title: Effect of IL-1β on mesenchymal stem cells

status: Public on Jun 22 2012

city: Valencia

first: Francisco

middle: García

last: García

address: Eduardo Primo Yúfera, 3

institute: CIPF

summary: Mesenchymal stem cells are often transplanted in inflammatory environments and they are able to survive and modulate host immune responses through mechanism poorly understood. In this paper we analyzed biological responses of MSC in response IL-1β as a representative inflammatory mediator. Microarray analysis of MSC treated with IL-1β revealed that this cytokine activates a set of biological process related with cell survival, cell migration, cell adhesion, chemokine production, induction of angiogenesis and modulation of immune response. Further analysis by real-time PCR and functional assays revealed that IL-1β mainly increases production of chemokines CCL5, CCL20, CXCL1, CXCL3, CXCL5, CXCL6, CXCL10, CXCL11 and CX3CL1, interleukins IL-6, IL-8, IL23A, IL32, Toll-like receptors TLR2, TLR4, CLDN1, metalloproteins MMP1 and MMP3, growth factors CSF2 and TNF, together with adhesion molecules ICAM1 and ICAM4. Functional analysis of MSC proliferation, migration and adhesion to extracellular matrix components revealed that IL-1β did not affect proliferation whereas constitute a throphic factor for MSC and increases adhesion mainly to collagen and laminin. Moreover, IL-1β treatment enhanced the ability of MSC to recruit monocytes and granulocytes cells in vitro. Blockade of NFkβ transcription factor activation with IκB kinase beta (IKKb) siRNA impaired MSC migration, adhesion and leucocyte recruitment, indicating that NF-kB signaling pathway is the main mechanism implicated in these biological processes. These findings are relevant for designing protocols that implicate MSC delivery into inflammatory environments.

overall_design: Comparison between two experimental conditions, one sample for each condition

first: Carrero

last: Rubén

first: Cerrada

last: Inmaculada

first: Lledó

last: Elisa

first: Dopazo

last: Joaquín

first: García-García

last: Francisco

first: Rubio

last: Paz

first: Trigueros

last: César

first: Dorronsoro

last: Akaitz

first: Ruiz-Sauri

last: Amparo

first: Montero

last: Anastasio

first: Sepúlveda

last: Pilar


title: Gene expression signatures in anti-FGFR2IIIc monoclonal antibody-treated human colorectal cancer cells

status: Public on Jun 08 2012

city: Tokyo

first: Yoko

last: Matsuda

address: 1-1-5, Sendagi, Bunkyo-ku

department: Department of Pathology

country: Japan

institute: Nippon Medical School

summary: To investigate the underlying mechanisms of the inhibitory effects of human anti-human FGFR2IIIc antibody on growth and migration of colorectal cancer cells, we used DNA microarray analysis to examine the cell signaling pathway alterations following the administration of anti-FGFR2IIIc antibody.

overall_design: Cells were plated at a density of 2.5 × 105 cells in a 60-mm dish, and grown overnight. Then 100 μg/mL of monoclonal anti-human FGFR2IIIc antibody was added in each dish. For control groups, an equal amount of anti-GFP antibody was added in another dish. After 48 hr, total RNA was isolated from cells. For use in DNA microarray analysis, 50 ng RNA from each group of cells was labeled using the Low Input Quick Amp Labeling kit. Labeled RNA was further purified using the Qiagen RNeasy Mini kit. Labeled cRNA was hybridized to the Agilent human 44k oligonucleotide microarray, and washed using Agilent Gene Expression washing buffer.

first: Toshiyuki

last: Ishiwata


title: Tumor-derived Tissue Factor Activates Coagulation and Enhances Thrombosis in a Mouse Xenograft Model of Human Pancreatic Cancer

status: Public on Jul 12 2012

city: Chapel Hill

first: Jen Jen

last: Yeh

state: NC

address: LCCC, 450 West Drive

department: Surgical Oncology

country: USA

institute: University of North Carolina at Chapel Hill

summary: Cancer patients often have an activated clotting system and are at increased risk for venous thrombosis. In this study, we analyzed tissue factor (TF) expression in four different human pancreatic tumor cell lines for the purpose of producing derivative tumors in vivo. We found that two of the lines expressed TF and released TF-positive microparticles (MPs) into the culture medium. The majority of TF protein in the culture medium was associated with MPs. Importantly, only TF-positive cell lines activated coagulation in nude mice, and this activation was abolished by an anti-human TF antibody. Of the two TF-positive lines only one produced detectable levels of human MP TF activity in the plasma when grown orthotopically in nude mice.  Surprisingly, <5% of human TF protein in plasma from tumor-bearing mice was associated with MPs. Mice with TF-positive tumors and elevated levels of circulating TF-positive MPs had increased thrombosis in a saphenous vein model. In contrast, we observed no difference in thrombus weight between tumor bearing and control mice in an inferior vena cava stenosis model. Our studies suggest that in a xenograft mouse model tumor TF activates coagulation, whereas TF on circulating MPs may trigger venous thrombosis.

overall_design: 8 human tumor pancreatic cell lines

first: Jian-Guo

last: Wang

first: Jen-Jen

first: Nigel

last: Mackman


title: Gene expression networks in COPD: microRNA and mRNA regulation

status: Public on Jun 27 2012

city: Seattle

first: Ji-Hoon

last: Cho

state: WA

address: 401 Terry Avenue North

institute: Institute for Systems Biology

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

summary: 70 miRNAs and 2667 mRNAs were differentially expressed between lung tissue from subjects with COPD and smokers without COPD. miRNA and mRNA expression profiles enriched for biological pathways that may be relevant to the pathogenesis of COPD including the transforming growth factor b, Wnt and focal adhesion pathways. miR-223 and miR-1274a were the most affected miRNAs in subjects with COPD compared with smokers without obstruction. miR-15b was increased in COPD samples compared with smokers without obstruction and localised to both areas of emphysema and fibrosis. miR-15b was differentially expressed within GOLD classes of COPD. Expression of SMAD7, which was validated as a target for miR-15b, was decreased in bronchial epithelial cells in COPD.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Lung tissue from smokers with no evidence of obstructive lung disease and smokers with COPD was examined for miRNA and mRNA expression followed by validation. We then examined both miRNA and mRNA expression to enrich for relevant biological pathways

first: Michael

middle: E

last: Ezzie

first: Melissa

last: Crawford

first: Robert

last: Orellana

first: Shile

last: Zhang

first: Richard

last: Gelinas

first: Kara

last: Batte

first: Lianbo

last: Yu

first: Gerard

last: Nuovo

first: David

last: Galas

first: Philip

last: Diaz

first: Kai

first: Patrick

last: Nana-Sinkam


title: DCK is frequently inactivated in acquired gemcitabine-resistant human cancer cells.

status: Public on May 09 2012

city: Sendai

first: yuriko

last: saiki

state: Miyagi

address: 2-1 Seiryo-machi, Aoba-ku

department: Molecular Pathology

institute: Tohoku University School of Medicine

summary: We examined the microarray-based expression profiles of the cells to identify genes associated with gemcitabine resistance

overall_design: Using three set of parental and resistant cell lines, PK-9 and RPK-9, PK-1 and RPK-1, and PK-59 and RPK-59, we studied mRNA transcription levels by microarray analysis to see if there are any of the key molecules for development of acquisition of the GEM resistance.

first: Yuriko

last: Saiki

first: Akira

last: Horii


title: A Key Role for Chd1 in Histone H3 Dynamics at the 3' Ends of Long Genes in Yeast (Rpb3 to input)

city: Santa Cruz

first: Grant

middle: A

last: Hartzog

state: CA

address: 349 Sinsheimer Labs

department: MCD Biology

institute: UC Santa Cruz

type: Genome binding/occupancy profiling by array

summary: Chd proteins are ATP-dependent chromatin remodeling enzymes implicated in biological functions from transcriptional elongation to control of pluripotency. Here, we examine roles of Chd1 in replication- independent dynamics of histone H3 in yeast.  Using genome-wide ChIP on chip analysis, we find that Chd1 influences histone turnover at the 5’ and 3’ ends of genes, accelerating H3 replacement at the 5’ ends of genes while protecting the 3’ ends of genes from excessive H3 turnover. Although consistent with a direct role for Chd1 in exchange, these results may indicate that Chd1 stabilizes nucleosomes perturbed by transcription. Curiously, we observe a strong effect of gene length on Chd1’s effects on H3 turnover. Finally, we show that Chd1 also affects histone H3K4 and H3K36 methylation patterns over genes, likely as a consequence of its effects on histone replacement. In control experiments, we measure effects of deletion of CHD1 on RNA polymerase II distribution across the genome and on gene expression.  We also examine the effect of deleting the TOP1 gene, alone and in combination with deletion of CHD1, on histone replacement.  Taken together, our results emphasize a role for Chd1 in histone replacement in both budding yeast and Drosophila, and surprisingly show that the major effects of Chd1 on turnover occur at the 3’ ends of genes.

overall_design: ChIP on chip experiments, compare IP to input, with dye-flips, comparing distribution of RNA polymerase II in chd1 deletion to wild type cells.

first: Marta

last: Radman-Livaja

first: Tiffani

middle: K

last: Quan

first: Lourdes

last: Valenzuela

first: Jennifer

last: Armstrong

first: Tibor

last: van Welsem

first: TaeSoo

last: Kim

first: Laura

middle: J

last: Lee

first: Stephen

last: Buratowski

first: Fred

last: van Leeuwen

first: Oliver

last: Rando


title: A Key Role for Chd1 in Histone H3 Dynamics at the 3' Ends of Long Genes in Yeast (H3K4me3 or H3K36me3 to input)

overall_design: ChIP on chip experiments, comparing IP to input.


title: The unique role of GATA1s in Down syndrome acute megakaryocytic leukemia biology and therapy

status: Public on Jun 01 2012

city: Detroit

first: Yubin

last: Ge

state: MI

address: 110 East Warren Ave.

institute: Karmanos Cancer Institute

summary: Microarray gene expression profiling of lentivirus shRNA knockdown of the GATA1 gene in a DS AMkL cell line, CMK (harbors a mutated GATA1 gene and only expresses GATA1s).

overall_design: Cell culture samples from two CMK clones (CMK-5a and CMK-5b) were compared against a negative control infection sample (CMK-neg). Two dye-swap microarrays were completed for each clone.

first: Alan

last: Dombkowski

first: Jeffrey

last: Taub


title: A Key Role for Chd1 in Histone H3 Dynamics at the 3' Ends of Long Genes in Yeast

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

overall_design: Refer to individual Series


title: Molecular events in endometrial carcinosarcomas and the role of high mobility group AT-hook 2 in endometrial carcinogenesis.

status: Public on Nov 01 2012

city: Madrid

first: Gema

last: Moreno-Bueno

state: Madrid

address: Arturo Duperier

department: Biochemistry

country: Spain

institute: IIB

summary: The molecular events implicated in the development of endometrial carcinosarcoma remain poorly understood. Using complementary DNA microarrays, we analyzed a group of 15 endometrial carcinosarcomas and compared their gene expression profiles with those obtained from a group of 23 endometrioid endometrial carcinomas. We demonstrated changes in the expression of genes modulating processes such as the epithelial to mesenchymal transition, muscle differentiation, the expression of cancer/testis antigens, and immune response in endometrial carcinosarcomas. The high mobility group AT-hook 2 gene is an embryonic nuclear factor that mediates epithelial to mesenchymal transition in various tumor models, and it was among the genes overexpressed in endometrial carcinosarcomas. High mobility group AT-hook 2 overexpression was confirmed in 54% of endometrial carcinosarcomas by quantitative real time-polymerase chain reaction and immunohistochemistry. Moreover, we found a significant inverse correlation between the expression of high mobility group AT-hook 2 and let-7b, a member of the let-7 family of microRNAs that represses high mobility group AT-hook 2 expression. These changes were also associated with overexpression of Lin28B, a suppressor of microRNA biogenesis that is implicated in cancer progression and metastasis. Finally, high mobility group AT-hook 2 overexpression, which was detected in less than 3% of endometrioid endometrial carcinomas, was observed in many nonendometrioid carcinomas (46% of 28 samples). This pattern of expression, restricted to nonendometrioid carcinomas and endometrial carcinosarcomas, reflects a role for high mobility group AT-hook 2 in endometrial carcinogenesis that is associated with aggressive phenotypes and points to its potential use as a marker to distinguish between endometrioid and nonendometrioid tumors.

