title: Mouse Prostate Developmental Timecourse

city: Seattle

first: Ilsa

last: Coleman

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

summary: Studies centered at the intersection of embryogenesis and carcinogenesis have identified striking parallels involving signaling pathways that modulate both developmental and neoplastic processes. In the prostate, reciprocal interactions between epithelium and stroma are known to influence neoplasia and also exert morphogenic effects via the urogenital sinus mesenchyme. In this study, we sought to determine molecular relationships between aspects of normal prostate development and prostate carcinogenesis. We first characterized the gene expression program associated with key points of murine prostate organogenesis spanning the initial in utero induction of prostate budding through maturity. We identified a highly reproducible temporal program of gene expression that partitioned according to the broad developmental stages of prostate induction, branching morphogenesis, and secretory differentiation. Comparisons of gene expression profiles of murine prostate cancers arising in the context of genetically engineered alterations in the Pten tumor suppressor and Myc oncogene identified significant associations between the profile of branching morphogenesis and both cancer models. Further, the expression of genes comprising the branching morphogenesis program, such as PRDX4, SLC43A1, and DNMT3A, was significantly altered in human neoplastic prostate epithelium. These results indicate that components of normal developmental processes are active in prostate neoplasia and provide further rationale for exploiting molecular features of organogenesis to understand cancer phenotypes.

overall_design:
Whole male UGS (E14.5, E15.5, E16.5, and E17.5) or separated prostate lobes (P7, P30, and DP90) were dissected from C57BL6/J mice and snap frozen in liquid nitrogen. For each biological replication, we pooled 3 to 10 mice representing one or two litters. RNA from pools of UGS or specific prostate lobes (vp, ap, and dlp) was prepared using the Qiagen RNeasy Mini kit. We included an on-column DNaseI treatment to remove contaminating DNA. Before RNA amplification, we combined equal quantities of RNA from vp, ap, and dlp for the postnatal prostate samples. We amplified 1 ug of total RNA from each sample through one round using the Arcturus RiboAmp kit. For the E14.5 UGS reference sample, a second round of amplification was done to provide enough RNA for all microarrays. Each developmental sample was hybridized against the E14.5 UGS reference sample with a dye swap, for a total of 42 arrays.

Warning: the normalized data for this study which was made public on December 1, 2009, was swapped for some samples.  All normalized data has now been corrected as of February 25, 2010.  Raw data was not affected.

first: C

last: Pritchard

first: B

last: Mecham

first: R

last: Dumpit

first: I

first: M

last: Bhattacharjee

first: Q

last: Chen

last: Sikes

first: P

last: Nelson


title: S. cerevisiae cells: control vs positive supercoiling accumulation in absence of telomere silencing after 0 and 120 min

status: Public on Dec 01 2009

city: Barcelona

first: Benjamin

last: Pina

address: Jordi Girona, 18

country: Spain

institute: IDAEA-CSIC

summary:
Positive DNA helical stress accumulates in vivo by the unbalanced relaxation of positive and negative DNA supercoils in Δtop1, top2ts, pGPD:TopA yeast cells. The resulting overwinding of DNA greatly diminishes overall RNA synthesis. Here we show that whereas most genes reduce their transcript levels by several fold, genes situated at less than 100 kb from the chromosomal ends (near 15% of the  genome) are gradually unaffected. This positional effect denotes that chromosomal ends are topologically open, thus precluding the accumulation of DNA helical stress in telomere-proximal regions. The progressive escape from the transcription stall observed in all the chromosome extremities indicates also that friction restrictions to DNA twist diffusion, rather than tight topological boundaries, suffice to confine DNA helical tension along eukaryotic chromatin.

Keywords: Time course of positive helical tension accumulation in absence of telomere silencing.

overall_design: Two-condition experiment: delta top1 delta sir3-TOPA vs delta top1 delta sir3 top2-ts-TOPA. 2 time points: 0min, 120min. 3 biological replicates per condition and time point, independently grown in leu- selective media and harvested.

first: Ricky

middle: S

last: Joshi

first: Joaquin

last: Roca

last: Piña


title: Saccharomyces cerevisiae cells: control vs positive supercoiling accumulation

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

overall_design: Refer to individual Series


title: Chicken versus Quail

status: Public on Dec 03 2009

city: Saint Louis

first: Kara

last: Powder

state: MO

address: 4566 Scott Ave

department: Genetics

country: USA

institute: Washington University in St Louis

summary:
Avian beaks show extreme species-specific variability in morphology, though they develop from the same primordial structures. In both humans and birds, cranial neural crest cells are the primary source of mesenchyme for the frontonasal prominence; previous work has shown that these cells contain molecular information that regulate species-specific facial variation.  To determine the molecular basis of avian craniofacial patterning, we have gene expression profiled micro-dissected cranial neural crest cells from the frontonasal prominence of three bird species (chickens, quails, and ducks) during embryonic development.  These changes in gene expression were measured on a custom built, cross-species, long oligonucleotide microarray that interrogates the vast majority of transcription factor (TF) genes plus a wide variety of signaling pathways.  Samples were isolated at two developmental stages, before (Hamilton Hamburger stage [HH] 20) and after (HH25) morphological distinctions between the species are evident.
Keywords: cross-species comparison

sample_organism:
Gallus gallus
Coturnix japonica

platform_organism:
Gallus gallus
Homo sapiens
Mus musculus

overall_design: Frontonasal mesenchymal cells were micro-dissected two developmental stages, before (Hamilton Hamburger stage [HH] 20) and after (HH25) morphological distinctions between the species are evident.  For each sample, mesenchyme from 40 embryos was pooled. For each stage-matched comparison between chicken and quail, experiments include technical replicates as well as dye-switches for a total of 12 microarrays.

middle: E

first: Samantha

middle: A

last: Brugmann

first: Jill

last: Helms

first: Michael

last: Lovett


title: Microvesicular mRNA profiling of SW480 human colorectal adenocarcinoma cells

city: Pohang

first: Yong Song

last: Gho

address: San 31, Hyoja-dong, Nam-gu

country: South Korea

institute: Pohang University of Science and Technology

summary:
We analyzed mRNA profile of SW480-derived microvesicles using microarray
Keywords: Microvesicular mRNA profiling

overall_design: The total RNA was extracted from purified microvesicles derived from SW480 by the single-step isolation method using TRIzol reagent (Invitrogen Corporation, Carlsbad, CA) according to the manufacturer’s protocol. For microarray hybridizations, we followed protocol described in the instruction manual of Illumina TotalPrep RNA Amplification kit (Ambion, Austin, TX). In brief, 640 ng of total RNA from microvesicles was used to synthesize single-stranded cDNA using T7-Oligo(dT) promoter primer and RNase H-facilitated second-strand cDNA, which was purified and served as a template in the subsequent in vitro transcription. The in vitro transcription was carried out in the presence of T7 RNA polymerase and a biotinylated NTP mixture for cRNA. There are four replicate hybridizations. Same amount (Each 1.5 μg) of cRNA was hybridized to arrays, and subsequently labeled with Cy3-streptavidin (Amersham Biosciences, Little Chalfont, UK) and scanned with a Bead Station (Illumina, San Diego, CA).

first: YongSong

first: Daehee

last: Hwang

first: Boksil

last: Hong

first: Ji-Hoon

last: Cho

first: Hyunjung

last: Kim


title: The gene expression signature of genomic instability in breast cancer is an independent predictor of clinical outcome

city: Lübeck

first: Jens

middle: K

last: Habermann

address: Ratzeburger Allee 160

department: Department of Surgery

country: Germany

institute: University Clinic Schleswig-Holstein (UKSH), Campus Lübeck

summary:
Recently, expression profiling of breast carcinomas has revealed gene signatures that predict clinical outcome, and discerned prognostically relevant breast cancer subtypes.  Measurement of the degree of   genomic instability provides a very similar stratification of prognostic groups.  We therefore hypothesized that these features are linked.  We used gene expression profiling of 48 breast cancer specimens that   profoundly differed in their degree of genomic instability and identified a set of 12 genes that defines the two groups.  The biological and prognostic significance of this gene set was established through survival prediction in published datasets from patients with breast cancer.  Of note, the gene expression signatures that define specific prognostic subtypes in other breast cancer datasets predicted genomic instability in our samples.  This remarkable congruence suggests a biological dependency of poor-prognosis gene signatures, breast cancer subtypes, genomic instability, and clinical outcome.

Keywords: disease state analysis

overall_design: 44 samples


title: A Tool for Sheep Product Quality: Custom Microarray from Public Databases

status: Public on Nov 30 2009

city: Viterbo

first: Alessio

last: Valentini

address: via San Camillo de Lellis

department: IBAF

country: Italy

institute: University of Tuscia

summary: Milk and dairy products are an essential food and an economic resource in many countries. Milk component synthesis and secretion by the mammary gland involve expression of a large number of genes whose nutritional regulation remains poorly defined. We aim at understanding the genomic influence on milk quality and synthesis by comparing two sheep breeds, with different milking attitude, Sarda and Gentile di Puglia, using sheep-specific microarray technology. From sheep ESTs deposited at NCBI, we generated the first annotated microarray developed for sheep with a covering of most of the genome.

overall_design: Whole tissue samples of mammary gland were collected from 4 lactating individuals of two sheep (Ovis aries) breeds, Gentile di Puglia and Sarda. Biopsies of lactating mammary tissue were taken at two lactation stages (first record, stage 01: 6 days after lambing; second record, stage 02: 44 days after lambing) in both breeds. Tissues from mammary gland were immersed in RNAlater (Sigma) immediately after biopsy and stored at -20°C.

first: Silvia

last: Bongiorni

first: Giovanni

last: Chillemi

first: Gianluca

last: Prosperini

first: Susana

last: Bueno

first: Lorraine

last: Pariset


title: Saccharomyces cerevisiae cells: control vs positive supercoiling accumulation after 0, 30 and 120 min

first: Benjamin

last: Pina

summary:
Positive DNA helical stress accumulates in vivo by the unbalanced relaxation of positive and negative DNA supercoils in Δtop1, top2ts, pGPD:TopA yeast cells. The resulting overwinding of DNA greatly diminishes overall RNA synthesis. Here we show that whereas most genes reduce their transcript levels by several fold, genes situated at less than 100 kb from the chromosomal ends (near 15% of the  genome) are gradually unaffected. This positional effect denotes that chromosomal ends are topologically open, thus precluding the accumulation of DNA helical stress in telomere-proximal regions. The progressive escape from the transcription stall observed in all the chromosome extremities indicates also that friction restrictions to DNA twist diffusion, rather than tight topological boundaries, suffice to confine DNA helical tension along eukaryotic chromatin.

