title: Human LSD2/KDM1b/AOF1 regulates gene transcription by modulating H3K4me2 methylation (Affymetrix)

city: Boston

first: Yujiang

last: Shi

address: 221 Longwood Ave

department: Medicine

institute: Brigham & Women's Hospital

summary:
Dynamic histone H3K4 methylation is an important epigenetic component of transcriptional regulation. However, most of our current understanding of this histone mark is confined to regulation of transcriptional initiation. We now show that human LSD2/KDM1b/AOF1, the human homolog of LSD1, is a novel H3K4me1/2 demethylase that specifically regulates histone H3K4 methylation within intragenic regions of its target genes. Genome-wide mapping reveals that LSD2 associates predominantly with the gene bodies of actively transcribed genes, but is markedly absent from promoters. Depletion of endogenous LSD2 results in an increase of H3K4me2 as well as a decrease of H3K9me2 at LSD2 binding sites, and a consequent dysregulation of target gene transcription. Furthermore, characterization of LSD2 complex revealed that LSD2 forms active complexes with euchromatic histone methyltransferases EHMT1/2 and NSD3 as well as cellular factors involved in active transcription elongation. These data provide a possible molecular mechanism linking LSD2 to transcriptional regulation post initiation.
We used microarray analysis to identify the subset of genes that are differentially expression after depletion of endogenous LSD2/KDM1b/AOF1.

overall_design: Retroviral shRNA targeting human LSD2 (5’-GTGGGACCACAATGAATTCTT -3’) and control shRNA was used to infect HeLa. RNA was purified 70 hours post infection and processed for Human Genome U133 Plus 2.0 Array (Affymetrix) hybridization per manufacture’s instructions. Biological duplicates were analyzed.

first: Shi

last: Yujiang

first: Fang

last: Rui


title: E. coli BW25113 frdC vs. E. coli BW25113 HW2

status: Public on Oct 31 2010

city: State College

first: Thomas

middle: K.

last: Wood

state: PA

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

country: USA

institute: Pennsylvania State University

summary: Glycerol is an attractive feedstock for biofuels since it accumulates as a byproduct during biodiesel operations; hence, it is interesting to consider converting glycerol to hydrogen using the formate hydrogen lyase system of Escherichia coli which converts pyruvate to hydrogen.  Starting with Escherichia coli BW25113 frdC that lacks fumarate reductase to eliminate the negative effect of accumulated hydrogen on glycerol fermentation and by using both adaptive evolution and chemical mutagenesis combined with a selection method based on increased growth on glycerol, we obtained an improved strain, HW2, that produces 20-fold  more hydrogen in glycerol medium (0.68 mmol/L/h)  compared to that of frdC mutant.  HW2 also grows 5-fold faster (0.25 1/h) than BW25113 frdC on glycerol, so it achieves a reasonable growth rate.  Corroborating the increase in hydrogen production, glycerol dehydrogenase activity in HW2 increased 4-fold compared to BW25113 frdC.  In addition, a whole-transcriptome study revealed that several pathways that would decrease hydrogen yields were repressed in HW2 (fbp, focA, and gatYZ) while a beneficial pathway, eno which encodes enolase was induced.

overall_design: the overnight aerobic culture of HW2 and the frdC mutant in LB (25mL) were sparged with nitrogen for 5 min. Sealed crimp-top vials (60 mL) were also purged with nitrogen for 5 min. Inside an anaerobic glove-box, 30 mL of sparged uninoculated glycerol medium and 3 mL of sparged overnight culture were added to each vial, then the vials were kept at 37oC with shaking for 5 h for cell collection and RNA isolation.

first: Hongbo

last: Hu

middle: K


title: Human LSD2/KDM1b/AOF1 regulates gene transcription by modulating H3K4me2 methylation

status: Public on Nov 01 2010

state: MA

type: Genome binding/occupancy profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC

summary: The global transcriptional regulator Hha of Escherichia coli controls hemolysin activity, biofilm formation, and virulence expressions.  Earlier, we have reported that Hha represses initial biofilm formation and disperses biofilms as well as controls prophage excision in E. coli.  Since biofilm dispersal is a promising area to control biofilms, here we rewired Hha to control biofilm dispersal and formation.  The Hha variant Hha13D6 was obtained to have enhanced biofilm dispersal activity along with increased toxicity compared to wild-type Hha (Hha13D6 induces dispersal 60%, whereas wild-type Hha induces dispersal at early biofilms but not at mature biofilms).  Toxic Hha13D6 caused cell death probably by the activation of proteases HslUV, Lon, and PrlC, and deletion of protease gene hslV with overproducing Hh13D6 repressed biofilm dispersal, indicating Hha13D6 induces biofilm dispersal through the activity of protease HslV.  Furthermore, another Hha variant Hha24E9 was also obtained to decrease biofilm formation 4-fold compared to wild-type Hha by regulation of gadW, glpT, and phnF.  However, the dispersal variant Hha13D6 did not decrease biofilm formation, while the biofilm variant Hha24E9 did not induce biofilm dispersal.  Hence, Hha may have evolved two ways in response to environmental factors to control biofilm dispersal and formation, but both controlling mechanisms come from different regulatory systems.

overall_design: For the whole-transcriptome study of BW25113 hha/pCA24N-hha13D6 versus BW25113 hha/pCA24N-hha biofilm dispersal, cells were grown in 250 mL of LB glucose (0.2%) for 16 h at 125 rpm with 10 g of glass wool (Corning Glass Works, Corning, NY, USA) in 1 L Erlenmeyer flasks to form a robust biofilm (Ren et al., 2004) and incubated an additional 1 h with 1 mM IPTG to induce wild-type Hha and Hha13D6.  Similarly, for the whole transcriptome study of BW25113 hha/pCA24N-hha24E9 versus BW25113 hha/pCA24N-hha biofilm formation, cells were grown in 250 mL of LB glucose (0.2%) containing 1 mM IPTG for 7 h at 250 rpm with 10 g of glass wool to form biofilms.  Biofilm cells were obtained by rinsing and sonicating the glass wool in sterile 0.85% NaCl solution at 0°C, and RNALater buffer® (Applied Biosystems, Foster City, CA, USA) was added to stabilize RNA during the RNA preparation steps.  Total RNA was isolated from biofilm cells using a bead beater (Biospec, Bartlesville, OK, USA).  cDNA synthesis, fragmentation, and hybridizations to the E. coli GeneChip Genome 2.0 array (Affymetrix, Santa Clara, CA, USA; P/N 511302).  Genes were identified as differentially expressed if the expression ratio was higher than the standard deviation: 2.0-fold (induced and repressed) cutoff for Hha13D6 DNA microarrays (standard deviation 1.3-fold) and 10.0-fold (induced) or 4.0-fold (repressed) for Hha24E9 DNA microarrays (standard deviation 4.0-fold), and if the p-value for comparing two chips was less than 0.05.


title: Expression profiles in WT and MLL1-KO MEF at two different circadian time point

status: Public on Oct 28 2010

city: Irvine

first: Sayako

last: Katada

state: CA

address: Rm2226B GNRB Dep. Pharmacology UC Irvine

institute: UC Irvine

summary: We found that a H3K4 specific histone methyltransferase MLL1, a mammalian homologue of Drosophila trithorax, is essential for circadian transcription. MLL1 is in a complex with CLOCK:BMAL1 and contributes to their rhythmic recruitment to circadian promoters and cyclic H3K4 tri-metylation. To analyze the function of MLL1 on circadian gene regulation, we performed comparative microarray analysis of global gene expression levels in WT and MLL1-deficient MEF, at two different circadian time points (CT18 and CT30). This analysis identified several genes whose expression levels were remarkably changed between CT18 and CT30 in WT and MLL1-KO MEF. Typical clock-regulated genes such as Per2, Per3, Bmal1, or Dbp were found to be changing in WT but not in MLL1-KO MEFs.

overall_design: Wild-type and MLL1-KO MEF at two circadian time point (CT18 and 30), three replicates for each hour.

first: Paolo

last: Sassone-Corsi


title: MEFs, iPS, and ES expression profiles, and OKS mediated reprogramming regulated by Sox2 and Klf4

status: Public on Oct 27 2010

city: Guangzhou

first: liu

last: jing

state: guangdong

address: 190 Kai Yuan Avenue

country: China

institute: GIBH


title: Differential Gene Expression of Soluble CD8+ T-cell mediated suppression of HIV replication in three older children

city: Chicago

first: Ben

last: Katz

state: IL

address: 2300 Children's Plaza, Box # 20

department: Division of Infectious Diseases

institute: Children's Memorial Hospital

summary:
Goal: To compare the gene expression profiles from pediatric patients with each other, with those reported in adults and in those related to exosomes.
Background: Suppression of human immunodeficiency virus (HIV) replication by CD8+ T-cells (CD8 suppression) contributes to survival in adults and children < 1 year. Soluble CD8 suppression can also be seen in some older children with AIDS. The factor responsible, CD8-derived antiviral factor (CAF), acts at the level of HIV RNA transcription. Differential gene expression techniques have been used to define the gene(s) mediating this phenomenon in adults. Recently, CAF has been linked to exosomes secreted by CD8+ T-cells.
Objective: To compare the gene expression profiles from pediatric patients with each other, with those reported in adults and in those reportedly related to exosomes.
Design/Methods: We used differential gene expression to study 3 older children with HIV infection, 1 who did demonstrate soluble CD-8 suppression and 2 who did not, and compared our results with those reported in 2 previous studies in adults and their relatedness to exosome components secreted by CD8+ T-cells.
Results: 18 differentially expressed genes were also seen in 1 adult study (p=0.002, χ2 test), and 38 such genes (p < 0.0001, χ2 test) in a second adult study. In addition, two exosome components and some RNA’s related to exosomal proteins were also differentially expressed.
Conclusions: In children with HIV infection, we found significant differentially expressed genes that correlated to those previously reported in 2 studies in adults. Our data also lends some support to the recent identification of CAF with exosomes secreted by CD8+ T-cells.

overall_design:
Differential gene expression was used to study 3 older children with HIV infection, 1 who did demonstrate soluble CD-8 suppression and 2 who did not, and compared our results with those reported in 2 previous studies in adults and their relatedness to exosome components secreted by CD8+ T-cells.
Three vertically-HIV-1-infected adolescent boys were studied. This study was approved by the Children’s Memorial Institutional Review Board. After informed consent was obtained, 20 - 40 ml of heparinized peripheral blood was collected in association with regularly scheduled, clinically-indicated blood sampling.
Keywords: differential gene expression; soluble CD8 suppression; gene array; pediatric HIV infection; CD8-derived antiviral factor

first: Samantha

middle: L

last: Gadd


title: Expression profile of early stage in OKS mediated reprogramming regulated by Sox2 and Klf4

summary:
Klf4 and Sox2 are among the core reprogramming factor, and have different function in reprogramming. Klf4 is supposed to trigger MET in the early stage of reprogramming ,Sox2 is well known plutipotent relative gene.
Klf4 and Sox2 play important role in induced reprogramming. We performed this experiment to identify the targets regulated by Sox2 and Klf4 respectively.

overall_design: We perform a expression profile analysis at Day3 between OK plus TetOn-Sox2 infected MEFs and OS plus TetOn-Klf4 infected MEFs in iCD1(a optimized medium for robust reprograming) medium with or without Dox.

