title: Identifying Nuclear Matrix–attached DNA across the Genome (Affymetrix)

status: Public on Oct 06 2016

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

department: Biochemistry

institute: University of Vermont

summary: Experimental approaches to define the relationship between gene expression and nuclear matrix attachment regions (MARs) have given contrasting and method-specific results. We have developed a next generation sequencing strategy to identify MARs across the human genome (MAR-Seq). The method is based on crosslinking chromatin to its nuclear matrix attachment sites to minimize changes during biochemical processing. We used this method to compare nuclear matrix organization in MCF-10A mammary epithelial-like cells and MDA-MB-231 breast cancer cells and evaluated the results in the context of global gene expression (array analysis) and positional enrichment of gene-regulatory histone modifications (ChIP-Seq). In the normal-like cells, nuclear matrix–attached DNA was enriched in expressed genes, while in the breast cancer cells, it was enriched in non-expressed genes. In both cell lines, the chromatin modifications that mark transcriptional activation or repression were appropriately associated with gene expression. Using this new MAR-Seq approach, we provide the first genome-wide characterization of nuclear matrix attachment in mammalian cells and reveal that the nuclear matrix–associated genome is highly cell-context dependent.

overall_design: Microarray expression data for 2 cell lines

first: Jason

last: Dobson

first: Gary

last: Stein


title: Identification of DHT induced cell cycle dependent trascriptome in prostate cancer cells

status: Public on Oct 05 2016

city: Philadelphia

first: Christopher

last: McNair

state: PA

address: 833 Chestnut Street Ste 1140

department: Medical Oncology

country: USA

institute: Thomas Jefferson University

summary: Evaluation of the genome wide impact of cell cycle position on DHT stimulated gene expression programs.  Results show differential cell cycle regulated gene expression in different cell cycle phases.

overall_design: 20 samples were analyzed using a GeneChip 1.0 ST Array in LNCaP cells arrested in the indicated stages of the cell cycle and stimulated with DHT

first: Karen

middle: E

last: Knudsen


title: Expression profiling on lactation day 2 mammary epithelial cells from constitutive miR-150 expressing mice compared to controls.

status: Public on Oct 01 2016

city: Aurora

first: Jennifer

middle: K

last: Richer

state: CO

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

department: Pathology

institute: University of Colorado Anschutz Medical Campus

summary: Constitutive expression of miR-150 in mammary epithelium causes severe lactation defects. Mammary epithelial cells (MECs) at lactation day 2 were isolated from four homozygous ROSA26-lox-STOP-lox-miR-150 (Stop-150) mice with WAP-driven Cre (WAP-Cre) and compared to MECs from four WAP-Cre control mice. Statistical analysis of the mRNA changes between the two genotypes identified supression of many lipid and cholesterol synthesis genes due to constitutive expression of miR-150.

overall_design: 4 replicates from each genotype (Stop-150fl/fl; WAP-Cre+ versus Stop-150-; WAP-Cre+) were hybridized onto Affymetrix GeneChip® Mouse Transcriptome Array 1.0 ( probesets)

first: R

last: Heinz

first: K

middle: T

last: Butterfield

first: N

middle: S

last: Spoelstra

first: B

middle: L

last: Babbs

first: H

last: Gu

first: J


title: Celiac disease T cell clone response to CD3/CD28 stimulation

status: Public on Sep 30 2016

city: Leiden

first: Martijn

middle: H

last: Brugman

address: Albinusdreef 2

department: IHB

country: Netherlands

institute: LUMC

summary: To identify the CD4+ T cell cytokines responsible for the proliferation of the Lin-IEL lines CD4+ T cell clone L10, which recognises DQ2-glia-α1, one of the immunodominant T cell epitopes in celiac disease, was stimulated for 3 hours in IMDM with plate-bound CD3/CD28-specific (2.5 µg/ml each) or control antibodies coated onto 6-well non-tissue culture treated plates. Three independent biological replicates were performed, each time including 6 million Ficoll-purified live cells per condition. RNA was purified from these cells using the RNAeasy mini kit (Qiagen, Venlo, the Netherlands). cDNA was amplified using the Applause WT-Amp system (NuGEN technologies, Bemmel, the Netherlands) and biotin-labelled with the Encore Biotin Module (NuGEN). Human Gene 1.0 ST arrays (Affymetrix, High Wycombe, UK) were employed to quantify global gene expression.

overall_design: CD4+ T clone L10 cells, isolated from a duodenal biopsy of a celiac disease patient (Petersen et al., 2014, Nat. Struct. Biol. 21:480-488) were stimulated for 3 hours in IMDM with plate-bound CD3/CD28-specific (2.5 µg/ml each) or control antibodies. Three independent biological replicates were performed, each time including 6 million Ficoll-purified live cells per condition.

first: Jeroen

last: van Bergen


title: Characterization of a P-REX1 gene signature in breast cancer cells

status: Public on Sep 07 2016

city: La Plata

first: Martin

middle: Carlos

last: Abba

state: Buenos Aires

country: Argentina

institute: School of Medical Sciences - UNLP

summary: The Rac nucleotide Exchange Factor (Rac-GEF) P-Rex1 is highly expressed in breast cancer, specifically in the luminal subtype, and is an essential mediator of actin cytoskeleton reorganization and cell migratory responses induced by ErbB and other tyrosine-kinase receptors. Heregulin, a growth factor highly expressed in mammary tumors, causes the activation of P-Rex1 and Rac1 in breast cancer cells via ErbB3, leading to a motile response. Since there is limited information about P-Rex1 downstream effectors, we carried out a microarray analysis to identify genes regulated by P-Rex1 in the context of HRG stimulation. In T-47D breast cancer cells, HRG treatment caused major changes in gene expression, including genes associated with motility, adhesion, invasiveness and metastasis. Silencing P-Rex1 expression from T-47D cells using RNAi altered the induction and repression of a subset of HRG-regulated genes, among them genes associated with extracellular matrix organization, migration, and chemotaxis. HRG induction of MMP10, a gene encoding for metalloproteinase-10, was found to be highly sensitive both to P-Rex1 depletion as well as inhibition of Rac1 function by the GTPase Activating Protein (GAP) 2-chimaerin, suggesting the dependence of the P-Rex1/Rac1 pathway for the induction of genes critical for breast cancer invasiveness. Notably, there is a significant association in the expression of P-Rex1 and MMP10 in human luminal breast cancer, and their co-expression is indicative of poor prognosis.

overall_design: T-47D cells were serum starved and then stimulated with HRG (20 ng/ml) or vehicle (PBS) for 6 h in 60-mm plates. Three biological replicates for each experimental condition were used. For the analysis of P-Rex1-regulated genes, T-47D parental, NTC, P-Rex1#1 and P-Rex1#2 cells, with and without HRG treatment, were used (24 samples)

first: Marcelo

middle: G

last: Kazanietz


title: Expression data from hMSC-TERT4 cells during osteoblast differentiation

status: Public on Sep 01 2016

city: Sydney

first: Natalie

last: Twine

address: High Street, Kensington

country: Australia

institute: University of New South Wales

summary:
Differentiation of human skeletal stem cells (hMSC) into osteoblasts is regulated by a few well described transcription factors. Our study used clustering and gene expression data to identify a novel transcription factor. ZNF25, which we showed is involved in osteoblast differentiation.
We used microarrays to study gene expression of hMSC-TERT4 cells during osteoblast differentiation.

overall_design: hMSC-TERT4 cells were induced to differentiated into osteoblasts in vitro with siZNF25. Gene expression was analysed using Affymetrix microarrays at days 0, 1, 3, 6, 9 and 12 post osteoblast induction.

middle: A

first: Marc

middle: R

last: Wilkins

first: Linda

last: Harkness

first: Moustapha

last: Kassem


title: MiroRNA expression from pig endometrium exposed to developing pre-implantation embryo versus unfertilized oocytes in vivo

status: Public on Oct 04 2016

city: Sheffield

first: Tamer

last: Nafee

address: The Jessop Wing, Tree Root Walk

department: AURDM

country: United Kingdom

institute: University of Sheffield

summary: In vivo evidence suggests a dynamic change of microRNA expression with the phase of the endometrial cycle to achieve endometrial receptivity. In vivo animal studies outlined post – implantation changes in microRNA profiles. Little information is available on the role of microRNAs in the early stages of the embryonic – endometrial dialogue prior to established implantation .Our aim is to investigate the possible role of microRNAs the early endometrial response to the developing pre- attachment blastocyst prior to established implantation

overall_design: Three sows were laparoscopically inseminated with semen in one oviduct and with diluent in the contra lateral oviduct. Whole endometrial homogenates were surgically collected from the tip of both uterine horns after microscopically confirming the presence of oocytes / blastocysts. An affymetrix GeneChip miRNA 3.0 microarray was used to compare the microRNA expression profiles of the endometrium exposed to unfertilised oocytes vs developing embryos

first: Alireza

last: Fazeli


title: Affymetrix CytoScan HD array data of iPSCs and iPSC-derived-NSPCs

status: Public on Sep 14 2016

city: Shinjuku-ku

first: Keiko

last: Sugai

state: Tokyo

address: 35 Shinanomachi

country: Japan

institute: Keio University School of Medicine

type: Genome variation profiling by genome tiling array

summary: Cytoscan HD analysis on DNA samples from iPSCs, iPS-derived NSPCs

overall_design: Affymetrix CytoScan HD array analyses were performed according to the manufacturer's directions on DNA extracted from three iPSCs, and their neural induced derivatives (NSPCs) using two different protocols. Each NSPC was cultured over 10 passages, and then their DNAs were also analyzed.

first: Masaya

last: Nakamura


title: Gene expression data from lung tumor biopsie

status: Public on Sep 17 2016

city: DISTRITO FEDERAL

first: Camilo

last: Molina Romero

state: Distrito Federal

address: Av. San Fernando No. 22

department: Thoracic Oncology Unit and Laboratory of Personalized Medicine

country: Mexico

institute: INCan

summary: We analyzed the differences in the genetic expression of adenocarcinoma subtypes according to the new WHO 2015 classification.

overall_design: Microarray gene expression analysis was performed on a cohort of 29 NSCLC patients treated at the Instituto Nacional de Cancerología of Mexico from 2008 to 2011. All patients had an available biopsy sample and were classified into four different subtypes of adenocarcinoma (2015 WHO classification).

first: Molina

last: Camilo

first: Rangel

last: Claudia


title: Tumor Touch Imprints as Source for Whole Genome Analysis of Neuroblastoma Tumors

status: Public on Aug 31 2016

city: Vienna

first: Clemens

last: Brunner

address: Zimmermannplatz 10

department: Tumor Biology

country: Austria

institute: Children's Cancer Research Institute

summary: Tumor touch imprints (TTIs) are routinely used for the molecular diagnosis of neuroblastomas by interphase fluorescence in-situ hybridization (I-FISH). However, to enable an up-to-date molecular diagnosis of neuroblastomas and to identify new markers to refine risk and therapy stratification methods, whole genome approaches are demanded. We tested whether an ultra-high density SNP array platform identifying copy number changes of varying sizes down to few exons can be applied to detect genomic changes on DNA extracted from TTIs.

overall_design: DNA was extracted from TTIs of 44 neuroblastoma, 1 Ewing tumor, 1 desmoplastic small round cell tumor, 1 medulloblastoma and 1 osteosarcoma. The DNAs were processed with the Cytoscan HD platform.

