title: CAV-2 vector-transduced human neurospheres transcriptome profiles

status: Public on Oct 24 2014

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

summary:
Brain gene transfer using viral vectors will likely become a therapeutic option for several disorders. Helper-dependent (HD) canine adenovirus type 2 vectors (CAV-2) are well suited for this goal. Indeed, these vectors are poorly immunogenic, efficiently transduce neurons, are retrogradely transported to afferent structures in the brain, and lead to long-term transgene expression. CAV-2 vectors have been exploited to unravel behavior, cognition, neural networks, axonal transport and therapy for orphan diseases. Here we describe the HD-CAV-2 vector induced transcriptional response of human dopaminergic neurospheres derived from midbrain progenitors. In  this 3D model system, brain cell functions and dynamics mimic several aspects the dynamic nature of human brain. With the goal of better understanding and characterizing HD CAV-2 for brain therapy, we analyzed the transcriptomic modulation induced by HD-CAV-2 in this brain model system.
We found that dopaminergic neurospheres are readily transduced by HD-CAV-2, and that transduction generates two main responses: a DNA damage response, and alteration of centromeric and microtubule probes. We suggest that the first effect is linked to viral DNA, while the second would be related to the interaction of the HD-CAV-2 fibre with CAR.

overall_design: Total RNAs extracted from 3D cultures of transduced hmNPCs cells at 2 h and 5 days post-infection with HD-CAV-2 vector were hybridized on Affymetrix microarrays and pair wise comparisons were performed between the mock and vector transduced hmNPCs cells. Each condition was tested in three replicates.

first: Stefania

last: Piersanti

first: Romina

last: Burla

first: Catarina

last: Brito

first: Mattia

last: la Torre

first: Paula

last: Alves

first: Daniel

last: Simao

first: Carla

last: Mottini

first: Sara

last: Salinas

first: Rodolfo

last: Negri

first: Enrico

last: Tagliafico

first: Eric

middle: J

last: Kremer

first: Isabella

last: Saggio


title: Retroviral overexpression or siRNA mediated knockdown of FOXP1 in DLBCL cell lines and primary human B cells

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

summary: To provide insight into the role of and target genes of the transcription factor FOXP1 in mature human B cells and in B cell non-Hodkgin lymhomas, we performed gene expression microarray studies, upon ectopic overexpression or silencing of FOXP1 in these cells.

overall_design: human memory B cells from 2 separate donors were transduced with LZRS-FOXP1-IRES-YFP or LZRS-IRES-YFP (negative control); DLBCL cell lines OCI-Ly1, OCI-Ly7, and OCI-Ly10 were transduced with LZRS-FOXP1-IRES-YFP or LZRS-IRES-YFP (negative control);  DLBCL cell lines OCI-Ly1, OCI-Ly7, and OCI-Ly10  were transiently transfected with siRNA targeting FOXP1 or sigenome non-targeting siRNA (negative control), using the Lonza nucleofection system.

first: Martine

last: van Keimpema

first: Leonie

last: Grüneberg

first: Steven

middle: T

last: Pals

first: Marcel

last: Spaargaren


title: An Investigation of Biomarkers Derived from Legacy Microarray Data for Their Utility in the RNA-Seq Era

status: Public on Oct 22 2014

city: Shanghai

first: Leming

last: Shi

address: 2005 Songhu Road

department: School of Life Sciences

country: China

institute: Fudan University

type: Expression profiling by high throughput sequencing

summary:
Gene expression microarray has been the primary biomarker platform ubiquitously applied in biomedical research, resulting in enormous data, predictive models and biomarkers accrued. Recently, RNA-seq has looked likely to replace microarrays, but there will be a period where both technologies coexist. This raises two important questions: can microarray-based models and biomarkers be directly applied to RNA-Seq data? Can future RNA-Seq-based predictive models and biomarkers be applied to microarray data to leverage past investment? We systematically evaluated the transferability of predictive models and signature genes between microarray and RNA-seq using two large clinical data sets. The complexity of cross-platform sequence correspondence was considered in the analysis and examined using three human and two rat data sets, and three levels of mapping complexity were revealed. Three algorithms representing different modeling complexity were applied to the three levels of mappings for each of the eight binary endpoints and Cox regression was used to model survival times with expression data. In total, 240,096 predictive models were examined. Signature genes of predictive models are reciprocally transferable between microarray and RNA-seq data for model development, and microarray-based models can accurately predict RNA-seq-profiled samples; while RNA-seq-based models are less accurate in predicting microarray-profiled samples and are affected both by the choice of modeling algorithm and the gene mapping complexity. The results suggest continued usefulness of legacy microarray data and established microarray biomarkers and predictive models in the forthcoming RNA-seq era.

Definitions of characteristics:
EFS day: number of days for event free survival
EFS bin: binary classification of event free survival
OS day: number of days for overall survival
OS bin: binary classification of overall survival
High Risk: Indicating whether a sample belongs to high risk group or not
A_EFS_All: binary class label for event free survival for all samples
B_OS_All: binary class label for overall survival for all samples
C_SEX_All: binary class label for sex
D_FAV_All: binary class label for favorable and unfavorable samples
E_EFS_HR: binary class label for event free survival of High Risk group
F_OS_HR: binary class label for overall survival of High Risk group.

The same set of Samples is submitted under GEO accession GSE49711. This Series is a reanalysis of the data.

overall_design: The same set of RNA samples were profiled with microarray and RNA-Seq platforms. We explore the transferability of predictive models and signature genes between microarray and RNA-Seq data

first: Zhenqiang

last: Su

first: Matthias

last: Fischer

first: Weida

last: Tong


title: Longitudinal expression data from CD4+ T cells responding to LCMV-Armstrong or LCMV-Clone 13

city: Philadelphia

first: E

middle: John

last: Wherry

address: 421 Curie Blvd.

country: USA

institute: University of Pennsylvania

summary: During acute viral infections, naïve CD4+ T cells differentiate into effector CD4+ T cells and, after viral control, into memory CD4+ T cells. Memory CD4+ T cells are highly functional, proliferate rapidly upon reinfection and persist long-term without antigen. In contrast, during chronic infections, CD4+ T cells become less functional. To compare the development of functional memory T cells with poorly functional T cells from chronic viral infection, we generated longitudinal transcriptional profiles for each.

overall_design: Naive CD44Lo CD4+ T cells were isolated and sorted from uninfected C57BL/6 mice and H2-IAb GP66-specific CD4+ T cells were sorted using MHC-II tetramers at d6, 8, 15, and 30 p.i. with either LCMV Arm or LCMV clone 13. RNA from these CD4+ T cells was processed, amplified, labeled, and hybridized to Affymetrix GeneChip MoGene 1.0 st microarrays.

first: Alison

last: Crawford

first: Jill

last: Angelosanto


title: Expression data from two sorted lymphatic endothelial cell (LEC) populations, podoplanin-high versus podoplanin low

status: Public on Oct 20 2014

city: Vienna

first: Bernhard

last: Schweighofer

address: Lazarettgasse 14

department: Department of Dermatology

country: Austria

institute: Medical University of Vienna

summary: Extracorporeal shockwave treatment was shown to improve orthopaedic diseases, wound healing and to stimulate lymphangiogenesis in vivo. The aim of this study was to investigate in vitro shockwave treatment (IVSWT) effects on lymphatic endothelial cell (LEC) behavior and lymphangiogenesis. We analyzed migration, proliferation, vascular tube forming capability and marker expression changes of LECs after IVSWT compared with HUVECs. Finally, transcriptome- and miRNA analyses were conducted to gain deeper insight into the IVSWT-induced molecular mechanisms in LECs. The results indicate that IVSWT-mediated proliferation changes of LECs are highly energy flux density-dependent and LEC 2D as well as 3D migration was enhanced through IVSWT. IVSWT suppressed HUVEC 3D migration but enhanced vasculogenesis. Furthermore, we identified podoplaninhigh and podoplaninlow cell subpopulations, whose ratios changed upon IVSWT treatment. Transcriptome- and miRNA analyses on these populations showed differences in genes specific for signaling and vascular tissue. Our findings help to understand the cellular and molecular mechanisms underlying shockwave-induced lymphangiogenesis in vivo.

overall_design: Immortalized lymphatic endothelial cells were flow-sorted in two populations according to their differences in FSC and SSC values and subjected to Affymetrix analysis in triplicate samples

first: Sabrina

last: Rohringer

first: Wolfgang

last: Holnthoner

last: Hackel

first: Anna

middle: M

last: Weihs

first: Dominik

last: Ruenzler

first: Susanna

last: Skalicky

first: Michael

last: Karbiener

last: Scheideler

first: Johannes

last: Proell

first: Christian

last: Gabriel

first: Marion

last: Groeger

first: Andreas

last: Spittler

last: Grillari

first: Heinz

last: Redl


title: Gene expression in juvenile spondyloarthritis

status: Public on Oct 31 2014

city: Zagreb

first: Fran

last: Borovecki

address: Salata 2

department: Center for Translational anc Clinical Research

country: Croatia

institute: University of Zagreb School of Medicine

summary:
Association of juvenile spondyloarthritis (jSpA) with the HLA-B27 genotype is well established, but there is little knowledge of other genetic factors with a role in disease development. The aim of the present study was to identify and confirm gene signatures and novel biomarkers in various cohorts of untreated and treated patients diagnosed with jSpA and other forms of juvenile idiopathic arthritis (JIA).
DNA microarray gene expression was performed in 11 patients with jSpA and in four healthy controls, along with bioinformatics analysis of retrieved data (DAVID, GSEA, IPA).

overall_design: Total RNA was isolated from whole blood of 45 children with known HLA genotype and diagnosis of jSpA according to ILAR criteria, 11 children with oligo- and polyarticular forms of JIA, as well as 12 age and sex matched control participants without diagnosis of chronic inflammatory disease. Of those 11 patient and 4 controls were utilized in the microarrays experiments, while the rest were used in the follow-up qPCR analyses

first: Miroslav

last: Harjacek

first: Lovro

last: Lamot


title: Ethanol treatment of lymphoblastoid cell lines from alcoholics and non-alcoholics causes many subtle changes in gene expression

city: Indianapolis

first: Jeanette

middle: Nance

last: McClintick

state: IN

address: 635 Barnhill Dr.

department: Biochemistry & Molecular Biology

institute: Indiana University School of Medicine

summary:
Compared gene expression in lymphoblasoid cell lines from alcholics and controls and 24 hr treatment with ethanol.
To elucidate the effects of a controlled exposure to ethanol on gene expression, we studied lymphoblastoid cell lines (LCLs) from 21 alcoholics and 21 controls. We cultured each cell line for 24 h with and without 75 mM ethanol and measured gene expression using microarrays. Differences in expression between LCL from alcoholics and controls were modest, but included 13 genes previously identified as associated with alcoholism or related traits in one or more GWAS, including KCNA3, DICER1, ZNF415, Catalase and PPARGC1B. The paired design allowed us to detect very small changes due to ethanol treatment: ethanol altered the expression of 37% of the probe sets (51% of the unique named genes) detectably expressed in these LCLs, but most by very modest amounts. 99% of the named genes expressed in the LCLs were also expressed in at least 1 of 9 brain regions tested, suggesting that LCLs are a reasonable and accessible proxy for brain tissues. Key pathways affected by ethanol include cytokine, TNF and NF-kB signaling. Among the genes affected by ethanol were ANK3, EPHB1, SLC1A1, SLC9A9, NRD1, and SH3BP5, which were reported to be associated with alcoholism or related phenotypes in 2 genome wide association studies. Genes that either differed in expression between alcoholics and controls or were affected by ethanol exposure are candidates for further study.