first: Jiekai

last: Chen

first: Duanqing

last: Pei

first: Jing

last: Liu


title: Changes in gene expression resulting from expression of MN1 in human CD34+ cells

status: Public on Oct 26 2010

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

summary: Reintroduction of CEBPA in MN1-overexpressing hematopoietic cells prevents their hyper-proliferation and restores myeloid differentiation. Forced expression of MN1 in primitive mouse hematopoietic cells causes acute myeloid leukemia and impairs all-trans retinoic acid (ATRA) induced granulocytic differentiation. Here, we studied the effects of MN1 on myeloid differentiation and proliferation using primary human CD34+ hematopoietic cells, lineage depleted mouse bone marrow cells, and bipotential (granulocytic/monocytic) human AML-cell lines. We show that exogenous MN1 stimulated the growth of CD34+ cells, which was accompanied by enhanced survival and increased cell cycle traverse in cultures supporting progenitor cell growth. Forced MN1 expression impaired both granulocytic and monocytic differentiation in vitro in primary hematopoietic cells and AML cell lines. Endogenous MN1 expression was higher in human CD34+ cells compared to both primary and in vitro differentiated monocytes and granulocytes. Microarray and real time RT-PCR analysis of MN1-overexpressing CD34+ cells showed down regulation of CEBPA and its downstream target genes. Re-introduction of conditional and constitutive CEBPA overcame the effects of MN1 on myeloid differentiation and inhibited MN1-induced proliferation in vitro. These results indicate that down regulation of CEBPA activity contributes to MN1-modulated proliferation and impaired myeloid differentiation of hematopoietic cells

overall_design: Human BM derived CD34+ cells (Stemcell Technologies, Vancouver, BC, Canada) were expanded for 2 days and transduced with MSCV-IRES-GFP or MSCV-MN1-IRES-GFP retrovirus for another 2 days. One day later RNA was isolated from GFP+/CD34+ FACS-sorted cells using Trizol (Sigma) and samples were subjected to micro array analysis following Affymetrix protocols (Affymetrix, Santa Clara, CA) using the GeneChip Human U133 Plus 2.0 array

first: Ayten

last: Kandilci

first: Gerard

last: Grosveld


title: Large intergenic non-coding RNAs as novel modulators of reprogramming: ESCs, fibroblast, and fibroblast-derived iPSC (gene expression)

status: Public on Nov 10 2010

city: Cambridge

first: Nataly

middle: Moran

last: Cabili

address: 7  Cambridge Center

institute: Broad Institute ;  Harvard University

summary: Gene expression profiles of human embryonic stem cells, fibroblasts, and fibroblast-derived induced pluripotent stem cells

overall_design:
Total RNA was extracted from human ESCs, fibroblast, and fibroblast-derived iPSC lines, then hybridized to Affymetrix arrays
Affymetrix Human Genome U133 Plus 2.0 Array [Affy_HG-U133_Plus_2]

first: Sabine

last: Loewer

first: George

middle: Q

last: Daley

first: John

last: Rinn


title: Expression profile of MEFs, iPS, and ES in different culture condition

summary:
MEFs can be reprograming to ES by defined reprogramming factors, the derived ES-like cells were termed iPSc. Completely reprogrammed iPSc have identifed gene expression profle  with ES.
Culture condition may influent the pluripotency of iPSCs.iPS/ES cultured in differient ES medium may have different gene expression profile.

overall_design: We preform an experiment to analyze the gene expression difference among MEFs cultured in FBS and iCD1,iPSc cultured in KSR medium and N2B27 supplementary with 2i medium , and ES cultured in  N2B27 supplementary with 2i medium.


title: Gene expression data from brain striatal and spinal cord regions of MPTP-intoxicated mouse following acupuncture

status: Public on Oct 23 2010

city: Seoul

first: Sabina

last: Lim

address: #1 Hoegi-dong Dongdaemoon-gu

country: South Korea

institute: East-West Medical Research Institute, Kyung Hee University


title: Expression data from human macrophages treated with Porphyromonas gingivalis and its components

first: Han

last: Hu

address: 44 Cummington St

department: Bioinformatics

institute: Boston University

summary:
Periodontitis is the most common human infection affecting tooth-supporting structures. It was shown to play a role in aggravating atherosclerosis. To deepen our understanding of the pathogenesis of this disease, we exposed human macrophages to an oral bacteria Porphyromonas gingivalis (P. gingivalis) either as live bacteria, or its lipopolysaccharide (LPS) or fimbria.

Microarray data from treated macrophages or control cells were analyzed to define molecular signatures. We focused our analysis on three important groups of genes. Group PG (genes differentially expressed by live bacteria only); Group LFG (genes differentially expressed in response to exposure to LPS and/or FimA); Group CG (core gene set jointly activated by all 3 stimulants). A total of 842 macrophage genes were differentially expressed in at least one of the three conditions compared to naïve cells. Using pathway analysis, we found that group CG activates the initial phagocytosis process and induces genes relevant to immune response, whereas group PG can de-activate the phagocytosis process associated with phagosome-lysosome fusion. LFG mostly affected RIG-I-like receptor signaling pathway.

overall_design: 12 samples in total. 4 conditions (treatment with live P. gingivalis, P. gingivalis LPS, P. gingivalis fimbriae, or saline) were used, and triplicates were performed for each condition. We considered the following comparisons: PG vs. Control (saline), PG-LPS vs. Control, and PG-fimbriae vs. Control. Fold-change > 2.0 and FDR < 0.25 were used to select significantly expressed genes.

first: Wen-han

last: Yu

first: Qingde

last: Zhou

first: Salomon

last: Amar


title: Identification of genes and molecular pathways associated with anti-miR-182 treatment.

status: Public on Oct 21 2010

city: LYON

first: Jiri

last: ZAVADIL

state: Other

address: 150 COURS ALBERT THOMAS

country: France

institute: IARC WHO

summary:
To identify genes differentially modulated by anti-miR-182 treatment in a liver melanoma metastasis mouse model.
Targeting oncogenic microRNAs is emerging as a promising strategy for cancer therapy. Here we provide proof-of-principle for the safety and efficacy of miRNA targeting against metastatic tumors. We tested the effect of targeting miR-182, a pro-metastatic miRNA frequently overexpressed in melanoma, whose silencing represses invasion and induces apoptosis in vitro. In particular, we assessed the effect of anti-miR-182 oligonucleotides synthesized with 2’ sugar modifications and a phosphorothioate backbone in a mouse model of melanoma liver metastasis. Luciferase imaging showed that mice treated with anti-miR-182 had an appreciably lower burden of liver metastases compared to the control. We confirmed that miR-182 levels were effectively downregulated in the anti-miR treated tumors relative to the scrambled treated tumor both in the liver and in the spleen. This downregulation was accompanied by an upregulation of miR-182 direct targets. Transcriptome analysis of mouse tissues treated with anti-miR-182 or scramble oligonucleotides revealed an enrichment for genes controlling survival, adhesion and migration modulated in response to anti-miR-182 treatment. These data indicate that in vivo administration of anti-miRs allows for efficient miRNA targeting and concomitant upregulation of target levels. Our results suggest that the use of anti-miR-182 is a promising therapeutic strategy for metastatic melanoma and provide solid proof-of-principle for similar strategies against other metastatic tumors.

Keywords: Differentially expressed genes (mRNAs) in response to miRNA inhibition

overall_design: Quadruplicate (n=4) samples of anti-miR-182 treated human melanoma metastasis compared to quadruplicate control treated metastasis.

first: Eva

last: Hernando

last: Zavadil

first: Chanh

last: Huynh

first: Miguel

last: Segura

first: Avita

last: Gaziel

first: Silvia

last: Menendez

first: Farbod

last: Darvishian

first: Iman

last: Osman

first: Luis

last: Chiriboga

first: Brandi

last: Levin

first: Daniel

last: Meruelo


title: Transcriptome profiling of dendritic cell subtypes

city: DEBRECEN

first: LAJOS

last: SZELES

address: Egyetem tér

country: Hungary

institute: UNIVERSITY OF DEBRECEN

summary:
In this study transcriptome profiling of dendritic cell subtypes was performed using various human dendritic cells.

Monocyte-derived DC:
CD14+ monocytes were obtained from buffy coats by Ficoll - gradient centrifugation and immunomagnetic cell separation using anti-CD14-conjugated microbeads. Monocytes were resuspended into 6-well culture dishes at a density of 1.5 x 10 million  cells/ml and cultured in RPMI 1640 supplemented with 10% FBS containing 800 U/ml GM-CSF and 500 U/ml IL-4. Cells were cultured for 5 days and the IL-4 and GM-CSF addition was repeated at day 2.

Dermal DC (DDC) and Langerhans Cells (LC) from skin:
Human skin specimens were obtained from healthy donors undergoing corrective breast or abdominal plastic surgery after informed consent. Thick slices (3 mm) of skin containing the epidermis and the dermis were cut by use of a dermatome. Slices of skin were cut in pieces of 1 cm2 and incubated with Dispase II for 30–60 min at 37°C. The epidermis and dermis were separated with tweezers and washed with PBS. To isolate LC, the epidermal sheets were incubated with PBS with 0.05% trypsin  for 10 min at 37°C, and a single-cell suspension was prepared by pushing the tissue through 100 µm pore nylon cell strainers with a plunger of a 2-ml syringe. Epidermal cell suspension was enriched for LC by density centrifugation over Lymphoprep and CD1a-guided MACS (Miltenyi Biotec). To isolate DDC, the dermis was incubated with PBS containing  Dispase and Collagenase A at 37°C for 2 h, after which, a single-cell suspension was prepared by pushing through 100 µm pore nylon cell strainers with a plunger of a 2-ml syringe. Cell suspension was enriched for DDC by CD1a-guided MACS.