overall_design: 15 endometrial carcinosarcomas and 23 endometrioid endometrial carcinoma

first: L

last: Romero-Pérez

first: M

last: Castilla

last: López-García

first: J

last: Díaz-Martín

last: Biscuola

first: S

last: Ramiro-Fuentes

first: E

last: Oliva

first: X

last: Matias-Guiu

last: Prat

first: A

last: Cano

first: G

last: Palacios


title: Epidermolysis bullosa associated cutaneous SCC fibroblast expression profiling

status: Public on May 16 2012

city: Dundee

first: Andrew

last: South

address: Ninewells Hopsital and Medical School

department: Division of Cancer Research

country: United Kingdom

institute: University of Dundee

summary: Patients with the genetic skin blistering disease recessive dystrophic epidermolysis bullosa (RDEB) develop aggressive cutaneous squamous cell carcinoma (cSCC). Metastasis leading to mortality is greater in RDEB than in other patient groups with cSCC. Here we investigate the dermal component in RDEB using mRNA expression profiling to compare cultured fibroblasts isolated from individuals without cSCC and directly from tumor matrix in RDEB and non-RDEB samples. While gene expression of RDEB normal skin fibroblasts resembled that of cancer-associated fibroblasts, RDEB cancer-associated fibroblasts exhibited a distinct and divergent gene expression profile, with a large proportion of the differentially expressed genes involved in matrix and cell adhesion. RDEB cancer-associated fibroblasts conferred increased adhesion and invasion to tumor and non-tumor keratinocytes. Reduction of COL7A1, the defective gene in RDEB, in normal dermal fibroblasts led to increased type XII collagen, thrombospondin-1 and Wnt-5A, while re-expression of wild type COL7A1 in RDEB fibroblasts decreased type XII collagen, thrombospondin- 1, and Wnt-5A expression, reduced tumor cell invasion in organotypic culture, and restricted tumor growth in vivo. Overall our findings demonstrate that matrix composition in patients with RDEB is a permissive environment for tumor development, and type VII collagen directly regulates the composition of matrix proteins secreted by dermal and cancer-associated fibroblasts.

overall_design: 16 samples

middle: P

first: Yi

middle: Z

last: Ng


title: Differential Gene Expression between African American and European American Colorectal Cancer Patients

status: Public on May 23 2012

first: Felix

last: Araujo-Perez

address: 103 Mason Farm Road-MBRB 7336

institute: University of North Carolina

summary: The incidence and mortality of colorectal cancer (CRC) is higher in African Americans (AAs) than in other ethnic groups in the U. S., but reasons for the disparities are unknown. We performed gene expression profiling and microsatellite instability (MSI) analysis of sporadic CRCs from AAs vs. European Americans (EAs) to assess the contribution to CRC disparities. We evaluated gene expression of 43 AA and 43 EA CRC tumors matched by stage and 40 normal colon tissues using the Agilent human whole genome 4x44K cDNA arrays. Gene and pathway analysis were performed using Significance Analysis of Microarrays (SAM), 10-fold Cross Validation (10-fCV) and Ingenuity Pathway Analysis (IPA). MSI analysis was assessed with five NIH Bethesda markers. SAM revealed that 95 genes were differentially expressed between AA and EA patients at a false discovery rate of <5%. A 10f-CV demonstrated that 9 genes were differentially expressed between  AA and EA with an accuracy of 97%. Nine genes (CRYBB2, PSPH, ADAL, VSIG10L, C17orf81, ARSE, ANKRD36B, ZNF835, ARHGAP6) were validated and differential expression confirmed by qRT-PCR in independent test set of 21 patients (10 AA, 11 EA). We also analyzed MSI in 57 of the CRC subjects. Overall, 15.8% of CRC patients had MSI, with a higher rate observed in EA (20%) than  in AA (12%). MSI distribution by tumor site was 77% right and 23% left colon. Previously, genetic, epigenetic and environmental factors have been implicated in the etiology of CRC. Our results are the first to implicate differential gene expression in CRC disparities and support the existence of distinct tumor microenvironments in these two patients' populations.

overall_design: 126 total samples: 1) 43 white cancer samples; 2) 43  black cancer samples; 3)  27 white control samples; 4) 13 black control samples.

first: Biljana

last: Jovov

first: Temitope

last: Keku


title: Whole genome analysis regulation in HepG2 cells exposed to cadmium

status: Public on May 01 2012

city: Ispra (VA)

first: marco

last: fabbri

address: Via E. Fermi, 2749

department: Institute for Health and Consumer Protection

country: Italy

institute: European Commission - Joint Research Centre

summary: Cadmium (Cd) is a metal present in working and living environments known to be toxic and carcinogenic, but its mechanism of action remains still unclear.  We investigated the gene expression modulation in human hepatoma cell line HepG2 after exposure to 2 µm and 10 µm cadmium using Agilent Whole human genome expression microarray.

overall_design: HepG2 cells were treated for 24 hours with 2 μM and 10 μM Cd and normal medium as control. Three independent replicates were used for the each type of stimuli.

first: Fabbri

last: Marco

first: Urani

last: Chaiara

first: Sacco

last: Maria Grazia

first: Procaccianti

last: Claudio

first: Gribaldo

last: Laura


title: Gene expression profiling in Tie-2-Etv2 endothelial and/or hematopoietic precursors

status: Public on May 10 2012

city: Kobe

first: Hiroshi

last: Kataoka

state: Hyogo

address: 2-2-3 Minatojima-minamimachi, Chuo-ku

department: Stem Cell Biology

institute: Riken Center for Developmental Biology

summary: Etv2 transgene was expressed from ROSA26 locus by removing floxed STOP cassette by Tie-2 Cre transgene. VE-Cad+/CD45= or VE-Cad+/CD45+ cells were sorted from control or tie-2-Etv2 E11.5 embryos (YS;yolk sac and Emb;embryo proper)and compared for gene expression in duplicate.

overall_design:
Sample ID
#1 VECAD+CD45-P3;Emb;Control
#2 VECAD+CD45-P3;Emb;Tg
#3 VECAD+CD45+P4;Emb;Control
#4 VECAD+CD45+P4;Emb;Tg
#5 VECAD+CD45-P3;YS;Control
#6 VECAD+CD45-P3;YS;Tg
#7 VECAD+CD45+P4;YS;Control
#8 VECAD+CD45+P4;YS;Tg

first: Misato

last: Hayashi

first: Matteo

last: Pluchinotta

first: Asuka

last: Momiyama

first: Yosuke

last: Tanaka

first: Shin-Ichi

last: Nishikawa


title: Gene expression profiling in Vav-Etv2 KSL and Granulocyte hematopoietic cells

summary: Etv2 transgene was expressed from ROSA26 locus by removing floxed STOP cassette by Vav Cre transgene. KSL or Mac1+/Gr1+ cells were sorted from control or Vav-Etv2 bone marrow and compared for gene expression in duplicate. This study will reveal the effect of Etv2 transgene in adult hematopoietic cells. The effect of Etv2 overexpression in relevant mouse tissue will be important to understand its effect in comparison with in ES cells. Genes aberrantly regulated by Etv2 overexpression will help to understand the caveat when using Etv2 to induce endothelial and hematopoietic cells in vitro.

overall_design:
Sample ID
#1;KSL;Control
#2;KSL;Control
#3;KSL;Tg
#4;KSL;Tg
#5;Gr;Control
#6;Gr;Control
#7;Gr;Tg
#8;Gr;Tg


title: Systems-wide RNAi analysis of CASP8AP2 / FLASH

status: Public on May 07 2012

city: Goettingen

first: Frank

last: Kramer

address: Humboldtallee 32

department: Department of Medical Statistics

country: Germany

institute: University Medical Center Göttingen

summary: We have used a combination of RNAi based functional and molecular genomic approaches to investigate in detail two proteins required for the survival of CRC cells.

overall_design: Set1 has 22 samples, 10 siNeg controls, 6 siRNA transfections for FLASH and NUP62 each. Set2 has 67 samples, siNeg controls at timepoint: 10hrs (5), 24hrs (6), 48hrs (6), 72hrs (5), siRNA FLASH at timepoint:  10hrs (8), 24hrs (8), 48hrs (8), 72hrs (8), untreated controls at timepoint:  10hrs (3), 24hrs (3), 48hrs (4), 72hrs (3).

first: Amanda

middle: B

last: Hummon

first: Jason

last: Pitt

first: Jordi

last: Camps

first: Susan

middle: M

last: Skube

first: Konrad

last: Huppi

first: Tamara

middle: L

last: Jones

first: Tim

last: Beissbarth

first: Marian

last: Grade

first: Michael

last: Difilippantonio

first: Thomas

last: Ried

first: Natasha

last: Caplen


title: Microarray analysis of gene expression differences in prostate specific antigen negative (PSA-ve) cells versus PSA+ve cells in human prostate cancer (HPCa) samples

city: Smithville

first: Dean

middle: G

last: Tang

state: TX

address: 1808 Park road 1C

department: Carcinogenesis

institute: U.T M. D. Anderson Cancer Center

summary: Prostate cancer (PCa) is heterogeneous containing both phenotypically differentiated and undifferentiated tumor cells. An important unanswered question is whether these two populations of PCa cells are functionally different. Here we report the distinct molecular, cellular, and tumor-propagating properties of PCa cells that express high (i.e., PSA+) and low (PSA-/lo) levels of the differentiation marker PSA (prostatespecific antigen). PSA-/lo PCa cells are quiescent and resistant to multiple stresses including androgen deprivation, exhibit high clonogenic potential, and possess long-term tumor-propagating capacity in male mice. They preferentially express stem cell-associated genes and can undergo asymmetric cell division generating PSA+ cells. Importantly, PSA-/lo PCa cells can initiate robust tumor development in castrated hosts, survive androgen deprivation, and harbor highly tumorigenic castration-resistant PCa cells that can be further enriched using the ALDH+CD44+α2β1+ phenotype. In contrast, PSA+ PCa cells possess more limited tumor-propagating capacity, mainly undergo symmetric division, and are sensitive to castration. Together, our study suggests that PSA-/lo and PSA+ PCa cells are functionally distinct and PSA-/lo cells may represent one critical source of castration-resistant PCa cells.

overall_design: There are 4 sets of human samples in this study corresponding to 4 different prostate cancer patients labeled as HPCa46T, HPCa47T, HPCa49T and HPCa51T. Each set includes 3 technical triplicates (except HPCa46T) that were performed on dual color arrays and each individual array includes comparisons between PSA- (Cy5) and PSA+ (Cy3) cells of the respective patient prostate tumor.