Keywords: Time course of positive helical tension accumulation.

overall_design: Two-condition experiment: delta top1-TOPA vs delta top1 top2-ts-TOPA. 3 time points: 0min, 30min, 120min. 3 biological replicates per condition and time point, independently grown in leu- selective media and harvested.

first: Ricky

last: Joshi

first: Joaquin

last: Roca

last: Piña


title: Tbx3 improves the germ-line competency of induced pluripotent stem cells

status: Public on Nov 25 2009

city: Singapore

first: Henry

last: Yang

address: 8A Biomedical Grove

department: Bioinformatics Group

country: Singapore

institute: SIgN

summary: Induced pluripotent stem (iPS) cells can be obtained through the introduction of defined factors into somatic cells. The combination of Oct4, Sox2 and Klf4 (OSK) constitutes the minimal requirement for generating iPS cells from mouse embryonic fibroblasts (MEFs). These cells are thought to resemble embryonic stem cells (ESCs) based on global gene expression analyses; but, few studies have tested their ability and efficiency in contributing to chimerism, colonization of germ tissues, and most importantly, germ-line transmission and life-birth from iPS cells produced with tetraploid complementation. Through the genomic analyses of ESC genes that have roles in pluripotency and fusion-mediated somatic cell reprogramming, we identified Tbx3 as a transcription factor that significantly improves the quality of iPS cells. Induced-PS cells generated with OSK + Tbx3 (OSKT) are superior in both germ cell contribution to the gonads and germ-line transmission frequency. However, global gene expression profiling could not distinguish between OSK and OSKT iPS cells. Genome-wide ChIP-sequencing analysis of Tbx3 binding sites in ESCs suggests that Tbx3 regulates pluripotency-associated and reprogramming factors, in addition to sharing many common downstream regulatory targets with Oct4, Sox2, Nanog and Smad1. This study underscores the intrinsic qualitative differences between iPS cells generated by different methods and highlights the need to rigorously characterize iPS cells beyond in vitro studies.

overall_design: Total RNA obtained from 8 clones for OSE, 11 clones for OSK, and 11 clones for OSKT compared to 4 biological replicates for R1 ESCs and 2 biological replicates for D3 ESCs.

first: Jianyong

last: Han

first: Ping

last: Yuan

first: Jinqiu

last: Zhang

first: Boonseng

last: Soh

first: Jungliang

last: Tay

first: Siewlan

last: Lim

first: Yuriy

last: Orlov

first: Thomas

last: Lufkin

first: Huckhui

last: Ng

first: Waileong

last: Tam

first: Bing


title: IL6 - IFNγ crosstalk experiment

status: Public on Nov 19 2009

city: Edmonton

first: Branko

last: Braam

department: Medicine / Nephrology

country: Canada

institute: Univ. of Alberta

summary: This experiment tested whether pretreatment of human microvascular endothelial cells (HMECs) with interferon-gamma (IFNγ) for 2h affected the transcriptional response to 1h exposure to interleukin-6 (IL-6).

overall_design:
Human microvascular endothelial cells in culture; exposure to IFNγ 1 ng/ml for 3 h alone, with IFNγ 1 ng/ml for 2 h and then with IL6 50 U/ml for 1 h, with IL6 50 U/ml alone, or with neither. 4 replicates for each condition. RNA isolation, Illumina expression arrays.

The supplementary file 'GSE19082_non-normalized_data.txt' contains non-normalized data for Samples GSM472434-GSM472449.

first: Mehdi

last: Rastmanesh

first: Hans

last: Bluyssen

first: Kim

last: Jie

first: Sebastiaan

last: Wesseling


title: Evaluation of the effects of shear stress on human dermal microvascular blood and lymphatic endothelial cells

city: Lausanne

first: Melody

last: Swartz

address: EPFL  Station 15

department: Science de la Vie

country: Switzerland

institute: Ecole Polytechnique Federal de Lausanne

summary:
The lymphatic system removes fluid from the interstitial space and returns it to the blood with a tremendous capacity: during inflammation, lymph flow rates can increase dramatically; however, during chronic lymphedema, there is little or no flow. The ability of lymphatic endothelium to sense and actively regulate this function is unknown, and shear stress is likely a key indicator of lymph flow. We profiled gene expression in human dermal microvascular lymphatic endothelial cells exposed to 0, 2 and 20 dyn/cm2 shear stress as representative of chronic lymphedema, normal, and acute inflammatory conditions, respectively. We found important adaptive responses correlated to multiple aspects of lymphatic function. Importantly, shear stress upregulated intracellular water and solute transporters while decreasing cell-cell adhesion and basement membrane components and increasing cell-matrix interactions. This data indicate that during high loading conditions, both passive and active drainage function increases, while conversely when fluid drainage is blocked, transport function is diminished in the lymphatic endothelium. These data demonstrate the first functional-adaptive response of lymphatic endothelium to flow conditions, thus indicating that the lymphatic endothelium plays an active role in regulating their function.
Keywords: Shear stress, dose response, cell type comparison

overall_design: Lymphatic endothelial cells were subjected to 0, 2, or 20 dyn/cm2 shear stress; blood endothelial cells were subjected to 0 or 20 dyn/cm2 shear stress. Four samples were used for each cell type/shear level group for a total of 20 samples. Each sample was independently compared to human universal reference RNA via two-color microarray analysis for a total of 20 arrays.  In all cases, the experimental samples were labeled with Cy5 dye while the reference RNA was labeled with Cy3.

first: Carolyn

last: Yong

first: Eric

last: Bridenbaugh

first: Veronique

last: Borel

first: Alexander

middle: P

last: Dorr

first: David

middle: C

last: Zawieja


title: Analysis of global gene expression in uninduced and β-estradiol treated G1E-ER-GATA cells

city: Madison

first: Emery

middle: H.

last: Bresnick

state: WI

address: 1300 University Avenue 383 MSC

department: Pharmacology

institute: University of Wisconsin-Madison

summary: Total RNA was analyzed from either uninduced or β-estradiol treated G1E-ER-GATA cells to determine changes in gene expression upon induction of erythroid maturation (treated).

overall_design: Array data profiling expression in untreated and β-estradiol-treated (1 uM, 24 h) G1E-ER-GATA-1 cells (2 independent experiments).

first: Tohru

last: Fujiwara

first: Henriette

last: O'Geen

first: Sunduz

last: Keles

first: Kimberly

last: Blahnik

first: Amelia

last: Linnemann

first: Yoon-A

last: Kang

first: Kyunghee

last: Choi

first: Peggy

middle: J

last: Farnham

middle: H


title: Stable Patterns of Gene Expression Regulating Carbohydrate Metabolism Determined by Geographic Ancestry

status: Public on Oct 31 2009

city: Chapel Hill

first: Jonathan

last: Schisler

state: NC

address: MBRB, Rm 2340C

department: McAllister Heart Institute

institute: The University of North Carolina at Chapel Hill

summary:
Individuals of African descent in the United States suffer disproportionately from diseases with a metabolic etiology (obesity, metabolic syndrome, and diabetes), and from the pathological consequences of these disorders (hypertension and cardiovascular disease).  Using a combination of genetic/genomic and bioinformatics approaches, we identified a large number of genes that were both differentially expressed between American subjects self-identified to be of either African or European ancestry and that also contained single nucleotide polymorphisms that distinguish distantly related ancestral populations.  Several of these genes control the metabolism of simple carbohydrates and are direct targets for the SREBP1, a metabolic transcription factor also differentially expressed between our study populations.  These data support the concept of stable patterns of gene transcription unique to a geographic ancestral lineage.  The coordinated transcriptional adaptation of carbohydrate metabolism to dietary environmental pressures suggests a genetic and transcriptional mechanism for the disproportionate levels of obesity, diabetes, and cardiovascular disease observed in Americans with African ancestry.

Keywords: Ancestry-dependent gene expression, functional genomics, personalized medicine, multi-factoral disease, nutrition, diabetes

overall_design: We utilized a “sample x reference” experimental design strategy in which RNA extracted from human peripheral blood mononuclear cells was hybridized to the microarray slide in the presence of labeled Universal Human Reference RNA (UHRR, Stratagene, LaJolla, CA).  A total of 161 subjects were used in this analysis.  Briefly, five hundred nanograms of total RNA were used for gene expression profiling following reverse transcription and T-7 polymerase-mediated amplification/labeling with Cyanine-5 CTP.  Labeled subject cRNA was co-hybridized to Agilent G4112A Whole Human Genome 44K oligonucleotide arrays with equimolar amounts of Cyanine-3 labeled UHRR. Slides were hybridized, washed, and scanned on an Axon 4000b microarray scanner.  The data were processed using GenePix Pro 6 software

first: Peter

last: Charles

first: Joel

last: Parker

first: Eleanor

middle: G

last: Hilliard

first: Sabeen

last: Mapara

first: Dane

last: Meredith

first: Robert

last: Lineberger

first: Samuel

last: Wu

first: Brian

middle: D

last: Alder

first: George

last: Stouffer

first: Cam

last: Patterson


title: G9a selectively represses a class of late-replicating genes at the nuclear periphery

status: Public on Nov 03 2009

city: Tallahassee

first: Ichiro

last: Hiratani

state: FL

address: 319 Stadium Dr

department: Biological Science

institute: Florida State University

type: Genome variation profiling by genome tiling array


title: G9a selectively represses a class of late-replicating genes at the nuclear periphery (Expression)

summary: We have investigated the role of the histone methyltransferase G9a in the establishment of silent nuclear compartments. Following conditional knockout of the G9a methyltransferase in mouse ESCs, 167 genes were significantly up-regulated, and no genes were strongly down-regulated. A partially overlapping set of 119 genes were up-regulated after differentiation of G9a-depleted cells to neural precursors. Promoters of these G9a-repressed genes were AT rich and H3K9me2 enriched but H3K4me3 depleted and were not highly DNA methylated. Representative genes were found to be close to the nuclear periphery, which was significantly enriched for G9a-dependent H3K9me2. Strikingly, although 73% of total genes were early replicating, more than 71% of G9a-repressed genes were late replicating, and a strong correlation was found between H3K9me2 and late replication. However, G9a loss did not significantly affect subnuclear position or replication timing of any non-pericentric regions of the genome, nor did it affect programmed changes in replication timing that accompany differentiation. We conclude that G9a is a gatekeeper for a specific set of genes localized within the late replicating nuclear periphery.

overall_design: 4 cell states each in duplicate (i.e. a total of 8 individual replicates)

first: Tomoki

last: Yokochi


title: Comparison of gene expression in melanoma of wild-type and VAP-1 -/- mice

status: Public on Oct 27 2009

city: Turku

first: Kaisa

last: Auvinen

address: Tykistökatu 6

department: Medicity Research Laboratory

country: Finland

institute: University of Turku

summary: Vascular adhesion protein-1 (VAP-1) is an endothelial cell-surface protein. It is also an enzyme posessing semicarbazide-sensitive amine oxidase activity (EC.1.4.3.6). VAP-1 is involved in leukocyte traffic. To study the role of VAP-1 in tumor immunity, we compared gene expression profiles in melanomas growing in VAP-1 -/- mice and their wid-type littermates.

overall_design: The B16-F10-Luc-G5 melanoma cells (Xenogen) were injected subcutaneously into abdominal area of 2 wild-type and 2 VAP-1 -/- mice. Tumors were grown until day 10 when mice were euthanized. Tumors were dissected and total RNA was isolated using the Qiagen RNA extraction kit.