overall_design: Lymphoblastoid cells from 21 alcoholics and 21 controls were treated with 75mM ethanol for 24 hours.

middle: N

first: Jay

middle: A

last: Tischfield

first: Howard

last: Edenberg


title: L1CAM overexpression in mouse lung endothelial cells (lECs)

status: Public on Oct 21 2014

city: San Giovanni Rotondo (FG)

first: Fabrizio

last: Bianchi

state: Outside U.S. & Canada

address: Viale Padre Pio 7

country: Italy

institute: Fondazione IRCCS Casa Sollievo della Sofferenza

summary: In an attempt to elucidate the molecular mechanisms underlying the multiple roles of L1 in endothelium, we checked whether manipulating its expression affected the transcriptome of lECs. To this purpose, we compared the gene expression profiles of L1-overexpressing and control lECs by Affymetrix, which revealed a remarkable effect of L1 overexpression on lECs transcriptome.

overall_design: Mouse lung-derived EC (lECs), kindly provided by E. Dejana (Milan, Italy), were stably transfected with a pcDNA3.1/Hygro(-) vector containing mouse LICAM full length or with and empty  pcDNA3.1/Hygro(-) vector as control. Three independent experimental replicates were performed.

first: Elena

last: Magrini

first: Ugo

last: Cavallaro


title: Expression data from macroH2A1/2 double knockout fetal mouse liver

status: Public on Oct 15 2014

first: John

last: Pehrson

state: PA

address: 3800 Spruce Street

summary:
MacroH2As core histone variants have a unique structure that includes C-terminal nonhistone domain. MacroH2As are highly conserved in vertebrates, and are thought to regulate gene expression. However the nature of genes regulated by macroH2As and the biological significance of macroH2As for the organism remain unclear. Here we examine macroH2A function in vivo by knocking out both macroH2A1 and macroH2A2 in the mouse.
We used microarrays to examine how the absence of macroH2A.1 and macroH2A.2 histone variants affect gene expression late fetal mouse liver.

overall_design: Wild-type and macroH2A1/2 double knockout pre-implantation embryos were collected, mixed and implanted into wild-type recipient females. Livers were collected from the resultant fetuses at 18.5 days post coitum and snap frozen with liquid nitrogen. Total RNA was extracted from the livers using Trizol.

middle: R


title: Pd-1 High and Intermediate CD8+ T cells

first: E

last: Wherry

summary: During acute viral infections, naïve CD8+ T cells differentiate into effector CD8+ T cells and, after viral control, into memory CD8+ T cells. Memory CD8+ T cells are highly functional, proliferate rapidly upon reinfection and persist long-term without antigen. In contrast, during chronic infections, CD8+ T cells become “exhausted” and have poor effector function, express multiple inhibitory receptors, possess low proliferative capacity, and cannot persist without antigen. Exhuasted CD8+ T cells can be further segregated by their expression of the inhibitory cell surface receptor PD-1. We performed transcriptional profiling on both PD-1 High and PD-1 Intermediate H2-Db GP33-specific CD8+ T cells.

overall_design: H2-Db GP33-specific CD8+ T cells were sorted from C57BL/6 mice 30 days p.i. with LCMV clone 13. These cells were then segregated by their expression of the inhibitory cell surface receptor PD-1 into PD-1 High and PD-1 Intermediate subpopulations. We performed transcriptional profiling on these subpopulations.

first: Alison

last: Crawford

first: Jill

last: Angelosanto


title: Cellular retinoic acid binding protein 2 (CRABP2) inhibits tumor growth by two distinct mechanisms

status: Public on Oct 14 2014

city: Cleveland

first: Liraz

last: Levi

state: OH

address: 9500 Euclid Avenue

department: Cellular and Molecular Medicine

institute: Lerner Research Institute; Cleveland Clinic

summary:
CRABP2 potently suppresses carcinoma cell growth, yet the mechanism(s) that underlie this activity remain incompletely understood. Two distinct functions are known for CRABP2: 1) the classical function of this protein is to directly deliver retinoic acid (RA) to the nuclear retinoic-acid receptorthereby activate gene expression, and 2)  in the absence of RA, CRABP2 directly binds to the RNA-binding and stabilizing protein, HuR, and  markedly strengthens its interactions with target mRNAs.
We used microarray experiments to elucidated genes regulated by HuR and/or CRABP2 in the absence of retinoic acid.

overall_design: Two experiments were preformed: 1) Transcriptome profiles of MCF-7 cells overexpresssing shHuR were compared to control cells, both in the absence of retinoic acid. 2) Transcriptome profiles of MCF-7 cells overexpresssing shCRABP2 were compared to control cells, both in the absence of retinoic acid.

first: Amanda

middle: C

last: Vreeland

first: Wei

last: Zhang

first: Daniel

last: Berry

first: Noa

last: Noy


title: Gene expression signatures of 64 T-ALL patient diagnosis samples

city: Gent

first: Sofie

last: Peirs

address: De Pintelaan 185

country: Belgium

institute: Ghent University

summary: Genetic studies have shown that human T-ALLs can be divided into subgroups that are characterized by unique gene expression signatures and relate to stages of T-cell differentiation at which the leukemic cells arrest. Each molecular subgroup has characteristic genetic abnormalities that cause aberrant activation of specific T-ALL transcription factor oncogenes, including LYL1/MEF2C, HOXA, TLX1, TLX3 and TAL1/LMO2. Notably, the recently described Early T-cell Precursor ALL (ETP-ALL) patients have leukemic cells that show an early block in T-cell differentiation and significantly overlap with LYL1-positive T-ALL and MEF2C-dysregulated immature T-ALL. We studied the gene expression profiles of 64 primary T-ALL samples and found a high BCL-2 expression in immature T-ALL patients compared to patients belonging to other subgroups.

overall_design: Gene expression profiling of 64 T-ALL patient samples

first: Pieter

last: Van Vlierberghe

first: Jean

last: Soulier

first: Frank

last: Speleman

first: Bruce

last: Poppe


title: Colony stimulating factor-1 receptor signaling networks inhibit macrophage inflammatory responses by induction of microRNA-21

status: Public on Oct 23 2014

city: New York

first: E. Richard

last: Stanley

state: New York

address: 1300 Morris Park Ave

department: Dev and Molecular Biology

institute: Albert Einstein College of Medicine

summary:
Macrophage polarization between the M2 (repair, pro-tumorigenic) and M1 (inflammatory) phenotypes is seen as a continuum of states. The detailed transcriptional events and signals downstream of CSF-1R that contribute to amplification of the M2 phenotype and suppression of the M1 phenotype are largely unknown. Macrophage CSF-1R pTyr-721 signaling promotes cell motility and enhancement of tumor cell invasion in vitro. Combining analysis of cellular systems for CSF-1R gain-of-function and loss-of-function with bioinformatic analysis of the macrophage CSF-1R pTyr-721-regulated transcriptome, we uncovered miR-21 as a downstream molecular switch controlling macrophage activation and identified ERK1/2 and NF-κB as CSF-1R pTyr-721-regulated signaling nodes. We show that CSF-1R pTyr-721 signaling suppresses the proinflammatory phenotype, predominantly by induction of miR-21. Profiling of the miR-21-regulated mRNAs revealed that 80% of the CSF-1-regulated canonical miR-21 targets are pro-inflammatory molecules. Additionally, miR-21 positively regulates M2 marker expression. Moreover, miR-21 feeds back to positively regulate its own expression and to limit CSF-1R-mediated activation of ERK1/2 and NF-κB. Consistent with an anti-inflammatory role of miRNA-21, intraperitoneal injection of mice with a miRNA-21 inhibitor increases the recruitment of inflammatory monocytes and enhances the peritoneal monocyte/macrophage response to lipopolysaccharide (LPS).
These results identify the macrophage miR-21 network as a novel target for controlling macrophage polarization.

overall_design: We performed microarray-based analysis on four mouse macrophage cell lines, two CSF-1R pTyr-721-expressing cell lines (M-/-.WT and M-/-.3ABY721) and two  CSF-1R Tyr-721-deficient lines (M-/-.Y721F and M-/-.3AB). Total RNA (two biological replicates) was extracted from CSF-1-starved cells (UR)  or  from cells constitutively grown in CSF-1 (CONST). Additionally, CSF-1-starved M-/-.WT and M-/-.Y721F cell lines were stimulated with CSF-1 for 0min, 20 min, 60 min and 180 min and used for total RNA extraction. Total RNA preparations with Ribosomal Integrity Numbers (RIN) > 9.5 were used for microarray analysis. A total of 100 ug/cell line/replicate was used for gene expresion analysis on the Affymetrix Mouse Gene ST1.0 chips at the Genomics Core at Einstein, according to manufacturer’s instructions. Differential expression analysis was performed using the ‘limma’ package of R/Bioconductor to identify significantly differentially expressed mRNAs over time, in response to CSF-1 treatment and to the genotype. CSF1-regulated genes were identified according to the cutoff with both expression folder change > 1.5 and p-value < 0.05.

first: Cristina

middle: I

last: Caescu

first: Xingyi

last: Guo

first: Deyou

last: Zheng

first: Lydia

last: Tesfa

first: Tushar

middle: D

last: Bhagat

first: Amit

last: Verma


title: In vitro expansion of human gastric epithelial stem cells and their primary response to bacterial infection

status: Public on Oct 13 2014

first: Richard

last: Volckmann

summary: We previously established long-term 3D organoid culture systems for several murine tissues (intestine, stomach, pancreas and liver) as well as human intestine and pancreas. Here, we describe culture conditions to generate long-term 3D culture from human gastric stem cells. The technology can be applied to study the epithelial response to infection with Helicobacter pylori. Human gastric cultures can expand indefinitely in 3D Matrigel. Cultures can be generated from normal tissue, from single sorted stem cells, or from tumor tissue. Organoids maintain many characteristics of the respective tissue in terms of histology, marker expression and euploidy. Organoids from normal tissue express markers of four lineages of the stomach and self-organize in gland and pit-domains. They can be directed to specifically express either lineages of the gastric gland, or the gastric pit by addition of Nicotinamide and withdrawal of Wnt. While gastric pit lineages react marginally to bacterial infection, gastric gland lineages mount a strong inflammatory response. The gastric culture system provides a unique tool to study gastric pathologies.

overall_design: We generated 2 sets of experiments. The first set contains organoids in 4 conditions: (1) organoids in expansion condition ENRWFGNiTi ("gland-type organoids") from 3 donors, (2) organoids as in 1 but differentiated for 4 days in differentiation condition ENR_FGNiTi ("pit'type organoids"), (3) organoids as in 1 but infected with Helicobacter pylori strain P12 MOI 50 for 2 h, (4) organoids as in 2 but infected as in 3. All 4 conditions were tested on the same organoid line in parallel. This experiment was conducted independently with cultures from 3 different donors. The second set of experiments compares freshly isolated glands with organoids. Samples from 2 patients were analyzed. Each patient received a total gastrectomy. From each patient, glands from corpus region or pyloric antrum were isolated. From each isolation, one aliquod was stored for microarray analysis and one aliquod used to generate organoids. Organoids and glands were subsequently lysed and analyzed in parallel.