first: Jichao

last: Qin

first: Xin

last: Liu

first: Brian

last: Laffin

last: Chen

first: Grace

last: Choy

first: Collene

last: Jeter

first: Tammy

last: Calhoun-Davis

first: Hangwen

last: Li

first: Ganesh

middle: S

last: Palapattu

first: Shen

last: Pang

first: Kevin

last: Lin

first: Jiaoti

last: Huang

first: Ivan

last: Ivanov

first: Wei

first: Mahipal

middle: V

last: Suraneni


title: Gene expression profile in HHUA treated with scytonemin

status: Public on Apr 12 2012

city: Yufu-shi

first: Noriyuki

last: Takai

state: Oita

address: 1-1 Idaigaoka, Hasama-machi

department: Obstetrics and Gynecology

institute: Oita University Faculty of Medicine

summary: To identify potential and novel target genes responsive to the anticancer effect in scytonemin-treated gynecological cancer cells, we examined the global changes in gene expression in HHUA endometrial cancer cells after treatment with scytonemin.

overall_design: Gene expression profile in HHUA endometrial cancer cells treated with scytonemin

first: Naoko

last: Kira


title: Gene expression profiling in Tie-2-Etv2 YS hematopoietic precursors

first: Hiroshi

last: Kataoka

summary:
Etv2 transgene was expressed from ROSA26 locus by removing floxed STOP cassette by Tie-2 Cre transgene.VE-Cad+/CD45+ cells were sorted from control or tie-2-Etv2 E10.5 embryosYS(yolk sac) and compared for gene expression in duplicate. This study will reveal the effect of Etv2 transgene in E10.5 mouse embryo yolk sac. The effect of Etv2 overexpression in relevant mouse tissue will be important to understand its effect in comparison with in ES cells.
Genes aberrantly regulated by Etv2 overexpression will help to understand the caveat when using Etv2 to induce endothelial and hematopoietic cells in vitro.

overall_design:
Sample ID
YS- ; (VECAD+CD45+;YS;Control)
YS+12; (VECAD+CD45+;YS;Tg)
YS+22 ; (VECAD+CD45+;YS;Tg)

first: Misato

last: Hayashi

first: Matteo

last: Pluchinotta

first: Asuka

last: Momiyama

first: Yosuke

last: Tanaka

first: Shin-Ichi

last: Nishikawa


title: EpCAM knock-down in FaDu head and neck carcinoma cells

status: Public on Apr 14 2012

city: Munich

first: Olivier

last: Gires

address: Marchioninistr. 15

department: Head and Neck Research Dept

institute: University Clinics Munich

summary:
Epithelial cell adhesion molecule EpCAM is a single transmembrane protein, which is involved in numerous cellular processes including cell adhesion, proliferation, maintenance of stemness of embryonic cells and progenitors, migration, and invasion. Activation of signal transduction by EpCAM is warranted by regulated intramembrane proteolysis and nuclear translocation of the intracellular domain EpICD. Here, we describe matrix metalloproteinase 7 (MMP-7) as a target gene of EpCAM signalling via EpICD nuclear translocation. EpCAM and MMP-7 expression pattern and levels positively correlated in vitro and in vivo, and were strongly elevated in primary carcinomas of the head and neck area. Hence, MMP-7 is a novel target of EpCAM signalling.
FaDu hypopharynx carcinoma cells were transiently transfected with a control siRNA or an EpCAM-specific siRNA. After two days, expression of EpCAM was assessed upon flow cytometry with antibodies, which specifically bind within the EGF-repeat in the extracellular domain of EpCAM (Balzar, et al., 1999). Compared to control siRNA, EpCAM siRNA induced a mean 43% reduction of EpCAM expression at the cell surface. Reduction of EpCAM expression upon siRNA treatment was confirmed by RT-PCR and qPCR. EpCAM down-regulation resulted in diminished cell proliferation assessed upon cell counting. The observed 43% decrease in cell surface expression of EpCAM translated in cell numbers diminished by 35%. This is a confirmation of earlier findings on the reduced proliferation of breast and colon cancer cell lines following siRNA-mediated knock-down of EpCAM (Maetzel, et al., 2009, Munz, et al., 2004, Osta, et al., 2004). Equal amounts of total RNA (RIN score = 10) from control- and EpCAM-siRNA-treated FaDu cells were next subjected to a single, explorative cDNA microarray analysis with the aim to identify potential target genes of the signal transduction cascade of EpCAM. All genes, which were up- or down-regulated by at least two-fold (>2-fold; 716 genes up-regulated, 552 genes down-regulated), were then subjected to a Panther classification software analysis (http://www.pantherdb.org/). Special emphasis was put on the regulation of genes associated with signalling pathways. Angiogenesis, Alzheimer's disease-presenilin pathway, Wnt signalling pathway, inflammation and cadherin signalling pathways were most strongly affected by EpCAM knock-down. mRNA levels of selected genes differently regulated following partial knock-down of EpCAM included the co-regulated genes for secreted frizzled-related protein 5, protocadherin 10, dickkopf homolog 2, MMP24, SPARC, Myst3, ErbB4, MMP12, WISP2, MMP7, Nanos1, WNT9A, and the counter-regulated genes for MMP11, fibronectin 1, DACT3, WNT2B, WNT5A, APC2, Spondin 1, and cateninα2. All genes except for protocadherin 10, Myst3, ErbB4, and WNT2B were validated in RT-PCR assays. Since several matrix metalloproteases were regulated after EpCAM knock-down and EpCAM is known to correlate with invasion, we chose this protein family for in-depth analysis. Matrix metalloprotease 7 (MMP-7) is a soluble factor, which, unlike other family members, is preferentially expressed in epithelial cells (Wilson, et al., 1995). Since EpCAM also displays highest expression in epithelia, we chose to proceed with the analysis of MMP7. SiRNA-mediated knock-down of EpCAM resulted in a comparable 50% down-regulation of MMP7 mRNA levels in RT-PCR and qPCR.

overall_design: Comparison of FaDu cells expressing EpCam vs FaDu cells with downregulated EpCam


title: HepG2 treated with Polycyclic Aromatic Hydrocarbons (PAHs)

status: Public on Apr 18 2012

city: Seoul

first: Mi-Kyung

last: Song

address: 39-1 Hwawol-gok-dong, Wolsong-gil5, Seongbuk-gu-seoul

country: South Korea

institute: Korea Institute of Science & Technology

summary: Assessing the potential carcinogenicity of human toxins represents an ongoing challenge. Chronic rodent bioassays predict human cancer risk with limited reliability, and are expensive and time-consuming. To identify alternative prediction methods, we evaluated a transcriptomics-based human in vitro model to classify carcinogens by their modes of action. The aim of this study was to determine the transcriptomic response and identify specific molecular signatures of polycyclic aromatic hydrocarbons (PAHs), which can be used as predictors of carcinogenicity of environmental toxins in human in vitro systems. We found that characteristic molecular signatures facilitate identification and prediction of carcinogens.

overall_design: To evaluate the change in gene expression levels, human hepatocellular carcinoma (HepG2) cells were exposed to nine different PAHs (benzo[a]pyrene, dibenzo[a,h]anthracene, 3-methylcholanthrene, naphthalene, chrysene, phenanthrene, benzo[a]anthracene, benzo[k]fluoranthene, and indeno[1,2,3-c,d]pyrene) for 48 h. Gene expression analysis was conducted using a 44K whole human genome microarray (Agilent Technologies, USA).

first: Jae-Chun

last: Ryu

first: Mee

first: Han-Seam

last: Choi


title: Comparison of host cell gene expression in cowpox, monkeypox or vaccinia virus infected cells reveals virus-specific regulation of immune response genes

status: Public on Apr 15 2012

city: Berlin

first: Daniel

last: Bourquain

state: Berlin

address: Seestraße 10

department: Centre for Biological Threats and Special Pathogens 1

institute: Robert Koch Institute

summary: Orthopoxviruses are large DNA viruses which can cause disease in numerous host species. Even though the eradication of variola virus - the causative agent of human smallpox – succeeded, with the end of vaccinations several other orthopoxviruses emerged as potential threat to human health. For instance, animal-borne monkeypox virus, cowpox virus and closely related vaccinia virus are all capable of establishing zoonotic infections in humans. The disease caused by each virus differs in terms of expression and severity, but we still know little about the reasons for these different phenotypes. They may be explained by the unique repertoire of host cell modulating factors encoded by each virus. In this study, we aimed at characterizing the specific modulation of the host cells gene expression profile by orthopoxvirus infection. In our study we analyzed changes in host cell gene expression of HeLa cells after infection with cowpox virus, monkeypox virus or vaccinia virus and compared these to each other and to the gene expression profile of non-infected cells using Agilent Whole Genome Microarray technology.  We could identify major differences in viral modulation of host cell immune response genes, especially an induction of genes involved in leukocyte migration and Toll-like receptor signalling in cowpox and monkeypox virus infected cells. This was not observed following vaccinia virus infection. If these differences contribute to the different clinical manifestation of cowpox, monkeypox and vaccinia virus infections in certain host species remains to be elucidated.

overall_design: We analyzed the gene expression profile of HeLa cells wich were either mock-infected or infected with Vaccinia virus strain IHD-W, Cowpox virus strain Brighton Red or Monkeypox virus strain MSF#6 at a multiplicity of infection of 5. Experiments were performed in duplicate. At 6 h post infection total RNA was isolated from infected cells and used for microarray analysis.

middle: R

first: Piotr

middle: W

last: Dabrowski

first: Andreas

last: Nitsche


title: Mapping Clinical and Expression QTL in a Sex-Dependent Effect of Host Susceptibility to Influenza H3N2/HK/1/68-MA20

status: Public on May 02 2012

city: Montreal

first: Rob

last: Sladek

state: QC

address: 740 ave Dr. Penfield

country: Canada

institute: McGill University

summary: Seasonal influenza outbreaks and recurrent influenza pandemics present major challenges to public health. By studying immunological responses to influenza in different host species, it may be possible to discover common mechanisms of susceptibility in response to various influenza strains. This could lead to novel therapeutic targets with wide clinical application. Using a mouse-adapted strain of influenza (A/HK/1/68-MA20 [H3N2]), we produced a mouse model of severe influenza (p-flu) that reproduces the hallmark high viral load and overexpression of cytokines associated with susceptibility to p-flu in humans. We mapped genetic determinants of the host response using a panel of 29 closely related mouse strains (AcB/BcA panel of recombinant congenic strains) created from influenza-susceptible A/J and influenza-resistant C57BL/6J (B6) mice. Combined clinical quantitative trait loci (cQTL) and lung expression QTL (eQTL) mapping identified candidate genes for two sex-specific QTLs on chromosomes 2 and 17. The former includes the previously described Hc gene, a deficit of which is associated with the susceptibility phenotype in females. The latter includes the phospholipase gene Pla2g7 and Tnfrsf21, a member of the tumor necrosis factor receptor superfamily. Confirmation of the gene underlying the chromosome 17 QTL may reveal new strategies for influenza treatment.

overall_design:
To identify eQTLs, we reanalyzed lung expression data previously obtained by Lee et al (2006) on MGU74Av2 microarrays (Affymetrix) for 54 mice (13BcA, 12AcB, B6 and A/J mice in duplicate) using Custom CDFv12 to reorganize oligonucleotide probes based on the latest genome and transcriptome information. We inferred an A/J or B6 strain of origin for each gene based on the genotype of surrounding markers with a call rate of 96.7%. If a gene was in between A/J and B6 markers for a given RCS, it was coded as NA. Expression values were normalized using the Robust Multi-array Analysis (RMA) for Affymetrix gene chips. To define the association between differentially expressed genes and genotypes, ANOVA was conducted on a per-gene basis using the linear model Expression ~ DSO + BG + DSO*BG, where background (BG) and donor strain of origin (DSO) were coded as binary phenotypes corresponding to A/J or B6. The cutoff for genome-wide significance was computed using the Benjamini–Hochberg correction.