first: Peter

middle: F

last: Ambros


title: Differential expression of miR-4520a associated with gain-of-function mutations in Familial Mediterranean Fever (FMF)

status: Public on Sep 21 2016

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

country: Germany

institute: Deutsches Rheuma-Forschungszentrum

summary: We knocked down the Mediterranean fever (MEFV) gene by RNA interference (siRNA) in human myelomonocytic cells that express endogenous pyrin, aiming to identify microRNAs (miRNAs) that are differentially expressed in siMEFV treated cells. The purpose of this study was to better understand the pathophysiology of FMF, through the identification of novel miRNAs involved in the regulation of MEFV.

overall_design:
The MEFV gene was knocked down by RNA interference (siRNA) in human myelomonocytic cells that express endogenous pyrin, aiming to identify microRNAs (miRNAs) that are differentially expressed in siMEFV treated cells using Affymetrix miRNA-3_0 chips. Heat maps from the significant differentially expressed microRNAs were produced and gene networks have been constructed to correlate pyrin with other known pathways and identify potential effectors regulated by pyrin. Microarray analyses revealed 29 significantly differentially regulated and most relevant miRNAs implicated in pathways associated with regulation of cellular integrity and survival. Bioinformatics analyses showed that miR-4520a is predicted to target genes implicated in autophagy through regulation of RHEB/mTOR signaling. Differential expression levels of RHEB were confirmed by luciferase reporter gene assays providing further evidence that RHEB is directly targeted by miR-4520a.
Total RNA was extracted using the RNeasy Mini kit (Qiagen). The integrity of isolated RNA was assessed for each sample using an Agilent 2100 Bioanalyzer (Agilent, Waldbronn, Germany) and amount was checked with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). Double-stranded complementary RNA was synthesized from 1 µg total RNA using Message AmpII Biotin (Ambion, USA). Fifteen micrograms of fragmented cRNA of each sample were hybridized to miRNA-3_0 chips (Affymetrix). Hybridization was performed in a Hybridization Oven 640, and chips were washed and stained in the Fluidics Station 400 (both Affymetrix). Finally, the arrays were scanned with a GeneChip Scanner 3000 using the Expression Console 1.3.1 software, both Affymetrix. The RMA or not RMA normalized data of quality checked microarrays were analyzed with High Performance Chip Data Analysis (HPCDA), using Access databases also for HPCDA-Score, HPCDA-Volcano-Plot and Gene List Significance Index (GLSI) calculations. Not RMA normalized data were further normalized with four different methods or only scaled. With HPCDAs of all the seven differently normalized Signals, seven lists of significant differentially expressed miRNAs were generated. With GLSI, HPCDA-Score and HPCDA-Volcano-Plot, the 29 most relevant miRNAs were defined.

first: H

last: Latsoudis

first: M

last: Mashreghi

first: J

last: Grün

middle: D

last: Chang

first: B

last: Stuhlmüller

first: A

last: Repa

first: I

last: Gergiannaki

first: E

last: Kabouraki

first: G

last: Vlachos

first: K

last: Doukoumetzidis

first: T

last: Häupl

last: Radbruch

first: P

last: Sidiropoulos

first: D

last: Kardassis

middle: B

last: Niewold

last: Boumpas

middle: N

last: Goulielmos


title: Gene expression profiling of miR-22-expressing Rhabdomyosarcoma cells

status: Public on Sep 15 2016

city: Torino

first: Ugo

last: Ala

address: Via Nizza 52

department: Dept. of Molecular Biotechnology and Health Sciences

country: Italy

institute: University of Torino

summary: The aim of this study was to identify genes regulated  by doxycycline-mediated induction (IND) of miR-22 expression (NpBI-22) in RD18 Rhabdomyosarcoma cells.

overall_design: The experiment included 6 samples: two biological replicates of RD18 NpBI-22 cells either treated with doxycycline for 6 days (IND) or left untreated (NI). RD18 NpBI-206AS cells, both induced (IND) and non-induced (NI) were included as additional controls.

first: Francesca

last: Bersani

first: Marcello

last: Lingua

first: Riccardo

last: Taulli


title: Gene expression profiling in primary human skeletal myotubes with small molecule inhibitors of lipid accumulation

status: Public on Aug 08 2016

city: Orlando

first: Rick

last: Vega

state: FL

address: 303 E. Princeton

institute: AdventHealth

summary: The development of insulin resistance is strongly associated with accumulation of intracellular lipid in tissues outside of adipose including skeletal muscle, liver and heart. In obese humans, intramyocellular lipid (IMCL) is negatively correlated with whole body insulin sensitivity. The skeletal myocyte imports fatty acids (FA) into the cell from circulating free fatty acids or lipoprotein particles such as VLDL, to support energy production. Once transported into the cell, FAs are oxidized for ATP production, used to build membranes, or stored as triglyceride. However, in the long term, increased delivery of fatty acids can exceed mitochondrial oxidative capacity and set the stage for a vicious cycle of cellular lipotoxicity. We have recently identified a novel small molecule inhibitor of lipid accumulation in skeletal mycytes termed SBI-477. Microarray transcriptomics was performed in primary human skeletal myotubes following oleate loading and treatment with SBI-477. This was also compared to A922500, a diacylglycerol transferase 1 (DGAT1) inhibitor. SBI-477 treatment reversed many of the transcriptomic effects of oleate loading in these cells but also produced a transcriptomic profile distinct from the DGAT1 inhibitor.

overall_design: Microarray expression profiling was performed with total RNA isolated from differentiated primary human skeletal myotubes. These cells were treated with BSA (control for oleate), 100micromolar oleic acid, oleate + 10micromolar SBI-477 and oleate + 1micromolar A922500 for 24 hours. Oleate and test compound were added at the same time to the cells. Two biologic replicates for each condition were included.

first: Mangala

last: Soundarapandian

first: Byungyong

last: Ahn

first: Daniel

middle: P

last: Kelly


title: microRNA (miRNA) expression data from normal human epidermal keratinocytes exposed to sulfur mustard and nitrogen mustard in the presence and absence of hydrocortisone treatment

status: Public on Aug 30 2016

city: Aberdeen Proving Ground

first: E Chepchumba

last: Yego

state: MD

address: 3100 Ricketts Point Road

department: Research

institute: US Army Medical Research Institute of Chemical Defense

summary: The bifunctional alkylating agent sulfur mustard (SM; bis-(2-dichloroethyl) sulfide) is a potent vesicating chemical that has previously been used as a chemical warfare agent.   studies have shown that exposure to CWNA compounds induces damage in the brain and heart.

overall_design: Normal human epidermal keratinocytes (NHEK) were pretreated for 24 hours with control vehicle (1.25% ethanol) or hydrocortisone (500µM HC) and then exposed to either 200µM SM or 200µM NM for 1 hour or 8 hours.

middle: C

first: Cristin

last: Rothwell

first: Heidi

middle: M

last: Hoard-Fruchey

first: James

last: Dillman


title: Expression data from healthy control human peripheral blood mononuclear cells (PBMC) treated with wild-type IL-2 or F42K

city: Houston

first: Radvanyi

last: Laszlo

address: 7455 Fannin St

institute: UT MD Anderson Cancer Center

summary:
IL-2 mutant (F42K) is a variant of IL-2 that binds preferentially to the lower affinity IL-2Rβγ and has minimal binding to CD25, on Tregs, effector NK and T-cell subsets. Our recent study has uncovered that in contrast to WT IL-2, F42K did not efficiently induce the expansion of highly suppressive ICOS+ Tregs in PBMC from healthy controls and melanoma patients whereas it did promote the expansion of NK cells.
We used microarray to study the differences of gene profiles induced by wild-type (WT) IL-2, F42K and IL-15 when treated on freshly isolated human peripheral blood mononuclear cells (PBMC) from healthy control.

overall_design: Human peripheral blood mononuclear cells (PBMC) were isolated from buffy coat and were stimulated with 0.4nM WT IL-2, F42K or IL-15 for 24 hr. Total RNA was extracted from each WT IL-2, F42K and IL-15 treated PBMCs and Sense RNA was reverse-transcribed via RT reaction into DNA and labeled with biotin using Affymetrix labeling kits and hybridized on human Affymetrix microarray chip.

first: Geok

last: Sim

first: Chengwen

last: Liu

first: Ena

last: Wang

first: Hui

first: Caitlin

last: Creasy

first: Zhimin

last: Dai

first: Willem

middle: W

last: Overwijk

first: Jason

last: Roszik

first: Francesco

last: Marincola

first: Patrick

last: Hwu

first: Elizabeth

last: Grimm

first: Laszlo

last: Radvanyi


title: Effects of black currant extract on gene expression on MCF10A

status: Public on Aug 06 2016

city: Aomori

first: Naoki

last: Nanashima

state: Aomori

address: 58-1 Mase, Hamadate

department: Department of Nutrition

institute: Aomori University of Health and Welfare

summary: To investigate new health functions by blackcurrant extract (BCE), we compare altered of the genes expression before and after BCE (50μg/ml) treatment in MCF10A.

overall_design: MCF10A cells were seeded in culture dish and maintain to confluent. Then medium replace with  mammary epithelial cell growth medium kit with or without BCE (50μg/ml). After the cells were incubated for 24 h at 37 °C 5% CO2.


status: Public on Aug 23 2016

city: Memphis

first: Jiyang

last: Yu

state: TN

address: 262 Danny Thomas Place, MS 1135

department: Computational Biology

institute: St. Jude Children's Research Hospital

summary: Expression Profiles of SUM149 cell treated by ACY1215 at 0h, 3h, 6h and 12h by Agilent SurePrint G3 Human GE v3 8x60K.

first: Ruth

last: Rodriguez-Barrueco

first: Andrea

last: Califano

first: Jose

last: Silva


title: Gene expression profiling  in Human mammary epithelial cell (MCF10A) by repression of KRT81 expression

summary: To investigate new health functions of hair keratin KRT81 in MCF10A, we compare altered of the genes expression.

overall_design: The expression of KRT81 was blocked by transient transfection with KRT81 siRNA in MCF10A cells.


title: Identification of a novel risk factor for intracranial aneurysms in ADPKD using iPSC models

status: Public on Aug 04 2016

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

institute: CyberomiX Inc

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

overall_design: Refer to individual Series


title: RNAPol2 accounts for tumor cells liability to JQ1 [Affymetrix]

status: Public on Aug 25 2016

city: milano

first: stefano

last: campaner

address: via adamello 16

department: Center for Genomic Science

institute: fondazione Istituto italiano di tecnologia

summary: We here use B-cell tumors as a model to address the mechanism of action of JQ1, a widely used BET inhibitor.

overall_design: 250000 cells/mL of RAJI cells were cultured in a total volume of 40 mL. 24h after the plating DMSO or 100 nM of JQ1 were added to the culture for 24h. Total RNA from 107 RAJI was purified using TRIzol reagent (Invitrogen) according to manufacturer’s instructions, treated with TurboDNase (Ambion) and processed for oligonucleotide microarray profile through Affymetrix Human Gene 1.0 ST arrays platform.

first: Stefano

last: Campaner

first: Ottavio

last: Croci

first: Elisa

last: Donato

first: Heiko

last: Muller


title: Expression and exosome incorporation of microRNA by leukemia versus nonmalignant hematopoietic progenitors

status: Public on Aug 18 2016

city: Portland

first: Noah

last: Hornick

state: OR

address: 3181 S.W. Sam Jackson Park Rd.