first: Fumiko

last: Marttila-Ichihara

first: Sirpa

last: Jalkanen

first: Marko

last: Salmi


title: Wild type vs. Nova2 KO mouse: Exon junction array data

status: Public on Nov 04 2009

city: Cleveland

first: Donny

last: Licatalosi

state: OH

address: 10900 Euclid Ave

institute: Case Western Reserve University

type: Genome binding/occupancy profiling by array

summary: To assess the requirement of Nova2 for alternative processing of RNA in mouse brain. Protein-RNA interactions play critical roles in all aspects of gene expression. Here we develop a genome-wide means of mapping protein-RNA binding sites in vivo, by high throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP).  HITS-CLIP analysis of the neuron-specific splicing factor Nova2 revealed extremely reproducible RNA binding maps in multiple mouse brains. These maps provide genome-wide in vivo biochemical footprints confirming the previous prediction that the position of Nova binding determines the outcome of alternative splicing; moreover, they are sufficiently powerful to predict Nova action de novo.  HITS-CLIP revealed a large number of Nova-RNA interactions in 3’ UTRs, leading to the discovery that Nova regulates alternative polyadenylation in the brain. HITS-CLIP, therefore, provides a robust, unbiased means to identify functional protein-RNA interactions in vivo.

overall_design: RNA from the cortex of 3 wild type and 3 Nova2 KO P10 CD1 mice.  One array per biological replicate.

middle: B

last: Darnell


title: Expression profiling of different adult female tissues isolated from Anopheles gambiae females

status: Public on Oct 30 2009

city: Manhattan

first: Kristin

last: Michel

state: KS

address: 267 Chalmers Hall

department: Biology

institute: Kansas State University

summary: Insect hemocytes mediate important cellular immune responses including phagocytosis and encapsulation, and also secrete immune factors such as opsonins, melanization factors, and antimicrobial peptides. In Anopheles, they contribute to the defense against malaria parasite invasion during the early sporogonic cycle. We used microarrays to identify transcripts that are specific or enriched in circulating hemocytes compared to either neuronal or to the rest of the body.

platform_organism:
Plasmodium falciparum
Anopheles gambiae

overall_design: Hemocytes, heads and carcasses were isolated from naïve adult females 1-2 days after eclosion.

first: S

last: Pinto

first: F

last: Kafatos

first: K


title: Expression profiling of hemocytes from Anopheles gambiae after malaria parasite infection

summary:
Insect hemocytes mediate important cellular immune responses including phagocytosis and encapsulation, and also secrete immune factors such as opsonins, melanization factors, and antimicrobial peptides. In Anopheles, they contribute to the defense against malaria parasite invasion during the early sporogonic cycle.
We used microarrays to identify if and to what degree circulating hemocytes have altered global expression profiles after infection with the rodent malaria parasite, Plasmodium berghei

overall_design: Hemocytes were isolated 24-28h after infection using the infectious EGFP-CON P. berghei strain (experiment) or an invasion-deficient, Circumsporozoite- and TRAP-related protein (CTRP) knockout strain with the same genetic background as GFP-CON (CTRPko/GFP, control).


title: Human monocyte-derived dendritic cells: Control vs Tolerogenic

status: Public on Nov 13 2009

city: Mexico City

first: Carmen

last: Sánchez-Torres

department: Molecular Biomedicine

country: Mexico

institute: CINVESTAV-IPN

summary: Transcriptional profiling of human dendritic cells (DC) comparing control (DC generated with GM-CSF plus IL-4) with three different treatments of tolerogenic (DC generated with GM-CSF plus IL-4 and IL-10, or IL-4, IL-10, and IL-6, or IL-4, IL-10, and TGF-b1)

overall_design: Three two-condition experiments, control (N) vs tolerogenic DC with three different treatments. Pool of 4 indivuduals for each condition. One replicate per array.

last: Sanchez-Torres

first: Honorio

last: Torres-Aguilar


title: WT vs. PPARd-/- Macrophages

status: Public on Oct 18 2009

city: Palo Alto

first: Alexander

last: Red Eagle

state: CA

address: 3230 CCSR

institute: Alexander Red Eagle

summary:
Macrophages rapidly engulf apoptotic cells to limit the release of noxious  cellular contents and to restrict autoimmune responses against self antigens.   Although factors participating in recognition and engulfment of apoptotic cells have  been identified, the transcriptional basis for the sensing and silently disposing of  apoptotic cells is unknown.  Here we show that peroxisome proliferator activated  receptor delta (PPARdelta) is induced when macrophages engulf apoptotic cells and  functions as a transcriptional sensor of dying cells.  Genetic deletion of PPARdelta  decreases expression of opsonins, such as C1qb, resulting in impairment of  apoptotic cell clearance and reduction in anti-inflammatory cytokine production.  This  increases autoantibody production and predisposes global and macrophage-specific  PPARdelta deficient mice to autoimmune kidney disease, a phenotype resembling the  human disease systemic lupus erythematosus.  Thus, PPARdelta plays a pivotal role in  orchestrating the timely disposal of apoptotic cells by macrophages, ensuring that  tolerance to self is maintained.
HoxA9 immortalized ES cell derived myeloid precursors were created and differentiated as in Odegaard et al, 2007. After expansion, macrophages were differentiated for 8 days in the presence of MCSF in 20% L929 conditioned media with 2.5% bovine serum albumin in low glucose media. Macrophages were harvested for RNA using Qiagen's RNeasy Kit. A common reference was generated using e17.5 C57Bl/6 embryos. 30ug of either reference or macrophage RNA was labeled with Cy3 and Cy5 (Amersham) and hybridized to Stanford Functional Genomics Facility mouse cDNA microarrays for 16 hours. The arrays were washed and scanned on an Agilent G2505A ChipScan v. A.6.3.1. Florescence values were extracted using GenePix Pro v. 5.0.0.51. The data were normalized using regression correlation. Subsequently, missing values were imputed and significantly differentially expressed genes were found with Significance Analysis of Microarrays. For the Nature Medicine manuscript, significantly differentially expressed genes including genes involved in the process of uptake of apoptotic cells were extracted and clustered by complete linkage using Cluster and visualized using TreeView.
Key to genotypes: "J1 untreated" are WT differentiated macrophages; "18 Untreated" are PPARd-/- differentiated macrophages
Genotype: Wild type (WT) or PPAR delta minus (PPARd -/-) macrophages

first: Justin

last: Odegaard


title: Gene expression profiling of BRCA1-mutated breast tumors

status: Public on Oct 14 2009

city: Madrid

first: Ricardo

last: Fernández-Ramires

state: Madrid

address: Melchor Fdez Almagro, 3

department: Human Cancer Genetics Program

institute: Spanish National Cancer Center

summary:
Background: Breast cancer is a complex disease, encompassed by different clinically and molecularly stratified entities. In 2000, Perou and colleagues demonstrated that tumor phenotypic diversity correlates with differences in global gene expression patterns, which in turn reflect aspects of the biological behavior of the tumors. Gene expression profiling has distinguished sporadic breast tumor sub-classes with genetic, histopathological and clinical differences, however, little is known about the molecular classification of hereditary breast tumors. It has been recently suggested that most tumors arising in BRCA1 mutation carriers display a basal-like phenotype, with the percentages reported in different studies ranging from 44 to almost 100%. In the present study we used expression profiling to produce a molecular classification of BRCA1-associated breast tumors and applied an integrative approach to examine biological dependencies or differences.

Methods and Findings: We used frozen tumor tissue from fourteen patients all of which harbored germline pathological mutations in BRCA1. Total RNA extraction, amplification and labeling with Cy5 were performed using standard protocols. Universal Human Reference RNA (Stratagene) was used as a reference and labeled with Cy3. Each pair of Cy3/Cy5 samples was hybridized onto the CNIO human OncoChip V2, which consists of a spotted microarray with 11,675 cDNA clones from the I.M.A.G.E. Consortium. Two channel ratios (Cy5/Cy3) for each spot were generated and quantified using GenePix Pro 5.1 (Axon Instruments, Inc., Union City, CA, USA). Data were normalized and filtered and multiple statistical analyses were performed. The data are deposited in the GEO database under the accession number GSE12350. A tissue microarray (TMA) containing an independent series of 15 BRCA1 tumors was used to validate some of the results obtained.

We have described molecular signatures that define BRCA1 subclasses depending on the expression of the gene encoding for Estrogen Receptor, ESR1. Signatures were found to be molecularly associated with different biological processes and transcriptional regulatory programs. The signature of ESR1-positive tumors was mainly linked to cell proliferation-related processes and, therefore, regulated by the estrogen receptor, while the signature of ESR1-negative tumors was mainly linked to the immune response and possibly regulated by transcription factors of the REL/NFκB family. These signatures were then verified in an independent series of hereditary and sporadic breast tumors, which revealed a possible prognostic value for each subclass. Over-expression of immune response genes appears to be a common feature of ER-negative sporadic and hereditary breast cancer and is associated with good prognosis. Interestingly, the ESR1-negative tumors were sub-stratified into two groups presenting light differences in the magnitude of the expression of immune response transcripts and REL/NFκB transcription factors, and this could be dependent on the type of germline alteration. In addition, analysis of the human protein-protein interaction network provides the wiring diagram of critical molecular associations in BRCA1 tumorigenesis and identifies close relationships between the different signatures.

Conclusions: In summary, in the present study we have established the gene expression profiling of a series of BRCA1 tumors and found that there is a further degree of heterogeneity beyond the main classification by the expression of ESR1 and the presence or absence of a basal-like phenotype. We have identified specific signatures for ESR1-positive and ESR1-negative BRCA1 tumors, the latter characterized by the enrichment of immune response and cell cycle genes, and have found that slight differences in the level of expression of the immune response stratify the ESR1-negative BRCA1 tumors into two additional sub-groups (A and B) with possible prognostic differences. NFkB could be a major driver responsible for the levels of both immune response and apoptotic genes in this group of tumors, which could in turn be related to the type of germline mutation in BRCA1. This study reveals the molecular complexity of BRCA1 breast tumors, which are found to display similarities to sporadic tumors, and suggests possible prognostic implications.

overall_design: 14 samples (primary breast tumors containing a BRCA1 mutation) were hybridized to a cDNA microarray in order to investigate the possible heterogeneity within the BRCA1 group.

first: Ana

last: Osorio


title: Expression changes associated with siRNA-mediated down regulation of TRMT12

status: Public on Oct 01 2009

city: Bethesda

first: Christopher

last: Pan

state: MD

address: Rm 5228, Bldg 50, South Dr.

department: NHGRI

institute: NIH

summary: A microarray study was performed to identify the genes and pathways to shed light on our observation of TRMT12 overexpression in breast cancer cell lines. In this study, we compared the differential gene expression profiles of the breast cancer cell line SKbr3 treated with TRMT12 siRNA and control siRNA.  RNA was extracted and linearly amplified once, then dye-labeled and co-hybridized to a microarray with over 35,000 oligos (Human Qiagen version 3 set).

overall_design:
A 35k expression arrays were generated by printing Oligo nucleotides from the Human Qiagen version 3 set onto epoxy slides. Total RNA from SKbr3 siRNAs treated cells was amplified using an Ambion kit (Cat#1753), labeled with Cy dyes and hybridized overnight to the oligo chip in a MAUI chamber.  Three different TRMT12 siRNAs were used. Each TRMT12 siRNA is compared to the same control siRNA in triplicate, including one dye swap, for a total of nine hybridizations.