For reference, the paper by Lee (2006):
http://www.ncbi.nlm.nih.gov/pubmed/16449383

first: Gregory

last: Boivin

first: Julien

last: Pothlichet

first: Emil

last: Skamene

first: Earl

last: Brown

first: J

middle: C

last: Loredo-Osti

first: Silvia

last: Vidal

first: Peter

middle: D

last: Lee

first: Bing

last: Ge

first: Celia

last: Greenwood

first: Donna

last: Sinnett

first: Yannick

last: Fortin

first: Sebastien

last: Brunet

first: Anny

first: Marina

last: Takane

first: Tomi

last: Pastinen

first: Michael

last: Hallett

first: Thomas

last: Hudson

first: Robert


title: DNA methylation regulates lineage-specifying genes in the human vascular system [expression array].

status: Public on Apr 10 2012

city: Bergisch Gladbach

last: Rueberg

address: Friedrich-Ebert-Str. 68

department: Genomic Services Department

institute: Miltenyi Biotec GmbH

summary: During embryonic development, the lymphatic system emerges by transdifferentiation from the cardinal vein. Although lymphatic and blood vasculature share a close molecular and developmental relationship, they display distinct features and functions. However, even after terminal differentiation, transitions between the two endothelial cell types have been reported. Since changes in phenotypic plasticity and cellular differentiation processes frequently involve epigenetic mechanisms, we wondered whether DNA methylation might play a role in regulating cell type-specific expression in endothelial cells. By analyzing global gene expression and methylation patterns of primary human dermal lymphatic and blood endothelial cells, we identified a highly significant set of genes, which were differentially methylated and expressed. Pathway analyses of the differentially methylated and upregulated genes in lymphatic endothelial cells revealed involvement in developmental and transdifferentiation processes. We further identified a set of novel genes, which might be implicated in regulating BEC-LEC plasticity and could serve as therapeutic targets and/or biomarkers in vascular diseases associated with alterations in the endothelial phenotype.

overall_design: Expression profile of 10 lymphatic endothelial cells was compared to that of 6 blood endothelial cells, no replicates, no control samples.

first: Marc

last: Winnefeld

first: Simone

last: Brönneke

first: Sabine

last: Hagemann


title: Examination of the role of peptidylarginine deiminase 2 (PAD2) in gene expression in MCF-7 breast cancer cells

status: Public on Apr 07 2012

city: Ithaca

first: Scott

last: Coonrod

state: NY

address: 1 Hungerford Hill

department: J.A. Baker Institute for Animal Health

institute: Cornell University

summary: To investigate the potential role of peptidylarginine deiminase 2 (PAD2) in gene expression, we created stable shRNA scrambled control and PAD2 knockdown MCF-7 breast cancer cell lines.  After validating the specific knockdown of PAD2 at the mRNA and protein level, we utilized an Agilent microarray platform to compare the gene expression profile of the two cell lines to generate a candidate list of genes regulated by PAD2.

overall_design: Control and PAD2 knockdown cells were created by stably transfecting shRNA constructs into MCF-7 cells.  Stable cells were selected using puromycin and knockdown validate at the mRNA and protein level.  Microarray data represents 4 independent biological replicates contain control and PAD2 knockdown samples.

first: Brian

last: Cherrington

first: Xuesen

last: Zhang

first: John

last: McElwee

first: Wei

last: Wang

first: Jennifer

last: Mosher


title: Colon Cancer cell line YB5 untreated cells vs YB5 treated 24h with Depsipeptide at 20 nM

status: Public on Apr 04 2012

city: Philadelphia

first: Noel

middle: J-M

last: Raynal

state: Pennsylvania

address: 3307 N. Broad Street

department: Fels Institute for Cancer and Molecular Biology

institute: Temple University

summary: Study the effect of HDACi Depsipeptide on gene expression. We combined these data with whole genome DNA methylation microarray to test the reactivation of genes that have an hypermethylated promoter region.

overall_design: We did two independant experiments with 2 untreated and 2 treated different batch of cells

first: Marcos

last: Estecio


title: Expression and DNA methylation of colon cancer cell lines

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Differential expression of metabolic genes in tumor and stromal components in primary and metastatic loci in pancreatic adenocarcinomas

status: Public on Apr 29 2012

city: Chapel Hill

first: Jen Jen

last: Yeh

address: LCCC, 450 West Drive

institute: University of North Carolina at Chapel Hill

summary: Background:Pancreatic cancer is the fourth leading cause of cancer related deaths the United States with a five-year survival rate of 6% (1). It is characterized by extremely aggressive tumor growth rate and high incidence of metastasis. One of the most common and profound biochemical phenotypes of animal and human cancer cells is their ability to metabolize glucose at high rates, even under aerobic conditions (2-5). However, the contribution of metabolic interrelationships between tumor cells and cells of the surrounding microenvironment to the progression of cancer is not well understood. We evaluated differential expression of metabolic genes and hence, metabolic pathways in primary tumor and metastases of patients with pancreatic adenocarcinoma. Methods and Findings:We analyzed the metabolic gene (those involved in glycolysis, tri-carboxylic acid pathway, pentose-phosphate pathway and fatty acid metabolism) expression profiles of primary and metastatic lesions from 35 pancreatic cancer patients by Affymetrix expression arrays. We observed two principal results: genes that were upregulated in primary and most of the metastatic lesions; and genes that were upregulated only in specific metastatic lesions in a site-specific manner. Immunohistochemical (IHC) analyses of several metabolic gene products confirmed the gene expression patterns at the protein level. The IHC analyses also revealed differential tumor and stromal expression patterns of metabolic enzymes that were correlated with the metastasis sites. Conclusions: Here, we present the first comprehensive studies that establish differential metabolic status of tumor and stromal components and elevation of aerobic glycolysis gene expression in pancreatic cancer. Furthermore, we identify key metabolic genes that can be targeted to diminish overall cancer progression and others that can be targeted to prevent cancer metastasis at specific organ sites.

overall_design: reference x sample

first: Nina

last: Chaika

first: Jen

first: Pankaj

last: Singh


title: A Key Role for Chd1 in Histone H3 Dynamics at the 3' Ends of Long Genes in Yeast (Flag-tagged histone H3 to total histone H3)

status: Public on Jun 08 2012

city: Santa Cruz

first: Grant

last: Hartzog

address: 349 Sinsheimer Labs

institute: UC Santa Cruz

summary: Chd proteins are ATP-dependent chromatin remodeling enzymes implicated in biological functions from transcriptional elongation to control of pluripotency. Here, we examine roles of Chd1 in replication- independent dynamics of histone H3 in yeast.  Using genome-wide ChIP on chip analysis, we find that Chd1 influences histone turnover at the 5’ and 3’ ends of genes, accelerating H3 replacement at the 5’ ends of genes while protecting the 3’ ends of genes from excessive H3 turnover. Although consistent with a direct role for Chd1 in exchange, these results may indicate that Chd1 stabilizes nucleosomes perturbed by transcription. Curiously, we observe a strong effect of gene length on Chd1’s effects on H3 turnover. Finally, we show that Chd1 also affects histone H3K4 and H3K36 methylation patterns over genes, likely as a consequence of its effects on histone replacement. In control experiments, we measure effects of deletion of CHD1 on RNA polymerase II distribution across the genome and on gene expression.  We also examine the effect of deleting the TOP1 gene, alone and in combination with deletion of CHD1, on histone replacement.  Taken together, our results emphasize a role for Chd1 in histone replacement in both budding yeast and Drosophila, and surprisingly show that the major effects of Chd1 on turnover occur at the 3’ ends of genes.

overall_design: ChIP on chip experiments, compares IP of newly expressed, Flag-tagged histone H3 to total histone H3.

first: Marta

last: Radman-Livaja

first: Tiffani

last: Quan

first: Lourdes

last: Valenzuela

last: Armstrong

first: Tibor

last: van Welsem

first: TaeSoo

last: Kim

first: Laura

last: Lee

first: Stephen

last: Buratowski

first: Fred

last: van Leeuwen

first: Oliver

last: Rando


title: Integrative array-based approach identifies MZB1 as a frequently methylated putative tumor-suppressor in hepatocellular carcinoma (expression)

status: Public on Mar 31 2012

city: Tokyo

first: satoshi

last: matsumura

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

department: Dept. of Mol. Cytogenet.

institute: Inst. of Med. Sci., Tokyo Med. & Dent. Univ.

summary: Gene expression was profiled using a 4x44K Human Whole Genome Ver. 2.0 gene expression array (Agilent Technologies) according to the manufacturer's instructions (Microarray-based gene expression analysis protocol ver. 5.0.1, Agilent Technologies)

overall_design: Total RNAs extracted from Hep3B, HepG2, and HuH-7 cell lines and from these cell lines treated with 10 μM 5-aza-dCyd for 5 days were used for conventional and pharmacological unmasking analyses, respectively.  Total RNAs from two normal livers (C20 and C40) were used as controls.

first: Issei

last: Imoto

first: Ken-ichi

last: Kozaki

first: Takeshi

last: Matsui

first: Tomoki

last: Muramatsu

first: Mayuko

last: Furuta

first: Shinji

last: Tanaka

first: Michiie

last: Sakamoto

first: Shigeki

last: Arii

first: Johji

last: Inazawa


title: Integrative array-based approach identifies MZB1 as a frequently methylated putative tumor-suppressor in hepatocellular carcinoma


title: HDAC inhibitors promote the pro-myogenic activity of Sca1-positive interstitial cells in regenerating dystrophic muscles

status: Public on Apr 01 2012

city: La Jolla

first: Roy

last: Williams

address: 3030 Science Park Road

department: Regenerative Medicine

institute: The Scripps Research Institute

summary: We report here on the identification and functional characterization of Sca1-positive muscle interstitial cells that contribute to regeneration or fibroadipogenic degeneration of dystrophic muscles and mediate the beneficial effects of HDAC inhibitors (HDACi) in mdx mice. We found that the phenotype adopted by these cells and their biological activity are influenced by changes in muscle environment. While Sca1-positive muscle interstitial cells from healthy muscles spontaneously adopt a fibro-adipogenic phenotype, Sca1-positive muscle interstitial cells isolated from dystrophic muscles of young mdx mice show a latent myogenic phenotype that is implemented by the exposure to HDACi. Co-culture assays in vitro and co-transplantation experiments in vivo demonstrate that HDACi also improve Sca1-positive muscle interstitial cell ability to enhance the differentiation potential of adjacent satellite cells. Importantly, HDACi-induced myogenic phenotype and pro-regeneration activity were not observed in Sca1-positive muscle interstitial cells isolated from muscles of old mdx mice. The different phenotype of Sca1-positive muscle interstitial cells from mdx mice at different stages of disease progression correlated with the stage-dependent beneficial effect of HDACi, which were effective only at early stages of disease. Transplantation of Sca1-positive muscle interstitial cells isolated from regenerating young muscles into muscles of old mdx mice restored HDACi ability to increase myofiber size. These results indicate that Sca1-positive muscle interstitial cells are key cellular determinants of disease progression and mediate the beneficial effect of HDACi in a mouse model of muscular dystrophy.

overall_design: Isolation of Sca1+ muscle interstitial cells from TSA treated DMD/MDX mice and MuSc from DMD/MDX mice


title: Enhanced expression of Ficolin 1 is a specific gene marker of Takayasu's vasculitis

status: Public on Mar 27 2012

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Takayasu's arteritis (TA) Vasculitis (angiitis) is a chronic inflammatory disease involving large blood vessels. We here identify the genes whose mRNA levels are commonly augmented in the peripheral blood mononuclear cells (PBMCs) from TA patients regardless of the patient's symptom, active or inactive phase, compared with those of normal volunteers. Among them, ficolin 1 (FCN1) was notable because its mRNA level was more than 4.0 fold in all 8 patients examined.

