptives may increase susceptibility to HIV and other infections; however, underlying mechanisms involving the upper female reproductive tract are undefined. To determine the effects of depot medroxyprogesterone acetate (DMPA) and the levonorgestrel intrauterine system (LNG-IUS) on gene expression and physiology of the human endometrial and cervical transformation zone (TZ), microarray analyses were performed on whole tissue biopsies. In endometrium, activated pathways included leukocyte chemotaxis, attachment, and inflammation in DMPA (z>2.5) and LNG-IUS (z>3.5) users, and regulation of pattern recognition receptors and other immune mediators. In cervical TZ, progestin treatment altered expression of tissue remodeling and viability genes, but not those of immune functions. Together, these results indicate that progestins influence expression of immune-related genes in endometrium that would be expected to result in the local recruitment of HIV target cells, and thus may increase HIV susceptibility. It is important to consider the upper reproductive tract in the assessment of effects of contraceptives that may influence susceptibility to pathogens, such as HIV.

overall_design: Cross-sectional study conducted at an academic medical center. Cervical transformation zone and endometrial biopsies were obtained from 3 groups of volunteers: those using no hormonal contraceptives (controls, mid-secretory phase, n=20 cervix, 11 endometrium), DMPA users (150mg, n=15, 8), or LNG-IUS users (n=17, 13). DMPA and LNG-IUS groups had used these contraceptives for at least 6 months.

first: Gabriel

last: Goldfien

first: Fatima

last: Barragan

first: Joseph

last: Chen

first: Margaret

last: Takeda

first: Juan

middle: C

last: Irwin

first: Jean

last: Perry

first: Ruth

middle: M

last: Greenblatt

first: Karen

middle: K

last: Smith-McCune


title: Molecular Mechanisms Regulating the Defects in Fragile X Syndrome Neurons Derived from Human Pluripotent Stem Cells

status: Public on Oct 28 2014

city: Jerusalem

first: Nissim

last: Benvenisty

state: Israel

address: Edmond Safra Campus Givat Ram

department: Genetics

country: Israel

institute: Hebrew University

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

summary: Fragile X syndrome (FXS) is caused by the absence of the fragile X mental retardation protein (FMRP). We have previously generated FXS-induced pluripotent stem cells (iPSCs) from patients' fibroblasts. In this study, we aimed at unraveling the molecular phenotype of the disease. Our data revealed aberrant regulation of neural differentiation and axon guidance genes in FXS-derived neurons, which are regulated by the RE-1 silencing transcription factor (REST). Moreover, we found REST to be elevated in FXS-derived neurons. As FMRP is involved in the microRNA (miRNA) pathway we employed microRNA-array analyses and uncovered several miRNAs dysregulated in FXS-derived neurons. We found hsa-mir-382 to be down-regulated in FXS-derived neurons, and introduction of mimic-mir-382 into these neurons was sufficient to repress REST and up-regulate its axon guidance target genes. Our data link, FMRP and REST, through the miRNA pathway, and show a new aspect in the development of FXS.

platform_organism:
Homo sapiens
synthetic construct

overall_design:
Affimetrix miRNA array of two WT and two fragile X syndrome derived neurons
Gene expression analysis was performed on a total of 14 human cell lines, including WT and FXS fibroblasts, iPSCs and Neurons

first: Tomer

last: Halevy

first: Christian

last: Czech


title: Exosome Transfer from Stromal to Breast Cancer Cells Regulates Therapy Resistance Pathways [set 1]


title: Somatic transcriptome priming gates lineage specific differentiation potential of human induced pluripotent stem cell states

status: Public on Nov 28 2014

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

country: Canada

institute: McMaster University

summary: Human induced pluripotent stem cells (hiPSCs) provide an invaluable source for regenerative medicine; but are limited by proficient lineage specific differentiation. Here we reveal that hiPSCs derived from dermal skin fibroblasts (Fib) vs. human cord blood (CB) cells exhibit equivalent and indistinguishable pluripotent properties, but harbor important propensities for neural and hematopoietic lineage differentiation, independent of reprogramming factors used. Genes associated with germ layer specification were identical in both Fib or CB derived iPSCs; whereas patterns of lineage specific marks emerge upon differentiation induction of hiPSCs that were correlated to the cell type of origin used to create hiPSCs. Functionally, CB-iPSCs predominantly differentiate into hematopoietic cells and even adopt definitive hematopoiesis as evidenced by adult β-globin positive red blood cell development whereas Fib-iPSCs possess enhanced neural capacity. These clear differentiation propensities come at the expense of other lineages and cannot be overcome with additional external stimuli for alternative cell fates. Moreover, these differences in developmental potential are encoded within cultures of CB vs. Fib derived hiPSCs that can be used to predict differentiation propensity.

overall_design: To examine molecular properties of human iPSCs derived from different somatic sources, we generated iPSCs from CD34+CD45+ umbilical cord blood cells (CB) and compared to iPSCs from human adult dermal fibroblasts (Fib). All hiPSC lines were derived by transduction with Oct4, Sox2, Nanog and Lin28 (OSNL) or Oct4, Sox2, c-Myc and Klf4 expressing lentiviral vectors (OSMK). Human dermal fibroblasts (ScienCell) or human cord blood cells were obtained from healthy donors (two independent fibroblasts donors and three cord blood samples). Informed consent was obtained from all sample donors in accordance with Research Ethics Board-approved protocols at McMaster University and the London Health Sciences Centre. CD34+ cord blood cells, used for hCB-iPSCs generation, were isolated by immunomagnetic separation. Transduced cells were maintained on irradiated feeder MEFs in DMEM/F12 (Gibco) supplemented with 20% Knockout Serum Replacement (Gibco), 100 mM b-mercaptoethanol, 100 mM nonessential amino acid (Gibco), 1 mM L-glutamine (Gibco), and 10 ng/ml bFGF. After iPSC generation cells were maintained in MEF conditioned medium + 8ng/ml.

first: Jong-Hee

last: Lee

first: Jung

first: Zoya

last: Shapovalova

first: Aline

last: Fiebig-Comyn

first: Ryan

middle: R

last: Mitchell

first: Sarah

last: Laronde

first: Eva

last: Szabo

first: Yannick

middle: D

last: Benoit


title: Temporal Dynamics of Human Cerebrospinal Fluid Vesicle microRNAs

status: Public on Nov 24 2014

city: Clemson

first: David

middle: Matthew

last: Feliciano

state: South Carolina

address: 132 Long Hall

department: Biological Sciences

institute: Clemson University

summary:
To determine whether the microRNA content of CSF vesicles changes throughout life we performed experiments including miRNA microarrays.
Hierarchical clustering analysis indicated that the miRNA content of CSF vesicles changes when patients less than 2 years are compared to those older than 70 years of age.

overall_design: CSF vesicles were fractionated and isolated from patients of different ages, total RNA extracted, and subjected to miRNA microarray analysis


title: Expression data from OVCAR-3 cells overexpressing histone H1.3

status: Public on Oct 31 2014

city: Atlanta

first: Yuhong

last: Fan

state: Georgia

address: IBB 2313, 315 Ferst Drive

department: School of Biology and the Petit Institute for Bioengineering and Bioscience

institute: Georgia Institute of Technology

summary: Ovarian cancer is a deadly gynecological malignancy for which novel biomarkers and therapeutic targets are imperative for improving survival. To investigate the role of histone H1 in ovarian cancer cells, we overexpress a histone H1 variant, H1.3, in the OVCAR-3 epithelial ovarian cancer cell line.  RNA was extracted from OV-3/H1.3(H) cells (OVCAR-3 with overexpression of H1.3) and control cells of OVCAR-3 transfected with vectors without H1.3.  The microarray chip used was human Affymetrix ST1.0 array.  Gene expression changes caused by overexpression of H1.3 in OVCAR-3 cells were identified.

