title: Paternally-induced transgenerational environmental reprogramming of metabolic gene expression in mammals (small RNA)

city: Jerusalem

first: naomi

last: habib

address: Givat-Ram

department: Computer Scince

country: Israel

institute: Hebrew University

type: Non-coding RNA profiling by high throughput sequencing

summary: Characterized the small (19-35 bp) RNA population from control and low protein offspring livers by high throughput sequencing. Eight sequencing lanes, one for each animal, with an average of 3.7 million mappable reads per lane. A number of miRNAs changed expression in the offspring from low protein diet fathers.

overall_design: Examination of the effect of 2 different paternal diets, control diet  and low-protein diet, on the small RNA expression in the liver of the offsprings. 8 samples: 4 are control diets and 4 are low protein diets

first: Benjamin

last: Carone

first: Lucas

last: Fauquier

first: Naomi

last: Habib

first: Jeremy

middle: M

last: Shea

first: Caroline

middle: E

last: Hart

first: Ruowang

last: Li

first: Christoph

last: Bock

first: Chengjian

first: Phillip

last: Zamore

first: Alexander

last: Meissner

first: Zhiping

last: Weng

first: Hans

last: Hofmann

first: Nir

last: Friedman

first: Oliver

last: Rando


title: Paternally-induced transgenerational environmental reprogramming of metabolic gene expression in mammals (Affymetrix)

status: Public on Jan 14 2011

summary:
Epigenetic information can be inherited through the mammalian germline, and represents a plausible transgenerational carrier of environmental information. To test whether transgenerational inheritance of environmental information occurs in mammals, we carried out an expression profiling screen for genes in mice that responded to paternal diet.
Characterising the change in RNA expression in sperm in response to different paternal diets.

overall_design: Examination of the effect of different diets, control diet, low-protein diet and caloric-restriction diet, on the RNA expression in the sperm. 8 samples: 3 are control diets and 2 are low protein diets 1 caloric restriction diet, and 2 samples from Epidydimal tissue.

middle: R

middle: D

middle: A

middle: J


title: VEGFR-1 expressed by malignant melanoma initiating cells is required for tumor growth

status: Public on Jan 13 2011

city: Boston

first: Natasha

middle: Y

last: Frank

state: MA

address: 320 Longwood Avenue

department: Medicine

country: USA

institute: Children's Hospital Boston

summary: Melanoma growth is driven by malignant melanoma initiating cells (MMIC) identified by  expression of the ATP-binding cassette (ABC) member, ABCB5. ABCB5+ melanoma  subpopulations have been shown to overexpress the vasculogenic differentiation markers CD144  (VE-cadherin) and TIE-1 and are associated with CD31-negative vasculogenic mimicry (VM),  an established biomarker associated with increased patient mortality. Here we identify a critical  role for VEGFR-1 signaling in ABCB5+ MMIC-dependent VM and tumor growth. Global gene  expression analyses, validated by mRNA and protein determinations, revealed preferential  expression of VEGFR-1 on ABCB5+ tumor cells purified from clinical melanomas and  established melanoma lines. In vitro, VEGF induced in a VEGFR-1-dependent manner  expression of CD144 in ABCB5+ subpopulations that constitutively expressed VEGFR-1, but not  in ABCB5- bulk populations that were predominantly VEGFR-1-negative. In vivo, melanomaspecific  shRNA-mediated knockdown of VEGFR-1 blocked the development of ABCB5+ VM  morphology and inhibited ABCB5+ VM-associated production of the secreted melanoma  mitogen, laminin. Moreover, melanoma-specific VEGFR-1 knockdown markedly inhibited  tumor growth (by >90%). Our results demonstrate that VEGFR-1 function in MMIC regulates  VM and associated laminin production, and show that this function represents one mechanism  through which MMIC promote tumor growth.

overall_design: Microarray analyses were performed on purified ABCB5+ (n=5) and ABCB5- (n=5) cell subsets derived from the established human melanoma cell lines G3361 and A375 and from three distinct clinical melanoma specimen. Total RNA was extracted, processed and hybridized onto Affymetrix human HG-U133Plus2 GeneChip microarrays (Affymetrix, Santa Clara, CA).

first: Markus

middle: H


title: Paternally-induced transgenerational environmental reprogramming of metabolic gene expression in mammals

first: naomi

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Human and mouse gene expression data from LPS-exposed mouse lungs treated with human MSCs

city: Temple

first: Joni

last: Ylostalo

state: TX

address: 5701 Airport Rd., Module C

department: Institute for Regenerative Medicine

institute: Texas A&M

summary: Multipotent stromal cells (MSCs) are currently in clinical trials for a number of inflammatory diseases. Recent studies have demonstrated the ability of MSCs to attenuate inflammation in rodent models of acute lung injury (ALI) suggesting that MSCs may also be beneficial in treating ALI. To better understand how human MSCs (hMSCs) may act in ALI, the lungs of immunocompetent mice were exposed to lipopolysaccharide (LPS) and 4 hr later bone marrow derived hMSCS were delivered by oropharyngeal aspiration (OA). Administration of hMSCs significantly reduced the expression of pro-inflammatory cytokines, neutrophil counts and total protein in bronchoalveolar lavage. There was a concomitant reduction in pulmonary edema as indicated by a decrease in lung wet/dry weight ratio. The anti-inflammatory effects of hMSCs were not dependent on localization to the lung, as intraperitoneal administration of hMSCs also attenuated LPS-induced inflammation in the lung. Microarray analysis revealed significant induction of TNF-α-induced protein 6 (TSG-6) expression by hMSCs 12 hr after OA delivery to LPS-exposed lungs. Knockdown of TSG-6 expression in hMSCs by RNA interference abrogated most of their anti-inflammatory effects. In addition, intra-pulmonary delivery of recombinant human TSG-6 reduced LPS-induced inflammation in the lung. These results show that hMSCs recapitulate the observed beneficial effects of rodent MSCs in animal models of ALI and suggest that the anti-inflammatory properties of hMSCs in the lung are explained, at least in part, by activation of hMSCs to secrete TSG-6.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Eight- to 10-week-old female BALB/C mice were treated with either 1 mg/kg lipopolysaccharide (LPS) in 100 μl PBS or an equal volume of PBS, as vehicle control, by oropharyngeal aspiration (OA). Four hours after LPS exposure, 250,000 human multipotent stromal cells in 100 μl of PBS were given by OA and 30 min later a second dose of equal concentration was administered, for a total of 500,000 hMSC. As a control, 200 μl PBS was delivered as described above. After 12 h, total RNA was isolated from (A) lungs of LPS-exposed mice treated with either hMSCs (LPS+MSC) or PBS (LPS+PBS), and (B) lungs of PBS-exposed mice treated with hMSCs (PBS+MSC). To obtain additional controls, hMSCs were mixed in vitro with either LPS- (LPS+MSC in vitro mix) or PBS-exposed (PBS+MSC in vitro mix) mouse lungs just before RNA isolation. RNA samples containing mouse and human RNA were first analyzed for amount of human RNA based on human GAPDH signal from real-time RT PCR. Samples with similar human RNA content were used for both mouse and human microarrays

first: Deborah

last: Sullivan


title: Tribbles 3 - a novel regulator of TLR2-mediated signaling in response to Helicobacter pylori lipopolysaccharide

status: Public on Jan 12 2011

city: Dublin 8

first: Sinead

middle: Marian

last: Smith

address: St. James's Hospital

country: Ireland

institute: Trinity College Dublin

first: Anthony

middle: P

last: Moran

first: Shane

last: Duggan

first: Salah

last: Ahmed

first: Abdelhafeez

middle: S

last: Mohamed

first: Henry

last: Windle

first: Luke

last: O'Neill

first: Dermot

last: Kelleher


title: Changes in gene expression in MKN45 cells in response to Helicobacter pylori lipopolysaccharide

summary:
This study set out to identify global changes in gene expression in MKN45 gastric epithelial cells following 8 hours stimulation with 10 μg/ml lipopolysaccharide (LPS) from the gastric pathogen H. pylori.
Microarray analysis was used to compare changes in gene expression between cells treated with 10 μg/ml H. pylori LPS and untreated cells at the same time point.

overall_design: Total RNA was harvested from MKN45 cells following treatment with LPS for 8h or untreated cells at the same time-point. 2 independent experiments were carried out. RNA was labeled and hybridized to GeneChips to analyse changes in gene expression.


title: Changes in gene expression in HEK-TLR2 cells in response to Helicobacter pylori lipopolysaccharide

summary:
This study set out to identify global changes in gene expression in human embryonic kidney (HEK) cells stably transfected with Toll-like receptor 2 (TLR2) over a 48 hour time-course, following stimulation with 10 μg/ml lipopolysaccharide (LPS) from the gastric pathogen H. pylori.
Microarray analysis was used to compare changes in gene expression between cells treated with 10 μg/ml H. pylori LPS and untreated cells at the same time point.

overall_design: Total RNA was harvested from HEK-TLR2 cells following treatment with LPS for 2, 4, 8, 24 and 48h or untreated cells at the same time-point. 2 independent experiments were carried out. RNA was labeled and hybridized to GeneChips to analyse changes in gene expression.


title: Human CD200+CD49+ hair follicle keratinocytes versus CD200-CD49+ keratinocytes

city: Baltimore

first: Luis

middle: Andres

last: Garza

state: MD

address: 1550 Orleans St. Suite 204 CRBII Koch

department: Dermatology

institute: Johns Hopkins School of Medicine

summary:
Human hair follicles from normal areas of the scalp were disassociated to single cells, sorted and tested by microarrray
To compare the expression of human CD200+ CD49+ hair follicle keratinocytes versus CD200-CD49+ keratinocytes

overall_design: 3 independent biologic replicates  (each from a distinct human subject) were sorted for both CD200+CD49+ and CD200-CD49+ populations

first: Tailun

last: Zhou

first: Hanz

last: Blat

first: Michelle

last: Lee

first: Hellen

last: He

first: David

middle: C

last: Stanton

first: Lee

last: Carrasco

first: John

last: Tobias

first: Chao

last: Yang

first: George

last: Cotsarelis


title: Bald scalp retains hair follicle stem cells but lacks CD200-rich and CD34-positive hair follicle progenitor cells

summary:
Androgenetic alopecia (AGA) or common baldness results from a marked decrease in hair follicle size. This miniaturization may be related to loss of hair follicle stem or progenitor cells. To test this hypothesis, we analyzed bald and non-bald scalp from the same individuals for the presence of hair follicle stem and progenitor cells using flow cytometry to quantitate cells expressing CYTOKERATIN 15 (KRT15), CD200, CD34 and ALPHA-6-INTEGRIN (ITGA6). High levels of KRT15 expression correlated with stem cell properties of small cell size and quiescence. Cells with the highest level of KRT15 expression were maintained in bald scalp; however, distinct populations of CD200high ITGA6high cells and CD34-positive cells were markedly diminished. Consistent with a progenitor cell phenotype, the diminished populations localized closely to the stem-cell rich bulge area but were larger and more proliferative than the bulge stem cells. In functional assays, analogous CD200 high /Itga6 high cells from murine hair follicles were multipotent and generated new hair follicles in skin reconstitution assays. These findings suggest that a defect in stem cell activation plays a role in the pathogenesis of AGA.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series.


title: Expression data analyzed with LPIA in A549 lung carcinoma cells treated with geldanamycin.

