title: Suppression of breast tumor growth and metastasis by an engineered transcription factor

status: Public on Aug 23 2011

city: CHAPEL HILL

first: PILAR

last: BLANCAFORT

state: NORTH CAROLINA

address: 4009 MASON FARM RD

department: PHARMACOLOGY

institute: UNIVERSITY OF NORTH CAROLINA AT CHAPEL HILL

summary:
Abstract
Maspin is a tumor and metastasis suppressor playing an essential role as gatekeeper of tumor progression. It is highly expressed in epithelial cells but is silenced in the onset of metastatic disease by epigenetic mechanisms. Reprogramming of Maspin epigenetic silencing offers a therapeutic potential to lock metastatic progression. Herein we have investigated the ability of the Artificial Transcription Factor 126 (ATF-126) designed to upregulate the Maspin promoter to inhibit tumor progression in pre-established breast tumors in immunodeficient mice. ATF-126 was transduced in the aggressive, mesenchymal-like and triple negative breast cancer line, MDA-MB-231. Induction of ATF expression in vivo by Doxycycline resulted in 50% reduction in tumor growth and totally abolished tumor cell colonization. Genome-wide transcriptional profiles of ATF-induced cells revealed a gene signature that was found over-represented in estrogen receptor positive (ER+) “Normal-like” intrinsic subtype of breast cancer and in poorly aggressive, ER+ luminal A breast cancer cell lines. The comparison transcriptional profiles of ATF-126 and Maspin cDNA defined an overlapping 19-gene signature, comprising novel targets downstream the Maspin signaling cascade.  Our data suggest that Maspin up-regulates downstream tumor and metastasis suppressor genes that are silenced in breast cancers, and are normally expressed in the neural system, including CARNS1, SLC8A2 and DACT3. In addition, ATF-126 and Maspin cDNA induction led to the re-activation of tumor suppressive miRNAs also expressed in neural cells, such as miR-1 and miR-34, and to the down-regulation of potential oncogenic miRNAs, such as miR-10b, miR-124, and miR-363. As expected from its over-representation in ER+ tumors, the ATF-126-gene signature predicted favorable prognosis for breast cancer patients. Our results describe for the first time an ATF able to reduce tumor growth and metastatic colonization by epigenetic reactivation of a dormant, normal-like, and more differentiated gene program.

overall_design: A total of six cell lines were used for gene expression analyses: CONTROL –DOX, CONTROL +DOX, ATF-126 –DOX, ATF-126 +DOX (all with 3 technical replicates), p-RetoX-Tight-Maspin –DOX, and p-RetoX-Tight-Maspin +DOX (with 2 technical replicates). For each cell line, total RNA was purified, amplified, labeled, and hybridized [46] using Agilent Agilent 4X44K oligo microarrays (Agilent Technologies, United States). The probes/genes were filtered by requiring the lowest normalized intensity values in both –DOX and +DOX samples to be >10. The normalized log2 ratios (Cy5 sample/Cy3 control) of probes mapping to the same gene were averaged to generate independent expression estimates. We also used available microarrays from the breast cancer cell lines [21], the UNC337-patient [20], the MERGE 550-patient dataset [47] and the NKI (295 patients [48,49]). All microarray cluster analyses were displayed using Java Treeview version 1.1.3. Average-linkage hierarchical clustering was performed using Cluster v2.12 [50]. ANOVA tests for gene expression data were performed using R (http://cran.r-project.org).

first: Adriana

last: Beltran

first: Pilar

last: Blancafort


title: Non-overlapping functions for Notch1 and Notch3 during murine steady state thymic lymphopoiesis.

status: Public on Aug 03 2011

city: jupiter

first: howard

middle: t

last: petrie

state: FL

address: 130 scripps way

department: cancer biology

country: USA

institute: the scripps research instititute

summary:
Notch1 signaling is absolutely essential for steady-state thymic lymphopoiesis, but the role of other Notch receptors, and their potential overlap with the function of Notch1, remains unclear. Here we show that like Notch1, Notch3 is differentially expressed by progenitor thymocytes, peaking at the DN3 progenitor stage. Using mice carrying a gene-trapped allele, we show that thymic cellularity is slightly reduced in the absence of Notch3, although progression through the defined sequence of TCR-αβ development is normal, as are NKT and TCRγδ cell production.
The absence of a profound effect from Notch3 deletion is not explained by residual function of the gene-trapped allele, since insertion mapping suggests that the targeted allele would not encode functional signaling domains. We also show that although Notch1 and Notch3 are co-expressed on some early intrathymic progenitors, the relatively mild phenotype seen after Notch3 deletion does not result from the compensatory function of Notch1, nor does Notch3 function explain the likewise mild phenotype seen after conditional (intrathymic) deletion of
Notch1. Our studies indicate that Notch1 and Notch3 carry out non-overlapping functions during thymocyte differentiation, and that while Notch1 is absolutely required early in the lymphopoietic process, neither receptor is essential at later stages.