overall_design: Affymetrix Human Exon 1.0 ST array was used to identify the changes in transcriptome of OVCAR-3 caused by overexpression of H1.3

first: Magdalena

last: Medrzycki

first: Yunzhe

last: Zhang

first: Weijia

first: Chenyi

last: Pan


title: MicroRNA Profiling Analysis and Target Gene Prediction in Laryngeal Squamous Cell Carcinoma

status: Public on Oct 30 2014

city: Beijing

first: Jugao

last: Fang

address: No. 1 Dongjiao Min Xiang, Dongcheng District

country: China

institute: Capital University of Medical Sciences attaches to Beijing Tongr

summary:
Background: Laryngeal squamous cell carcinoma (LSCC) is the most common type in head and neck squamous cell carcinoma (HNSCC), and the development of LSCC are multistep processes accompanied by changes of molecular biology.
Objective: The purpose of this study was to investigate the miRNAs basis of tumorigenesis in LSCC, and analyze the microRNAs dysregulation related with the six targeted genes (CDK1,CDK2, CDK4, MCM2, MCM3, MCM4) which were related to tumorigenesis from the screened miRNAs.
Methods: A total number of 5 patients who underwent surgery for primary laryngeal squamous cell carcinoma were recruited for miRNA array analysis. LSCC tissues compared with corresponding adjacent non-neoplastic tissues were analysed by the Affymetrix GeneChip miRNA Array 3.0 to screen effective miRNAs, then mirfocus  3.0 database (http://mirfocus.org/index.php)  was adopted to  select putative regulated miRNAs of the six targeted genes. Moreover, the selected putative regulated miRNAs were also validated by qRT-PCR in another 36 patients diagnosed for LSCC.
Results: Analysed by the miRNAs arrays, there were 127 miRNAs significantly related to tumorigenesis ,and 78  showed  a  higher expression  in  tumor  than  in  non-tumor  tissue while  49 presented  the  contrasting pattern(P<0.01).Then analyzed by mirfocus  3.0 database, there were 2 putative regulated miRNAs, hsa-miR-24-3p and hsa-miR-183-5p, corresponding to three of the six targeted genes. Among the 2 putative miRNAs, hsa-miR-24-3p regulated MCM4,CDK1 and CDK4,while hsa-miR-183-5p regulated MCM4 only. Another miRNA we should focus on is hsa-miR-30a-5p, a tumor-suppressive factor, which was down-expressed obviously analysed by the miRNAs arrays. The expression of the 3 putative regulated miRNAs were also validated by qRT-PCR in another 36 patients (P<0.05).
Conclusions: The research revealed 127 miRNAs expression signature of tumorigenesis in laryngeal squamous cell carcinoma,and analyzed 3 putative regulated miRNAs, hsa-miR-24-3p, hsa-miR-183-5p and hsa-miR-30a-5p, as potential diagnostic and therapeutic markers in LSCC. The result will contribute to the understanding of the molecular basis of LSCC and help to improve the treatment.

overall_design: A total number of 5 patients who underwent surgery for primary laryngeal squamous cell carcinoma were recruited for miRNA array analysis. LSCC tissues compared with corresponding adjacent non-neoplastic tissues were analysed by the Affymetrix GeneChip miRNA Array 3.0 to screen effective miRNAs, then TargetScan,PITA and microRNAorg were used for target gene prediction in GeneSpring 12.5 software.Moreover, pathway-based methods were adopted to analyse physiological processes of the target genes. The screened miRNAs and the significant target genes were also validated by qRT-PCR in another 36 patients diagnosed for LSCC.

first: Meng

last: Lian

first: Xiaoqin

last: Liu


title: Identification of candidate rhinovirus C (RV-C) receptors by gene expression analysis

status: Public on Nov 01 2014

city: Madison

first: Yury

last: Bochkov

state: WI

address: 600 Highland Ave, K4/945 CSC

department: Pediatrics

institute: University Of Wisconsin-Madison

summary: Members of rhinovirus C (RV-C) species are more likely to cause wheezing illnesses and asthma exacerbations compared to other rhinoviruses. The cellular receptor for these viruses was heretofore unknown. We measured gene expression (Human Gene 1.0 ST Array, Affymetrix) in two series of experiments involving cells that were either susceptible or not susceptible to RV-C infection. In one experimental series, susceptible cells included whole sinus mucosal tissue specimens (n = 5), epithelial cell suspension from sinus tissue, and nasal epithelium obtained via brushing, while non-susceptible cells included monolayers of primary undifferentiated epithelial cells and transformed cell lines (n = 5). In a second experimental series, we compared three pairs of undifferentiated and fully differentiated (ALI) sinus epithelial cell cultures. We identified a total of 12 genes upregulated in RV-C susceptible cells (represented by 14 probe sets) encoding proteins localized to plasma membrane, and/or with predicted or functionally demonstrated receptor activity, including members of the Human MHC class II, stomatin, guanine nucleotide-binding, type I cytokine and atypical chemokine receptor and cadherin protein families.

overall_design: Sinus and bronchial epithelial tissue samples were obtained from residual surgical specimens. Primary airway epithelial cells were cultured submerged (undifferentiated monolayers) or at air-liquid interface (fully-differentiated). Established cell lines (HeLa, NCI-H358 and WisL) were cultured submerged. Epithelial tissue samples were placed in RNAlater solution (Life Technologies) to stabilize and protect cellular RNA; cultured cells were lysed directly and total RNAs were isolated using TRIzol reagent (Life Technologies). Gene expression was analyzed using the Human Genome 1.0 ST GeneChip arrays (Affymetrix, Santa Clara, CA).

first: Shamaila

last: Ashraf

first: James

last: Gern


title: Expression study of human embryonic stem cells, dental pulp cells (DPCs) and induced pluripotent stem cells (iPSC) obtained from DPC for characterization of iPSC

status: Public on Oct 23 2014

city: La Jolla

first: Alysson

middle: Renato

last: Muotri

address: Scenic Road - Sanford Consortium, Room 3005

department: Dept. Cellular & Molecular Medicine

institute: University of California San Diego

summary: iPSC were obtained from DPC from TRPC6-mut patient, a idiopathic autistic patient and a control. Original DPC and iPSC obtained were submited to expression analysis in order to check if the expression pattern obtained for the iPSC cells were closer related to embyonic cells than to the original DPC

overall_design: DPCs were grown until reach 80-90% of confluency in DMEM/F12 media supplemented with 15% fetal bovine serum (Hyclone, TX), 1% penicillin/streptomycin, and 1% non-essential amino acids and maintained under standard conditions (37°C, 5% CO2). RNA samples were extracted from cells in passage 5 to 7. iPSC were grown until reaches 70% of confluency in mTSER medium (Stem Cells Technologies). RNA samples were extracted from cells in passage 12 to 15.

first: Karina

last: Griesi-Oliveira

first: Allan

last: Acab

first: Abha

last: Gupta

first: Daniele

middle: Y

last: Sunaga

first: Thanathom

last: Chailangkarn

first: Xavier

last: Nicol

first: Yanelli

last: Nunez

first: Michael

last: Walker

first: John

last: Murdoch

first: Stephan

last: Sanders

first: Thomas

middle: V

last: Fernandez

first: Weizhen

last: Ji

first: Richard

last: Lifton

first: Estevão

last: Vadasz

first: Alexander

last: Dietrich

first: Dennis

last: Pradhan

first: Hongjun

last: Song

first: Guo-li

last: Ming

first: Xiang

last: Guoe

first: Gabriel

last: Haddad

first: Maria

last: Marchetto

first: Nicholas

last: Spitzer

last: Passos-Bueno

first: Matthew

middle: W

last: State


title: Expression study between dental pulp cells from TRPC6-mut individual and control individuals

first: Alysson

last: Muotri

summary: As TRPC6 channel induces CREB-mediated trancription, Dental pulp cells from TRPC6-mut patient and from 6 controls were analyzed in order to verify if the disruption of TRPC6 leads to transcriptional changes.

overall_design: Cells were grown until reach 80-90% of confluency in DMEM/F12 media supplemented with 15% fetal bovine serum (Hyclone, TX), 1% penicillin/streptomycin, and 1% non-essential amino acids and maintained under standard conditions (37°C, 5% CO2). RNAs samples were extracted from cells in passage 5 to 7.

first: Karina

last: Griesi-Oliveira

first: Allan

last: Acab

first: Abha

last: Gupta

first: Daniele

last: Sunaga

first: Thanathom

last: Chailangkarn

first: Xavier

last: Nicol

first: Yanelli

last: Nunez

middle: F

last: Walker


title: Modeling non-syndromic autism and the impact of TRPC6 disruption in human neurons

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

overall_design: Refer to individual Series


title: Altered gene expression pattern in peripheral blood mononuclear cells in patients with acute myocardial infarction

city: Warsaw

first: Beata

last: Burzynska

address: Pawinskiego 5A

country: Poland

institute: Institute of Biochemistry and Biophysics

summary:
Despite a substantial progress in diagnosis and therapy, acute myocardial infarction (MI) is a major cause of mortality in the general population. A novel insight into the pathophysiology of myocardial infarction obtained by studying gene expression should help to discover novel biomarkers of MI and to suggest novel strategies of therapy. The aim of our study was to establish gene expression patterns in leukocytes from acute myocardial infarction patients.
ST-segment elevation myocardial infarction alters expression of several groups of genes. On admission, several genes and pathways that could be directly or indirectly linked with lipid/glucose metabolism, platelet function and atherosclerotic plaque stability were affected (signaling of PPAR, IL-10, IL-6). Analysis at discharge highlighted specific immune response (upregulation of immunoglobulins). Highly significant and substantial upregulation of SOCS3 and FAM20 genes expression in the first 4-6 days of myocardial infarction in all patients is the most robust observation of our work

overall_design: Twenty-eight patients with ST-segment elevation myocardial infarction (STEMI) were included. The blood was collected on the 1st day of myocardial infarction, after 4-6 days, and after 6 months. Control group comprised 14 patients with stable coronary artery disease (CAD), without history of myocardial infarction. Gene expression analysis was performed with Affymetrix GeneChip® Human Gene 1.0 ST microarrays and GCS3000 TG system.