Please note that the data for dye-swap experiments ( hv35565, hv35568, hv35571) was reversed in the raw data already, so that the ratios are in the same direction as the first two replicates.

first: Virginia

last: Rodriguez

first: Abdel

last: Elkahloun

first: Settara

last: Chandrasekharappa


title: Cdx and Hox genes differentially regulate posterior axial growth in mammalian embryos -13 somites embryonic stage

status: Public on Oct 19 2009

city: Utrecht

first: Jacqueline

last: Deschamps

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Hox and Cdx transcription factors regulate embryonic positional identities. Cdx mutant mice display posterior body truncations of the axial skeleton, neuraxis, and caudal uro-rectal structures. We show that trunk Hox genes stimulate axial extension as they can largely rescue these Cdx mutant phenotypes. Conversely, posterior  (paralog group 13) Hox genes can prematurely arrest posterior axial growth when precociously expressed. Our data suggest that the transition from trunk to tail Hox gene expression successively regulates construction and termination of axial structures in the mouse embryo. Thus, Hox genes seem to differentially orchestrate posterior expansion of embryonic tissues during axial morphogenesis as an integral part of their function in specifying head-to-tail identity. In addition, we present evidence that Cdx and Hox transcription factors exert these effects by controlling Wnt signaling. Concomitant regulation of Cyp26a1 expression, restraining retinoic acid signaling in the posterior growth zone, may likewise play a role in timing the trunk-tail transition.

overall_design: A micro-array screen of down regulated and upregulated genes in Cdx2+/-Cdx4-/-  mutant embryos versus wildtype embryos was performed at the embryonic stage of 13 somites. RNA was isolated from the posterior part of the embryos dissected at the same axial level using the last somite boundary as a landmark.  Posterior tissues from pools of 7 embryos of each genotype were pooled. The labeled cRNAs were hybridized on 4X44K Agilent Whole Mouse Genome dual colour Microarrays (G4122F) in a dye swap experiment, resulting in two individual microarrays.


title: Gene Expression Analysis of IgM+CD27+ B Cells in HCV-Infected Individuals with Mixed Cryoglobulinemia

city: New York

first: Edgar

middle: D.

last: Charles

state: NY

address: 1230 York Avenue, Box 64

department: Virology and Infectious Disease

institute: Rockefeller University

summary: Analysis of IgM+CD27+ B cells in individuals with hepatitis C virus (HCV)-associated mixed cryoglobulinemia (MC). We have previously shown that HCV+MC+ individuals have clonal expansions of IgM+ memory B cells. This study aims to characterize differentially expressed genes in peripheral IgM+CD27+ B cells in HCV RNA+MC+ individuals, compared to HCV RNA+MC- subjects and HCV RNA- healthy controls. IgM+ B cells were isolated form donor PBMCs by immunomagnetic negative selection, and the CD27+ subset was further purified by positive selection. 2ng RNA was isolated from cells and amplified using the Nugen WT-Ovation Amplification Kit. cDNA was synthesized, biotin labeled, and hybridized to Illumina human v2 microarrays. Data were collected and analyzed with Illumina Genome Studio. Raw data were normalized by transforming measurements less than 0.01 to 0.01, normalizing per chip to the 50th percentile, and normalizing per gene to the median. Normalized data were then filtered to remove genes with control signals <170. Genes that were significantly upregulated in HCV RNA+MC+ vs HCV RNA+MC- subjects' IgM+CD27+ B cells were identified using a Welch t-test with p-calue cutoff 0.05 and Benjamini-Hochberg false discovery rate of 0.05. The resulting gene list was then filtered for genes showing >2-fold differential expression.

overall_design:
5 HCV Ab-,7 HCV AB+/HCV RNA-, 12 HCV RNA+/IgM MC-, and 15 HCV RNA+/IgM MC+ samples analyzed.
Supplementary file GSE18084_non-normalized_data.txt (Combined III_raw.xls) contains non-normalized data.

first: E

first: L

last: Dustin


title: Fuel Ethanol Yeast Strains

status: Public on Sep 24 2009

city: Stanford

first: Barbara

last: Dunn

institute: Stanford University

summary:
Fuel ethanol is now considered a global energy commodity that is fully competitive with gasoline.  We have determined genome copy number differences that are common to five industrially important fuel ethanol yeast strains responsible for the production of billions of gallons of fuel ethanol per year from sugarcane.  The fuel strains used were CAT1, BG1, PE2, SA1, and VR1 (note that two independent isolates were analyzed, denoted by "-1" and "-2").  These array-CGH data were compared with array-CGH data from nine other non-fuel industrial yeasts: An ale brewing strain ("Sc-ale"), four wine strains (GSY2A, GSY3A, GSY10A, GSY11B), and 4 bakers' yeast strains (GSY149, GSY150, GSY154, GSY155). Our results reveal significant amplifications of the telomeric SNO and SNZ genes only in the fuel strains, whose protein products are involved in the biosynthesis of vitamins B6 (pyridoxine) and B1 (thiamin).  We show that these amplifications allow these yeasts to grow efficiently, especially at high sugar concentrations, regardless of the presence or absence of either of the two vitamins.  Our results reveal important genetic adaptations that have been selected for in the industrial environment, which may be required for the efficient fermentation of biomass-derived sugars from other renewable feedstocks.
A strain or line experiment design type assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species.
Strain Name: fuel strains used for aCGH

first: Boris

last: Stambuk


title: HOXA3 expression in wound tissue

status: Public on Oct 13 2009

city: Manchester

first: Kimberly

last: Mace

address: Michael Smith Building, Oxford Road

department: Division of Cell Matrix Biology & Regenerative Medicine

country: United Kingdom

institute: University of Manchester

summary:
To investigate how HOXA3 expression in wound tissue alters gene expression to control selective recruitment of bone marrow-derived cell populations, we utilized murine whole genome expression arrays (MEEBO arrays) to identify differentially expressed genes in cutaneous wounds from db/db (diabetic) mice treated with either CMV-HOXA3 or control plasmid.  In addition to unwounded control skin, we chose day 4 as the time point to harvest the wounds for RNA isolation, which represents the transition from inflammatory to proliferative phase of wound repair, and precedes the observed differences in BMDC mobilization and recruitment at day 7.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Disease State: cutaneous wound/control skin

overall_design: unwounded skin, wounded skin treated with control plasmid, wounded skin treated with HOXA3

first: John

last: Rinn


title: Genome functional screening identifies GAB2 as a key promoter of anchorage independence in normal and neoplastic cells

status: Public on Oct 21 2009

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

institute: Candiolo Cancer Institute, University of Torino

summary: Acquisition of independence from anchorage to the extracellular matrix is a critical event for onset and progression of solid cancers. To identify and characterize new genes conferring anchorage independence, we transduced MCF10A human normal breast cells with a retroviral cDNA expression library and selected them by growth in suspension. Microarray analysis targeted on library-derived transcripts revealed robust and reproducible enrichment, after selection, of cDNAs encoding the scaffolding adaptor Gab2. Gab2 was confirmed to strongly promote anchorage-independent growth when overexpressed. Interestingly, downregulation by RNAi of endogenous Gab2 in neoplastic cells did not affect their adherent growth, but abrogated their growth in soft agar. Gab2-driven anchorage independence was found to specifically involve activation of the Src-Stat3 signaling axis. A transcriptional “signature” of 205 genes was obtained from GAB2-transduced, anchorage-independent MCF10A cells, and found to contain two main functional modules, respectively controlling proliferation and cell adhesion/migration/invasion. Extensive validation on breast cancer datasets showed that the Gab2-signature provides a robust prognostic classifier for breast cancer metastatic relapse, largely independent from existing clinical and genomic indicators and from estrogen receptor status. This work highlights a pivotal role for GAB2 and its transcriptional targets in anchorage-independent growth and breast cancer metastatic progression.

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Experiment I ("Xenoarray"), 8 samples (GSM455814-GSM455821): four control sample transduced with GFP, of which two selected for growth in the absence of anchorage, and four samples transduced with a mouse testis retroviral expression library, of which two selected for growth in the absence of anchorage. The cells are human, the expression arrays are murine to trace the abundance of library-derived murine transcripts before and after selection.

Experiment II, 12 samples (GSM455826-GSM455837): biological duplicates of MCF10A cells in six different experimental conditions.

first: Alessia

last: Mira

first: Claudio

last: Isella


title: Effect of maternal tobacco smoke exposure on the placental transcriptome

status: Public on Sep 15 2009

city: Prague 2

first: Hana

last: Bruchova

address: U nemocnice 1

department: Molecular Genetics

country: Czech Republic

institute: Institute of Hematology and Transfusion

summary: Smoking in pregnancy increases a woman's risk of preterm delivery resulting in serious health problems during the newborn period, chronic lifelong disabilities (such as cerebral palsy, mental retardation and learning problems), and even death.  Further, smoking women have placental problems such as placenta previa (a low-lying placenta that covers part or all of the opening of the uterus), placental abruption (in which the placenta peels away, partially or almost completely before delivery) often resulting in bleeding during delivery. Gene expression profiles in placentas from women exposed to tobacco smoke in pregnancy and from those without the exposure were determined by Illumina HumRef8 Beadchips with 20,589 gene probes. Comparative analysis, smokers versus non-smokers, revealed differential expression of 241 genes at p<0.05. In smokers we identified deregulated genes that represent general biomarkers of exposure as well as candidate genes likely involved in placental abnormalities found in smoking women. Functional annotation determined deregulated processes that were mainly related to development, metabolism, ion transport, and adhesion.

overall_design: The study comprised 76 women who gave birth to a baby at the Children Hospital of Motol in Prague. All participants provided written informed consent and filled in the questionnaire including information about their smoking history in pregnancy, life style, pregnancy history, delivery course and newborn characteristics. To study effect of tobacco smoke on placental transcriptome, we performed gene expression profiling in placentas from women exposed to tobacco smoke in pregnancy (N=12) and from those without the exposure (N=64).

first: Alzbeta

last: Vasikova

first: Michaela

last: Merkerova

first: Jan

last: Topinka

first: Ivan

last: Balascak

first: Radim

last: Sram

last: Brdicka


title: Whole genome analysis in A549 cells treated for short incubation periods with various concentrations of triptolide

status: Public on Oct 16 2009

city: Toulouse

first: Stéphane

last: VISPE

address: 3 Rue des Satellites

country: France

institute: Laboratoires Pierre Fabre

summary: The purpose of this study was to identify the genes primarily affected by a short treatment of A549 cells with grading concentrations of the natural compound triptolide. The cells were exposed to this molecule before RNA was extracted, then used for whole human genome microarray experiments.

overall_design: 12 samples, corresponding to untreated cells plus three concentrations (0.05, 0.15, 0.45 µM) of tripolide for each time point (1, 2, and 4 hours). Each sample was analysed in triplicate, i.e. three microarray for each condition, making a total of 36 microarrays.