Blood Cd1c+ DC:
Blood CD1c+ DC were isolated from periferal blood. BDCA1+ (CD1c) DCs were incubated with a lineage-specific PE-labeled Ab mixture, HLA-DR-allophycocyanin, and BDCA1-FITC. Lineage-negative and HLA-DRhigh DCs, positive for BDCA1 were sorted on a FACS and collected in tubes containing 1 ml of 100% FBS. A total of 40,000–100,000 cells was isolated (>98% pure).

overall_design: Dendritic cell subtypes were differentiated in vitro from monocytes and primary dendritic cells were isolated from human skin and blood.

first: Lajos

last: Szeles

first: Malin

last: Lindstedt

first: Saskia

last: Santegoets

first: Istvan

last: Szatmari

first: Laszlo

last: Nagy


title: Gene expression data from striatal regions of MPTP-intoxicated mouse brain by acupuncture

first: Sabina

last: Lim

summary:
Acupuncture at acupoints GB34 and LR3 has been reported to inhibit nigrostriatal degeneration in parkinsonism models, yet the genes related to this preventive effect of acupuncture on the nigrostriatal dopaminergic system remain elusive.
We investigated gene expression profile changes in the striatal region of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced parkinsonism models after acupuncture at the acupoints GB34 and LR3

overall_design: C57BL/6 mice were divided into four experimental groups; ① C: Control, ② M: MPTP-treatment only, ③ MA: MPTP- and acupuncture-treatment at acupoints GB34 and LR3, ④ MNA: MPTP- and acupuncture-treatment at non-acupoints. Total RNA was isolated from two brains' striatal regions of each experimental group (4 experimental group × 2 samples of each experimental group = total 8 samples).

first: Yeong-Gon

last: Choi

first: Sujung

last: Yeo

first: Yeon-Mi

last: Hong


title: Effects of shikonin on the gene expression of human lymphoma U937 cells

status: Public on Oct 20 2010

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

country: Japan

institute: University of Toyama

summary: Shikonin is a active component isolated from the roots of the traditional Chinese herb Lithospermum erythrorhizon and exhibits multiple pharmacological properties, such as anti-oxidant, anti-inflammatory, and anti-tumor effects. Here, the effects of shikonin on the gene expression of human lymphoma U937 cells were investigated using an Affymetrix GeneChip system. The cells were treated with 100 nM shikonin, and followed by incubation for 3h at 37°C. Flow cytometry analysis with Annexin-V and propidium iodide demonstrated that no cell death was observed in the cells at 100 nM shikonin. Of approximately 47,000 probe sets analyzed, many genes that were differentially expressed by a factor 2.0 or greater were identified in the cells treated with the compound.

overall_design: U937 cells, a human lymphoma cell line, were treated with 100 nM shikonin and followed by incubation for 3h at 37°C. The cells treated with dimethyl sulfoxide were served as control. Total RNA samples were prepared from the cells. Gene expression was analyzed by an Affymetrix GeneChip® system with a Human Genome U133-plus 2.0 array for analysis of over 47,000 transcripts. Sample preparation for array hybridization was carried out as described in the manufacturer’s instructions.

first: Kanwal

last: Ahmed

first: Yukihiro

last: Furusawa

first: Takashi

last: Kondo


title: STAT3 protects from liver injury and fibrosis in a mouse model of sclerosing cholangitis.

city: Vienna

first: Stefanie

last: Tauber

address: Dr. Bohr-Gasse 9

department: CIBIV

country: Austria

institute: MFPL

summary: Background and aims: Signal transducer and activator of transcription 3 (Stat3) is the main mediator of interleukin-6 type cytokine signaling required for hepatocyte proliferation and hepatoprotection but its role in sclerosing cholangitis (SC) and other cholestatic liver diseases remains unresolved.                                               Methods: We investigated the role of Stat3 in inflammation-induced cholestatic liver injury and used mice lacking the multidrug resistance gene 2 (mdr2-/-) as a model for SC.                                                                                Results: We demonstrate that conditional inactivation of stat3 in hepatocytes and cholangiocytes (stat3Δhc) of mdr2-/- mice strongly aggravated bile acid-induced liver injury and fibrosis. Similarly, stat3Δhc mice are more sensitive to cholic acid feeding than control mice. Global gene expression analysis demonstrated that hepatoprotective signals via epidermal growth factor and insulin-like growth factor 1 are affected upon loss of Stat3.                                                                                Conclusions: Our data suggest that Stat3 protects cholangiocytes and hepatocytes from bile acid-induced damage thereby preventing liver fibrosis in cholestatic diseases.

overall_design: Affymetrix microarray analyses was performed to identify metabolic and molecular pathways in stat3Δhc mdr2-/- mice that lead to cholestasis and bile acid-induced liver injury. To avoid false positive results that are due to differential cellular composition, we defined the onset of fibrosis and expression of fibrogenic factors in stat3Δhc mdr2-/- mice.

first: Markus

last: Mair

first: Robert

last: Eferl


title: Expression data of lentivirus sponge MicroRNA16 (miR16) downregulated RPMI 8226 and MMS1 multiple myeloma (MM) cell lines compared with control lentivirus sponge

first: Daniel

middle: Ruben

last: Carrasco

address: 44 Binney St

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Multiple myeloma is characterized by frequent chromosomal alterations. Deletion of chr 13, especially band 13q14, is commonly observed in early stages of MM, suggesting the presence of tumor suppressor genes (TSG) within this region. We sought to functionally validate the role of the microRNAs-15a/16 cluster, centered at the deleted region, as TSGs and delineate their downstream target genes in MM. Using “sponge” lentiviral vectors to competitive stably inhibit mature microRNAs in vitro and in vivo, we have documented enhanced proliferative and invasive capacity of cells with stably inhibition of miR-16. Expression profiling analysis of miR-16-deficient cells identified a large number of downstream target genes. This loss-of-function system, which mimics the 13q chromosomal deletion, provides a valuable tool to investigate their function in MM pathogenesis and their potential use as therapeutic targets.

overall_design: We used microarrays to detail the global programme of gene expression underlying miR16 downregulation, simulating the 13q- cytogenetic changes related to MM in order to identified distinct classes of up-regulated genes during this process. MM cell lines were stably tranduced and sorted with miR16 lentiviruses expressing miR downregulating sponges or control sponges, and analyzed for GEP to asses possible miR16 target genes. Cells were lysed and the RNA extraction and hybridization was peformed on Affymetrix microarrays. We sought to obtain homogeneous populations of cells and therefore collected all at the same timepoint.

first: Moshe

last: Gat

first: Ruben

middle: D


title: A molecular signature of normal breast epithelial and stromal cells from Li-Fraumeni syndrome mutation carriers

city: Indianapolis

first: Brittney-Shea

last: Herbert

state: IN

address: 975 W. Walnut st.

department: Medical & Molecular Genetics

institute: Indiana University School of Medicine

summary: Specific changes in gene expression during cancer initiation should enable discovery of biomarkers for risk assessment, early detection and targets for chemoprevention. It has been previously demonstrated that altered mRNA and proteome signatures of morphologically normal cells bearing a single inherited “hit” in a tumor suppressor gene parallel many changes observed in the corresponding sporadic cancer. Here, we report on the global gene expression profile of morphologically normal, cultured primary breast epithelial and stromal cells from Li-Fraumeni syndrome (LFS) TP53 mutation carriers. Our analyses identified multiple changes in gene expression in both morphologically normal breast epithelial and stromal cells associated with TP53 haploinsufficiency, as well as interlocking pathways.  Notably, a dysregulated p53 signaling pathway was readily detectable. Pharmacological intervention with the p53 rescue compounds CP-31398 and PRIMA-1 provided further evidence in support of the central role of p53 in affecting these changes in LFS cells and treatment for this cancer. Because loss of signaling mediated by TP53 is associated with the development and survival of many human tumors, identification of gene expression profiles in morphologically normal cells that carry “one-hit” p53 mutations may reveal novel biomarkers, enabling the discovery of potential targets for chemoprevention of sporadic tumors as well.

overall_design: compare gene expression from different cell types

first: Rebecca

middle: A

last: Chanoux

first: Yunlong

last: Liu

first: Peter

middle: H

last: Baenziger

first: Chirayu

middle: P

last: Goswami

first: Jeanette

middle: N

last: McClintick

first: Howard

middle: J

last: Edenberg

middle: E

last: Pennington

first: Steve

middle: M

last: Lipkin

first: Levy

last: Kopelovich


title: Gene Expression differences between replication error deficient and proficient colorectal cancers: the dominant role of deletions in 3’UTR poly T sequences

status: Public on Oct 19 2010

city: John Radcliffe hospital

first: Jenny

last: Wilding

state: Headington, Oxford

address: Weatherall institute of molecular medicine

department: oncology

country: United Kingdom

institute: University of Oxford

summary:
16 replication error proficient (RER-/MSI-) and 14 replication error deficient (RER+/MSI+) colorectal cancer cell lines
Replication error deficient (RER+) colorectal cancers are a distinct subset of colorectal cancers, characterised by inactivation of the DNA mismatch repair system.  They are typically pseudodiploid, accumulate mutations in repetitive sequences as a result of their mismatch repair deficiency, and have distinct pathologies.  Regulatory sequences controlling all aspects of mRNA processing, including especially message stability are found in the 3’UTR sequence of most genes.  The relevant sequences are typically A/U rich elements and/or U repeats. Microarray analysis of 14 RER+ (deficient) and 16 RER- (proficient) colorectal cancer (CRC) cell lines confirms a striking difference in expression profiles. Analysis of the incidence of mononucleotide repeat sequences in the 3’UTRs, 5’UTRs and coding sequences of those genes most differentially expressed in RER+ versus – cell lines has shown that much of this differential expression can be explained by the occurrence of a massive enrichment of genes with 3’UTR T repeats longer than 11 base pairs in the most differentially expressed genes. This enrichment was confirmed by analysis of two published consensus sets of RER differentially expressed probe sets for a large number of primary colorectal cancers.   Sequence analysis of the 3’UTRs of a selection of the most differentially expressed genes shows that they all contain deletions in these repeats in all RER+ cell lines studied. These data strongly imply that deregulation of mRNA stability through accumulation of mutations in repetitive regulatory 3’UTR sequences underlies the striking difference in expression profiles between RER+ and RER- colorectal cancers.

overall_design: 16 replication error proficient (RER-/MSI-) and 14 replication error deficient (RER+/MSI+) colorectal cancer cell lines.

first: Walter

middle: F

last: Bomder

first: Jennifer


title: Intestinal ablation of CKIalpha highlights invasiveness control

city: Jerusalem

first: Gady

last: Cojocaru

address: Kiryat Hadassah

department: Pathology

country: Israel

institute: hadassah medical center

summary: Wnt signaling, which drives the rapid self-renewal of the gut epithelium is causally associated with intestinal neoplasia. Here we show that CKIalpha is a activation depends on p53 and p21Waf1/Cip1: CKIα ablation provokes activation of p53 and p21, which assume a pivotal role in suppressing invasive cancer. Dual loss of CKIalpha and either p53 or p21 results in rapid, rampant malignant signature denoted p53supinv (p53-suppressed invasiveness) that is conditionally induction of invasiveness. Like invasiveness control, the transcriptional suppression of p53supinv genes is largely mediated by p21, independently of cell cycle control, representing a novel tumor suppressor function of wild-type p53.

overall_design: 13 arrays of mice entrocytes herto or homozygot for gut specific KO of CKI alpha. Crossed with p53 or p21 KO mice.

first: Ela

last: Elyada

first: Ariel

last: Pribluda

last: Goldstein

first: Yael

last: Morgenstern

first: Guy

last: Brachya

first: Irit

last: Snir-Alkalay

first: Ido

last: Burstain

last: Haffner-Krausz

first: Steffen

last: Jung

first: Zoltan

last: Wiener

first: Kari

last: Alitalo

last: Oren

first: Eli

last: Pikarsky

first: Yinon

last: Ben-Neriah


title: Gene profiling of the cell death induced by heat stress in HSC-3 human oral squamous carcinoma cells

first: Yoshiaki

last: Tabuchi

summary: Hyperthermia is widely used to treat patients with various cancers. The 42.5˚C is well known as inflection point of hyperthermia and generally up to 42˚C of hyperthermia is used in clinical case to combine with other therapy. Here, the effects of heat stress at 42 or 44˚C for 90 min on the gene expression in HSC-3 human oral squamous carcinoma cells were investigated using an Affymetrix GeneChip system. The cells were treated with heat stress (42 or 44°C for 90 min) and followed by incubation for 0, 6, or 12 h at 37°C. The percentage of cell death was 5.0 ± 1.5 (mean ± SD) at 42°C for 12 h and 17.4 ± 0.6 at 44°C for 12 h. Of approximately 47,000 probe sets analyzed, many genes that were differentially expressed by a factor 2.0 or greater were identified in the cells treated with heat stress at 42 and 44°C.