first: Sina

last: Bartfeld

first: H

last: Clevers


title: Beta-tubulin and Actin Filament-Associating Small GTPase GIMAP4 is Required for IFN-Ɣ Secretion During Early Human CD4+ T Cell Activation

status: Public on Oct 09 2014

city: Turku

first: Kartiek

last: Kanduri

address: Tykistokatu 6

country: Finland

institute: Turku Centre for Biotechnology

summary: The aim of the dataset was to study on a genome-wide level the effect of GTPase of the human immune associated protein 4 (GIMAP4) knockdown on the gene expression of resting T cells and immediately after T cell activation and Th1(Act+IL12) polarizing conditions of human cord blood-derived CD4+ T cells.

overall_design: Total RNA from GIMAP4 siRNA-treated cord blood CD4+ T cells 48 hours after siRNA treatment, before TCR activation and corresponding cells cultured for 2h in TCR activating (antiCD3+antiCD28) plus IL-12 conditions was compared to total RNA from nonspecific control siRNA-treated cells. Samples from 3 biological replicates were analysed.

first: Mirkka

last: Heinonen

first: Harri

last: Lähdesmäki

first: Riitta

last: Lahesmaa

first: Tiina

last: Henttinen


title: Gene expression data on human keratinocytes with knockdown or overexpression of SNAI2

city: La Jolla

first: George

last: Sen

state: CA

address: 9500 GIlman Drive

department: Dermatology/CMM

institute: UCSD

summary:
1. Keratinocytes infected with retroviruses expressing control or SNAI2 shRNAs were cultured in growth medium and Affymetrix HG-U133 plus 2.0 arrays were used to determine global gene expression profiles.
2. Keratinocytes infected with retroviruses overexpressing LACZ or SNAI2 were cultured in growth medium and Affymetrix HG-U133 plus 2.0 arrays were used to determine global gene expression profiles.

overall_design: Keratinocytes with knockdown or overexpression of SNAI2 were used to determine gene expression profiles

first: Devendra

last: Mistry


title: Effect of glucose, endothelin-1 and cortisol on human iPS-derived cardiomyocytes

status: Public on Oct 10 2014

city: Basel

first: Laura

last: Badi

address: Grenzacherstrasse

country: Switzerland

institute: Hoffmann La Roche LTD

summary: Analysis of human iPS-derived cardiomyocytes exposed to glucose, endothelin-1 and cortisol in vitro. Treatment produces a surrogate diabetic cardiomyopathic phenotype. Results provide insight into the pathways regulated by the treatment in the cardiomyocyte.

overall_design: The RNA for each vehicle-control treated and glucose endothelin cortisol treated iPS derived cardiomyocytes from 4 replicate samples, were extracted and hybridized to 8 individual human HG-U133 Plus2.0 Affymetrix microarray gene chips, whereby each chip represented the expression profile for one cell culture at 2 days.

first: F

last: Drawnel

first: R

last: Lacone


title: Microarray Gene Expression Analysis of control and UBF knockdown in NIH3T3 cells

status: Public on Oct 19 2014

city: East Melbourne

first: Elaine

last: Sanij

state: VIC

address: 1 St Andrews Place

department: Research

country: Australia

institute: Peter MacCallum Cancer Centre

summary: UBF is an essential RNA Polymerase I (Pol I)-transcription factor. Our research investigates extra roles for UBF in regulation of Pol II gene expression. Our gene expression data identifies genes that are differentially regulated following UBF knockdown by siRNA.

overall_design: RNA was extracted from NIH3T3 cells after 48 hour of transfection with two independent siRNA oligonucleotides targeting UBF, sirEGFP or Mock control. A total of 12 samples were analysed using Affymetrix arrays.We include the expression data from three  biological replicate experiments

first: E

last: Hannan


title: Comparative DNA methylome analysis of endometrioid adenocarcinoma, uterine papillary serous carcinoma, and normal endometrium

status: Public on Oct 12 2014

city: SAINT LOUIS

first: Daofeng

last: Li

state: MO

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St. Louis

type: Methylation profiling by high throughput sequencing

summary: Classically, there are two types of endometrial cancer, endometrioid adenocarcinoma (EAC), or Type I; and uterine papillary serous carcinoma (UPSC), or Type II. These two types of cancers exhibit distinct DNA methylation levels in promoters of many genes. In EAC, many tumor suppressor genes were silenced due to DNA hypermethylation at their promoter region. However, promoters of many of these genes remained unmethylated in UPSC. Here, we described complete DNA methylome maps of endometrioid adenocarcinoma, uterine papillary serous carcinoma, and normal endometrium, by applying a combined strategy of methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylation-sensitive restriction enzyme sequencing (MRE-seq).

overall_design: We took a complementary and orthogonal approach to identify DNA methylation changes unique to the two endometrial cancer subtypes in an unbiased fashion. We generated complete DNA methylome maps for endometrioid adenocarcinoma (EAC, three samples), uterine papillary serous carcinomas (UPSC, three samples), and normal endometrium (pooled samples) by integrating data from methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylation-sensitive restriction enzyme sequencing (MRE-seq).

first: Bo

last: Zhang

first: Ting

last: Wang

first: Paul

last: Goodfellow


title: Mastermind-like protein 1 regulates DNA methylation and expression of early developmental gene clusters in human embryonic kidney cells (methylation)

status: Public on Oct 08 2014

city: Huddinge

first: Milica

last: Putnik

address: Hälsovägen 7

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

summary:
Mastermind-like 1 (MAML1) is a transcriptional coregulator that has been associated with early development of many systems such as neuronal, muscular, cardiovascular and urogenital. The present study aimed to explore the genome-wide effects of MAML1 on gene expression and DNA methylation in human embryonic kidney cells. RNA expression was measured using a microarray that screens approximately 36,000 transcripts, and DNA methylation was determined for 450,000 CpG sites. 225 genes were found to be differentially expressed, while 11802 CpG sites were found to be differentially methylated in MAML1-expressing cells. A subset of 211 differentially methylated loci was associated with the expression of 85 genes. Gene ontology analysis revealed that these genes are involved in the regulation of urogenital system development, cell adhesion and embryogenesis.
The aim of the study was to identify genes regulated by mastermind-like pritein 1 and DNA methylation, using genome-wide approach.

overall_design: We assayed the effects of MAML1 overexpression, as well as knock-down, on global DNA methylation profiles in HEK293 cells. 11802 CpG sites were found to be differentially methylated in MAML1-overexpressing cells. However, no significant changes were observed by comparing HEK293_H_siControl with HEK293_H_siMAML1.

first: David

last: Brodin

first: Fredrik

last: Fagerström-Billai

first: Karin

last: Dahlman-Wright

first: Annika

middle: E

last: Wallberg


title: Mastermind-like protein 1 regulates DNA methylation and expression of early developmental gene clusters in human embryonic kidney cells

type:
Expression profiling by array
Methylation profiling by array

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

overall_design: Refer to individual Series


title: Lysine acetylation effect in gene expression in Escherichia coli

status: Public on Oct 07 2014

city: Murcia

first: Sara

last: Castaño Cerezo

address: Faculty of Chemistry. Campus de Espinardo. University of Murcia

department: Dpt. Biochemistry and Molecular Biology B and Immunology

country: Spain

institute: University of Murcia

summary:
Although protein acetylation is widely observed, it has been associated with few specific regulatory functions making it poorly understood. To interrogate its functionality, we analyzed the acetylome in Escherichia coli knockout mutants of cobB, the only known sirtuin-like deacetylase, and patZ, the best-known protein acetyltransferase. For four growth conditions, more than 2,000 unique acetylated peptides, belonging to 809 proteins, were identified and differentially quantified. Nearly 65% of these proteins are related to metabolism. The global activity of CobB contributes to the deacetylation of a large number of substrates and has a major impact on physiology. Apart from the regulation of acetyl-CoA synthetase, we found that CobB-controlled acetylation of isocitrate lyase contributes to the fine-tuning of the glyoxylate shunt. Acetylation of the transcription factor RcsB prevents DNA binding, activating flagella biosynthesis and motility, and increases acid stress susceptibility. Surprisingly, deletion of patZ increased acetylation in acetate cultures, which suggests that it regulates the levels of acetylating agents. The results presented offer new insights into functional roles of protein acetylation in metabolic fitness and global cell regulation.
In this study we aimed to discover how the deregulation of protein acetylation could alter physiology in E. coli. We observed that the deletion of both cobB or patZ genes in E. coli altered gene expression, specially those genes related with motility, chemotaxis and acid stress response.

overall_design: We used three biological replicates in this study and each condition. The control in these experiments was E. coli BW25113

last: Castaño-Cerezo

first: Vicente

last: Bernal


title: Mouse ureter: wild type vs miR-143/145 knock out

city: Charlottesville

first: Roberto

last: Gomez

state: VA

address: 409 Lane Rd Room 2001

department: Pediatrics

institute: University of Virginia

summary:
mRNA profiling of mouse ureters comparing wild-type ureter vs. ureters from mice having whole body deletion of miR-143 and miR-145 which results in abnormal ureter peristalsis and hydronephrosis
We used microarrays to detail the global program of gene expression in wild-type and miR-143/145-deficient ureters which revealed dysregulation of genes linked to smooth muscle morphology and function.

overall_design: Two condition experiment: wild type vs miR-143/145 KO; biological replicates: individual mice - 2 wild type, 2 mutant. One replicate per array.

first: Maria

middle: S

last: Sequeira-Lopez

first: Silvia

last: Medrano


title: Gene expression signature in advanced colorectal cancer patients select drugs and response for the use of leucovorin, fluorouracil, and irinotecan

status: Public on Oct 06 2014

city: Sutton

first: Anguraj

last: Sadanandam

state: Surrey

address: 15 Cotswold Road

department: Molecular Pathology

country: United Kingdom

institute: Institute of Cancer Research (ICR), London

summary: In patients with advanced colorectal cancer, leucovorin, fluorouracil, and irinotecan (FOLFIRI) is considered as one of the reference first-line treatments. However, only about half of treated patients respond to this regimen, and there is no clinically useful marker that predicts response. A major clinical challenge is to identify the subset of patients who could benefit from this chemotherapy. We aimed to identify a gene expression profile in primary colon cancer tissue that could predict chemotherapy response.  Patients and Methods:- Tumor colon samples from 21 patients with advanced colorectal cancer were analyzed for gene expression profiling using Human Genome GeneChip arrays U133. At the end of the first-line treatment, the best observed response, according to WHO criteria, was used to define the responders and nonresponders. Discriminatory genes were first selected by the significance analysis of microarrays algorithm and the area under the receiver operating characteristic curve. A predictor classifier was then constructed using support vector machines. Finally, leave-one-out cross validation was used to estimate the performance and the accuracy of the output class prediction rule. Results:- We determined a set of 14 predictor genes of response to FOLFIRI. Nine of nine responders (100% specificity) and 11 of 12 nonresponders (92% sensitivity) were classified correctly, for an overall accuracy of 95%. Conclusion:- After validation in an independent cohort of patients, our gene signature could be used as a decision tool to assist oncologists in selecting colorectal cancer patients who could benefit from FOLFIRI chemotherapy, both in the adjuvant and the first-line metastatic setting.