first: Marek

last: Kiliszek

first: Marcin

last: Michalak

first: Monika

last: Gora

first: Aleksandra

last: Winkler

first: Agata

last: Maciejak

last: Leszczynska

first: Ewa

last: Gajda

first: Janusz

last: Kochanowski

first: Grzegorz

last: Opolski


title: Expression data of osteoarthritic and healthy human labrum cells

status: Public on Nov 17 2014

city: Ghent

first: Dirk

last: Elewaut

state: België

address: de pintelaan 185

department: Rheumatology

country: Belgium

institute: Ghent University

summary:
Osteoarthritic cartilage has largely been investigated, however supporting structures as the acetabular labrum are less investigated. In this studies we aimed to identify differences in gene expression between healthy and osteoarthritic labrum cells
we used the microarray as a discovery tool to identify possible new targets in hip osteoarthritis pathology

overall_design: We isolated labrum cells by enzymatic digestion of the acetabular labrum and cultures the cells in for 7 days in a 3D alginate culture systems which gives rise to a stable phenotype.

first: Aad

last: Dhollander

first: Stijn

last: Lambrecht


title: Effects of RUNX1 knockdown in AR signaling

status: Public on Oct 18 2014

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

country: Japan

institute: Tokyo Metropolitan Institute of Gerontology

summary:
Prostate cancer is the most common cancer in men and AR downstream signalings promote prostate cancer cell proliferation. We identified RUNX1 is an androgen-regulated gene.
In order to investigate the RUNX1 function in prostate cancer cells, we performed gene expression in AR-positive prostate cancer cell lines after siRUNX1 treatment. We also treated cells with vehicle or androgen to analyzed the effects of RUNX1 on AR function.

overall_design: Observation of androgen dependent gene expression changes after treatmet with siRNAs targeting RUNX1 with microarray.

first: K

first: S

last: Inoue


title: PRC2 loss amplifies Ras-driven transcription and confers sensitivity to BRD4-based therapies [expression array]

status: Public on Oct 21 2014

city: Boston

first: Thomas

last: De Raedt

state: MA

address: 77 Avenue Louis Pasteur

department: Medicine

institute: Harvard Medical School -  Brigham Women's Hospital

summary: The polycomb repressive complex 2 (PRC2) exerts oncogenic effects in many tumour types1. However, loss-of-function mutations in PRC2 components occur in a subset of haematopoietic malignancies, sug- gesting that this complex plays a dichotomous and poorly understood role in cancer2,3. Here we provide genomic, cellular, and mouse mod- elling data demonstrating that the polycomb group gene SUZ12 func- tions as tumour suppressor in PNS tumours, high-grade gliomas and melanomas by cooperating with mutations in NF1. NF1 encodes a Ras GTPase-activating protein (RasGAP) and its loss drives cancer by activating Ras4. We show that SUZ12 loss potentiates the effects of NF1 mutations by amplifying Ras-driven transcription through effects on chromatin. Importantly, however, SUZ12 inactivation also triggers an epigenetic switch that sensitizes these cancers to bromodomain inhib- itors. Collectively, these studies not only reveal an unexpected con- nection between the PRC2 complex, NF1 and Ras, but also identify a promising epigenetic-based therapeutic strategy that may be exploited for a variety of cancers.

overall_design: 9 samples in triplicates, 3x LacZ control, 3x SUZ12 over expression, 3x JQ1 treatment

first: Karen

last: Cichowski


title: The role of  AR-associated factors in androgen signaling

summary:
Prostate cancer is the most common cancer in men and AR downstream signalings promote prostate cancer cell proliferation. We identified androgen-regulated genes, CTBP2, FOXP1 and RUNX1. These factors interact with AR ligand dependently.
In order to investigate androgen-regulated gene functions in prostate cancer cells, we performed gene expression in AR-positive prostate cancer cell lines after siRNA treatment. We also treated cells with vehicle or androgen to analyzed the effects of these genes on AR function.

overall_design: Observation of androgen dependent gene expression changes after treatment with siRNAs targeting FOXP1, CTBP2 and FOXA1 with microarray.

first: Satoshi


title: Expression data from HUVEC with YAP siRNA knockdown

status: Public on Oct 17 2014

city: Philadelphia

first: Zhewei

last: Shen

address: BRB II/III Rm 527, 421 Curie Blvd.,

institute: University of Pennsylvania

summary: YAP knockdown in HUVEC elicits proliferation and cell cycle preogression defects. YAP deficient cells caused arrest in G1 and defects in S-phase entry. The microarray analysis was conducted to identify potential YAP targets that are involved in HUVEC cell cycle regulation

overall_design: mRNA samples were collected from siRNA treated HUVECs 30 hour after transfection. Four biological replicates were used for each condition: control (RISC-free) and knockdown (siYAP#1 and siYAP#2)

first: Z

first: B

middle: Z

last: Stanger


title: miR-671-5p promotes epithelial-to-mesenchymal transition by downregulating FOXM1 expression in breast cancer

status: Public on Oct 16 2014

city: Washington

first: Sidney

last: Fu

state: DC

address: 2300 Eye St. NW, Ross 402C

institute: George Washington University

summary:
microRNA (miRNA) dysfunction is associated with a variety of human diseases including cancer. Our previous study showed that miR-671-5p was deregulated during breast cancer progression. We aim to decipher the functional mechanism of miR- 671-5p in breast cancer.
We used microarrays to detail the global programme of gene expression after overexpression miR-671-5p in several breast cancer cell lines, and those altered genes might potentially under regulation of miR-671-5p contibuting to breast cancer developemtn.

overall_design: miR-671-5p or scramble control nucleotide were tranfected into breast cancer cell lines, including MCF7, MDA231 and SKBR3.  Total RNA were extracted and hybridized on Affymetrix microarrays. We sought to identify the potential downstream target genes that under miR-671-5p regulation by overexpress miR-671-5p. Potential targets were predicted to see if it has binding sites matching miR-671-5p sequence by miRNA target prediction softwares.

first: Xiaohui

last: Tan

first: Yebo

first: Liang

last: Chen


title: MiR-21 function in T-lymphocytes

status: Public on Oct 15 2014

city: Rome

first: Teresa

last: Colombo

address: p.le A. Moro 7

department: Institute of Molecular Biology and Pathology (IBPM)

institute: Consiglio Nazionale delle Ricerche (CNR)

summary: T-lymphocyte activation is efficiently mimicked in vitro by treatment with anti CD3 / anti CD28 antibodies. We report miR-21 induction upon CD3/CD28 stimulation of primary T-lymphocytes. In order to assess the function of miR-21 in T-lymphocytes we interfered with miR-21 function by lentiviral transduction of a miR-21 sponge construct. MRNA profile of miR-21 sponge and control transduced T-lymphocytes 48hrs after stimulation.

overall_design: mRNA microarray profile of T-lymphocytes tranduced with either a miR-21 sponge or control construct. 3 biological replicas have been performed.

first: Claudia

last: Carissimi

first: Nicoletta

last: Carucci

first: Silvia

last: Piconese

first: Gianluca

last: Azzalin

first: Emanuela

last: Cipolletta

first: Franca

last: Citarella

first: Vincenzo

last: Barnaba

first: Giuseppe

last: Macino

first: Valerio

last: Fulci


title: Differential Gene Expression in Angelman syndrome deletion vs. int dup(15) Human Lymphocytes

status: Public on Oct 09 2014

city: Memphis

first: Lawrence

middle: T.

last: Reiter

state: TN

address: 855 Monroe Ave., Link 415

department: Neurology

institute: UTHSC

summary: Angelman syndrome (AS) and interstitial duplication 15q autism (int dup(15)) are  reciprocal genomic disorders caused by maternal deletion or duplication of the 15q11.2-q13 region.  While AS is caused by maternal loss of 15q and maternal duplications of 15q can cause autism implicating the maternally expressed UBE3A gene in these phenotypes.  We investigated chromatin and gene expression changes in blood and cell lines from three int dup(15) and three reciprocal AS deletion subjects to identify global genomic and gene expression changes that may influence both the AS and autism phenotypes.  Using formaldehyde-assisted isolation of regulatory elements (FAIRE) we identified 1104 regions of differential open chromatin in AS deletion and 2344 regions int dup(15) indicating changes in chromatin could influence gene expression in these regions.  Microarray analysis revealed 1225 genes that were elevated in AS deletion vs int dup(15) and 976 genes that were elevated in int dup(15) vs AS deletion PBMC (pvalue<0.05).  Significant differences in expression were found for genes at the 15q locus like UBE3A, ATP10A and HERC2. A larger set of genes involved in chromatin remodeling, DNA repair and neurogenesis were found, at FAIRE peaks in AS deletion samples but had increased transcription in int dup(15) samples. There was a significant enhancement for genes with FOXP1 binding sites in the int dup(15) gene set and elevated FOXP1 protein could be detected in the nucleus of int dup(15) as compared to AS deletion cell lines. This analysis provides the first insights into transcriptional changes which may unveil new sets of genes and pathways contributing to both AS and autism pathogenesis.