overall_design: Thymuses from 10 male C57BL6 mice at 5 weeks old were used for sorting thymocytes (DN1, DN2, DN3, preDP, DP).  These samples were used for subsequent RNA purification, labeling and hybridization to Affymetrix arrays.

first: Howard

middle: T

last: Petrie

first: Jianjun

last: Shi

first: Mohammad

last: Fallahi


title: LNCaP Prostate Cancer Cells: Control vs. siRNA-PCAT1 Treated

status: Public on Jul 28 2011

city: Ann Arbor

first: Matthew

last: Iyer

state: MI

address: 5316 CCGC 0940 1400 E. Medical Center Drive

department: Michigan Center for Translational Pathology

institute: University of Michigan

summary:
Transcriptional profiling of LNCaP prostate cancer cells comparing control siRNA-treated LNCaP cells with LNCaP cells treated with siRNAs targeting Prostate Cancer Associated Transcript-1 (PCAT1), an uncharacterized long non-coding RNA.

High-throughput sequencing of polyA+ RNA (RNA-Seq) in human cancer shows remarkable potential to identify both novel disease-specific markers for clinical uses and uncharacterized aspects of tumor biology, particularly non-coding RNA (ncRNA) species.  To illustrate this approach, we employed RNA-Seq on a cohort of 102 prostate tissues and cells lines and found that aberrant expression profiles of novel tissue-specific ncRNAs distinguished benign, cancerous, and metastatic tumors.  Among these, a novel prostate-cancer specific ncRNA (termed PCAT-1) defined a subset of aggressive cancers with low expression of the epigenetic regulator EZH2, a component of the Polycomb Repressive Complex 2 (PRC2) commonly upregulated in metastatic cancers.   In vitro assays for core PRC2 genes indicated that the PRC2 complex directly binds and represses PCAT-1, and that the PCAT-1 transcript reciprocally binds PRC2, suggesting a regulatory feedback mechanism.  Importantly, knockdown of PCAT-1 in cells with high levels of endogenous PCAT-1 transcript showed changes in cell proliferation and transcriptional regulation of several key biological processes, including cell cycle.   Finally, we showed that ncRNA expression signatures, including PCAT-1, were effective for the non-invasive detection of prostate cancer, and that high ncRNA expression signature values correlate with high-grade histology.  The findings presented herein establish the utility of RNA-Seq to comprehensively identify unannotated ncRNAs that define human disease states and characterize PCAT-1 as a novel regulator of cell proliferation mechanistically linked to PRC2 and contributory to translational clinical tests for prostate cancer.

overall_design: Two-condition experiment: Control-siRNA-treated versus PCAT1-siRNA-treated LNCaP cells. Biological replicates: 3 control replicates, 3 treatment replicates.

middle: K

first: John

last: Prensner

first: Arul

middle: M

last: Chinnaiyan

first: Xuhong

last: Cao

first: Xiaojun

last: Jing


title: Bystander responses to 0.5Gy of alpha-particles in a human 3-dimensional skin model in 4h after exposure to ionizing radiation

status: Public on Aug 31 2011

city: New York

first: Alexandre

last: Mezentsev

state: NY

address: 630 west 168th Street, VC 15-204

department: Dermatology

institute: Columbia University

summary: Direct irradiation of 3-dimensional skin model, Epi-200, with alpha-particles led to differential regulation of 545 genes at 4 h postirradiation. Unlike the traditional 2-dimensional in vitro systems, Epi-200 made of the primary cells, epidermal human keratinocytes. It mimics the structure of the human epidermis Global gene expression is a powerful tool for uncovering both fundamental signaling processes and the mechanistic basis of cellular or physiological effects. By comparing irradiated tissues with non-irradiated control, we have been able to measure global gene expression responses and reveal the affected biological pathways and molecular functions. The data were analyzed using BRB-Array Tools (NIH), and further gene ontology analysis was performed with Panther (Applied Biosystems). The responding pathways were identified jointly and separately for up- and downregulated genes. Receptors (12 genes, p=0.0467), including nuclear hormone receptors (3 genes, p=8.2 x E-04) and Ser/Thr receptors (3 genes, p=5.3 x E-03), chemokines (2 genes, p=0.0155) and signaling molecules were overrepresented among 123 upregulated genes while DNA binding proteins (27 genes, p=5.07 x E-04), particularly helicases (6 genes, p=3.61 x E-03) and, G-protein modulators (16 genes, p=4.4 x E-03) were overrepresented among 403 downregulated genes. Remarkably, 6 differentially regulated genes in this group were represented by helicases and methyltransferases (6 genes, p=0. 0534) involved in methylation of histones and DNA. These changes confirmed an importance in the biological response of two its basic components: receptor-regulated pathways and chromatin remodeling. Upregulation the first group supposes to increase sensitivity of irradiated cells to chemokines and cytokines while downregulation of the second group would likely affect the DNA methylation pattern and stimulate the transcription.