status: Public on Jan 11 2011

first: Lisa

last: Christadore

address: 24 Cummington Street

department: Chemistry

institute: Boston University

summary: The statsitcal model, latent pathway identification analysis (LPIA), was implemented for the analysis of A549 lung carcinoma cells treated with geldanamycin. Control and treated samples were assayed with Affymetrix HG_U133_plus_2 arrays and analyzed using LPIA. LPIA looks for statistically signﬁcant evidence of dysregulation in a network of pathways constructed in a manner that explicitly links pathways through their common function in the cell. Geldanamycin (geld) is known to inhibit the molecular chaperone protein, Hsp90, and plays a role in preventing the malignant transformation and proliferation of healthy cells during oncogenesis. LPIA successfully identified pathways specific to geldanamycin effects at the gene transcription level.

overall_design: A549 lung carcinoma cells were allowed to adhere for 24h and further incubated in the presence of geldanamycin at a concentration equivalent to the determined IC50 of 40 nM or IC20 of 10 nM, or with vehicle DMSO (final concentration 0.4%). After 24h and 48 h, cells were harvested and total RNA was purified and processed for Affymetrix HG_U133_Plus_2.0 microarray analysis. Raw probe intensities were RMA-normalized and avereaged for three replicates for each condition. Probe sets for 54,120-annotated open reading frames were included in LPIA analysis.

last: Pham

first: Scott

last: Schaus

first: Eric

last: Kolaczyk


title: HeLa gene expression profile

status: Public on Jan 07 2011

city: Charlottesville

first: Anindya

last: Dutta

state: VA

address: 1300 Jefferson Park Ave

department: Biochemistry & Molecular Genetics

institute: University Of Virginia

summary:
Gene expression in HeLa cells was profiled using Affymetrix gene expression Human HG-U133_Plus_2 array.  Transcript signal was mapped against the chromosome coordinates (probe-by-probe basis) using the HG-U133A_2 Annotations CSV file for hg18 build of the human genome provided by Affymetrix.
Karnani N, Taylor C, Malhotra A, Dutta A (2007) Pan-S replication patterns and chromosomal domains defined by genome-tiling arrays of ENCODE genomic areas. Genome Res 17: 865-876.

overall_design: Total RNA from asynchronously growing HeLa cells was isolated and subjected to micrarray analysis for gene expression.

first: Neerja

last: Karnani

first: Ankit

last: Malhotra


title: Killer cell Ig-like receptor (KIR) 3DL1 downregulation enhances inhibition of type 1 diabetes by autoantigen-specific regulatory T cells

status: Public on Jan 06 2011

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

summary:
Varied genes may be responsible for the functional differences of distinct subsets of T cells. As a result, it is possible that regulatory T cells and pathogenic T cells may display a different set of gene profile regulating their functional status.
To identify genes contributing to the functional role of T cells, we used microarrays to examine the global gene expression in regulatory T cells, pathogenic T cells, and control non-regulatory, non-pathogenic T cells.

overall_design: BDC, N79, N206 and NR206 CD4+ T cells were cultured in RPMI medium plus 5% fetal bovine serum in vitro. N206 and NR206 were used as Tregs, BDC were used as Tpath cells and N79 were used as neutral control cells . BDC, N79, N206 and NR206 were cultured for RNA extraction and hybridization on Affymetrix microarrays.

first: Hanjun

last: Qin

first: Zunde

last: Wang

first: Weiting

last: Du

first: Wen-Hui

first: Arthur

last: Riggs

first: Chih-Pin

last: Liu


title: Expression data from WASF3 knockdown stable MDA-MB-231 cells and control cells

city: Augusta

first: yong

last: teng

address: 1120 15th Street

institute: Medical College of Georgia

summary:
We recently showed that inactivation of the WASF3/WAVE3 gene in breast cancer cells results in loss of cell motility and invasion in vitro and metastasis in vivo. To obtain a better understanding of molecular mechanisms of action of WASF3, we have established the stable  WASF3 knockdown  MDA-MB-231 cells using shRNA strategy.
We used microarrays to detail the global programme of gene expression after silencing WASF3 and identified distinct classes of up or down-regulated genes associated with breast cancer cell migration and motility

overall_design: The three stable WASF3 knockdown single clones and three control clones were selected for RNA extraction and hybridization on Affymetrix microarrays.  To identify altered gene expression patterns in the knockdown cells, we compared gene expression levels between three different knockdown and three different control clones.

first: Y

last: Teng

first: J

middle: K

last: Cowell


title: Expression profiling of vascular endothelial cells using minimal input material

city: Dundee

first: Gino

last: Miele

address: James Arrot Drive, Ninewells Hospital

country: United Kingdom

institute: Translational Medicine Research Collaboration

summary: Expression profiling using minimal endothelial cell numbers isolated from 2 phenotypic groups (condition A and B). In total 64 GeneChips were processed, 12 Genechips for condition A and 52 GeneChips for condition B.

overall_design: Vascular endothelial cell scraping biopsies were collected and endothelial cells postively enriched (CD-146) from 2 different phenotypic groups. RNA extraction and probe generation were carried out using workflows optimised for use with minimal input material.

first: Laura

last: Kennedy

first: Chim

last: Lang

first: Mahesh

last: Pauriah


title: High-throughput ectopic expression screen for tamoxifen resistance

city: Manhattan

first: Ross

last: Levine

state: NY

address: RRL

institute: MSKCC

summary: Resistance to tamoxifen in breast cancer patients is a serious therapeutic problem and major efforts are underway to understand underlying mechanisms. Resistance can be either intrinsic or acquired. We derived a series of subcloned MCF7 cell lines that were either highly sensitive or naturally resistant to tamoxifen and studied the factors that lead to drug resistance. Gene-expression studies revealed a signature of 67 genes that differentially respond to tamoxifen in sensitive vs. resistant subclones, which also predicts disease-free survival in tamoxifen-treated patients. High-throughput cell-based screens, in which >500 human kinases were independently ectopically expressed, identified 31 kinases that conferred drug resistance on sensitive cells. One of these, HSPB8, was also in the expression signature and, by itself, predicted poor clinical outcome in one cohort of patients. Further studies revealed that HSPB8 protected MCF7 cells from tamoxifen and blocked autophagy. Moreover, silencing HSBP8 induced autophagy and caused cell death. Tamoxifen itself induced autophagy in sensitive cells but not in resistant ones, and tamoxifen-resistant cells were sensitive to the induction of autophagy by other drugs. These results may point to an important role for autophagy in the sensitivity to tamoxifen.

overall_design: For defined estrogen culture experiments, sensitive (MCF7-B7TamS) and resistant (MCF7-G11TamR) subclones, were plated in 10-cm dish (Nunc) in DMEM supplemented with 5% FBS. The day after plating, the media was changed to steroid depleted media (phenol red-free DMEM) supplemented with 5% charcoal-dextran treated FBS and grown for 2 d. On day 3, cells were rinsed three times with PBS and treated in triplicate using one of four different conditions: (i) estrogen-depleted medium (control); (ii) estrogen (E) at 10 to 9 M; (iii) 4-OHT at 1 uM; and (iv) E plus 4-OHT, both drugs at the same concentrations as in (ii) and (iii). After 4 h, RNA was isolated and processed for gene-expression profiling according to the Affymetrix protocol (Human Genome U133 plus 2.0 Array) at the Microarray Core Facility at the Dana Farber Cancer Institute. The gene-expressionCEL files were normalized using dChip, using the invariant method and PM-MM difference methods for background subtraction. We identified genes that are differentially regulated by tamoxifen using the following criteria: (i) Genes that responded to estrogen in both MCF7-B7TamS andMCF7-G11TamR were identified if cells under tamoxifen treatment were more than 1.1-fold either up- or down-regulated [90% confidence interval (CI)] relative to its corresponding control cells; (ii) Genes unresponsive to tamoxifen in resistant cells: genes that showed more than 1.1-fold up- or down-regulation (90% CI) in MCF7-G11TamR but not in MCF7-B7TamS when comparing cells treated with both estradiol and tamoxifen with those treated with drug only.

first: Lihua

last: Zou

last: Gonzalez-Malerva


title: Comparative expression profiles of human embryonic stem cells among different feeders and conditioned media

city: Taipei

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

summary:
Background: The hES-T3 cell line with normal female karyotype was used to differentiate into autogeneic fibroblast-like cells (T3HDF) as feeder to support the undifferentiated growth of hES-T3 cells (T3/HDF) for 14 passages. A feeder-free culture on Matrigel in hES medium conditioned by these autogeneic feeder cells (T3HDF) was established to maintain the undifferentiated growth of hES-T3 cells (T3/CMHDF) for 8 passages. Results: The gene expression profiles of mRNAs, microRNAs and proteins between the undifferentiated T3/HDF and T3/CMHDF cells were shown to be very similar, and their expression profiles were also found to be similar to those of T3/MEF and T3/CMMEF cells grown on MEF feeder and feeder-free Matrigel in MEF-conditioned medium, respectively. The abundantly expressed genes of T3/HDF, T3/CMHDF, T3/MEF and T3/CMMEF cells were found to play prominent roles in signaling pathways and GO process networks. The miR-302/367 cluster and miR-371/372/373 cluster were extremely abundantly expressed in undifferentiated T3/HDF and T3/CMHDF as well as T3/MEF andT3/CMMEF cells. The undifferentiated state of T3/HDF and T3/CMHDF cells was evidenced by the very high expression levels of ¡§stemness¡¨ genes and low expression levels of differentiation markers of ectoderm, mesoderm and endoderm in addition to the strong staining of OCT4 and NANOG. Conclusion: The T3HDF feeder and T3HDF-conditioned medium were able to support the undifferentiated growth of hES cells, and they would be useful for drug development and toxicity testing in addition to the reduced risks of xenogeneic pathogens when used for medical applications such as cell therapies.

Keywords: genetic modification

overall_design:
In this investigation, both miRNA and mRNA expression profiles from human embryonic stem cells (hES-T3) grown on MEF feeder (T3_MEF), feeder-free Matrigel in MEF-conditioned medium (T3_CMMEF), T3HDF (hES-T3 differentiated fibroblast-like cells) feeder and feeder-free Matrigel in T3HDF-conditioned medium were quantitatively determined. Several target genes of T3BA and T3CM cells-specific miRNAs were identified.