overall_design: Gene expression was performed using 100ng of total RNA from each subject as starting material for amplification and cRNA synthesis in accordance Affymetrix protocols (http://tinyurl.com/3j7dcp6).  Hybridizations were performed to the Affy HumanGene_st_v1 chip and the signal data normalized using internal chip controls.  Normalized expression data was then exported to a text file for subsequent expression analysis using the EXPANDER software analysis suite.

middle: T


title: Early pre-symptomatic and progressive signatures of non-coding RNAs in ALS patients and mutation carriers

city: Ulm

first: Karlheinz

last: Holzmann

address: Helmholtzstreet 8/1

department: Medical Faculty

institute: Ulm University

summary: Knowledge about the nature and timepoint of pathomolecular alterations preceding onset of symptoms in amyotrophic lateral sclerosis (ALS) is largely lacking. It could not only pave the way for valuable therapeutic targets but might also govern future concepts of pre-manifest disease modifying treatments. MicroRNAs (miRNAs) are central regulators of transcriptome plasticity and participate in pathogenic cascades and/or mirror cellular adaptation to insults. We obtained expression profiles of miRNAs as well as other non-coding RNAs (ncRNAs) in the serum of sporadic ALS patients (sALS), familial ALS cases (fALS), asymptomatic mutation carriers and healthy controls. We observed a strikingly homogenous ncRNA profile in fALS patients that, to a large extend, was independent to the underlying disease gene and different to heterogeneous ncRNA signatures in sALS patients. Moreover, we identified 68 significantly dysregulated ncRNAs in pre-manifest ALS mutation carriers, more than 20 years before the estimated time window of disease onset. 91% of ncRNA alterations in mutation carriers overlapped with the fALS patients revealing progressive changes towards and during the disease. Our data thus demonstrate a high epigenetic heterogeneity amongst sALS patients and suggest common denominators regarding molecular pathogenesis of different ALS genes. We describe the earliest pathomolecular alterations in ALS known to date, which provide a basis for the development of predictors of disease onset as well as the discovery of novel therapeutic targets and strongly argue for studies evaluating pre-symptomatic disease-modifying treatment in ALS.

overall_design: Serum ncRNA pofiles of sporadic and familiar ALS patients as well as asymptomatic ALS mutation carriers were compared to age and gender matched healthy controls using a total of 53 Affymetrix miRNA 3.0 arrays. In detail, a total of 9 fALS patients (analyzed in 6 arrays) were compared to 10 controls, a total of 18 ALS mutation carriers (analyzed in 12 arrays) were compared to 8 controls and 18 sALS patients were compared to 16 controls.

first: Axel

last: Freischmidt

first: Kathrin

last: Müller

first: Lisa

last: Zondler

first: Patrick

last: Weydt

first: Alexander

middle: E

last: Volk

first: Michael

last: Walther

last: Bonin

first: Benjamin

last: Mayer

first: Markus

last: Otto

first: Christine

last: von Arnim

first: Peter

last: Andersen

first: Albert

last: Ludolph

first: Karin

last: Danzer

first: Jochen

middle: H

last: Weishaupt


title: Gene expression profiling regulated by PDGF in pBSMCs

status: Public on Oct 06 2014

city: LA

first: Sungyong

last: You

address: Beverly Blvd 8400

department: Surgery

institute: Cedars-Sinai Medical Center

summary: To explore global molecular changes in smooth muscle in response to PDGFR activation, primary human bladder smooth muscle cells were treated with 1 nM PDGF-BB (hereafter PDGF) for 0, 4 or 24 h. Total RNA were prepared, and analyzed using expression profiling, and subjected to bioinformatic and functional interrogation.

overall_design: To identify molecular signatures of bladder smooth muscle peturbed by PDGF, primary human bladder smooth muscle cells were treated with 1 nM PDGF-BB (hereafter PDGF) for 0, 4 or 24 h.

first: Rosalyn

last: Adam


title: Corneal Gene Expression Analysis

status: Public on Oct 02 2014

city: Dublin

first: colin

last: clarke

address: Dublin City University

country: Ireland

institute: Dublin City University

summary: Transplantation of amniotic membrane-expanded limbal epithelium (AMLE) in place of donor tissue grafts results in significantly improved outcomes for patients suffering from severe limbal stem cell deficiency; however the reasons for such superior results are unclear. The purpose of this study was to identify transcriptional gene profiles specific to AMLE and donor central corneal epithelium (CE), which may contribute to the divergent clinical outcomes observed following transplant. Limbal fibroblasts which underlie the epithelium and secrete extracellular matrix proteins following injury/surgery were also profiled. Using cell culture, immunofluorescence, microarray gene expression profiling and qRT-PCR validation; this study aims to identify enriched biological processes and pathways which characterise AMLE and CE tissues.  We hope the study outcomes will shed light onto the factors which contribute to provide the improved clinical outcomes associated with AMLE transplantation.

overall_design: Gene expression profiling of three central corneal buttons, three amniotic membrane-expanded limbal epithelial cultures and three limbal fibroblast cultures

first: Clair

last: Gallagher

first: Colin

last: Clarke

first: Sinéad

last: Aherne

first: Kishore

last: Katikireddy

first: Padraig

last: Doolan

first: Vincent

last: Lynch

first: William

last: Murphy

first: Andra

last: Bobart Hone

first: Conor

first: Martin

last: Clynes

last: Power

first: Finbarr

last: O'Sullivan


title: Human CA2 ES cells undergoing stepwise differentiation to airway epithelium and challenged with TNFa and LPS

status: Public on Oct 01 2014

city: Hamilton

first: Mickie

last: Bhatia

address: 1200 Main Street West

institute: McMaster University

summary: This study examines the innate immune response of human pluripotent stem cell derived airway epithelium. Immune challenge was performed with TNF-alpha or bacterial lipopolysaccharide (LPS)

overall_design: Airway epithelium differentiated from the ES line CA2 was compared to paired differentiated cells stimulated with either TNF-alpha or LPS

first: Brendan

last: McIntyre

first: Zoya

last: Shapovalova

first: Rahul

last: Kushwah

first: Rami

last: Mechael

first: Cantas

last: Alev


title: Comparison of transcriptomes of pre-ameloblasts (PAB) and secretory ameloblasts (SAB) in tooth development

city: Köln

first: Yulong

last: Niu

state: Nordrhein-Westfalen

address: Carl-von-Linne-Weg 10

department: Plant Microbe Interactions

institute: Max Planck Institute for Plant Breeding Research

summary:
Ameloblast differentiation is the most critical stepwise process in amelogenesis, and it is controlled by precise molecular events. To better understand the mechanism controlling pre-ameloblasts (PABs) differentiation into secretory ameloblasts (SABs), a more precise identification of molecules and signaling networks will elucidate the mechanisms governing enamel formation and lay a foundation for enamel regeneration.
We analyzed transcriptional profiles of human PABs and SABs. From a total of 28,869 analyzed transcripts, we identified 923 differentially expressed genes (DEGs) with p < 0.05 and Fold-change > 2. Among the DEGs, 647 genes showed elevated expression in PABs compared to SABs. Notably, 38 DEGs displayed more than eight-fold changes. Comparative analysis revealed that highly expressed genes in PABs were involved in cell cycle control, DNA damage repair and apoptosis, while highly expressed genes in SABs were related to cell adhesion and extracellular matrix. Moreover, coexpression network analysis uncovered two highly conserved sub-networks contributing to the differentiation, containing transcription regulators (RUNX2, ETV1 and ETV5), solute carrier family members (SLC15A1 and SLC7A11), enamel matrix protein (MMP20), and a polymodal excitatory ion channel (TRPA1).
By combining comparative analysis and coexpression networks, this study provides novel biomarkers and research targets for ameloblast differentiation and the potential for their application in enamel regeneration.

overall_design: Human tooth buds (18-22 weeks) were obtained from fetal cadaver tissue within 3 hours after legal abortion. Teeth were dissected from the mandibles under a laminar flow hood, embedded in OCT compound, and cryosectioned at 10-μm thickness. These sections were used for laser capture microdissection (LCM). In total of 3 pre-ameloblasts and 3 secretory ameloblasts pooled samples were used for RNA extraction and hybridization on Affymetrix microarray.

first: Cheng

last: Liu


title: Stability analysis of B25MOL cells

status: Public on Sep 29 2014

city: Berlin

first: Kerstin

last: Heinrich

address: Fabeckstraße 30

institute: Mologen AG

summary: Stability of B25MOL cells was proven by comparative transcriptome analysis. Expression profile (mRNA) was determined for cells of different age (4 time points) indicated by passage number.

overall_design: Cells from primary tumor of human kidney were propagated for 20, 28, 29, 36, and 40 rounds of seeding/growth/harvest and subjected to mRNA isolation.