overall_design: A total of 8 two color arrays were performed and each individual array included a target sample and a control sample.

first: Shigeto

last: Kobayashi

first: Hiroshi

last: Nojima


title: Gene expression profile in HHUA treated with telmisartan

status: Public on Mar 22 2012

first: Noriyuki

last: Takai

summary: To identify potential and novel target genes responsive to the anticancer effect in telmisartan-treated gynecological cancer cells, we examined the global changes in gene expression in HHUA endometrial cancer cells after treatment with telmisartan.

overall_design: Gene expression profile in HHUA endometrial cancer cells treated with telmisartan

first: Naoko

last: Kira


title: Microarray analysis of genes impacted by 5 day knockdown of SLC24A5 in normal human melanocytes.

status: Public on Apr 26 2012

city: Sharnbrook

first: Fei Ling

last: Lim

state: Bedfordshire

address: Colworth Science Park

institute: Unilever

summary: A major development in pigmentation research was the discovery of the involvement of SLC24A5 in natural variation in skin colour. This study used Agilent whole-genome microarrays to examine the impact of SLC24A5 knockdown on the transcriptome of normal human melanocytes derived from lightly and darkly pigmented donors.

overall_design: 2 melanocyte cell lines were treated for 6h, with 2 separate siRNA duplexes to target SLC24A5. Treatment of the cells with a non-targeting siRNA control duplex, lipofectamine transfection reagent alone and unchallenged cells, cultured alongside the cellular treatments comprised the controls for the experiment. All treatments and controls were conducted in triplicate, in both cell lines.

first: Karen

middle: H

last: Abraham

first: Sarah

middle: E

last: Askew

first: Martin

last: Green


title: Expression data from LSK cells from mice with knock-out of Ezh1 versus LSK control

status: Public on Mar 06 2012

city: Madrid

first: Antonio

middle: Herrera

last: Merchan

address: Melchor Fernández Almagro, 3

department: Regenerative Cardiology

institute: CNIC

summary: Ezh1 is a protein member of PRC2. Ezh1 has been described as a functional repressor gene, such as its homologous Ezh2. We are investigating the role of Ezh1 in hematopoietic stem cells, aging, self-renewal and differentiation. We used microarrays to detail the global program of gene expression in LSK cells from mice with knocked-down expression of Ezh1.

overall_design: LSK cells from EZH1 knockout and control mice were marked and isolated by fluorescence-activated cell sorting. 2 replicates each.

first: Susana

last: González

first: Isabel

last: Gavilan


title: Transcriptional profiling of  Lung H1299-BRG1 inducible cells

status: Public on Mar 12 2012

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

institute: IDIBELL

summary: Global Transcriptional analysis of BRG1 in lung cancer cells

overall_design: Comparative transcriptional profile comparing the expression in lung cancer cells  before and after  restoring the  Wild type  BRG1 or Mutant BRG1 expression controlled by the  Tet-ON system ( doxicycline depending expression)

first: Octavio

middle: A

last: Romero Ferraro

first: Montse

last: Sanchez-Cespedes


title: Translatome of Jurkat cells: control vs. stress treatment.

status: Public on Mar 02 2012

first: Ivan

last: Ventoso

address: Nicolas cabrera 1. Universidad Autonoma de Madrid

department: Virology and Microbiology

institute: Centro de Biología Molecular Severo Ochoa

summary: Translation efficiencies of Jurkat mRNAs in control and in cells treated with thapsigargin 10microM for 1h and 3h.

overall_design: Three-conditions experiments. Biological replicates: 1 from three pooled control experiments, 1 from three pooled 1h stress experiment, 1 from three pooled 3h stress experiment.

first: Iván

first: Javier

last: Santoyo

first: Joaquín

last: Dopazo

first: David

last: Montaner


title: Mediators in Crohn’s disease influence the gene expression profiles of mesenchymal progenitor cells differentiated into the osteoblastic lineage.

status: Public on Mar 16 2012

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: Crohn’s disease (CD) is associated with a higher prevalence of osteoporosis, a complication that is increasingly recognised as a significant cause of morbidity. Its pathogenesis is still controversial, but activity of CD is thought to be one contributing factor.

overall_design: Two-Color DRLL-IS-Design [Landgrebe et.al 2004: Efficient two-sample designs for microarray experiments with biological replications. In Silico Biology 4] including 12 Arrays, osteoporosis samples from 4 mc patients, control samples from 3 mc patients without osteoporosis

first: Martina

last: Blaschke

first: Julia

last: Cortis

first: Mike

last: Baums

first: Regine

last: Köpp

first: Dirk

last: Raddatz

first: Norbert

last: Schuetze

first: Nikolai

last: Miosge

last: Salinas-Riester

first: Heide

last: Siggelkow


title: HNRPA2B1 RIP-chip

status: Public on Feb 28 2012

city: San Francisco

first: Hani

last: Goodarzi

department: Biochemistry and Biophysics

institute: UCSF

summary: Expression and cross-linking of tagged HNRRPA2B1 in MDA-MB-231 to identify this proteins binding partners.

overall_design: Two differentially labeled co-IP versus input samples

first: Hamed

last: Najafabadi

first: Panos

last: Oikonomou

first: Todd

last: Greco

first: Lisa

last: Fish

first: Reza

last: Salavati

first: Ileana

last: Cristea

first: Saeed

last: Tavazoie


title: A1-2 expression analysis of GR activation

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary:
A1-2 cells treated with 100 nM Dexamethasone or ethanol vehicle for 8h.
The ability of steroid hormone receptors to initiate a genetic program is tightly regulated by the chromatin environment of the responsive regions.  Using the glucocorticoid receptor (GR) as a model factor for transcriptional initiation, we classified chromatin structure through Formaldehyde Assisted Isolation of Regulatory Elements (FAIRE), a technique designed to identify regulatory regions and open chromatin within the genome.  We looked at dynamic changes in FAIRE signals prior to and following activation of GR with its ligand, dexamethesone, specifically at regions of receptor interaction.  We have found a distribution of GR responsive regions that respond to activation by varying degrees of chromatin modulation. The majority of regions that demonstrate GR interaction also demonstrate increases in FAIRE signal in response to ligand.  Most of these GR responsive regions fell within a narrow window of FAIRE signal in the basal chromatin state, suggesting a preferred chromatin structure for GR recruitment.  Supporting this notion, global FAIRE-seq data indicated an enrichment of signal surrounding the GR binding site prior to activation.  FAIRE signal induction correlated to an increase in nuclease sensitivity and overall FAIRE signal also represented a general accessibility of the chromatin.  Further investigation into the requirement of ATPase-dependent chromatin remodeling showed response element specific effects of Brg-1 knockdown. FAIRE induction was universally decreased by Brg-1 depletion, but to varying degrees in a target specific manner.  Taken together, these data suggest classes of nuclear receptor response regions that react to activation through different chromatin regulatory events and identify a novel identifier of chromatin structure that classifies the majority of response elements tested.

overall_design: Experiment performed in triplicate. 3 biological replicates of A1-2 cells treated with dexamethasone and 3 biological replicates of A1-2 cells treated with ethanol

first: Craig

middle: J

last: Burd

first: Trevor

middle: K

last: Archer

first: Valerie

last: Davis

first: Dhiral

last: Phadke

first: Grace

last: Kissling

first: Ruchir

last: Shah


title: Gene expression analysis of mesenchymal stem cells (MSC), osteoblasts and the U2OS (osteosarcoma) cell line

city: BALTIMORE

first: hari

last: easwaran

state: MD

address: 1650 Orleans Street, CRB1, Room 530

department: Oncology

institute: Johns Hopkins University

summary: Transcriptional profiling of MSC, Osteoblasts and U2OS cells. The aim was to quantitate relative gene expression in MSC, osteoblasts and U2OS. MSC and osteoblasts were used as normal cells in this study because osteosarcoma most likely originates from MSC or osteoblasts.

overall_design:
Cell culture and treatment: U2OS cells were cultured in McCoys 5A media (Invitrogen) containing 10% FBS. MSC and osteoblasts were cultured as described by Jaiswal et al. (J Cell Biochem 64, 295-312; 1997). Cells were treated with 5 uM 5-Azadeoxycytidine (5-Aza-CdR) or 300 nM Trischostatin-A (TSA) for 96 hours or 18 hours, respectively.

Microarray analysis: Total RNA was extracted using the Qiagen kit according to the manufacturer's instructions, including a DNase step. RNA was quantified using the NanoDrop ND-100, followed by quality assessment with the 2100 Bioanalyzer (Agilent Technologies). RNA concentrations for individual samples were greater than 200ng/ul, with 28s/18s ratios greater than 2.2 and RNA integrity numbers of 10 (highest). Sample amplification and labeling procedures were carried out using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies) according to the manufacturer's instructions. The labeled cRNA was purified using the RNeasy mini kit (Qiagen) and quantified. RNA spike-in controls (Agilent Technologies) were added to the RNA samples before amplification. 0.75 microgram of samples labeled with Cy3 or Cy5 were mixed with control targets (Agilent Technologies), assembled on Oligo Microarray, hybridized, and processed according to the Agilent microarray protocol. Scanning was performed with the Agilent Scanner G2505B under the default settings recommended by Agilent Technologies.

Data analysis: All arrays were subject to the quality checks recommended by the manufacturer. Images were visually inspected for artifacts, and distributions of signal and background intensity of both red and green channels were examined to identify anomalous arrays. No irregularities were observed, and all arrays were retained and used. All calculations were performed using the R statistical computing platform and packages from the Bioconductor bioinformatics software project. To determine the expression levels of genes in MSC, Osteoblasts and U2OS, the data were LOWESS-normalized, the probe intensities of the mock channel (no drug treatment) were extracted and set to the same scale by quantile normalization. Mean of replicate samples were calculated for each probe.

first: Hariharan

last: Easwaran

first: Stephen

middle: B

last: Baylin


title: Activation of different signaling pathways in the regulation of biological properties of human pancreatic cancer cells by the mucin MUC4 and the oncogenic receptor ErbB2 genes

status: Public on Mar 20 2012

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

summary: The mucin MUC4 and its membrane partner the ErbB2 oncogenic receptor are potential actors and partners in pancreatic tumourigenesis. However, the way they function is still largely unknown. We thus undertook in this work to identify the cellular mechanisms and the intracellular signalling pathways under the control of both ErbB2 and MUC4. Using co-immunoprecipitation, we show that MUC4 and ErbB2 interact in the human pancreatic adenocarcinomatous cell line CAPAN-2. Stable Knocked-Down (KD) cellular clones for both MUC4 and ErbB2 were raised by a shRNA approach. Biological properties of these cells were then studied in vitro and in vivo. Our results show that ErbB2-KD cells are more apoptotic and less proliferative (decreased cyclin D1 and increased p27kip1 expression) while migration and invasive properties were not altered. MUC4-KD clones were less proliferative with decreased cyclin D1 expression, G1 cell cycle arrest and altered ErbB2/ErbB3 expression. Their migration properties were reduced whereas invasive properties were increased. Importantly, inhibition of ErbB2 and MUC4 expression did not impair the same signalling pathways (inhibition of MUC4 expression affected the JNK pathway whereas that of ErbB2 altered the MAPK pathway). Finally, ErbB2-KD and MUC4-KD cells showed impaired tumour growth in vivo. This indicates that ErbB2 and MUC4, that physically interact, activate different intracellular signalling pathways to regulate biological properties of pancreatic cancer cells. Altogether, these data bring new information regarding molecular mechanisms under the control of both MUC4 and ErbB2 that will have to be taken into account for developing efficient targeting of both proteins in order to slow down/stop pancreatic tumourigenesis.