department: Pediatric Hematology Oncology

institute: OHSU

type:
Non-coding RNA profiling by array
Third-party reanalysis

summary: Exosomes are paracrine regulators of the tumor microenvironment. However, their complex cargo can hamper an understanding of their specific action in target cells. We therefore sought to identify the changes in exosome miRNA content that occur with malignant transformation by comparing two myeloid cancer cell lines to their nonmalignant predecessors, CD34+ human hematopoietic progenitor cells. We employed microarrays to evaluate which miRNA are present at altered concentrations before and after transformation as well as before and after incorporation into exosomes.

overall_design: This experiment sought to compare the cells and exosomes of CD34+ nonmalignant progenitors to those of malignant myeloid cell lines HL-60 and MOLM-14. Cells were cultured under 1% O2 conditions for 48 hours, after which cells and exosomes were collected, and miRNA was extracted for microarray comparison. Normalization included comparison to the additional MOLM-14 cell and exosome samples grown at 1% O2 in GSE55025 (GSM1328048, GSM1328049, GSM1328044, GSM1328045). The complete_normalized_data.txt contains 16 data columns (12 new samples + 4 re-analyzed data).

first: Peter

last: Kurre

first: Jianya

last: Huan

middle: I

first: Christina

last: Harrington

first: Solange

last: Mongoue-Tchokote

first: Amiee

last: Potter

first: Mark

last: Fisher


title: Gene expression profiling of Calu-6 lung cancer cells transfected with scrambled siRNA and LAPTM4B-specific siRNA

status: Public on Aug 01 2016

first: Humam

last: Kadara

state: TX

address: 2130 W. Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

summary:
We recently characterized the adjacent airway field of cancerization in NSCLC by whole transcriptome expression analysis and demonstrated that lysosomal protein transmembrane 4 beta (LAPTM4B) was an elevated field cancerization marker in NSCLCs and in adjacent but not in distant normal-appearing airways.
We also found that LAPTM4B was up-regulated in NSCLCs compared to normal lung and promoted anchorage-dependent growth of lung cancer cells. Previous reports suggested that LAPTM4B is activated following metabolic and genotixc stress. The precise role of LAPTM4B in lung cancer cell survival and NSCLC pathogenesis is still elusive.

overall_design: In the present study we sought to examine how LAPTM4B expression levels impact downstream expression profiles and cell signaling in order to gain better insights into the function of this putative oncogene in lung cancer. Calu-6 lung cancer cells were transfected with SMARTpool (Dharmacon)control/scrambled siRNA or siRNA targeting LAPTM4B. Following transfection, cells were cultured in the presence or absence of 10% fetal bovine serum (FBS). Three independent transfections for each condition were performed representing three biological replicates per condition (total number of samples = 12). RNA interference-mediated knock-down of LAPTM4B in samples was confirmed by quantitative real-time PCR. Total RNA was profiled using the Human Gene 1.0 ST platform.

first: Yuho

last: Maki


title: Integrative analysis of microRNA and gene expression profiles identifies microRNAs as potential regulators in alcoholic hepatitis

status: Public on Aug 02 2016

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

summary: Background & aims: The role of microRNAs (miRNAs) in Alcoholic Hepatitis (AH) and their potential as therapeutic targets in liver disease has not been explored yet. This study aims at profiling miRNA in AH and identifying dysregulated miRNAs involved in AH pathophysiology.  Methods: miRNA expression arrays were performed in 13 AH, 5 alcohol liver disease-induced cirrhosis (ALD-CH), 5 nonalcoholic steatohepatitis induced cirrhosis (NASH-CH), 4 HCV-induced cirrhosis (HCV-CH) and 6 non-injured liver control samples. Genome wide expression profile was retrieved for 12 paired AH and control samples. MiRNA and mRNA expression data was integrated and identified miRNAs were validated in AH samples and in animal models of liver injury.   Results: The miRNA array showed 111 upregulated and 66 downregulated miRNAs in AH versus healthy subjects. The comparison of miRNA profile in liver samples from AH among ALD-CH, HCV-CH and NASH-CH identified 18 miRNAs specifically dysregulated in AH. Integrative miRNA and mRNA analysis in AH identified dysregulated miRNAs for which their target genes were also dysregulated. A functional analysis of identified miRNAs and their targets revealed their involvement in the regulation of canonical pathways related to apoptosis, fatty acid metabolism and cell cycle among others. miRNAs expression (miR-182, miR-21, miR-155, miR-214, miR-432, miR-422a) was validated in an independent cohort of AH. MiR-182 expression correlated with cholestasis, disease severity and short-term mortality. Moreover, miR-182 expression is associated to cholestasis with ductular reaction but not to fibrosis and inflammation in animal models of liver injury.  Conclusions: AH is characterized by an important dysregulation of miRNA expression with a unique miRNA profile. MiRNAs specifically expressed in AH are associated to cholestasis… Uncovered miRNAs are involved in important pathophysiological features in AH suggesting ta regulation of he role of miRNAs in the regulation of AH, and highlight miR-182 as a potential regulator of its pathophysiology.

overall_design: miRNA expression arrays were performed in 13 AH(Alcoholic hepatitis), 5 alcohol liver disease-induced cirrhosis (ALD-CH), 5 nonalcoholic steatohepatitis induced cirrhosis (NASH-CH), 4 HCV-induced cirrhosis (HCV-CH) and 6 non-injured liver control samples(CTRL).

first: J

middle: J

first: D

last: Blaya

first: P

last: Sancho-Bru


title: Methyl-CpG-Binding Protein MBD2 plays a critical role in maintenance and spread of DNA methylation of CpG islands and shores in cancer (expression)

status: Public on Aug 24 2016

city: Darlinghurst

first: Elena

last: Zotenko

state: NSW

address: 384 Victoria St.

department: Genomics and Epigenetics

institute: Garvan Institute of Medical Research

summary: Cancer is characterised by DNA hypermethylation and gene silencing of CpG island-associated promoters, including tumour suppressor genes The methyl-CpG-binding domain (MBD) family of proteins bind to methylated DNA and can aid in the meditation of gene silencing by interaction with histone deacetylases and histone methyltransferases.  However the mechanisms responsible for eliciting CpG island hypermethylation in cancer, and the potential role that MBD may proteins play in modulation of the methylome remain unclear.  Our previous work demonstrated that MBD2 preferentially binds to the hypermethylated GSTP1 promoter CpG island in prostate cancer cells.  Here, we use functional genetic approaches to investigate if MBD2 plays an active role in promoting DNA methylation.  First, we show that loss of MBD2 results in inhibition of both maintenance and spread of de novo methylation of a transfected construct containing the GSTP1 promoter CpG island in prostate cancer cells and Mbd2-/- mouse fibroblasts. De novo methylation was rescued by transient expression of Mbd2 in Mbd2-/- cells. Second, we show that MBD2 depletion triggers significant hypomethylation genome-wide in prostate cancer cells with concomitant loss of MBD2 binding at promoter and enhancer regulatory regions.  Finally, CpG islands and shores that become hypomethylated after MBD2 depletion in LNCaP cancer cells show significant hypermethylation in clinical prostate cancer, highlighting a potential active role of MBD2 in promoting cancer specific hypermethylation.  Importantly, co-immunoprecipiation of MBD2 reveals that MBD2 associates with DNA methyltransferase (DNMT) enzymes 1 and 3A.  Together our results demonstrate that MBD2 plays a critical role in “rewriting” the cancer methylome at specific regulatory regions.

overall_design: LNCaP prostate cancer cell line clones with reduced MBD2 expression were establised by using shRNA to MBD2 and scrambled control clones were established with scrambled control shRNA. To interrogate expression changes induced by MBD2 knock-down we profiled three stably transfected scrambled control clones and three MBD2 knockdown clones on Affymetrix HuGene 1.0ST expression arrays. Differential expression analysis was carried out to identified genes up-/down-regulated by MBD2 knockdown.


title: Affymetrix SNP array data of melanoma cell lines from lymph node metastates

status: Public on Jul 27 2016

city: Essen

first: Klaus

middle: Georg

last: Griewank

address: Hufelandstr. 55

department: Dermatology

institute: University of Duisburg-Essen

summary:
Melanoma recurrence frequently occurs after a latency period of several years. In vivo studies demonstrated that tumor cells overcoming latency show a T cell-edited phenotype, suggesting a relevant role for CD8+ T cells in maintaining metastatic latency. Here, in a patient model of multiple recurrent lesions, we illustrate the genetic evolution of poorly immunogenic melanoma phenotypes, evolving in the presence of autologous tumor antigen-specific CD8+ T cells. Melanoma cells from two of three late recurrent metastases, developing within a 6-year latency period, lacked HLA class I expression. HLA class I-negative tumor cells became clinically apparent 1.5 and 6 years into stage IV disease. Genome profiling by SNP arrays revealed total T-cell resistance in both metastases originating from a shared chromosome 15q alteration and independently acquired focal B2M gene deletions. A third HLA class I-positive lesion developed in year 3 of stage IV disease. By HLA haplotype loss lesion-derived melanoma cells acquired resistance towards dominant T-cell clonotypes targeting early stage III tumor cells. Early disease melanoma cells showed a dedifferentiated MITFnegative phenotype, recently described to be associated with immunosuppression, in contrast to the MITFhigh phenotype of T cell-edited tumor cells from late metastases. In summary, our study demonstrates that tumor recurrences after long-term latency develop towards T-cell resistance by independent genetic events, suggesting a mechanism of T cell-driven genetic evolution of melanoma as a means to evade immune recognition and tumor immunotherapy.

Genetic alterations lead to loss of tumor antigen presentation.

overall_design:
Cell lines were generated from tumor material, differences in T cell recognition were observed and Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from the cell lines.
SNP analysis of different melanoma cell lines obtained from one melanoma patient (4 cell lines from different metastasis of one patient with matching germline DNA).

first: Annette

last: Paschen


title: Expression data from NKYS transfected with siRNAs or plasmids

status: Public on Jul 26 2016

city: Singapore

first: Chong-Lei

last: Bi

address: #12-02, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive

country: Singapore

institute: Cancer Science Institute Singapore

summary:
The siRNA transfection includes JAK3 and EZH2 siRNAs. The plasmid transfection includes EZH2 WT and its mutants.
We used gene expression data from JAK3 siRNA to test whether it affected epigenetic regulation, and used EZH2 mutants to study how it affected EZH2 canonical function.