first: Heinrich

last: Kerstin


title: The prognostic ease and difficulty of invasive breast carcinoma

status: Public on Oct 08 2014

city: Lausanne

first: Eric

last: Paquet

state: Vaud

address: Station 15  CH - 1015

department: Life sciences

country: Switzerland

institute: EPFL

summary: Breast carcinoma (BC) have been extensively profiled by high-throughput technologies for over a decade, and broadly speaking, these studies can be grouped into those that seek to identify patient subtypes (studies of heterogeneity) or those that seek to identify gene signatures with prognostic or predictive capacity. The shear number of reported signatures has led to speculation that everything is prognostic in BC. Here we show that this ubiquity is an apparition caused by a poor understanding of the inter- relatedness between subtype and the molecular determinants of prognosis. Our approach constructively shows how to avoid confounding due to a patient's subtype, clinicopathological or treatment profile. The approach identifies patients who are predicted to have good outcome at time of diagnosis by all available clinical and molecular markers, but who experience a distant metastasis within five years. These inherently difficult patients (~7% of BC) are prioritized for investigations of intra-tumoral heterogeneity.

overall_design: 321 samples from breast cancer patients.

first: Matthew

last: Suderman

first: Ali

last: Tofigh

first: Julie

last: Livingstone

first: Nicholas

last: Bertos

first: Hong

last: Zhao

first: Margarita

last: Souleimanova

first: Sean

last: Cory

first: Robert

last: Lesurf

first: Solmaz

last: Shahalizadeh

first: Sadiq

last: Saleh

first: Norberto

last: Garcia Lopez

first: Yasser

last: Riazalhosseini

first: Attila

last: Omeroglu

first: Josie

last: Ursini-Siegel

first: Morag

last: Park

first: Vanessa

last: Dumeaux

first: Michael

last: Hallett


title: Tissue- and Aging-specific DNA-Methylation Patterns are erased in Mesenchymal Stromal Cells derived from Induced Pluripotent Stem Cells. [Expression profiling]

status: Public on Sep 24 2014

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

summary: Standardization of mesenchymal stromal cells (MSCs) remains a major obstacle in regenerative medicine. Starting material and culture expansion affect cell preparations and render comparison between studies difficult. In contrast, induced pluripotent stem cells (iPSCs) assimilate towards a ground-state and may therefore give rise to more standardized cell preparations. We reprogrammed bone marrow MSCs into iPSCs which were subsequently re-differentiated towards MSCs. These iPS-MSCs revealed similar morphology, immunophenotype, in vitro differentiation potential, and gene expression profiles as primary MSCs. DNA methylation (DNAm) profiles of iPSCs maintained some donor-specific characteristics, whereas tissue-specific, senescence-associated, and age-related DNAm patterns were erased during reprogramming. iPS-MSCs reacquired senescence-associated DNAm during culture expansion but they remained rejuvenated with regard to age-related DNAm. Overall, iPS-MSCs and MSCs are similar in function but differ in their epigenetic makeup.

overall_design: 8 samples were hybridized to the GeneChip Human Gene 1.0 ST Array (Affymetrix)

first: Joana

last: Frobel

first: Hatim

last: Hemeda

last: Lenz

first: Bernd

last: Denecke

first: Tomo

last: Šarić

first: Martin

last: Zenke


title: Global brown adipose transcript data from fasted male BXD strains on chow diet

status: Public on Sep 26 2014

first: Johan

last: Auwerx

address: Station 15

department: SV IBI NCEM

institute: École Polytechnique Fédérale de Lausanne

summary:
Transcript data from brown adipose tissue from fasted-state male BXD strains on chow or high fat diet
We used microarrays to compare the brown adipose expression differences across males from the BXD strain family and across two diverse diets

overall_design: 29-week-old male mice were fasted overnight (6pm-9am), anesthetized under isoflurane, and perfused, then brown adipose tissue was snap-frozen in liquid nitrogen for RNA extraction and RNEasy cleanup. Each dietary and strain cohort consisted of ~5 animals which were prepared independently then pooled evenly by µg RNA before the Affymetrix arrays were run.

first: Evan

middle: G

last: Williams


title: Gene expression profile of activated CD4 T cells from adults and newborns

status: Public on Sep 21 2014

city: London

first: Deena

middle: L

last: Gibbons

state: UK

address: 2nd Floor Borough Wing

department: Peter Gorer Department of Immunobiology

country: United Kingdom

institute: Kings College London

summary: Given their precipitous encounter with the environment, newborn infants might be expected to possess abundant immunoprotective mechanisms. Paradoxically, their T cells display grossly impaired Th1 anti-bacterial and anti-viral responses. This study identifies factors produced by neonatal CD4 T cells when compared with adult naive CD4 T cells and highlights CXCL8 as a pivotal effector molecule in neonatal T cells. Using Affimetrix microarray we compared gene expression in cord blood derived CD4 T cells with naive CD4 T cells from adults after polyclonal stimulation.

overall_design: The Affymetrix GeneChip Human Genome 1.0 ST array were used to define gene expression profiles in each of the CD4 T cell samples.

first: Adrian

last: Hayday


title: The transcriptome of Legionella pneumophila-infected human monocyte-derived macrophages

status: Public on Sep 19 2014

city: Louisville

first: Christopher

last: Price

address: 505 S HANCOCK ST CTR ROOM 633

department: Microbiology and Immunology

institute: University of Louisville

summary:
Analysis of the human monocyte-derived macrophage (hMDM)  transcriptional response to L. pneumophila infection at 8 hours post-infection
We used microarrays to probe the hMDM transcriptional response to wild type L. pneumophila AA100 infection and its isogenic ankB and T2SS mutants. We identified up-regulation of innate immunity pathways and down-regulation of protein translation pathways

overall_design: hMDMs were isolated from healthy donors and infected with L. pneumophila AA100 and its isogenic ankB and T2SS mutants for 8 h prior to isolation of total RNA and hybridization to Affymetrix microarrays.

first: Yousef

middle: A

last: Kwaik


title: Transcriptomic analysis unveils correlations between regulative apoptotic caspases and genes of cholesterol homeostasis in human brain

status: Public on Sep 13 2014

city: udine

first: raffaella

last: picco

address: piazzale kolbe 4

department: department of medical and biological sciences

institute: university of Udine

summary: Caspases are cysteine-proteases with key roles in the execution phase of apoptosis. Additional cellular activities, unrelated to cell death seem to be influenced by these enzymes. Identification of genes co-regulated with caspases could help to ascertain new biological roles for these proteases.To identify genes and pathways under the influence of caspase-2 we silenced its expression in U87MG glioblastoma cell line. Transcriptional expression profiles of cells transfected with caspase-2 siRNA or control siRNA were compared.

overall_design: Gene expression profiling was evaluated from 2 replicates of U87MG cells transfected with CASP2-siRNA, or with Control-siRNA.

first: Raffaella

last: Picco

first: Andrea

last: Tomasella

first: Federico

last: Fogolari

first: Claudio

last: Brancolini


title: Genomic analysis of low-grade serous ovarian carcinomas [EXP]

city: East Melbourne

first: Dariush

last: Etemadmoghadam

address: St Andrew's Place

country: Australia

institute: Peter MacCallum Cancer Centre

summary: Low-grade serous ovarian carcinomas are typically Ras-pathway mutated, TP53 wild-type, have limited chromosomal aberration, and are frequently associated with borderline tumors. By contrast, high-grade serous ovarian carcinoma lack Ras-pathway mutations, are invariably TP53 mutated, show widespread genomic change, and are commonly BRCA-pathway disrupted. We sought to identify differentially expressed genes between co-existing borderline and invasive components of serous carcinoma.

overall_design: Paired co-existing borderline and invasive tumor components were profiled from tumors from 7 patients

first: Anna

last: deFazio

first: David

last: Bowtell

first: Catherine

last: Emmanuel

first: Yoke-Eng

last: Chiew

first: Joshy

last: George


title: Time course expression measured by microarray of fresh CD4+ response to activation from healthy individuals

status: Public on Aug 28 2014

city: Boston

first: Liang

last: Yang

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

summary:
Variation in individuals' adaptive immune response is believed to influence susceptibility to complex diseases in humans. The genetic basis of such variation is poorly understood.
We measured gene expression from resting and activated CD4+ T cells derived from the peripheral blood of healthy individuals. We activated the primary T cells with anti-CD3/CD28 beads alone or with IFNb or Th17 polarizing cytokines.

overall_design: We collected peripheral blood from each human donor. We isolated peripheral blood mononuclear cells by Ficoll, and negatively selected for CD4+ T cells using RosettaSep. We then either left cells unstimulated or stimulated them with beads conjugated with anti-CD3 and anti-CD28 either without additional cytokines, or with IFNb, or with Th17 cocktail. Cells were harvest at up to 8 time points (0hr, 45min, 2hr, 4hr, 10hr, 24hr, 48hr and 72hr), lysed and RNA isolated to be profiled on microarray.