last: Vispé

first: Natacha

last: Novosad

first: Jérome

last: Verdier

first: Laurent

last: Créancier

last: Besse

first: Sophie

last: Bréand

first: Nicolas

last: Guilbaud

first: Jean-Marc

last: Barret

first: Christian

last: Bailly


title: Induction of developmental and inflammatory transcriptomes in PGP fibroblasts

status: Public on Sep 30 2009

city: Boston

first: Je

middle: Hyuk

last: Lee

state: MA

address: 3 Blackfan Circle, CLSB 528

department: Wyss Institute

institute: Harvard Medical School

summary: To identify genetic polymorphisms responsible for common phenotypic variants, one must examine single nucleotide polymorphisms (SNPs) affecting the protein function, or the gene regulation. Since SNPs in the non-coding region are vastly more common, the latter may play a larger role; however, this requires examining the transcriptome from multiple tissues. While induced pluripotent stem cells (iPS) can be used to generate multiple cell types in vitro, a high throughput method for targeted cell reprogramming will be more practical and interpretable. We induce developmental plasticity by transiently expressing pluripotency factors using retrovirus or adenovirus. The induced plasticity brings out differences not ordinarily seen among fibroblasts. We also show that the innate immune response triggered by adenovirus has additional effects on the cellular development and induces multiple markers of inflammation. Because of its scalability, it may enable broad examination of normal and medically relevant complex traits in a large number of individuals.

overall_design: In order see the new transcripts captured by transient pluripotency infection using retrovirus and adenovirus, we took primary fibroblasts and infected them with appropriate viral vectors. The total RNA was extracted and used to see newly induced genes induced by these factors (above the background level). The aim was to see any additional genes captured using transient reprogramming in addition to fibroblasts.

first: Jehyuk

first: In-Hyun

last: Park

first: Nimet

last: Maherali

first: Jie

last: Deng

first: Jun

last: Li

first: Jin

first: Konrad

last: Hochedlinger

first: George

middle: Q

last: Daley

first: Kun

last: Zhang

middle: M

last: Church


title: Differential Gene Expression Profiles in CD34+ Myelodysplastic Syndrome Marrow cells to Disease Subtype and Progression

status: Public on Nov 01 2009

first: Kunju

last: Sridhar

address: 3801 Miranda Ave, bldg 100, Rm E4-230

department: Hematology

summary: Microarray analysis with 40,000 cDNA gene chip arrays determined differential gene expression profiles (GEPs) in CD34+ marrow cells from myelodysplastic syndrome (MDS) patients compared to normal individuals.  Using focused bioinformatics analyses, we found 1175 genes significantly differentially expressed by MDS vs Normal, requiring a minimum of 39 genes to separately classify these patients. Major GEP differences were demonstrated between Normal and MDS patients and between several MDS subgroups: (1) those whose disease remained stable (sMDS) and those who subsequently transformed (tMDS) to acute myeloid leukemia (AML); (2) between del(5q) and other MDS patients. A 6-gene ‘poor risk’ signature was defined which was associated with AML transformation and provided additive prognostic information for IPSS Intermediate-1 patients. Over-expression of genes generating  ribosomal proteins and for other signaling pathways was demonstrated in the tMDS patients. Comparison of del(5q) to the remaining MDS patients showed 1924 differentially expressed genes, with under-expression of 1014 genes, 11 of which were within the 5q31-32 Commonly Deleted Region. These data demonstrated (1) GEPs distinguishing MDS patients from normal and between those with differing clinical outcomes (tMDS vs sMDS) and cytogenetics [eg, del(5q)] ; and (2) molecular criteria refining prognostic categorization and associated biologic processes in MDS.

overall_design: Gene expression profiles from CD34+ cells of 35 MDS subjects and 6 Normals were compared.

first: Doug

last: Ross

first: Robert

last: Tibshirani

first: Atul

last: Butte

first: Peter

middle: L

last: Greenberg


title: HCT116 cells isogenic for p53 expression upon treatment with actinomycin D and nutlin-3

status: Public on Sep 01 2009

city: Singapore

first: Meng Ling

last: Choong

address: 31 Biopolis Way, #03-01 Nanos

department: Drug Discovery

institute: Experimental Therapeutics Centre

summary:
HCT116 wild type cells express p53. The isogenic HCT116 p53KO cells have the p53 gene knocked out. Cells were treated for 16 hours. Dosages for actinomycin D treatment was 1 nM, 10 nM, and 100 nM. Dosage for nutlin-3 was 4 uM.

Keywords: dose response

overall_design: Measuring the gene expression profile of the isogenic cell lines when the cells were treated with 2 different drugs at different concentrations

first: Meng

first: May-Ann


title: Time-series transcriptome profilings of control and Fenretinide-treated human NB4 cells

city: Bristol

first: Hai

last: Fang

address: Woodland Road

department: Department of Computer Science

institute: University of Bristol

summary: Pharmacological intervention of redox balance in cancer cells often results in oxidative stress-mediated apoptosis, attracting much attention for the development of a new generation of targeted therapy in cancer. However, little is known about mechanisms underlying the conversion from oxidative signaling to downstream activities leading cells to death. We here report a systematic detection of transcriptome changes in response to oxidative signals generated in leukemia cells upon fenretinide treatment, implicating the occurrence of numerous stress-responsive events during the fenretinide induced apoptosis, such as redox response, endoplasmic reticulum stress/unfolded protein response, translational repression and proteasome activation. Moreover, the configuration of these relevant events is primarily orchestrated by stress responsive transcription factors, as typically highlighted by NF-E2-related factor-2 (NRF2) and heat shock factor 1 (HSF1). Several lines of evidence suggest that the coordinated regulation of these transcription factors and thus their downstream genes are involved in converting oxidative signaling into downstream stress-responsive events regulating pro-apoptotic and apoptotic activities at the temporal and spatial levels, typifying oxidative stress-mediated programmed death rather than survival in cancer cells. This study provides a roadmap for understanding oxidative stress-mediated apoptosis in cancer cells, which may be further developed into more sophisticated therapeutic protocols, as implicated by synergistic induction of cell apoptosis using proteasome inhibitors with fenretinide.

overall_design: Time-series experiment, fenretinide treated NB4 cells at 19 time points (i.e., 0.25, 0.5, 1, 2, 4, 6, 8, 10, 12, 15, 18, 21, 24, 30, 36, 42, 48, 54 and 60 hours) and untreated NB4 cells at 4 time points (i.e., 0, 8, 12 and 15 hours).

first: Kan-kan

last: Wang

first: Ji


title: Effects of Hfe-/- and dietary iron overload on gene expression in the liver and duodenum of mice

status: Public on Sep 05 2009

city: Tampere

first: Alejandra

last: Rodriguez-Martinez

address: Biokatu 6

department: Institute of Biomedical Technology

institute: University of Tampere

summary: Iron is an essential trace element whose absorption is usually tightly regulated in the duodenum. HFE-related hereditary hemochromatosis (HH) is characterized by abnormally low expression of the iron-regulatory hormone, hepcidin, which results in increased iron absorption. The liver is crucial for iron homeostasis as it is the main production site of hepcidin. The aim of this study was to explore and compare the genome-wide transcriptome response to Hfe deficiency and dietary iron overload in murine liver and duodenum.

overall_design: C57BL/6 male mice were used following the next scheme: 3 Hfe knockout mice and 2 wild type mice as their controls; 3 mice with dietary iron overload and 2 mice fed a standard diet as their controls. 2 tissues were analyzed from all the described mice, liver and duodenum. As an exception, the duodenum samples of only 2 Hfe knockout mice, instead of 3, were used. This makes a total of 19 samples: 10 liver samples and 9 duodenum samples.

last: Rodriguez

first: Tiina

last: Luukkaala

last: Fleming

middle: S

last: Britton

first: Bruce

middle: R

last: Bacon

first: Seppo

last: Parkkila


title: Gene regulation in a novel therapeutic approach that involves ceramide-induced apoptosis pathways

status: Public on Aug 27 2009

city: Toronto

first: Azza

last: Al-Mahrouki

address: 2075 Bayview Avenue

department: Radiation Oncology & Imaging Research

institute: Radiation Oncology, Sunnybrook Health Sciences Centre

summary: We have used human umbilical vein endothelial cell line (HUVEC) as a model to investigate the effect of ultrasound (US) activated micro-bubbles on sensitizing the tumour response to radiation and to check the implication of this approach on gene expression. The use of micro-bubbles in cancer therapy is a novel approach that is being recently investigated, and patterns of gene expressions were not yet characterized. Gene analysis has identified about 19,264 genes; where, 239 – 517 genes have shown more than two folds up-regulation in response to the different treatments. This included a number of genes that are known to be involved in apoptosis and ceramide-induced apoptosis pathways, such as Sphingomyelin phosphodiesterase 2, neutral sphingomyelinase (SMPD2), sphingomyelin phosphodiesterase 1, acid lysosomal (ASM; SMPD1), UDP-galactose ceramide galactosyltransferase (UGT8), cytochrome c oxidase (COX6B1), Caspase-9 and mitogen-activated protein kinase kinase 1 (MAP2K1). To verify these results, we have performed Real time RT-PCR, which indicated an up-regulation that ranged from 2 to 200 folds, specifically in the combined treatment of US, 3.3% micro-bubbles and 8 Gy. The observed higher levels of  expression of UGT8, SMPD2 and Caspase 9-alpha when compared to the control or to radiation only indicated the involvement of  ceramide, which possibly induces apoptosis . These results support the hypothesis that micro-bubbles play a role in increasing sensitization to radiation, and can prove to be an effective cancer therapeutic approach.

middle: A

first: Raffi

last: Karshafian

first: Anoja

last: Giles

first: Gregory

last: Czarnota


title: Circadian Rhythm of Gene Expression Patterns in Liver of Mouse

status: Public on Aug 31 2009

city: Seoul

first: YoungJi

address: 28 Yongon-dong Chongno-gu

institute: Seoul National University Biomedical Informatics

summary:
Genes encoding the circadian pacemaker in the hypothalamic suprachiasmatic nuclei (SCN) of mammals have recently been identified, but the molecubasis of circadian timing in peripheral tissue is not well understood. We used a bead-based microarray to identify mouse liver transcripts that show circadian cycles of abundance under constant conditions.

Keywords: Time course

overall_design: microarray-based expression profiling of mRNA with triplicates in mouse liver for 48 hours at 4-hour intervals

first: Y

first: J

last: Kim


title: Coordinated posttranscriptional mRNA population dynamics during T-cell activation

status: Public on Aug 19 2009

city: Durham

first: Neelanjan

last: Mukherjee

address: 101 Science Drive

department: Institute for Genome Sciences & Policy

institute: Duke University

summary:
Although RNA-binding proteins (RBPs) coordinate many key decisions during cell growth and differentiation, the dynamics of RNA–RBP interactions have not been extensively studied on a global basis. We immunoprecipitated endogenous ribonucleoprotein complexes containing HuR and PABP throughout a T-cell activation time course and identified the associated mRNA populations using microarrays. We used Gaussian mixture modeling as a discriminative model, treating RBP association as a discrete variable (target or not target), and as a generative model, treating RBP-association as a continuous variable (probability of association). We report that HuR interacts with different populations of mRNAs during T-cell activation. These populations encode functionally related proteins that are members of the Wnt pathway and proteins mediating T-cell receptor signaling pathways. Moreover, the mRNA targets of HuR were found to overlap with the targets of other posttranscriptional regulatory factors, indicating combinatorial interdependence of posttranscriptional regulatory networks and modules after activation. Applying HuR mRNA dynamics as a quantitative phenotype in the drug-gene-phenotype Connectivity Map, we identified candidate small molecule effectors of HuR and T-cell activation. We show that one of these candidates, resveratrol, exerts T-cell activation-dependent posttranscriptional effects that are rescued by HuR. Thus, we describe a strategy to systematically link an RBP and condition-specific posttranscriptional effects to small molecule drugs.