overall_design: Whole genome microarray comparison of JAK3/EZH2 manipulations and control

first: Yan

last: Junli

first: Eric

last: Liang

first: Bi

last: Chonglei

first: Chng

last: Joo


title: Phenotypic, transcriptomic and genomic characterization of clonal plasma cells in light chain amyloidosis [Gene expression profiling]

status: Public on Jul 22 2016

city: Pamplona

first: Bruno

last: Paiva

address: Av. Pio XII, 55

institute: Clinica Universidad de Navarra

summary: Immunoglobulin light-chain amyloidosis (AL) is a rare clonal plasma cell (PC) disorder that remains largely incurable. AL and multiple myeloma (MM) share the same cellular origin, but while knowledge about MM PC biology has improved significantly, the same does not apply for AL. Here, we undertook an integrative phenotypic, molecular, and genomic approach to study clonal PCs from 22 newly-diagnosed AL patients. Through principal-component-analysis, we demonstrated highly overlapping phenotypic profiles between AL and MGUS or MM patients. However, in contrast to MM, highly-purified FACSs-sorted clonal PCs in AL (n=9/22) show virtually normal transcriptomes with only 68 deregulated genes as compared to normal PCs, including a few tumor suppressor (CDH1, RCAN) and pro-apoptotic (GLIPR1, FAS) genes. Notwithstanding, clonal PCs in AL (n=11/22) were genomically unstable with a median of 9 copy-number-abnormities (CNAs) per case; many of which similar to those found in MM. Whole-exome sequencing (WES) was performed in three AL patients and revealed a median of 10 non-recurrent mutations per case. Altogether, we showed that although clonal PCs in AL display phenotypic and CNA profiles similar to MM, their transcriptome is remarkably similar to that of normal PCs. First-ever WES revealed the lack of a unifying mutation in AL

overall_design:
A total of 22 patients with confirmed diagnosis of AL based on the presence of amyloid-related systemic syndrome, positive amyloid tissue staining with Congo red, and evidence of PC clonality were studied. Samples were collected after informed consent was given, in accordance with local ethical committee guidelines and the Helsinki Declaration.
GEP was performed in 9/22 AL cases with adequate RNA extracted from FACS-purified clonal PCs according to patient-specific aberrant phenotypes, and compared to that of normal PCs from 5 healthy individuals (FACSAriaIIb, BDB; ≥95% purity). RNA was hybridized to the Human Gene 1.0 ST Array (Affymetrix, Santa Clara, CA, USA) and normalization was carried using the expression console (Affymetrix) with the RMA algorithm which includes background correction, normalization and calculation of expression values (log2). Differentially expressed genes between classes were identified using the Significant Analysis of Microarrays (SAM) algorithm (http://www-stat.standford.edu/-tibs/SAM), and significant genes were selected based on the lowest q-value (<10-5).

first: Joaquin

last: Martinez-Lopez

first: Luis

last: Corchete

first: Noemi

last: Puig

first: Maria

last: Luz Sanchez

first: Paloma

last: Barcena

first: Diego

last: Alignani

first: Marta

last: Lasa

first: Alfonso

last: García de Coca

first: Emilia

last: Pardal

first: Fernando

last: Escalante

first: Tomás

last: González-López

first: José

last: Alonso

first: Magdalena

last: Sierra

first: Abelardo

last: Bárez

last: Hernández

first: Josefina

last: Galende

first: Felipe

last: Prosper

first: Alberto

last: Orfao

first: Maria-Belen

last: Vidriales

first: Norma

last: Gutierrez

first: María-Victoria

last: Mateos

first: Juan-Jose

last: Lahuerta

first: Jesús

last: San Miguel


title: Identification of a novel risk factor for intracranial aneurysms in ADPKD using iPSC models [Affymetrix]

first: Akira

last: Watanabe

summary: Cardiovascular complications are the leading cause of death in autosomal dominant polycystic kidney disease (ADPKD), and intracranial aneurysm (ICA) causing subarachnoid hemorrhage is among the most serious complications. The diagnostic and therapeutic strategies for ICAs in ADPKD have not been fully established. We here generated induced pluripotent stem cells (iPSCs) from seven ADPKD patients, including four with ICAs. The vascular cells differentiated from ADPKD-iPSCs showed altered Ca2+ entry and gene expression profiles compared with those from control-iPSCs. We found that the expression level of a metalloenzyme gene, matrix metalloproteinase (MMP) 1, was specifically elevated in the iPSC-derived endothelia from ADPKD patients with ICAs. Furthermore, we confirmed a statistically significant correlation between the serum MMP1 levels and the development of ICAs in 354 ADPKD patients, indicating that the serum MMP1 levels may be a novel risk factor and become more beneficial when combined with other risk factors. These results suggest that cellular disease models with ADPKD-specific iPSCs can be used to study the disease mechanisms and to identify novel disease-related molecules or risk factors.

overall_design: The gene expression profiles of vascular endothelia and smooth muscle cells derived from ADPKD-iPSCs were analyzed.  Seven ADPKD-iPSC derived ECs, and seven ADPKD-iPSC derived SMCs were analyzed.

first: Tomonaga

last: Ameku

first: Fumihiko

last: Shiota

first: Fumiyo

last: Kitaoka

first: Naoki

last: Amano

first: Masahiro

last: Nakamura

first: Kenji

last: Osafune


title: Phenotypic, transcriptomic and genomic characterization of clonal plasma cells in light chain amyloidosis

first: Bruno

last: Paiva

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


title: Gene Expression Profiling of OPM2 treatment with VS-5584 (SB2343).

first: Nurulhuda

last: Mustafa

address: 14 Medical Drive, Level 12

department: Yong Loo Lin School of Medicine

institute: National University of Singapore

summary:
The PI3K/mTOR pathway is a constitutively active in multiple myeloma. Single inhibition of mTOR usually confers reactivation of the pathway. VS-5584 (SB2343) is a bispecific PI3K/mTOR inhibitor which effectively and specifically inhibits the target pathways and shows potent anti-myeloma activity.
We utilised a gene microarray analysis to analyse and identify the genes that were sensitively regulated by VS-5584 treatment in OPM2.

overall_design: OPM2 cells were either treated with DMSO(drug solvent) or with 125nM of VS-5584(SB2343) which is half the IC50 concentration of the drug at 48h in OPM2 cells. The cells were harvested at  24h in order to detect the regulation of relatively early response genes.

first: Bi

last: Lei

first: Chung

middle: T

last: Hoon

first: Chng

last: Joo


status: Public on Jul 21 2016

city: Stirling

first: Kevin

last: Petrie

state: Stirling

address: Stirling

department: Biological and Environmental Sciences

institute: University of Stirling

summary: Targeted interference of sin3a-tgif1 function by SID decoy treatment inhibits WNT signaling and invasion in triple negative breast cancer cells.  MDA-MB-231 cells were treated with scrambled SID control, 2.5µM SID peptide or untreated for 24h.

overall_design: Sub-confluent cultures of MDA-MB-231 cells were treated with scrambled SID control, 2.5µM SID peptide or untreated for 24h. Experiments were performed as three independent replicates.

first: Yordan

last: Sbirkov


title: Gene expression data from PNU 96415E treated human glioblastoma derived neural stem cells (GNS)

status: Public on Jul 15 2016

city: Toronto

first: Peter

last: Dirks

state: ON

address: 686 Bay Street

department: Developmental and Stem Cell

country: Canada

institute: Hospital for Sick Children

summary:
Glioblastomas grow in a rich neurochemical mileu, but targeting neurochemical signaling as a potential therapeutic avenue for these incurable tumors has been underexplored.  Thus, we probed patient derived glioblastoma stem cells with a focused library of neurochemicals, to identify new therapeutic targets.  Dopaminergic, serotonergic and cholinergic pathways were found to be active against glioblastoma. In particular, dopamine receptor D4 (DRD4) antagonists selectively inhibited glioblastoma growth in vitro and in vivo, in addition to showing synergistic effect with temozolomide.  Small molecule or genetic antagonism of DRD4 suppressed ERK1/2 signaling and impaired autophagic flux causing accumulation of autophagic vacuoles and ubiquitinated proteins, associated with G0/G1 cell cycle arrest.  These data suggest a new mechanism for treating glioblastoma through modulating dopamine DRD4 signaling.
We used Affymetrix microarrays to characterize the mechanism of action for dopamine receptor D4 antagonist (PNU 96415E) in human glioblastoma derived neural stem cells.

overall_design: We treated the human glioblastoma derived neural stem cells (GNS cells) with PNU 96415E for period of 0h, 24h and 48h and extracted RNA for hybridaization on Affymetrix microarrary (Human gene 1.0 ST array) on two GNS lines.

first: Sonam

last: Dolma


title: Chromosomal Instability and Molecular Defects in Induced Pluripotent Stem Cells with Nijmegen Breakage Syndrome

status: Public on Jul 19 2016

city: Jerusalem

first: Nissim

last: Benvenisty

state: Israel

address: Edmond Safra Campus Givat Ram

department: Genetics

country: Israel

institute: Hebrew University

summary: Nijmegen breakage syndrome (NBS) results from the absence of the NBS1 protein, responsible for detection of DNA double-strand breaks (DSBs). NBS is characterized by microcephaly, growth retardation, immunodeficiency, and cancer predisposition. Here we show successful reprogramming of NBS fibroblasts into induced pluripotent stem cells (NBS-iPSCs). Our data suggest a strong selection for karyotypically normal fibroblasts to go through the reprogramming process. NBS-iPSCs then acquire numerous chromosomal aberrations and show a delayed response to DSB induction. Furthermore, NBS-iPSCs display slower growth, mitotic inhibition, a reduced apoptotic response to stress and abnormal cell cycle-related gene expression. Importantly, NBS neural progenitor cells (NBS-NPCs) show down-regulation of neural developmental genes, which seems to be mediated by P53. Our results demonstrate the importance of NBS1 in early human development, shed new light on the molecular mechanisms underlying this severe syndrome and further expand our knowledge of the genomic stress cells experience during the reprogramming process.

overall_design: Gene expression analysis was performed on a total of 6 human cell lines, including WT and NBS Neural progenitor cells (NPCs) and NBS-iPSCs

first: Tomer

last: Halevy

first: Shira

last: Akov

first: Martina

last: Bohndorf

first: Barbara

last: Mlody

first: James

last: Adjaye

first: Michal

last: Goldberg


title: Screening and validation of lncRNAs and circRNAs as miRNA sponges

status: Public on Jul 06 2016

city: Copenhagen SV

first: Shizuka

last: Uchida

email: heart.lncrna@gmail.com, suc@dcm.aau.dk

address: Frederikskaj 10B, 2. (building C)

department: Department of Clinical Medicine

country: Denmark

institute: Aalborg University

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

platform_organism:
Homo sapiens
synthetic construct


title: Expression of Cyclic AMP associated genes on primary culture human myometrial cells

status: Public on Jul 01 2016

city: London

first: Suren

last: Sooranna

address: Du Cane Road

department: Surgery and Cancer

institute: Academic Obstetrics and Gynaecology

summary:
During pregnancy, the myometrium remains quiescent but at term, switches to a state capable of producing a series of coordinated contractions for the delivery of the fetus. Myometrial contractions of labour signify the normal physiological end-point of pregnancy but the biochemical onset of labour may occur at or before term via a series of changes in expression of labour associated genes that are responsible for controlling the activity of the uterus during pregnancy and parturition. There is increasing evidence that components of the cAMP-signalling pathway are up-regulated in the human myometrium during pregnancy to promote the relaxation of the myometrium until term. Our aim was to determine which cAMP-associated genes are important during pregnancy and parturition by exposing myometrial cells to forskolin and performing an a gene array. We then plan to study the trend of the cAMP-associated genes at different stages of gestation and during labour.
In this study, we used microarrays to elucidate forskolin responsive genes in human myometrium. These data may provide a broader view of gene networks and cellular functions regulated by forskolin in human myometrial cells. In our future study, this will also help us understand the role of cAMP in human parturition.

overall_design: Primary cultures of human myometrial cells were grown from myometrial biopsies obtained at the time of elective caesarean section at term. Cells were exposed to forskolin (100 µM) for 48 hours, and then total RNA were extracted from each culture. Two comparisons were carried out including: 1. Control 2. Forksolin

first: Angela

last: Yulia

first: Mark

last: Johnson


title: Gene expression anlaysis of laser-capture microdissected tumor and stroma from triple negative breast cancer

city: Nashville

first: Brian

middle: David

last: Lehmann

address: 2220 Pierce Ave

department: Biochemistry

institute: Vanderbilt University

summary: LCM was perfomed on adjacent tumor and stromal cells to identify differentially expressed genes in triple negative breast cancer.