overall_design: HSC-3 human oral squamous carcinoma cells were treated with heat stress (42 or 44°C for 90 min) and followed by incubation for 0, 6, or 12 h at 37°C. Non-treated cells were served as control. Total RNA samples were prepared from the cells. Gene expression was analyzed by an Affymetrix GeneChip® system with a Human Genome U133-plus 2.0 array for analysis of over 47,000 transcripts. Sample preparation for array hybridization was carried out as described in the manufacturer’s instructions.

first: Shigehito

last: Wada

first: Yukihiro

last: Furusawa


title: Viable Mice Produced from 3-factor Induced Pluripoent Stem (iPS) Cells through Tetraploid Complementation

city: Dalian

first: Lan

last: Kang

address: 9 West Section, Lvshun South Road

department: Institute of Cancer Stem Cell

institute: Dalian Medical University

summary: Ectopic expression of four transcription factors including Oct4, Sox2, Klf4 and c-Myc in differentiated fibroblast cells could reset the cell fate of fibroblast cells to pluripotent state. Subsequently, fully pluripotency of these so-called induced pluripotent stem cells (iPSCs) has been demonstrated as viable mice could be generated autonomously from iPS cells through tetraploid blastocyst complementation. Moreover, the generation of human and patient-specific iPS cells have raised the possibility of utilizing iPS cells clinically. However, the utilization of c-Myc in iPS cells induction greatly increased the incidence of tumorigenecity in the iPS-chimeric mice and also might hinder the clinical application of human iPS cells in the future. Fortunately, c-Myc has been recently found dispensable for iPS induction even though the iPS induction efficiency is greatly reduced in the absence of c-Myc. However, it remains unknown if these three factors-induced iPS cells are fully pluripotent. In the present study, we have successfully demonstrated that 3-factor iPS cells could also be fully pluripotent as viable mice could be generated from 3-factor iPS cells autonomously via tetraploid complementation and moreover, our data indicated that the pluripotency regulatory mechanism in 3-factor iPS cells might be distinct from 4-factor iPS cells.

overall_design: We compared the gene expression profile of iPS cells with and without the tetraploid embryo complementation competence. Three biological repeats were included for each line.

first: Tong

last: Wu

first: Yu

last: Tao

first: Ye

last: Yuan

first: Jing

last: He

last: Zhang

last: Luo

first: Zhaohui

last: Kou

first: Shaorong

last: Gao


title: Gene expression differences between highly enriched normal and chronic myelogenous leukemia quiescent stem/progenitor cells and correlations with biological abnormalities

status: Public on Oct 16 2010

city: New York

first: quincy

last: mo

state: NY

address: 1275 York Avenue

institute: Memorial Sloan-Kettering Cancer Center

summary: In comparing gene expression of normal and CML CD34+ quiescent (G0) and proliferating (G1/S/G2/M) cells, 292 genes were down-regulated and 192 genes were up-regulated in the CML G0 cells. The differentially expressed genes were grouped according to their reported functions and correlations were sought with biological differences previously observed between the same groups. The most apparent correlations include: i) Normal and CML G0 cells are more primitive than G1/S/G2/M cells; ii) CML G0 cells are in a more advanced stage of development and more poised to begin proliferating than normal G0 cells; iii) When CML G0 cells are stimulated to proliferate, they undergo further differentiation and maturation more rapidly than normal G0 cells, but both granulopoiesis and erythropoiesis are less efficient than normal; iv) Whereas normal G0 cells form only granulocyte/monocyte (GM) colonies when stimulated by cytokines, CML G0 cells consistently form a combination of GM and erythroid clusters and colonies; and v) Prominin-1 (CD133) is the gene most down-regulated in CML G0 cells and its down-regulation appears to be associated with the spontaneous formation of erythroid colonies by CML progenitors without EPO. The gene most over-expressed in CML G0 cells is LepR, but its role in contributing to the myeloid expansion and other abnormalities is unknown. It was hoped that LepR might serve as a therapeutic target, but leptin had no stimulatory or inhibitory effect on either normal or CML G0 cells, our attempts to make a specific LepR antibody were unsuccessful, and no other potentially targetable over-expressed surface antigens were identified.

overall_design: A total of eight patients diagnosed with Ph+ CML (three in accelerated phase and five in chronic phase) were used in this study. The CML samples were all obtained from patients hospitalized at the Memorial Sloan Kettering during the period 1990-2006. The four normal bone marrow samples were purchased from Cambrex (Cambrex Bio Science Rockland,Inc., Rockland, Maine 04841, USA).

first: Maurizio

last: Affer

first: Su

last: Dao

first: Charlotte

last: Liu

first: Qianxing

last: Mo

first: Agnes

last: Viale

first: Caryl

last: Lambek

first: Tom

last: Marr

first: Bayard

last: Clarkson


title: PTPN22 autoimmune susceptibility gene affects the removal of human developing autoreactive B cells

city: New Haven

first: Laurence

last: Menard

state: CT

address: 300 George st

department: Immunobiology-HTI

institute: Yale School of Medicine

summary:
Protein tyrosine phosphatase nonreceptor type 22 (PTPN22) gene segregates with most autoimmune diseases; its risk allele encodes overactive PTPN22 phosphatases that alter B cell receptor (BCR) signaling potentially involved in the regulation of central B cell tolerance.  To assess whether PTPN22 risk allele affects the removal of developing autoreactive B cells, we tested by ELISA the reactivity of recombinant antibodies isolated from single B cells from asymptomatic healthy individuals carrying one or two PTPN22 risk allele(s). We found that new emigrant/transitional and mature naive B cells from PTPN22 risk allele carriers contained high frequencies of autoreactive clones compared to non-carrier control donors.  Hence, a single PTPN22 risk allele has a dominant effect on altering autoreactive B cell counterselection, suggesting that early B cell tolerance checkpoint defects precede the onset of autoimmunity.  In addition, gene array experiments comparing mature naïve B cells from healthy individuals carrying or not PTPN22 risk allele(s) revealed that the strength of association of PTPN22 for autoimmunity, second in importance only to the MHC, may not only be due to BCR signaling alteration but also to the regulation of other genes, which themselves have also been identified as involved in the development of autoimmune diseases.

The PTPN22 risk allele is a single nucleotide change (cytidine to thymidine) at residue 1858, which results in a single amino acid substitution from arginine to tryptophan at position 620 of the PTPN22/Lyp protein.

overall_design: Data from mature naïve B cell populations from patients carrying 1 or 2 PTPN22 T alleles and non-carrier patients were compared in order to characterize the impact of PTPN22 polymorphism on B cell physiology. RNA was extracted from batch-sorted CD19+CD10-CD21+CD27- conventional mature naive B cells using the Absolutely RNA microprep kit (Stratagene).  100-200 ng of RNA was obtained per sample, and the quality of the purified RNA was assessed by the Bioanalyzer from Agilent.  Using the Ovation biotin system kit from Nugen, 30-50ng of RNA was amplified and labeled to produce cDNA.  Labeled cDNA was hybridized on chips containing the whole human genome (Human Genome U133 Plus 2.0 from Affymetrix).

first: David

last: Saadoun

first: Isabelle

last: Isnardi

first: Yen-Shing

last: Ng

first: Greta

last: Meyers

first: Clara

last: Abraham

first: Roja

last: Motaghedi

first: Jane

last: Buckner

first: Peter

last: Gregersen

first: Eric

last: Meffre


title: Expression data for naïve IL-2 and IL-12 primed Pmel-1 CD8+ T-cells

city: Los Angeles

first: Robert

last: Prins

address: 1506 Gonda

department: Neurosurgery

institute: UCLA

summary: The expansion, trafficking and functional effectiveness of adoptively transferred CD8+ T-cells play a critical role in mediating effective anti-tumor immunity.  However, the mechanisms which program the highly proliferative and functional state of CD8+ T-cells are not completely understood.   We hypothesized that IL-12, a cytokine commonly induced by TLR activation, could enhance T-cell priming by altering responsiveness to antigen and cytokines.   Priming of tumor specific CD8+ T-cells in the presence of IL-12 induced the acquisition of a 'polyfunctional' effector response and increased the generation of memory cells.   Moreover, IL-12 priming also promoted high levels of the IL-2 receptor alpha-chain (CD25) and robust IL-2 mediated activation of STAT5.  This sensitivity to IL-2 translated into enhanced in vivo proliferation of adoptively transferred CD8+ T-cells.  Furthermore, real-time, in vivo imaging of T-cell trafficking confirmed the ability of IL-12 priming to drive in vivo proliferation.  IL-12 priming enhanced the anti-tumor function of adoptively transferred cells by reducing established subcutaneous tumor burden, and significantly increasing survival in an established intracranial tumor model.  Finally, IL-12 priming of human PBMCs generates tumor specific T-cells phenotypically and functionally similar to IL-12 primed Pmel-1 T-cells.  These results highlight IL-12 as an important mediator of CD8+ T-cell effector function and anti-tumor immunity.

overall_design:
We primed Pmel-1 TCR transgenic CD8+ T-cells with cognate antigen and either IL-2 or IL-12 and compared their gene expression profiles.  This was used to identify pathways or genes necessary for anti-tumor activity in vivo.
RNA was isolated from Pmel-1 T-cells primed with antigen and cytokine for 6 days and hybridized to Affymetrix arrays.

first: Dominique

last: Lisiero


title: Transcriptome analysis of wild type E. coli (K-12 MG1655) comparing to mutant E. coli strain (ECOM4) under aerobic and anaerobic conditions

status: Public on Oct 15 2010

city: La Jolla

first: Bernhard

last: Palsson

address: 9500 Gilman Dr.

department: Bioengineering

institute: UCSD

summary:
Cytochrome oxydases and quinol monooxygenase were removed from the E. coli genome resulting in oxygen-independent physiology
We used microarray profiling to identify perturbed metabolic or regulatory functionality resulting in the inability to undergo aerobic-anaerobic shift.

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

overall_design: Affimetrics E. coli Arrays 2.0, Experiment (ECOM4) under both conditions (+O2/-O2) were analyzed in triplicates and compared to control (MG1655) under same conditions in triplicates

first: Vasiliy

last: Portnoy

last: Scott

first: Nathan

last: Lewis

first: Yekaterina

last: Tarasova

first: Andrei

last: Osterman


title: Gene Expression Profile of Medullary Epithelial Cells isolated from thymus of Bone Marrow (BM) reconstituted RAG1 null (control) and SCID NOD mouse

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary:
We identified DNAPK as one of the major proteins that physically interact with Autoimmune regulator (Aire). To establish physiological significance of DNAPK in Aire-driven expression of PTA genes in MECs, we utilized BM-reconstituted SCID mice (which express non functional DNAPK in their MECs) and RAG1 null mouse as a control.
MECs from these mutated/reconstituted mice  were sorted by Flow cytomety and their expression profile was analyzed using Affymetrix chips. The analysis shows that Aire-dependent PTA  genes are significantly underexpressed in reconstituted SCIDS vs. RAGs (Controls), suggesting the involvement of DNAPK in Aire-mediated gene expression.