Keywords: Timecourse, RIP, Immunoprecipitation, HuR, ELAVL1, PABP, T cell activation

overall_design: Timecourse experiment: 0hr, 4hr, and 12hr post-activation of Jurkat cells. Four samples collected: HuR-IP, PABP-IP, Neg-IP and Total RNA. 3 Biological replicates per condition and sample that were independently grown and harvested.

first: Patrick

last: Lager

first: Matthew

last: Friedersdorf

first: Marshall

last: Thompson

first: Jack

last: Keene


title: Gene expression profiles of thymic neuroendocrine tumors (carcinoids) with ectopic ACTH syndrome

status: Public on Aug 13 2009

first: Hai

last: Fang

summary: Although there has been increased knowledge about the molecular biology of neuroendocrine tumors (NETs), little is known about thymic carcinoids and even less about those with excessive hormone disorders, such as ectopic ACTH syndrome. This study was designed to gain insights into molecular networks underlying the tumorigenesis of thymic carcinoids with ACTH secretion. By an approach integrating cDNA microarray and methods of computational biology, we compare gene expression profile between ACTH-producing thymic carcinoids and normal thymus. Totally there are 63 biological categories increased and 108 decreased in thymic carcinoids. Cell proliferation was stimulated which may explain the relatively uncontrolled cell growth of the tumor. Dysregulation of Notch signaling pathway was likely underlying the neuroendocrine features of this type of tumors. Moreover, the inhibition of the immunity and the increased neuropeptide signaling molecules, POMC and its sorting molecule CPE, made the clinical manifestation reasonable and thus validated the array data. In conclusion, thymic carcinoids have distinguished gene expression pattern from the normal thymus and they are characterized by deregulations of a series of biofunctions, which may be involved in the development of neuroendocrine tumor. This study hence has provided not only a detailed comprehension of the molecular pathogenesis of thymic carcinoid with ectopic ACTH syndrome, but also a road map to approach thymic neuroendocrine tumors at the system level.

overall_design: Transcriptome profilings were performed to identify differentially expressed cDNAs between five samples (NCs) from thymic tumor-suffering patients with ectopic ACTH syndrome (i.e., NC1, NC2, NC3, NC4, NC5, NC6) and six samples (ACs) of the noncancerous thymuses (i.e., AC1, AC2, AC3, AC4, AC5).

first: Kan

middle: K

last: Wang

first: Ji

last: Zhang

first: Yu

middle: F

last: Bi

first: Rui

middle: X

last: Liu

first: Guang

last: Ning


title: Genetic changes in high-grades serous ovarian cancer

status: Public on Oct 02 2009

city: Houston

first: Samuel

last: Mok

state: TX

address: 1515 Holcombe Blvd

institute: University of Texas M.D. Anderson Cancer Center

summary: Comparative genomic hybridization analysis on advanced stage high-grade serous ovarian cancer.

overall_design: CGH was performed on 42 DNA isolated from microdissected advanced stage high-grade serous ovarian cancer.

middle: C

first: Michael

last: Birrer

first: Kwong-kowk

last: Wong


title: CGH data from AID WT vs AID KO BCR-ABL1 mouse leukemia cells

status: Public on Aug 15 2009

city: Los Angeles

first: Markus

last: Müschen

address: 4650 Sunset Blvd

department: Childrens Hospital Los Angeles

institute: University of Southern California

summary:
Activation-induced cytidine deaminase (AID) specific amplifications and deletions in BCR-ABL1 positive Leukemia mouse cells.

Bone marrow from Balb/CJ WT and Balb/CJ AID KO mice was transduced with BCR-ABL1. The AID specific amplifications and deletions where analyzed with an Agilent 244A mouse whole Genome CGH Array.

overall_design:
The AID specific amplifications and deletions where analyzed with an Agilent 244A mouse whole Genome CGH Array.
3 WT samples where compared to AID KO samples.

1.) WT MIG1_Cy5 vs KO MIG_Cy3
2.) WT MIG2_Cy5 vs KO MIG_Cy3
3.) WT MIG3_Cy5 vs KO MIG_Cy3


title: Microarray analysis on tumours of mice supplemented with oil palm phenolics (OPP)

status: Public on Aug 12 2009

city: Kajang

first: Soon-Sen

last: Leow

state: Selangor

address: No. 6, Persiaran Institusi, Bandar Baru Bangi

country: Malaysia

institute: Malaysian Palm Oil Board

summary: OPP (1500 ppm gallic acid equivalent (GAE)) was supplemented to BALB/c mice inoculated subcutaneously with J558 myeloma cells at the dorsum of the neck in order to observe possible anti-cancer effects. Tumours which developed were harvested four weeks after inoculation of the cells for gene expression studies. Results show that genes involved in the cell cycle were differentially expressed, and that OPP may have anti-cancer properties in vivo.

overall_design: Total RNA obtained from J558 tumours which developed in BALB/c mice given OPP (four weeks after subcutaneous inoculation of J558 myeloma cells) were compared to controls given distilled water (three replicates in the treatment group versus four replicates in the control group)

first: Soon

first: Sekaran

last: Devi

first: Sambanthamurthi

last: Ravigadevi


title: Profiling the target genes for ZIP repressor in MCF-7

status: Public on Aug 21 2009

city: Beijing

first: Yongfeng

last: Shang

address: 38 Xue Yuan Road

department: Biochemistry and Molecular Biology

country: China

institute: Peking University

summary: Using ChIP-DSL technology from Aviva Systems Biology to find out the whole genome targets for ZIP transcription repressor

overall_design: We analyzed arrays using specific ZIP antibody and negative control to acquire the enriched ratio of each gene


title: Macrophage-specific inhibition of NF-κB activation impairs foam cell survival

status: Public on Aug 11 2009

city: Utrecht

first: Joost

middle: Ougust

last: Fledderus

address: Heidelberglaan 100, Huispostnummer G02-402

department: Vascular Medicine

institute: University Medical Center Utrecht

summary:
Macrophage death in advanced atherosclerotic lesions is a key event in the conversion of benign lesions to vulnerable plaques. One fundamental transcription factor that has been shown to play a pivotal role in cell death/survival is nuclear factor kB (NF-kB). Still, the relevance of this key transcription factor for macrophage-derived foam cell survival has not been unequivocally resolved at the molecular level. THP-1 monocytic cell lines were generated in which NF-kB activation is specifically inhibited by overexpression of a trans-dominant, non-degradable form of IkBa (IkBa (32A/36A)) under control of the macrophage-specific SR-A promoter. A diminished lipid loading during NF-κB inhibition during foam cell formation was accompanied by increased cell death. A genome-wide expression profile of NF-kB-dependent genes during foam cell formation was established showing a widespread effect on the macrophage transcriptome. The three largest functional gene clusters identified and validated by independent techniques, were those involved in lipid metabolism, apoptosis and oxidative stress. The net result of these complex gene expression changes invoked by inhibition of NF-κB activation during lipid loading is a reduction of foam cell survival through caspase-dependent apoptosis. Thus, the NF-kB-dependent gene repertoire seems essential for sustained macrophage survival during the process of pathological lipid loading.

Keywords: genetic modification, lipid loading, timecourse

overall_design: THP-1 cells and two different THP-1 IkB mutants (A3 and A12) were exposed to PMA to induce macrophage differentiation and subsequently loaded with oxidized LDL or vehicle for 5 or 8 days. One replicate per array, a total of 15 arrays. A common reference pool, composed of an equimolar mixture of all samples, was labeled with Cy3 and hybridized against the Cy5-labeled experimental sample.

first: Valerie

last: Ferreira

middle: O

first: Anton

middle: J

last: Horrevoets


title: Microarray analysis of heat and/or drought sensitivity of early grain development in wheat (Triticum aestivum L.)

status: Public on Sep 24 2009

city: Szeged

first: Attila

last: Szűcs

address: Somogyi utca 4

department: Faculty of Medical Research

country: Hungary

institute: University of Szeged

summary: Based on EST-based in silico gene expression analysis a 15k oligonucleotid microarray has been developped in order to monitor environmental stress-dependent gene expression changes in the wheat caryopsis. Using this array, the effect of water withdrawal, with and and without additional heat stress, during the first five days of grain development (0-5 DAA) has been investigated on two wheat cultivars differing in their drought sensitivity. The combined effect of heat and drought (DH) on gene expression was much significant (8-10% of the investigated genes changed >2-fold) in contrast to drought alone (1.5%). Drought and heat stress resulted in the co-ordinated change of the expression of storage proteins, some enzymes involved in sugar/starch metabolism, cell division-related and histone proteins, certain transcription factors, heat shock proteins, proteases and aquaporins. The potential link between the observed gene expression changes and the parallel histological observations indicating the accelerated development of the stressed grains is discussed.

overall_design: 8 samples with 2 biological replicate using dye swap


title: Profiling the target genes for LSD1, MTA1, MTA2, and MTA3 in MCF-7

summary: Using ChIP-DSL technology from AVIVA SYSTEMS BIOLOGY to find out the whole genome targets for LSD1, MTA1, MTA2, and MTA3

overall_design: We analyzed arrays using antibodies against LSD1, MTA1, MTA2, or MTA3 and negative control to acquire the enriched ratio of each gene.


title: Expression profiling of Muscle tissue from C57BL/6J X C3H/HeJ)F2 and (C3H/HeJ X C57BL/6J)F2

status: Public on Aug 10 2009

first: Leslie

last: Ingram-drake

department: Medicine/MIMG/Human Genetics

institute: UCLA

summary: The purpose of this experiment was to determine the expression traits in animals from F2 intercross of inbred strains C57BL/6J, C3H/HeJ. (N=309, 164 males and 145 females).

overall_design: Muscle from 285 F2 female and male mice were generated by intercrossing F1 mice. Mice were fed chow diet containing 4% fat (Ralston-Purina Co., St. Louis, MO) until 8 weeks of age and then were placed on a high-fat "Western" diet containing 42% fat and 0.15% cholesterol (Teklad 88137, Harlan Teklad, Madison WI) for 12 weeks. At 20 weeks mice were sacrificed, after a 12-hour fast Muscle tissues were dissected and flash frozen in LN2 and stored at -80°C. Keywords=Genetics of Gene Expression Keywords Keywords=C57B1/J6 Keywords=C3H/HeJ


title: Breast tumor gene expression profiling for assessment of sufficient tumor cells for microarray diagnostic

status: Public on Aug 17 2009

city: Amsterdam

first: Paul

last: Roepman

address: Science Park 406

institute: Agendia

summary: Gene expression profiling of breast cancer primary tumor was performed to identify gene expression that is related to the presence of sufficient tumor cells. These gene profile can be used for identification of tumor samples that are eligible for microarray diagnostics.