***This submission represents the mRNA expression component of the study only***

first: SL

last: Li


title: Expression data from Adam10 knock out mice and wild type

city: Kiel

first: Robert

last: Haesler

address: Schittenhelmstr. 12

department: IKMB / 1st Dept. of Medicine

country: Germany

institute: University Clinic of Schleswig Holstein

summary:
Adam10, a cell surface protease, cleaving many proteins including TNF-alpha and E-cadherin. Here we investigate the genome wide effects of Adam10 knock out on the transcriptome.
Commercial microarrays (Affymetrix Mouse Gene ST 1.0) were used to generate genome wide mRNA profiles.

overall_design: Mouse tissue samples from n=4 wiltype skin and n=4 Adam10 knockout skin were used in the study.

last: Häsler

first: Silvio

last: Weber

first: Paul

last: Saftig


title: Transcriptome data for human ES, IMR90 and IMR90-derived iPS (ESIMR90) cells

status: Public on Jan 05 2011

city: Singapore

first: Yee Jiun

last: Kok

address: 20 Biopolis Way, #06-01 Centros

country: Singapore

institute: Bioprocessing Technology Institute

summary:
Assessing relevant differences between human induced pluripotent stem (iPS) cells and human embryonic stem (ES) cells is important, given that such differences may impact their potential therapeutic use.
We used microarray to profile the changes in global gene expression arising from the reprogramming of somatic cells to induced pluripotent stem cells.

overall_design: Comparison of gene expression between human embryonic stem cells (HES-3), induced pluripotent stem cells (ESIMR90) and its parental fibroblasts (IMR90). A pair of biololical replicates were analysed for each cell line.

first: Angela

last: Chin

first: Andre

last: Choo

first: Vanessa

last: Ding

first: Albert

last: Heck

first: Yee

first: Teck

last: Low

first: Javier

last: Muñoz


title: Transcriptome data for human ES, FORESKIN and FORESKIN-derived iPS (ES4SKIN) cells

overall_design: Comparison of gene expression between human embryonic stem cells (HES-3), induced pluripotent stem cells (ES4SKIN) and its parental fibroblasts (FORESKIN). A pair of biololical replicates were analysed for each cell line.


title: Transcriptome data for human induced pluripotent stem (iPS) cells and human embryonic stem (ES) cells


title: Gene expression changes in alpha GABA receptors in the mice brains after prolonged ketamine administration

status: Public on Jan 04 2011

city: Hong Kong

first: sijie

last: tan

country: China

institute: Chinese university of Hong Kong

summary: Transcriptome analysis of global gene epression changes in the mouse prefrontal cortex after long term treatment with sub-aesthetics dose of ketamine.

overall_design: We analyzed brain tissues from 2 ketamine treated mice and 2 saline treated mice using the Affymetrix Mouse Gene 1.0 st v1 platform. Array data was processed by Affymetrix Exon Array Computational Tool. No techinical replicates were performed.

first: Sijie

last: Tan

first: David

middle: T

last: Yew


title: Expression data from In vitro induced C2  M cells in the presence of commensal bacteria

status: Public on Jan 01 2011

city: Cork

first: John

middle: Andrew

last: Mac Sharry

state: Cork

address: College Road

department: APC, Biosciences Instiute

institute: UCC

summary:
M cells are the main site of bacterial translocation in the intestine. We used the in vitro M cell model to study the effect of the commensal bacteria; Lactobacillus salivarius, Eschericha coli and Bacteroides fragilis, on M cell gene expression.
Bacterial translocation across the gut mucosa has traditionally been based on the detection of commensals in the mesenteric lymph node. Differential rates of commensal translocation have been reported in vivo, however fewer studies have examined translocation of commensals at the level of the gut epithelial M cell. In this study we employed an in vitro M cell model to quantify translocation of various bacteria. C2BBe1 cells were differentiated into M cells and the gene expression profile and transport kinetics of different bacterial strains, namely Lactobacillus salivarius, Escherichia coli, and Bacteroides fragilis, was assessed. For comparison with M cell uptake, the THP-1 monocytic cell line was used to analyze bacterial internalization and resulting cytokine production. The commensal bacterial strains were translocated across M cells with different efficiencies; E. coli and B. fragilis translocated with equal efficiency while L. salivarius translocated with less efficiency. In contrast, L. salivarius was internalized by THP-1 cells to a higher degree than B. fragilis or E. coli and was associated with a different cytokine profile. Microarray analysis showed both common and differential gene expression amongst the bacteria and control polystyrene beads. In the presence of bacteria, but not beads, upregulated genes were mainly involved in transcription regulation and dephosphorylation, e.g. EGR1, JUN; whereas proinflammatory and stress response genes were primarily upregulated by E. coli and B. fragilis, but not L. salivarius nor beads, e.g. IL8, TNFAIP3. These results demonstrate that M cells have the ability to discriminate between different commensal bacteria and modify subsequent immune responses.

overall_design: C2bbe1 cells were converted to M cells (C2M) following 21 days of culture on Transwells in the presence of Raji B cells. C2M cells were co-cultured alone, Lactobacillus salivarius, Eschericha coli, Bacteroides fragilis and control beads. Total RNA was extracted and processed for Affymetrix array hybridisation

first: Susan

last: Lapthorne

last: MacSharry


title: The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli

city: Bethesda

first: Chase

middle: Lawrence

last: Beisel

address: 18 Library Dr. MSC 5430

department: CBMP

institute: NICHD

summary: Bacteria selectively consume some carbon sources over others through a regulatory mechanism termed catabolite repression. Here, we show that the base pairing RNA Spot 42 plays a broad role in catabolite repression in Escherichia coli by directly repressing genes involved in central and secondary metabolism, redox balancing, and the consumption of diverse non-preferred carbon sources. Many of the genes repressed by Spot 42 are transcriptionally activated by the global regulator CRP. Since CRP represses Spot 42, these regulators participate in a specific regulatory circuit called a multi-output feedforward loop. We found that this loop can reduce leaky expression of target genes in the presence of glucose and can maintain repression of target genes under changing nutrient conditions. Our results suggest that base pairing RNAs in feedforward loops can help shape the steady-state levels and dynamics of gene expression.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: MG1655 lacIq cells harboring the control vector pBRplac or the Spot 42-inducible vector pSpot42 were grown in LB to an ABS600 of ~0.4 and treated with 1 mM IPTG. After 7 min, total RNA was isolated using the hot phenol extraction procedure.

first: C

middle: L

first: G

last: Storz


title: The antitumor mechanism of Desmosdumotin C Analog

status: Public on Jan 03 2011

first: Sung-Liang

last: Yu

summary:
In our continuing study of the desmosdumotin C (1) series, twelve new analogues, 21–32, mainly with A-ring modifications, were prepared and evaluated for in vitro anticancer activity against several human tumor cell lines. Among them, the 4′-iodo-3,3,5-tripropyl-4-methoxy analogue (31) showed significant cytotoxicity against multiple human tumor cell lines with ED50 values of 1.1–2.8 microM. Elongation of the C-3 and C-5 carbon chains reduced activity relative to propyl substituted analogues; however, activity was still better than that of natural 1. Among analogues with various ether groups on C-4, compounds with methyl (2) and propyl (26) ethers inhibited cell growth of multiple tumor cells lines, while 28 with an iso-butyl ether showed selective cytotoxicity against lung cancer A549 cells (ED50 1.7 microM). The gene expression profiles showed that 3 may modulate the spindle assembly checkpoint (SAC) and chromosome separation, and thus, arrest cells at the G2/M-phase.
We used microarrays to elucidate the underlying antitumor mechanism induced by Desmosdumotin C Analog

overall_design: Analogue 3 showed potent cytotoxicity against the highly invasive non-small-cell lung cancer cell line CL1-5 with an ED50 value of 0.11 µM. To determine which genes were differentially expressed upon CL1-5 treatment with analogue 3, the genome-wide mRNA expression profiles of 3-treated cells and control cells were determined using Affymetrix human genome U133 plus 2.0 GeneChip according to the Manufacturer’s protocols

first: Kyoko

last: Nakagawa-Goto

first: Kuo-Hsiung

last: Lee


title: Background analysis using yeast RNA on the mouse and human array

city: Atlanta

first: Michael

last: Zilliox

state: GA

address: 1510 Clifton Road

department: Microbiology and Immunology

institute: Emory University School of Medicine

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

overall_design: Refer to individual Series


title: Microarray expression data from whole murine knee joints at early time points post surgery in the destabilization of medial meniscus (DMM) model of OA

city: London

first: Annika

last: Burleigh

address: 65 Aspenlea Road

department: Kennedy Institute of Rheumatology

institute: Imperial College London

summary:
Mechanical Stimuli are arguably the most important aetiolgical factors in osteoarthritis (OA) development.  Not only do we see disease arising from joints where the cartilage has sustained direct (e.g. intraarticular fracture) or indirect (e.g. meniscal injury) trauma, but mechanical factors are considered, at least partly, to explain the disease associations with aging and obesity.  It is now well established that OA is not simply due to repeated wear and tear, leading to attrition of the articular surfaces, but that it requires activation of a number of inflammatory genes, which drive catabolic protease activity in the joint.  These enzymes lead to breakdown of the major extracellular matrix components of cartilage, namely type II collagen, and the proteoglycan, aggrecan.  Although it is unclear precisely which enzymes are responsible for matrix breakdown in human OA, Glasson et al showed that deletion of the aggrecan degrading enzyme, ADAMTS5 substantially protected the joint from surgically induced murine OA suggesting that it is a major aggrecanase in the mouse.
This study was part of a wider study using the surgical model of murine OA, induced by destabilising the medial meniscus (DMM), to confirm the dependence of joint loading on disease progression and to reveal mechanosensitive genes within the joint which may be involved in the development of OA.
Using this model we, and others, have shown that there is a robust degradation of articular cartilage over 4-12wks in male C57B/6 mice.  We identified the gene response in joints early following induction of OA, prior to cartilage degradation, by extracting RNA from whole joints (after skin and muscle had been removed) 6hrs, 3 days and 7 days following sham and DMM surgery.  An Affymetrix ST1 gene array was performed.  Significantly regulated genes (>1.4 fold above naive and sham samples at any timepoint), or those considered to have a putative role in OA pathogenesis were selected for quantitative validation using Taqman low density microfluidic card arrays (TLDA).

overall_design: Gene expression in whole knee joints at 3 early time points post DMM surgery (before cartilage loss), 6hrs, 3days and 7days was examined.  Two controls were identified, the first control consisted of age matched naïve mice that had undergone 15 minutes of anaesthesia but were not operated on (0hrs post surgery).  The second control included mice which had undergone sham surgery (capsulotomy alone).  For this RNA was taken at the same time points post surgery as DMM samples (6hrs, 3days and 7days).  There were three biological replicates per condition (total of 21 samples).  The right (ipsilateral) knee joint was taken and RNA extracted and processed for microarray analysis using the Affymetrix Mouse Gene 1.0 st v1 platform.

first: Tonia

last: Vincent

first: Jeremy

last: Saklatvala


title: Analysis of Ppif-/- hearts

city: Cincinnati

middle: W

last: Elrod

state: OH

address: 240 Albert Sabin Way

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital and Medical Center

summary: To identify differences in gene expression between peptidylprolyl isomerase F (cyclophilin D; Ppif)-null hearts and WT control hearts.

overall_design: RNA was isolated from mice 8 weeks of age to discover gene changes prior to myocardial dysfunction. Three replicates each of Ppif-/- and WT mice.

first: Jeffery

last: Molkentin

first: Bruce

last: Aronow

first: Bhuvana

last: Sakthievel


title: Background analysis using yeast RNA on the U133 plus 2.0 array

summary: We used yeast RNA to estimate background binding for each probe on the human U133 plus 2.0 array.

overall_design: Yeast RNA was hybridized to the human microarray.

first: Matthew

middle: N

last: McCall

first: Rafael

last: Irizarry


title: Phase II trial melphalan ILI plus ADH-1 for treatment of in-transit extremity melanoma

city: Durham

first: Christina

last: Augustine

state: NC

address: VAMC RmE4001 508 Fulton St.