first: Chun

last: Ye

first: Ting

last: Feng

first: Aviv

last: Regev

first: Christophe

last: Benoist


title: Copy number variation analysis of pheochromocytoma and paraganglioma

city: Melbourne

first: Aidan

last: Flynn

state: Victoria

address: St Andrews Place, Melbourne East

department: Research

summary: Cytogenetic analysis of 36 pheochromocytoma and four paraganglioma using high density arrays

overall_design: A series of 36 pheochromocytoma and four paraganglioma were analysed for genomic structural alterations using high density copy number arrays

first: Richard

last: Tothill


title: Gene expression profiles in patients with multiple myeloma receiving adjuvant treatment with an extract from the mushroom agaricus blazei Murill in addition to chemotherapy

city: Oslo

first: Jon-Magnus

last: Tangen

address: Kirkeveien 166

country: Norway

institute: Oslo University Hospital

summary: The edible mushroom Agaricus blazei Murill has immunomodulating and antiproliferative effects. In a clinical study 33 patients with multiple myeloma were randomized to receive treatment with Agaricus (16 patients) or placebo (17 patients) in addition to chemotherapy.

overall_design: Gene expression profiles were analyzed before and after treatment in 8 patients in the agaricus group and in 6 patients in the control group and the differences were calculated

first: Ole

middle: K

last: Olstad


title: Expression data measured by microarray of CD4+ T cells from healthy individuals stimulated with anti-CD3/CD28

country: USA

summary:
This SubSeries in the ImmVar project investigates the response of selected genes in T cells from healthy human individuals to ascertain the impact of genetic or non-genetic variation on T cell activation parameters.
We measured gene expression from resting and activated CD4+ T cells derived from the peripheral blood of healthy individuals. We activated the primary T cells with anti-CD3/CD28 beads alone or with IFNb or Th17 polarizing cytokines.

overall_design: We collected peripheral blood from each human donor. We isolated peripheral blood mononuclear cells by Ficoll, and negatively selected for CD4+ T cells using RosettaSep. We then either left cells unstimulated or stimulated them with beads conjugated with anti-CD3 and anti-CD28. Cells from 15 individuals were harvested at up to 5 conditions, lysed and RNA isolated to be profiled on microarray.


title: miRNA profile of the bovine pretransfer endometrium based on pregnancy success after in vivo and in vitro produced embryos transfer

status: Public on Sep 05 2014

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

institute: Leibniz Institute for Farm Animal Biology (FBN)

summary: In summary the main goal of this study is to determine the miRNA transcriptional profile of bovine endoemtrium at early stage of development in relation to pregnancy success after transfer of in vivo and in vitro derived blastocysts

overall_design: 24 pool of bovine endometrium based on out come of pregnancy sucess

first: Siriluck

last: Ponsuksili


title: Genomic analysis of low-grade serous ovarian carcinomas

first: Dariush

last: Etemadmoghadam

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

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

overall_design: Refer to individual Series


title: Expression data from from hTR and hTERT knockdown in human CD4 T cells

city: San Francisco

first: Elizabeth

last: Blackburn

state: CA

address: 600 16th St Genentech Hall S316

institute: UCSF

summary:
We have found that knockdown of the human telomerase RNA template, hTR, induces Bim-mediated apoptosis independent of telomere length in primary human CD4 T cells, whereas knockdown of the telomerase enzymatic protein, hTERT does not induce apoptosis in the timeframe of our studies.
We used microarray analysis to determine any gene changes in human primary CD4 T cells that could provide mechanistic insight into hTR knockdown induced apoptosis. Cells with control shScramble, shTERT, and shTR were used in this experiment

overall_design: Primary human CD4 T cells were trandsuced in biological triplicates with lentivirus containing shRNAs against a scrambled sequence, hTERT, and hTR 24 hours after CD3 CD28 stimiulation.  Cells were cultured in the presence of puromycin to select for cells with shRNAs. shTERT and shTR were compared to shScramble results.

first: Francesca

middle: S

last: Gazzaniga


title: Affymetrix SNP array data for NUP98 rearranged acute leukemias

status: Public on Aug 26 2014

city: Perugia

first: Cristina

last: Mecucci

address: Santa Maria della Misericordia University Hospital

institute: University of Perugia

summary: We assessed lineage involvement by NUP98 translocations in myelodysplastic syndromes (MDS), acute myeloid leukemia (AML), and T-cell acute lymphoblastic leukemia (T-ALL). Single cell analysis by FICTION (Fluorescence Immunophenotype and Interphase Cytogenetics as a Tool for Investigation of Neoplasms) showed that NUP98-translocations with various partners, i.e. NSD1, DDX10, RAP1GDS1, and LNP1, always affected a CD34+/CD133+ hematopoietic precursor. Interestingly, in MDS/AML myelomonocytes, erythroid cells, B- and T- lymphocytes belonged to the abnormal clone, while in T-ALL only CD7+/CD3+ cells were involved. The partner did not appear to play a major role in determining the leukemia phenotype as shown in AML and T-ALL with the same NUP98-RAP1GDS1 fusion. Additional hits, namely mutations of FLT3 and CEBPA in MDS/AML and mutation of NOTCH1 plus MYB duplication in T-ALL, were identified in leukemias with, respectively, myeloid or T-lymphoid phenotype.

overall_design: Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from cryopreserved diagnostic bone marrow or peripheral blood samples. Copy number and Copy neutral LOH analysis of with Affymetrix Cytogenetic 2.7 and Cytoscan HD SNP arrays was performed on 6 NUP98 rearranged leukemias.

first: Gianluca

last: Barba


title: Transient expression of CHD5 in KELLY cells

status: Public on Sep 23 2014

first: Timur

last: Yusufzai

address: 450 Brookline Ave

institute: DFCI

summary:
Loss of the tumor suppressor CHD5 frequently occurs during neuroblastoma progression.
We used microarray analyses to identify genes that change expression following transient transfection of human CHD5 into KELLY cells

overall_design: KELLY cells were transiently transfected with the human CHD5 cDNA or the empty vector.  RNA was extracted and hybridized on Affymetrix microarrays

first: Jinhua

last: Quan


title: Maturation of the thalidomystery

city: Be'er Yacob

first: Yossi

last: Cohen

state: Zerifin

address: Assaf Harofhe, Institute of Hematology

department: Hematology

institute: Asaf Harofhe Hospital

summary: Gene expression profile (GEP) was analyzed from cultured bone marrow (BM) samples of patients with lenalidomide-responsive versus lenalidomide-resistant myeloma after 24 hours incubation in vitro with thalidomide (Thal) (0.8 µg/ml), lenalidomide (Len) (0.5 µg/ml)  or with DMSO (control).

overall_design: Comparative gene expression profile of cultured bone marrow samples from patients with lenalidomide responsive versus lenalidomide resistant myeloma after 24 hours incubation in vitro with thalidomide, lenalidomide or DMSO (control).

first: Osnat

last: Garach-Jehoshua

first: Adina

last: Bar-Chaim

first: Abraham

last: Kornberg


title: Affymetrix SNP array data for cone precursor derived retinoblastoma like samples

status: Public on Aug 25 2014

city: New York

first: Xiaoliang Leon

last: Xu

state: NY

institute: MSKCC

type: Genome variation profiling by genome tiling array

summary: Retinoblastoma is a childhood retinal tumor that initiates in response to biallelic RB1 inactivation. We show that post-mitotic human cone precursors are uniquely sensitive to the oncogenic effects of Rb depletion.  Rb knockdown induced cone precursor proliferation in prospectively isolated populations.   SNP-array analysis of two Rb/p130-depleted cone precursor cell lines, revealing no megabase-size loss of heterozygosity (LOH) or copy number alterations (CNAs). SNP-array analysis of one Rb/p130-depleted (tumor 1) or one Rb-depleted (tumor 2) cone precursor-derived tumors, revealing no megabase-size LOH or CNAs, consistent with the lack of DNA copy number alterations in some retinoblastomas.  Thus, the cone precursor tumors resembled human retinoblastomas at the molecular cytogenetic level.

overall_design:
High resolution SNP-array DNA copy number analyses were performed using CytoScan® HD (Affymetrix, 901835) according to the manufacturer's directions. Data were analyzed using Chromosome Analysis Suite 2.0 (Affymetrix).
DNA was extracted from two Rb/p130 depleted cone precursor cell lines and two cryopreserved mouse retinoblastoma samples from eyes xenograted with Rb/p130 or Rb depleted cone precursors. Affymetrix SNP analysis on retinoblastoma cell lines Y79, RB176, and WERI were used as control. Normal human genome 19 was used as reference.

first: Xiaoliang

first: Suresh

last: Jhanwar

first: David

last: Cobrinik


title: CD47-dependent immunomodulatory and angiogenic activities of extracellular vesicles produced by T cells

status: Public on Sep 01 2014

city: BETHESDA

first: abdel

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

summary: Intercellular communication is critical for integrating complex signals in multicellular eukaryotes.  Vascular endothelial cells and T lymphocytes closely interact during the recirculation and trans-endothelial migration of T cells.  In addition to direct cell-cell contact, we show that T cell derived extracellular vesicles can interact with endothelial cells and modulate their cellular functions.  Thrombospondin-1 and its receptor CD47 are expressed on exosomes/ectosomes derived from T cells, and these extracellular vesicles are internalized and modulate signaling in both T cells and endothelial cells.  Extracellular vesicles released from cells expressing or lacking CD47 differentially regulate activation of T cells induced by engaging the T cell receptor.   Similarly, T cell-derived extracellular vesicles modulate endothelial cell responses to vascular endothelial growth factor and tube formation in a CD47-dependent manner. Uptake of T cell derived extracellular vesicles by recipient endothelial cells globally alters gene expression in a CD47-dependent manner. CD47 also regulates the mRNA content of extracellular vesicles in a manner consistent with some of the resulting alterations in target endothelial cell gene expression. Therefore, the thrombospondin-1 receptor CD47 directly or indirectly regulates intercellular communication mediated by the transfer of extracellular vesicles between vascular cells.

