title: The transcriptomes of two heritable cell types illuminate the circuit governing their differentiation

city: Foster City

first: Brian

last: Tuch

address: 850 Lincoln Center Dr.

country: USA

institute: Life Technologies

type: Expression profiling by high throughput sequencing

summary: The differentiation of cells into distinct cell types, each of which is heritable for many generations, underlies many biological phenomena. White and opaque cells of the fungal pathogen Candida albicans are two such heritable cell types, each thought to be adapted to unique niches within their human host.  To systematically investigate the differences between the two cell types, we performed strand-specific massively-parallel sequencing of RNA from C. albicans white and opaque cells. Combining the resulting data from both cell types, we first substantially re-annotated the C. albicans transcriptome, finding 1443 novel coding and non-coding transcriptionally active regions.  Using the new annotation, we compared differences in transcript abundance between the two cell types with the genomic regions bound by the master regulator of the white-opaque switch (Wor1).  We found that the revised transcriptional landscape considerably alters our understanding of the circuit governing differentiation.  In particular, we can now resolve the poor concordance between binding of the master regulator and the differential expression of adjacent genes, a discrepancy observed in many other studies of cell differentiation.  More than one third of the Wor1-bound differentially-expressed transcripts were previously unannotated, which explains the formerly puzzling presence of Wor1 at these positions along the genome.  Indeed, many of these newly identified Wor1-regulated genes are non-coding and transcribed antisense to coding transcripts.  We also found that 5' and 3' untranslated regions (UTRs) of mRNAs in the circuit are unusually long and that 5' UTRs often differ in length between white and opaque cells.  These observations suggest that the use of alternative promoters is widespread in the circuit and that important regulatory information is carried in the long UTRs.  Further analysis revealed that the revised Wor1 circuit bears several striking similarities to the Oct4 circuit that specifies the pluripotency of mammalian embryonic stem cells.  Additional characteristics shared with the Oct4 circuit suggest a set of general hallmarks characteristic of heritable differentiation states in eukaryotes.

overall_design: RNA-Seq was applied to Candida albicans white and opaque cells to identify novel transcripts and UTRs that are differentially regulated between the two cell types. Two biological replicates each of white and opaque cell cultures. One of the white cell RNA samples was split just after isolation to allow a comparison of the poly(A)-selection and ribo-depletion sample preparation strategies.

first: Quinn

last: Mitrovich

first: Cinna

last: Monighetti

first: Clarissa

last: Nobile

first: Alexander

last: Johnson


title: Expression data from Complex genetics sarcomas (cohort 1 and 2)

status: Public on Jun 30 2010

city: Bordeaux

first: fred

last: chibon

address: 229 cours de l'argonne

department: Pathology

country: France

institute: Institut Bergonie

summary:
For this study, we selected, from the French Sarcoma Group (FSG) database, soft tissue sarcomas with no recurrent chromosomal translocations and for which a frozen tissue of the untreated primary tumor was available. Three hundred and ten sarcomas  have been studied. They are split in two cohorts.
We used microarrays to detail the global programme of gene expression underlying the tumor biology

overall_design: Every cases has been histologically reviewed by the pathologist subgroup and classified according to the 2002 WHO classification using histology, immunohistochemistry and molecular genetic and cytogenetic when needed

first: Frederic

last: Chibon

first: Jean-Michel

last: Coindre

first: Alain

last: Aurias


title: Effects of Rituximab on global gene expression profiles in the RA synovium

status: Public on Oct 19 2010

city: Brussels

first: Bernard

middle: Robert

last: Lauwerys

address: Avenue Hippocrate 10

department: Institut de Recherches Expérimentales et Cliniques

country: Belgium

institute: Université catholique de Louvain

summary:
Objective: Rituximab displays therapeutic benefits in the treatment of rheumatoid arthritis (RA) patients resistant to TNF blockade. However, the precise role of B cells in the pathogenesis of RA is still unknown. In this study we investigated the global molecular effects of rituximab in synovial biopsies obtained from anti-TNF resistant RA patients before and after administration of the drug.

Methods: Paired synovial biopsies were obtained from the affected knee of anti-TNF resistant RA patients before (T0) and 12 weeks after initiation of rituximab therapy (T12). Total RNA was extracted, labeled according to standard Affymetrix procedures and hybridized on GeneChip HGU133 Plus 2.0 slides. Immunohistochemistry and quantitative real-time PCR experiments were performed to confirm the differential expression of selected transcripts.

Results: According to paired Student’s t-tests, 549 out of 54,675 investigated probe sets were differentially expressed between T0 and T12. Pathway analysis revealed that genes down-regulated between T0 and T12 were significantly enriched in immunoglobulin genes, and genes involved in chemotaxis, leucocyte activation and immune responses (Gene Ontology annotations). By contrast, genes up-regulated between T0 and T12 were significantly enriched in transcripts involved in cell development (Gene Ontology annotation) and wound healing (GSEA). At baseline, higher synovial expression of immunoglobulin genes was associated with response to therapy.

Conclusion: Rituximab displays unique effects on global gene expression profiles in synovial tissue of RA patients. These observations open new perspectives in the understanding of the biological effects of the drug and in the selection of patients likely to benefit from this therapy.

overall_design:
Twenty patients with RA (17 women and 3 men, average age +/- SEM: 52,6+/-3,8 years) were included in the study. All patients met the American College of Rheumatology classification criteria for the diagnosis of RA. All patients had active disease at the time of tissue sampling and were resistant to TNF blockade. They all had erosive changes imaged on conventional x-rays of the hands and/or feet. All of them had a swollen knee at inclusion. Rituximab therapy was administrated at a dose of 1,000 mg IV at baseline (T0) and at week 2, together with 125 mg IV Methylprednisolone. Clinical parameters at baseline (T0) and 12 weeks after the initiation of therapy (T12) was evaluated using DAS(28)-CRP scores and clinical responses were assessed using EULAR response criteria. Synovial biopsies were obtained by needle-arthroscopy of an affected knee from all patients at T0 and T12. For each procedure, 4 to 8 synovial samples were kept overnight at 4°C in a RNA stabilizing solution (RNALater, Ambion, Applied Biosystems, TX, USA) and then stored at –80°C for later RNA extraction. The same amount of tissue was snap-frozen in liquid nitrogen and kept at –80°C for immunostaining experiments on frozen sections. The remaining material was fixed in 10% formaldehyde and paraffin embedded for conventional optical evaluation and immunostaining of selected markers. All the experiments (RNA extraction, histology, immunohistochemistry) were performed on at least 4 biopsies harvested during every procedure in order to correct for variations related to the potential heterogeneous distribution of synovial inflammation. The study was approved by the ethics committee of the Université catholique de Louvain and informed consent was obtained from all patients.

At least 1 µg total RNA could be extracted from 12 paired samples at T0 and T12 for further processing.

first: Ilse

last: Gutierrez-Roelens

middle: R


title: Genome-wide detection of STAT6 binding sites in IL-4 treated naive human CD4+ T cells

status: Public on Jun 25 2010

city: Turku

first: Henna

last: Kallionpää

address: P.O. Box 123

department: Turku Centre for Biotechnology

country: Finland

institute: University of Turku

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
STAT6 is a major transcription factor driving the polarization of Th2 cells in response to IL-4. STAT6 is phosphorylated by Jak1 and Jak3 kinases at the IL-4 receptor, after which phosphorylated STAT6 forms a homodimer and translocates into the nucleus. There STAT6 binds to specific DNA sequences, regulating the transcription of its target genes. Here we have analyzed on a genome wide level the STAT6 binding sites, after 1h and 4h of IL-4 induction, in naive human CD4+ T cells.

Keywords: SRA

overall_design: Altogether 5 samples from 1 biological replicate were analyzed. Activated and IL-4 treated samples were compared to only activated or untreated samples to identify unique STAT6 binding sites after IL-4 induction.

first: Laura

last: Elo

last: Järvenpää

first: Soile

last: Tuomela

first: Sunil

last: Raghav

first: Helena

last: Ahlfors

first: Bhawna

last: Gupta

first: Johanna

last: Tahvanainen

first: Riikka

last: Lund

first: Laurila

last: Kirsti

first: Lähdesmäki

last: Harri

first: Omid

last: Rasool

first: Matej

last: Oresic

first: Kanury

last: Rao

first: Tero

last: Aittokallio

first: Riitta

last: Lahesmaa

first: David

last: Hawkins


title: Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities

status: Public on May 27 2010

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

summary: Genome-scale studies have revealed extensive co-localization of transcription factors in a given cell type as well as substantial differences in the binding patterns of specific transcription factors between cell types. Several mechanisms have been proposed to explain these observations, including targeting of transcription factors to accessible chromatin marked by lysine 4-monomethylated histone H3 (H3K4me1) and interactions between transcription factors that enable nucleosome displacement. Here we demonstrate that collaborative interactions of PU.1 with small sets of macrophage- or B cell-lineage-determining transcription factors establish common and cell-specific binding sites that are associated with the majority of promoter-distal H3K4me1-marked genomic regions in macrophages and B cells, respectively. PU.1 binding initiates nucleosome remodeling followed by H3K4 monomethylation at large numbers of genomic regions associated with both broadly and specifically expressed genes. These sites are representative of locations that serve as beacons for additional factors, exemplified by liver X receptors, which drive both cell-specific gene expression and signal-dependent responses. In concert with analysis of transcription factor binding and H3K4me1 patterns in other cell types, these studies suggest that simple combinations of lineage-determining transcription factors can specify the genomic sites ultimately responsible for both cell identity and cell type-specific responses to diverse signaling inputs.

overall_design: ChIP-Seq and gene expression profiling was performed in macrophages, B cells, and a variety of genetically modified primary cells and cell lines approximating developmental stages of macrophage and B cell development.

first: Sven

last: Heinz

first: Nathanael

last: Spann

first: Eric

last: Bertolino

first: Yin

middle: C

last: Lin

first: Peter

last: Laslo

first: Jason

middle: X

last: Cheng

first: Cornelis

last: Murre

first: Harinder

last: Singh

middle: K

last: Glass


title: Integrated molecular genetic profiling of pediatric-high grade gliomas reveals key differences with adult disease

status: Public on Jun 16 2010

city: Memphis

first: Chunxu

last: Qu

state: TN

address: 262 Danny Thomas Pl

institute: St Jude Children's Research Institute

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

summary:
Purpose:  To define copy number alterations and gene expression signatures underlying pediatric high-grade glioma (HGG). Patients and Methods: We conducted a high-resolution analysis of genomic imbalances in 78 de novo pediatric HGG, including 7 diffuse intrinsic pontine gliomas, and 10 HGG cases arising in children who received cranial irradiation for a previous cancer, using Affymetrix 500K GeneChips.  Gene expression signatures for 53 tumors were analyzed with Affymetrix U133v2 arrays.  Results were compared with publicly available data from adult tumors. Results:  Pediatric and adult glioblastoma were clearly distinguished by frequent gain of chromosome 1q (30% vs 9%) and lower frequency of chromosome 7 gain (13% vs 74%), respectively.  The most common focal amplifications also differed, with PDGFRA and EGFR predominant in childhood and adult populations respectively. These common alterations in pediatric HGG were detected at higher frequency in irradiation-induced tumors, suggesting that these are initiating events in childhood gliomagenesis. CDKN2A was the most common tumor suppressor gene targeted by homozygous deletion in pediatric HGG. No IDH1 hotspot mutations were found in pediatric tumors, highlighting molecular differences in pathogenesis between childhood HGG and adult secondary glioblastoma. Integrated copy number and gene expression data indicated that deregulated PDGFRA signaling plays a major role in pediatric HGG. Conclusions:  Integrated molecular profiling showed substantial differences in the molecular features underlying pediatric and adult HGG, indicating that findings in adult tumors cannot be simply extrapolated to younger patients.  PDGFRA may be a useful target for pediatric HGG including diffuse pontine gliomas.