department: Surgery

institute: Duke University Medical Center

summary:
An evaluation of biopsies from patients with in-transit extremity melanoma who have been treated with ADH-1 followed by melphalan in the setting of isolated limb infusion
Gene expression profiles were obtained from 28 lesions across 15 patients and evaluated for expression values that correlated with ADH-1 treatment given 4-8hrs prior to melphalan isolated limb infusion

overall_design:
Chemotherapy response analysis:  complete response - CR; partial response - PR; stable disease - SD; progressive disease - PD; lost to follow-up - LTU/F
ADH-1 treatment classification:  'pre' - lesions obtained prior to any treatment with ADH-1; 'post' - lesions obtained just prior to ILI with melphalan after 1 treatment with ADH-1; '2nd' - lesions obtained after a 2nd dose of ADH-1 given 8 days after melphalan ILI

first: Douglas

last: Tyler


title: Phenotype, Function and Gene Expression Profiles of PD-1 high CD8 T cells in Healthy Human Adults

first: Jaikumar

last: Duraiswamy

address: 1510, Clifton Road, G211, Rollins Research Center

department: Emory Vaccine Center and Department of Microbiology & Immunology

institute: Emory Univesity

summary: T cell dysfunction is an important feature of many chronic viral infections. In particular, it was shown that PD-1 regulates T cell dysfunction during chronic LCMV infection in mice and PD-1 high cells exhibit an intense exhausted gene signature. These findings were extended to human chronic infections such as HIV, HCV and HBV. However, it is not known if PD-1 high cells of healthy humans have the traits of exhausted cells. In this study, we provide a comprehensive description of phenotype, function and gene expression profiles of PD-1 high versus PD-1 low CD8 T cells in the peripheral blood of healthy human adults as following: 1) The percentage of naive and memory CD8 T cells varied widely in the peripheral blood cells of healthy humans and PD-1 was expressed by the memory CD8 T cells. 2) PD-1 high CD8 T cells in healthy humans did not significantly correlated with the PD-1 high exhausted gene signature of HIV specific human CD8 T cells or chronic LCMV specific CD8 T cells from mice. 3) PD-1 expression did not directly affect the ability of CD8 T cells to secrete cytokines in healthy adults. 4) PD-1 was expressed by the effector memory (TEM) compared to ‘terminally differentiated effector’ (TEMRA) CD8 T cells. 5) Finally, an interesting inverse relationship between CD45RA and PD-1 expression was observed.

overall_design: We used highly purified PD-1 high and PD-1 low from six healthy adult individuals and naive CD8 T cell populations from four of those individuals for gene expression studies

first: Rafi

last: Ahmed


title: Epstein Barr virus Nuclear Antigen 3C regulated genes in Lymphoblastoid Cell Lines

city: Boston

first: Bo

last: Zhao

address: 181 Longwood Ave

institute: Brigham and Women's Hospital

summary: Epstein Barr virus (EBV) nuclear antigen 3C (EBNA3C) is an essential transcription factor for initiating and maintaining human B lymphocyte transformation to lymphoblastoid cell lines (LCLs). To comprehensively identify EBNA3C regulated cell genes in LCLs, oligonucleotide arrays were used to compare RNA abundances in 3 different LCLs transformed by an EBV that conditionally expresses EBNA3C. Cell RNA levels were assessed in actively growing LCLs, under non-permissive or permissive conditions or under non-permissive conditions after transcomplementation with wild type EBNA3C. A two-way ANOVA model with covariates including the 3 different clone effects and the 3 EBNA3C expression levels, identified 550 EBNA3C regulated genes, with False Discovery Rate <0.01 and >1.5 fold change. A seeded Bayesian network analysis of the 80 most significantly EBNA3C regulated genes that changed >1.5 fold, positioned RAC1, LYN and TNF upstream of other EBNA3C regulated genes. Further, Gene Set Enrichment Assay (GSEA) identified EBNA3C regulated genes to be enriched for MAP kinase signaling, cytokine-cytokine receptor interactions, JAK-STAT signaling, and cell adhesion molecule effects, implicating these pathways in LCL growth or survival. Moreover, 106 EBNA3C regulated genes could be placed in protein interaction networks. Since CXCL12 and CXCR4 signaling are implicated in LCL growth and were EBNA3C up-regulated, up-regulation of CXCL12 was validated by qRT-PCR and effects on induced LCL migration were confirmed. EBNA3C regulated genes significantly overlapped with EBNA2 and EBNA3A regulated genes, consistent with a central role for RBP/CSL in these effects.

overall_design: RNAs from three different Lymphoblastoid Cell Lines(LCLs) expressing conditional EBNA3C grown under permissive or non-permissive conditions for 7 days; the same LCLs transcompletemented with  EBNA3C expressed in trans at full wild-type level were used to identify EBNA3C regualted cellular genes. Total cell RNAs were hybrdized to Affymetrix U-133 Plus 2.0 microarrays. A two way ANOVA  model was developed with covariates including the 3 different clone effects and the 3 EBNA3C expression levels and identified 550 EBNA3C regulated genes.

first: Jessica

last: Mar

first: Seiji

last: Maruo

first: Sungwook

first: Benjamin

last: Gewurz

first: Eric

last: Johannsen

first: Kristina

last: Holton

first: Renee

last: Rubio

first: Kenzo

last: Takada

first: John

last: Quackenbush

first: Elliott

last: Kieff


title: Changes in gene expression in AGS cells in response to Helicobacter pylori lipopolysaccharide

city: Dublin 8

first: Sinead

last: Smith

address: St. James's Hospital

institute: Trinity College Dublin

summary:
This study set out to identify global changes in gene expression in AGS gastric epithelial cells following 8 hours stimulation with 10 μg/ml lipopolysaccharide (LPS) from the gastric pathogen H. pylori.
Microarray analysis was used to compare changes in gene expression between cells treated with 10 μg/ml H. pylori LPS and untreated cells at the same time point.

overall_design: Total RNA was harvested from AGS cells following treatment with LPS for 8h or untreated cells at the same time-point. 2 independent experiments were carried out. RNA was labelled and hybridized to GeneChips to analyse changes in gene expression.

middle: M

first: Anthony

last: Moran

first: Shane

last: Duggan

first: Dermot

last: Kelleher


title: The effects of SMYD2 overexpression on ectopic RB in SAOS cells

city: Stanford

first: Julien

last: Sage

address: 265 Campus Drive, SIM1 G2078

department: Pediatrics

institute: Stanford University

summary: Expression analysis of wild-type SAOS cells and SAOS cells transiently transfected with RB, SMYD2, or RB and SMYD2.

overall_design: Four samples of wild-type, rb1, smyd2 and rb1-smyd2 were analyzed on the Human Genome U133 Plus 2.0 array.

first: Louis

last: Saddic


title: Gene expression data in estrogen receptor alpha positive breast tumors with and without PIK3CA mutations.

status: Public on Jan 10 2011

city: SAINT-CLOUD

first: clairac

last: geraldine

address: 35 rue Daily

department: Oncogenetique

country: France

institute: Centre Rene Huguenin

summary:
PI3K/AKT pathway plays one of pivotal roles in breast cancer development and maintenance. PIK3CA, coding PIK3 catalytic subunit, is the oncogene which shows the high frequency of gain-of-function mutations leading to the PI3K/AKT pathway activation in breast cancer. In particular in the ERα-positive breast tumors PIK3CA mutations have been observed in 30% to 40%. However, genes expressed in connection to the pathway activation in breast tumorigenesis remain largely unknown.
To identify downstream relevant target genes (and signaling pathways) turned on by the aberrant PI3K/AKT signal in breast tumors, we analyzed gene expression by pangenomic oligonucleotide microarray in a series of 43 ERα-positive tumors with and without PIK3CA mutations.

overall_design: 43 ERα-positive breast tumors including 14 tumors with PIK3CA mutations and 29 tumors without PIK3CA mutattions were used as screening set for microarray.

first: Magdalena

last: Cizkova

first: Géraldine

last: Cizeron-Clairac

first: Sophie

last: Vacher

first: Aurélie

last: Susini

first: Catherine

last: Andrieu

first: Laétitia

last: Marisa

first: Aurélien

last: de Reyniès

first: Rosette

last: Lidereau

first: Ivan

last: Bièche


title: Microarray analysis identifies the gene signature of surviving motor neurons in human SOD1-related motor neuron disease

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

institute: University of Sheffield

summary:
Gene expression profiling has been performed previously on motor cortex and spinal cord homogenates and of sporadic ALS cases and controls, to identify genes and pathways differentially expressed in ALS. More recent studies have combined the use of laser capture microdissection (LCM) with gene expression profiling to isolate the motor neurons from the surrounding cells, such as microglia and astrocytes, in order to determine those genes differentially expressed in the vulnerable cell population – i.e. motor neuron.
The aim of the present study is to combine LCM and microarray analysis to determine those genes and pathways differentially expressed in MNs from human SOD1-related MND and to establish potential pathways for therapeutic intervention.

Keywords: Human motor neurons

overall_design:
The aim of this study was to determine the gene expression profiles from a small subset of cases which all carry mutations in the SOD1 gene. Expression profiles from isolated motor neurons in SOD1-related ALS cases were compared to those from control motor neurons, in order to establish the pathways implicated in SOD1-related motor neuronal cell death.

The 'control' samples were originally submitted to GEO as GSE19332.

first: Janine

last: Kirby

first: Ke

last: Ning

first: Laura

last: Ferraiuolo

middle: R

first: Azza

last: Ismail

first: Su-wei

last: Kuo

first: Chiara

last: Valori

last: Cox

first: Basil

last: Sharrack

first: Stephen

middle: B

last: Wharton

middle: G

last: Ince

first: Pamela

last: Shaw

first: Mimoun

last: Azzouz


title: Early and Late gene expression responses to Salmonella infection in the mouse intestine

status: Public on Feb 16 2011

city: Rochester

first: Jun

last: Sun

state: MN

address: 575 Elmwood Ave

institute: university of rochester

summary:
We used microarrays to detail the global programme of gene expression of  the mouse colon responses to Salmonella (SL1344 and SB1117) infection at the early phase (8 hours) and the late phase (4 days).
We specifically examined the the differentillay gene expression profiles in mouse colon when it responded to pathogenic Salmonella stain SL1344 (with AvrA expression) or SB1117 (without AvrA expression).

overall_design: Mice were infected with 1x107 CFU of samonella stains, SL1344 and SB1117 respectively (100µl suspension in HBSS) or treated with sterile HBSS (control) by oral gavage as previously described.  At 8 hours and 4 days after infection, mice were sacrificed and RNA tissue samples from the intestinal tracts were removed for analysis.

first: Xingyin

last: Liu

first: Rong

last: Lu

first: Shaoping

last: Wu

first: Yinglin

last: Xia


title: Molecular plasticity of regulatory T cells in allogeneic stem cell transplantation

status: Public on Dec 31 2010

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary:
Graft-versus-host disease (GvHD) is still one of the major complications following allogeneic stem cell transplantation (SCT) triggered by alloreactive donor T cells. Whereas murine data have clearly shown the beneficial effects of regulatory T cells (Tregs) on the development of GvHD, data from the human system are rare mainly due to low cell numbers of circulating or organ-infiltrating Tregs in lymphopenic patients. Here, we present a comparative analysis of Tregs from patients with and without acute/ chronic GvHD designed as a dynamical approach studying the whole genome profile over the first 6 months after SCT. For this purpose, blood samples were collected monthly for FACS-based isolation of CD4+CD25highCD127low/- Tregs. The Treg transcriptome showed a high stability in the first half year representing the most sensitive time window for tolerance induction. However, the comparison of the Treg transcriptome from patients with and without GvHD uncovered regulated gene transcripts that point to a reduced suppressive function of Tregs with diminished migration capacity to the target organs likely contributing to the development of GvHD. These findings highlight the critical role of human Tregs in the pathophysiology of GvHD and identify novel targets for the manipulation of Tregs to optimize cellular immune intervention strategies.