overall_design: HuVEC cells were cocultured with exosomes derived either from Jurkat or JinB8 cells culture media. Each condition was done in triplicate. Also, Exosome RNA from Jurkat or JINB8 cells were compared to each other in triplicate.

first: Abdel

first: Sukhbir

last: Kaur

middle: D

last: Roberts

first: Weiwei

last: Wu


title: BCL6 target genes in a Burkitt's lymphoma cell line with inducible BCL6 expression.

status: Public on Aug 22 2014

city: Leicester

first: Simon

middle: David

last: Wagner

address: Lancaster Road

department: CSMM

institute: University of Leicester

summary: In order to determine BCL6 target genes an EBV negative Burkitt's lymphoma cell line, DG75, was stably transfected with a tetracycline transactivator and tight doxycycline responsive expression of GFP was established. The endogenous BCL6 genes of this cell line were disrupted by homologous recombination and a BCL6 cDNA downstream of tetracycline responsive elements (TRE) was inserted to produce Bcl6-/-:tetBCL6-HA cells. Westerns demonstrated doxycycline dependent BCL6 expression.Bcl6-/-:tet. BCL6-HA cells (clone AB7) were either grown without doxycycline (control) or with 1 ug/ml doxycycline for 16, 48 or 96 hours. Total RNA was extracted using RNeasy minipreps (Qiagen) and concentration and quality were checked on the NanoDrop® ND- 1000 spectrophotometer (NanoDrop Technologies, USA) and the RNA Nano 6000 kit (Agilent Technologies) on a 2100 Bioanalyzer (Agilent Technologies). One hundred ng of total RNA was processed with the GeneChip® Eukaryotic Whole Transcript Sense Target Labelling Assay kit (Affymetrix) according to the manufacturer's details. Hybridisation and scanning of GeneChips® was carried out at the CSC/IC Microarray Centre, MRC Clinical Sciences Centre Imperial College London and data analysis by Bioinformatics Support Service, Imperial College London. Briefly, pre- processing of data was performed using GeneSpring GX 10.0.2 software (Agilent Technologies) which applied the "Exon RMA16"¸ algorhithm to the data set. Exon RMA16 performs background correction, quantile normalisation, median polish summarisation and variance stabilisation of 16.  In background correction, intensity values of each individual array are corrected for non-specific binding by subtracting the average signal intensity of the area between spots from each probe set. Normalisation is required so multiple chips can be compared to each other. Quantile normalisation adjusts the distribution of probe intensity of each array analysed and so that the distribution of probe intensities for each array in a set of arrays is the same. Probe summarisation refers to the conversion of probe level values (there are approximately 26 probes per gene on each GeneChip®) to a single probe set expression value. Variance stabilisation of 16 refers to the addition of the value 16 to the expression values. By increasing the expression value, the variance of the data set is reduced and the distribution (defined by its mean and its variance) is stabilised.

overall_design: A control sample at time (t)=0 was compared to samples at t=16 hours, t=48 hours and t=96 hours following addition of doxycycline.

first: Andrew

last: Porter

first: Jennifer

last: Zobel


title: Comparative gene expression analysis of the human dental pulp in deciduous and permanent teeth

status: Public on Aug 21 2014

city: Seoul

first: Seong-Oh

last: Kim

address: 250 Seongsanno, Seodaemun-gu

department: Pediatric dentistry

country: South Korea

institute: Yonsei University College of Dentistry

summary: Human deciduous and permanent teeth exhibit different developmental processes, morphologies, histological characteristics and life cycles. In addition their pulp tissues react differently to external stimuli, such as the pulp sensitivity test, dental trauma and pulp therapy materials. These differences are attributable to their genetic backgrounds. Therefore the purpose of this study is to compare the differences of dental pulp in deciduous and permanent teeth.

overall_design:
Pulp samples were obtained from permanent premolars (n=6, aged 11-14 years) and deciduous teeth (n=6, aged 11-14 years). Comparative cDNA microarrary analysis revealed several differences in gene expression between the deciduous and permanent pulp tissues.
Each GSM record represents a pulp sample pooled from two teeth samples.

first: Seong

middle: O


title: KDELR activation

city: Naples

first: Jorge

last: Cancino

address: Pietro Castellino 111

department: Life Sciences

institute: IBP

summary:
HeLa cells transfected to express KDELR1 and HeLa cells incubated with KDEL-Bodipy peptide
Cells were transfected to express KDELR1 for 72 hours, or tretaed with 1 micromolar KDEL-Bodipy peptide for 6 hours

overall_design: 1 control and 2 treatments

first: Alberto

last: Luini


title: Comparative gene expression analysis of dental follicle and periodontal ligament in humans

summary: The aim of this study was to evaluate and compare the gene expression profiles of dental follicle and periodontal ligament in humans, which can possibly explain their functions of dental follicle and PDL such as eruption coordination and stress resorption. That may apply this information to clinical problem like eruption disturbance and to periodontal tissue engineering.

overall_design: PDL samples were obtained from permanent premolars (n=11) and dental follicle samples were obtained during extraction of supernumerary teeth (n=4). Comparative cDNA microarray analysis revealed several differences in gene expression between permanent PDL and dental follicles.


title: Whole saliva expression data from human populations stratified by psychosocial stress exposure

status: Public on Sep 04 2014

city: Menlo Park

first: Aaron

last: Wacholder

address: 333 Ravenswood Ave

department: Molecular Genetics Program

institute: SRI International

summary:
The objective of this study was analysis of the whole saliva transcriptome to search for biomarkers of psychosocial stressor exposure and substance use in young adults drawn from a population-based longitudinal cohort, the Oregon Youth Substance Use Project. We conducted genome-wide gene expression analysis on whole saliva RNA from 48 individuals stratified by psychosocial stressor exposure using an Affymetrix Gene ST 1.0 array. We applied Weighted Gene Co-expression Network Analysis (WCGNA) to characterize the high-level structure in the data and to relate expression patterns among samples to participant clinical characteristics. This approach finds clusters of correlated genes (modules) which can reflect clinical, histological, or intracellular organization and function.

Using WCGNA, we constructed a gene expression network from saliva genome-wide gene expression data, which we found to be similar to a network we constructed from publicly available cell-free saliva genome-wide gene expression data. Functional characterization of the WGCNA modules suggested that the samples varied in composition between an expression profile similar to circulating antigen presenting cell types and a glycoprotein-containing expression profile. We identified a significant relation between one module of whole saliva genome-wide gene expression and smoking behavior, and one with psychosocial stressor exposure. The smoking-related module was related to mitochondrial gene expression, and ever-smokers were found to have reduced overall mitochondrial gene expression. To determine whether reduced expression could be explained by reduction in mitochondrial DNA, we measured mtDNA copy number variation within genomic DNA from 400 OYSUP participants. Surprisingly, we found that more frequent smoking is associated with increased mtDNA copy number. The network structure of whole saliva and its association with clinically assessed exposures and behaviors are reported here for the first time.

overall_design: Two groups of 24 individuals each were selected from a sample of 132 based on results from the Life Events and Difficulties Schedule, an assesment of chronic psychosocial stress exposure. The two groups were selected from each end of the stress exposure distribution, composing a high stress and low stress group. One sample (4H) failed and was removed from the study.

first: Denise

last: Nishita

first: Jessica

last: Bowers

first: Judy

last: Andrews

last: Bergen


title: Myeloid malignancies with chromosome 5q deletions acquire a dependency on an intrachromosomal NF-κB gene network

status: Public on Aug 23 2014

city: Columbia

first: Jing

last: Fang

state: SC

address: 715 Sumter Street

department: Drug Discovery and Biomedical Sciences

institute: University of South Carolina

summary: Chromosome 5q deletions (del(5q)) are common in high-risk (HR) Myelodysplastic Syndrome (MDS) and Acute Myeloid Leukemia (AML); however, the gene regulatory networks that sustain these aggressive diseases are unknown. Reduced miR-146a expression in del(5q) HR-MDS/AML and miR-146a-/- hematopoietic stem/progenitor cells (HSPC) results in TRAF6/NF-κΒ activation. Increased survival and proliferation of HSPC from miR-146alow HR-MDS/AML is sustained by a neighboring haploid gene, SQSTM1 (p62), expressed from the intact 5q allele. Overexpression of p62 from the intact allele occurs through NF-κB-dependent feedforward signaling mediated by miR-146a deficiency. p62 is necessary for TRAF6-mediated NF-κB signaling, as disrupting the p62-TRAF6 signaling complex results in cell cycle arrest and apoptosis of MDS/AML cells. Thus, del(5q) HR-MDS/AML employs an intrachromosomal gene network involving loss of miR-146a and haploid overexpression of p62 via NF-κB to sustain TRAF6/NF-κB signaling for cell survival and proliferation. Interfering with the p62-TRAF6 signaling complex represents a therapeutic option in miR-146a-deficient and aggressive del(5q) MDS/AML.