overall_design: profiling of pancreatic cells depleted for ErbB2 and MUC4

first: Nicolas

last: Jonckheere


title: Identification of new genes involved in human adipogenesis and fat storage

first: Silvia

last: Rueberg

institute: Miltenyi Biotec GmbH

summary:
Since the worldwide increase in obesity represents a growing challenge for the health care systems, new approaches are needed to treat obesity and associated disease effectively. The food intake is primarily stored in the adipose tissue and therefore this organ is in focus to develop new anti-obesity treatments.
To provide a systematic analysis of genes that regulate adipose tissue biology and to establish a target-oriented compound screening, we performed a high throughput siRNA screen with primary (pre)adipocytes, using a druggable siRNA library targeting 7,784 human genes. Beside well known regulators of adipogenesis and neutral lipid storage (like PPAR?, RXR, Perilipin A) the screening revealed a large number of genes which were not previously described in the context of fatty tissue biology. An enrichment of genes was observed for axonemal dyneins. Five out of ten anxonemal dyneins were identified in our primary screen and retested positive with independent siRNAs and cell-donors. Quantitative RT-PCR- and immunoblot analysis revealed that axonemal dyneins are expressed in preadipocytes and maturing adipocytes. Using microarray analysis, we further characterize the remaining genes identified in our primary screen to determine their expression pattern during adipogenesis. In the course of fat cell differentiation, 149 among the 459 positive genes were regulated on the gene expression level. Assuming that an adipogenesis-specific expression pattern is another independent hind, that these genes are involved in neutral lipid storage and/or adipocyte differentiation, we retested this gene-pool with independent siRNAs and cell donors. Finally, to show that the genes identified are per se druggable we performed a proof of principle experiment using an antagonist for one randomly chosen gene. The results showed a very similar phenotype compared to knock-down experiments proofing the druggability.
Thus, we identified new adipogenesis-associated genes and those involved in neutral lipid storage. Moreover, by using a druggable siRNA library the screen data provides a very attractive starting point, to identify anti-obesity compounds targeting the adipose tissue.

overall_design: For microarray analysis, RNA was isolated at 3 different points in time during adipogenesis (day 0, day 3 and day 7 after induction of differentiation). This experiment was carried out with cells obtained from three different donors. No replicates are included for each point in time.

first: Marc

last: Winnefeld

first: Jörn

last: Söhle


title: Analysis of Gene expression of human Th17 and Th1 clones

status: Public on Feb 27 2012

city: Napoli

first: Raffaele

last: De Palma

address: via Pansini 5

department: Clinical & Experimental Medicine

institute: Second University of Naples

summary: Human T cell clones were derived according to standard protocols using different mix of cytokines, once assessed for their functional profile were studied for gene expression. The purpose of this study is to analyze human Th1 and Th17 clones with and without stimulation with PMA and Ionomycin to measure differences in gene expression that can distinguish the two lineages.

first: Laura

last: Maggi

first: Veronica

last: Santarlasci

first: Elena

last: D'Aiuto

first: Luca

last: Beltrame

first: Lorenzo

last: Cosmi

first: Francesco

last: Annunziato

last: DePalma


title: Expression correlates of the full-length androgen receptor and its splicing variants

status: Public on Mar 17 2012

city: baltimore

first: Jun

last: Luo

address: 600 N Wolfe st

summary: Continued androgen receptor (AR) signaling is an established mechanism underlying castration-resistant prostate cancer (CRPC), and suppression of AR signaling remains a therapeutic goal of CRPC therapy. Constitutively active androgen receptor splicing variants (AR-Vs) lack the AR ligand-binding domain (AR-LBD), the intended target of androgen deprivation therapies (ADT) including new CRPC therapies such as abiraterone and MDV3100.  While the canonical full-length AR (AR-FL) and AR-Vs are both increased in CRPC, their expression regulation, associated transcriptional programs, functional relationships, and respective roles in mediating responses to endocrine therapies have not been dissected. In this study, we show that suppression of canonical AR-FL signaling by targeting AR-LBD leads to increased AR-V expression in two cell line models of CRPC. Importantly, treatment-induced AR-Vs activate a distinct expression signature enriched for cell cycle genes without requiring the presence of AR-FL. Conversely, activation of AR-FL signaling suppresses the AR-V signature but activates expression programs mainly associated with macromolecular synthesis, metabolism, and differentiation. In prostate cancer cells and CRPC xenografts treated with MDV3100 and abiraterone, increased expression of two constitutively active AR-Vs, AR-V7 and ARV567ES, but not AR-FL, parallels increased expression of the AR-driven cell cycle gene UBE2C.  In addition, protein expression of AR-V7, but not AR-FL, is positively correlated with UBE2C in clinical CRPC specimens. The cumulative in vitro and in vivo evidence support an adaptive shift toward AR-V-mediated signaling in at least a subset of CRPC tumors as the AR-LBD is rendered inactive, suggesting an important mechanism contributing to drug resistance to CRPC therapies.

overall_design: LNCaP cells lacking AR-V were transfected with AR-V7 with or without androgen stimulation of AR-FL (4 conditions); LNCaP95 cells expressing AR-Vs were treated with control siRNA or siRNA trageting AR-LBD or AR-DBD, with or without androgen stimulation of AR-FL (6 conditions); VCaP cells expressing AR-Vs in the presence of androgen were treated with control siRNA, siRNA trageting AR-LBD, DMSO or MDV3100 to inhibit AR-FL (4 conditions). Total 14 arrays with no replicates.


title: FOXA1 actively represses the molecular phenotype of basal breast cancers.

status: Public on Mar 09 2012

city: Columbus

first: Gina

last: Sizemore

state: OH

address: 460 W. 12th Avenue

institute: Ohio State University

summary: Breast cancer is a heterogeneous disease comprised of at least five major subtypes. Luminal subtype tumors confer a more favorable patient prognosis, which is in part, attributed to the Estrogen Receptor-α (ER) positivity and anti-hormone responsiveness of these tumors. Expression of the forkhead box transcription factor, FOXA1, also correlates with the luminal subtype and patient survival, but is present in a subset of ER-negative tumors. Similarly, FOXA1 is consistently expressed in luminal breast cancer cell lines even in the absence of ER. In contrast, basal breast cancer cell lines do not express FOXA1, and loss of FOXA1 in luminal cells increases migration and invasion, characteristics of the basal subtype. To delineate an ER-independent role for FOXA1 in maintaining the luminal phenotype, and hence a more favorable prognosis, we performed cDNA microarray analyses on luminal FOXA1-positive, ER-positive (MCF7, T47D) and FOXA1-positive, ER-negative (MDA-MB-453, SKBR3) cell lines in the presence or absence of transient FOXA1 silencing. This resulted in three FOXA1 transcriptomes: (1) a luminal-signature (consistent across cell lines), (2) an ER-positive signature (restricted to MCF7 and T47D) and (3) an ER-negative signature (restricted to MDA-MB-453 and SKBR3). Use of Gene Set Enrichment Analyses (GSEA) as a phenotyping tool revealed that FOXA1 silencing resulted in a transcriptome shift from luminal to basal gene expression signatures. FOXA1 binds to both luminal and basal genes within luminal breast cancer cells, suggesting that it not only transactivates luminal genes, but also represses basal-associated genes. From these results we conclude that FOXA1 controls plasticity between basal and luminal cells, playing a dominant role in repressing the basal phenotype, and thus tumor aggressiveness, in luminal breast cancer cells. Although it has been proposed that FOXA1-targeting agents may be useful for treating luminal tumors, these data suggest that this approach may promote transitions toward a more aggressive cancer.

overall_design: FOXA1 siRNA treated breast cell lines compared directly to nonspecific siRNA treated cell lines using Agilent 4X44 microarrays.

middle: M

last: Bernardo

first: Charles

last: Ginther

first: Gurkan

last: Bebek

first: Dennis

last: Slamon

first: Ruth

last: Keri


title: HepG2 Cell: Control vs. HGF treated

status: Public on Feb 23 2012

city: Taipei

first: Yung-Ming

last: Jeng

address: 7 Chung-Shan South Road

country: Taiwan

institute: National Taiwan University Hospital

summary: Transcription profile of HepG2 cells treated with hepatocyte growth factor and control cells

overall_design: Two condition experiment, Hep G2 vs. Hep G2-HGF. Biological replicates: 1 control and 1 HGF-treated (no replication)


title: Control shRNA- vs. obscurin shRNA-expressing MCF10A cells

status: Public on Feb 02 2012

city: Baltimore

first: Aikaterini

last: Kontrogianni-Konstantopoulos

address: 108 N Greene St

institute: University of Maryland, Baltimore

summary: Obscurins (~70-870kDa), encoded by the single OBSCN gene, are cytoskeletal proteins originally identified in striated muscles with structural and regulatory roles.  Recently, analysis of 13,023 genes in breast and colorectal cancers identified OBSCN as one of the most frequently mutated genes, implicating it in cancer formation.  Herein, we studied the expression profile of obscurins in breast, colon and skin cancer cell lines, and their involvement in cell survival.  Immunoblot analysis demonstrated significant reduction of obscurins in cancer cells, resulting from decreased mRNA levels and/or the presence of mutant transcripts.  In normal epithelium, obscurins localize in cytoplasmic puncta, the cell membrane and the nucleus.  Accordingly, subcellular fractionation demonstrated the presence of two novel nuclear isoforms of ~110 and ~120kDa.  Non-tumorigenic MCF10A breast epithelial cells stably transduced with shRNAs targeting giant obscurins exhibited increased viability (~30%) and reduced apoptosis (~20%) following exposure to the DNA damaging agent, etoposide.  cDNA microarrays followed by Gene Ontology profiling indicated a substantial number of transcripts related to apoptosis and survival are differentially regulated upon obscurin knock-down.  Quantitative RT-PCR further indicated that the anti-apoptotic genes BAG-4 and HAX-1 were up-regulated (1.5 and 1.4 fold, respectively), whereas initiator caspase-9 and death caspase-3 transcripts were down-regulated (0.8 and 0.6 fold, respectively).  Our findings are the first to pinpoint critical roles for obscurins in cancer development by contributing to the regulation of cell survival.

overall_design: Two-condition experiment: control shRNA- vs. obscurin shRNA-expressing MCF10A cells exposed to 150 uM etoposide. 3 independent replicates per condition.

first: Nicole

last: Perry

first: Marey

last: Shriver

first: Marie

last: Mameza

first: Bryan

last: Grabias

first: Eric

last: Balzer


title: sRSM1 synthetic decoy vs. scrambled transfections in MDA-MB-231 cells

first: Hani

last: Goodarzi

state: CA

summary: Transcriptional profiling of MDA-MB-231 comparing the regulatory consequences of transfecting synthetic decoys carring sRSM1 motifs versus synthetic scrambled oligos

overall_design: Two decoy/scrambled sets, each with two biological replicates

first: Hamed

last: Najafabadi

first: Panos

last: Oikonomou

first: Todd

last: Greco

first: Lisa

last: Fish

first: Reza

last: Salavati

first: Ileana

last: Cristea

first: Saeed

last: Tavazoie


title: Hypoxia-induced modulation of gene expression in human adipocytes - A microarray study

first: Fei Ling

last: Lim

summary: Obesity is characterised by expansion of white adipose tissue, accompanied by an inflamatory response.  It has been proposed that the inflammatory state observed may be linked to relative hypoxia in clusters of adipocytes distant from vasculature.  Adipose tissue hypoxia has been observed in both animal models and human studies in obesity, and has been linked to insulin resistance.  This study has used Agilent whole-genome microarrays to examine the effects of acute hypoxia on the global gene expression in human adipocytes.