overall_design: All tissue samples were maintained at −180°C (liquid nitrogen) until RNA extraction and were weighed before homogenization. Tissue samples were then disrupted directly into a lysis buffer using Mixer Mill MM 300 (Qiagen, Valencia, CA). Total RNA was isolated from tissue lysates using the RNeasy Mini Kit (Qiagen), and additional DNAse digestion was performed on all samples during the extraction process (RNase-Free DNase Set Protocol for DNase treatment on RNeasy Mini Spin Columns; Qiagen). After each extraction, a small fraction of the total RNA preparation was taken to determine the quality of the sample and the yield of total RNA. Controls analyses were performed by UV spectroscopy and analysis of total RNA profile using the Agilent RNA 6000 Nano LabChip Kit with the Agilent 2100 Bioanalyser (Agilent Technologies, Palo Alto, CA) to determine RNA purity, quantity, and integrity.

first: Maguy

last: Del Rio


title: Depletion of p62 reduces nuclear inclusions and paradoxically ameliorates disease phenotypes in Huntington’s model mice

city: Tokyo

first: Yoshihiro

last: Kino

address: 2-522-1 Noshio, Kiyose

country: Japan

institute: Meiji Pharmaceutical University

summary:
Huntington’s disease (HD) is a dominantly inherited genetic disease caused by mutant huntingtin (htt) protein with expanded polyglutamine tracts.  A neuropathological hallmark of HD is the presence of neuronal inclusions of mutant htt.  p62 is an important regulatory protein in selective autophagy, a process by which aggregated proteins are degraded, and it is associated with several neurodegenerative disorders including HD.  Here we investigated the effect of p62 depletion in three HD model mice: R6/2, HD190QG and HD120QG mice.  We found that loss of p62 in these models led to longer lifespans and reduced nuclear inclusions, although cytoplasmic inclusions increased with polyglutamine length.  In mouse embryonic fibroblasts (MEFs) with or without p62, mutant htt with a nuclear localization signal (NLS) showed no difference in nuclear inclusion between the two MEF types. In the case of mutant htt without NLS, however, p62 depletion increased cytoplasmic inclusions.  Furthermore, to examine the effect of impaired autophagy in HD model mice, we crossed R6/2 mice with Atg5 conditional knockout mice.  These mice also showed decreased nuclear inclusions and increased cytoplasmic inclusions, similar to HD mice lacking p62.  These data suggest that the genetic ablation of p62 in HD model mice enhances cytoplasmic inclusion formation by interrupting autophagic clearance of polyQ inclusions. This reduces polyQ nuclear influx and paradoxically ameliorates disease phenotypes by decreasing toxic nuclear inclusions.
Gene expression profiles were analyzed to examine the effects of p62 depletion in mouse with or without mutant huntingtin exon 1

overall_design: To examine the effect of p62 depletion on the transcriptome of Huntington's disease model mice, we crossed p62 knockout mice with HD model mice. We extracted total RNA from the striatum of these mice at 8 weeks and used for a microaaray analysis. The samples are HD transgenic mice with p62 knockout (HD_p62KO), HD mice with normal p62 (HD_p62WT), non-HD-transgenic mice with p62 knockout (NT_p62KO), and non-HD-transgenic mice with normal p62 (NT_p62WT).

first: Masaru

last: Kurosawa

first: Nobuyuki

last: Nukina


title: Gene expression in WT and podoplanin (PDPN)-deficient MEFs

city: Boston

first: Jillian

middle: Leigh

last: Astarita

state: MA

address: 450 Brookline Ave

department: Cancer Immunology and AIDS

institute: Dana Farber Cancer Institute

summary:
MEFs were grown from WT and PDPN-deficient mouse embryos and gene expression was analyzed. The aim was to determine whether a lack of PDPN caused significant global changes in gene expression in primary fibroblasts.
Here, we performed a microarray on WT and PDPN-deficient mouse embryonic fibroblasts to determine whether there were signficiant underlying changes in gene expression.

overall_design: Two replicates each of WT and PDPN KO MEFs from C57BL6/J mice

middle: L


title: C10ORF10/DEPP, a transcriptional target of FOXO3 regulates ROS-sensitivity by destabilizing peroxisomes in human neuroblastoma

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

institute: Eurac Researc

summary:
FOXO transcription factors control cellular formation of reactive oxygen species (ROS), which critically contribute to cell survival and cell death in neuroblastoma. Here, we report that C10orf10, also named “Decidual Protein induced by Progesterone (DEPP)”, is a direct transcriptional target of FOXO3 in human neuroblastoma. As FOXO3-mediated apoptosis involves a biphasic ROS accumulation, we analyzed cellular ROS levels in DEPP-knockdown cells by live-cell imaging. Knockdown of DEPP prevented the primary and secondary ROS accumulation during FOXO3 activation and attenuates FOXO3-induced apoptosis, whereas its overexpression raises cellular ROS levels and sensitizes to cell death. In neuronal cells, cellular steady state ROS are mainly detoxified in peroxisomes by the enzyme CAT/catalase. As DEPP contains a peroxisomal-targeting-signal-type-2 (PTS2) sequence at its N-terminus that enables protein import into peroxisomes, we analyzed the effect of DEPP on peroxisomal function by measuring the catalase enzyme activity. Catalase activity was reduced by conditional DEPP overexpression and significantly increased in DEPP-knockdown cells. Using live cell imaging and fluorescent peroxisomal and mitochondrial probes we demonstrate that DEPP localizes to peroxisomes and mitochondria in neuroblastoma cells. The combined data indicate that DEPP reduces peroxisomal activity and thereby impairs the cellular ROS detoxification capacity and contributes to death sensitization.
SH-EP, NB15 neuroblastoma cells and CCRF-CEM-C7H2 acute lymphoblastic leukemia cells were infected with the retrovirus plasmid pLIB-FOXO3(A3)-Ertm-iresNeo.

overall_design: Gene expression measures of samples with activated FOXO3 transcription factor (3h OHT treated) have been compared to untreated samples (0h time point). To rule out gene regulations by estrogen samples treated for 3 hours with tamoxifen have been compared to the untreated samples. Only genes that were more than two-fold regulated in the first, but not in the second comparison were defined to be FOXO3 regulated.

first: S

last: Salcher

first: K

last: Geiger

first: J

last: Hagenbuchner

first: M

last: Seiter

first: R

last: Kofler

first: U

middle: K

last: Kohlendorfer

last: Ausserlechner

first: P

last: Obexer


title: NFAT transcriptional activity is associated with metastatic capacity in colon cancer

city: Nashville

first: Jing

last: Zhu

state: TN

institute: Vanderbilt University

summary: Colorectal carcinoma is the third leading cause of cancer-related death in the United States. In order to understand the mechanism/signaling pathways responsible for invasion, migration and metastasis in colorectal cancer, we developed an integrative and comparative genetic approach to infer transcriptional regulatory mechanisms underlying colon cancer progression.   Accordingly, we filtered fourteen human colorectal cancer (CRC) microarray data sets, from an immune competent mouse model of metastasis to identify known and novel transcriptional regulators in CRC. Using this approach, Nuclear Factor of Activated T cells (NFAT) family of transcription factors were identified as metastasis driver of colon cancer.  NFAT family of transcription factors  is known to induce gene transcription in various disease processes, including carcinogenesis. We used parental and metastatic derivatives of MC38 mouse colon cancer cells (MC38Par and MC38Met, respectively) to evaluate the role of NFATc1 in cancer cell invasiveness.  We found that high NFATc1 expression correlates with significantly increased (p<0.0001) Trans-Endothelial Invasion (TEI) in MC38Met cells. Conversely, RNAi-based inhibition of NFATc1 expression and functional inhibition with calcineurin inhibitor FK506 in MC38Met cells, both resulted in significant decreased TEI (p=0.0193 & p=0.0003). Furthermore, a set of  predicted NFATc1 target mRNAs identified in our original analysis were downregulated by knock-down of NFATc1 or functional inhibition with FK506 in MC38Met cells.  The expression level (mRNA) of predicted gene targets were high in human CRC specimens which had higher than median NFATc1 mRNA expression (n=11 out of total 22). The tumor-associated NFATc1 co-regulated gene signature is significantly correlated with both disease-specific and disease-free survival in Stage II and III CRC patients. We have successfully demonstrated a bioinformatics approach to identify a tumor promoter driver gene NFATc1. Our studies suggest a role of NFATc1 towards invasion and its co-regulated gene signature for poor outcomes in colorectal cancer.

overall_design:
We developed an integrative and comparative genetic approach to infer transcriptional regulatory mechanisms underlying colon cancer progression. Using this approach, the Nuclear Factor of Activated T cells (NFAT) family of transcription factors were identified as metastasis driver of colon cancer. We used parental and metastatic derivatives of MC38 mouse colon cancer cells (MC38Par and MC38Met, respectively) to evaluate the role of NFATc1 in cancer cell invasiveness [GSE19073]. We found that high NFATc1 expression correlates with significantly increased (p<0.0001) Trans-Endothelial Invasion (TEI) in MC38Met cells. Conversely, RNAi-based inhibition of NFATc1 expression and functional inhibition with calcineurin inhibitor FK506 in MC38Met cells, both resulted in significant decreased TEI (p=0.0193 & p=0.0003). Furthermore, a set of predicted NFATc1 target mRNAs identified in our original analysis were downregulated by knock-down of NFATc1 or functional inhibition with FK506 in MC38Met cells. Finally, we generated a microarray gene expression dataset based on tumor samples collected from 122 CRC patients and tested whether the tumor-associated NFATc1co-regulated gene signature is correlated with patient survival.