Keywords: gene mutation

overall_design: Since SCID mice lack mature thymocytes and as a result thymic stroma, we reconstituted these animals by BM transfer (IP injection into 2-4d pups) 6 hrs post-irradiation (200rad). Reconstituted thymi were analyzed 6-8w after transfer.

first: Jakub

last: Abramson

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Bortezomib resistance in Mantle Cell Lymphoma (MCL) is associated with plasmacytic differentiation

status: Public on Oct 13 2010

city: Bethesda

first: Patricia

last: Perez-Galan

state: MD

address: 10 center drive

department: Hematology Branch

institute: NHLBI-NIH

summary:
Bortezomib-induced resistant MCL cell lines (HBL2 BR and JEKO BR) were generated by continuous cultured of corresponding parental cell lines (HBL2 PT and JEKO PT) with increasing bortezomib concentrations
The IC50 of bortezomib of BR cell lines was 80 fold higher than the IC50 of the parental clone for HBL2-BR and 40 fold higher for JEKO-BR.RNA was isolated from cells collected at different time points within the period of one month in triplicate for HBL2 and in duplicate for JEKO subclones. This material was used for gene expression analysis using Affymetrix platform.

Keywords: RNA

overall_design: Comparision of gene expression profiling in matched pairs of PT and BR cell lines

first: Adrian

last: Wiestner


title: Gene Expression Profile of 293T and 293T-Aire-expressing cells

summary:
To analyze the impact of Aire on gene expression profile in a model cell line, we used 293T cells and transfected them either with an Aire expression plasmid pCMV-Aire (where mAire is driven by CMV promoter) or with a control plasmid pCMV2B.
Total RNA was extracted 48 hours post transfection, processed and used for gene expression profiling by Affymetrix. The data demonstrate that Aire has a very broad impact, effecting (upregulating and downregulating) hundreds of differents genes, however these genes differ dramatically from its targets in medullary epithelial cells.

Keywords: transfection

overall_design: 293T cells were seeded on 10cm plates and were grown in DMEM containing 10% FBS under standard TC conditions. Next day, the cells were transfected either by pCMV-Aire (6ug/plate) or empty pCMV (6ug/plate) using Mirus reagent, according to manufacturer's instructions. Total RNA was extracted 48 hrs post transfection by Trizol protocol according to the manufacturer's instructions. 3 biological replicates were used for Aire transfection and 2 replicates for transfection with a control plasmid.


title: Expression data from white and brown adipose tissue (WAT and BAT) of per2-/- and control mice

city: Irvine

first: benedetto

last: grimaldi

address: 2226B Gillespie NRF

department: pharmacology

institute: university of california, irvine

summary: We found that the circadian protein PER2 interacts with the nuclear receptor PPARgamma to repress its activity. PPARgamma is a master regulator of adipogenesis and lipid metabolism and is very abundant in adipose tissue. We used microarrays to detail the global program of gene expression in adipose tissue lacking the per2 gene. This analysis identified several PPARgamma target genes up-regulated in adipose tissue from per2-/- mice.

overall_design: Per2-/- and per2+/+ male mice (Bae et al., 2001) were housed under 12 hr light/12 hr dark (LD) cycles. Mice 20 weeks old were sacrificed at the same time and adipose tissue (WAT and BAT) was collected for RNA extraction. 3 biological replicates per mouse/tissue.

first: Benedetto

last: Grimaldi

first: Paolo

last: Sassone-Corsi


title: Expression data from synovium, bone marrow and nucleus pulposus

status: Public on Oct 11 2010

city: Tokyo

first: Takashi

last: Miyamoto

address: 1-5-45 Yushima, Bunkyo-ku

department: Department of Orthopedic Surgery

institute: Tokyo Medical and Dental University

summary:
Synovial and bone marrow mesenchymal stem cells after intradiscally injection show regenerative effects of nucleus pulposus.
Microarray analyses of rats were performed to investigate the closeness of the gene profiles between the nucleus pulposus cells and the synovial or bone marrow mesenchymal stem cells. To investigate interaction between synovial mesenchymal stem cells and nucleus pulposus cells, human synovial mesenchymal stem cells and rat nucleus pulposus cells were co-cultured, and species specific microarray were performed.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: Synovium of knee joints, bone marrow and nucleus pulposus were harvested from rat or human, and cells were isolated for RNA extraction and hybridization on Affymetrix microarrays. To compare the gene profiles each other, isolated cells were mono-cultured respectively, and human synovial mesenchymal stem cells and rat nucleus pulposus cells were co-cultured.

first: Ichiro

last: Sekiya

first: Kenji

last: Matsumoto


title: Expression data from human Ea.hy926 cells in response to epoxomicin and in dependency of TCF11 presence

status: Public on Oct 08 2010

city: Berlin

first: Elke

last: Krueger

address: Monbijoustr. 2

department: Institute of Biochemistry

country: Germany

institute: Charité Universitaetsmedizin Berlin

summary:
Coordinated regulation of the ubiquitin-proteasome system is crucial for the cell to adjust its protein degradation capacity to changing proteolytic requirements. The transcription factor TCF11 has been identified as a  regulator for 26S-proteasome formation in human cells to compensate for reduced proteolytic activity. To expand the current knowledge of other UPS-related TCF11 target genes in response to epoxomicin, we performed microarray analyses of cells exposed to epoxomicin and with or without depletion of TCF11.

Keywords: siRNA depletion

overall_design: Human Ea.hy926 cells were harvested 24 hours following treatment with 10nM epoxomicin or DMSO as a solvent control and with transfection of control siRNA or TCF11-specific siRNA for RNA extraction and hybridization on Affymetrix microarrays.

first: Janos

last: Steffen

last: Krüger


title: Developmental ablation of Id1 and Id3 genes in the vasculature leads to postnatal cardiac phenotypes

status: Public on Oct 07 2010

city: Newark

first: Saleena

last: Ghanny

address: 185 South Orange Ave

institute: Rutgers University

summary:
Rationale: The Id1 and Id3 genes play major roles during cardiac development, despite their expression being confined to non-myocardial layers (endocardium – endothelium - epicardium). We previously described that Id1–/–Id3–/– double knockout (dKO) mouse embryos die at mid-gestation from multiple cardiac defects, but early demise precluded the studies of the roles of Id in the adult mice.
Objective: To elucidate postnatal roles of Id genes in the heart.
Methods and Results: We ablated Id1 gene in the vasculature and Id3 gene globally to generate Tie2Cre+Id1F/–Id3–/– and Tie2Cre+Id1F/FId3–/– conditional KO (Id cKO) embryos. Half of the Id cKO mice die at birth. Postnatal demise was associated with cardiac underdevelopment, enlargement, muscular ventricular septal and endothelial defects. Surviving Id cKO mice exhibited dilated, fibrotic cardiomyopathy associated with defects in the vasculature. The adult cardiac phenotype progressed into heart failure and resembled endomyocardial fibroelastosis. An abnormal vascular response was also observed in the healing process of excisional skin wounds of Id cKO mice. Expression patterns of vascular, fibrotic and hypertrophic markers were altered in the Id cKO hearts, but addition of Insulin-Like Growth Factor binding protein-3 (IGFbp3) reversed gene expression profiles of vascular and fibrotic, but not hypertrophic markers.
Conclusions: Conditional ablation of Id genes in the vasculature leads to dilated fibrotic cardiomyopathy. The findings could reveal important insights into the role(s) of the endocardial network of the endothelial lineage to the development of dilated fibrotic cardiomyopathy and identify a potential therapeutic target, IGFbp3, in its treatment.

overall_design: Total RNA from heart tissue was isolated (RNeasy, QIAGEN) from P180 WT, Id control, Id cKO, IGFbp3 incubated Id cKO, and control incubated Id cKO.  RNA was converted to cDNA, cRNA, and hybridized to DNA sequences contained in the GeneChip Mouse Gene 1.0 ST Array (Affymetrix). Information from at least duplicate samples was compared and filtered by fold change >2 (Id cKO vs WT, Id control vs WT, IGFbp3 incubated Id cKO vs. control incubated Id cKO) and statistical p-value<0.001.

first: Diego

last: Fraidenraich

first: Qingshi

last: Zhao

first: Amanda

last: Beck

first: Joseph

last: Vitale

first: Joel

middle: S

last: Schneider

first: Shumin

last: Gao

first: Genie

last: Elson

first: Samuel

last: Leibovich

first: Hyung-song

last: Nam


title: Effect of Imatinib on chronic myelogenous leukemia

status: Public on Oct 10 2010

first: Markus

last: Müschen

address: 4650 Sunset Blvd

department: Childrens Hospital Los Angeles

institute: University of Southern California

summary: The Philadelphia chromosome (Ph) encodes the oncogenic BCR-ABL1 tyrosine kinase, which is present in almost every patient with chronic myeloid leukemia. In this study, the tyrosine kinase inhibitor Imatinib was used for pharmacological inhibition of BCR-ABL1. Gene expression profiles of CML cell lines were analyzed in response to Imatinib treatment.

overall_design: Three CML cell lines (KU-812, KCL-22, JURL-MK1) were either treated with 10 µM STI571 (Imatinib) for 16 hours or cultured in absence of STI571.

first: Cihangir

last: Duy

first: Christian

last: Hurtz

first: Seyedmehdi

last: Shojaee

first: Leandro

last: Cerchietti

first: Huimin

last: Geng

first: Srividya

last: Swaminathan

first: Lars

last: Klemm

first: Soo-mi

last: Kweon

first: Rahul

last: Nahar

first: Melanie

last: Braig

first: Eugene

last: Park

first: Yong-mi

last: Kim

first: Wolf-Karsten

last: Hofmann

first: Sebastian

last: Herzog

first: Hassan

last: Jumaa

first: Phillip

last: Koeffler

first: Jessica

last: Yu

first: Nora

last: Heisterkamp

first: Hong

last: Wu

first: Hilda

middle: B

last: Ye

first: Ari

last: Melnick


title: Three non-invasive protein biomarkers for solid-organ transplant rejection found through integrative genomics

status: Public on Oct 12 2010

city: Stanford

first: Li

last: Li

address: 300 pastuer dr.,

department: Pediatric

institute: Stanford University

summary: We integrated three transplant rejection microarray studies examining gene expression in samples from pediatric renal, adult renal, and adult heart transplants. We performed one study ourselves and retrieved two others from the NCBI Gene Expression Omnibus (GEO)(GSE4470 and GSE1563). We identified 45 genes that were upregulated in common in acute rejection. Half were involved in one immune-related pathway. Among ten proteins we tested by serum ELISA, three successfully distinguished acute rejection from stable transplants. These were CXCL9, PECAM1, and CD44, with areas under the receiver operating characteristic curves of 0.844, 0.802, and 0.738, respectively. Immunohistochemistry showed that the PECAM1 protein was increased in acute rejection in renal, liver and heart transplants versus normal tissues. Our results show that integrating publicly-available gene expression data sets is a fast, powerful, and cost-effective way to identify serum-detectable diagnostic biomarkers.

overall_design: For new microarray experiments, we collected 18 acute rejection (AR) and 18 stable (STA) biopsy samples from pediatric renal allograft recipients at Stanford University. Written informed consent was obtained from all the subjects. The study was approved by the Stanford University Institutional Review Board. Nucleic acids from the samples were hybridized to Affymetrix U133 Plus 2.0 microarrays. AR samples were obtained at the time of a biopsy-proven acute rejection episode according to the Banff classification (IA, IIA, IIB). Prior to including the samples in this study, the diagnosis of acute rejection was confirmed by a pathologist. STA samples were obtained from patients with stable graft function during regular post-transplantation follow-up protocol biopsies. All three data sets (pediatric renal, adult renal, and adult heart) were normalized by the quantile-quantile method using dChip software. Ten proteins in serum were measured by using commercial ELISA kits.