Keywords: disease state analysis

overall_design:
78 samples for SNP analysis, including 10 samples arising in children who received cranial irradiation for a previous cancer and 7 diffuse pontine gliomas;  53 of them with gene expression analysis; 2 tumor grades

To have access to SNP CEL files, please contact Dr. Suzanne Baker (suzzane.baker@stjude.org).

first: Barbara

middle: S

last: Paugh

first: Chris

last: Jones

first: Zhaoli

last: Liu

first: Martyna

last: Adamowicz-Brice

first: Junyuan

last: Zhang

first: Dorine

middle: A

last: Bax

first: Beth

last: Coyle

first: Jennifer

last: Barrow

first: Darren

last: Hargrave

first: James

last: Lowe

first: Amar

last: Gajjar

first: Wei

last: Zhao

first: Alberto

last: Broniscer

middle: W

last: Ellison

first: Richard

middle: G

last: Grundy

first: Suzanne

middle: J

last: Baker


title: Array CGH with DNA extracted from Candida albicans strains 3153A and its derivative Sor55, which is monosomic for chromosome 5

status: Public on Jun 14 2010

city: Rochester

first: Elena

last: Rustchenko

state: NY

address: 601 Elmwood Ave., Box 712

department: Biochemistry & Biophysics

institute: University of Rochester

type: Genome variation profiling by genome tiling array

summary: Goal of this experiment was to confirm the proposed monosomy condition of chromsome 5 genes in the mutant Sor55

overall_design: Different batches of total DNA were prepared from the parental strain 3153A and its derivative Sor55. Hybridization included different combinations of two independent batches of DNA from 3153A or Sor55, as well as one dye-swap. Parental/mutant ratio data was analyzed.

first: Anatoliy

last: Kravets

first: Qinshan

last: Gao

first: Hong

last: Qin

first: Ausaf

last: Ahmad

first: Gabor

last: Bethlendy


title: Affymetrix SNP array for CSES1, CSES8, CSES1 maternal, and CSES8 maternal

status: Public on May 06 2010

city: Los Angeles

first: Tamar

last: Dvash

state: CA

address: 695 Charles E. Young Drive South

department: Human Genetics

institute: University of California Los Angeles

summary: These SNP arrays were used to genotype hESCs and their corresponding matenal sample. Expression analysis of some of the SNPs located on the X chromosome was used to identify the pattern of X Chromosome inactivation in these human embryonic stem cells

overall_design: Affymetrix 250k Sty SNP arrays were used to genotype CSES1 and CSES8 embryonic stem cell lines and CSES1 maternal and CSES8 maternal DNA

first: Guoping

last: Fan


title: Human bone-derived mesenchymal stem cells: SLE patients vs normal controls

city: Nanjing

first: Yu

last: Tang

state: Jiangsu Province

address: 321 Zhongshan Road

department: Department of Rheumatology and  Immunology

country: China

institute: The Affiliated Drum Tower Hospital of Nanjing University Medical School

summary: Previous studies showed that bone marrow derived-mesenchymal stem cells (BMMSCs) from patients with systemic lupus erythematosus (SLE) and lupus animal models have deficiency in their capacities of proliferation, differentiation, secretion of cytokines and other functions. In this study, we aim to investigate the different gene patterns of BMMSCs between normal and SLE individuals using genome-scale DNA microarrays. We found that among all the genes investigated in microarray slides, a total of 1, 905 genes were differentially expressed by BMMSCs SLE patients, in which 652 genes were up-regulated and 1253 genes were down-regulated. Gene ontology analysis showed that the majority of these genes were related to cell cycle and protein binding. Pathway analysis showed that differentially regulated signal pathways involved actin cytoskeleton, focal adhesion, tight junction and TGF-β pathway. Our data suggested that there were differential gene expression patterns of BMMSCs between normal and SLE individuals, and further studies are needed to reveal the mechanisms for such differences.

overall_design: Bone marrow (BM) was obtained from 4 patients with SLE and 4 normal controls. BMMSCs were cultured and mRNA was extracted. Standard human reference RNA were purchased. Every slide: SLE or normal vs control, then SLE vs normals.

first: Lingyun

last: Sun


title: Sub-populations of c-Myb in MCF-7 cells

status: Public on May 01 2010

city: Albuquerque

first: Gavin

last: Pickett

state: NM

address: 2325 Camino de Salud NE

department: Genomics

institute: UNM

type: Genome binding/occupancy profiling by genome tiling array

summary: We compared two independent c-Myb antibodies during cellular confluence and estrogen stimulation to determine endogenous c-Myb target genes. Interestingly, we discovered that c-Myb specificity was estrogen dependent and multiple antibodies recognize distinct sets of endogenous targets suggesting that epitope masking and domains within the c-Myb protein play a critical role in the activity of the c-Myb protein.

overall_design: MCF-7 cells were plated to 90% confluence in DMEM supplemented with 10% FBS for 24 hours. Cells were subjected to ChIP assay with anti-c-Myb (Upstate (Millipore)) or VKN immune serum (independently developed) and analyzed for enrichment at known c-Myb targets. These samples were compared to ChIP assays performed on cells plated to a high density in DMEM supplemented with 5% Charcoal stripped serum for 48 hours and subsequently induced for 24 hours with purified 17-beta-estradiol. Verified ChIP samples were linearly amplified with a modified version of the Affymetrix whole genome amplification protocol and amplified DNA (6ug) was hybridized to human promoter tiling array 1.0R. Analysis was performed with MAT software for promoter tiling array analysis.

first: Anita

middle: M

last: Quintana

first: Scott

last: Ness


title: Estrogen-mediated Epigenetic Repression of Large Chromosomal Regions through DNA Looping

status: Public on Apr 29 2010

city: Columbus

first: Pei-Yin

last: Hsu

state: OH

address: BRT836, 460W 12th Ave

institute: OSU

type: Methylation profiling by genome tiling array

summary: The current concept of epigenetic repression is based on one repressor unit corresponding to one silent gene. This notion, however, cannot adequately explain concurrent silencing of multiple loci observed in large chromosome regions. The long-range epigenetic silencing (LRES) can be a frequent occurrence throughout the human genome. To comprehensively characterize the influence of estrogen signaling on LRES, we analyzed transcriptome, methylome, and estrogen receptor alpha (ESR1)-binding datasets from normal breast epithelia and breast cancer cells. This ?omics? approach uncovered 11 large repressive zones (range: 0.35~5.98 megabases), including a 14-gene cluster located on 16p11.2. In normal cells, estrogen signaling induced transient formation of multiple DNA loops in the 16p11.2 region by bringing 14 distant loci to focal ESR1-docking sites for coordinate repression. However, the plasticity of this free DNA movement was reduced in breast cancer cells. Together with the acquisition of DNA methylation and repressive chromatin modifications at the 16p11.2 loci, an inflexible DNA scaffold may be a novel determinant used by breast cancer cells to reinforce estrogen-mediated repression.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design:
ChIP-seq: E2-preexposed or DMSO-preexposed mammosphere-derived epithelial cells (MDECs); MCF-7 cells with 4hr of DMSO or E2 stimulation.

MeDIP-chip: Methylated DNA from MCF7 cells was immunoprecipitated by the antibody against 5-methyl cytidine. The immunoprecipitated methylated DNA fragments were processed by the NimbleGen Methylation Microarray Service. Methylation analysis was performed on the NimbleGen Two-Array HG18 Promoter Set.

mRNA profiling by array: Four sets of total RNA samples from the mammary gland of each 50-day-old rat with prepubertal exposure of BPA. Each sample set includes one BPA-exposed and one sesame oil-exposed rat RNA.

first: Julia

last: Pereira

first: Ricardo

last: Lopez

first: Jose

last: Russo

first: Coral

last: Lamartiniere

first: Pearlly

last: Yan

first: Joseph

last: Liu

first: Gregory

last: Singer


title: CGH analysis of UMASS Type A strain

status: Public on Apr 08 2010

city: Atlanta

first: Brian

middle: H

last: Raphael

state: GA

address: 1600 Clifton Road

department: Enteric Diseases Laboratory Branch

institute: Centers for Disease Control and Prevention

summary: C. botulinum UMASS Type A strain was compared to the ATCC 3502 Type A reference strain.

overall_design: Genomic DNA from the UMASS Type A strain was labled with Cy3 and cohybridzied with Cy5 labeled genomic DNA isolated from the ATCC 3502 Type A strain using a custom comparative genomic hybridization microarray.  Differences in gene content between the were assessed by examining the log2 ratio data of the signal intensities.

first: Ping-Ke

last: Fang

first: Susan

middle: E

last: Maslanka

first: BalRam

last: Singh

first: Shuowei

last: Cai


title: Expression data from cultured macrophages and osteoclasts

status: Public on Mar 22 2010

city: Shinjuku-ku

first: Takeshi

last: Miyamoto

state: Tokyo

address: 35 Shinanomachi

department: School of Medicine

country: Japan

institute: Keio University

summary:
Osteoclastogenesis is induced by the stimulation of RANKL. In the early stage of osteoclast differentiation, the osteoclast progenitor cells are primed by M-CSF, following a tightly controlled genetic program where specific sets of genes are up-regulated by RANKL. Some of them, for instance, control differentiation, cell-cell fusion and bone resorption.
We used microarrays to detail the global program of gene expression underlying osteoclastogenesis and identified various up-regulated genes during this process.

overall_design: Macrophages and osteoclasts were cultured for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain homogeneous populations of macrophages and osteoclasts in order to increase the temporal resolution of expression profiles. To that end, mouse bone marrow cells were cultured in the presence of M-CSF for three days and harvested as macrophage and oseteoclast common progenitor cells. Then common progenitor cells were further cultured in the presence of M-CSF alone for macrophages and M-CSF plus RANKL for osteoclasts, respectively.


title: Activated Notch-induced transcriptional profile modulation in human primary dermal lymphatic endothelial cells

status: Public on Mar 20 2010

city: los angeles

first: Young Kwon

last: Hong

address: 1441 Eastlake Ave NOR6336

institute: Norris Cancer Center

summary:
Human Notch1 intracellular domain (NICD) was overexpressed in human primary lymphatic endothelial cells (LECs) for 10 and 24 hours by adenovirus. A GFP-control adenovirus-infected cells (24hours) and uninfected cells were also analysed as controls.
Total RNAs were harvested and subjected to Affymetrix U133A microarray.

overall_design:
Human primary lymphatic endothelial cells (LECs) were isolated from human foreskin and cultured and expanded to population passages 5~6. Healthy subconfluent primary LECs were infected with adenovirus expressing human Notch1 intracellular domain (NICD) for 10 or 24 hours. In parallel, LECs were also infected with a GFP-expressing control adenovirus for 24 hours. Uninfected LECs were also used as a negative control in the same experiments