overall_design: Human adipocytes (Zen-bio cells) were incubated in hypoxic conditions (1% O2) for 24 h.  Control human adipocytes were incubated under normoxic conditions (21% O2).  Eight biological replicates were prepared for each experimental condition, and RNA was pooled from two biological replicates, giving a total of n=4 array replicates.

first: Dawn

last: Mazzatti

first: Fei-Ling

first: Adrian

last: O'Hara

first: I

last: Wood

first: Paul

last: Trayhurn


title: Mouse primary osteoblasts treated with/without BMP2

status: Public on Mar 30 2012

first: Dai

last: Suzuki

address: 1-5-8 Hatanodai, Shinagawa

department: Biochemistry

institute: Showa University

summary: Bone morphogenetic proteins (BMPs) regulate many aspects of skeletal development, including osteoblast and chondrocyte differentiation, cartilage and bone formation, and cranial and limb development. Among them, BMP2, one of the most potent osteogenic signaling molecules, stimulates osteoblast differentiation.

overall_design: We used cDNA microarrays to elucidate regulators of BMP-2-induced osteoblast differentiation.

first: Yo

last: Shibata


title: Systems-level analysis of age-related macular degeneration reveals global and subtype-specific functional pathways

status: Public on Feb 14 2012

city: Santa Barbara

first: Monte

middle: J.

last: Radeke

address: Neuroscience Research Institiute

department: Neuroscience Research Institute

institute: University of California, Santa Barbara

summary: Age-related macular degeneration (AMD) is a leading cause of human blindness in developed countries. While significant inroads have been made over the past decade, an integrated description of the molecular mechanisms underlying AMD has yet to emerge. Here we describe a systems-level transcriptome analysis of the retina and retinal pigmented epithelium (RPE)-choroid complex from 31 normal, 26 AMD, and 11 potential pre-AMD human eyes derived from the University of Iowa. Our analysis identifies cell-mediated immune responses as the central feature of dry AMD, wet AMD, and geographic atrophy (GA), and we confirm this finding using a second cohort of donor eyes obtained from the Lion's Eye Bank of Oregon. In addition, in the RPE-choroid, we identify the major up-regulated pathways in GA and wet AMD as apoptosis and angiogenesis, respectively. In the retina, a graded up-regulation of wound response, complement, and neurogenesis pathway genes strongly correlates with advanced stages of AMD, in parallel with a progressive down-regulation of key phototransduction processes. Finally, using expression signatures enriched in functional pathways, we assemble two detailed AMD interactomes that highlight modular gene expression programs that delineate and interconnect dry, wet, and GA AMD subtypes across both RPE-choroid and retina tissues. In total, these interactomes are comprised of over 150 genes of which 23 have been previously associated with AMD. These data provide new insights into the expression landscape of AMD pathophysiology, and reveal numerous new targets for AMD pharmaceuticals and diagnostics.

overall_design:
177 samples from the macular or extramacular region of human donor eye RPE-choroids and 118 samples from the macular or extramacular region of human donor retina with no reported ocular disease, possible preclinical AMD or AMD were analyzed using a two-color universal reference design. The reference RNA was comprised of a 1:1 mixture of pooled RPE-choroid and retina RNA from normal and AMD eyes. Except for two samples, no replicates were performed. The dyes used to label the experimental samples and the reference samples were alternated.

The non-Iowa donor eye data was used as a second cohort for verification purposes of global (i.e., non-subtype-specific) expression.

first: Aaron

last: Newman

first: Don

last: Anderson

first: Lincoln

last: Johnson

first: Gregory

last: Hageman


title: Epstein-Barr Virus (EBV)-positive B-cell strain, 28-2: Low v. High latent membrane protein 1 (LMP1)-mRFP expression

status: Public on Feb 01 2012

city: Madison

first: Zachary

last: Pratt

state: WI

address: 1400 University Avenue

institute: University of Wisconsin-Madison

summary: Expression of mRNAs in an EBV-positive B-cell strain, 28-2.  28-2 are infected with a derivative of the B-958 strain of EBV, which expresses eGFP constitutively and LMP1 fused to mRFP from its native promoter.  Single cells were sorted by flow cytometry for their levels of LMP1-mRFP (5% expressing the lowest levels of LMP1-mRFP or 5% expressing the highest levels of LMP1-mRFP)

overall_design: Two-condition experiment: Low v. High LMP1-mRFP expression.  Biological replicates: 3 Low LMP1-mRFP, 3 High LMP1-mRFP.  Samples were normalized to the expression of mRNAs in a pool of unsorted 28-2 cells.

middle: L

first: Bill

last: Sugden


title: adipose tissue Glut4 overexpression or knockout

status: Public on Jan 28 2012

city: Boston

first: Mark

last: Herman

state: MA

address: 330 Brookline Avenue

department: Medicine / Endocrine

institute: Beth Israel Deaconess Medical Center

summary: The goal of this study is to determine the effects of adipose-specific Glut4 overexpression or knockout on changes in adipose tissue global gene expression

overall_design: Three mice from each of four genotypes were studied using a total of 12 microarray chips: aP2-Cre transgenic mice (controls for adipose-Glut4-/- mice), adipose-Glut4-/- mice; FVB mice (littermate controls for adipose-GLUT4-Tg mice) and adipose-GLUT4-Tg mice with Glut4 transgenically overexpressed under the control of the aP2 promoter. Total RNA from perigonadal adipose tissue was extracted using the RNeasy Mini Kit from Qiagen. Affymetrix gene chip hybridization and analysis were performed at the Genomics Core Facility of the Beth Israel Deaconess Medical Center.

first: Barbara

last: Kahn

first: Odile

last: Peroni


title: Transcriptomic analysis of normal and Ino-RNA treated cells.

status: Public on Feb 09 2012

first: NIEHS

last: Microarray Core

summary: During virus infections, host machinery is mobilized to defend against the invading pathogen. The recognition of a viral infection is accomplished by interaction of viral components with host cells. Viral proteins and double-stranded RNA have been previously reported to be potent activator of host cells. We have identified that recognition of virus infections by host cells is the presence of inosines in RNA, which is rare under normal growing conditions but is significantly increased during virus infections. This recognition leads to a robust activation of innate immune responses both in vitro in human epithelial cell cultures and in vivo in a mouse model. This study uncovers a novel structure for activation of innate immune responses during virus infections.

overall_design: Primary human bronchial epithelial cells were treated with 20 ug/ml of normal or Ino-RNA (10% inosines). After 2 hr, total cellular RNA was isolated and used in global transciptomic analysis. All experiments were done in triplicate. Genes that were highly induced by Ino-RNA were selected and categorized into genes of anti viral responses, innate and adaptive immunity, and cell signaling.

first: Jieying

last: Liao

first: Sheetal

last: Thakur

first: Chrissy

last: Prater

last: Zalinger

first: John

last: Gibbs

first: Kevin

last: Gerrish

first: Farhad

last: Imani


title: Whole-genome decay rate measurements in MDA-MB-231 cells transfected with HNRPA2B1 siRNAs versus controls

first: Hani

last: Goodarzi

summary: Transcriptional profiling of MDA-MB-231 samples taken at 0, 1, 2 and 4hr timepoints upon exposure to alpha-amanitine, comparing the siRNA-mediated HNRPA2B1 knock-downs versus mock-transfected controls

overall_design: 4 biological replicates for each time point for the siRNA transfections and controls respectively

first: Hamed

middle: S

last: Najafabadi

first: Panos

last: Oikonomou

first: Todd

last: Greco

first: Lisa

last: Fish

first: Reza

last: Salavati

first: Ileana

last: Cristea

first: Saeed

last: Tavazoie


title: ESlncRNA (AK148461) over-expression on gene expression

status: Public on Jan 06 2012

city: Cambridge

first: Wenqian

last: Hu

address: 9 Cambridge Center

institute: Whitehead Institute

summary: We over-expressed ESlncRNA (AK148461) in fetal liver erythroid progenitor cells (Lin-cells), followed by microarray analysis to examine the global changes of gene expression level. We showed that ESlncRNA has an anti-apoptotic activity during mouse erythropoiesis.

overall_design: Compare the gene expression level in vector transduced fetal liver erythroid progenitor cells (Lin-cells) with that in ESlncRNA transduced fetal liver erythroid progenitor cells (Lin-cells).

first: Bingbing

last: Yuan

first: Johan

last: Flygare

first: Harvey

middle: F

last: Lodish


title: siRNA-mediated HNRPA2B1 knock-down in MDA-MB-231 cells

summary: Transcriptional profiling of MDA-MB-231 comparing the siRNA-mediated HNRPA2B1 knock-downs versus mock-transfected controls

overall_design: Three siRNA vs mock transfections


title: Bone marrows infiltrating human neuroblastoma cells express high levels of calprotectin and HLA-G proteins.

status: Public on Jan 20 2012

city: Genova

first: PAOLA

last: SCARUFFI

state: GE

address: LARGO R. BENZI, 10

institute: "San Martino" Hospital

summary: In neuroblastoma (NB) patients metastasis are the main cause of death, thus understanding the biological and genetic features of the metastatic NB cells is needed to reach efficient target-based therapies for high risk patients. In recent years, several prognostic signatures derived from gene expression profiles, DNA abnormalities, and non-coding RNAs have been proposed as sensitive indicators of tumor aggressiveness in NB patients. Although efforts have been performed in order to validate each gene classifier on independent patient cohorts, the major challenge remains to identify specific signature of in vivo metastatic NB cells. Based on the above considerations, we evaluated the gene expression profile of the bone-marrow (BM) infiltrating metastatic NB cells in comparison with that of primary tumor cells, in order to identify the genes differentially expressed in vivo and to validate potential markers and/or therapeutic targets for metastatic cells. We show that BM infiltrating metastatic NB cells express, together with typical NB markers, genes commonly expressed by the hematopoietic lineages. A among the proteins up-regulated in the metastatic cells, calprotectin, a potent inflammatory protein, and HLA-G, a potent tolerogenic protein, may represent novel diagnostic and prognostic markers as well as potential targets for biologically driven therapy of high risk NB patients.

overall_design: We analyzed gene expression profiles of 32 RNA samples from NB patients stage 4, divided into three groups: 11 samples are neuroblasts freshly isolated from metastatic bone marrow, 11 samples are primary tumors from patients stage 4 alive at 5 years follow-up, 10 samples are primary tumors from patients stage 4 dead with disease at 5 years follow-up.