The following clinical information can be found in the characteristics fields of each sample;
AJCC_STAGE: stage of cancer classified by AJCC (American Joint Committee on Cancer) staging system
DFS_EVENT: disease free survival; cancer recurrence=1, no recurrence=0
DFS_TIME: disease free survival time (months)
DSS_EVENT: disease specific survival; death from cancer=1,no death=0
DSS_TIME: disease specific survival time (months)

last: Beauchamp

first: Bing

last: Zhang

first: Xi

last: Chen

first: Natasha

middle: G

last: Deane

last: Washington

first: Kristen

last: Ciombor

last: Smith


title: Expression data comparing Rb/p53 and p53 deficient mammary tumors and  normal mammary tissue

status: Public on Oct 03 2014

city: Guelph

first: Robert

last: Jones

address: 50 Stone Rd

department: Biomedical Sciences

country: Canada

institute: University of Guelph

summary: To investigate the impact of combined Rb and p53 loss in mammary tumorigenesis, we used transgenic  and viral approaches to delete Rb and p53 floxed alleles specifically in the mouse mammary epithelium.  Although MMTV-Cre (NLST) targets stem/bi-potent progenitors in the mammary gland, a subset of MMTV-Cre:Rbf/f;p53f/f mice developed non-mammary tumors. Thus, freshly isolated primary mammary epithelial cells from these animals were transplanted into the mammary fat pads of immunodeficient mice and monitored for tumor formation. In addition, primary MECs were isolated from Cre-negative Rbf/f;p53f/f mice, infected with Ad-Cre followed by orthotopic transplantation.  In all these cases, resulting tumors shared similar spindle-shape histology, expressed high levels of vimentin, a mesenchymal marker, but not E-cadherin, a luminal marker, and were classified as adeno-sacrcomatoid/spindle-cell/mesenchymal-like breast cancer. We used microarrays to detect differentially expressed genes in the Rb/p53 double-knock-out vs p53 single deletion or normal mammary tissue.

overall_design: Total RNA was extracted from tumors developed by double Trizol method and hybridized on Affymetrix microarrays

first: Jeff

last: Liu

first: Eldad

last: Zacksenhaus


title: Expression data from PARK2 overexpression in U251 cells

city: Los Angeles

first: DECHEN

last: LIN

address: 8700 Beverly Boulevard

institute: Cedars-Sinai Medical Center

summary:
PARK2 (PARKIN) is an E3 ubiquitin ligase whose dysfunction has been associated with the progression of Parkinsonism and human malignancies, and its role in cancer remains to be explored. In this study, we investigated its role in glioma.
We used microarrays to detail the global programme of gene expression upon PARK2 overexpression in U251 cells

overall_design: U251 cells with PARK2 overexpression or control (GFP) were subjected for RNA extraction and hybridization on Affymetrix microarrays.

first: Dechen

last: Lin

first: H

middle: P

last: Koeffler


title: Effects of SGI-110 on A2780 ovarian cancer xenografts

status: Public on Oct 02 2014

city: Indianapolis

first: Horacio

last: Cardenas

address: 980 West Walnut Street

institute: Indiana University

type: Methylation profiling by genome tiling array

summary: Genome-wide DNA methylation profiles of SGI-110-treated ovarian cancer xenografts were obtained using next generation Illumina Infinium 450k assay which includes over 450,000 GpG sites.

overall_design: DNA from 6 samples were hybridized to the Illumina's Infinium HumanMethylation 450 BeadChip

first: Daniela

last: Matei

first: Yunlong

first: Matthew

middle: W

last: Segar


title: Gene expression profile of human epidermal keratinocytes in response to IFNgamma, IL-4, IL-6, IL-17A and IL-22

city: Seoul

first: Minsoo

last: Noh

address: 1 Gwanak-ro, Gwanak-gu

department: Pharmacy

country: South Korea

institute: Seoul National University

summary:
To understand the role of epidermal keratinocytes in immunopathology of skin diseases with predominant T helper (Th) cell responses, we measured the genome-wide transcriptional profile of human keratinocytes in response to IFNgamma, IL-4, IL-17A or IL-22, major cytokines produced by Th1, Th2, Th17 or Th22 cells, respectively.
IL-6 was also included in the transcriptional profile analysis because a variety of pro-inflammatory stimuli stimulate human keratinocytes to produce IL-6 that has an autocrine or paracrine role in epidermal immunity.

overall_design: We aimed to discover commonly expressed genes in human keratinocytes in response to pro-inflammatory cytokines, which would be associated with common pathophysiological responses in various skin diseases such as skin permeability barrier disruption or epidermal hyperplasia. Normal human keratinocytes (NHKs) were stimulated with IFNγ, IL-4, IL-6, IL-17A and IL-22 for 24 hours and harvested for total RNA extraction and hybridization on Affymetrix microarrays.


title: CD4+CD+8 double positive T-cell mRNA expression profiles from patients with granulomatotis with polyangiitis (GPA) compared to healthy controls

city: Kiel

last: Haesler

address: Schittenhelmstr. 12

department: IKMB / 1st Dept. of Medicine

country: Germany

institute: University Clinic of Schleswig Holstein

summary:
Expansion of circulating CD4+CD8+ double positive (DP) T-cells in a disease context is poorly understood.
The study aims to identify mechanisms which may drive expansion of CD4+CD8+ double positive t-cells in GPA.

overall_design: PBMCs from 3 GPA patients and 3 healthy controls were used to generate mRNA profiles from CCD4+CD8+ double positive T-cells in a disease context

first: R

last: Häsler


title: RNA Expression Profiling of Human iPSC-Derived Cardiomyocytes in a Cardiac Hypertrophy Model [mRNA expression]

city: Milwaukee

first: Ulrich

last: Broeckel

state: WI

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

summary:
Cardiac hypertrophy is an independent risk factor for cardiovascular disease and heart failure. There is increasing evidence that microRNAs (miRNAs) play an important role in the regulation of messenger RNA (mRNA) and the pathogenesis of various cardiovascular diseases. However, the ability to comprehensively study cardiac hypertrophy on a gene regulatory level is impacted by the limited availability of human cardiomyocytes. Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) offer the opportunity for disease modeling.
We utilized a previously established in vitro model of cardiac hypertrophy to interrogate the regulatory mechanism associated with the cardiac disease process. We performed miRNA sequencing and mRNA expression analysis on endothelin 1 (ET-1) stimulated hiPSC-CMs to describe associated RNA expression profiles. MicroRNA sequencing revealed over 250 known and 34 predicted novel miRNAs to be differentially expressed between ET-1stimulated and unstimulated control hiPSC-CMs. Messenger RNA expression analysis identified 731 probe sets with significant differential expression. Computational target prediction on significant differentially expressed miRNAs and mRNAs identified nearly 2000 target pairs.

overall_design: To characterize miRNA and mRNA expression patterns we utilized iCell Cardiomyocytes derived from human iPSCs (hiPSC-CMs). Based on preliminary dose-response and time-course studies, we stimulated these cells with ET-1 at 10-8M for 18h. We used unstimulated control (control-CM) and ET-1 stimulated (ET1-CM) hiPSCs from 3 separate experiments as triplicate data for this study. mRNA expression for the control-CM and ET1-CM samples was analyzed using GeneChip 3’IVT express arrays (Affymetrix).

first: Praful

last: Aggarwal

first: Amy

last: Turner

first: Andrea

last: Matter

first: Steven

middle: J

last: Kattman

first: Alexander

last: Stoddard

first: Rachel

last: Lorier

first: Bradley

last: Swanson

first: Donna

last: Arnett


title: Genome-wide DNA methylation and expression analysis of lung carcinoma

status: Public on Oct 05 2014

city: Lund

first: Johan

last: Staaf

address: Medicon Village

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University


title: Expression data from immortalized and transformed WT and HGPS cell lines

city: Bethesda

first: Patricia

last: Fernandez Ferri

state: MD

address: 41 Library Drive, B513

institute: NCI/NIH

summary:
Primary skin fibroblasts from HGPS patients and an age-matched control wild-type individuals were challenged in a standard transformation assay by retroviral introduction of TERT (T), V12-HRAS (R) and SV40 large and small T antigens (S). TERT-Immortalized cell lines from the same sources were also generated.
Abstract: Advanced age and DNA damage accumulation are strong risk factors for cancer.  The premature-aging disorder Hutchinson Gilford Progeria Syndrome (HGPS) provides a unique opportunity to study the interplay between DNA damage and aging-associated tumor mechanisms, since HGPS patients do not develop tumors despite elevated levels of DNA damage. Here, we have used HGPS patient cells to identify a protective mechanism to oncogenesis. We find that HGPS cells are resistant to neo-plastic transformation. This resistance is mediated by the bromodomain protein BRD4, which exhibits altered genome-wide binding patterns in transformation-resistant cells leading to inhibition of oncogenic de-differentiation.  BRD4 also in-hibits, albeit to a lower extent, the tumorigenic potential of transformed cells from healthy individuals and BRD4-mediated tumor protection is clinically relevant, since a BRD4 gene signature predicts positive clinical outcome in breast and lung cancer.  Our results demonstrate a protective function for BRD4 and suggest tissue-specific functions for BRD4 in tumorigenesis.

overall_design: 2 independent cell lines are included for each of the 4 groups (TERT-WT, TRS-WT, TERT-HGPS and TRS-HGPS)

last: Fernandez

first: Paola

last: Scaffidi

first: Tom

last: Misteli


title: Genome-wide DNA methylation analysis of lung carcinoma

summary:
Lung cancer is the worldwide leading cause of death from cancer. DNA methylation in gene promoter regions is a major mechanism of gene expression regulation that may promote tumorigenesis. However, whether clinically relevant subgroups based on DNA methylation patterns exist in lung cancer is not well studied.

We performed whole-genome methylation analysis using 450K Illumina BeadArrays on 124 tumors including 83 adenocarcinomas, 23 squamous cell carcinomas, one adenosquamous cancer, five large cell carcinomas, nine large cell neuroendocrine carcinomas (LCNEC), three small cell carcinomas (SCLC) and 12 normal lung tissues. Unsupervised class discovery was performed to identify DNA methylation subgroups with clinicopathological and molecular features. Subgroups were validated in two independent NSCLC cohorts.

Unsupervised analysis identified five DNA methylation subgroups (epitypes). One epitype was distinctly associated with neuroendocrine tumors (LCNEC and SCLC). For adenocarcinoma, in both discovery and validation cohorts, remaining four epitypes were associated with differences in clinicopathological and molecular features, including global hypomethylation, promoter hypermethylation, copy number alterations, expression of proliferation-associated genes, association with unsupervised and supervised gene expression phenotypes, KRAS, TP53, KEAP1, SMARCA4, and STK11 mutations, smoking history, and patient outcome.

Based on a multicohort approach we conducted a comprehensive survey of genome-wide DNA methylation in lung cancer, identifying a distinct neuroendocrine epitype and four adenocarcinoma epitypes associated with molecular and clinicopathological characteristics, and patient outcome. Our results bring further understanding of the epigenetic characteristics and molecular diversity in lung cancer generally and in adenocarcinoma specifically.

overall_design: Genome-wide DNA methylation analysis of 124 lung carcinomas and 12 normal lung tissues using Illumina Human Methylation 450K v1.0 Beadchips.

first: Anna

last: Karlsson

first: Mats

last: Jönsson

first: Martin

last: Lauss

first: Hans

last: Brunnström

first: Per

first: Göran

first: Markus

last: Ringner

first: Maria

last: Planck


title: A 3'-UTR KRAS-variant is associated with cisplatin resistance in patients with recurrent and/or metastatic head and neck squamous cell carcinoma.

city: Baltimore

first: Elana

middle: Judith

last: Fertig

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

summary: To determine the differential expression of KRAS-variant HNSCC (head and neck squamous cell carcinoma) cell lines.

overall_design: Total RNA collected from a panel of HNSCC cell lines.

first: C

middle: H

last: Chung

first: E


title: Gene Expression data from Pdx-1CreAPC+/LP53L/L pancreatic ductal adenocarcinoma (PDAC) cells versus Pdx-1CreP53L/L normal pancreatic ductal cells

status: Public on Oct 01 2014

city: Kaohsiung

first: Tzu-Lei

last: Kuo

state: Taiwan

address: 70 Lien-Hai Rd

department: Institute of Biomedical Sciences

country: Taiwan

institute: National Sun Yat-Sen University

summary:
Analysis of primary PDAC cells established from Pdx-1CreAPCL/+p53L/L and Pdx-1Crep53L/L mice.
APC haploinsufficiency combined with P53 loss in the pancreas drives MCN progression in mice. Results provide insight into  molecular mechanisms  invloved in the MCN formation of Pdx-1Cre APCL/+P53L/L mice.