*** CEL files unavailable/unrecoverable. ***

first: Young


title: Aberrant heterochromatic foci are associated to deregulation of the GMCL1 gene in CH1 lymphoma B cells

status: Public on Mar 10 2010

city: Grenoble

first: Mary

middle: Bridgid

last: Callanan

address: Rond point de la Chantourne, La Tronche

department: Cell differentiation and transformation

institute: INSERM-UJF U823, Institut Albert Bonniot

summary:
Chromosome 1 pericentric heterochromatin rearrangements : potent drivers of nuclear architecture perturbations and gene deregulation in human B cell lymphoma

Epigenetic perturbations are increasingly described in cancer cells where they are thought to contribute to deregulated gene expression and genome instability. Here, we report the first evidence, that a distinct category of chromosomal translocation observed in human tumours – those targeting 1q12 satellite DNA - can directly mediate such perturbations by promoting the formation of aberrant heterochromatic foci (aHCF). By detailed investigations of a 1q12 translocation to chromosome 2p, in a case of human B cell lymphoma, aberrant aHCF were shown to be localised to the nuclear periphery and to arise as a consequence of long range ‘pairing’ between the translocated 1q12 and chromosome 2 centromeric regions. Remarkably, adjacent 2p sequences showed increased levels of repressive histone modifications, including H4K20me3 and H3K9me3, and were bound by HP1. aHCF were associated to aberrant spatial localisation and deregulated expression of a novel 2p gene (GMCL1) that was found to have prognostic impact in B cell lymphoma. Thus constitutive heterochromatin rearrangements can contribute to tumourigenesis by perturbing gene expression by via long range epigenetic mechanisms.

overall_design: The formation of aberrant heterochromatic foci, coupled to abnormal enrichment of adjacent 2p sequences in repressive heterochromatin marks (H4K20me3, H3K9me3 and HP1), delayed replication and repositioning of the rearranged chromosome 2 to the nuclear periphery, could be associated to altered gene expression of at least those genes brought into close proximity to heterochromatin. To assess this question, global gene expression profiling was performed in the lymphoma B cells presenting the aberrant heterochromatin foci (CH1), treated or not with the histone deacetylase inhibitor, trichostatin A.


title: Non adherent macrophage of mafb null and WT

status: Public on Feb 23 2010

city: TSUKUBA

first: Michito

last: Hamada

state: IBARAKI

address: 1-1-1 tennodai

department: anatomy and embryogy

institute: University of Tsukuba

summary: MafB is a member of the large Maf family of transcription factors that share similar basic region/leucine zipper DNA binding motifs and N-terminal activation domains.Although it is well known that MafB is specifically expressed in  macrophages, characterization of the null mutant phenotype in these tissues has not been previously reported. To investigate suspected MafB functions macrophages, we generated mafB/green fluorescent protein (GFP) knock-in null mutant mice. MafB deficiency was found to dramatically suppress F4/80 expression in nonadherent macrophages. To investigate detail function of MafB in nonadherent macrophages, we performed microarray analysis.

overall_design: Macrophages were derived from	day	14.5	fetal	livers 	of	mafB- /- and WT	mice. 	Suspensions of single fetal liver cells were prepared by mechanical disruption . A total of 106 cells in suspension were centrifuged at 1,200 rpm for 5 min, and the cell pellet was resuspended in Dulbecco’s modified Eagle’s medium  supplemented with 10% fetal calf serum (heat inactivated), streptomycin and penicillin (100 units/ml), and macrophage colony-stimulating factor (M-CSF) (10 ng/ml) and then seeded either onto a nonadhesive dishes coated with hydrophilic polymers (Hydrocell; Cell Seed, Tokyo). The culture medium was not changed throughout the experiment. M-CSF (final concentration, 10 ng/ml) was added every day from day 4 onwards. One, 2, 4, and 6 days after seeding, the cells were harvested and analyzed by flow cytometry. After 6 day culture, macrophages of Mafb-/- and WT were use microarray analysis .


title: Expression profiling of early-stage squamous cell non-small cell lung cancer.

status: Public on Mar 05 2010

city: Vancouver

first: Kim

middle: Marie

last: Lonergan

state: British Columbia

address: 675 West 10th Avenue

department: Cancer Genetics and Developmental Biology

country: Canada

institute: British Columbia Cancer Research Centre

summary:
We are investigating the molecular development of squamous cell lung carcinoma based upon analysis of global gene expression profiles representing progressive stages of cancer development, consisting of precancerous, carcinoma-in-situ, and invasive cancer.
Keywords: global gene expression analysis, lung cancer development

overall_design: In this study, we have generated 13 SAGE libraries, consisting of five carcinoma-in-situ libraries, six early invasive squamous cell carcinoma libraries, and two reference libraries representing precancerous squamous development.

first: Raj

last: Chari

first: Wan

middle: L

last: Lam


title: Human thymic epithelial cell: untransfected control vs. scramble-siRNA transfected vs. CD49e-siRNA transfected

status: Public on Feb 28 2010

city: Rio de Janeiro

first: Marcelo

last: Ribeiro-Alves

state: RJ

address: Avenida Brasil 4365. Manguinhos.

department: Centro de Desenvolvimento Tecnológico em Saúde

country: Brazil

institute: Fundação Oswaldo Cruz

summary: BACKGROUND: The thymus is a central lymphoid organ, in which bone marrow-derived T cell precursors undergo a complex process of maturation. Developing thymocytes interact with thymic microenvironment in a defined spatial order. A component of thymic microenvironment the thymic epithelial cells (TEC) are crucial for the maturation of T-lymphocytes because the secretion of extracellular matrix compounds, thymic hormones and cytokines and also by cell-cell contacts which can be mediated by extracellular matrix compounds and its receptors, integrins. There is evidence that extracellular matrix molecules play a fundamental role in localizing the different thymocyte stages in the thymus. The interaction between alpha5beta1 (CD49e/CD29; VLA-5) and fibronectin is essential for thymocyte adhesion. Previous results from our laboratory have shown that adhesion of thymocytes to cultured TEC line is enhanced in the presence of fibronectin. And we also demonstrated that anti-VLA-5 antibody when applied to growing TEC prior to the co-culturing with thymocytes, significantly prevented their adhesion to the epithelial. RESULTS: Herein, we studied the role of integrin alpha5 subunit in thymocyte and thymic epithelial cell interactions. We investigate the in vitro effects of silencing alpha5 integrin subunit in human thymic epithelial cell line by RNA interference. After silence a great deal of interest has arisen on intracellular signaling due the absence of alpha5 integrin subunit silence. The expression profile using cDNA microarrays of alpha5 subunit silenced cells showed 131 genes differential expression. Our data showed downregulation in two genes with cell adhesion function: neuronal cell adhesion molecule (NrCAM) and Activin receptor-like kinase 1 gene and in genes related with integrin pathway like, Phosphatidylinositol-4-phosphate 5-kinase, Phospholipase C gamma1 and SHC (Src homology 2 domain containing) transforming protein 1. We also assessed the effect of the loss of alpha5beta1 expression on TEC-thymocytes interaction and ours experiments confirm that alpha5beta1 contribute to adhesion rate. CONCLUSION: Conjointly, our data reinforce the importance of VLA-5 in TEC thymocyte interactions in the process of thymocyte differentiation and we hypothesize a decrease in stress fibers due absence of alpha5 integrin subunit and a compensatory pathway because of downregulation of neuropilin-2, vascular endothelial growth factor and plexin A.

overall_design: Three-condition experiment, control TEC vs. Scramble-siRNA TEC vs. CD49e-siRNA TEC. Biological replicates: 3 control, 3 Scramble-siRNA TEC and 3 CD49e-siRNA TEC transfected, independently grown and harvested. Two replicate per array.

first: Leandra

last: Linhares-Lacerda

first: Danielle

last: Magalhães

first: Geraldo

last: Passos

first: Wilson

last: Savino


title: Foreskin Melanocyte: control vs. treated with pIC/pIC+PEI

status: Public on Feb 01 2010

city: Madrid

first: Maria

last: Soengas

address: Melchor Fernandez Almagro, 3

department: Molecular Pathology

country: Spain

institute: Spanish National Cancer Research Institute

summary: Transcriptional profiling of Foreskin Melanocyte comparing control untreated cells with cells treated with 1ug/ml of polyinosine-polycytidylic acid (pIC) or 1ug/ml of pIC with polyethyleneimine (PEI) for 4 or 10 hours.

overall_design: Four-condition experiment, Foreskin Melanocyte untreated vs. Foreskin Melanocyte treated with pIC/pIC+PEI at 4 and 10 hours. One replicate per array.

first: Damia

last: Tormo


title: Molecular Stratification of Clear Cell Renal Cell Carcinoma Reveals Distinct Subtypes and Survival Patterns

status: Public on Feb 17 2010

city: Nashville

first: Kimryn

last: Rathmell

address: 2220 Pierce Ave

institute: Vanderbilt

summary:
Renal cell carcinoma (RCC) tumors express varying gene profiles, dependent on varying genetic events.
Here we analyzed a series of ccRCC tumors to show that two subtypes of  ccRCC exist based on their molecular signature. These subtypes (ccA and ccB) are identifiable by a robust set of genes representing distinct biological pathways and are correlated with patient survival post-nephrectomy.

Keywords: Patient sample study

overall_design: RNA from 48 clear cell RCC tumors specimens and 18 corresponding non-tumor samples was hybridized against a modified commercial reference RNA (Perou CM, Sorlie T, Eisen MB, et al. Molecular portraits of human breast tumours. Nature 2000;406:747–752) for gene expression analysis.

first: A

last: Brannon

first: Anupama

last: Reddy

first: Michael

last: Seiler

first: Alex

last: Arreola

last: Pruthi

first: Eric

last: Wallen

first: Huiqing

last: Liu

first: Shridar

last: Ganesan

first: Gyan

last: Bhanot

first: W


title: Expression data from Epstein-Barr virus -positive and negative Akata Burkitt's Lymphoma Clones

status: Public on Jan 20 2010

city: Shreveport

first: Rona

middle: S.

last: Scott

state: LA

address: 1501 Kings Highway

department: Microbiology and Immunology

institute: Louisiana State University Health Sciences Center-Shreveport

summary:
Transition of Akata Burkitt lymphoma (BL) cells from a malignant to nonmalignant phenotype upon loss of Epstein-Barr virus (EBV) genomes in vitro is evidence for a viral contribution to tumor maintenance despite the tightly restricted pattern of EBV gene expression in BL. Akata cells retaining virus manifest increased resistance to apoptosis under growth limiting conditions, although ambiguity exists regarding the exact mechanisms involved.  By examining global cellular gene expression differences in Akata subclones that had either retained or lost EBV, we identified spermidine/spermine N1-acetyltransferase (SSAT), an inducible acetylating enzyme whose catabolism of polyamines affects both apoptosis and cell growth, as one of a limited number of cellular genes up-regulated upon loss of EBV.