overall_design: A cohort of 403 early-stage primary breast cancer tumors was analyzed against a breast cancer reference pool

first: Arenda

last: Schuurman

first: Leonie

last: Delahaye

first: Anke

middle: T

last: Witteveen

first: Arno

middle: N

last: Floore

first: Annuska

last: Glas


title: Sex-dependent gene regulatory networks of the heart rhythm

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

summary: Expression level, control and intercoordination of 66 selected heart rhythm determinant (HRD) genes were compared in atria and ventricles of 4 male and 4 female adult mice. We found that genes encoding various adrenergic receptors, ankyrins, ion channels and transporters, connexins and other components of the intercalated discs form a complex network that is chamber dependent and differs between the two sexes. In addition, most HRD genes in atria had higher expression in males than in females, while in ventricles expression levels were mostly higher in females than in males. Moreover, significant chamber-differences were observed between the sexes, with higher expression in atria than ventricles for males and higher expression in ventricles than atria for females. We have ranked the selected genes according to their prominence in controlling the HRD gene web through expression coordination with the other web genes and protecting the web though their own expression stability. Interestingly, the prominence hierarchy was substantially different between the two sexes. Taken together these findings indicate that the organizational principles of the heart rhythm transcriptome are sex-dependent, with the newly introduced prominence analysis allowing identification of genes that are pivotal for the sexual dichotomy.

overall_design: Four adult male (M) and 4 adult female (F) mice were decapitated, the hearts removed and atria (A) and ventricles (V) collected in separate tubes. 20 µg total RNA extracted in Trizol from each of the 16 samples was reverse transcribed in the presence of fluorescent Alexa Fluor®_647 and Alexa Fluor®_555-aha-dUTPs (Invitrogen, CA) to obtain labeled cDNAs  Red and green-labeled samples of biological replicas were then co-hybridized (“multiple yellow” strategy) overnight at 50°C with mouse MO36k oligonucleotide arrays printed by Duke University (http://microarray.genome.duke.edu/spotted-arrays) with Operon Mouse Oligo Set, version 4.0. After washing (0.1% SDS and 1% SSC) to remove the non-hybridized cDNA, each array was scanned with GenePix 4000B scanner (MDS, Toronto, Canada) and images were primarily analyzed with GenePixPro 6.0 (Axon Instruments, CA).

first: Sanda

first: Neil

last: Thomas

first: David

last: Spray


title: DIDS protects against neuronal injury

city: La Jolla

first: Hang

last: Yao

address: 9500 Gilman Dr

institute: UCSD

summary: Using long-oligo beadschip arrays, we examined the global gene expression profile in cultured hippocampal slices under the simulated ischemic condition with and without the presence of DIDS .

overall_design:
Control-ACSF: cultured hippocampal slices were incubated with ACSF for 2 hours and were analysed on whole-genome expression chips to determine the gene expression profile. This group was used as controls for IS-treated groups and ACSF+DIDS-treated grous.

IS: cultured hippocampal slices were treated wtih IS for 2 hours and the gene expression was analyzed and compared with the control group.

IS+DIDS: cultured slices were treated with both IS and DIDS for 2 hours and the gene expression profile was determined. Differentially expression genes were identified by comparing with IS group.

ACSF+DIDS: cultured slices were incubated with both ACSF and DIDS for 2 hours and gene expression profile was determined. This group was used as a control for IS+DIDS group.

ACSF: artificial cerebral spinal fluid
DIDS: 4,4'-diisothiocyanatostilbene-2,2'-disulfonic acid
IS: ischemic solution


title: CAST/EiJ x C57BL/6J cross data

first: Tomas

last: Babak

state: ON

address: 112 College St

department: Banting and Best Department of Medical Research

institute: Best Institute

summary: Here we introduce a test for lineage-specific selection of cis-regulation that can be applied to any gene set of interest.  Applying the test to hundreds of gene sets in two diverged subspecies of mouse, we find evidence for selection acting on the cis-regulation of several functional classes, including those involved in both physiology (e.g. mitochondria-related genes and growth regulators) and behavior (e.g. locomotory-related genes and memory-related genes).  These positively selected gene sets implicate potential targets of positive selection that are supported by quantitative trait loci, and accurately predict a number of phenotypic differences between the two subspecies, suggesting that the divergence in these traits may have been driven by adaptive evolution.

overall_design:
Dual-channel ratio data for 23,653 genes across 3 tissues in 443 CASTxB6 F2 mice

NO RAW DATA HAS BEEN SUBMITTED TO GEO AT THIS TIME. THIS SUBMISSION WAS APPROVED AT THE REQUEST OF THE SUBMITTER TO ALLOW PUBLICATION REVIEWER ACCESS.

first: Hunter

last: Fraser

first: Eric

middle: E

last: Schadt


title: Expression profiling of Liver tissue from C57BL/6J X C3H/HeJ)F2 and (C3H/HeJ X C57BL/6J )F2

overall_design: Liver from 302 F2 female and male mice were generated by intercrossing F1 mice. Mice were fed chow diet containing 4% fat (Ralston-Purina Co., St. Louis, MO) until 8 weeks of age and then were placed on a high-fat "Western" diet containing 42% fat and 0.15% cholesterol (Teklad 88137, Harlan Teklad, Madison WI) for 12 weeks. At 20 weeks mice were sacrificed, after a 12-hour fast liver tissues were dissected and flash frozen in LN2 and stored at -80°C. Keywords=Genetics of Gene Expression Keywords Keywords=C57B1/J6 Keywords=C3H/HeJ


title: Expression profiling of Adipose tissue from C57BL/6J X C3H/HeJ)F2 and (C3H/HeJ X C57BL/6J )F2

overall_design:
Adipose from 295 F2 female and male mice were generated by intercrossing F1 mice. Mice were fed chow diet containing 4% fat (Ralston-Purina Co., St. Louis, MO) until 8 weeks of age and then were placed on a high-fat "Western" diet containing 42% fat and 0.15% cholesterol
(Teklad 88137, Harlan Teklad, Madison WI) for 12 weeks. At 20 weeks mice were sacrificed, after a 12-hour fast adipose tissues were dissected and flash frozen in LN2 and stored at -80°C. Keywords=Genetics of Gene Expression Keywords Keywords=C57B1/J6 Keywords=C3H/HeJ

first: Aldons

last: Lusis


title: Gene expression changes associated with myocarditis and fibrosis in hearts of mice with chronic chagasic cardiomyopathy

status: Public on Aug 07 2009

summary: Chronic chagasic cardiomyopathy is a leading cause of heart failure in Latin American countries. About 30% of Trypanosoma cruzi-infected individuals develop this severe symptomatic form of the disease, characterized by intense inflammatory response accompanied by fibrosis deposition in the heart. We performed a microarray analysis of a mouse model of this disease and identified >5% alterations of gene expression in the heart. Most of the upregulations were associated with immune-inflammatory responses (chemokines, adhesion molecules, cathepsins and MHC molecules) and fibrosis deposition (extracellular matrix components, lysyl oxidase and Timp1). Our results indicate potentially relevant factors involved in the pathogenesis of the disease that may provide new therapeutic targets in chronic Chagas’ disease.

overall_design: The heart transcriptomes of 4 age-mached Trypanosoma cruzi-infected and 4 control C57Bl/6 mice were profiled and compared using Duke Mouse 30k Oligonucleotide Arrays (Operon V3.0.1) hybridized in the "multiple yellow" strategy described in Iacobas et al,  Biochem Biophys Res Commun. 2006 349(1):329-38.

first: Milena

middle: B

last: Soares

first: Ricardo

last: de Lima

first: Leonardo

last: Rocha

first: Juliana

last: Vasconcelos

first: Silvia

last: Rogatto

last: dos santos

first: Regina

last: Goldenberg

first: Herbert

last: Tanowitz

first: Antonio

last: de Carvalho

first: david


title: CHO cells with enhanced and abolished gamma-secretase activity

status: Public on Aug 01 2009

city: Lausanne

first: Patrick

last: Fraering

state: Vaud

address: station no15

department: Life Sciences / Brain Mind Institute

institute: Swiss Federal Institute of Technology

summary: γ-secretase is an intra-membrane-cleaving aspartyl protease implicated in the processing of a wide range of type I membrane proteins including the Notch receptor and the amyloid-β precursor protein (APP). It thus regulates a diverse array of cellular and biological processes including the differentiation of neuronal embryonic stem cells, or intestinal stem cells, with the latter controlling the self-renewing of the intestinal epithelium. Indeed, proteolysis of these proteins by  γ-secretase triggers signaling cascades by releasing intracellular domains (ICDs) which, following association with adaptor proteins and nuclear translocation, modulate the transcription of different genes by binding directly to their promoters. The pronounced proliferative and regenerative effects of Notch signaling and its implication in the generation of the Aβ-peptides, makes  γ-secretase a therapeutic target for several types of cancer and for Alzheimer’s disease. To investigate the broad effects of γ-secretase activity onto the cellular transcriptome, Chinese hamster ovary (CHO) cells with enhanced γ-secretase were compared to cells with abolished γ-secretase activity via a microarray designed for a genetically close species, mouse. Our findings will potentially help to decipher the biology of γ-secretase, including a better understanding of the roles of this enzyme in gene transcription.

overall_design: We compared the transcriptomes of two CHO cell lines displaying extreme differences in γ-secretase activity. The S-1 cell line overexpressed the four components of γ-secretase (NCT, APH1aL, PS1, and PEN2) and was characterized by a marked increase in the level of PS1 heterodimers associated with 8-fold increased γ-secretase activity compared to untransfected controls. The other cell line consisted of wild type CHO cells incubated with DAPT, a well-known γ-secretase inhibitor. The two cell lines were used in combination with a mouse microarray to analyze gene transcription under enhanced γ-secretase. Two samples, S1 and DAPT treated CHO- were used in biological triplicates each.

first: Alexandra

middle: I

last: Magold

first: Matthias

last: Cacquevel

first: Keith

last: Harshman


title: A gene expression fingerprint in mental retardation reflects disease causing defects in the histone demethylase KDM5

status: Public on Jul 29 2009

city: Berlin

first: Lars

middle: Riff

last: Jensen

address: Ihnestrasse 73

department: Human Molecular Genetics

institute: Max Planck Institute

summary: Mutations in KDM5C, (previously named SMCX or JARID1C) a gene that encodes a transcriptional regulator with histone-demethylase activity specific for di- and tri-methylated H3K4, are a comparatively frequent cause of non-syndromic X-linked mental retardation (NS-XLMR). Specific transcriptional targets of KDM5C, however, are still unknown and the effects of KDM5C deficiency on gene expression have not yet been investigated. Here we present the results of gene expression profiling performed on lymphoblastoid cell lines as well as blood from patients with mutations in KDM5C. Using whole genome expression arrays and QRT-PCR we identified several genes, including CMKOR1, JARID1B and KIAA0469 that were consistently deregulated in both tissues. These findings shed light on the patho-mechanisms underlying mental retardation and may have implications for future diagnostics of this heterogeneous disorder.

overall_design: We compared the mRNA expression of a patient lymphoblastoid cell line deficient for KDM5C with that of three controls to identify genes that are deregulated in the patient cell line.