first: Rong

last: Chen

first: Tara

last: Sigdel

first: Neeraja

last: Kambham

first: Sue

last: Hsieh

first: Bryan

last: Klassen

first: Minnie

last: Sarwal

first: Atul

last: Butte


title: Genechip analysis of bone marrow osteoprogenitors exposed to microgravity

city: Genova (GE)

first: Massimiliano

last: Monticone

address: Largo R. Benzi, 10

country: Italy

institute: IRCCS AOU San Martino – IST, Genova

summary:
In March 2006, murine Bone Marrow Stromal Cells (BMSC) were flown in the Soyuz 12S to the International Space Station to investigate the effects of microgravity on their osteogenic potential in a three-dimensional environment. BMSC were grown in porous bioceramic Skelite disks (Φ 9 mm x T 1.2 mm). The constructs were exposed to microgravity for ca. 8 days, then fixed for RNA extraction. While the flight experiment was performed in fully automated hardware inside the KUBIK incubator, one group of control samples were incubated inside manually operated hardwares (flight control), and the other control group was incubated under routine laboratory conditions (lab control). The altered gene expression profile was analyzed by Mouse Gene 1.0 ST array (Affymetrix) representing whole-transcript coverage. Each one of the 28853 genes is represented on the array by approximately 26 probes spread across the full length of the gene, providing a more complete and more accurate picture of gene expression than the 3’ based expression array design.
A few days of microgravity were sufficient to determinate, at least at the molecular level, an effect in the BMSC; this response expressed a stress condition able to determinate consequences on several compartments and cellular functions. In particular, it seems to promote a gene expression, known to be associated with neurogenic activity (e.g. axon guidance), perhaps promoting the BMSC capability to be committed in that direction. The osteo-induction, by dexamethasone-based medium, due to the short duration of stimulation, did not have the possibility to manifest itself at the phenotypic level but only partially at the molecular level.
Keywords: gene expression array-based, count

overall_design: Comparison of microgravity effects on bone marrow stromal cells maintained both in growth and in osteo-inductive conditions.

first: Natalija

last: Pujic

first: Federico

last: Tortelli

first: Yi

last: Liu

first: Ranieri

last: Cancedda


title: Analysis of normal lung cells treated with 5-aza-dC to induce DNA demethylation

city: Baltimore

first: Chad

last: Glazer

address: 1550 Orleans St. CRB II-574

institute: Johns Hopkins Medical Institutions

summary: Analysis of 2 cultured normal lung cell lines, Normal Human Bronchial Epithelial (NHBE) and Human Small Airway Epithelial (SAEC) cells (Lonza, Walkersville, MD), following treatment with 5-aza-dC to induce DNA demethylation. These results provide insight into the role of epigenetic alterations, specifically demethylation, in differential gene expression in various lung neoplasms.

overall_design: Two normal lung cell lines, NHBE and SAEC, were treated with 5uM 5-aza deoxycytidine for 72 hours and Trichostatin A for 24 hours prior to harvesting total RNA for expression array analysis using the Affymetrix Human Genome U133 Plus 2.0 expression platform.  Signal intensity and statistical significance was established for each transcript using dChip version 2005. Two-fold increase based on the 90% confidence interval of the result and expression minus baseline >50 was used as the statistical cutoff value after 5Aza-dC and/or TSA treatment to identify upregulated candidate genes.

first: Joseph

last: Califano


title: Hdac3 is essential for the maintenance of chromatin structure and genome stability

city: Nashville

first: srividya

last: bhaskara

address: PRB room 512

department: Biochemistry

institute: Vanderbilt University

summary:
Deletion of Hdac3 impaired DNA repair and greatly reduced chromatin compaction and heterochromatin content. Liver-specific deletion of Hdac3 culminated in hepatocellular carcinoma. The loss of genomic stability and the impaired response to DNA damage suggested that a high mutation rate stimulated the development of HCC.  To begin to assess what pathways were involved in the formation of HCC, we performed gene expression analysis using cDNA microarrys.
In the array data, we noted the enhanced expression of c-Myc, a commonly over expressed oncogene and signatures consistent with activation of the Ras pathway and impairment of the p53 pathway were also identified in this analysis.

overall_design: We isolated total RNA from livers obtained from ~10 month old control (Hdac3FL/+; AlbCre+) or null (Hdac3FL/-; AlbCre+) male mice.

first: Srividya

last: Bhaskara

first: Sarah

last: Knutson

first: Guochun

last: Jiang

first: Mahesh

last: Chandrasekharan

first: Andrew

last: Wilson

first: Siyuan

last: Zheng

first: Ashwini

last: Yenamandra

first: Kimberly

last: Locke

first: Jia-ling

last: Yuan

first: Alyssa

middle: R

last: Bonine-Summers

first: Christina

last: Wells

first: Jonathan

last: Kaiser

first: Kay

last: Washington

first: Zhongming

last: Zhao

first: Florence

last: Wagner

first: Zu-Wen

last: Sun

first: Fen

last: Xia

first: Edward

last: Holson

first: Dineo

last: Khabele

first: Scott

middle: W

last: Hiebert


title: Gene expression data from FLCN-restored UOK257-2 renal cancer cells

first: Seung-Beom

last: Hong

address: 10 Center Dr.

department: National Cancer Institute

institute: National Institutes of Health

summary: UOK257 cell line was derived from a BHD patient. It harbors a germline mutation in FLCN (c.1285dupC) and LOH. UOK257-2 cells were generated from UOK257 cells by introducing wildtype FLCN using retrovirus. FLCN inactivation induces TFE3 transcriptional activity by increasing its nuclear localization. Thus expression microarray was used to identify the genes regulated by FLCN and TFE3.

overall_design: UOK257-2 cells expressing wildtype FLCN were transfected with 1) scrambled, 2) FLCN, 3) TFE3 and 4)FLCN/TFE3 siRNAs with Lipofectamine 2000 transfection reagent. Cells were harvested 3 days after transfection and RNAs were isolated using Trizol reagent and RNeasy Mini Kit. The genes induced by FLCN siRNA and reduced by TFE3 siRNA were chosen as a candidate genes regulated by FLCN and TFE3.

first: Seung

first: Baba

last: Masaya

first: Laura

last: Schmidt

first: William

last: Linehan


title: Temporal and regional regulation of gene expression by calcium-stimulated adenylyl cyclase activity during fear memory

first: Lindsay

last: Wieczorek

address: 1115 Light Hall

department: Pediatrics

summary: Mice with the two calcium-stmulated adenylyl cyclase isoforms (AC1 and AC8; DKO mice) knocked-out show conditioned fear memory deficits.  We assessed gene expression changes at baseline and several time points after conditioned fear learning to assess transcriptional changes at different stages of learning.  Transcriptional changes were assessed in the amydgdala and hippocampus of DKO and wild-type mice.

overall_design: Mice either received no treatment (baseline) or were subjected to conditioned fear training (one 0.7mA x 2 sec shock).  Amygdala and hippocampal tissue from wild-type and DKO (AC1 and AC8 KO) mice was used.  Samples were extracted at baseline (-5 min before conditioned fear training), 0 hr, 1 hr, or 48 hr after a 5 min conditioned fear training trial, or at 1 wk after a 5 min conditioned fear testing trial.  RNA samples from 5-10 mice were pooled per array with one array per genotype/brain region/time point for a total of 20 arrays.  mRNA was reverese transcribed, labeled and hybridized to Affymetric Mouse Gene ST 1.0 Arrays.

first: Louis

last: Muglia


title: Microglia in ischemic brain injury

status: Public on Oct 05 2010

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary: Microglia are resident CNS immune cells that are active sensors in healthy brain and versatile effectors under pathological conditions. Cerebral ischemia induces a robust neuroinflammatory response that includes marked changes in the gene expression and phenotypic profile of a variety of endogenous CNS cell types (astrocytes, neurons, microglia) as well as an influx of leukocytic cells (neutrophils, macrophages, T-cells) from the periphery. Many molecules and conditions can trigger a transformation of “resting” (or surveying) microglia to an “activated” (alerted/reactive) state. Here we review recent developments in the literature that relate to microglial activation in the experimental setting of in vitro and in vivo ischemia. We also present new data from our own laboratory demonstrating the direct effects of in vitro ischemic conditions on the microglial phenotype and genomic profile. Emphasis is placed on the role of specific molecular signaling systems such as hypoxia inducible factor-1 (HIF-1) and toll-like receptor-4 (TLR4) in regulating the microglial response in this setting. We then review histological and recent novel radiological data that confirms a key role for microglial activation in the setting of ischemic stroke in humans. We discuss recent progress in the pharmacological and molecular targeting of microglia in acute ischemic stroke. Finally, we explore how recent studies on ischemic preconditioning have increased interest in preemptively targeting microglial activation in order to reduce stroke severity.

overall_design: 12 arrays, 4 experimental groups, 3 replicates in each group, CN is control normoxia, CH is control hypoxia, TN is TLR4 knockout normoxia, TH is TLR4 knockout hypoxia.

first: Richard

last: Beyer

last: Weinstein

first: Ines

last: Koerner

first: Thomas

last: Möller


title: Investigation of the gene expression profile of LYVE-1-positive macrophages

status: Public on Oct 02 2010

city: Adelaide

first: Emma

last: Gordon

state: South Australia

address: Frome Road

department: Haematology

country: Australia

institute: SA Pathology

summary:
LYVE-1-positive macrophages were observed to be closely spatially associated with the developing lymphatic vasculature. The role of this population of macrophages in the embryo is uncharacterised.
We used microarray analyses to investigate which genes are differentially regulated between LYVE-1-positive and LYVE-1-negative macrophages

overall_design: Macrophage populations were isolated from cell suspensions prepared from digested embryonic day (E) 15.5 skin and prepared for RNA extraction and hybridization on Affymetrix microarrays.

first: Natasha

last: Harvey


title: Low dose human chorionic gonadotropin hCG

city: Brussel

first: Inge

last: Van Vaerenbergh

address: Laarbeeklaan 103

department: EXPA

country: Belgium

institute: Vrije Universiteit Brussel

summary:
Influence of ovarian stimulation with 200 IU of hCG, (administered in the late follicular phase among ICSI patients undergoing a GnRH-antagonist protocol), on the endometrium on the day of oocyte pick-up.
The purpose of the present study is to assess the influence of the administration of low dose hCG on the endometrium.  In addition, by analysing the correlation of the morphological pattern and gene expression profile of human endometrium on the day of oocyte retrieval in patients of both treatment groups, we want to study the implantation potential.