Keywords: cell type comparison

overall_design: Relative gene expressions were determined by normalized intensity values. GeneSpring analysis was performed using the Treg transcriptome data with following comparisons: no GvHD d90 versus no GvHD d150, no GvHD d90 versus acute GvHD, no GvHD d150 versus chronic GvHD, acute GvHD versus chronic GvHD, acute GvHD versus GvHD d90 and chronic GvHD versus GvHD d150 (Figure 2). Cut-off was a transcript fold change of 2 or -2 in at least one comparison. Student´s t-test was used to identify significant expression changes.

first: R

first: A

last: Franzke

first: Sya

last: Ukena


title: gene expression data from cep701 treated HEL cells and shPRMT5 knocking down HEL cells

city: New York

first: Jeffrey

last: Zhao

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

summary: compare the gene expression profile between cep701 treated HEL cells with shPRMT5 knockingdown HEL cells. HEL cells contain homologous alells with mutation Jak2V617F. We found JAK2V617F can inactivate PRMT5 activity by directly phosphorylating PRMT5 through histone methylation.

first: Xinyang

first: Fabriana

last: Perna

last: Nimer


title: Changes in Hepatic Gene Expression upon Oral Administration of Taurine-Conjugated Ursodeoxycholic Acid in ob/ob Mice

city: Pohang

first: Jae-Seong

last: Yang

address: San 31 Hyoja-dong

department: School of Interdisciplinary Bioscience and Bioengineering

country: South Korea

institute: Pohang University of Science and Technology

summary: We examined the effect of oral TUDCA treatment on hepatic steatosis and associated changes in hepatic gene expression in ob/ob mice.

overall_design: We administered TUDCA to ob/ob mice at a dose of 500 mg/kg twice a day by gastric gavage for 3 weeks. Body weight, glucose homeostasis, endoplasmic reticulum (ER) stress, and hepatic gene expression were examined in comparison with control ob/ob mice and normal littermate C57BL/6J mice.

first: Jin

last: Kim

first: Jouhyun

last: Jeon

first: Ho

last: Park

first: Gyeong

middle: H

last: Kang

first: Kyong

first: Hong

last: Lee

first: Sanguk

first: Young

last: Cho


title: SDF-1 induced transcriptional changes in human cord blood CD34+ cells

first: Kathy

middle: YY

last: Chan

address: Rm84041, 6/F, Clinical Science Building, Prince of Wales Hospital, Shatin, N.T.

department: Paediatrics

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: We have employed whole genome microarray expression profiling to identify genes differentially expressed in cord blood enriched CD34+ cells(>95%) after a short-term exposure to the chemokine stromal cell-derived factor-1 (SDF-1).

overall_design: SDF-1 induced gene expressions of cord blood enriched CD34+ cells were measured at 4 hours. Four biological replicates were performed for each treatment group.

first: Karen

last: Li

first: Kam

last: Leung

middle: Y


title: MEK5 is Activated by Shear Stress, Activates ERK5 And Induces KLF4 To Modulate TNF Responses in Human Dermal Microvascular Endothelial Cells

city: Ridgefield

first: Adedayo

last: Hanidu

address: 175 Briar Ridge Rd

summary:
MEK5 is activated by shear stress in large vessel endothelial cells (ECs) and contributes to the suppression of pro-inflammatory changes in the arterial wall. We used microarray analyses of total RNA from MEK5/CA-transduced HDMECs compared to LacZ control-transduced HDMECs to identify distinct classes of several regulated genes, including KLF4, eNOS, and ICAM.
We conclude that MEK5 activation by shear stress may modulate inflammatory responses in the microvasculature, and these actions are partly mediated by KLF4.

overall_design: Total RNA was isolated from 8 separate paired (derived from same primary isolate) MEK5/CA and LacZ transduced HDMEC lines

first: Paul

last: Clark

first: Todd

last: Jensen

first: Martin

middle: S

last: Kluger

first: Zhenhao

last: Qi

first: Maurice

last: Morelock

first: Revati

middle: J

last: Tatake

first: Jordan

last: Pober


title: The differentially expressed genes induced by EV71 infection

city: Taipei

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

institute: National Taiwan University

summary: Virus infection may shut off host protein synthesis in order to achieve the replicative advantage over host cells. It is well known that human pathogenic viruses, particularly the picornaviruses, can block host protein synthesis by cleavage or inhibition of eukaryotic initiation factors (eIFs). In this study we found a novel mechanism that microRNA (miRNA) is involved in viral pathogenesis. Infection of enteroviruses can disturb the expression of host miRNAs, in which miR-141 is up-regulated and inhibits host protein synthesis by post-transcriptional repression of the target gene eIF4E, a key element for cap-dependent translation of host proteins. Knockdown of miR-141 by a specific siRNA, antagomiR-141, could restore host eIF4E expression, delay the occurrence of cytopathic effect (CPE), and impair virus propagation. We demonstrated that EV71 infection could increase early growth response 1 (EGR1) expression which induced miR-141 causing the eIF4E suppression; while silencing of EGR1 attenuated virus production. Our results suggest that enterovirus infection causes the EGR1-mediated upregulation of host miR-141, further lead to the translational switch from cap-dependent to cap-independent protein synthesis in the host cells, an environmental beneficial for viral propagation. This novel mechanism may highlight a new approach for future development of antiviral therapy.

overall_design:
Enteroviruses in the Picornaviridae family are important human pathogens which can cause fatal diseases, including cardiopulmonary failure, aseptic meningitis, paralysis, myocarditis, and encephalomyelitis. Virus infection may induce shutoff of host protein synthesis, particularly in picornavirus, whose protein translation is cap-independent. It is known that poliovirus 2A protease cleaves eIF4G, a scaffold component of mammalian cell translational complex, leading to the shut down of host protein synthesis. Nevertheless, the cleavage of eIF4G may not be sufficient for the complete shutoff of host protein synthesis. Previous studies showed that cleavage of polyA-binding protein (PABP) by viral protease 3C and dephosphorylation of the translational repressor, eIF4E binding protein 1 (4E-BP1), also contribute to this process. The cap-binding protein, eIF4E, is the most crucial factor in determining whether cap-dependent or -independent translation takes place. The mechanism by which viral infection modulates host cell protein synthesis through interfering eIF4E expression is not yet known. miRNAs are a newly discovered class of small non-protein-coding RNAs that may act via endogenous RNA interference. Our understanding of its role in the dynamic interplay between virus and host components is quite limited. Since both virus infection and miRNAs could hinder cellular protein synthesis, whether miRNAs are involved during virus infection in shutting off host protein synthesis is still unknown. To address this issue, we analyze the altered gene and microRNA expression after EV71 infection.

***This submission represents the mRNA expression component of the study only***

first: Bing-Ching

last: Ho

first: Chun-Nan

first: Pan-Chyr

last: Yang


title: Functional Analysis and Gene Expression Profile of Umbilical Cord Blood Regulatory T Cells

city: Rome

first: Sabina

last: Chiaretti

address: Via Benevento, 6

department: Cellular Technologies and Hematology

country: Italy

institute: Division of Hematology

summary: Since the role of cord blood (CB) regulatory T cells (Tregs) for the suppression of the allogeneic T-cell response is under investigation, we analyzed and compared the functional properties and gene expression profile of Tregs expanded from CB units or from the peripheral blood (PB) of helathy donors. Tregs were purified from 23 CB units and from the PB of 13 donors and expanded for 6 days with anti-CD3, anti-CD28 and IL-2. Immunophenotypic analyses were performed, and suppressor activity of expanded Tregs was measured in mixed lymphocyte reaction (MLR) cultures. The IL-10 production capacity was tested and gene expression profile experiments were performed on 6 Tregs from PB and 4 from CB. CB and PB Tregs had similar immunophenotypic features. Tregs from CB presented a higher expansion capacity and  genomic characterization showed in CB-derived Tregs a significant enrichments of genes involved in cell proliferation, chromatin modification and regulation of gene expression in CB-derived Tregs. All samples were positive for the Foxp3 gene and protein after expansion. CB and PB expanded Tregs exerted a comparable and potent suppressive function of MLR and presented a high in vitro IL-10 production capacity. Gene profile analysis also revealed for PB Tregs a significant enrichments of genes involved in the adaptive immune response.

overall_design:
Comparison of the transcriptional profile of T-REGS derived either from cord blood or peripheral blood.
6 highly purified T-regs samples derived from peripheral blood of healthy donors were compared to highly purified T-regs from cord blood.

first: Giovanni

last: Torelli


title: Comparative Gene Expression Profiling of HUVEC and Ocular Vascular Endothelial Cells

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

institute: Newcastle University

summary:
To compare the gene expression profiles of unpassaged, proliferating HUVEC and human iris, retinal and choroidal microvascular endothelial cells.
Gene expression profiling revealed significant differences between HUVEC and ocular microvascular endothelial cells suggesting that HUVE cells may not be a suitable surrogate when studying pathophysiological mechanisms of ocular disorders. There were significant differences in the gene expression of important cell signalling pathways in human retinal and choroidal ECs. These differences may be important in the mechanisms and treatment of choroidal and retinal neovascularisation.

overall_design: 12 arrays are included.  Endothelial cells were derived from 4 tissues: iris, retina, choroid and human umbilical vein.  RNA extracts from cells were hybridised to Affymetrix HGU133plus2 arrays in triplicate.

first: Andrew

middle: C

last: Browning

first: Daniel

last: Swan


title: Identification of the receptor tyrosine kinase AXL in triple negative breast cancer as a novel target for the human miR-34a microRNA (gene expression)

city: Bethesda

first: Mark

last: Mackiewicz

address: 37 Convent Drive

department: National Cancer Institute

institute: National Institutes of Health

summary:
Triple negative breast cancer (TNBC) is histologically characterized by the absence of the hormone receptors estrogen and progesterone, in addition to having a negative immunostain for HER-2.  The aggressiveness of this disease and lack of targeted therapeutic options for treatment is of high clinical importance.  MicroRNAs are short 21- to 23 nucleotide endogenous non-coding RNAs that regulate gene expression by binding to mRNA transcripts, resulting in either decreased protein translation or mRNA degradation.  Dysregulated expression of miRNAs is now a hallmark of many human cancers.  In order to identify a miRNA/mRNA interaction that is biologically relevant to the triple negative breast cancer genotype/phenotype, we initially conducted a miRNA profiling experiment to detect differentially expressed miRNAs in cell line models representing the triple negative (MDA-MB-231), ER+ (MCF7), and HER-2 overexpressed (SK-BR-3) histotypes.  We identified human miR-34a expression as being  >3-fold down (from its median expression value across all cell lines) in MDA-MB-231 cells, and identified AXL as a putative mRNA target using multiple miRNA/target prediction algorithms.  The miR-34a/AXL interaction was functionally characterized through ectopic overexpression experiments with a miR-34a mimic.  In reporter assays, miR-34a binds to the putative target site within the AXL 3’UTR to affect luciferase expression.  We also observed degradation of AXL mRNA and decreased AXL protein levels, as well as cell signaling effects on AKT phosphorylation and phenotypic effects on cell migration.  Finally, we present an inverse correlative trend in miR-34a and AXL expression for both cell line and patient tumor samples.
Comparison of the changes in gene expression as a result of transfections with miR-34a mimic molecules (representing two different vendors; Qiagen and Dharmacon) in MDA-MB-231 cells.