overall_design: Radiation induced gene expression in 3-dimensional tissue model, Epi-200, was measured at 4 hours after exposure to  0.5 Gy of alpha-particles. Three independent experiments were performed using one tissue sample per a data point.

first: Sally

middle: A

last: Amundson

middle: V


title: Genomic differences distinguish the myofibroblast phenotype of distal lung from airway fibroblasts

status: Public on Jul 22 2011

city: Pittsburgh

first: XIUXIA

last: ZHOU

state: PA

address: 3459 fifth ave

department: Medicine

institute: University of Pittsburgh

summary: ABSTRACT  Primary human distal lung/parenchymal fibroblasts (DLF) exhibit a different phenotype from airway fibroblasts (AF), including the expression of high levels of a-smooth muscle actin (a-SMA). The scope of the differences and the mechanisms driving them are unknown. To determine whether distinct fibroblast characteristics and function based on lung region are predicted by a broad range of genomic differences in AF vs DLF. Matched human fibroblast pairs isolated from proximal and distal lung in 18 asthmatic and 4 normal subjects were studied. Microarray analysis was performed on 12 matched fibroblast pairs (8 asthmatic and 4 normal subjects) and validated by quantitative real-time PCR (qRT-PCR). The functional impact of these molecular differences on AF and DLF was then revealed using computational approaches. Microarray data demonstrated 474 transcripts upregulated in AF, and 611 transcripts upregulated in DLF, when the asthmatic and normal fibroblasts were combined for all the analysis. Further gene ontology (GO) and network analysis identified distinct pathway activation patterns between AF and DLF, including identification of the SMAD3 and MAPK8 signaling pathways. These results demonstrated that marked molecular and functional differences exist between these two lung regional fibroblast populations. These striking differences identify multiple potential mechanisms by which AF and DLF differ in their responses to injury, regeneration and remodeling in the lungs.

overall_design: In order to better identify the underlying molecular differences between AF and DLF, microarray analysis was performed on 12 different matched pairs of fibroblasts (4 pairs from normal subjects and 8 pairs from asthmatics).

first: Xiuxia

last: Zhou

first: Wei

last: Wu

first: Haizhen

last: Hu

first: Jadaranka

last: Milosevic

first: Kazuhisa

last: Konishi

first: Naftali

last: Kaminski

middle: E

last: Wenzel


title: Expression signature in a human colorectal cancer cell line HCT116 transfected with miR-1 precursor molecule

status: Public on Jul 01 2011

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

country: Japan

institute: Sapporo Medical University

summary: We identified that miR-1 is silenced in association with CpG island hypermethylation in a colorectal cancer (CRC) cell line, HCT116. To determine whether miR-1 serves as a tumor suppressor in CRC, we transfected CRC cell lines with a miR-1 precursor molecule or a negative control, and carried then out a series of MTT assays.  Forty-eight hours after transfection, we observed that ectopic expression of miR-1 moderately suppressed growth in all three cell lines. To further clarify the effect of the miRNA, we next performed gene expression microarray analysis in HCT116 cells transfected with a miR-1 precursor molecule or a negative control.  We found that 2769 probe sets were downregulated (> 1.5-fold) by ectopic miR-1 expression, and gene ontology analysis revealed that “extracellular regions”, “membrane” and “response to wound healing” genes were significantly enriched among the downregulated genes.

overall_design: HCT116 cells were transfected with a Pre-miR-1 miRNA Precursor Molecule (Ambion) or Pre-miR miRNA Molecules Negative Control #1 (Ambion). Forty-eight hours after transfection, total RNA extraction were carried out, and gene expression signatures were analyzed.