Keywords: Disease state analysis

overall_design: We used Affymetrix microarrays to examine variations in global gene expression between the paired EBV-positive (1B6) and EBV-negative (2A8) Akata Burkitt's lymphoma clones.   EBV-negative Akata clones  were generated by treatment with hydroxyurea, an inhibitor of ribonucleotide reductase that forced rapid loss of EBV episomes and compared to their EBV-positive counterparts.  Logarithmically growing EBV-negative and positive Akata EBV clones were seeded at 2.5x10^5 cells/ml in RPMI1640 supplemented with 10% fetal bovine serum, 2mM glutamine, and 100units/ml penicillin/streptomycin.  The next day, the cells were incubated for 4 hours in media containing 1% fetal bovine serum (low serum), 2mM glutatmine and 100units/ml penicillin/streptomycin to begin selection of the Akata tumor phenotype.  The short incubation time was intended to minimize cell death and other potential downstream effects of low serum treatment, while at the same time initiating expression changes contributing to the tumorigenic phenotype.

first: John

last: Sixbey


title: MicroRNAs regulated by DAC

city: Yushima, Bunkyo-ku

first: Yutaka

last: Hashimoto

department: Molecular Oncology

institute: Tokyo Medical and Dental University Graduate School

summary: Aberrant expression of microRNA (miRNA) has been reported in various cancers. To clarify the role of miRNA in gastric carcinogenesis, we performed miRNA microarray analysis and investigated expressional changes of miRNAs in a 5-aza-2'-deoxycytidine (DAC)-treated gastric cancer cell line, KATO-ІІІ.

sample_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design:
A gastric cancer cell line KATO-III was daily treated with DAC for 72 h. MiRNAs up- or down-regulated by DAC was compared with unteated KATO-III.

The list of all up-regulated miRNAs in KATO-III by drug treatment can be found in supplementary file, GSE16006_miRNA_list.txt, below.

first: Yoshimitsu

last: Akiyama

first: Takeshi

last: Otsubo

first: Shu

last: Shimada

first: Yasuhito

last: Yuasa


title: Systematic planning of genome-scale experiments in poorly studied species.

status: Public on Jan 24 2010

city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

institute: University of Washington

summary: Genome-scale datasets have been used extensively in model organisms to screen for specific candidates or to predict functions for uncharacterized genes. However, despite the availability of extensive knowledge in model organisms, the planning of genome-scale experiments in poorly studied species is still based on the intuition of experts or heuristic trials. We propose that computational and systematic approaches can be applied to drive the experiment planning process in poorly studied species based on available data and knowledge in closely related model organisms. In this paper, we suggest a computational strategy for recommending genome-scale experiments based on their capability to interrogate diverse biological processes to enable protein function assignment. To this end, we use the data-rich functional genomics compendium of the model organism to quantify the accuracy of each dataset in predicting each specific biological process and the overlap in such coverage between different datasets. Our approach uses an optimized combination of these quantifications to recommend an ordered list of experiments for accurately annotating most proteins in the poorly studied related organisms to most biological processes, as well as a set of experiments that target each specific biological process. The effectiveness of this experiment- planning system is demonstrated for two related yeast species: the model organism Saccharomyces cerevisiae and the comparatively poorly studied Saccharomyces bayanus. Our system recommended a set of S. bayanus experiments based on an S. cerevisiae microarray data compendium. In silico evaluations estimate that less than 10% of the experiments could achieve similar functional coverage to the whole microarray compendium. This estimation was confirmed by performing the recommended experiments in S. bayanus, therefore significantly reducing the labor devoted to characterize the poorly studied genome. This experiment-planning framework could readily be adapted to the design of other types of large-scale experiments as well as other groups of organisms.

platform_organism:
Saccharomyces bayanus
Saccharomyces cerevisiae

overall_design:
This dataset contains 53 experiments as follows:
(experiment: number of datasets (number of arrays))

growth at different temperatures: 1 (3)
heat shock: 4 (18)
ammonium: 1 (6)
cadmium: 1 (4)
copper: 1 (6)
lead: 1 (6)
nickel: 1 (5)
sulfite toxicity: 1 (6)
zinc: 1 (6)
ethanol toxicity: 1 (6)
sorbitol: 1 (6)
bleach: 1 (6)
hydrogen peroxide: 3 (17)
2-deoxyglucose: 1 (6)
hydroxyurea: 1 (6)
lovastatin: 1 (4)
MG-132: 1 (5)
MMS: 1 (6)
rapamycin: 1 (6)
tunicamycin: 1 (6)
zeocin: 1 (6)
chronological aging: 3 (13)
diauxic shift: 1 (6)
galactose: 5 (38)
glycerol: 1 (4)
sucrose: 1 (4)
auxotroph starvation: 1 (11)
nutrient limited chemostat growth: 3 (7)
mating type and ploidy: 1 (3)
alpha factor: 1 (8)
cell cycle: 1 (30)
sporulation: 3 (18)
strain backgrounds: 1 (4)
cross progeny: 1 (22)
Tn7 insertions: 1 (27)
555.11 and 670.20 knockout tetrads: 2 (8)

Timecourse datasets:

heat shock, ammonium, cadmium, copper, lead, nickel, sulfite toxicity, zinc, ethanol toxicity, sorbitol, bleach, hydrogen peroxide, 2-deoxyglucose, hydroxyurea, lovastatin, MG-132, MMS, rapamycin, tunicamycin, zeocin, chronological aging, diauxic shift, galactose, glycerol, sucrose, auxotroph starvation, alpha factor, cell cycle, sporulation

Single timepoint datasets:

growth at different temperatures, strain backgrounds, cross progeny, Tn7 insertions, nutrient limited chemostat growth, mating type and ploidy, 555.11 and 670.20 knockout tetrads

Almost all samples were hybridized versus a common reference prepared from a mixture of RNA from Mat a, Matx, and Mata/x cells sampled in both exponential and stationary phase.  Additionally, RNA from stress conditions was included: hydrogen peroxide treatment sampled at 10, 30 and 45 minutes, and heat shock from 25 to 37 degrees sampled at 10 and 30 minutes.

Samples from the following datasets were not hybridized versus the common reference (reference used in parenthesis and in array annotations): cell cycle (asynchronous culture), constant temperatures (log phase culture), mating type and ploidy (log phase culture), diauxic shift (log phase culture), and strain backgrounds (log phase culture).

Replicates and dye swaps were not used.


title: Transcriptome analysis of porcine PMBCs after stimulation by LPS or PMA/ionomycin using SLA-RI/NRSP8-13K chip

status: Public on Jan 31 2010

city: Jouy en Josas

first: Yu

last: GAO

address: INRA, BAT440

department: Animal Genetics

institute: GABI-GIS

summary:
Background: During the past 25 years, selection of production traits highly increased pig production but diseases have emerged that may cause economic loss of extreme importance. Designing sustainable animal production that better balances productivity with resistance to disease is a major concern and challenge for the next decade. In order to address questions related to immunity and resistance to disease, it is necessary to increase knowledge on the pig immune system and to produce efficient tools dedicated to this species. In this context we produced a generic array enriched in immunity genes and validated its relevance by studying innate immune response of pigs by stimulating porcine mononuclear cells with lipopolysaccharide (LPS) or a mixture or phorboml myristate acetae (PMA) and ionomycin for 24 hours.  Results: A long oligonucleotide-based chip was produced by combining a generic set of 13K probes targeting 8541 genes to a newly designed SLA-RI set that targets all genes and pseudogenes of the pig major histocompatibility complex region (SLA complex) in both orientations (906 probes) and immunity genes outside the SLA complex (2957 porbes). The porcine chip was referred to as SLA-RI/NRSP8-13K. Transcripotme analysis of PBMCs stimulated by LPS or PMA/ionomycin was carried out. Ten times more genes were up regulated after PMA/ionomycin stimulation by comparison to LPS stimulation. The LPS response was more related to the catalog Diseases and Disorders and the PMA/ionomycin response to the catalog Molecular and Cellular Function. LPS stimulation induced a general inflammation response with over-expression of SAA1, pro-inflammatory chemokines IL8, CCL2, CXCL5, CXCL3, CXCL2 and CCL8 as well as genes related to oxidative processes (SOD2) and calcium pathways (S100A9 and S100A12). PMA/ionomycin stimulation induced a stronger up-regulation of T cell activation than B cell activation with dominance toward a Th1 response, including IL2, CD69 and TNFRSF9 genes. In addition, a very intense repression of THBS1 was observed, suggesting a predominant role of this matricellular glycoprotein during T/B cell stimulation by tumor inducers.   Repression of MHC class I genes was observed after PMA/ionomycin stimulation despite an up-regulation of the gene cascade involved in peptide processing and repression of MHC class II genes was observed after both stimulations. A significant reduction of antigen presentation to T cells was shared by the two types of responses that is likely to be due to separate mechanisms that need further elucidation. In addition, our results provided preliminary data suggesting a role of antisense transcripts mapping to the SLA complex during immune response.  Conclusion: The SLA-RI/NRSP8-13K was highly relevant to. On the one hand the SLA-RI/NRSP8-13K was shown to be relevant and accurate to decipher two distinct innate immune responses by PBMCs indicating that this chip will constitute a valuable tool to further study immunity and resistance to disease in pig. On the other hand, the transcriptom analysis revealed specific and common features of the innate immune response according to stimulation that increase knowledge on pig immunity.

Keywords: immune response activation in pig PBMCs

overall_design: Two-condition experiment, LPS stimulated PBMCs vs. mock-stimulated PBMCs, PMA_ionomycine stimulated PBMCs vs.mock-stimulated PBMCs. Biological replicates: 1 control, 1 LPS stimulated and 1 PMA_ionomycine stimulated from 7 animals independently grown and harvested. Dye-swap design. One replicate per array. 28 slides.

last: Gao

first: Laurence

last: Flori

first: Jérome

last: Lecardonnel

first: Diane

last: Esquerre

first: Claire

last: Rogel-Gaillard


title: Genome wide DNA methylation profiling of diabetic nephropathy in type 1 diabetes mellitus

status: Public on Mar 01 2010

city: London

first: Andrew

last: Teschendorff

address: 72 Huntley Street

department: UCL Cancer Institute/Institute for Women's Health

country: United Kingdom

institute: University College London

summary:
The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in whole blood samples from a case-control study of 192 Irish patients with type 1 diabetes mellitus (T1D). Cases had T1D and nephropathy whereas controls had T1D but no evidence of renal disease.
emails: christopher.bell@cancer.ucl.ac.uk, a.teschendorff@ucl.ac.uk

Keywords: DNA methylation

overall_design: Bisulphite converted DNA from the 192 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

first: Christopher

last: Bell


title: Expression data from DM1, DM2 and Normal Adult Skeletal Muscle Biopsies

status: Public on Jan 28 2010

city: Houston

first: Mario

last: Sirito

state: TX

address: 1515 Holcombe blvd

department: Cancer Genetics

institute: M. D. Anderson Cancer Center

summary:
DM1 and DM2 biopsies from patients were compared to Normal adult individuals
Keywords: 3 groups of samples

overall_design: 10 DM1 biopsies, 20 DM2 biopsies, and 6 Normal individuals biopsies

first: Ralf

last: Krahe


title: Identification of miR-145 or miR-133a target genes in bladder cancer

status: Public on Jan 05 2010

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1, Inohana

department: Functional Genomics

institute: Chiba University

summary: We recently identified a subset of down-regulated miRNAs such as miR-145 and miR-133a in bladder cancer. Cell growth inhibitions occurred in miR-145 and miR-133a transfectants compared with the controls, suggesting that both miRNAs function as tumor suppressors. The aims of our expression studies were identification of these miRNAs target genes.

overall_design: miR-145 transfected cancer cells vs control cells, miR-133a transfected cancer cells vs control cells


title: The target genes of transcript factor ZNF191

status: Public on Dec 31 2009

city: ShangHai

first: Jianzhong

last: Li

address: GuoHe Road 325#

department: Department of Biochemical Pharmacy

institute: Second Military Medical University

summary:
Transcriptional profiling of human embryo kidney cells comparing control HEK293 transfected with empty vectors cells with HEK293 cells transfected with pcDNA3-ZNF191 (or ZNF191 siRNA vector).
We searched for early ZNF191 target genes by using a transient overexpression and knockdown strategy in the human embryo kidney (HEK293) cells.