overall_design: MDA-MB-231 cells were transfected in 6-well dishes (600,000 cells) with either AllStar negative control, Qmimic, or Dmimic at 10 nM final concentration using Lipofectamine™ 2000 (Invitrogen; Carlsbad, CA).  All transfections were performed in triplicate.  Forty-eight hours post-transfection, total RNA was isolated from each sample using Qiagen’s miRNeasy extraction kit (Qiagen; Germantown, MD).  Total RNA samples were sent to the Laboratory of Molecular Technology (National Cancer Institute at Frederick; Frederick, MD), for processing on Affymetrix GeneChip Human Genome U133 Plus 2.0 microarrays (Affymetrix; Santa Clara, CA).  Expression values were normalized using Robust Multichip Averaging (RMA).  Only gene probes (AllStar vs. Mimic) that passed a log2 1.5-fold change, p < 0.05 threshold using an Empirical Bayes moderated t statistics with a Benjamini-Hochberg correction for the false discovery rate were reported.  All analyses were performed with Bioconductor packages AFFYGUI and LIMMA on a R environment.

first: Konrad

last: Huppi

first: Jason

last: Pitt

first: Robert

last: Cornelison

first: Tiffany

last: Dorsey

first: Stefan

last: Ambs

first: Natasha

last: Caplen


title: Identification of the receptor tyrosine kinase AXL in triple negative breast cancer as a novel target for the human miR-34a microRNA

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

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

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Refer to individual Series


title: The effect of IAN on E. coli O157:H7 EHEC biofilm formation

city: Gyeongsan-Si

first: Jintae

last: Lee

state: Gyeongsangbuk-Do

address: 214-1 Daedong

department: Chemical engineering

institute: Yeungnam University

summary: Intercellular signal indole and its derivative hydroxyindoles inhibit Escherichia coli biofilm and diminish Pseudomonas aeruginosa virulence.  However, indole and bacterial indole derivatives were unstable in microbial community due to the widespread of diverse oxygenases that could quickly degrade them.  Hence, we sought to identify novel non-toxic, stable, and potent indole derivatives from plant sources for inhibiting biofilm formation of E. coli O157:H7 and P. aeruginosa PAO1.  Here, plant auxin 3-indolylacetonitrile (IAN) was found to inhibit biofilm formation of both E. coli O157:H7 and P. aeruginosa without affecting its growth.  IAN inhibited biofilms more effectively than indole for both E. coli and P. aeruginosa.  Additionally, IAN decreased the production of virulence factor pyocyanin in P. aeruginosa.  DNA microarray analysis indicated that IAN repressed genes involved in curli formation and glycerol metabolism, while IAN induced indole-related genes and prophage genes in E. coli.  It appears that IAN inhibits biofilm formation of E. coli by reducing curli formation and inducing indole production.  Furthermore, unlike bacterial indole derivatives, plant-originated IAN was stable in the presence of either E. coli or P. aeruginosa.

overall_design: For the microarray experiments, E. coli O157:H7 were inoculated in 25 ml of LB medium in 250 ml shake flasks with overnight cultures that were diluted 1:100.  IAN (100 μg/ml) dissolved in 25 μl DMSO or 25 μl DMSO alone as a control was added.  Cells were cultured in LB at 37C with 250 rpm shaking until an absorbance of 1.0 at 600 nm.  Cells were immediately chilled with dry ice and 95% ethanol (to prevent RNA degradation) for 30 sec before centrifugation in 50 ml centrifuge tubes at 13,000 g for 2 min; cell pellets were frozen immediately with dry ice and stored -80°C.  RNA was isolated using Qiagen RNeasy mini Kit (Valencia, CA, USA).  RNA quality was assessed by Agilent 2100 bioanalyser using the RNA 6000 Nano Chip (Agilent Technologies, Amstelveen, The Netherlands), and quantity was determined by ND-1000 Spectrophotometer (NanoDrop Technologies, Inc., DE, USA).

first: Jin-Hyung


title: gene expression profiling of three type of grade II gliomas

city: Luoyang

first: Zhiqiang

last: Yao

state: Henan

address: No.288, Zhongzhou Road

department: Neurosurgery

institute: No.150 Military Central Hospital

summary: In this study we performed gene expression profiling of 14 cases of grade II gliomas. The results of these analysis were used in unsupervised analyses to compare correlations between the histological subtype of grade II gliomas and gene expression profiles

overall_design: Total RNA was isolated from 14 tumor tissue of patients, which included 5 astrocytomas WHO grade II (T2), 5 oligodendro-gliomas WHO grade II (T2) and 4 ependymomas WHO grade II (T2) samples, in additional to 4 normal tissues. The genome-wide expression analysis was first performed by directly comparing the expression profile of highly enriched different kinds of grade II gliomas and normal tissues, we then applied various data-mining methods to process the 14 different types of grade II gliomas tissues sample.

first: Zhongyu

last: Liu


first: Hans-Ulrich

last: Klein

department: Neurology

institute: Columbia University Medical Center

summary:
Full Title: Multilineage Dysplasia (MLD) in AML correlates with MDS-related cytogenetic abnormalities and a prior history of MDS or MDS/MPN but has no independent prognostic relevance: A comparison of 408 cases classified as “AML not otherwise specified” or “AML with myelodysplasia-related changes”

The WHO classification of acute myeloid leukemia (AML) is hierarchically structured and integrates genetic information, data on patients’ history, and multilineage dysplasia (MLD). The category “AML with MDS-related changes” (AML-MRC) is separated from AML not otherwise specified (AML-NOS) by the presence of either MLD, MDS-related cytogenetics or MDS history. To clarify whether MLD alone is clinically relevant, we analyzed 408 adult patients categorized as AML-MRC or AML-NOS. EFS (Median 13.8 months vs. 16.0 months) and 3-year-OS (45.8% vs. 53.9%) did not differ significantly between patients with MLD and without. However, MLD correlated with pre-existing MDS (p<0.001) and MDS-related cytogenetics (p=0.035). Patients with MLD as sole AML-MRC criterion (AML-MLD-sole; n=90) had less frequently FLT3-ITD (p=0.032), and a lower median age than AML-NOS (n=232), but EFS, OS, and WBC did not differ significantly. Contrarily, patients with AML-NOS plus AML-MLD-sole (n=323) versus patients with MDS history or MDS-related cytogenetics (n=85) had better EFS (16.9 vs. 10.7 months; p=0.005) and 3-year-OS (55.8% vs. 32.5%; p=0.001). Gene expression profiles were measured for a subset of 96 patients. Analysis of the expression data showed distinct clusters for AML-MLD-sole and AML-NOS versus AML with MDS-related cytogenetics or MDS history. Thus, MLD demonstrated no independent clinical impact, while cytogenetics and MDS history were of prognostic relevance. This data suggest modifications in a revised WHO proposal.

overall_design: All 96 bone marrow samples were obtained from untreated patients at the time of diagnosis. Cells used for microarray analysis were collected from the purified fraction of mononuclear cells after Ficoll density centrifugation.

first: Miriam

last: Miesner

first: Claudia

last: Haferlach

first: Ulrike

last: Bacher

first: Tamara

last: Weiss

first: Katja

last: Macijewski

first: Alexander

last: Kohlmann

first: Martin

last: Dugas

first: Wolfgang

last: Kern

first: Susanne

last: Schnittger

first: Torsten


title: Expression data after miR-99a transfection in C4-2 prostate cancer cells

status: Public on Dec 29 2010

city: Charlottesville

first: Anindya

last: Dutta

department: Biochemistry and Molecular Genetics

institute: University of Virginia

summary: MicroRNAs (miRNAs) have been globally profiled in cancers but there tends to be poor agreement between studies including in the same cancers. Additionally, few putative miRNA targets have been validated. To overcome the lack of reproducibility, we profiled miRNAs by next generation sequencing and locked nucleic acid miRNA microarrays, and we verified concordant changes by quantitative RT-PCR. Notably, miR-125b and the miR-99 family members miR-99a, -99b, -100 were down-regulated in all assays in advanced prostate cancer cell lines relative to the parental cell lines from which they were derived. All four miRNAs were also down-regulated in human prostate tumor tissue compared to normal prostate.  Transfection of miR-99a, -99b or -100 inhibited the growth of prostate cancer cells and decreased the expression of prostate-specific antigen (PSA), suggesting potential roles as tumor suppressors in this setting. To identify targets of these miRNAs, we combined computational prediction of potential targets with experimental validation by microarray and polyribosomal loading analysis. Three direct targets of the miR-99 family that were validated in this manner were the chromatin remodeling factors SMARCA5 and SMARCD1 and the growth regulatory kinase mTOR. We determined that PSA is post-transcriptionally regulated by the miR-99 family members at least partially by repression of SMARCA5. Together, our findings suggest key functions and targets of miR-99 family members in prostate cancer suppression and prognosis.

overall_design: C4-2 cells were transfected with miR-99a and harvested after 48hr. si-GL2 was used as control.

first: Dandan

last: Sun

first: YongSun

first: Ankit

last: Malhotra

first: HakKyun

last: Kim

first: Mirela

last: Matecic

first: Clive

last: Evans

first: Roderick

last: Jensen

first: Christopher

last: Moskaluk


title: Effects of acLDL loading on macrophage

city: Seattle

first: David

middle: K

last: Pritchard

state: WA

address: 815 Mercer Street Rm.  418

department: Pathology

institute: University of Washington

summary:
acLDL loading of mouse peritoneal macrophage is an in vitro foam cell model.
We have used microarray analysis and proteomics to characterize the effects of acLDL loading on the cells.

overall_design: Macrophages were harvested from the peritoneum of C57Bl/6J mice 5 days after injection of thioglycolate.  Thioglycollate elicited macrophage were cultured for 2 days in DMEM + 10%FBS either in the presence or absence of 50 microgram/mL acLDL. 4 indepdendent biological replicates were used for each condition.

first: Masashi

last: Suzuki

first: Jay

last: Heinecke


title: Gene expression analysis of embryonic photoreceptor precursor cells using BAC-Crx-EGFP transgenic mouse.

status: Public on Dec 25 2010

city: Suita

first: Takahisa

last: Furukawa

state: Osaka

address: 6-2-4 Furuedai

department: Developmental Biology

country: Japan

institute: Osaka Bioscience Institute

summary: We generated a transgenic mouse line which express EGFP in the retina driven by the Crx promoter using BAC transgenesis. We sorted EGFP-positive photoreceptor precursors at E17.5 using FACS, and subsequently performed microarray analysis of the FACS-sorted cells.

overall_design: In order to clarify a molecular role of Crx in developing cone photoreceptor precursors, we investigated the expression profile of the BAC-Crx-EGFP-positive cells compared with that of the BAC-Crx-EGFP-negative cells at E17.5.

first: Yuki

last: Muranishi


title: Gene Expression Analysis of Deer Antler

city: Toledo

first: Manuel

last: Nieto-Diaz

state: Toledo

address: Finca La Peraleda s/n

department: Unidad de Neurología Experimental

country: Spain

institute: Hospital Nacional de Parapléjicos (SESCAM)

summary: Identification of the changes in gene expression between the antler velvet and mesenchyme, pedicle skin and frontal skin tissues from adult male deers (Cervus elaphus). Hybridization data were analysed using MAS5, RMA, GCRMA and Dchip algorithms to maximize the chances of identifying gene expression changes.

overall_design: Comparison of 4 tissues with 3 biological replicates each. Samples were obtained from Velvet, Mesenchyme, Pedicle, and Frontal tissues of 3 adult males.

first: Wolfgang

last: Pita-Thomas

last: Nieto-Sampedro


title: Comparison of gene expression between ruptured and unruptured human intracranial aneurysms

status: Public on Dec 24 2010

city: Kuopio

first: Mitja

last: Kurki

address: Yliopistonranta 1 E

country: Finland

institute: University of Eastern Finland

summary:
Background and Purpose
Aneurysmal subarachnoid hemorrhage, almost always from saccular intracranial aneurysm (sIA), is a devastating form of stroke that affects working age population. Cellular and molecular mechanisms predisposing to the rupture of the sIA wall are largely unknown. Such knowledge would facilitate the design of novel diagnostic tools and therapies for the sIA disease.