overall_design: To determine differences in tumor and adjacent stromal tissue, laser-capture microdissction was perfomed on 10 triple negative breast cancer specimans to isolate tumor and stromal cells for gene expression analysis. RNA was isolated from captured cells and hybridized to affymetrix gene expression microarrays.

first: Jennifer

last: Pietenpol


title: Identification of the possible molecules by which acquired platinum resistance induces EMT-like changes in urothelial carcinoma

city: Shinjuku

first: Nobuyuki

last: Tanaka

address: 35 Shinanomachi

institute: School of Medicine, Keio University

summary: To identify the possible targets in EMT-acquisition after developing acquired platinum resistance in urothelial carcinoma (UC), we examined the changes in global gene expression before and after development of acquired platinum resistance. Comparing two types of acquired platinum resistant UC cells and their corresponding parent cells, in the end we identified 49 genes (25 up-regulated and 24 down-regulated genes) which were commonly changed in two acquired platinum resistant UC cells.

overall_design: Four invasive UC cell lines, T24, 5637, and those acquired platinum-resistant sublines T24PR and 5637PR, were used for microarrays. T24PR and 5637PR cells were newly established in our laboratory, which were grown and passaged upon reaching confluence in medium containing CDDP over a 6-month period. In preliminary studies, we found that these cell lines had an altered phenotype with morphologic and molecular changes consistent with EMT, and exhibited a marked difference in migratory potential before and after developing platinum resistance.


title: CNV anlysis of human parthenogenetic haploid ESCs (hPGES)

status: Public on Jul 13 2016

city: shanghai

first: cuiqing

last: zhong

address: yueyang road 320

country: China

institute: institute of biochemistry and cell biology

summary: The genomic DNA sample of hPGES were compared to UCSC Human genome19 by CNV data. The data confirmed that the human parthenogenetic haploid ESCs sustained normal genome integrity

overall_design: The analysis was performed on Affymetrix CytoHD to check the chromosome number variations in hPGES, and the CNV data of UCSC Human genome 19 was used as control.

first: Jinsong

last: Li


title: Identification miRNA expression profiles of human granulosa cells obtained from PCOS patients and control individuals

status: Public on Jul 14 2016

city: Ankara

first: Bala

last: Gur Dedeoglu

address: Ankara University Tandogan Campus

department: Biotechnology Institute

country: Turkey

institute: Ankara University

summary: The miRNA expression profiles of mural granulosa cells (MGCs) which were obtained from PCOS patients and control individuals were identified and compared.

overall_design: MGCs in follicular fluid were obtained from PCOS patients and control individuals during oocyte pick up for in vitro fertilization (IVF) procedure. Total RNA of MGCs was isolated with QIAzol Lysis Reagent (Qiagen). 500 ng of total RNA was labelled with FlashTag Biotin HSR RNA Labelling Kits (Affymetrix) and hybridised to Affymetrix GeneChip miRNA 3.0 array which were were washed, stained and scanned according to the manufacturer’s instructions.

first: Alp

last: Aydos


title: Microarray gene-expression profiles of 69 pancreatic tumors and 61 adjacent non-tumor tissue from patients with pancreatic ductal adenocarcinoma

city: Bethesda

first: Perwez

middle: S

last: Hussain

address: 37 Convent Drive, Building 37, Room3044B

country: USA

institute: National Cancer Institute

summary: In order to identify biologically relevant tumor markers , we  analyzed gene expression profiling of tumor and adjacent non-tumor tissues from PDAC cases. We compared the microarray gene-expression profiles of MIF-high and MIF low expressing tumors as detrmined by qRT-PCR. Affymetrix gene-expression analysis was done in two sets. Affymetrix data from sample number 1-90 were earlier submited by us as GEO accession#: GSE28735. The batch effect between the two sets of data was removed using Partek Genomic Suite and this normalized data was submitted to GEO in this submission. All the analysis was performed using the merged data set.

overall_design: We compared gene expression profile of 69 pancreatic tumor and adjacent non-tumor tissues using Affymetrix GeneChip Human Gene 1.0 ST arrays to identify microRNA targets associated with MIF signaling. Using Partek, we peformed ANOVA and Cox-regression analysis to identify differentially expressed genes that were also associated with survival. The list of genes was then subjected to pathway and biomarker analyses using Ingenuity Pathways Analysis (IPA).

first: S


title: Huh-7-Mock and Huh-7-HBV

status: Public on Jun 18 2016

city: Xuzhou

first: Fanyun

last: Kong

state: Jiangsu

address: 209 Tongshan Road

department: Department of Pathogenic Biology and Immunology

institute: Xuzhou Medical University

summary:
The expression profiling of HBV-transfected Huh-7 cells and control cells.
Hepatocellular carcinoma (HCC) is one of major malignant disease worldwide, and patients with chronic hepatitis B virus (HBV) infection have a high risk of developing HCC. Via microarray gene expression analysis, we detected the gene alteration in HBV transfected hepatoma cells.

overall_design: To investigate the role of HBV on gene alteration of hepatoma cells, the pUC18-HBV1.2 plasmid and control plasmid were transfected into Huh-7 cells (named as Huh-7-HBV and Huh-7-Mock). After 48 hours, the total RNA was extracted and gene expression profiling of both HBV transfected cells and control cells were carried out on Affymetrix GeneChip Human Gene 1.0 ST array.

first: Renxian

last: Tang


title: Gene expression profiling of MDA-MB-468 cells following p53-R273H mutant knock-down

status: Public on Jun 30 2016

city: Bukit Jalil

first: Chee-Onn

last: Leong

country: Malaysia

institute: International Medical University

summary: A total of 58 genes were up-regulated (> 1.5 fold-change) while 117 genes were down-regulated

overall_design: Microarray experiments were performed in duplicate as follows: MDA-MB-468 cells were transduced with lentiviral shRNA targeting endogenous p53-R273H mutant (p53si-1)or a non-targeting shRNA (NS). Total RNA from cells was extracted using Qiagen RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturers’ protocol. RNA purity was examined by spectrophotometric determination at 260/280 nm. The microarray hybridizations were carried out using the Affymetrix Human Gene 1.0 ST arrays.


title: Gene expression profile of HGPS skin fibroblasts upon treatment with JH4

status: Public on Jul 08 2016

city: BUSAN

first: Bum-Joon

last: Park

address: Busandaehak-ro 63

department: Molecular Biology

country: South Korea

institute: Pusan National University

summary:
To gain further insight into the biological effects of JH4, we investigated its impact on gene expression profiles.
We defined a set of genes such as IL33, BRCA1, BLM, Rad51, IL6, IL8, and TNFSF18 whose expression is restored by JH4 treatment

overall_design: 4 total RNA samples from HGPS, JH4-treated HGPS, young (9-yr; N9) and old (81-yr; N81) fibroblasts are anlayzed. Young fibroblast (9-yr) was used control

first: Su-Jin

last: Lee

first: Ah-Young

last: Oh


title: Expression profiling of skin fibroblast, iPSC, iPSC-derived neural progenitors, and iPSC-derived neurons from Autism Spectrum Disorder male patients and their unaffected normal male siblings

first: Owen

last: Rennert

address: 10 Center Drive, MSC 1255, Building 10, Room 1C-250

department: NICHD

institute: National Institutes of Health

summary: Autism spectrum disorder (ASD) is an early onset neurodevelopmental disorder, which is characterized by disturbances of brain function and behavioral deficits in core areas of impaired reciprocal socialization, impairment in communication skills, and repetitive or restrictive interests and behaviors. ASD is known to have a significant genetic risk, but the underlying genetic variation can be attributed to hundreds of genes. The molecular and pathophysiologic basis of ASD remains elusive because of its genetic heterogeneity and complexity, its high comorbidity with other diseases, and the paucity of brain tissue for study. The invasive nature of collecting primary neuronal tissue from patients might be circumvented through reprogramming peripheral cells to induced pluripotent stem cells (iPSCs), which are able to generate live neurons carrying the genetic variants of disease. This breakthrough allows us to access the cellular and molecular phenotypes of patients with ‘intrinsic autism’, that is patients without known genetic disorders or identifiable syndromes or malformations. To do this, we studied a relatively homogeneous patient population of boys with intrinsic autism by excluding patients with known genetic disease or recognizable phenotypes or syndromes, as well as those with profound mental retardation or primary seizure disorders. We generated iPSCs from patients with intrinsic autism, their unaffected male siblings and age-, and sex-matched unaffected controls. And these stem cells were subsequently differentiated into electrophysiologically active neurons. The expression profile for autistic and their unaffected siblings' iPSC-derived neurons were compared. A distinct expression profile was found between autism and sib control. The significantly differentially expressed genes (> 2-fold, FDR < 0.05) in autistic iPSC-derived neurons were significantly enriched for processes related to synaptic transmission, such as neuroactive ligand-receptor signaling and extracellular matrix interactions (FDR < 0.05), and were significantly enriched for genes previously associated with ASD (p < 0.05). Our findings suggest approaches such as iPSC-derived neurons will be an important method to obtain tissue for study that appropriately recapitulates the complex dynamics of an autistic neural cell.

overall_design: We generated induced pluripotent stem cells (iPSCs) from male patients with intrinsic autism, their unaffected male siblings, and age-, and sex-matched unaffected controls. And these stem cells were subsequently differentiated into electrophysiologically active neurons following 80 days of post-mitotic neural differentiation. These samples, including fibroblast, iPSC, iPSC-derived neural progenitors (NPC) and iPSC-derived neurons, were analyzed for the change of gene expression profile by whole genome microarray.

first: Xiaozhuo

last: Liu

first: Lucile

last: Thouennon

first: Hoi

last: Cheung


title: Generation of clinical grade CD19-specific CAR-modified CD8+ memory stem cells for the treatment of B-cell malignancies

status: Public on Jun 29 2016

first: Luca

last: Gattinoni

address: 9000 Rockville Pike

department: Experimental Transplantation and Immunology Branch

institute: NCI - National Cancer Institute

summary: Long-lived, self-renewing, multipotent T memory stem cells (TSCM) can trigger profound and sustained tumor regression but their rareness poses a major hurdle to their clinical application. Presently, clinically compliant procedures to generate relevant numbers of this T cell population are undefined. Here, we provide a strategy for deriving large numbers of clinical grade tumor-redirected TSCM cells starting from naïve precursors. CD8+CD62L+CD45RA+ naïve T cells enriched by streptamer-based serial positive selection were activated by CD3/CD28 engagement in the presence of IL-7, IL-21 and the glycogen synthase-3β inhibitor TWS119, and genetically engineered to express a CD19-specific chimeric antigen receptor (CD19-CAR). These conditions allowed for the generation of CD19-CAR modified TSCM cells that were phenotypically, functionally and transcriptomically equivalent to their naturally occurring counterpart. Compared with T cell products currently under clinical investigation, CD19-CAR modified TSCM cells exhibit enhanced metabolic fitness, persistence and anti-tumor activity against systemic acute lymphoblastic leukemia xenografts. Based on these findings, we have initiated a phase 1 clinical study to evaluate the activity of CD19-CAR modified TSCM in patients with B-cell malignancies refractory to prior allogeneic hematopoietic stem cell transplantation.