A table of gene targets of transcription factor ZNF191 commonly identified by both strategies is appended below as a supplementary file.

overall_design: ZNF191 overexpression experiment, the cells of ZNF191 overexpression  vs Control. ZNF191 siRNA experiment, ZNF191 siRNA cells vs Control.


title: Expression data of the thymus from 15weeks old Hexb-/- and Hexb+/- mice

status: Public on Dec 25 2009

city: Yokohama City

first: Akira

last: Yamaguchi

state: Kanagawa

address: 3-9 Fukuura

department: Department of Pathology

institute: Yokohama City University School of Medicine

summary:
Sandhoff disease (SD) is a lysosomal storage disorder characterized by the absence of β-hexosaminidase and storage of GM2 ganglioside and related glycolipids. We found the alterations in the thymus during the development of mild to severe progressive neurologic disease.
To elucidate the molecular basis of thymic involution, we performed cDNA microarray analysis to identify the changes in gene expression that accompanied the involution of the thymus.
8018 probes were found to be relatively increased in the thymus of the Hexb-/- mice, an animal model for SD, compared with that of the Hexb+/- mice. On the other hand, the expression of 7604 probes was relatively decreased. The cohort of up-regulated sequences was dominated by genes that play a role in the immune response. In addition, some of these genes are expressed in macrophage lineages such as macrophage expressed gene 1, and colony stimulating factor 2 receptor beta 1. Th2 cytokines were mostly upregulated in the Hexb-/- mice, although Th1 cytokines did not show this increase. In addition, B cell related genes such as CD19, CXCL13 were increased, whereas the T cell-related genes were mostly decreased, in Hexb-/- mice compared with Hexb+/- mice.

overall_design: Pooled thymic RNA samples were obtained from two 15 weeks old Hexb-/- mice and two strain-matched, 15 weeks old Hexb+/- mice. cDNA were synthesized from 10 μg total RNA. Biotinylated cRNA were synthesized. Following fragmentation, 10 μg of cRNA were hybridized on GeneChip Mouse Genome 430 2.0 Array.

first: Seiichi

last: Kanzaki

first: Syoji

last: Yamanaka


title: Exon level integration of proteomics and microarray data

status: Public on Nov 24 2009

first: Danny

middle: Asher

last: Bitton

address: Darwin Building, Gower Street

department: Department of Genetics, Evolution & Environment

summary: Background: Previous studies comparing quantitative proteomics and microarray data have generally found poor correspondence between the two. We hypothesised that this might in part be because the different assays were targeting different parts of the expressed genome and might therefore be subjected to confounding effects from processes such as alternative splicing.  Results: Using a genome database as a platform for integration, we combined quantitative protein mass spectrometry with Affymetrix Exon array data at the level of individual exons. We found significantly higher degrees of correlation than have been previously observed (r=0.808). The study was performed using cell lines in equilibrium in order to reduce a major potential source of biological variation, thus allowing the analysis to focus on the data integration methods in order to establish their performance.  Conclusion: We conclude that much of the variation observed when integrating microarray and proteomics data may occur as a consequence both of the data analysis and of the high granularity to which studies have until recently been limited. The approach opens up the possibility for the first time of considering combined microarray and proteomics datasets at the level of individual exons and isoforms, important given the high proportion of alternative splicing observed in the human genome.

overall_design: This data set contains three technical replicates of the cell lines MCF7 and MCF10A

first: Michal

last: Okoniewski

first: Yvonne

last: Hey

first: Stuart

middle: D

last: Pepper

last: Connolly

first: Crispin

last: Miller


title: Gene expression profiling on mouse models of cardiomyopathies

status: Public on Dec 12 2009

city: Berlin

first: Henning

last: Witt

address: Ihnestrasse 65

department: Hans Lehrach

country: Germany

institute: Max Planck Institute for Molecular Genetics

summary: Adjuvant chemotherapy of anthracycline derivatives with antibodies against erbB2 (i.e. trastuzumab, herceptin) is highly effective for a subset of mammary tumors overexpressing erbB2 oncogen. However, an undesired effect of the combined treatment is the increase incidence of dilated cardiomyopathies that may affect a 30% subpopulation of these patients. The accumulating evidence demonstrates the essential role of neuregulin signaling in the adult heart, and morerover, indicates that an impaired neuregulin signaling exacerbates the doxorubicin-mediated cardiac toxicity.  Despite this strong evidence, the precise molecular interactions and the specific cardiomyocyte targets of the active erbB2/erbB4 heterodimer remain unknown.  In this study, we examined potential molecular targets and mechanisms underlying the synergistic cardiotoxicity of anthracyclines in the ventricular muscle specific erbB4 knockout mouse. We employed a DNA microarray to assess the characteristic gene expression profile, whose partial data was verified by real time RT-PCR and then, grouped in functional categories and pathways. From this study, we demonstrate the upregulation of genes related to the classical signature of a hypertrophic response, shared by the 3 models. In addition, these results revealed an erbB-dependent hypertrophic response through the interaction with G-protein coupled receptors, a commonality in the 3 models. A robust upregulation of EGF and HB-EGF and pleitrophin implicated in cardiac growth together with the remarkable downregulation of IGF-I/PI 3`Kinase pathway characterize the doxorubicin-treated erbB4-KO mice. This defect together with metabolic abnormalities appears to be underlying the phenotypic modification of cardiomyocytes in doxorubicin-treated erbB4-KO mouse.

overall_design: For each mouse model investigated RNA of 4-8 individuals was pooled and targets were hybridised in four technical replicates on agilent cDNA microarrays. In a two color approach two dye swaps were performed with the cardiomyopathy samples and their wildtype/healty controls.

first: Cecilia

last: Hertig

first: Patricia

last: Ruiz Noppinger


title: Myeloid progenitor cells lacking p53 exhibit delayed upregulation of Puma, prolonged survival after cytokine deprivation

status: Public on Dec 07 2009

city: Parkville

first: Anissa

last: Jabbour

state: Victoria

address: 1G Royal Parade

department: Cell Signalling and Cell Death

country: Australia

institute: Walter and Eliza Hall Institute

summary: We generated WT and p53-/- Factor Dependent Myeloid (FDM) cells and found that p53-/- cells were protected against IL-3 withdrawal. A survival advantage was also observed in untransformed p53-/- hematopoietic progenitor cells cultured in the presence or absence of cytokines. Array analysis was perfomed on RNA extracted from WT and p53-/- FDM cells.

overall_design: Total RNA obtained from WT and p53-/- FDM cells cultured in the presence or absence of IL-3

first: Paul

last: Ekert

first: Lavinia

middle: C

last: Gordon


title: Expression profiling of HONE1 cell line stably transfected with LMP1

status: Public on Nov 05 2009

city: Guangzhou

first: Chen

last: Jing

address: 651 Dong Feng Road East

department: Dept. of Pathology

institute: Sun Yat-Sen University Cancer Center

summary: Using gene expression profiling technology from Capitalbio to find out the whole genome influence after LMP1 stably transfectted to HONE1 cell line.

overall_design: We analyzed gene expression change by LMP1 in HONE1 cell to find the active pathway and related biology function.

first: Jing

last: Chen


title: Control of gene expression by the Retinoic acid-related Orphan Receptor alpha in HepG2 human hepatoma cells

status: Public on Nov 04 2009

city: Grenoble

first: Gaelle

last: Saint-Auret

address: 17 rue des martyrs

institute: CEA

summary:
Retinoic acid-related Orphan Receptor alpha (RORalpha; NR1F1) is a nuclear receptor involved in several physiological and patho-physiological functions including lipid metabolism, inflammation, angiogenesis, and circadian rythm. It is widely distributed. In order to better understand the role of this nuclear receptor in liver, we aimed at displaying genes controlled by RORalpha in liver cells. HepG2 human hepatoma cells stably over-expressing RORalpha were designed. Genes whose expression was altered in these cells versus control cells were displayed using micro-arrays and qRT-PCR. Expression of these genes was also altered in cells in which RORalpha was transiently over-expressed after adenoviral infection. Some genes are involved in functions controlled by RORalpha. This is the case for LPA, NR1D2 and ADIPOQ in lipid metabolism, ADIPOQ and PLG in inflammation, PLG in fibrinolysis and NR1D2 and NR1D1 in circadian rhythm. This study also revealed that genes such as G6PC, involved in glucose homeostasis, and AGRP, involved in the control of body weight, are also controlled by RORalpha. Lastly, SPARC, involved in cell growth and adhesion and associated with liver carcinogenesis, was up-regulated by RORalpha. It is a new direct RORalpha target gene since it possesses, in its promoter, a functional RORE as evidenced by EMSAs and transfection experiments. It is likely the case for most of the other genes we found regulated by RORalpha contain putative ROREs in their regulatory regions. These results open new routes to think about the role of RORalpha in glucose metabolism and carcinogenesis within cells of hepatic origin.

Keywords: Comparison of HepG2 cells expressing RORalpha or control HepG2 cells cultured in 20% oxygen or 2% oxygen during 24h.

overall_design: RNAs were extracted from HepG2 cells transfected by pCMX-hRORa1 and expressing RORalpha or from control HepG2 cells transfected by pCMX (empty vector). Before the extraction, these cells were cultured in 20% oxygen or 2% oxygen (hypoxic treatment) during 24h. Each sample was hybridized on Human Whole Genome Oligonucleotides Microarrays 44k (G4112F).

first: Caroline

last: Chauvet

first: Brigitte

last: Bois-Joyeux

first: Christophe

last: Duhem

first: Gaëlle

first: Bart

last: Staels

first: Jean-Louis

last: Danan


title: Expression data from murine embryonic stem (ES) cells exposed to oxidative stress

status: Public on Oct 23 2009

city: New York

first: Christine

last: Richardson

address: St Nicholas Av

department: Institute for Cancer Genetics

institute: Columbia University

summary:
Elevated reactive oxidative species (ROS) may be crucial for cellular transformation and tumor progression. Defining the response of stem cells to ROS is critical to understanding the unique sensitivity of stem cells to ROS-mediated transformation and tumor initiation.
We examined both the immediate transcriptional and phospho-proteomic responses of murine ES cells induced by a single brief dose of hydrogen peroxide (H2O2) to create a more complete understanding of cell response to ROS.

overall_design: Murine ES cells were briefly exposed to low and high dose of H2O2 then allowed to recover for 1 hour in maintenance medium before RNA extraction and MG_U74Av2 microarray hybridization.

first: Raymond

last: Mouzannar


title: IFN-a-induced monocyte phenotype in chronic unsuppressed HIV infection

status: Public on Oct 09 2009

city: San Francisco

first: Bing

last: Sun

address: B1, R103, 4150 Clement St

institute: San Francisco VA Medical Center

summary:
Abstract

Objectives: HIV infection dysregulates the innate immune system and alters leukocyte gene expression. The objectives were two fold: to characterize the impact of HIV infection on peripheral monocyte gene expression and to identify the predominant factor(s) responsible for altered gene expression.