Keywords: gene expression analysis

overall_design: In total 10 samples from patients without pregnancy following embryo transfer were analyzed for gene expression analysis with microarrays, 5 patients from group A (rFSH group) and 5 patients from group B (hCG group) were compared

first: Christophe

last: Blockeel

first: Human

last: Fatemi

first: Michel

last: De Vos

first: Leentje

last: Van Lommel

first: Claire

last: Bourgain

first: Paul

last: Devroey


title: Expression data from WT and TCF-1-deficient memory CD8 T cells

status: Public on Oct 04 2010

city: Nutley

first: Hai-Hui

last: Xue

state: NJ

address: 111 Ideation Way

department: Center for Discovery and Innovation

institute: Hackensack University Medical Center

summary:
TCF-1 is an HMG family transcription factor which is known to be activated by the canonical Wnt signaling pathway and modulated by other signals such as those derived from T cell receptor. We found that during CD8 T cell responses, TCF-1 deficiency impaired long-term maintenance of antigen-specific memory CD8 T cells.
We used microarrays to detect gene expression changes in memory CD8 T cells caused by TCF-1 deficiency.

overall_design: Host mice that received WT or TCF-1-deficient OT-I CD8 T cells were infected with attenuated Listeria monocytogenes expressing Ova peptide. In memory phase (i.e., more than 80 days post infection), antigen-specific T cells were ioslated by cell sorting. RNA was extracted and hybridized to GeneChip Mouse GENE 1.0 ST arrays (Affymetrix).

first: Xinyuan

last: Zhou


title: Ras-Association Domain Family 1C Protein Promotes Breast Cancer Cell Migration

first: xinmin

last: Li

address: 1000 Veteran Ave

institute: UCLA

summary:
RASSF1C, unlike RASSF1A, is not a tumor suppressor, but instead may play a role in stimulating metastasis and survival in breast cancer cells
RASSF1C over-expression enhances T47D cell invasion/migration in vitro

overall_design: Three RASSF1C over-expression samples vs three controls

first: Yousef

last: Amaar

first: Xinmin


title: Lack of chemokine signaling through CXCR5  causes mortality, ventricular dilatation and  deranged matrix during pressure overload

status: Public on Oct 01 2010

city: Oslo

first: Ståle

last: Nygård

address: Institute for Experimental Medical Research, Oslo University Hospital - Ulleval

country: Norway

institute: University of Oslo

summary: Inflammatory mechanisms have been suggested to play a role in  the development of heart failure (HF), but a role for chemokines is  largely unknown. The aim of this study was to analyze the role of  the chemokine CXCL13 and its receptor CXCR5 in cardiac  pathophysiology leading to HF

overall_design: A microarray study was performed on seven mice harboring a systemic knockout of the CXCR5 (CXCR5-/-) and seven wildtype mice. Four of the knockouts and four of the wild type mice were subjected to aorta banding and three of each to sham operations.

first: Anne

last: Wæhre

first: Geir

last: Christensen


title: Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis

first: Douglas

last: Warner

address: 136 Harrison

department: Molecular Biology & Microbiology

institute: Tufts University

summary: Mutation of marA, rob, and soxS causes a clinical strain of E.coli to be attenuated at d3 post-infection in a mouse model of pyelonephritis, here we extract RNA at d2 post infection to analyze transcriptional differences between the two strains.

overall_design: In order to purify enough bacterial RNA to perform microarray, we chose a time point (day 2 post-infection) just before the triple mutant begins to decrease in bacterial load.  Mouse kidneys were extracted, homogonized, and samples were pooled in RNALater (Ambion) before extraction and analysis of the transcriptomes

first: Stuart

last: Levy


title: Gene epression profile in human BM-MSC

city: Taipei

first: Wei-Lun

last: Hwang

address: No.155, Sec.2, Linong Street

department: Department of Biotechnology and Laboratory Science in Medicine

country: Taiwan

institute: National Yang Ming Chiao Tung University

summary: Gene expression profiles of human BM-MSC isolated form normal donor to elucidate potential molecular network for clinical application

overall_design: Fresh isolated BM-MSC cells were cultured on defined condition. Functional assay was performed prior to gene expression analysis

first: Tse-Shun

last: Huang

first: Jui-Yu

last: Hsieh

first: Hsei-Wei

last: Wang


title: Effect of Growth hormone on podocytes

city: Ann Arbor

first: Ram

last: Menon

state: MI

address: 1500 East Medical Center Drive, D1205 MPB

department: Pediatric Endocrinology

institute: University of Michigan

summary: Transcriptome analysis of growth hormone dependant genes in glomerular podocytes

overall_design: Differentiated human glomerular podocytes in culture exposed to growth hormone for 0 min, 2 min, 5 min, 15 min, and 30 min. Total RNA is extracted and subjected to microarray analysis.

middle: K

first: Prapai

last: Dejkhamron

first: Kateryna

last: Kotlyarevska

first: Chunxia

last: Lu

first: Pasupulati

last: Kumar


title: Expression data of MMTV-PyMT mice mammary tumor with or without JAM-A

city: Milano

first: gabriele

last: bucci

address: via olgettina 58

department: CTGB

institute: IRCCS Ospedale San Raffaele

summary: Junction Adhesion Molecule-A (JAM-A) is present on leukocytes and platelets where it promotes cell adhesion and motility. We are interested in an interaction between JAM-A and tumor progression/metastases. To address this point, we mated JAM-A-/- mice and mouse mammary tumor model MMTV-PyMT mice which, which express polyoma middle T antigen under the control of mouse mammary tumor virus. MMTV-PyMT mice show 100% penetration of mammary tumor and highly metastases to lung. MMTV-PyMT mice without JAM-A show less primary tumor progression, therefore JAM-A enhance primary tumor progression. Then we are addressing the molecular mechanism of this phenomenon by in vivo. Furthermore, we would like to examine JAM-A deficient MMTV tumor signature.

overall_design: Each 3 MMTV-PyMT JAm-A+/+ (JamA+) and 3 MMTV JAM-A-/- (JamA-) mammary tumor were resected at early stages of tumor development for RNA extraction and hybridization on Affymetrix microarrays.

first: Masato

last: Murakami


title: Transcript variation in C57BL/6J mice under normal laboratory conditions

city: Bar Harbor

first: Peter

middle: Thomas

last: Vedell

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

summary:
BACKGROUND: The transcript levels of many genes exhibit significant variation in tissue samples from inbred laboratory mice. A microarray experiment was designed to separate transcript abundance variation across samples from adipose, heart, kidney, and liver tissues of C57BL/6J mice into within-mouse and between-mouse components. Within-mouse variance captures variation due to heterogeneity of gene expression within tissues, RNA-extraction, and array processing. Between-mouse variance reflects differences in transcript levels between these genetically identical mice. Many biological sources can contribute to heterogeneous transcript levels within a tissue sample including inherent stochasticity of biochemical processes such as intrinsic and extrinsic noise within cells and differences in cell-type composition which can result from heterogeneity of stem and progenitor cell populations. Differences in global signaling patterns between individuals and micro-environmental influences such as interactions with pathogens and cage mates can also contribute to variation, but are likely to contribute more to the between-mouse variance component.
RESULTS: The nature and extent of transcript abundance variation differs across tissues. Adipose has the largest total variance and the largest within-mouse variance.  Liver has the smallest total variance, but it has the most between-mouse variation. Genes with high variability can be classified into groups with correlated patterns of expression that are enriched for specific biological functions. Variation between mice is associated with circadian rhythm, growth hormone signaling, immune response, androgen regulation, lipid metabolism, and the extracellular matrix. Genes showing correlated patterns of within mouse variation were also associated with biological functions, spatial connectivity of stochastic variation and heterogeneity of cell types within tissues.
CONCLUSIONS: Genetically identical mice are individuals and they can experience different outcomes for medically important traits. This is reflected in the stochastic variation in gene expression observed between genetically identical mice. Much of the stochasticity has organismal, tissue, or spatial connectivity. Prior knowledge of the genes and functional classes of genes that are likely to vary in the absence of experimental perturbations, whether these are genetic or environmental, can inform experimental design decisions and the interpretation of gene expression data. Variation in gene expression in genetically identical mice sheds light on the impact of stochastic and micro-environmental factors and their phenotypic consequences.

overall_design:
Four tissues were sampled from twelve 10-week old male mice.  Six pairs of siblings were co-housed from weaning under uniform environmental conditions.  From each mouse we obtained duplicate samples of adipose (inguinal fat pad), heart, kidney, and liver tissues by splitting whole organs or tissues prior to homogenization and RNA extraction. Adipose, heart, and liver tissues were coarsely cut into pieces and divided into two samples that were homogenized separately prior to RNA extraction.  The left and right kidneys were processed separately. This sampling design allows us to partition the variance for each gene into within-mouse and between-mouse components, with a division line that corresponds to the step of splitting tissues.

[Stochastic Variation of Transcript Abundance in C57BL/6J Mice]: The liver tissues were sampled from twelve 10-week old male mice.  Six pairs of siblings were co-housed from weaning under uniform environmental conditions.  From each mouse we obtained duplicate samples by splitting whole organs or tissues prior to homogenization and RNA extraction. Each whole tissue was coarsely cut into pieces and divided into two samples that were homogenized separately prior to RNA extraction.  This sampling design allows us to partition the variance for each gene into within-mouse and between-mouse components, with a division line that corresponds to the step of splitting tissues.

middle: T

first: Karen

middle: L

last: Svenson

first: Gary

last: Churchill


title: The lymph node microenvironment promotes B-cell receptor signaling, NF-κB activation, and tumor proliferation in chronic lymphocytic leukemia (CLL)

city: Bethesda

first: Adrian

last: Wiestner

address: 10 Center Dr

department: Hematology Branch

institute: NHLBI/NIH

summary:
To elucidate effects of tumor host interactions in vivo in CLL, purified tumor cells were obtained concurrently from blood, bone marrow and/or lymph node and analyzed by gene expression profiling.

Keywords: RNA

overall_design: Comparision of gene expression  profiling in matched pairs of peripheral blood (PB) vs.  bone marrow (BM) or lymph nodes (LN) derived CLL cells

first: Yair

last: Herishanu

first: Delong

last: Liu


title: Comparison of gene expression profiles between paired primary and metastasis colorectal carcinoma

status: Public on Oct 06 2010

first: Chan-Yen

last: Tsai

institute: Yang-Ming University

summary: Paired tissues (normal colon, primary colorectal carcinoma, normal liver, liver metastasis of colorectal carcinoma) from 2 colorectal carcinoma patients in Taiwan were processed to generate total RNA, which was subsequently analyzed for gene expression using Affymetrix U133 plus 2.0 arrays.

overall_design: Comparison of gene expression profiles between paired normal colon and primary colorectal carcinoma;  between primary colorectal carcinoma and liver metastasis colorectal carcinoma


title: Gene expression data from stage IV melanoma patients

city: Rochester

first: Alexey

middle: Aleksandrovich

last: Leontovich

state: MN

address: 200 First street

department: Health Science Research

institute: Mayo Clinic

summary: In this study we tested the hypothesis that pregnancy, a physiologic condition of transient, organ system-based immune evasion, can integrate known and identify new mechanisms of immune modulation pertinent to metastatic melanoma.

overall_design: Total RNA was extracted from tissue samples of frozen melanoma tumor biopsies.

first: Shernan

middle: G

last: Holtan

first: Aaron

last: Mansfield

middle: A

first: Vera

last: Suman

first: Douglas

last: Creedon

first: Lori

last: Erickson

first: Svetomir

last: Markovic


title: Highly efficient reprogramming to pluripotency and directed differentiation using synthetic mRNA

status: Public on Sep 30 2010

city: Boston

first: Hu

last: Li

state: MA

address: 3 Blackfan Circle

institute: Wyss Institute

summary: Clinical application of induced pluripotent stem (iPS) cells is limited by low efficiency of iPS derivation, and protocols that permanently modify the genome to effect cellular reprogramming. Moreover, safe and effective means of directing the fate of patient-specific iPS cells towards clinically useful cell types are lacking. Here we describe a simple, non-mutagenic strategy for reprogramming cell fate based on administration of synthetic mRNA modified to overcome innate anti-viral responses. We show that this approach can reprogram multiple human cell types to pluripotency with efficiencies that greatly surpass established protocols. We further show that the same technology can be used to efficiently direct the differentiation of RNA-induced pluripotent stem (RiPS) cells into terminally differentiated myogenic cells. Our method represents a safe, efficient strategy for somatic cell reprogramming and directing cell fates that has broad applicability for basic research, disease modeling and regenerative medicine.

overall_design: We isolated RNA from human RNA derived iPS cells, viral derived iPS cells, different human fibroblasts and human embryonic stem cells for hybridization to the Affymetrix gene expression microarrays.

first: Derrick

last: Rossi

first: James

last: Collins


title: Transcriptional Profiling of B19 Virus Nonstructure Protein (NS1) transduced CD36+ Erythoid Progenitor Cells (EPCs)

status: Public on Nov 03 2010

first: Ning

last: zhi

address: 9000 Rockville Pike

department: hematology

institute: NIH

summary:
B19V NS1 is known to be cytotoxic and involved in the pathogenesis of B19V infection. Our previous data demonstrated that NS1 impaired the cell-cycle progression of the CD36+ EPCs by inducing a stable G2 arrest. Microarray analysis was used to identify genes whose expressions were associated with the NS1-induced G2 arrest. A total of 1045 genes displayed a  more than 1.5-fold differential expression in the NS1-transduced cells. Out of 1045 differentially expressed genes, 177 were involved in cell-cycle regulation and 51 were involved in the regulation of cell differentiation.