overall_design: Three healthy human blood donors provided lymphocyte-enriched apheresis blood for this study after informed consent. From all samples, total RNA was isolated using an miRNeasy Mini Kit (Qiagen), processed by Ambion’s WT expression kit, fragmented and labeled with a WT Terminal Labeling Kit (Affymetrix), hybridized to WT Human Gene 1.0 ST arrays (Affymetrix) and stained on a Genechip Fluidics Station 450 (Affymetrix), all according to the respective manufacturer's instructions. Samples represent exon-level and gene-level analyses.

first: Marianna

last: Sabatino

first: Jinhui

last: Hu

first: Michele

last: Sommariva

first: Sanjivan

last: Gautam

first: Vicki

last: Fellowes

first: Sean

last: Dougherty

first: Haiying

last: Qin

first: Carl

middle: H

last: June

first: Terry

last: Fry

first: Ronald

middle: E

last: Gress

first: James

last: Kochenderfer

first: Lothar

last: Germeroth

first: David

last: Stroncek

first: Yun

last: Ji


title: TUMOR INITIATING CELLS AND IGF/FGF SIGNALING CONTRIBUTE TO SORAFENIB RESISTANCE IN HEPATOCELLULAR CARCINOMA

status: Public on Jun 16 2016

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

institute: CIBEREHD

summary: OBJECTIVE: Sorafenib is effective in hepatocellular carcinoma (HCC), but patients ultimately present disease progression. Molecular mechanisms underlying acquired resistance are still unknown. Herein, we characterize the role of tumor-initiating cells (T-ICs) and signaling pathways involved in sorafenib resistance. DESIGN: HCC xenograft mice treated with sorafenib (n=22) were explored for responsiveness (n=5) and acquired resistance (n=17). Mechanism of acquired resistance were assessed by: 1) Role of T-ICs by in vitro sphere formation and in vivo tumorigenesis assays using NOD/SCID mice, 2) Activation of alternative signaling pathways and 3) Efficacy of anti-FGF and anti-IGF drugs in experimental models. Gene expression (microarray, qRT-PCR) and protein analyses (immunohistochemistry, western blot) were conducted. A novel gene signature of sorafenib resistance was generated and tested in 2 independent cohorts. RESULTS: Sorafenib-acquired resistance tumors showed significant enrichment of T-ICs (164 cells needed to create a tumor) vs. sorafenib-sensitive tumors (13400 cells) and non-treated tumors (1292 cells), p<0.001. Tumors with sorafenib-acquired resistance were enriched with IGF and FGF signaling cascades (FDR<0.05). In vitro, cells derived from sorafenib-acquired resistant tumors and two sorafenib-resistant HCC cell lines were responsive to IGF or FGF inhibition. In vivo, FGF blockade delayed tumor growth and improved survival in sorafenib-resistant tumors. A sorafenib-resistance 175-gene signature was characterized by enrichment of progenitor-cell features, aggressive tumoral traits and predicted poor survival in 2 cohorts (n=442 HCC patients). CONCLUSION: Acquired resistance to sorafenib is driven by tumor initiating cells with enrichment of progenitor markers and activation of IGF and FGF signaling. Inhibition of these pathways would benefit a subset of patients after sorafenib progression.

overall_design: Transcriptomic profile of subcutaneous Huh7 cells-derived tumors treated with sorafenib that developed acquired resistance to the drug (n=4), remain responsive to sorafenib (n=3) or were treated with brivanib after development of resistance (n=3). Gene profiling of hepatospheres generated from tumors with acquired resistance to sorafenib (n=3) and non-treated tumors (n=3) was also analyzed.

first: V

last: Tovar

first: H

last: Cornella

first: A

last: Moeini

first: S

last: Vidal

first: Y

last: Hoshida

first: D

last: Sia

first: J

last: Peix

first: L

last: Cabellos

first: C

last: Alsinet

last: Torrecilla

first: I

last: Martinez-Quetgas

last: Desbois-Mouthon

first: M

last: Solé

last: Domingo-Domenech

last: Villanueva

last: Llovet


title: Screening and validation of lncRNAs and circRNAs as miRNA sponges [siRNA, HuGene-1_0-st]

first: Shizuka

last: Uchida

summary: Intensive research in past two decades has uncovered the presence and importance of noncoding RNAs (ncRNAs), which includes microRNAs (miRs) and long ncRNAs (lncRNAs). These two classes of ncRNAs interact to a certain extent, as some lncRNAs bind to miRs to sequester them. Such lncRNAs are collectively called 'competing endogenous RNAs' or 'miRNA sponges'. In this study, we screened for lncRNAs that may act as miRNA sponges using the publicly available data sets and databases. To uncover the roles of miRNA sponges, loss-of-function experiments were conducted, which revealed the biological roles as miRNA sponges. LINC00324 is important for the cell survival by binding to miR-615-5p leading to the de-repression of its target BTG2 LOC400043 controls several biological functions via sequestering miR-28-3p and miR-96-5p, thereby changing the expressions of transcriptional regulators. Finally, we also screened for circular RNAs (circRNAs) that may function as miRNA sponges. The results were negative at least for the selected circRNAs in this study. In conclusion, miRNA sponges can be identified by applying a series of bioinformatics techniques and validated with biological experiments.

overall_design: Using HEK-293 cells, we performed microarray experiments (n=2) for siRNA-mediated silencing of LINC00324 and LOC40043.

first: Giuseppe

last: Militello


title: Gene expression profiling reveals novel protective effects of Aminaphtone on ECV304 endothelial cells

status: Public on Jun 14 2016

city: Milano

first: Gualtiero

middle: Ivanoe

last: Colombo

address: Via Carlo Parea, 4

institute: Centro Cardiologico Monzino IRCCS

summary:
Aminaphtone, a drug used in the treatment of chronic venous insufficiency (CVI), showed a remarkable role in the modulation of several vasoactive factors, like endothelin-1 and adhesion molecules. We analysed in vitro the effects of Aminaphtone on whole-genome gene expression. ECV304 endothelial cells were stimulated with IL-1β 100 U/ml in the presence or absence of Aminaphtone 6 μg/ml. Gene expression profiles were compared at 1, 3, and 6 h after stimulation by microarray.
Microarrays showed a significant down-regulation at all times of a wide range of inflammatory genes. Aminaphtone appeared also able to modulate the regulation of immune response process (down-regulating cytokine biosynthesis, transcripts involved in lymphocyte differentiation and cell proliferation, and cytokine-cytokine receptor interaction) and to regulate genes engaged in homeostasis, secretion, body fluid levels, response to hypoxia, cell division, and cell-to-cell communication and signalling.

overall_design: Confluent ECV304 cells were incubated for 1, 3, and 6 h with recombinant interleukin-1β (IL-1β; Sigma-Aldrich) 100 IU/ml in the presence of Aminaphtone 6 μg/ml (treatment group) or an equal volume of medium alone (control group). All experiments were performed in three independent replicates for each time point. Total RNA was extracted and gene expression analysis was performed at all time points by Affymetrix GeneChip Human Gene 1.0 ST Arrays.

first: Giulia

last: Salazar

first: Katia

last: Todoerti


title: RNA profiling in metastatic colorectal cancer patients treated first-line with oxaliplatin

status: Public on Jun 09 2016

city: Aarhus

first: mads

middle: heilskov

last: rasmussen

state: Please Select

address: Brendstrupgårdsvej 21

institute: Aarhus University Hospital

summary: Oxaliplatin (oxPt) resistance in colorectal cancers (CRC) is a major medical problem, and predictive markers are urgently needed. Recently, miR-625-3p was reported as a promising predictive marker. Here, we have used in vitro models to show that miR-625-3p functionally induces oxPt resistance in CRC cells, and have identified signalling networks affected by miR-625-3p. The p38 MAPK activator MAP2K6 was shown to be a direct target of miR-625-3p, and, accordingly, was downregulated in patients not responding to oxPt therapy. miR-625-3p resistance could be reversed in CRC cells by anti-miR-625-3p treatment and by ectopic expression of a miR-625-3p insensitive MAP2K6 variant. In addition, by reducing p38 MAPK signalling using either siRNA technology, chemical inhibitors to p38 or by ectopic expression of dominant negative MAP2K6 protein we induced resistance to oxPt. Transcriptome, proteome and phosphoproteome profiles revealed inactivation of MAP2K6-p38 signalling as one likely mechanism a possible driving force behind of oxPt resistance.   Our study shows that miR-625-3p induces oxPt resistance by abrogating MAP2K6-p38 regulated apoptosis and cell cycle control networks, and corroborates the predictive power of miR-625-3p

overall_design: Cancer and normal epithelium cells were obtained by laser-microdissection from biopsies from first line oxaliplatin treated metastatic colorectal cancer patients.

first: Mads

last: Rasmussen

first: Iben

last: Lyskjær

first: Claus

middle: L

last: Andersen


title: Effect of Angiotensin Converting Enzyme Inhibitor or Angiotensin Receptor Blocker Exposure on Intragraft Gene Expression of Kidney Transplant Patients

status: Public on Jun 10 2016

city: Bronx

first: Pilib

last: Ó Broin

state: NY

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

summary:
Treatment with angiotensin converting enzyme inhibitors (ACEI) or angiotensin receptor blockers (ARB) has been shown to have anti-inflammatory effects such as decreased growth factors and cytokines in animal models, this effect however, has not been investigated in kidney transplant recipients.  We aimed to study the effect of ACEI or ARB treatment on intragraft gene expression profiles of transplant kidney biopsies using microarrays.
Both groups had similar demographic characteristics in terms of age, race, sex, type of transplant, previous history of transplantation or acute rejection, panel reactive antibody levels, and immunosuppressive treatment. There were no differences in acute and chronic Banff allograft injury scores between the 2 Groups. Intragraft gene expression profiles of ACEI or ARB treated Group 2 biopsies showed decreased gene transcripts of interferon-gamma and rejection-associated transcripts (GRIT) and constitutive macrophage-associated transcripts (CMAT) compared to Group 1 biopsies. There were no statistically significant differences in expression of cytotoxic T cell (CAT), regulatory T cell (TREG), B-cell (BAT), natural killer cell (NKAT), or endothelial cell-associated transcripts (ENDAT) between the 2 Groups.  Our data suggest that exposure to ACEI or ARB was associated with down-regulation of GRIT and CMAT. This anti-inflammatory effect of ACEI or ARB treatment could be an additional benefit in kidney transplant recipients.

overall_design: We identified 29 near normal biopsies with chronic sum allograft injury score (ct+ci+cv)  ≤ 3 for gene expression profiling comparing 2 groups; Group 1 (n=16), patients with no exposure of ACEI or ARB treatment and Group 2 patients (n=13) with exposure to ACEI or ARB at least 6 months prior to kidney biopsy.  Biopsies with a diagnosis of acute or chronic rejection, recurrent or de novo glomerular disease, or polyoma nephropathy were excluded.

first: Enver

last: Akalin


title: Expression data from Sertoli cells treated with 0.1μM NP, 0.1mM MBP, 0.1μM NP+0.1mM MBP and solvent control

city: Shanghai

first: Xiaoqin

last: Yin

state: Shanghai

address: No. 355 Luding Road, Shanghai 200062, P.R.China.

department: Shanghai Children’s Hospital

institute: School of medicine, Shanghai Jiao Tong University

summary:
The combined effects of NP and MBP were much more toxic than NP or MBP exposed alone.
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes and miRNAs after treated with 0.1μM NP, 0.1mM MBP, 0.1μM NP+0.1mM MBP and solvent control.