Design and methods: In a cross-sectional study, CD14+ monocytes were isolated from 11 HIV seronegative controls, 22 HIV seropositive subjects with low viral loads (LVL, <= 10,000 RNA copies/ml) and 22 HIV seropositive subjects with high viral loads (HVL, > 10,000 RNA/copies/ml). Total monocyte RNA was hybridized to 55K probes on high-density microarrays to obtained detailed gene expression profiles from control, LVL and HVL subjects. As potential candidates for immune disruption, we evaluated three HIV-related peripheral factors, interferon (IFN)-a, IFN-a and lipopolysaccharide (LPS) by treating HIV seronegative CD14+ monocytes for 48h and then analyzing gene expression. Plasma collected from the HIV subjects were quantified for LPS using a Pyrogene assay and for soluble (s) CD14 by ELISA.

Results: In this cross-sectional study of HIV subjects (n=44), viral loads above 10,000 RNA copies/ml were associated with an activated phenotype. Characterization of the gene expression pattern by Gene Ontology reveals an ongoing immune response to viral infection including inflammation and chemotaxis. Gene expression analysis of in vitro treated HIV seronegative monocytes with IFN-a, IFN-g or LPS demonstrated that IFN-a most accurately recapitulated the HIV HVL profile. There was no detectable LPS signature even in those HIV subjects with the highest LPS and sCD14 levels.

Conclusions: Monocyte gene expression in subjects with viremia is predominantly due to IFN-a, while subjects with LVL have a non-activated phenotype. In monocytes, there was no discernible expression profile linked to LPS exposure.

overall_design: Global gene expression analysis using high-density cDNA microarrays was performed on CD 14+ monocytes isolated from 55 subjects, 22 with HIV HVL, 22 with HIV LVL and 11 HIV seronegative controls. The categorization of high or low viral load was based on clinical criteria with LVL <10,000 RNA copies/ml and HVL as >10,000 RNA copies/ml. Subjects in the study were males between 30 and 66 years of age and the cohort was comprised of white (62%), black (19%), Hispanic (12%), Asian (4%) and other (3%) individuals. At the time of the study individuals in the LVL group were on highly active antiretroviral therapies (HAART), while subjects with HVL fell into one of three categories: on HAART (15); scheduled treatment interruption (6) or HAART naïve (1) (Table 1).

first: Hans

last: Remple

first: Cyrus

last: Calosing

first: Lynn

last: Pulliam


title: Allergen-challenged CD4+ cells from patients with seasonal allergic rhinitis

status: Public on Oct 16 2009

city: Gothenburg

first: Mikael

last: Benson

address: Smorslottsgatan

department: Paediatrics

country: Sweden

institute: Queen Silvia Children's Hospital

summary: Seasonal allergic rhinitis (SAR) is a complex disease that is caused by many interacting genes and environmental factors. It is also an excellent model disease for clinical studies; it is common, it is seasonal, and since it takes place in the nasal cavity it can be studied in vivo non-invasively. Furthermore, the key disease cell, the Th2 cell is known. We study SAR using allergen-challenged CD4+ cells from allergic patients.

overall_design: Samples were obtained from 3 patients with SAR; each separated into allergen-challenged samples and unchallenged controls.


title: Dendritic cell stimulation: 5 ligands, 9 time points

city: Cambridge

first: Tal

last: Shay

state: MA

institute: Broad Institute

summary: mouse primary BMDCs were stimulated with  tlr ligands and  gene expression changes were profiled on Affymetrix arrays

overall_design: BMDC were stimulated with 5 tlr ligands (LPS, pIC ,PAM, CpG, GRD) across 9 time points (.5, 1, 2, 4, 6, 8, 12, 16, 24  hours). Unstimulated cells were used as controls.

first: Ido

last: Amit


title: A Microarray approach for Identification of Candidate Genes Involved in Gyration of the Pig Cerebral Cortex

status: Public on Oct 08 2009

city: Aarhus

first: Karsten

middle: Bork

last: Nielsen

address: 4 Wilhelm Meyers Allé, Building 1242

department: Institute of Human Genetics

country: Denmark

institute: University of Aarhus

summary: In this study we examined brain gyration using the pig brain as model. Pig cortical tissue from two time points in development representing a non-folded, lissencephalic, brain (embryonic day 60) and primary-folded, gyrencephalic, brain (embryonic day 80) were examined by whole genome expression microarray studies.

overall_design: 3 samples from 3 litters mates representing the two time points E60 and E80 of the porcine gestation period

middle: B

first: Mogens

last: Kruhøffer

first: Ida

last: Holm

first: Arne

last: Jørgensen

first: Anders


title: Gene expression profiles of Herceptin-resistant breast cancer cells

status: Public on Aug 21 2009

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

summary:
Herceptin (trastuzumab) is a humanized monoclonal antibody targeted to the Her2 receptor tyrosine kinase.  Despite a robust response rate to Herceptin-based therapies in Her2-positive patients, resistance frequently arises within one year of the initial response.  To address the mechanism of Herceptin resistance, we selected clonal variants of Her2-positive BT474 human breast cancer cells (BT/HerR) that are highly resistant to the anti-proliferative effects of Herceptin in the presence of 0.2 uM or 1.0 uM Herceptin.  Our original report on these cell lines demonstrated sustained PI3K/Akt signaling and sensitivity to PI3K inhibitors in BT/HerR cells in the presence of Herceptin, suggesting dysregulation of that pathway as an essential component of Herceptin-resistant proliferation.
To address the mechanism by which BT/HerR cells and their PI3K/Akt signaling pathway became resistant to Herceptin, we analyzed gene expression profiles of two clones (BT/HerR1.0C and BT/HerR 1.0E) that were selected in 1.0 uM Herceptin and two clones (BT/HerR0.2D and BT/HerR 0.2J) that were selected in 0.2 uM Herceptin, in comparison to the Herceptin sensitive BT474 parent cells.

overall_design: Total cellular RNAs were extracted from BT474 (control) and four BT/HerR subclones, two that were originally selected in 1.0 uM Herceptin and two that were originally selected in 0.2 uM Herceptin.  Two RNA samples independently prepared from each clone were analyzed.

first: Susan

last: Kane

first: Long

last: Gu


title: Expression data from Bronchial Epithelial Cells exposed to Cyclic Stretch with and without LPS or TNFa

status: Public on Aug 31 2009

city: Toronto

first: Claudia

middle: Chimisso

last: dos Santos

state: ON

address: 30, Bond Street, room 4-011

department: University of Toronto

institute: Saint Michaels Hospital

summary:
Acute respiratory distress syndrome (ARDS) is a catastrophic form of acute lung injury (ALI). The necessity for mechanical ventilation (MV) renders patients at risk for ventilator induced lung injury (VILI). Exposure to repetitive cyclic stretch (CS) and/or over-inflation exacerbates injury. Reducing tidal volume (VT) is the only therapeutic strategy shown to mitigate morbidity and mortality. Cyclic stretch has been shown to differentially regulate gene expression in part through the activation of mammalian mitogen-activated protein kinase (MAPK). Although these studies have shown both molecular and cellular alterations, no unifying hypothesis to explain MV-induced lung injury has emerged.
In the current study, we hypothesized that coordinated expression of cyclic stretch (CS)-responsive genes relies on the presence of common CS-sensitive regulatory elements. To identify CS-responsive genes, we undertook a comparative examination of the gene expression profile of human bronchial epithelial airway (Beas-2B) cells in response to various injurious stimuli involved in the pathogenesis of acute lung injury (ALI)/Ventilator induced lung injury (VILI): cyclic stretch, tumor necrosis factor alpha (TNF-a), and lipopolysaccharide (LPS).

overall_design: Human Bronchial Epithelial Cells (Beas-B2) cells grown on silicon elastic plates coated with Type I collagen (Flexercell International, McKeesport, PA) were exposed to six regiments for 4 h: 1) control (static, [control]); 2) mechanical stretch (25 PKa, 30 cycles per min, [stretch]); 3) LPS (1 mcg/ml [LPS]); 4) TNF-α (20 ng/ml; [TNF]); 5) mechanical stretch plus LPS [LPS+S], and 6) mechanical stretch plus TNF-α [TNF+S]. Total RNA (duplicate experiments) was extracted using TRIZOL reagent (as per manufactures specifications) and purified using Qiagen mRNA purification Kit (as per manufacturers specifications). mRNA was hybridized to Affymetrix Human U133plus2.0 chips. Probe based analysis, background reduction, and quantile data normalization was performed in MeV 4.0 of TM4 using Robust Multi-array Average (RMA).

first: Ali

last: Akram

last: Han

first: Hussain

last: Masoom

last: Peng

first: Emily

last: Lam

first: Michael

last: Litvak

first: Xiaohui

last: Bai

first: Yuexin

last: Shan

first: Tsonwin

last: Hai

first: Arthur

middle: S

last: Slutsky

first: Haibo

last: Zhang

first: Jack

last: Haitsma

first: Mingyao

last: Liu


title: Transcriptomic and proteomic analyses of colon inflammation in interleukin-10 gene-deficient mice

status: Public on Sep 10 2009

city: Puddle Alley

first: Alan

middle: Francis

last: McCulloch

state: Mosgiel

address: Invermay

country: New Zealand

institute: AgResearch NZ

summary:
A total of 30 male IL10-/- (B6.129P2-Il10<tm1Cgn>/J) and 30 male C57 control (C57BL/6J) mice were obtained from The Jackson Laboratory (Bar Harbor, Maine, USA). All mice were between 28 and 35 days of age at the start of the study. For convenience and consistency in reporting, their age was defined as 35 days or 5 weeks of age. The mice were housed individually in standard shoebox size cages containing untreated wood shavings and maintained in an air-conditioned animal room with a 12-h light-dark cycle. Animals had free access to water and were fed an AIN-76A standard powder diet prepared in-house. This study was approved by the AgResearch Ruakura Animal Ethics Committee in Hamilton, New Zealand according to the Animal Protection Act (1960) and Animal Protection Regulations (1987) and amendments.
Four days after arrival, all mice were inoculated orally with a mixture of Enterococcus faecalis strains and bacteria commonly found in the intestinal lumen to obtain a more consistent and reproducible intestinal inflammation.
Mice were randomly assigned to five sampling groups (7, 8.5, 10, 12 and 14 weeks of age).

overall_design: For the comparison of gene expression levels, colonic RNA of IL10-/- and C57 at 7 and 12 weeks of age were compared because of a low HIS variability in the colon within those time points. A reference design with 15 arrays was used, where each individual RNA sample was hybridized with a reference sample onto the array, in a total of 3 or 4 biological replicates per treatment. Reference RNA was prepared by pooling equal amounts of purified total RNA extracted from small intestine, colon, kidney, liver and fetuses from normal, healthy Swiss mice.

first: Bianca

last: Knoch

first: Zaneta

last: Park-Ng


title: HES2 embryonic stem cells (ESCs) grown in standard conditions and FACs sorted for GCTM-2 and CD9

status: Public on Oct 01 2009

city: St Lucia

first: Sean

last: Grimmond

state: Q

address: Services Rd

department: Institute for Molecular Bioscience

institute: University of Queensland

summary:
HES2 ESCs were grown in standard ES culture conditions.  After 1 week, these cells were FACs sorted for the presence of GCTM-2 and CD9.