Keywords: RNA

overall_design: CD36+ EPCs were generated from CD34+ stem cells, and transduced with B19V NS1 or control-lentivirus for 12, 24,and 48 hours. Each sample has triplicates. There are 18 samples analyzed.

last: Zhi

first: Zhihong

last: Wan

first: Neal

last: Young


title: Identification of miR-145 targets involved in colon cancer

city: Coepnhagen N

first: Lea

middle: Haarup

last: Gregersen

address: Ole Maaloes vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

summary: MicroRNAs (miRNAs) have emerged as important gene regulators and are recognized as key players in tumorigenesis. miR-145 is reported to be down-regulated in several cancers, but knowledge of its targets in colon cancer remains limited. To investigate the role of miR-145 in colon cancer, we have employed a microarray based approach to identify miR-145 targets. Based on seed site enrichment analyses and unbiased word analyses, we found a significant enrichment of miRNA binding sites in the 3’-untranslated regions (UTRs) of transcripts down-regulated upon miRNA overexpression, which represent potential miR-145 targets. Gene Ontology analysis showed an overrepresentation of genes involved in cell death, gene expression, cancer, cell cycle, DNA replication, recombination and repair. A number of the identified miRNA targets have previously been implicated in cancer, including YES, FSCN1, ADAM17, BIRC2, VANGL1 as well as the transcription factor STAT1. Both YES and STAT1 were verified as direct miR-145 targets based on 3’UTR luciferase assays and western blots for endogenous proteins.

overall_design: DLD-1 cells were transfected with 50 nM miR-145 duplex or mock transfected. Total RNA was harvested 24 hours post-transfection and analyzed on Affymetrix HG-U133 Plus 2.0 human arrays.

first: L

middle: H

first: A

last: Jacobsen

last: Frankel

first: J

last: Wen

last: Krogh

last: Lund


title: Differential gene expression between human Cord blood transduced with HPIP-wt, mutant NRPID and control YFP

city: Muenchen

first: Pawandeep

last: Kaur

state: Bavaria

address: Marchioninstrasse 25

department: Hematology

institute: Helmholtz-Muenchen

summary: Background  Homeobox gene associated regulatory networks are among the key determinants of early hematopoietic development. Previously, the ‘hematopoietic PBX interacting protein’ (HPIP) has been identified as a novel interacting partner of the TALE homeodomain protein PBX1, forming a microtubule signalling complex. Expression of HPIP has been associated with increased tumorigenicity of the MCF7 breast cancer cell line. We now demonstrate that HPIP is a novel regulatory protein in human hematopoiesis: constitutive expression of HPIP in human umbilical cord blood derived CD34+ cells increased the absolute number of clonogenic progenitors in liquid expansion culture as well as in methylcellulose assays with a significantly enhanced formation of erythroid colonies compared to the control (p≤0.01, n=6). Limiting dilution LTC-IC assays confirmed the hematopoietic activity of the protein on primitive human progenitor cells with an over 5fold increase in the absolute number of LTC-ICs compared to non-transduced cells (n=8; p<0.05). In vivo HPIP expression induced a significant shift towards myeloid engraftment (n=8;p<0.05) and doubled the proportion of hCD34+CD38+ human cells in transplanted mice (p≤0.05, n=8). Structure – function analyses identified the C - terminal nuclear receptor/PBX interacting domain (NRPID; LXXLL domain) as a critical domain for the hematopoietic activity of HPIP. Gene expression data by microarray and Q-RT-PCR analysis demonstrated that HPIP induced particularly differential expression of genes involved in the MAPK pathway and cytokine-cytokine interaction. Taken together, these data demonstrate that proteins involved in the organization of microtubular signalling complexes such as HPIP can act as regulators of early human hematopoiesis.

overall_design: Stable PG13 packaging cell lines were used to perform transductions of human umbilical cord blood derived CD34+ cells. Phoenix amphotropic cells were used for transient transduction of PG13 with wt and ∆NRPID mutant viruses. Both cell lines were cultured in DMEM with 10% fetal bovine serum and plated on corning dishes for transfections and transient transduction ( 2.5 x 106 cells per 10 cm plate) a day prior to the experiment. Transient transductions were performed as described before in literature. Briefly, cells at 2x10e5/mL were prestimulated for 48 hours in Iscove´s IMDM( GIBCO-Invitrogen, Karlsruhe, Germany) containing a serum substitute (BITTM, Stem Cell Technologies), 10-4M β mercaptoethanol (Sigma-Aldrich, Taufkirchen, Germany), supplemented with the following recombinant human cytokines: 100 ng/mL Flt-3 Ligand, 100 ng/mL SF, 20 ng/mL IL-3, 20 ng/mL G-CSF, and 20 ng/mL IL-6 (Immunotools, Friesoythe, Germany). After 48 Hours, cells were resuspended in filtered virus-containing medium (VCM) supplemented with the same five cytokine cocktail and polybrene (5 µg/mL) on tissue culture dishes (Corning). The dishes were pre-loaded with VCM twice, each time for 45 mins. The procedure was repeated for a total of three infections.   Fresh RNA was prepared using RNA easy micro kit (Sigma) with ≤ 2x105 retrovirally transduced human cord blood CD34+HPIP-WT-YFP+, CD34+∆NRPID-HPIP-YFP+ or CD34+YFP+ cells. Total RNA was reverse transcribed (Superscript II, Invitrogen) by using oligo (dT) to prime cDNA synthesis. In vitro transcription was performed using a the GeneChip® Two-Cycle cDNA Synthesis Kit, uniquely configured and tested for GeneChip® target labeling. Two cycles of double-stranded cDNA synthesis containing the T7 promoter sequence were performed from 10 to 100 ng of total RNA using this Kit.


title: Transcriptome analysis of pancreatic cancer cell line that differ in metastatic potential

city: Munich

first: Stefan

last: Krebs

address: Feodor-Lynen-Str. 25

department: Gene Center

institute: Ludwig-Maximilian University

summary:
Two pancreatic cancer cell lines with different metastatic and growth potential were compared under hypoxic conditions and under normal atmospheric oxygen pressure. The FG cell lines shows very few metastases and slow growth in mouse xenograft models. L3.6pl, derived from FG by cycles re-implantation of metastatic cells obtained after orthotopic tumor growth in nude mice, shows high motility, aggressive growth and very high metastatic potential
By comparison of the two cell lines under different oxygen concentration we tried to simulate in vivo conditions of tumors at different growth stages. Differentially expressed genes and transcription factor regulating coexpressed genes identified by SOTA clustering were used to identify key genes that define metastatic potential of pancreatic cancer cells
Keywords: 2+2 factorial design

overall_design: 12 samples, two cell lines * two culture conditions(oxygen pressure) * three replicates

first: S

first: C

last: Bruns

last: Thieme

first: H

last: Blum

first: Peter

last: Camaj


title: Expression profiling of human adipose stromal cell (hASC) adipogenesis

city: Cambridge

first: Tarjei

last: Mikkelsen

address: 7 Cambridge Center

institute: Broad Institute

summary: Human abdominal adipose tissue was obtained with informed consent from a 33-year old Caucasian female (BMI = 32.96 Kg/m2) undergoing lipoaspiration. Adipose stromal cells (hASCs) were isolated and differentiated into adipocytes in vitro.

overall_design: Two technical replicates from 9 time points realtive to induction of adipogenesis (day 0). Also, two technical replicated from pre-adipocytes (day -2) grown without FGF. Two individual replicates (day 1 and day 7) were removed due to failed hybridizations.

first: Zhao

last: Xu

first: Jeffery

last: Gimble

first: Eric

last: Lander

first: Evan

middle: D

last: Rosen


title: Identification of molecular mechanisms involved in pathogenesis of MALT lymphoma from small sample size

city: London

first: Rifat

last: Hamoudi

address: 67-73 Riding House Street

department: Surgery

institute: University College London

overall_design: MALT lymphoma is characterized by t(11;18)(q21;q21)/API2-MALT1, t(1;14)(p22;q32)/BCL10-IGH and t(14;18)(q32;q21)/IGH-MALT1, which commonly activate the NF-κB pathway. Gastric MALT lymphomas harboring such translocation do not respond to H. pylori eradication, while those without translocation can be cured by antibiotics. To understand the molecular mechanism of these different MALT lymphoma subgroups, we performed gene expression profiling analysis of 24 MALT lymphomas (15 translocation-positive, 9 translocation-negative). Gene set enrichment analysis (GSEA) of the NF-κB target genes and 4394 additional gene sets covering various cellular pathways, biological processes and molecular functions showed that translocation-positive MALT lymphomas are characterized by an enhanced expression of NF-κB target genes, particularly TLR6, CCR2, CD69 and BCL2, while translocation-negative cases were featured by active inflammatory and immune responses, such as IL8, CD86, CD28 and ICOS.MALT lymphoma is characterized by t(11;18)(q21;q21)/API2-MALT1, t(1;14)(p22;q32)/BCL10-IGH and t(14;18)(q32;q21)/IGH-MALT1, which commonly activate the NF-κB pathway. Gastric MALT lymphomas harboring such translocation do not respond to H. pylori eradication, while those without translocation can be cured by antibiotics. To understand the molecular mechanism of these different MALT lymphoma subgroups, we performed gene expression profiling analysis of 24 MALT lymphomas (15 translocation-positive, 9 translocation-negative). Gene set enrichment analysis (GSEA) of the NF-κB target genes and 4394 additional gene sets covering various cellular pathways, biological processes and molecular functions showed that translocation-positive MALT lymphomas are characterized by an enhanced expression of NF-κB target genes, particularly TLR6, CCR2, CD69 and BCL2, while translocation-negative cases were featured by active inflammatory and immune responses, such as IL8, CD86, CD28 and ICOS.

first: Ming

middle: Q

last: Du