first: Minoru

last: Toyota


title: Gene expression comparison between undifferentiated H9 cells and trophoblasts

status: Public on Sep 19 2011

city: Baltimore

first: Hongkai

last: Ji

state: MD

address: 615 North Wolfe Street, Rm E3638

department: Department of Biostatistics

institute: Johns Hopkins Bloomberg School of Public Health

summary: Undifferentiated H9 express high levels of c-Myc.  Upon differentiation, Myc levels decrease.  Gene expression analysis was carried out between these 2 cell types

overall_design: H9 cells were treated with BMP-4 for 6 days in order to differentiate them toward a trophoblast lineage.

first: Karen

last: Zeller

first: Chi

last: Dang


title: Expression data from C2C12 murine myoblast cells infected with an inducible Msx1-ER fusion protein

status: Public on Aug 17 2011

city: Cambridge

first: Richard

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary:
The spatial and temporal control of gene expression during development requires the concerted actions of sequence-specific transcriptional regulators and epigenetic chromatin modifiers, which are thought to function within precise nuclear compartments. However, how these activities are coordinated within the dynamic context of the nuclear environment is still largely unresolved. Here we show that transcriptional repression by the Msx1 homeoprotein coordinates recruitment of Polycomb to genomic targets with localization to the nuclear periphery. Using genome-wide ChIP-Seq analyses to identify genomic binding sites for Msx1, we find that repressed target genes are enriched at the nuclear periphery in myoblast cells. We further show that the interaction of Msx1 with the Polycomb repressive complex PRC2 is required for transcriptional repression and regulation of myoblast differentiation, and promotes increased tri-methylation of lysine 27 on histone H3 (H3K27me3)  at Msx1 target genes. Furthermore, Msx1 genomic binding promotes the dynamic spatial redistribution of the H3K27me3 repressive mark to the nuclear periphery in developing embryos in vivo. Thus, our findings suggest a hitherto unappreciated spatial coordination of transcription factor binding, Polycomb recruitment, and subnuclear localization in regulation of developmentgene expression programs.
In order to identify genes regulated by Msx1, we infected C2C12 myoblast cells with a retrovirus expressing a tamoxifen-regulated Msx1 protein, Msx1-ER (or with empty vector as a control), followed by induction with 0.2 nM of tamoxifen or vehicle (DMSO) for 6 hours. Regulated genes were identified as those that changed in expression upon tamoxifen induction of the Msx1-ER protein but did not change in the empty vector control.

overall_design:
Experiments were performed in triplicate for each of the four experimental conditions (Msx1-ER + tamoxifen, Msx1-ER - tamoxifen, empty vector control + tamoxifen, empty vector control - tamoxifen), for a total of 12 independent array samples.

This submission represents the transcriptome component of the study.

first: Jingqiang

last: Wang

first: Roshan

last: Kumar

first: Vanessa

middle: J

last: Biggs

first: Hansol

last: Lee

first: Yun

last: Chen

first: Michael

middle: H

last: Kagey

first: Cory

last: Abate-Shen


title: Intrinsic differentiation potential of human postnatal MSC, Mab and MAPC reflected in their transcriptome

status: Public on Jul 12 2011

city: Leuven

first: Valerie

middle: Dina

last: Roobrouck

address: Herestraat 49 bus 804

department: Interdepartmental Stem Cell Institute Leuven

country: Belgium

institute: Catholic University Leuven

summary: We have employed whole genome microarray expression profiling to identify genes that characterize different populations of human postnatal stem cells and reflect their potency

overall_design:
MSC, Mab and MAPC cultures were established from at least three different donors and their transcriptome was assayed using the Agilent 4x44k whole human genome microarray; furthermore, the H9 ESC line from U of Wisconsin and MSC from Lonza were added for comparison

MSC = Mesenchymal Stem Cells, MAPC= Multipotent Adult Progenitor Cells, Mab= Mesoangioblasts, ESC= Embryonic Stem Cells

first: Catherine

last: Verfaillie

middle: D

first: Fernando

last: Ulloa-Montoya

first: Carlos

middle: C

last: Claver


title: Heart specific moderate over-expression of serum response factor (SRF) in 6mo mouse.