overall_design: Pdx-1CreAPC+/LP53L/L PDAC cell lines and 2  Pdx-1CreP53L/L ductal cell lines were analyzed.

first: Kuang-hung

last: Cheng


title: Mouse GM-CSF-related alveolar macrophage genome-wide expression data

city: Cincinnati

first: Takuji

last: Suzuki

address: 3333 Burnet Avenue

department: Pulmonary Biology

institute: Cincinnati Children's Hospital Medical Center

summary: GM-CSF receptor-β deficient (Csf2rb–/– or KO) mice develop a lung disease identical to hereditary pulmonary alveolar proteinosis (hPAP) in humans with recessive CSF2RA or CSF2RB mutations that impair GM-CSF receptor function. We performed pulmonary macrophage transplantation (PMT) of bone marrow derived macrophages (BMDMs) without myeloablation in Csf2rb–/–mice. BMDMs were administered by endotracheal instillation into 2 month-old Csf2rb–/– mice. Results demonstrated that PMT therapeutic of hPAP in Csf2rb–/– mice was highly efficacious and durable. Alveolar macrophages were isolated by bronchoalveolar lavage one year after administration subjected to microarray analysis to determine the effects of PMT therapy on the global gene expression profile.

overall_design: Total mRNA was isolated from alveolar macrophages PMT-treated Csf2rb–/–mice (PMT) and from age-matched, untreated KO mice (KO)  and wild-type (C57Bl/6) mice (WT). Total mRNA was evaluated using Affymetrix microarrays (Mouse Gene 1.0 ST Array) to compare the gene expression profiles among the three groups (3 mice/group).

first: T

first: B

last: Trapnell


title: Spinophilin silencing in the breast cancer cell line SUM159

city: Graz

last: Pichler

address: Auenbruggerplatz 15

department: Internal medicine, Division of Oncology

institute: Medical University of Graz

summary: Microarray profiling was used to determine the most abundantly expressed genes in spinophilin-silenced breast cancer cells compared to control cells in the cell line SUM159. We identified several differentially expressed genes in spinophilin-silenced cells.

overall_design: A total number of six samples were analyzed, each in three replicates. There are three SUM159 Control samples and three samples of the cell line SUM159 with silenced spinophilin.


title: Endometrial cancer cell lines treated with eribulin and paclitaxel

city: Andover

first: Zoltan

last: Dezso

address: 4 Corporate dr

institute: Eisai Inc

summary: Eribulin mesylate is a synthetic macrocyclic ketone analog of the marine sponge natural product halichondrin B. Eribulin is a mechanistically unique inhibitor of microtubule dynamics, leading to inhibition of microtubule growth in the absence of effects on microtubule shortening at microtubule plus ends, and formation of nonproductive tubulin aggregates. In this study, we investigated whether selective signal pathways were associated with eribulin activity compared to paclitaxel, which stabilizes microtubules, based on gene expression profiling of cell line panels of breast, endometrial, and ovarian cancer in vitro.

overall_design: 19 endometrial cancer cell lines treated with eribulin and paclitaxel for 24 hours at concentration 10xIC50. Three technical replicates were included. for eribulin , paclitaxel and untreated cell lines.

first: Judith

last: Oestreicher

first: Amy

last: Weaver

first: Stephanie

last: Santiago

first: Sergei

last: Agoulnik

first: Jesse

last: Chow

first: Yoshiya

last: Oda

first: Yasuhiro

last: Funahashi


title: Expression data from menadione, PERK inhibitor, or control-treated HMLE-shGFP and HMLE-Twist human mammary epithelial cells

city: Cambridge

first: Catherine

last: Del Vecchio

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary:
Malignant carcinomas that recur following therapy are typically de-differentiated and multi-drug resistant (MDR). De-differentiated cancer cells acquire MDR by upregulating reactive oxygen species (ROS)-scavenging enzymes and drug efflux pumps, but how these genes are upregulated in response to de-differentiation is not known. Here, we examine this question by using global transcriptional profiling to identify ROS-induced genes that are already upregulated in de-differentiated cells, even in the absence of oxidative damage.
Using this approach, we found that the Nrf2 transcription factor, which is the master regulator of cellular response to oxidative stress, is pre-activated in de-differentiated cells. In de-differentiated cells, Nrf2 is not activated by oxidation but rather through a non-canonical mechanism involving its phosphorylation by the ER membrane kinase PERK. In contrast, differentiated cells require oxidative damage to activate Nrf2. Constitutive PERK-Nrf2 signaling protects de-differentiated cells from chemotherapy by reducing ROS levels and increasing drug efflux. These findings are validated in therapy-resistant basal breast cancer cell lines and animal models, where inhibition of the PERK-Nrf2 signaling axis reversed the MDR of de-differentiated cancer cells. Additionally, analysis of patient tumor datasets showed that a PERK pathway signature correlates strongly with chemotherapy resistance, tumor grade, and overall survival. Collectively, these results indicate that de-differentiated cells upregulate MDR genes via PERK-Nrf2 signaling, and suggest that targeting this pathway could sensitize drug-resistant cells to chemotherapy.

overall_design: Differentiated human breast epithelial cells (HMLE-shGFP) or de-differentiated cells (HMLE-Twist) were treated in culture with 40uM menadione for 2 hours or 1uM PERK inhibitor for 48 hours and compared to control DMSO-treated cells.

first: Piyush

middle: B

last: Gupta


title: Ovarian cancer cell lines treated with eribulin and paclitaxel

overall_design: 21 ovarian cancer cell lines treated with eribulin and paclitaxel for 24 hours at concentration 10xIC50. Three technical replicates were included for eribulin , paclitaxel and untreated cell lines.


title: Breast cancer cell lines treated with eribulin and paclitaxel

overall_design: 27 breast cancer cell lines treated with eribulin and paclitaxel for 24 hours at concentration 10xIC50. Three technical replicates were included. for eribulin , paclitaxel and untreated cell lines.


title: Integrative Analysis of Gene and miRNA expression profiles in Primary Myelofibrosis CD34+ cells

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

institute: Centre for Regenerative Medicine

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

summary:
Ph-negative myeloproliferative neoplasms (MPNs) are characterized by many somatic mutations which have already been shown useful in the prognostic assessment of MPN patients. Moreover, aberrant microRNA (miRNA) expression seems to add to the molecular complexity of MPNs, as specific miRNA signatures capable of discriminating MPN cells from those of normal donors were previously reported. In order to have a comprehensive picture of miRNA deregulation and its relationship with differential gene expression in primary myelofibrosis (PMF) cells, we obtained gene- (GEP) and miRNA expression profiles (miEP) of CD34+ cells from 31 healthy donors and 42 PMF patients using Affymetrix technology (HG-U219 and miRNA 2.0 arrays). Differentially expressed genes (DEG) and miRNAs (DEM) were sorted out by means of  Partek Genomic Suite vs 6.6. Since each miRNA can target many mRNAs while a single mRNA can be targeted by multiple miRNAs, we performed Integrative Analysis (IA) by means of Ingenuity Pathway Analysis (IPA) to untangle this combinatorial complexity. In particular, IPA points out DEM-DEG pairs among experimentally validated interactions from TarBase, miRecords and Ingenuity Expert Findings as well as predicted microRNA-mRNA interactions from TargetScan. IPA microRNA Target Filter was then employed to select only the DEM-DEG pairs showing an anti-correlated expression pattern and to build regulatory networks. Finally, 3'UTR luciferase reporter assays were performed to validate IPA predicted miRNA-mRNA interactions.
This study allowed the identification of different networks possibly involved in PMF onset and progression, highlighting an aberrant cross-regulation in miRNA-targets involved in malignant hematopoiesis. Furthermore, Integrative analysis was proved a powerful tool to unravel miRNA-mRNA interactions in functional networks, shedding light on the potential contribution of miRNAs to PMF pathogenesis.

platform_organism:
Homo sapiens
synthetic construct

overall_design: Gene expression profile (GEP) and miRNA expression profile (miEP) were performed starting from the same totalRNA of CD34+ cells from 42 PMF patients and 31 healthy donors (n=16 PB CD34+, n=15 BM CD34+) (1 replicate for each sample). In particular, GEP and miEP were performed on 23 PMF patients carrying the mutation JAK2V617F and 19 wild-type  samples.

first: Ruggiero

last: Norfo

first: Roberta

last: Zini

first: Valentina

last: Pennucci

first: Paola

last: Guglielmelli

first: Tiziana

last: Fanelli

first: Costanza

last: Bogani

first: Elisa

last: Bianchi

first: Simona

last: Salati

first: Samantha

last: Ruberti

first: Zelia

last: Prudente

first: Giorgia

last: Sacchi

first: Sebastiano

last: Rontauroli

first: Daniela

last: Pietra

first: Silvia

last: Salmoiraghi

first: Andrea

last: Bisognin

first: Stefania

last: Bortoluzzi

first: Gianni

last: Barosi

first: Mario

last: Cazzola

first: Alessandro

last: Rambaldi

first: Enrico

last: Tagliafico

middle: M

last: Vannucchi


title: Molecular Classification of Endometriosis and Disease Stage Using High-Dimensional Genomic Data

city: San Francisco

first: Linda

last: Giudice

address: 513 Parnassus Ave. HSE 1619

department: OBGYN and RS

institute: University of California, San Francisco

summary: Endometriosis, an estrogen-dependent, progesterone-resistant, inflammatory disorder affects 10% of reproductive-age women. It is diagnosed and staged at surgery, resulting in an 11-year latency from symptom onset to diagnosis, underscoring the need for less invasive, less expensive approaches. Since the uterine lining (endometrium) in women with endometriosis has altered molecular profiles, we tested whether molecular classification of this tissue can distinguish and stage disease. We developed classifiers using genomic data from n=148 archived endometrial samples from women with endometriosis or without endometriosis (normal controls or with other common uterine/pelvic pathologies) across the menstrual cycle and evaluated their performance on independent sample sets.  Classifiers were trained separately on samples in specific hormonal milieu, using margin tree classification, and accuracies were scored on independent validation samples. Classification of samples from women with endometriosis or no endometriosis involved two binary decisions each based on expression of specific genes. These first distinguished presence or absence of uterine/pelvic pathology and then no endometriosis from endometriosis, with the latter further classified according to severity (minimal/mild or moderate/severe). Best performing classifiers identified endometriosis with 90-100% accuracy, were cycle phase-specific or independent, and utilized relatively few genes to determine disease and severity. Differential gene expression and pathway analyses revealed immune activation, altered steroid and thyroid hormone signaling/metabolism and growth factor signaling in endometrium of women with endometriosis. Similar findings were observed with other disorders versus controls. Thus, classifier analysis of genomic data from endometrium can detect and stage pelvic endometriosis with high accuracy, dependent or independent of hormonal milieu. We propose that limited classifier candidate-genes are of high value in developing diagnostics and identifying therapeutic targets. Discovery of endometrial molecular differences in the presence of endometriosis and other uterine/pelvic pathologies raises the broader biological question of their impact on the steroid hormone response and normal functions of this tissue.