first: Andreas

middle: W

last: Kuss


title: Expression profiling of Brain tissue from C57BL/6J X C3H/HeJ)F2 and (C3H/HeJ X C57BL/6J)F2

first: Leslie

last: Ingram-drake

overall_design: Brain from 292 F2 female and male mice were generated by intercrossing F1 mice. Mice were fed chow diet containing 4% fat (Ralston-Purina Co., St. Louis, MO) until 8 weeks of age and then were placed on a high-fat "Western" diet containing 42% fat and 0.15%cholesterol (Teklad 88137, Harlan Teklad, Madison WI) for 12 weeks. At 20 weeks mice were sacrificed, after a 12-hour fast Brain tissues were dissected and flash frozen in LN2 and stored at -80°C.


title: Systems biology analysis of Korean red ginseng effects on Immobilization stressed mice brain

status: Public on Aug 09 2009

city: Suwon

first: Sangdun

last: Choi

address: Woncheon-dong, Yeongtong-gu

department: Department of Molecular Science and Technology

institute: Ajou University

summary:
Here we present molecular mechanisms of Korean red ginseng (KRG) on immobilization stresses

Keywords: stress response

overall_design: Mice were divided into three groups (3 mice / group): control, stress + no treat, and stress + Korean Red Ginseng (KRG, 100 mg). Stress + KRG group were given KRG  100 mg orally for 7 days and then exposed to immobilization stress for 45 min. stress + no treat group were administrated with phosphate buffer saline (d-PBS, pH 7.4) together with IMO stress for 45 min.

first: Mi-Jeong

last: Lee

first: Eun-Hye

last: Kim

first: Soo-Cheol

first: DongKwon

last: Rhee


title: The Central Role of c-Myc during Malignant Conversion in Human Hepatocarcinogenesis

status: Public on Aug 04 2009

city: Bethesda

first: Snorri

middle: S

last: Thorgeirsson

address: 37 Convent Dr. # 4146

department: Laboratory of Experimental Carcinogenesis

institute: National Cancer institute/NIH

summary: Hepatocarcinogenesis is a multi-stage process in which precursor lesions progress into early hepatocellular carcinomas (eHCC) by sequential accumulation of multiple genetic and epigenetic alterations. To decode the molecular events during early stages of liver carcinogenesis, we performed gene expression profiling on cirrhotic (regenerative) and dysplastic nodules (DN) as well as eHCC. Although considerable heterogeneity was observed at the regenerative and dysplastic stages, clear differences were detected between DN and eHCC which included 460 differentially expressed genes. Functional analysis of the significant gene set identified the MYC oncogene as a plausible driver gene for malignant conversion of the dysplastic nodules. In addition, gene set enrichment analysis (GSEA) revealed a remarkable enrichment of MYC up-regulated gene set in eHCC versus dysplasia. Presence of the MYC signature significantly correlated with increased expression of CSN5 as well as with the higher overall transcription rate of genes located in the 8q chromosome region. Furthermore, a classifier constructed from MYC target genes could robustly discriminate eHCC from high- and low-grade dysplastic nodules. In conclusion, our study identified unique expression patterns associated with the transition of high-grade dysplastic nodules to early HCC and demonstrated that activation of the MYC transcription signature is critical for the malignant conversion of pre-neoplastic liver lesions.

overall_design: Samples from forty-nine nodular liver lesions including 24 regenerative (cirrhotic) nodules (CN), 3 low-grade (LGDN), 12 high-grade dysplastic nodules (HGDN) and 10 early hepatocellular carcinomas (Early HCC) were used. The Human Operon V2 oligonucleotide library containing 22K features representing expressed sequences was printed to glass arrays in the Advanced Technology Center (National Cancer Institute, Gaithersburg, MD). The aRNA probes were fragmented and hybridized to the microarray slides following the standard procedures. All samples were hybridized against a common amplified reference RNA pooled from normal liver samples. Experimental duplicates were prepared following a reverse-flour design.


title: Reconstruction of gene interaction networks by in vitro RNA interference and global expression analysis

city: Heidelberg

first: Mark

last: Fellmann

address: INF 580

department: Molecular Genome Analysis

institute: DKFZ

summary:
We here used the technology of RNA interference or selective treatment of the ESR1 and cDNA microarrays to reconstruct a network between genes known to be disregulated in ER-positive breast cancer diseases. Therefor single genes of high importance were silenced and the effect of this pertubation was measured with cDNA microarrays.

Keywords: Network Reconstruction, RNAi, siRNA, Interaction Network

overall_design: human ER-positive breast cancer cell line was cultivated as described and transfection with chemically synthesized siRNAs was performed according to standard HiPerFect transfection protocol by Qiagen (Hilden, Germany) At least 4 cDNA-microarrays were hybridized in dye-swap method for the silencing of every gene of interest. To minimize off-target effects we used at least two different siRNAs per gene.

first: Holger

last: Fröhlich

first: Markus

last: Ruschhaupt

first: Ruprecht

last: Kuner

last: Sültmann


title: Gene expression in LCMV-specific Blimp-1 deficient effector CD8+ T cells compared to wildtype effector CD8+ T cells

status: Public on Jul 22 2009

city: New Haven

first: Rachel

last: Rutishauser

state: CT

address: 1 Gilbert St., TAC Building

department: Immunobiology

institute: Yale University

summary: Antigen-specific effector CD8+ T cells deficient in Blimp-1 (Prdm1) do not acquire maximal effector functions, evade terminal differentiation, and more rapidly acquire some hallmark properties of memory CD8+ T cells. In this study, we compared the gene expression profiles of wildtype and Prdm1-/- LCMV-specific effector CD8+ T cells to better understand the molecular mechanisms underlying this striking phenotype.

overall_design: DNA microarray analysis was performed of DbGP33-41 and DbNP396-404 tetramer-positive effector CD8+ T cells FACS-sorted at day 8 post-LCMV infection from four independent samples of either Blimp-1 conditional knockout mice (CKO;  Blimp-1flox/flox x GranzymeB-cre+) or wildtype (WT) littermate controls.

middle: L

first: Gislaine

middle: A

last: Martins

first: Sergey

last: Kalachikov

first: Anmol

last: Chandele

first: Ian

last: Parish

first: Joshy

last: Jacob

first: Kathryn

last: Calame

first: Susan

middle: M

last: Kaech


title: Illumina HapMap (HumanCNV370-Duov1)

status: Public on Jul 27 2009

city: San Diego

last: Illumina Inc.

address: 9885 Towne Centre Drive

institute: Illumina Inc.

summary: HapMap samples

overall_design: 123 samples from Illumina_CNV370_Samples_Confidential.txt


title: Identification of novel markers for malignant pleural mesothelioma diagnosis

status: Public on Jul 25 2009

city: Nantes

first: Raluca

last: TEUSAN

address: 1, rue gaston veil

institute: INSERM U915

summary: Diagnosis of malignant pleural mesothelioma (MPM) is difficult, the most common differential diagnosis being benign pleural diseases and metastatic adenocarcinomas. In order to identify novel markers able to improve diagnostic accuracy, we performed a genome-wide gene expression analysis on tumor cells lines established from pleural effusions (13 MPM and 4 lung adenocarcinoma). Our microarray analysis led to the identification of genes encoding novel cellular and soluble markers whose expression was validated by RT-qPCR. Immunohistochemical staining of tumor biopsies with anti-type-III collagen antibodies were positive in mesothelioma cells but not in adenocarcinoma cells. Using ELISA, we showed that the C-C motif chemokine 2 (CCL2) concentration was significantly higher in pleural effusions from patients with mesothelioma (n = 61) than in subjects with adenocarcinoma (n = 25) or with benign pleural effusions (n = 15): median (interquartile range) = 2.99 ng/mL (1.76-6.01) versus 0.99 ng/mL (0.51-1.83) and 1.47 ng/mL (0.80-1.56), respectively, P < 0.0001. Conversely, the galectin-3 concentration was lower in mesothelioma: 11.50 ng/mL (6.73-23.53) versus 24.74 ng/mL (20.42-70.35) and 17.64 ng/mL (14.81-24.68), respectively, P < 0.0001. The AUC for CCL2 were 0.8030 and 0.7716 for differentiating mesothelioma from adenocarcinoma or benign effusions, respectively. Similarly, the AUC obtained for galectin-3 were 0.7980 and 0.6923, respectively. In conclusion, type-III collagen, CCL2 and galectin-3 are promising new diagnostic markers for mesothelioma.

overall_design:
two-condition experiment: ADCA vs MPM cell lines

13 MPM and 4 ADCA cell lines were independantly grown and harvested

3 biological replicates per cell line, one replicate per array

first: Fabien

last: Gueugnon

first: Sabrina

last: Leclercq


title: In vitro response of fibroblasts isolated from patients with immunodeficiencies

status: Public on Jul 15 2009

city: Dallas

first: Damien

last: Chaussabel

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

summary: Children with autosomal recessive deficiency suffer from life-threatening, often recurrent viral or bacterial infections. We have profiled transcriptional responses of fibroblast cell lines derived from patients deficient for key regulators of immune responses such as MYD88, IRAK4, UNC93B, STAT1 or NEMO. This systems immunology approach revealed distinct patterns or responsiveness to stimuli activating the Toll-like/IL1 Receptor pathway in either an MYD88-dependent (IL1B) or independent (poly(I:C)) fashion, or activating the TNF pathway. The prototypic signatures in cell lines derived from patients were as follows: NEMO-deficient cells were unresponsive to all three stimuli, UNC-93B-deficient cells did not respond to poly(I:C), and STAT1-deficient cells responded only weakly to poly(I:C) after eight hours (not shown). MyD88- and IRAK-4-deficient cells had indistinguishable phenotypes, both being unresponsive to IL-1B at both time points. The signatures obtained in response to TNF and poly(I:C) (via TLR3) in these cells were similar to that of control fibroblasts.

overall_design: Skin fibroblast cell lines were derived from controls (n=3), patients with deficiencies for MYD88 (n=1), IRAK4 (n=1), UNC93B (n=2), STAT1 (n=1) and NEMO (n=1). Cells were cultured for 2 or 8 hours in the presence of TNF, IL1B or poly(IC) or left unstimulated for the same length of time. Transcriptional profiles were acquired using Illumina Hu6 V2 BeadChips in two separate batches (2 hours, 8 hours)

first: Horst

last: von Bernuth

first: Capucine

last: Picard

first: Zhongbo

last: Jin

first: Rungnapa

last: Pankla

first: Hui

last: Xiao

first: Cheng-Lung

last: Ku

first: Maya

last: Chrabieh

first: Imen

last: Ben Mustapha

first: Pegah

last: Gandhil

first: Yildiz

last: Camcioglu

first: Júlia

last: Vasconcelos

first: Nicolas

last: Sirvent

first: Margarida

last: Guedes

first: Artur-Bonito

last: Vitor

first: María-José

last: Herrero-Mata

first: Juan-Ignacio

last: Aróstegui

first: Carlos

last: Rodrigo-Gonzalez de Liria

first: Laia

last: Alsina

first: Estibaliz

last: Ruiz-Ortiz

first: Manel

last: Juan

first: Claudia

last: Fortuny

first: Jordi

last: Yagüe

last: Antón

first: Mariona

last: Pascal

first: Ben-Zion

last: Garty

first: Helen

last: Chapel

first: Andrew

last: Issekutz

first: László

last: Maródi

last: Rodriguez-Gallego

first: Jacques

last: Banchereau

first: Laurent

last: Abel

first: Xiaoxia

last: Li

first: Anne

last: Puel

first: Jean-Laurent

last: Casanova