Methods
We compared the whole genome expression profile of eleven ruptured sIA wall samples, resected at a median of 15 hours after rupture, to that of eight unruptured ones. Signaling pathways enriched in the ruptured sIA walls were identified with bioinformatic analyses. Their transcriptional control was predicted in silico by seeking the enrichment of conserved transcription factor binding sites in the promoter regions of differentially expressed genes.

Results
Overall, 686 genes were significantly upregulated and 740 downregulated in the ruptured sIA walls. Significantly upregulated biological processes included: response to turbulent blood flow; chemotaxis; leukocyte migration; oxidative stress; vascular remodelling; and extracellular matrix degradation. Toll like receptor (TLR) signalling and NF-κB, HIF1A and ETS transcription factor binding sites were significantly enriched among the upregulated genes.

Conclusions
We identified pathways and candidate genes associated to the rupture of human sIA wall. These results provide a molecular basis analysis (a) to identify rupture-prone sIAs and (b) to prevent their rupture. Novel measures to prevent the rupture of sIA wall may include inhibition of response to turbulent blood flow, leukocyte migration, TLR signalling, or blockade of NF-κB, HIF1A and ETS transcription factors.

overall_design: Human aneurysm pouches were clipped intraoperatively and immediately snap frozen. RNA was extracted from 19 (11 ruptured and 8 unruptured) aneurysm samples and used in microarray hybridization.

middle: I

first: Sanna-Kaisa

last: Häkkinen

first: Juhana

last: Frösen

first: Riikka

last: Tulamo

first: Mikael

last: Fraunberg

first: Garry

last: Wong

first: Gerard

last: Tromp

first: Mika

last: Niemelä

first: Juha

last: Hernesniemi

middle: E

last: Jääskeläinen

first: Seppo

last: Ylä-Herttuala


title: Streptococcus agalactiae induced gene expression in human coronar artery endothelial cells

city: Wuerzburg

first: Claudia

last: Beyrich

address: Grombuehlstr. 12

department: IKBZ

institute: University of Wuerzburg

summary:
Early onset sepsis due to Group B streptococcus (GBS) leads to neonatal morbidity, increased mortality and long term neurological deficencies. Interaction between septicemic GBS and confluent monlayers of human coronary artery endothelial cells (HCAEC) was analyzed by a genome wide expression profiling. Regulation of selected genes and proteins identified in the gene array analysis was confirmed by Real Time RT-PCR assay (Granulocyte chemotactic protein 2 (CXCL6)), ELISA (Urokinase, Cyclooxygenase 2 (COX2), Granulocyte chemotactic protein 1 (IL8)) and Western Blotting (Heme oxygenase1, BCL2 interacting protein (BIM)) at various time points between 4 and 24 hours. In total, 124 genes were differentially regulated (89 upregulated, 35 downregulated) based on a more than 3-fold difference to unstimulated HCAEC. Regulated genes are involved in apoptosis, hemostasis, oxidative stress response,  infection and inflammation. We confirmed upregulation of urokinase (UPA), COX2, HMOX1 and BCL2 interacting protein and downregulation of CXCL6 and IL8. These results indicate that GBS infection might lead to impaired function of the innate immune system and might contribute to hemorrhagic and inflammatory complications during GBS sepsis.

Keywords: stimulated HCAEC (with S. agalactiae) vs unstimulated control cells

overall_design: total samples analysed are 2, including control

first: Jürgen

last: Löffler

first: Anna

last: Kobsar

first: Christian

middle: P

last: Speer

first: Susanne

last: Kneitz

first: Martin

last: Eigenthaler


title: Expression data from control and ZNF145-overexpressing human mesenchymal stem cells (MSCs)

status: Public on Dec 22 2010

city: Singapore

first: Tongming

last: Liu

address: 60 Biopolis street

department: Cancer stem group

institute: Genome Institute of Singapore

summary:
ZNF145 is shown to be upregulated during three linage differentiation of MSCs especially in chondrogenesis. To understand the molecular basis of ZNF145 underlying MSCs,  targets of ZNF145 in MSCs are determined by microarray
We used microarrays to detail the change in gene expression profile upon overexpression of ZNF145 compared with control in undifferentiated MSCs

overall_design: Control MSCs and ZNF145-overexpressing MSCs are processed for RNA extraction and hybridization on Affymetrix microarrays. To that end, we overexpressed ZNF145 in two patient-derived human MSCs.

first: Tong

first: Eng

last: Lee

first: Bing

last: Lim


title: An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer

city: Vancouver

first: Raj

last: Chari

state: BC

address: 675 West 10th Avenue

department: Cancer Genetics and Developmental Biology

country: Canada

institute: BC Cancer Research Centre

type: Genome variation profiling by genome tiling array


title: Chromatin Remodeling Complex Dosage Modulates Transcription Factor Function in Heart Development

city: San Francisco

first: Alisha

last: Holloway

address: 1650 Owens Street

institute: Gladstone Institutes

summary: Dominant mutations in cardiac transcription factor genes cause human inherited congenital heart defects (CHDs), but their molecular basis is not understood. Transcription factors and Brg1/Brm-associated factor (BAF) chromatin remodeling complex interactions suggest potential mechanisms, but the role of BAF complexes in cardiogenesis is not known. Here we show that dosage of Brg1 is critical for mouse and zebrafish cardiogenesis. Disrupting the balance between Brg1 and disease-causing cardiac transcription factors, including Tbx5, Tbx20, and Nkx2-5, causes severe cardiac anomalies, revealing an essential allelic balance between Brg1 and these cardiac transcription factor genes. This suggests that relative levels of transcription factors and BAF complexes are important for heart development, which is supported by reduced occupancy of Brg1 at cardiac genes in Tbx5 haploinsufficient hearts. Our results reveal complex dosage-sensitive interdependence between transcription factors and BAF complexes, providing a potential mechanism underlying transcription factor haploinsufficiency, with implications for multigenic inheritance of CHDs.

overall_design: We performed transcriptional profiling of E11.5 hearts from mice heterozygous for deletions of Brg1, Tbx5, or Nkx2-5, and mice that were compound  heterozygotes for Brg1 and each transcription factor gene (Tbx5 and Nkx2-5).

first: Benoit

last: Bruneau


title: Effects of MaxiK silencing in corporal smooth muscle cells

city: Bronx

first: Giulia

last: Calenda

address: 1300 Morris Park Avenue

department: Urology

institute: Albert Einstein College of Medicine

summary: The MaxiK potassium channel is a key modulator of smooth muscle tone. Due to its calcium and voltage sensitivity, MaxiK is activated following depolarization and Ca2+ mobilization, therefore relaxing the muscle. We investigate the effects of silencing MaxiK for 48h in corpus cavernosuml smooth muscle (CCSM) cells to identify possible mechanisms of compensation through molecular crosstalk between pathways regulating smooth muscle tone.

overall_design: Human CCSM cells were obtained from explant cell cultures. MaxiK channels were silenced for 48h then total RNA was extracted for hybridization on Affymetrix microarrays. Global gene expression of 48h siRNA treated cells was compared to that of untreated controls.

first: Kelvin

last: Davies


title: Increased placental expression and maternal serum levels of apoptosis-inducing TRAIL in recurrent miscarriage

city: Perth

first: Sulev

last: Koks

state: Western Australia

address: 90 South Street

department: Centre for Molecular Medicine and Innovative Therapeutics

country: Australia

institute: Murdoch University

summary:
INTRODUCTION:
Recurrent miscarriage (RM; ≥3 consecutive pregnancy losses) occurs in 1-3% of fertile couples. No biomarkers with high predictive value of threatening miscarriage have been identified. We aimed to profile whole-genome differential gene expression in RM placental tissue, and to determine the protein levels of identified loci in maternal sera in early pregnancy.
METHODS:
GeneChips (Affymetrix(®)) were used for discovery and Taqman RT-qPCR assays for replication of mRNA expression in placentas from RM cases (n = 13) compared to uncomplicated pregnancies matched for gestational age (n = 23). Concentrations of soluble TRAIL (sTRAIL) and calprotectin in maternal serum in normal first trimester (n = 35) and failed pregnancies (early miscarriage, n = 18, late miscarriage, n = 4; tubal pregnancy, n = 11) were determined using ELISA.
RESULTS:
In RM placentas 30 differentially expressed (with nominal P-value < 0.05) transcripts were identified. Significantly increased placental mRNA expression of TNF-related apoptosis-inducing ligand (TRAIL; P = 1.4 × 10(-3); fold-change 1.68) and S100A8 (P = 7.9 × 10(-4); fold-change 2.56) encoding for inflammatory marker calprotectin (S100A8/A9) was confirmed by RT-qPCR. When compared to normal first trimester pregnancy (sTRAIL 16.1 ± 1.6 pg/ml), significantly higher maternal serum concentration of sTRAIL was detected at the RM event (33.6 ± 4.3 pg/ml, P = 0.00027), and in pregnant women, who developed an unpredicted miscarriage 2-50 days after prospective serum sampling (28.5 ± 4.4 pg/ml, P = 0.039). Women with tubal pregnancy also exhibited elevated sTRAIL (30.5 ± 3.9 pg/ml, P = 0.035). Maternal serum levels of calprotectin were neither diagnostic nor prognostic to early pregnancy failures (P > 0.05).
CONCLUSIONS:
The study indicated of sTRAIL as a potential predictive biomarker in maternal serum for early pregnancy complications.

overall_design: 10 gene arrays, 6 in control group and 4 in cases

first: Kristiina

last: Rull

first: Kärt

last: Tomberg

last: Kõks

first: Jaana

last: Männik

first: Märt

last: Möls

first: Meeli

last: Sirotkina

first: Signe

last: Värv

first: Maris

last: Laan


title: Mature dendritic cells under hypoxic condition

city: Genoa

first: Paolo

last: Fardin

address: Largo G. Gaslini 5

department: Molecular Biology

institute: Istiuto Giannina Gaslini

summary: Dendritic cells (DCs) are professional antigen-presenting cells whose activity is intrinsically linked to the microenvironment. Hypoxia is a condition of low oxygen tension occurring in inflammatory tissues that creates a special microenvironment conditioning cell physiology. We studied the effects of hypoxia on the differentiation of human monocytes into DCs and maturation into mature DCs. Mature DCs were differentiated in vitro from human monocytes under normoxic or hypoxic  conditions and the gene expression profile was determined.

overall_design: The expression profile of mature dendritic cells under normoxia vs hypoxia was studied. Three healthy donors were used as biologial replicates.