overall_design: We analyzed endometrial samples from n=148 women without or with endometriosis and/or other uterine/pelvic pathologies, using whole genome microarrays.

first: John

last: Tamaresis

first: Juan

last: Irwin

first: Gabriel

middle: A

last: Goldfien

first: Joseph

middle: T

last: Rabban

first: Richard

middle: O

last: Burney

first: Camran

last: Nezhat

first: Louis

middle: V

last: DePaolo


title: Identification of genes associated with bone metastatic breast cancer cells

city: Barcelona

first: Evarist

middle: Planet

last: Letschert

state: Spain

address: C/ Baldiri Reixac 10

department: Biostatistics

institute: IRB Barcelona

summary: We used comparative RNA hybridization (Affymetrix) analysis between Bone metastatic derivatives isolated in vivo and parental cells and focused on changes affecting the expression of potential bone metastasis genes.

overall_design: Total RNA from biological and technical replicates of parental MCF7 and BoM2 bone metastasis derivatives grown for 48 hours in regular media (see growth protocol) was isolated from in vitro cultured control and MAF expressing MCF7 parental cells. Total RNA was extracted using the TRIzol® Plus RNA Purification Kit (Life Technologies).

first: Roger

last: Gomis


title: Gene Expression Profiling Reveals Epithelial Mesenchymal Transition (EMT) Genes Can Selectively Differentiate Eribulin Sensitive Breast Cancer Cells

first: Zoltan

last: Dezso

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

overall_design: Refer to individual Series


title: 16q22-24 DNA amplification specifically predicts and mediates, through MAF gene, breast cancer bone metastasis.

type: Genome binding/occupancy profiling by genome tiling array


title: Gene expression microarray profiling in mice hearts with pathological and physiological cardiac hypertrophy

city: Orlando

first: Ling

last: Lai

state: FL

address: 6400 Sanger Rd

institute: Sanford-Burnham Medical Research Institute

summary: Compelling evidence suggests that mitochondrial dysfunction contributes to the pathogenesis of heart failure, including defects in the substrate oxidation, and the electron transport chain (ETC) and oxidative phosphorylation (OXPHOS). However, whether such changes occur early in the development of heart failure, and are potentially involved in the pathologic events that lead to cardiac dysfunction is unknown. To address this question, we conducted transcriptomic/metabolomics profiling in hearts of mice with two progressive stages of pressure overload-induced cardiac hypetrophy: i) cardiac hypertrophy with preserved ventricular function achieved via transverse aortic constriction for 4 weeks (TAC)  and ii) decompensated cardiac hypertrophy or heart failure (HF) caused by combining 4 wk TAC with a small apical myocardial infarction.  Transcriptomic analyses revealed, as shown previously, downregulated expression of genes involved in mitochondrial fatty acid oxidation in both TAC and HF hearts compared to sham-operated control hearts. Surprisingly, however, there were very few changes in expression of genes involved in other mitochondrial energy transduction pathways, ETC, or OXPHOS. Metabolomic analyses demonstrated significant alterations in pathway metabolite levels in HF (but not in TAC), including elevations in acylcarnitines, a subset of amino acids, and the lactate/pyruvate ratio. In contrast, the majority of organic acids were lower than controls. This metabolite profile suggests “bottlenecks” in the carbon substrate input to the TCA cycle. This transcriptomic/metabolomic profile was markedly different from that of mice PGC-1a/b deficiency in which a global downregulation of genes involved in mitochondrial ETC and OXPHOS was noted. In addition, the transcriptomic/metabolomic signatures of HF differed markedly from that of the exercise-trained mouse heart. We conclude that in contrast to current dogma, alterations in mitochondrial metabolism that occur early in the development of heart failure reflect largely post-transcriptional mechanisms resulting in impedance to substrate flux into the TCA cycle, reflected by alterations in the metabolome.

overall_design: Microarray gene expression profiling was performed with bi-ventricle RNA isolated from (1) 3 month-old female C57Bl6/J mice with transverse aortic constriction (CH), vs sham-operated control (Sham-CH), (2) 3 month-old female C57Bl6/J mice with heart failure (HF), vs. sham-operated control (Sham-HF); (3) 2 month-old female C57Bl6/J mice with voluntary wheel training for 2 months (Run), vs. Sedentary control (Sed). Five biological replicates are included for each group.

first: Ola

last: Martin

first: Teresa

middle: C

last: Leone

first: Daniel

last: Kelly


title: Microarray profiling of total testicular transcriptome in mouse

city: Trivandrum

first: Pradeep

last: Kumar

state: Kerala

address: Thycaud, Poojappura

department: Molecular Reproduction

country: India

institute: Rajiv Gandhi Centre for Biotechnology

summary: Gene expression during spermatogenesis is highly variable and this differential pattern is very important for the successive culmination of different stages of the process, leading to production of the male gamete. Taking the time window of first wave of spermatogenesis, we did a microarray profiling of total testicular transcriptome in mouse and found several significant patterns of variable gene expression, forming upregulated and downregulated clusters among the three stages analyzed here.

overall_design: Mouse testis tissue were taken at three stages, 8 days, 16 days and 24 days, during first wave of spermatogenesis for RNA extraction and hybridization on the  Affymetrix microarrays. Three biological replicates per age group were included and comparisons were done as 16 days vs 8 days, 24 days vs 16 days and 24 days vs 8 days testis transcriptome profile.

first: Sreesha

last: Sree


title: Identification of MAF controlled genes in breast cancer cells

summary: To identify relevant genes transcriptionally controlled by MAF in breast cancer, we focused on genes whose expression changed accordingly to MAF transcriptiion factor overexpression in MCF7. We used comparative RNA hybridization (Affymetrix) to this end.

overall_design: Total RNA from parental and MAFshort or long isoform overexpressing MCF7 grown for 48 hours in regular media (see growth protocol) was isolated from in vitro cultured control and MAF expressing MCF7 parental cells. Total RNA was extracted using the TRIzol® Plus RNA Purification Kit (Life Technologies).


title: miRNA-mRNA networks in mouse testis during the 1st wave of spermatogenesis

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


title: Defining the role of oxygen tension in human neural progenitor fate

status: Public on Sep 30 2014

city: Los Angeles

first: William

last: Lowry

address: 621 Charles Young Drive South

department: Molecular, Cell and Developmental Biology

country: USA

institute: University of California, Los Angeles

summary:
Hypoxia augments human embryonic stem cell self-renewal via hypoxia-inducible factor 2α (HIF2α) activated OCT4 (POU5F1) transcription. Hypoxia also increases the efficiency of reprogramming differentiated cells to a pluripotent-like state. Combined, these findings suggest that low oxygen (O2) tension would impair the purposeful differentiation of pluripotent stem cells.  Here, we show that low O2 tension and HIF activity instead promotes appropriate hESC differentiation. Through gain and loss of function studies, we implicate O2 tension as a modifier of a key cell fate decision, namely whether neural progenitors differentiate towards neurons or glia.  Furthermore, our data show that even transient changes in O2 concentration can affect cell fate through HIF by regulating the activity of MYC, a regulator of LIN28/let-7 that is critical for fate decisions in the neural lineage.  We also identify key small molecules that can take advantage of this pathway to quickly and efficiently promote the development of mature cell types.
We used microarrays to detail the global gene expression of human neural progenitor cells (NPC) cultured in physiological (2%) oxygen tension. By comparing NPCs with activated Hypoxia inducible factor (HIF) activity (DFX treatment) and NPCs with diminished HIF activity (HIF1β knockdown), we identified genes that are important for NPC fate decision under physiological oxygen concentration. We also used microarrays to obtain a global gene expression profiling during embryoid bodies formation using ES cells with diminished HIF activity.

overall_design: In HIF activation experiments, two ES lines and one iPS line-derived NPC were used, with or without DFX treatment for 5 days. In HIF1β knockdown experiments, NPCs were derived from either shHIF1β or control ES lines. In embryoid body formation experiments, day0 (ES stage) and day6 EBs were generated from either shHIF1β or control ES lines in 2% oxygen.

first: Yuan

last: Xie


title: Microarray analysis of GFP-SAS cells treated with small interfering RNA (siRNA) specific for Akt1 (siAkt1)

city: Toon

first: Koh-ichi

last: Nakashiro

state: Ehime

address: 454 Shitsukawa

department: Oral and Maxillofacial Surgery

institute: Ehime University Graduate School of Medicine

summary:
Knockdown of Akt1 markedly inhibited the growth of GFP-SAS cells.
We investigated the molecular mechanisms of the growth inhibitory effect by siAkt1 using Affymetrix GeneAtlasTM System.

overall_design: Using Affymetrix GeneAtlas System, we determined the gene expression profiles of GFP-SAS cells treated with siAkt1 or non-targeting siRNA (siNT).

first: Hiroshi

last: Tanaka


title: Expression analysis on microfibrillar associated protein 5 (MFAP5) protein treated ovarian cancer cell line OVCA432

city: Houston

first: Tsz-Lun

last: Yeung

state: TX

address: 1515 Holcombe Blvd. Unit 1362

department: Gynecologic Oncology and Reproductive Medicine

institute: University of Texas MD Anderson Cancer Center

summary: Ovarian cancer is the fifth most common form of cancer in women in the United States. Among different types of ovarian cancer, epithelial ovarian cancer is the most common and is highly lethal, however, prognostic and predictive markers, which can be used to predict chemoresponse and patient survival, have not been thoroughly explored. One critically important yet often overlooked component to the tumor progression process is the tumor microenvironment. Primarily composed of fibroblasts and extracellular matrix proteins (ECM) as well as endothelial cells and lymphocytic infiltrate, the tumor microenvironment has been shown to directly affect cell growth, migration, and differentiation through secreted proteins, cell-cell interactions and matrix remodeling (Tlsty and Coussens, 2006). The tumor microenvironment has the potential to promote tumor initiation of normal epithelial cells and facilitate progression of malignant cells, thereby, presenting a unique approach to diagnosing, understanding and treating cancer. Using a whole-genome oligonucleotide array platform to perform transcriptome profiling on the fibroblastic stromal component microdissected from a series of advanced stage high-grade serous ovarian adenocarcinomas, we identified a transcriptome signature for the ovarian cancer associated fibroblast (CAF). We further functionally characterized one of the identified genes, MFAP5, and we showed that stromal MFAP5 is a prognostic marker associated with poor patient survival. In addition to that, to investigate the signaling machanism and the effect of MFAP5 treatment on ovarian cancer cells, transcriptome profiling of MFAP5 treated OVCA432 high-grade serous ovarian cancer cells was performed. Further functional studies showed that stromal MFAP5 modulated ovarian cancer cell motility and invasion potential.

overall_design: High grade serous ovarian cancer cell line OVCA432 was used. Total RNA was isolated from control samples and MFAP5 treated cancer cell samples at 48 hours post-treatment. Followed by cDNA synthesis, IVT and biotin labeling, samples were then hybridized onto Affymetrix Human genome U133 plus 2.0 microarrays. For each treatment group, three independent samples were prepared for the microarray experiment.