platform_organism:
Rattus norvegicus
synthetic construct

overall_design: Rat Sertoli cell were selected from rat testis for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain the differentially expressed genes and miRNAs in 0.1μM NP, 0.1mM MBP, 0.1μM NP+0.1mM MBP and solvent control treated Sertoli cells, respectively.

first: Dongmei

last: Li

first: Yang

last: Hu


title: Affymetrix Cytoscan HD Array Data for a patient with Partial Androgen Insensitivity Syndrome and Recto Sigmoid Cancer: a family study

status: Public on Jun 05 2016

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

summary: The present study was carried out on a proband affected by Partial Androgen Insensitivity Syndrome (PAIS) and his family. The patient developed the primary RSC at 27 years. Three years after primary surgery, the patient developed a second primary (metachronous) rectal cancer relapsed one year later. The PAIS was also diagnosed in his cousin. Both cousins were found positive for the same missense androgen receptor (AR) gene mutation that was inherited from their asymptomatic mothers. The aim of this study was to identify constitutional genetic events that could have played a role in early onset of RSC in the proband. SNP-array analyses were carried out to investigate Copy Number Variations and Uniparental Disomy events as possible genetic causes linked to Colorectal Cancer pathogenesis.

overall_design: Affymetrix CytoScan HD arrays were performed according to the manufacturer's directions on DNA extracted from peripheral blood samples of the proband (BT53I) and his relatives members (Father: CH92, Mother: CH90; Ount: CH91; Cousin: CH94). The secondary RSC tissue of the proband (BT56) was also analyzed using the same platform. Data were analyzed using Chromosome Analysis Suite 2.0 (Affymetrix).

first: Vittoria

last: Disciglio


title: Identification of a novel PPARβ/δ / miR-21-3p axis in UV-induced skin inflammation [human mRNA]

status: Public on Jun 03 2016

city: Lausanne

first: Mark

last: Ibberson

address: Genopode building

department: Vital-IT

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

summary: Although excessive exposure to UV is widely recognized as a major factor leading to skin perturbations and cancer, the complex mechanisms underlying inflammatory skin disorders resulting from UV exposure remain incompletely characterized. The nuclear hormone receptor PPARβ/δ is known to control cutaneous repair and UV-induced cancer development. Here, we describe a novel PPARβ/δ-dependent molecular cascade involving TGFβ-1 and miR-21-3p, which is activated in the epidermis in response to UV exposure. We establish that the passenger miRNA miR-21-3p, that we identify as a novel UV-induced miRNA in the epidermis, plays a pro-inflammatory function in keratinocytes, and that its high level of expression in human skin is associated with psoriasis and squamous cell carcinomas. Finally, we provide evidence that inhibition of miR-21-3p reduces UV-induced cutaneous inflammation in ex vivo human skin biopsies, thereby underlining the clinical relevance of miRNA-based topical therapies for cutaneous disorders.

overall_design: 6 samples from human immortalized keratinocytes HaCaT: 3 miR-21-3p mimic-overexpressing samples; 3 control samples

first: Liliane

last: Michalik

first: Ilenia

last: D'Errico


title: Patient-derived xenografts from pediatric liver cancer predict tumor recurrence and advise clinical management

city: Badalona

first: Carolina

last: Armengol

state: Barcelona

address: C/ Canyet, Camí de les Escoles, s/n

institute: Health Siences Research Institute Germans Trias i Pujol

summary: Identification of new treatments for relapsing pediatric cancer is an unmet clinical need and a societal challenge. Liver cancer occurrence in infancy, 1.5 for million children per year, falls far below the threshold of interest for the development of dedicated drug development programs, and this disease is too rare and heterogeneous to gather enough children into a clinical trial. Here, we present the establishment of an unprecedented preclinical platform of 24 pediatric liver cancer patient-derived xenografts (PLC-PDXs) from 20 hepatoblastomas, 1 transitional liver cancer tumor, 1 hepatocellular carcinoma and two rhabdoid tumors. SNP array and mutational analysis of the parental tumors and the corresponding PLC-PDXs show high conservation of the molecular features of the parental tumors. The histology of PLC-PDXs is strikingly similar to that observed in primary tumors, and recapitulates well the heterogeneity of recurrent disease observed in the clinic. Tumor growth in the mouse is strongly associated with elevated circulating alpha-fetoprotein (AFP), low rate of necrosis/fibrosis after treatment and gain of chromosome 20, all indicators of resistance to chemotherapy and poor outcome. Accordingly, the ability of a tumor to generate PLC-PDX is predictive of poor prognosis. Exposure of PLC-PDXs to standards of care or therapeutic options already in use for other pediatric malignancies revealed unique response profiles in these models. Among these combinations, irinotecan/temozolomide induced strong tumor regression in the transitional liver cancer tumor model and on a model derived from AFP-negative relapsing HB. These results provide promising evidence that this preclinical platform can strongly contribute to accelerate the identification and diversification of anti-cancer treatment for aggressive subtypes of pediatric liver cancer.

overall_design: We analyzed CN of 8 primary tumors and 2 recurrence and their PLC-PDXs (Pediatric Liver Cancer-Patient Derived Xenografts) from 9 patients.

first: Marina

last: Simon-Coma

first: Mar

last: Mallo


title: Identification of a new gene regulatory circuit involving B cell receptor activated signaling using a combined analysis of experimental, clinical and global gene expression data [timeSeries]

status: Public on Jun 07 2016

city: Regensburg

first: Christian

last: Kohler

state: Bavaria

address: Am BioPark 9

department: Institute of Functional Genomics

institute: University of Regensburg

summary: To discover new essential regulatory pathways in B lymphoma cells a combined analysis of experimental and clinical high throughput data was performed. Among others, a specific cluster of coherently expressed genes named BCR.1 was identified in primary lymphoma samples. These coherently expressed genes are suppressed by α-IgM treatment of lymphoma cells in vitro. This B cell receptor activation leads to a G2 phase prolongation, delayed entry into the M phase, an overall diminished capacity of the cells to enter into mitosis and defects in metaphases. Cytogenetic changes are detected under long term α-IgM treatment. Furthermore, an inverse correlation of BCR.1 genes with c-Myc coregulated genes in distinct groups of lymphoma patients is observed. In addition to the impact of c-Myc in the regulation of cell cycle regulators, BCR.1 genes are regulated by a combined action of IKK2, MAPK14 and JNK. Finally, the BCR.1 index discriminates activated B cell like and germinal centre B cell like diffuse large B cell lymphoma. Therefore, a new regulatory circuit is described affecting cell cycle and chromosome instability in B cells.

overall_design: 33 BL2 cell samples were hybridized to HuGene-1_0-st-v1 Affymetrix GeneChips.

first: Alexandra

last: Schrader

first: Katharina

last: Meyer

first: Neele

last: Walther

first: Ailine

last: Stolz

first: Maren

last: Schmidt

first: Elisabeth

last: Hand

first: Frederike

last: von Bonin

first: Maurits

last: Evers

first: Katayoon

last: Shirneshan

first: Martina

last: Vockerodt

first: Wolfram

last: Klapper

first: Monika

last: Szczepanowski

first: Paul

middle: G

last: Murray

first: Holger

last: Bastians

first: Lorenz

last: Trümper

first: Rainer

last: Spang

first: Dieter

last: Kube


title: Macrophage heterogeneity in human carotid artery atherosclerotic plaques: identification of novel markers for M1 and M2 that are independent of the activation status

status: Public on Jun 01 2016

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary:
Recent studies suggest the presence of both “classically activated” M1 and “alternatively activated” M2 macrophages in human atherosclerotic tissue, yet due to the lack of validated markers the reported localization patterns of these macrophage phenotypes within plaques are ambiguous. In the present study, we searched for  markers that indisputably can identify differentiated M1 and M2 macrophages independently of stimuli that affect the activation status of the two subpopulations. We used these validated markers to assess the presence of M1 and M2 macrophages in different zones of human carotid artery atherosclerotic plaques obtained from 12 patients. Using microarray and qPCR technology we show that the frequently used macrophage subpopulation markers MCP-1 and CD206 do not discriminate between M1 and M2 macrophages. However, we confirm the subtype specificity of the classical M2 marker CD163 and we report that the genes INHBA and DSP (both M1) and SEPP1 and MARCKS (both M2) are highly suitable for macrophage phenotyping. mRNA expression of the pan-macrophage marker CD68 in the shoulder zones of the plaques and in adjacent tissue segments correlated positively with mRNA expression levels of SEPP1, MARCKS and CD163 (r=0.86, 0.94 and 0.96, and r= 0.86, 0.98 and 0.69, respectively) but not with the expression of the M1 markers DSP and INHBA. In contrast, mRNA expression of CD68 in the core of the plaques correlated positively with expression of DSP and INHBA (r=0.73 and 0.49) but not with SEPP1, MARCKS and CD163. These findings suggest that M1 macrophages predominate in the core of human carotid atherosclerotic plaques while M2 macrophages prevail at the periphery of the plaque.

Keywords: Expression profiling by array

overall_design: Monocytes from healthy volunteers were differentiated into M1 and M2 macrophages by incubation with granulocyte-macrophage colony-stimulating factor (GM-CSF) or macrophage colony-stimulating factor (M-CSF), respectively. After 5 days cells were exposed to oxidized LDL. Total RNA was isolated and subjected to gene expression profiling.

first: L

last: van Tits

first: R

last: Stienstra

first: M

last: Netea

first: J

middle: A

last: Pol

last: Truijers

last: van der Vliet

first: G

last: Joosten

first: A

middle: F

last: Stalenhoef


title: Identification of a new gene regulatory circuit involving B cell receptor activated signaling using a combined analysis of experimental, clinical and global gene expression data

first: Christian

last: Kohler

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

overall_design: Refer to individual Series


title: Transcriptome data of multiple sclerosis patients receiving fingolimod therapy [HTA-2_0, CD56+ cells, exon level]

status: Public on May 20 2016

city: Rostock

first: Michael

last: Hecker

address: Gehlsheimer Str. 20

department: Department of Neurology

institute: University of Rostock

summary:
We analyzed the gene expression patterns of different blood cell types before and during fingolimod treatment in a group of patients with relapsing-remitting multiple sclerosis (RRMS).
Affymetrix Human Transcriptome Arrays (HTA) 2.0 were used to obtain gene expression profiles of immune cell populations from 10 RRMS patients within the first 3 months of fingolimod treatment.
This GEO entry provides the Affymetrix HTA 2.0 microarray data of peripheral blood CD56+ cells, preprocessed according to the exon level workflow.

overall_design:
EDTA blood samples were taken from all patients immediately before first and second fingolimod administration as well as after 3 months of therapy.
Total RNA of CD56+ cells positively selected from each blood sample was extracted, labeled and hybridized to high-density Affymetrix HTA 2.0 microarrays to quantify the transcript levels.

first: Dirk

last: Koczan

first: Uwe

middle: K

last: Zettl


title: Effects of enhanced external counterpulsation on skeletal muscle gene expression in patients with severe heart failure

city: Stockholm

first: Eric

last: Rullman

address: C1:82 Karolinska University Hospital, Huddinge

department: Laboratory Medicine

country: Sweden

institute: Karolinska Institutet

summary:
Male patients (n=6, mean age 62 years) with NYHA III-IV and an left ventricular ejection fraction of <35% despite pharmacological therapy received 35 hours of enhanced external counterpulsation (EECP) over a period of 7 weeks.
Before and after treatment, lateral vastus muscle biopsies were obtained and skeletal muscle gene expression was evaluated using the Affymetrix HuGene 1.0 platform.