first: Maria

last: Bosco

first: Daniele

last: Pierobon

first: Fabiola

last: Blengio

first: Federica

last: Raggi

first: Cristina

last: Vanni

first: Paola

last: Cappello

first: Marco

last: Gattorno

first: Franco

last: Novelli

first: Mirella

last: Giovarelli

first: Luigi

last: Varesio


title: Expression profile in HEK293T cells transfected with control or ZAPS expression vector

city: Sapporo

first: Akinori

last: Takaoka

address: Kita15, Nishi8, Kitat-ku

institute: Hokkaido University

summary: Analysis of HEK293T cells overexpressing ZAPS (zinc finger antiviral protein, short form; NP_078901), which is a member of the PARP (poly (ADP-ribose) polymerase)-superfamily. Results of gene profiles provide insight into the role of ZAPS in innate immunity.

overall_design: HEK293T cells were transfected with ZAPS expression vector or control, and forty-eight hours later, total RNA was prepared for the subsequent cDNA systhesis and microarray analysis (GeneticLab Pathology Center Co., Ltd) with the Human Genome U133 Plus 2.0 Array (Affymetrix). Data analysis was performed with GeneChip Operating Software (Affymetrix).


title: Gene expression profile in CD4+ and CD8+ T cells from identical twins discordant for Multiple sclerosis

city: Rome

first: Viviana

last: Annibali

address: Via di Grottarossa,1035

institute: University of Rome "Sapienza"

summary:
To gain insight into the etiopathogenesis of Multiple sclerosis (MS) we investigated gene expression changes in CD4+ and CD8+ T lymphocytes from monozygotic twins (MZ) discordant for relapsing remitting MS.
We studied 4 monozygotic twin pairs discordant for disease, with the affected co-twin free of disease modifying therapies (F/M = 3/1, mean age 36.25±3.9). Following leukapheresis, CD4+ and CD8+ T cells were separated and studied by Affymetrix GeneChip®

overall_design: For gene expression profiling, peripheral blood mononuclear cell (PBMC) were obtained from leukopheresis by density centrifugation over Ficoll-hypaque according to standard procedures. Briefly, heparinized blood was diluted with 1 volume of RPMI medium and gently layered over the Fycoll. Following centrifugation at 660 g for 30 minutes, cells at the interface of the gradient was collected and washed 3 times. Highly purified CD4+ and CD8+ (purity >95%) cell subsets were then sorted by flow cytometry on MoFlo high speed cell sorter (Beckman Coulter, Fullerton, CA) and frozen in Trizol (Invitrogen). Total RNA was extracted using TRIzol® (Invitrogen),  according to the manufacturer's instructions. RNA quality and purity were assessed with the use of the RNA 6000 Nano assay on Agilent 2100 Bioanalyzer (Agilent). Total RNA from each sample was prepared using GeneChip® one Cycle cDNA Synthesis kit and GeneChip® IVT Labeling kit (Affymetrix), according to the manufacturer’s protocols. Briefly, starting from 2.5µg total RNA, biotinylated cRNA was produced by one cycle of reverse transcription and in vitro transcription (IVT). Biotinylated cRNA was fragmented and hybridized for 16 h at 45°C onto GeneChip® Human Genome U133 Plus 2.0 arrays (Affymetrix). The statistical analysis was performed couple by couple using the Rosetta Resolver® system (Rosetta Biosoftware). The fold-change of each gene was calculated by comparing gene expression in the affected twin with that in the unaffected twin and the genes with the same trend in at least 3 twin pairs out of the 4 studied were selected as candidates to be validated by real-time RT-PCR.

first: Vivivana

first: Giovanni

last: Ristori

first: Daniela

last: F. Angelini

first: Barbara

last: Serafini

first: Rosella

last: Mechelli

first: Stefania

last: Cannoni

first: Silvia

last: Romano

first: Andrea

last: Paollillo

first: Hadi

last: Abderrahim

first: Adamo

last: Diamantini

first: Giovanna

last: Borsellino

first: Francesca

last: Aloisi

first: Luca

last: Battistini

last: Salvetti


title: The reduced form of Coenzyme Q10 decreases the expression of LPS-sensitive genes in human THP-1 cells

city: Kiel

first: Frank

last: Döring

address: Heinrich-Hecht-Platz 10

department: Human Nutrition and Food Science

institute: Christian-Albrechts-University Kiel

summary: Monocytes are key players in inflammatory processes which are triggered by lipopolysaccharide (LPS), the major outer membrane component of gram-negative bacteria. The present study in human monocytic THP-1 cells was designed in order to identify LPS-inducible genes which are down-regulated by the reduced form of CoQ10 (ubiquinol, Q10H2). For this purpose, THP-1 cells were incubated with 10 µM Q10H2 for 24 h. Subsequently, cells were stimulated for 4 h with 1µg/ml LPS and the resulting gene expression levels were determined using microarrays. 14 LPS-inducible genes were identified to be significantly (p < 0.05) down-regulated by Q10H2 pre-treatment between a factor of 1.32 and 1.65. The strongest effect of Q10H2 incubation was found for the nuclear receptor coactivator 2 gene (NCOA2). Gene Ontology (GO) terms revealed for the Q10H2-sensitive genes an involvement in e.g. signal transduction processes (CENTD1, NCOA2, PSD3, PPP2R5C), transcriptional regulation (NCOA2, POU2F1, ETV3) and cell proliferation pathways (CCDC100, EPS15). In conclusion, we provide evidence in THP-1 cells that the reduced form of CoQ10 (Q10H2) modulates LPS-induced gene expression.

overall_design: Whole genome expression profiles were analysed from monocytes pre-incubated with the reduced form of CoQ10 (ubiquinol, Q10H2) before subsequent stimulation with LPS. Stimulated (+LPS) and unstimulated (-LPS) monocytes were used as positive and negative controls, respectively. For every experimental group (3 groups in total), three Affymetrix Human Genome U133 Plus 2.0 arrays were used, thus resulting in the analysis of 9 microarrays.

first: Constance

last: Schmelzer


title: Identification of LPS-inducible genes down-regulated by ubiquinone in human THP-1 cells

summary: Coenzyme Q10 (CoQ10) is an obligatory element in the respiratory chain and functions as a potent antioxidant of lipid membranes. More recently, anti-inflammatory effects as well as an impact of CoQ10 on gene expression have been observed. To reveal putative effects of Q10 on LPS-induced gene expression, whole genome expression analysis was performed in the monocytic cell line THP-1. 1129 probe sets have been identified to be significantly up-regulated (p < 0.05) in LPS-treated cells when compared to controls. Text mining analysis of the top 50 LPS up-regulated genes revealed a functional connection in the NFκB pathway and confirmed our applied in vitro stimulation model. Moreover, 33 LPS-sensitive genes have been identified to be significantly down-regulated by Q10-treatment between a factor of 1.32 and 1.85. GeneOntology (GO) analysis revealed for the Q10-sensitve genes a primary involvement in protein metabolism, cell proliferation and transcriptional processes. Three genes were either related to NFκB transcription factor activity, cytokinesis or modulation of oxidative stress. In conclusion, our data provide evidence that Q10 down-regulates LPS-inducible genes in the monocytic cell line THP-1. Thus, the previously described effects of Q10 on the reduction of pro-inflammatory mediators might be due to its impact on gene expression.

overall_design: Whole genome expression profiles were analysed from monocytes pre-incubated with ubiquinone (Q10) before subsequent stimulation with LPS. Stimulated (+LPS) and unstimulated (-LPS) monocytes were used as positive and negative controls, respectively. For every experimental group (3 groups in total), three Affymetrix Human Genome U133 Plus 2.0 arrays were used, thus resulting in the analysis of 9 microarrays.


title: Expression data from cultured human lung tissue-derived fibroblasts and human vascular adventitial fibroblasts

status: Public on Dec 18 2010

city: Kashiwa

first: Ayuko

last: Hoshino

state: Chiba

address: 6-5-1 Kashiwanoha

institute: The University of Tokyo

summary: In order to find the difference between human lung tissue-derived fibroblasts and human vascular adventitial fibroblasts for enhancing tumor formation ablity of human lung adenocarcinoma cell line A549, we found that human vascular adventitial fibroblasts enhance A549 tumor formation in vivo compared to human lung tissue-derived fibroblasts.  To find the responsible genes for this phenomena, we used microarray analysis to find the expression difference between lung tissue-derived fibroblasts and vascular adventitial fibroblas

overall_design: Cultured human lung tissue-derived fibroblasts and human vascular adventitial fibroblasts were analyzed in replicates.

first: Hiroki

last: Sasaki

first: Kazuhiko

last: Aoyagi


title: Expression data from epithelial cells during the process of multistep pancreatic carcinogenesis

status: Public on Dec 23 2010

city: Tokyo

first: Nobuyoshi

last: Hiraoka

address: 5-1-1 Tsukiji, Chuo-ku

department: Pathology Division

institute: National Cancer Center Research Institute

summary:
The host antitumor immunity changes drastically during carcinogenesis. Intraductal papillary-mucinous neoplasm (IPMN) of the pancreas is a precursor lesion of pancreatic cancer and progresses according to adenoma-carcinoma sequence. We found that the host antitumor immune reaction changes from an immune response to immune tolerance between intraductal papillary-mucinous adenoma (IPMA) and intraductal papillary-mucinous carcinoma (IPMC).
In order to determine molecules affecting intraepithelial DC infiltration in IPMNs during multistep carcinogenesis, we examined the gene-expression profiles of entire transcripts of neoplastic cells at different stages.

overall_design: We collected normal and neoplastic epithelial cells from frozen tissue sections (normal main pancreatic duct, IPMA, IPMC, and invasive carcinoma originating in IPMN) by laser microdissection, extracted total RNA from them, and analyzed their gene expression profiles using Affymetrix microarrays.

first: Rie

last: Itoh

first: Yoshinori

last: Ishikawa

first: Tesshi

last: Yamada

first: Setsuo

last: Hirohashi

first: Yae

last: Kanai


title: Search for specific biomarkers of IFN-beta bioactivity in patients with MS

city: Barcelona

first: Ramil

last: Nurtdinov

address: Dr. Aiguader 88

department: Bioinformatics and Genomics

institute: Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology

summary: We aimed to identify specific biomarkers of IFN-beta bioactivity in order to compare their gene expression induction by type I IFNs with the MxA, and to investigate their potential role in MS pathogenesis. Gene expression microarrays were performed in PBMC from MS patients who developed neutralizing antibodies (NAB) to IFN-beta. Nine genes followed patterns in gene expression over time similar to the MX1 and were selected for further experiments: IFI6, IFI27, IFI44L, IFIT1, HERC5, LY6E, RSAD2, SIGLEC1, and USP18. In vitro experiments revealed specific induction of selected biomarkers by IFN-beta but not IFN-gamma, and several markers, in particular USP18 and HERC5, were significantly induced at lower IFN-beta concentrations and more selective than the MX1 as biomarkers of IFN-beta bioactivity. In addition, USP18 expression was deficient in MS patients compared with healthy controls (p=0.0004). We propose specific biomarkers that may be considered in addition to the MxA to evaluate IFN-beta bioactivity, and to further explore their implication in MS pathogenesis.

overall_design: Number of samples: 32. We analyzed PBMC from 8 patients at baseline and after 3, 12 and 24 months of IFN-beta treatment

first: Sunny

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