first: Sze

last: Leung

first: Tsz

first: Samuel

last: Mok


title: Gene expression of wild-type MLL infant ALL patients

city: Rotterdam

first: Marieke

middle: van der

last: Linden

address: Dr. Molenwaterplein 50

department: Pediatric Oncology

country: Netherlands

institute: Erasmus MC

summary:
Extensive molecular and prognostic characterization of wild-type MLL infant ALL.
Background: Approximately 20% of all infant ALL cases carry wild-type (or germline) MLL genes. To date, wild-type MLL infant ALL patients are generally regarded as young pediatric precursor B-ALL patients, but extensive characterization of this specific patient group largely remains unacknowledged.
Methods: We here studied a relatively large cohort of 78 wild-type MLL infant ALL samples, using clinical parameters, array-comparative genomic hybridization analysis, gene expression profiling, multiplex ligation-dependent probe amplification, and conventional sequencing.
Findings: Wild-type MLL infant ALL patients are generally characterized by a lower incidence of favourable prognostic factors than pediatric (non-infant) B-ALL patients, and patients at high risk of therapy failure typically display an immature pro-B immunophenotype or respond poorly to prednisone. Using gene expression profiling, we found MEIS1 expression to additionally be highly predictive for clinical outcome in wild-type MLL infant ALL with a favourable prognosis in the wild-type MLL infants with low MEIS1 expression (DFS 88%% versus 50%, p=0•01). Overall the incidence of DNA copy number variations and genetic abnormalities in genes involved in B-cell differentiation is lower in wild-type MLL infant ALL patients as compared with pediatric precursor B-ALL patients.
Interpretation: Wild-type MLL infant ALL represents a highly heterogeneous patient group, which cannot be unified by one or a few known recurrent genomic aberrations. High-level MEIS1 expression and an immature pro-B immunophenotype in high-risk wild-type MLL infant ALL patients shows parallel with the unfavourable prognosis of MLL-rearranged infant ALL patients. In contrast, wild-type MLL infant ALL patients expressing lower levels of MEIS1 and displaying more differentiated (pre-B or common) phenotypes may well be more related to pediatric precursor B-ALL patients older than 1 year of age. We advocate that a treatment strategy in wild-type MLL infant ALL based on MEIS1 expression could be beneficial for improving survival.

overall_design:
Gene expression profiling of wild-type MLL infant ALL.
Additional wild-type MLL infant ALL patient samples (n=17) to the earlier samples published under GSE19475 (GSM485309 to GSM485322).

first: M

last: van der Linden

first: R

last: Stam


title: DNA methylation dynamics during ex vivo differentiation and maturation of human dendritic cells

city: Davis

first: Hong

last: Ji

address: County Rd 98 & Hutchison Drive

institute: University of California Davis

summary: Genomewide DNA methylation profiling of monocyte isolated from humna blood, immature and mature dendritic cells generated ex vivo. The Illumina Infinium HumanMethylation450 beadchips were used to generate DNA methylation profiles.

overall_design: Bisulfite converted DNA were hybridized to the Illumina Infinium HumanMethylation450 beadchips

first: Xue

last: Zhang

first: Ashley

last: Ulm

first: Hari

last: Somineni


title: Gene expression profiling of Notch1 knockout mouse liver samples and murine hepatic angiosarcoma cell lines.

city: Basel

first: Zuzanna

last: Makowska

address: Hebelstrasse 20

department: Biomedicine

institute: University of Basel

summary:
This work is part of the paper: Generation of a murine hepatic angiosarcoma cell line and reproducible mouse tumor model, Rothweiler S et al, Laboratory Investigation, 2014
Hepatic Angiosarcoma (AS) is a rare and highly aggressive tumor of endothelial origin with dismal prognosis. Studies of the molecular biology of AS and treatment options are limited since animal models are rare. We have previously shown that inducible knockout of Notch1 in mice leads to spontaneous formation of hepatic AS. The aim of this study was to 1) establish and characterize a cell line derived from this murine AS, 2) to identify molecular pathways involved in the pathogenesis and potential therapeutic targets, and 3) to generate a tumor transplantation model. AS cells retained specific endothelial properties such as tube formation activity, as well as expression of CD31 and von Willebrand Factor. However, electron microscopy analysis revealed signs of dedifferentiation with loss of fenestrae and loss of contact inhibition. Microarray and pathway analysis showed substantial changes in gene expression and revealed activation of the Myc pathway. Exposing the AS cells to sorafenib reduced migration, filopodia dynamics, and cell proliferation but did not induce apoptosis. In addition, sorafenib suppressed ERK phosphorylation and expression of cyclin D2. Injection of AS cells into NOD/SCID mice resulted in formation of undifferentiated tumors confirming the tumorigenic potential of these cells.  Conclusion: We established and characterized a murine model of spontaneous AS formation and hepatic AS cell lines as a useful in vitro tool. Our data demonstrate antitumor activity of sorafenib in AS cells with potent inhibition of migration, filopodia formation, and cell proliferation, which support further evaluation of sorafenib as a novel treatment strategy. In addition, AS cell transplantation provides a subcutaneous tumor model useful for in vivo preclinical drug testing.

overall_design: Mouse liver samples (Notch1 knockout and wild type control, 3 animals per group) and angiosarcoma cell lines (3 independently derived lines) were analyzed.

first: Sonja

last: Rothweiler

first: Michael

last: Dill

first: Luigi

last: Terraciano

first: Luca

last: Quagliata

first: Ruslan

last: Hlushchuk

first: Valentin

last: Djonov

first: Markus

last: Heim

first: David

last: Semela


title: Expression data from mouse adult epidermis in response to physical or immune mediated damage

city: Irvine

first: William

last: Gordon

address: Sprague Hall

department: Biological Chemistry

institute: University of California Irvine

summary: Whether epidermal factors play a primary role in immune-mediated skin diseases such as psoriasis is unknown. We now show that the pro-differentiation transcription factor Grainyhead-like 3 (GRHL3), essential during epidermal development but dispensable in adult skin homeostasis, is required for barrier repair after adult epidermal injury. Consistent with activation of a GRHL3-regulated repair pathway in psoriasis, we find GRHL3 up-regulation in lesional skin where GRHL3 binds known epidermal differentiation gene targets. Furthermore, we show the functionality of this pathway in the Imiquimod mouse model of immune-mediated epidermal hyperplasia where loss of Grhl3 exacerbates the epidermal damage response, conferring greater sensitivity to disease induction, delayed resolution of epidermal lesions, and resistance to anti-IL-22 therapy. ChIP-seq and gene expression profiling studies show that while GRHL3 regulates differentiation genes both in development and during repair from immune-mediated damage, it targets distinct sets of genes in the two processes. In particular, GRHL3 suppresses a number of alarmin and other pro-inflammatory genes after immune injury.  This study identifies a GRHL3-regulated epidermal barrier repair pathway that suppresses disease initiation and helps resolve existing lesions in immune-mediated epidermal hyperplasia.

overall_design: A single timepoint was assessed after physical injury of the epidermal barrier and two timepoints were assessed after immune mediated injury of the epidermis following Imiquimod treatment (psoriasis mouse model)


title: mTORC1 activation blocks BrafV600E-induced growth-arrest but is insufficient for melanoma formation

status: Public on Sep 26 2014

city: New Haven

last: Damsky

state: CT

address: 333 Cedar St, LCI 501

department: Dermatology

institute: Yale School of Meicine

summary:
Expression profiling was performed using uncultured melanocytes and melanoma cell from various mouse models of BrafV600E induced melanocytic proliferation
Various genotypes were analyzed at different time points in melanomagenesis

overall_design: RNA was purifired and hydridized to Affymetrix microarrays

first: Marcus

last: Bosenberg


title: PCGF6, a polycomb group protein, regulates mesodermal lineage differentiation in murine ES cells and functions in iPS reprogramming

city: Aachen

first: Martin

last: Zenke

state: NRW

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

institute: Institute for Biomedical Engineering

summary: Polycomb group (PcG) proteins comprise a large group of evolutionary conserved factors with essential roles for embryonic development and adult stem cell function. PcG proteins constitute two main multiprotein polycomb repressive complexes (PRC1 and PRC2) that operate in a hierarchical manner to silence gene expression. Functionally distinct PRC1 complexes are defined by Polycomb group RING finger protein (PCGF) paralogs. So far, six PCGF paralogs (PCGF1-6) have been identified but paralog-specific functions are not well understood. In our studies, we observed that Pcgf6 showed the highest expression level in undifferentiated murine embryonic stem cells (ESCs), blastocysts and testes. When ESCs differentiated, Pcgf6 expression strongly declined. To further investigate Pcgf6 biology, we established dox-inducible shRNA knockdown (KD) ESCs. Following Pcgf6 KD in ESCs the expression of pluripotency genes decreased, while mesodermal- and spermatogenesis-specific genes were de-repressed. Concomitantly with the elevated expression of mesodermal lineage markers, Pcgf6 KD ESCs showed increased hemangioblastic and hematopoietic activities. Finally, PCGF6 replaced SOX2 but not KLF4 or c-MYC in the generation of germline-competent iPS cells. Forced expression of Pcgf6 in OSKM-driven reprogramming increases iPS efficiency while Pcgf6 KD reduces the formation of ESC-like colonies. Together, these analyses show that Pcgf6 is non-redundantly involved in maintaining the pluripotent nature of ESCs and functions in iPS reprogramming.

overall_design: 6 samples were hybridized GeneChip Mouse Gene 1.0 ST Arrays (Affymetrix)

first: Daniela

last: Zdzieblo

first: Xiaoli

last: Li

first: Qiong

last: Lin

first: Matthias

last: Becker

first: Albrecht

last: Müller


title: Th17 pathway is activated in early inflamed acne lesions

status: Public on Sep 25 2014

city: SOPHIA-ANTIPOLIS

first: Johannes

last: Voegel

address: 2400 route des colles

department: Research Department

country: France

institute: Galderma R&D

summary: The mechanisms of inflammation in acne are not well understood. This study performed in two separate patient populations focused on the activation of adaptive and innate immunity in early inflamed acne. Biopsies were collected from lesional and non-lesional skin of acne patients. Psoriasis patients and healthy volunteers were included in the study for comparison (not included in the records). Using Affymetrix Genechips, we observed significant elevation of the signature cytokines of the Th17 lineage in acne lesions compared to non-lesional skin. The increased expression of IL-17 was confirmed with real-time qPCR (RT-PCR) in two separate patient populations. Cytokines involved in Th17 lineage differentiation (IL-1beta, IL-6, TGF-beta; IL23p19) were remarkably induced at the RNA level. In addition, pro-inflammatory cytokines (IL-8, TNF-α), Th1 markers (IL12p40, CXCR3, T-bet, IFN-gamma), T regulatory cell markers (Foxp3, IL-10, TGF-β) and antimicrobial peptides (S100A7, S100A9, LNC2, hBD2, hBD3, hCAP18) were induced. Importantly, immunohistochemistry revealed significantly increased numbers of IL-17A positive T cells and CD83 dendritic cells in the acne lesions. In summary our results demonstrate the presence of IL17A positive T cells and the activation of Th17-related cytokines in acne lesions, indicating that the Th17 pathway may play a pivotal role in the disease process, offering new targets of therapy.

overall_design: Total of 24 chips. 12 patients : 2 biospies per patient: 1 lesional and 1 non lesional.

first: J