Keywords: Sorted cell comparison

overall_design: Three consecutive passages of HES2 cells were grown and subjected to FACs sorting. For each, 4 sorted populations of cells (p4, p5, p6, p7) were collected and these were subjected to microarray. A total of 12 samples: 3 replicates each of p4, p5, p6, and p7.

first: Gabriel

last: Kolle


title: Gene expression profiling of MIAPaCa2 cells re-expressing the alpha2 integrin or truncation mutations of alpha2 integrin

status: Public on Sep 26 2009

city: Durham

first: Jian-Liang

last: Li

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

summary: Previous reports demonstrate that the α2-integrin (α2) mediates pancreatic ductal adenocarcinoma (PDAC) cell interaction with collagens. We found that untransformed pancreatic ductal epithelial cells and well-differentiated PDAC cells use α2 exclusively to adhere and migrate on collagenI. In contrast, poorly-differentiated PT45P1 and MIAPaCa2 cells demonstrate reduced reliance on, or complete loss of α2, respectively. Further, well-differentiated PDAC lines exhibit reduced in vitro invasion compared to poorly-differentiated lines, and α2-blockade suppressed invasion of well-differentiated lines exclusively. Based on these data and the demonstrated role of α2 in maintaining tissue architecture in other organs, we hypothesized that α2 may actually suppress the malignant phenotype in PDAC. Accordingly, stable ectopic expression of α2 in MIAPaCa2 cells (MP2-α2) retarded in vitro invasion. MP2-α2 cells maintained on collagenI were more invasion-retarded than MP2-α2 cells maintained in standard tissue culture, and demonstrated higher α2β1 expression that was reflected in faster and more complete adhesion/migration on collagenI. Affymetrix gene expression profiling of α2-expressing and mock-transfected cells revealed that kallikrein-related peptidases (KLK)-5, 6 and 7 were specifically upregulated by α2. Accordingly, well-differentiated PDAC lines express KLK-5, 6 and 7 and KLK blockade increased invasion as well as collagenI-migration in KLK-positive lines. Importantly, an α2 cytoplasmic deletion mutant promoted KLK expression and retarded invasion, while an α9α2 chimera retarded invasion less efficiently, and did not impact KLK expression.  These data demonstrate for the first time that the α2-ectodomain and KLK’s coordinately regulate a less invasive phenotype in PDAC cells.

overall_design:
Affymetrix global gene arrays were used to analyse differences in gene expression patterns in MIAPaCa2 cells stably reexpressing the alpha2 integrin, a cytoplasmic deletion of the alpha2 integrin (dCYTO) or an alpha9 ectodomain and transmembrane domain/alpha2 cytoplasmic domain chimera, versus vector-only mock controls.  RNA was harvested from cells passaged identically and maitained under standard tissue culture conditions or on collagenI- or tenascin FNIII-coated plates..
Genetic manipulation (stable transgene expression)

first: Chia-Yao

last: Lee

first: Steve

last: Silletti


title: Expression Profiling Identifies Genes Involved in Emphysema

status: Public on Sep 21 2009

city: Brisbane

first: Santiyagu

middle: Mary

last: Savarimuthu Francis

state: Queensland

address: Level 1, Clinical Sciences Building, The Prince Charles Hospital, Rode Road

department: School of Medicine

institute: The University of Queensland

summary:
Chronic obstructive pulmonary disease (COPD) is a major public health problem. The aim of this study was to identify genes involved in emphysema severity in COPD patients.
Gene expression profiling was performed on total RNA extracted from non-tumor lung tissue from 30 smokers with emphysema. Class comparison analysis based on gas transfer measurement was performed to identify differentially expressed genes. Genes were then selected for technical validation by quantitative reverse transcriptase-PCR (qRT-PCR) if also represented on microarray platforms used in previously published emphysema studies. Genes technically validated advanced to tests of biological replication by qRT-PCR using an independent test set of 62 lung samples.
Class comparison identified 98 differentially expressed genes (p<0.01). Fifty-one of those genes had been previously evaluated in differentiation between normal and severe emphysema lung. qRT-PCR confirmed the direction of change in expression in 29 of the 51 genes and 11 of those validated, remaining significant at p<0.05. Biological replication in an independent cohort confirmed the altered expression of eight genes, with seven genes differentially expressed by greater than 1.3 fold, identifying these as candidate determinants of emphysema severity.
Gene expression profiling of lung from emphysema patients identified seven candidate genes associated with emphysema severity including COL6A3, SERPINF1, ZNHIT6, NEDD4, CDKN2A, NRN1 and GSTM3.

overall_design: Expression profiling using 22K element microarrays of 30 normal lung tissues.

first: Jill

last: Larsen

first: Sandra

middle: J

last: Pavey

first: Rayleen

middle: V

last: Bowman

first: Nick

middle: K

last: Hayward

first: Kwun

last: Fong

first: Ian

middle: A

last: Yang


title: LXR activation in RAW264.7 mouse macrophages expressing LXRalpha.

status: Public on Aug 01 2009

city: Madrid

first: ANTONIO

last: CASTRILLO

address: Arturo Duperier 4

department: metabolism and cellular signaling

institute: Instituto Investigaciones Biomedicas Alberto Sols CSIC

summary:
To identify novel LXR target genes, we conducted transcriptional profiling studies using RAW264.7 cells ectopically expressing
LXRalpha

overall_design:
Total RNA was isolated from RAW264.7 macrophages ectopically expressing LXRalpha as described in Venkateswaran et al. (2000); PNAS 97, 12097-12102. Cells were cultured with DMSO or GW3965 (1 μM) and
LG268 (100 nM). Transcriptional profiling was performed at the UCLA microarray core facility using murine Affymetrix 430 2.0 microarrays.

first: NOELIA

last: A-GONZALEZ

first: STEVEN

last: BENSINGER

first: CYNTHIA

last: HONG

first: SUSANA

last: BECEIRO

first: MICHELLE

last: BRADLEY

first: NOAM

last: ZELCER

first: JOSE

last: DENIZ

first: CRISTINA

last: RAMIREZ

first: MERCEDES

last: DIAZ

first: GERMAN

last: GALLARDO

first: CARLOS

last: GALARRETA

first: JON

last: SALAZAR

first: FELIX

last: LOPEZ

first: PETER

last: EDWARDS

first: JOHN

last: PARKS

first: MIGUEL

last: ANDUJAR

last: TONTONOZ


title: Gene expression in rat right ventricles during chronic pulmonary embolism

status: Public on Sep 01 2009

city: Charlotte

first: John

last: Zagorski

address: 1542 Garden Terrace, 301

department: Emergency Medicine

institute: Carolinas Medical Center

summary: Pulmonary vascular occlusions due to thromboemboli can result in pulmonary hypertension and right heart damage. Treatments to clear the vascular obstructions such as i.v. heparain or thrombolytics can resolve the hypertension but right ventricular damage often occurs first. Methods of protecting the right ventricle from hypertensive damage during the course of acute treatment to clear the thromboemboli are needed. Monocyte- and neutrophil-mediated inflammation and fibrosis are associated with chronic right ventricular damage but the pathways involved are not understood. A comprehesive survey of gene expression during chronic pulmonary embolism verses control rats has been conducted in this study.

overall_design: Pulmonary thromoembolism was simulated by injecting rats with 25-micron polystyrene microspheres into the right jugular vein. A dose of 2 million microspheres per 100 grams rat weight was used to generate chronic pulmonary embolism (~350 gram rats; injections ware 0.15 ml/100 gram of a 13 million microsphere per ml suspension in sterile 0.01% Tween-20). Control rats were injected with 0.01 ml/100 grams of Tween-20 "vehicle". After 6 weeks of PE or control, rats were euthanized and hearts surgically excised. Hearts were briefly perfused with buffer to remove blood. Right venticles were removed from whole hearts and separated into "apex" and "outflow-tract" (base) sections. Tisssues were then processed for RNA. More complete descriptions of these methods are available in PMID: 18430806, PMID: 18025228 and PMID: 16814320.

first: Maria

last: Obraztsova

first: Michael

last: Gellar

first: Jeffrey

last: Kline

last: Watts


title: Mouse gestational protein restriction: Newborn offspring liver and hindleg muscle

status: Public on Nov 07 2009

city: Copenhagen N

first: Ole

middle: Hartvig

last: Mortensen

address: Panum 6.5.28, Blegdamsvej 3

department: Department of Biomedical Sciences

institute: University of Copenhagen

summary: Gestational protein restriction is a model for low birth size. We hypothesized that taurine supplementation would protect against changes in newborn liver and muscle caused by a maternal low protein diet.

overall_design:
Pregnant mouse dams were subjected to different diet schemes from day 1 of pregnancy until birth. Pups were killed following birth and liver and hindleg skeletal muscle taken out and frozen at -80C until analysis.

Diet schemes: Normal Protein (20% casein; NP), Normal Protein + taurine (1% taurine supplementation in water ad libitum; NP+tau), Low Protein (8% casein; LP) and LP+tau

The liver and muscle samples were normalized separately.

middle: H

first: Hanne

last: Olsen

first: Lis

last: Frandsen

first: Peter

middle: E

last: Nielsen

first: Finn

first: Niels

last: Grunnet

first: Bjørn

last: Quistorff


title: Zebrafish embryos treated with Retinoic Acid or Retinoic acid antagonist during gastrulation and early somitogenesis.

status: Public on May 29 2009

city: Seattle

first: Lei

last: Feng

address: 1100 Fairview Ave. North, B2-152

department: Basic Science

institute: FHCRC

summary:
Retinoic acid (RA) is an important developmental signaling molecule responsible for the patterning of multiple vertebrate tissues. RA is also a potent teratogen, causing multi-organ birth defects in humans. Endogenous RA levels must therefore be tightly controlled in the developing embryo.
In order to understand the RA function and regulation at the genomic level, we used a microarray approach to identify genes that function as negative feedback regulators of retinoic acid signaling. To that end, we treated embryos with different chemicals: DMSO as control, AGN193019 as RA antagonist at high concentration 10uM and low concentration 1uM, as well as 0.33uM RA. Each treatment has four biological replicates. We screened for genes expressed in early somite-stage embryos that respond oppositely to treatment with RA versus RA antagonists, and validated them by whole-mount RNA in situ hybridization.

overall_design: Each treatment was performed four times, for a total of 16 independent samples (4 x 0.33 µM RA, 4 x 10 µM AGN193109, 4 x 1 µM AGN193109 and 4 x DMSO control).

first: Hernanderz

last: Rafael

last: Smith


title: Expression profile of cuticular genes of silkworm, Bombyx mori

city: Beibei

first: Jiubo

last: Liang

state: Chongqing

address: Tiansheng Road No. 2

department: Molecular Biology

institute: Institute of Sericulture and System Biology

summary: Insect cuticle plays essential roles in multiple physiological functions. During molting and metamorphosis, tremendous changes occur in silkworm cuticles. Silkworm is a model of Lepidoptera insects; however, little is known about the stage expression profiles of genes in cuticles of silkworm. In the present study, we selected 16 developmental stages, ranging from day 1 of the first instar larvae to day 8 of pupae, to perform microarray-based expression profiles. The data told us that various functions and physiological pathways were activated in the cuticle. Moreover, the expression profiles of cuticular protein genes, as the important components of cuticle, were investigated. The current study provides important insights for the functional study of insect cuticle and the regulation of insect cuticular protein genes.

overall_design: Transcription profiling experiments, 16 developmental stages (samples) were analyzed. Dual-channel experiments, with test samples labeled by Cy5 and common reference samples labeled by Cy3. Common reference sample was used for data normalization. One biological replicate. No dye-swaps.