first: Paola

last: Scaruffi

first: Fabio

last: Morandi

last: Gallo

first: Sara

last: Stigliani

first: Stefano

last: Moretti

last: Bonassi

first: Claudio

last: Gambini

first: Katia

last: Mazzocco

first: Paolo

last: Fardin

first: Riccardo

last: Haupt

first: Vito

last: Pistoia

first: GianPaolo

last: Tonini

first: MariaValeria

last: Corrias


title: Low Expression of SP1 has a Different Effect on Intestinal-type compared to Diffuse-type Gastric Adenocarcinoma

status: Public on Jan 01 2012

city: Seoul

first: Young kee

last: shin

address: 599 Gwanakro, Gwanak-gu

department: Department of Pharmacy

institute: Seoul national university

summary: Specificity protein 1 (SP1) is an essential transcription factor regulating multiple cancer-related genes. Since aberrant expression of SP1 was known to be related to cancer development and progression, we focused on SP1 expression in gastric carcinoma and its correlation with disease outcomes. We discovered a different relationship between SP1 expression and patient survival in intestinal- and diffuse-type gastric cancer. In diffuse-type gastric cancer, patient survival decreased as SP1 expression increased (P < 0.05) in accordance with previously published papers, whereas the lack of SP1 expression in intestinal-type gastric cancer was correlated significantly with poor survival (P < 0.05). When SP1 downregulation was forced in high SP1 expressor intestinal-type gastric cell line MKN28 with siRNA, both migration and invasion were increased but cell proliferation was decreased. In accordance with these results, microarray data in siRNA-transfected MKN28 showed that genes inhibiting migration were downregulated and the expression of genes negatively facilitating proliferation was increased. Both migration and invasion, however, in low SP1 expressor intestinal-type gastric cell line AGS were decreased by forced SP1 expression. In contrast to intestinal-type, in diffuse-type gastric cell line SNU484, high SP1 expressor, both migration and invasion were decreased by siRNA. Contrary to previous studies, which did not reflect differences between the 2 histological types, our results showed that low expression of SP1 is involved in cancer progression and metastasis, and has a different effect on intestinal-type compared to diffuse-type gastric adenocarcinoma.

overall_design: 2 samples for MKN28 cells: si-SP1 against si-control and dyeswap of it upon 72 hour

first: H

last: Lee

first: C

last: Park

first: E

last: Oh

first: Y

last: Shin


title: Transcription profiling of human olfactory ecto-mesenchymal stem cells (hOE-MSCs) from familial dysautonomia (FD) patients with or without kinetin treatment

city: MARSEILLE

first: El Chérif

last: Ibrahim

address: 27 Bd Jean Moulin

institute: Aix Marseille Université-CNRS

summary:
Human olfactory ecto-mesenchymal stem cells (hOE-MSCs) from controls and familial dysautonomia (FD) patients were cultured in either sphere-forming conditions (ITS + EGF + bFGF) or in the presence of retinoic acid, forskolin and Sonic Hedgehog (rafnshh) for 7 days to induce neuroglial differentiation and were also treated or not with kinetin (100 mM for 48h) which corrects the aberrant splicing of IKBKAP mRNA.
We used the recently described model of human olfactory ecto-mesenchymal stem cells to identify genes differentially expressed between controls and familial dysautonomia patients, and also the genes sensitive to kinetin which corrects aberrant splicing of IKBKAP mRNA

overall_design: Total RNAs were extracted from 20 samples including: 4 control and 4 FD hOE-MSCs-derived sphere cultures, 4 control and 4 FD rafnshh-treated hOE-MSCs, 4 FD rafnshh-treated hOE-MSCs in the presence of kinetin

first: Aurélie

last: Bergon

first: Béatrice

last: Loriod

first: Nathalie

last: Boone

first: ElChérif


title: Gene regulation by phosphomimetic Myc and retinoic acid

status: Public on Jan 05 2012

city: Barcelona

first: Luciano

last: Di Croce

address: Dr. Aiguader, 88

institute: Centre for Genomic Regulation

summary: We aimed to investigate the E-box and Max-independent functions of the oncogene Myc in gene regulation and differentiation of leukemic cells. Expression in HL60 leukemic cells of a mutant form of Myc with impaired Max and E-box interaction by replacing the phosphorylation sites of Pak2 kinase to aspartic acid (MycD), resulted in downregulation of 235 genes and, interestingly, upregulation of 586 genes. Eleven percent of the genes upregulated by MycD coincided with those stimulated by a short treatment of retinoic acid (RA) alone. When leukemic cells expressing MycD were stimulated with RA, the overlap with the RA-alone signature increased to 32% (492/1556 genes). Importantly, 320 of these 492 bona-fide direct RA target genes were specifically superactivated in presence of MycD (MycD+RA>RA), and not by MycA (MycD+RA>MycA+RA), further suggesting a synergy between the two pathways. The list of superactivated genes included important regulators of development and differentiation such as GATA6, ICAM1 and HOX genes, whose expression was validated in independent experiments by RT-qPCR.

overall_design: Induced gene expression in HL60 cells was measured after a short-treatment of retinoic acid (100nM, 4 hours). Cells were either wild-type or expressing ER-tagged MycD or MycA. Four biologically independent experiments were performed at each time.

first: Iris

last: Uribesalgo

first: Guglielmo

last: Roma


title: Gene Regulation by the Human Glucocorticoid Receptor Dimerization Domain Mutant dim4

status: Public on Dec 22 2011

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

institute: NIEHS

summary: A mutation in the dimerization domain of the mouse glucocorticoid receptor (GR), dim1, has recently been shown to bind DNA and regulate gene expression.  To expand these studies we created a stable osteosarcoma (U-2 OS) cell line expressing four mutations in the dimerization domain of the human GR, dim4 (N454D, A458T, R460D, D462C), and used whole human genome microarray analysis to compare differences in gene regulation between vehicle treated (CON) and those treated with the glucocorticoid receptor agonist dexamethasone (DEX) at 100nM concentration for 6 hours.

overall_design: Gene expression in U-2 OS hGRdim4 cells was measured after a 6 hour treatment with 100nM dexamethasone or vehicle (control) and the dexamethsone (dex) treated cells were compared to vehicle treated cells. The experiment was performed in triplicate.

first: Christine

last: Jewell

first: John

last: Cidlowski


title: Alterations in tumour necrosis factor signaling pathways associated with cytotoxicity and resistance to taxanes in tumour cells.

status: Public on Dec 30 2011

city: Sudbury

first: Baoqing

last: Guo

state: ON

address: 41 Ramsey Lake Road

department: Tumor Biology

institute: Advanced Medical Research Institute of Canada

summary: The taxanes are widely used in the treatment of breast and other cancers.  While their cytotoxicity has been attributed to the induction of cell cycle arrest in mitosis through the stabilization of microtubules, we found that docetaxel promotes soluble tumor necrosis factor alpha (TNF-alpha production in MCF-7 breast tumor cells.  TNF-alpha induces apoptotic cell death in a variety of cell types by binding to one of its receptors (TNFR1) which promotes death-inducing signaling complex (DISC) formation.  Consistent with this view, we also report that selection of MCF-7 cells for survival in increasing concentrations of paclitaxel or docetaxel results in selection of drug-resistant variants that are resistant to TNF-alpha cytotoxicity.  MCF-7 cells selected to 3-5 nM docetaxel produced >30-fold more TNF-alpha than control MCF-7CC cells but had strongly reduced levels of TNFR1.  In contrast, expression of TNFR2 was unchanged, resulting in enhanced cell survival through the activation of the NF-kappaB p50 and p65 subunits.  Gene expression profiling of docetaxel resistant MCF-7 cells compared to parental MCF-7 cells was performed for the changes of TNF related genes, and also confirmed in ovarian cell line A2780.

overall_design: Two docetaxel resistant cell lines of breast MCF-7 and ovarian A2780 were  generated for gene expression profilling. Two colour microarray of Agilent whole human genome nucleotide arrays was conducted with two replicate of both forward and reverse labellings for MCF-7. Four arrays were used for this experiments. And it was four replicate of both forward and reverse labellings for A2780 cells. Eight arrays were used for this experiments

first: Jason

last: Sprowl

first: Stephen

middle: X

last: Armstrong

first: Carita

last: Lanner

first: Kerry

last: Reed

first: Stacey

last: Hembruff

first: Irina

last: Kalatskaya

first: Lincoln

last: Stein

first: Amadeo

last: Parissenti


title: MYBPH, a novel transcriptional target of NKX2-1/TTF-1, inhibits ROCK1 and actomyosin assembly, and reduces cell motility and tumor metastasis

city: Nagoya

first: Takashi

last: Takahashi

state: Aichi

address: 1-1 Kanokoden, Chikusa-ku

institute: Aichi Cancer Center

summary: Cell migration driven by actomyosin filament assembly is a critical step in tumour invasion and metastasis. Herein, we report identification of myosin binding protein H (MYBPH) as a transcriptional target of NKX2-1 (also known as TTF-1 and TITF1), a lineage-survival oncogene in lung adenocarcinoma. MYBPH inhibits assembly competence-conferring phosphorylation of the myosin regulatory light chain (RLC) as well as activating phosphorylation of LIM domain kinase (LIMK). These are unexpectedly implemented through direct physical interaction of MYBPH with Rho kinase 1 (ROCK1) rather than with RLC. In addition, MYBPH is shown to directly bind with non-muscle myosin heavy chain IIA (NMHC IIA), resulting in inhibition of NMHC IIA assembly. Thus, MYBPH plays multi-facetted roles in negative regulation of actomyosin organization, which in turn reduces cell motility, invasion, and metastasis. Finally, we also show that MYBPH is epigenetically inactivated by promoter DNA methylation in a fraction of lung adenocarcinomas abundantly expressing NKX2-1, which appears to be in accordance with its deleterious function for lung adenocarcinoma invasion and metastasis, as well as with the paradoxical association of NKX2-1 expression with favourable prognosis in lung adenocarcinoma patients.

overall_design: Dye-swap experiment, vector control vs. transiently transfectanted with TTF-1 in HPL1D, immortalized human peripheral lung epithelial cell line.

first: Yasuyuki

last: Hosono

first: Tomoya

last: Yamaguchi

first: Eri

last: Mizutani

first: Kiyoshi

last: Yanagisawa

first: Chinatsu

last: Arima

first: Shuta

last: Tomida

first: Yukako

last: Shimada

first: Michiyo

last: Hiraoka

first: Seiichi

last: Kato

first: Kohei

last: Yokoi

first: Motoshi

last: Suzuki


title: Genome-Wide Expression Profiling of human tumor-infiltrating microglia/macrophages

status: Public on Dec 31 2011

city: Heidelberg

first: Grischa

last: Toedt

address: Im Neuenheimer Feld 280

department: Molecular Genetics (B060)

institute: German Cancer Research Center (DKFZ)

summary: Microglia isolated from glioma patients gain anti-tumor activities upon poly (I:C) stimulation.

overall_design: Expression profiles of human tumor-infiltrating microglia/macrophages before (untreated) and after treatment with poly (I:C) for 48h (induced). Tumor-infiltrating microglia/macrophages were isolated from freshly excised brain tumors

first: Tim

last: Kees

first: Jennifer

last: Lohr

first: Rodrigo

last: Mora

first: Georg

last: Gdynia

first: Aurelie

last: Ernst

first: Bernhard

last: Radelwimmer

first: Christine

last: Falk

first: Christel

last: Herold-Mende

first: Anne

last: Regnier-Vigouroux


title: Microarray Analysis of Genes Regulated by Macrophage-Conditioned Media Treatment of Human Pre-Adipocytes

status: Public on Dec 21 2011

city: Sharnbrook

first: Fei Ling

last: Lim

address: Colworth Science Park

institute: Unilever

summary: A major development in the study of obesity is the recognition that the condition is characterised by chronic mild inflammation.  Within adipose tissue, this involves the infiltration of macrophages, as well as the direct inflammatory response of the adipocytes and pre-adipocytes.  This study has used Agilent whole-genome microarrays to examine the effects of macrophage-conditioned medium on the global inflammatory response of human pre-adipocytes.

overall_design: Human pre-adipocytes (SGBS cells) were treated with macrophage (U937 cells) conditioned medium for 24 h.  Control pre-adipocytes were treated with unconditioned medium (control) or RPMI-1640 media alone to control for differences in media used to culture the U937 cells.  There were 5 biological replicates per group.

first: Adrian

last: O'Hara

first: FeiLing

first: Dawn

last: Mazzatti

first: Paul

last: Trayhurn