overall_design: Skeletal muscle gene expression before and after treatment with enhanced external counterpulsation for 7 weeks in 6 male patients with severe heart failure


title: Transcriptome data of multiple sclerosis patients receiving fingolimod therapy [HTA-2_0, CD19+ cells, exon level]

summary:
We analyzed the gene expression patterns of different blood cell types before and during fingolimod treatment in a group of patients with relapsing-remitting multiple sclerosis (RRMS).
Affymetrix Human Transcriptome Arrays (HTA) 2.0 were used to obtain gene expression profiles of immune cell populations from 10 RRMS patients within the first 3 months of fingolimod treatment.
This GEO entry provides the Affymetrix HTA 2.0 microarray data of peripheral blood CD19+ cells, preprocessed according to the exon level workflow.

overall_design:
EDTA blood samples were taken from all patients immediately before first and second fingolimod administration as well as after 3 months of therapy.
Total RNA of CD19+ cells positively selected from each blood sample was extracted, labeled and hybridized to high-density Affymetrix HTA 2.0 microarrays to quantify the transcript levels.


title: Transcriptome data of multiple sclerosis patients receiving fingolimod therapy [HTA-2_0, CD14+ cells, exon level]

summary:
We analyzed the gene expression patterns of different blood cell types before and during fingolimod treatment in a group of patients with relapsing-remitting multiple sclerosis (RRMS).
Affymetrix Human Transcriptome Arrays (HTA) 2.0 were used to obtain gene expression profiles of immune cell populations from 10 RRMS patients within the first 3 months of fingolimod treatment.
This GEO entry provides the Affymetrix HTA 2.0 microarray data of peripheral blood CD14+ cells, preprocessed according to the exon level workflow.

overall_design:
EDTA blood samples were taken from all patients immediately before first and second fingolimod administration as well as after 3 months of therapy.
Total RNA of CD14+ cells positively selected from each blood sample was extracted, labeled and hybridized to high-density Affymetrix HTA 2.0 microarrays to quantify the transcript levels.


title: Expression data of human tympanic membrane cells and epidermal keratinocytes [miRNA]

status: Public on May 31 2016

city: Lorenskog

first: Peder

last: Aabel

address: Sykehusvn. 27

department: ENT

country: Norway

institute: Akershus University Hospital

summary:
The data set compares the microRNA expression of two types of keratinocytes from the tympanic membrane and epidermis of the body. Healthy human samples were harvested for the analysis.
Cells were cultivated to evaluate the effect of keratinocytes only. Few Chip Ids (11) were considered differentially expressed between the cell types.

overall_design: Six samples were analyzed in total. Each cell type in biological triplicates. Genes of p-value <0.05 and fold change of ≥ 1.5 were considered significant.

first: Magnus

last: von Unge

first: Ole

last: Olstad


title: EFFECT OF A NOVEL PROBIOTIC PREPARATION ON INDUCTION AND MAINTENANCE OF REMISSION IN ULCERATIVE COLITIS PATIENTS: A DOUBLE-BLIND PLACEBO CONTROLLED TRIAL

status: Public on May 24 2016

city: Leuven

first: Ingrid

last: Arijs

address: Herestraat 49

department: Clinical and Experimental Medicine

country: Belgium

institute: KULeuven

summary: This study investigated the effect of a novel probiotic preparation on the colonic mucosal gene expression in UC patients, using whole genome gene expression microarrays.

overall_design: Total RNA, extracted from endoscopically-derived colonic mucosal biopsies from (in-)active UC patients before and after probiotics/placebo intake, was used to analyze the mRNA expression via Affymetrix Human Gene 1.0 ST arrays

first: Vicky

last: De Preter

first: Bruno

last: Pot

first: Henrike

last: Hamer

first: Leentje

last: Van Lommel

first: Frans

last: Schuit

first: Geert

last: Huys

first: Paul

last: Rutgeerts

first: Kristin

last: Verbeke


title: Inhibition of Hedgehog signaling in human osteoarthritic cartilage

city: toronto

first: benjamin

last: alman

state: ontario

address: 555 university avenue

department: Developmental and stem cell biology

institute: Hospital for Sick Children

summary:
Osteoarthritis (OA) is a common degenerative disease of the joint. Data from our lab indicates that Hedgehog (Hh) signaling is activated in human OA and murine models of OA (Lin et al., 2009, Nature Medicine). To identify Hh target genes, microarray analyses were performed to detect changes in gene expression when the Hh pathway was inhibited in human OA cartilage samples.
Identifying Hh target genes in chondrocytes will elucidate key regulatory networks that govern chondrocyte homeostasis and provide novel therapeutic strategies for OA.

overall_design: Articular cartilage from each sample was divided into two groups, one kept as control, one treated with a chemical Hh antagonist. Three biological replicates were used.

first: Shabana

last: Ali

first: Benjamin

last: Alman


title: Genome-wide transcriptomic analysis of hepatocyte-like cells upon ectopic miR-146a-5p expression

status: Public on May 09 2016

city: Strasbourg

first: Mirjam

middle: B.

last: Zeisel

address: 3, rue Koeberlé

country: France

institute: Inserm

summary:
Hepatitis C virus (HCV)-induced chronic liver disease is one of the leading causes of hepatocellular carcinoma (HCC). However, the molecular mechanisms underlying HCC development following chronic HCV infection remain poorly understood. MicroRNAs (miRNAs) play an important role in cellular homeostasis within the liver and deregulation of the miRNome has been associated with liver disease including HCC. While host miRNAs are essential for HCV replication, viral infection in turn appears to induce alterations of intrahepatic miRNA networks. Although the cross-talk between HCV and liver cell miRNAs most likely contributes to liver disease pathogenesis, the functional involvement of miRNAs in HCV-driven hepatocyte injury and HCC remains elusive. Here, we combined a hepatocyte-like based model system, high-throughput small RNA-sequencing, computational analysis and functional studies to investigate HCV-miRNA interactions that may contribute to liver disease and HCC. Profiling analyses indicated that HCV infection differentially regulated the expression of 72 miRNAs by at least two-fold including miRNAs that were previously described to target genes associated with inflammation, fibrosis and cancer development. Further investigation demonstrated that miR-146a-5p was consistently increased in HCV-infected hepatocyte-like cells and primary human hepatocytes as well as in liver tissues from HCV-infected patients. Genome-wide microarray and computational analyses indicated that miR-146a-5p over-expression is related to liver disease and HCC development. Furthermore, we showed that miR-146a-5p positively impacts on late steps of the viral replication cycle thereby increasing HCV infection. Collectively, our data indicate that the HCV-induced increase in miR-146a-5p expression both promotes viral infection and is relevant for pathogenesis of liver disease.
To explore the functional relevance of miR-146a-5p up-regulation, we performed a genome-wide transcriptomic analysis of hepatocyte-like cells upon ectopic miR-146a-5p expression.

overall_design: Hepatocyte-like cells (differentiated Huh7.5.1 cells) were reverse transfected with miR-146a-5p mimic (5 nM, Sigma-Aldrich; three samples) or non-targeting control (5 nM, GE Dharmacon; three samples) using RNAiMax reagent according to the manufacturer's instructions (Life Technologies). Seventy-two hours post-transfection, total RNA was extracted and subjected to genome-wide mRNA profiling using GeneChip Gene 1.0 ST array (Affymetrix TSA) at the IGBMC Microarray and Sequencing Platform (Illkirch, France).

first: Simonetta

last: Bandiera

first: Sophie

last: Pernot

first: Hussein

last: El Saghire

first: Sarah

middle: C

last: Durand

first: Christine

last: Thumann

first: Emilie

last: Crouchet

first: Tao

last: Ye

first: Isabel

last: Fofana

first: Jochen

last: Barths

first: Catherine

last: Schuster

first: Patrick

last: Pessaux

first: Markus

last: Heim

first: Thomas

last: Baumert

middle: B


title: Distinct Gene Regulatory Pathways for Human Innate Versus Adaptive Lymphoid Cells [gene expression]

status: Public on May 13 2016

city: Saint Louis

first: Eugene

middle: M

last: Oltz

state: Missouri

address: 660 Euclid Ave, Campus Box 8118

department: Pathology & Immumonolgy

institute: Washington University in St Louis

summary: Innate lymphoid cells (ILCs) serve as sentinels in mucosal tissues, sensing release of soluble inflammatory mediators, rapidly communicating danger via cytokine secretion, and functioning as guardians of tissue homeostasis. Although ILCs have been studied extensively in model organisms, little is known about these “first responders” in humans, especially their lineage and functional kinships to cytokine-secreting T helper cell (Th) counterparts. Here, we report gene regulatory circuitries for four human ILC–Th counterparts derived from mucosal environments, revealing that each ILC subset diverges as a distinct lineage from Th and circulating natural killer cells, but shares circuitry devoted to functional polarization with their Th counterparts. Super-enhancers demarcate cohorts of cell identity genes in each lineage, uncovering new modes of regulation for signature cytokines, novel molecules that likely impart important functions to ILCs, and potential mechanisms for autoimmune disease SNP associations within ILC–Th subsets.

overall_design: RNA was isolated from two to five replicates of ILC1, ILC3, Th1, Th2 and NK cells. Gene expression levels were determined using Affymetrix Human Gene 1.0 ST arrays.

first: Marco

last: Colonna

first: Olivia

middle: I

last: Koues

first: Marina

last: Cella


title: Nucleosome positioning changes during human embryonic stem cell differentiation.

status: Public on May 16 2016

city: Athens

first: wenjuan

last: zhang

state: GA

address: 120 Green street, Life Science Building, Room B304B

institute: University of Georgia

summary: Nucleosomes are the basic unit of chromatin. Nucleosome positioning (NP) plays a key role in transcriptional regulation and other biological processes. To better understand NP we used MNase-seq to investigate changes that occur as human embryonic stem cells (hESCs) transition to nascent mesoderm and then to smooth muscle cells (SMCs). Compared to differentiated cell derivatives, nucleosome occupancy at promoters and other notable genic sites, such as exon/intron junctions and adjacent regions, in hESCs shows a stronger correlation with transcript abundance and is less influenced by sequence content. Upon hESC differentiation, genes being silenced, but not genes being activated, display a substantial change in nucleosome occupancy at their promoters. Genome-wide, we detected a shift of NP to regions of higher G+C content as hESCs differentiate to SMCs. Notably, genomic regions with higher nucleosome occupancy harbor twice as many G↔C changes but fewer than half A↔T changes, compared to regions with lower nucleosome occupancy. Finally, our analysis indicates that the hESC genome is not rearranged and has a sequence mutation rate resembling normal human genomes. Our study reveals another unique feature of hESC chromatin, and sheds light on the relationship between nucleosome occupancy and sequence G+C content.

overall_design: Gene expression data for human embryonic cells (WA09-hESC), and embryonic cell differentiated derivatives (WA09-INM and WA09-SMC).

first: Wenjuan

last: Zhang

first: Yaping

last: Li

first: Michael

last: Kulik

first: Rochelle

last: Tiedemann

first: Keith

middle: D

last: Robertson

first: Stephen

last: Dalton

first: Shaying

last: Zhao