first: Liang

last: Zhang

first: Zhonghuai

last: Xiang

first: Ningjia

last: He


title: Genomic expression analysis of rat chromosome 4 for skeletal traits at femoral neck

status: Public on Mar 31 2009

city: Indianapolis

first: Charles

last: Turner

state: IN

address: 723 W. Michigan St. SL 220C

department: Biomedical Engineering

institute: Indiana University Purdue University Indiapanolis

summary:
Femoral neck bone mineral density and structure candidate gene analysis in Fischer 344 (F344) and Lewis (LEW) rats
Hip fracture is the most devastating osteoporotic fracture type with significant morbidity and mortality. Previously, we identified that the region of 4q21-q41 on chromosome (Chr) 4 uniquely harbors multiple femoral neck quantitative trait loci (QTLs) in inbred Fischer 344 (F344) and Lewis (LEW) rats. In this study we identified the candidate genes for femoral neck density and structure by correlating gene expression in the proximal femur with the femoral neck phenotypes linked to the QTLs on Chr 4. Microarray analysis was performed using RNA extracted from proximal femora of 4-week-old rats from F344, LEW and two other strains. A total of 104 genes in the 4q21-q41 region were differentially expressed (p<0.05) among all strains of rats with a false discovery rate (FDR) less than 10%. These 104 genes were then ranked based on the proportion of variation in femoral neck phenotypes in F2 animals homozygous for a particular strain’s allele at the Chr 4 QTL explained by the expression level of the gene in that strain. A total of 37 genes, including 21 candidate genes and 16 predicted genes, were strongly correlated (r2>0.50) with different femoral neck phenotypes and prioritized for further analysis.  Ingenuity pathway analysis revealed several direct or indirect relationships among the candidate genes related to bone metabolism including pathways related to beta-estradiol, interleukin 6, insulin growth factor 2, androgen receptor and tumor necrosis factor.
Keywords: Comparison of gene expression profiles between F344, LEW, COP and DA rats

overall_design: Comparison of differentially expressed genes at the chromosome 4 QTL identified in F344 and LEW F2 rats.

first: Imranul

last: Alam

first: Qiwei

last: Sun

first: Lixiang

last: Liu

first: Daniel

middle: L

last: Koller

first: Yunlong

first: Howard

last: Edenberg

last: Econs

first: Tatiana

last: Foroud


title: Relation between the "activation of the inflammation" in the encephalic death donor and the quality of the graft

status: Public on Aug 05 2009

city: Luxembourg

first: Yvan

last: Devaux

address: 120 route d'Arlon

country: Luxembourg

institute: LIH

summary:
Study of the relation between the activation of the inflammation in the encephalic death donor and the quality of the graft (time before the first rejection occurred). Diagnostic approach based on the profiling of the donor's inflammatory reaction.
Keywords: procalcitonin, graft, inflammation

overall_design:
The 22 patients of this study were divided in 2 groups corresponding to the extreme quartiles of PCT values. The first group are the patients with low PCT and the second group are the patients with high PCT.
Blood  sample: 2.5 mL harvested in PAXgene® Blood RNA tubes (PreAnalytix)
RNA extraction: PAXgene® Blood RNA kit (Qiagen)
We used a Universel Reference RNA (Stratagene)
RNA amplification and labelling: kit Amino Allyl MessageAmp II (Ambion)
We hybridized 4 microarrays per patient using pangenomic microarrays from the "Réseau National des Génopôles" (Illkirch, France). 2 slides were hybridized with reference RNA labelled Cy3 and patient RNA labelled Cy5, and 2 slides were hybridized with reference RNA labelled Cy5 and patient RNA labelled Cy3.
Hybridation : Agilent protocol with few modifications : 750 ng of each labelled RNA were hubriddized at 60°C during 17 hours in an Aglient hybridization oven.
After washings, Slides were scanned with a GenePix 4000B scanner (Molecular Devices). Image intensity data were extracted with GenePix Pro 6.0 analysis software.
Quantification of Cy3 and Cy5 and selection of good spots were performed using the MAIA software (Novikov E and Barillot E. Software package for automatic microarray image analysis (MAIA).
Bioinformatics. 2007 Mar 1;23(5):639-40.
The ACUITY software was then used to normalize log ratios Cy3/Cy5 with Lowess non linear normalization, to filter out genes not present in at least 3 slides out of 4, to evaluate the reproducibility of the 4 microarrays of each patient (hierarchical clustering, Self Organizing Maps). Statistical analyses to insure reproducibility was performed using Excel (correlation coefficients, ANOVA). Only slides that passed all reprocubility tests were validated.

first: Pascal

last: Barbry

first: Kevin

last: LeBrigand


title: Limited transcriptional responses of Rickettsia rickettsii exposed to environmental stimuli

status: Public on May 23 2009

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

summary: Rickettsiae are strict obligate intracellular pathogens that alternate between arthropod and mammalian hosts in a zoonotic cycle. Typically, pathogenic bacteria that cycle between environmental sources and mammalian hosts adapt to the respective environments by coordinately regulating gene expression such that genes essential for survival and virulence are expressed only upon infection of mammals. Temperature is a common environmental signal for upregulation of virulence gene expression although other factors may also play a role. We examined the transcriptional responses of Rickettsia rickettsii, the agent of Rocky Mountain spotted fever, to a variety of environmental signals expected to be encountered during its life cycle. R. rickettsii exposed to differences in growth temperature (25o C vs. 37o C), iron limitation, and host cell species displayed nominal changes in gene expression under any of these conditions with only 0, 5, or 7 genes, respectively, changing more than 3-fold in expression levels. R. rickettsii is not totally devoid of ability to respond to temperature shifts as cold shock (37o C vs. 4o C) induced a change greater than 3-fold in up to 57 genes. Rickettsiae continuously occupy a relatively stable environment which is the cytosol of eukaryotic cells. Because of their obligate intracellular character, rickettsiae are believed to be undergoing reductive evolution to a minimal genome. We propose that their relatively constant environmental niche has led to a minimal requirement for R. rickettsii to respond to environmental changes with a consequent deletion of non-essential transcriptional response regulators. A minimal number of transcriptional regulators in the R. rickettsii genome is consistent with this hypothesis.

platform_organism:
Coxiella burnetii
Rickettsia rickettsii
Chlamydia muridarum
Chlamydia pneumoniae AR39
Staphylococcus epidermidis RP62A
Staphylococcus epidermidis ATCC 12228
Staphylococcus aureus subsp. aureus MW2
Borreliella burgdorferi B31
Coxiella burnetii RSA 493
Chlamydia caviae GPIC
Chlamydia trachomatis D/UW-3/CX
Staphylococcus haemolyticus JCSC1435
Granulibacter bethesdensis

overall_design: various growth and environmental condition comparisons

first: Damon

middle: W

last: Ellison

first: Tina

middle: R

last: Clark

first: Kimmo

last: Virtaneva

first: Ted

last: Hackstadt


title: Expression data from Rat heterotopic cardiac transplants

status: Public on Nov 11 2009

city: Houston

first: Malgorzata

last: Kloc

address: 6565 Fannin Street

department: Surgery

institute: The Methodist Hospital

summary: Heterotopic cardiac transplants were constructed in male Wistar Furth (allograft donor) and ACI (host) rats. Rats were divided into three groups consisting of no treatment, treatment with a sub-therapeutic dose of cyclosporin A, and treated with combination of a sub-therapeutic dose of cyclosporin A and allochimeric peptide. The allografts were harvested at defined periods post-transplantation and RNA was harvested to monitor gene expression changes resulting from the various treatments in T-cells and in heart cells.

overall_design: There are 3 distinct treatment groups, with three timepoints in each group. Two tissue samples are isolated from each group: allograft heart tissue and T-cells, for a total of 18 samples. The no-treatment group can be considered a baseline sample set for the determination of gene expression changes resulting from the two treatments.


title: Expression data from wild-type, Dgcr8 knockout and Dicer knockout ES cells

status: Public on Sep 23 2009

city: San Francisco

first: Robert

last: Blelloch

state: CA

address: 513 Parnassus Avenue, Campus Box #0525

institute: University of California, San Francisco

summary: Dgcr8 and Dicer are both important components of the microRNA biogenesis pathway while Dicer is also implicated in biogenesis of other types of small RNAs such as siRNAs and mirtrons. Here we performed microarray analysis of WT, Dgcr8 and Dicer knockout ES cells to identify mRNAs differentially regulated upon loss of Dgcr8 and Dicer.

overall_design: Wild-type, dgcr8 knockout, and dicer1 knockout ES cells were plated on 60-mm plates in triplicate.

first: Yangming

last: Wang


title: Global transcriptome changes in HepG2 cells exposed to copper

status: Public on Jun 25 2009

city: RTP

first: Min Ok

last: Song

address: 111 T.W. Alexander Dr

department: DIR ETP

summary:
Our hypothesis is that copper modulates the activity of multiple intracellular signal transduction pathways to affect transcription. We have previously shown that copper activates transcription through both metal- and oxidative stress-responsive signal transduction pathways. Since the global molecular mechanisms underlying copper toxicity have not been well elucidated in humans, we have profiled transcriptome changes in HepG2 cells exposed to 100, 200, 400 and 600 uM copper for 4, 8, 12 and 24 hours using a human oligonucleotide microarray. Differentially expressed genes were identified, and integrated into biological and functional pathways through Gene Ontology analysis. Global gene expression profile was overlaid onto biomolecular interaction networks and signal transduction cascades using pathway mapping and interactome identification.
Keywords: copper toxicity, HepG2 cells, copper concentrations: 100, 200, 400 and 600 uM, exposure times: 4, 8, 12, and 24 h, expression profiles of copper-responsive genes

overall_design: To prepare RNA for microarray studies, HepG2 cells were plated and allowed to grow until they were 50% confluent.  Cells were then treated with 100, 200, 400 and 600 uM of copper sulfate (Sigma-Aldrich Chemical Co., St Louis, MO) for 4, 8, 12 and 24 h.  These exposure conditions concentrations were based on cytotoxicity results, previously reported and corresponded to LD's between LD5 to LD50.  Three independent sets of total RNAs were isolated from untreated and treated cells using RNeasy mini kits (Qiagen, Inc., Valencia, CA) following manufacturer's instructions.  The quality of the purified RNA was determined using a BioAnalyzer (Agilent Technologies, Palo Alto, CA), and then stored at -70°C until used. For microarray hybridizations, 100 ng of total RNA from metal-treated cells was amplified and labeled with Cy3 fluorescent dye, and a common reference pool (non-treated cells) was amplified and labeled with Cy5 using Agilent Technologies Low RNA Input Linear Amplification labeling kit following the manufactureâ€™s protocol.  The quantity and purity of the resulting fluorescently-labeled cRNA was evaluated using a Nanodrop ND-100 spectrophotometer (Nanodrop Technologies, Wilmington, DE), and the size distribution using an Agilent Bioanalyzer.  Equal amounts of Cy3- and Cy5-lableled cRNA were then hybridized to an Agilent Human Microarray (~22,000 k features) for 17 h at 65°C.  The hybridized microarrays were then washed and scanned using an Agilent G2565BA scanner.  Data were extracted from the scanned images using Agilent Feature Extraction software.  A total of 98 microarrays were analyzed in this study:  4 concentrations x 4 time points x 3 biological replicates x 2 (dye-flip/technical replicates).  This results in six measurements for each treatment condition. GeneSpring v.7 (Agilent Technologies) was used to identify genes that showed significant changes in gene expression with any treatment.  For global normalization of raw microarray data, per spot and per chip: intensity dependent (LOWESS) normalization was applied.

first: Min-Ok

first: Jianying

last: Li

first: Jonathan

last: Freedman