overall_design: Four del(5q) MDS/AML patients with low miR-146a expression (5284, 8839, 8285, 4233) and 5 with high miR-146a expression (7957, 5534, 4688, 4982, 8412) were selected for microarray assay. RNA was reverse transcribed and labeled, and hybridized onto the GeneChip Human Gene 1.0 ST Array. A total of nine samples were included, and two groups are assigned based on miR-146a expression. Comparison comprises mRNA expression profile of low miR-146a group v.s. high miR-146a group.

first: Brenden

last: Barker

first: Lyndsey

last: Bolanos

first: Xiaona

last: Liu

first: Andres

last: Jerez

first: Hideki

last: Makishima

first: Susanne

last: Christie

first: Xiaoting

last: Chen

first: Dinesh

last: Rao

first: Leighton

last: Grimes

first: Kakajan

last: Komurov

first: Matthew

last: Weirauch

first: Jose

last: Cancelas

first: Jaroslaw

middle: P

last: Maciejewski

first: Daniel

last: Starczynowski


title: Gene expression data from SOX2 knock-out 2102Ep and NTera-2 human embryonal carcinoma cell lines

status: Public on Aug 15 2014

city: Dublin

first: Sebastian

last: Vencken

address: Catherine McAuley Centre, Nelson Street

department: Clinical Research Centre

institute: University College Dublin

summary:
SOX2 is an oncogene and a core pluripotency transcription factor. SOX2 has multiple roles in various malignancies, in the maintainance of pluripotency and during various stages of embryonic development. Human embryonal carcinoma cells express SOX2 and the loss of this results in their differentiation.
We silenced SOX2 in two human embryonal carcinoma cell lines and measured whole-genome mRNA expression. Many genes related to embryogenesis and tissue morphogensis were upregulated. Other upregulated genes were markers of mesodermal development and epithelial-to-mesenchymal transition.

overall_design: A specific and validated siRNA against SOX2 was chemically transfected in undifferentiated 2102Ep and NTera-2 embryonal carcinoma cell lines. After three days of incubation under normal growth conditions we used Affymetrix microarrays to measure whole-genome mRNA transcript expression in three biological replicates of each cell line and compared this to whole-gene expression in identical samples transfected with a non-targeting, scrambled control siRNA. SOX2 silencing was validated using qRT-PCR and Western blot prior to whole-genome expression analysis.

first: Praveen

last: Sethupathy

first: Gordon

last: Blackshields

first: Cathy

last: Spillane

first: Salah

last: ElBaruni

first: Orla

last: Sheils

first: Michael

last: Gallagher

first: John

middle: J

last: O’Leary


title: Differential gene and microRNA expression in two SOX2-silenced human embryonal carcinoma cell lines

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


title: Cell Fusion Enhances Mesendodermal Differentiation of Human Induced Pluripotent Stem Cells

status: Public on Aug 06 2014

city: Aachen

first: Martin

last: Zenke

state: NRW

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

institute: Institute for Biomedical Engineering

summary: Human induced pluripotent stem cells (iPS cells) resemble embryonic stem cells and can differentiate into cell derivatives of all three germ layers. However, frequently the differentiation efficiency of iPS cells into some lineages is rather poor. Here, we found that fusion of iPS cells with human hematopoietic stem cells (HSC) enhances iPS cell differentiation. Such iPS hybrids showed a prominent differentiation bias towards hematopoietic lineages but also towards other mesendodermal lineages. Additionally, during differentiation of iPS hybrids expression of early mesendodermal markers - Brachyury (T), MIX1 Homeobox-Like Protein 1 (MIXL1) and Goosecoid (GSC) - appeared with faster kinetics than in parental iPS cells. Following iPS hybrid differentiation there was a prominent induction of NODAL and inhibition of NODAL signaling blunted mesendodermal differentiation. This indicates that NODAL signaling is critically involved in mesendodermal bias of iPS hybrid differentiation. In summary, we demonstrate that iPS cell fusion with HSC prominently enhances iPS differentiation.

overall_design: 11 samples were hybridized GeneChip Human Gene 1.0 ST Arrays (Affymetrix)

first: Jie

last: Qin

first: Stephanie

last: Sontag

first: Qiong

last: Lin

first: Saskia

last: Mitzka

first: Isabelle

last: Leisten

first: Rebekka

last: Schneider

first: Xiaoying

last: Wang

first: Anna

last: Jauch

last: Peitz

first: Oliver

last: Brüstle

first: Wolfgang

last: Wagner

first: Robert

middle: C

last: Zhao


title: Gene Expression Profiles in Chronic Idiopathic Urticaria

status: Public on Aug 12 2014

city: Aurora

first: Stephen

last: Dreskin

state: CO

department: Division of Allergy and Clinical Immunology, Department of Medicine

institute: University of Colorado Denver

summary: Lesions of chronic idiopathic urticaria (CIU) showed significant up-regulation of 506 genes and reduced expression of 51 genes.

overall_design: We enrolled 8 patients with CIU and 6 healthy controls and obtained 4mm punch biopsies of active lesions and unaffected skin of patients with CIU and of skin from normal controls. Routine histologic evaluation was performed, RNA was isolated and gene expression data was determined using an Affymetrix Human Gene 1.0 ST Array (www.affymetrix.com). Due to technical reasons, the final evaluation included 6 samples of lesional skin, 7 samples of non-lesional skin and 5 samples of normal skin.


title: Brown Adipose Tissue (BAT) in Visceral Fat Depot

city: Aarhus

first: Kasper

last: Thorsen

address: Brendstrupgaardsvej

institute: Aarhus University Hospital

summary:
Case story. A patient with massive infiltration of the visceral adipose tissue depot by BAT in a patient with a catecholamine secreting paraganglioma. BAT tissue was identified by protein expression of UCP1 (western blotting and immunostaining)
The goal of the study is to identify patterns of gene expression in BAT containing visceral fat compared to the patient's own subcutanous fat which did not express BAT. For comparison a pool of mRNA isolated from visceral fat from obese subjects was used.

overall_design: Patient Case, Gene expression array from a biopsy from the patient's visceral fat and a biopsy from the subcutaneous fat compared to one array of mRNA from the visceral depot pooled from a group of obese subjects

first: E

last: Sondergaard

first: N

last: Jessen


title: Naa10p's effect on gene expression profiles in MCF7 breast cancer cells

status: Public on Aug 01 2014

city: Beijing

first: Like

last: Qu

address: 52 Fucheng Road

institute: Peking Uiniversity Cancer Institute

summary: N-α-acetyltransferase 10 protein (Naa10p, also called ARD1), the catalytic subunit of N-acetyltransferase A, is a critical regulator of cell death and proliferation. Naa10p is also shown to regulate cancer metastasis by inhibiting cell motility, however its role in cancer metastasis is not fully understood. In this study, we found that high expression of Naa10p is positively correlated with the survival of patients with breast cancer, while negatively correlated with lymph node metastasisr. Naa10p inhibits breast cancer cell migration and invasion in vitro and decreases the xenograft growth and metastasis in nude mice. Microarray screening revealed that Naa10p down-regulates expression of several pro-invasive genes, which was validated by qRT-PCR analysis.

overall_design: To gain an insight into Naa10p’s inhibitory effect on cancer metastasis, we performed microarray analysis with RNA samples extracted from Naa10p-silenced MCF-7 (MCF-7SA) and control cells (MCF-7NC).

first: Y

last: Zeng

first: C

last: Shou


title: Comparative gene array analysis of progenitor cells from deep neck and subcutaneous adipose tissue

status: Public on Aug 05 2014

city: Ulm

first: Daniel

last: Tews

address: Eythstrasse 24

department: Department of Pediatric Endocrinology and Diabetes

institute: University Medical Center Ulm

summary:
Expression profiling of progenitor cells from human supraclavicular and subcutaneous adipose tissue. Studies in animal models revealed that brown and white adipocytes derive from different progenitor cells. Molecular characteristics of these cells have not been investigated in detail in humans.
Results provide evidence into the molecular basis of the difference of white and brown progenitor cells in humans.

overall_design: Progenitor cells from paired samples of supraclavicular and subcutaneous of six patients undergoing neck surgery were isolated by collagenase digestion and subsequently transferred to cell culture. After reaching subconfluency (7 days), we harvested RNA and analyzed differencens in gene expression by microarray analysis.

first: D

first: V

last: Schwar

first: K

last: Holzmann

first: P

last: Fischer-Posovszky

first: M

last: Wabitsch