city: Little Rock

first: Jeanne

last: Wei

address: 4301 West Markham Street

department: Geriatrics

institute: University of Arkansas for Medical Sciences

summary:
To identify in vivo new cardiac SRF target genes and to study the response of these novel genes to SRF overexpression, we employed a cardiac-specific, transgenic mouse model that has a phenotype in young adulthood which resembles that of the typically aged heart. Using this “cardiac aging” model, we identified 207 genes that are important to cardiac function that were differentially expressed in vivo. Among them, 192 genes had SRF binding motifs (56 with CArG and 136 with CArG-like elements) in their promoter region. Fifty-one of 56 genes with classic CArG elements were not previously reported. These SRF target genes were grouped into 12 categories based on their function. It was observed that genes associated with cardiac energy metabolism shifted toward that of carbohydrate metabolism and away from that of fatty acid metabolism. The expression of genes that are involved in transcription and ion regulation were decreased, but expression of cytoskeletal genes were significantly increased. Using public databases of mouse models of stress, we also found that altered expression of the SRF target genes occurred in these hearts as well.  Thus, SRF target genes are actively regulated under various physiological and pathological conditions, including hemodynamic stress. The mild elevation of SRF protein in the rodent heart that is observed during typical adult aging may have a major impact on many SRF target genes, thereby affecting cardiac structure and performance. In addition, these results could help to enhance our understanding of SRF regulation of cellular processes, including metabolic and cytoskeletal function.
The generation and characterization of transgenic mice with mild cardiac-specific overexpression of SRF was previously reported (Zhang et al., 2003). At 6 months of age, the transgenic mice manifested cardiac changes suggestive of an “aged heart” (Zhang et al., 2003). Therefore, 6-month-old transgenic and non-transgenic mice were used in this study.

overall_design: Cardiac gene expression in SRF Tg heart was compared to that of wild-type mice.

middle: Y


title: Determining IRF4 target genes using RNA interference in ABC-DLBCL and MM

city: Bethesda

first: Louis

middle: M.

last: Staudt

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

summary: Interferon regulatory factor 4 (IRF4) is a transcriptional regulator with critical roles in the normal development and malignant transformation of lymphocytes. Recently we have shown that plasma cell cancers (multiple myeloma, MM) are addicted to an aberrant gene expression program ochestrated by wild-type IRF4 for their survival. Here we show that an aggressive malignancy of mature B cells, the activated B cell for of Diffuse Large B Cell lymphoma (ABC-DLBC), also depends on IRF4 for survival. With genome-wide expression profiling and localization (ChIP-Seq) assays, we identified IRF4 target genes in ABC-DLBCL as members of diverse pathways related to B cell biology and malignant behavior, distinct from IRF4 targets in MM. For example, we find the gene encoding the NFkB signal transduction adapter protein CARD11 is a target of IRF4 activation, driving the critical NFkB pathway in ABC-DLBCL. Further, we find enrichment of DNA binding motifs for ETS-IRF factors in regions of IRF4 binding in ABC-DLBCL suggesting cooperative activity between IRF4 and an ETS family transcription factor. Through complementation assays we show that IRF4 and the critical ABC-DLBCL ETS factor SPIB interact with one another and are key to ABC-DLBCL survival. Together our data show that ABC-DLBCL is addicted to the interaction between IRF4 and SPIB, in part through a positive feedback loop invovling CARD11 and the activation of the NFkB pathway. These data suggest theraepeutic potential in targeting the IRF4:SPIB interface in ABC-DLBCL.

overall_design:
Gene expression was analyzed using Agilent human 4X44K oligo gene expression arrays. Cell lines (HBL1, OCILY3, TMD8-ABC-DLBCL; KMS12-MM) were infected with control (shControl, Cy3) or shIRF4_3'UTR (Cy5) constructs, and changes in gene expression were monitored over time after induction of the shRNA with doxycyclin. For each of the three ABC-DLBCL cell line a four timepoint series (24, 48, 72, 96 hrs) of shRNA induction was analyzed, for a total of 12 arrays. In HBL-1 a second shRNA targeting the IRF4 cds (shIRF4_cds) was used in a similar time course of shRNA induction (4 arrays). For the KMS12 MM cell line a three point time course was analyzed using the shIRF4_3'UTR with one technical (using the same RNA sample) duplicate time point measurement (4 arrays).

ChIP-Seq data not provided.


title: A human ESC model for MLL-AF4 reveals an impaired early human hemato-endothelial specification

status: Public on Jun 09 2011

city: MAdrid

first: Gustavo

last: Melen

state: Madrid

address: Avda. Menendez Pelayo 65

country: Spain

institute: FIB Hospital NIño Jesus

summary: The MLL-AF4 fusion gene is a hallmark genomic aberration in high-risk acute lymphoblastic leukemia in infants. Although it is well-established that MLL-AF4 arises pre-natally during human development, its effects on hematopoietic development  in utero remains unexplored. We have created a human-specific in vitro system to study early hemato-endothelial development in MLL-AF4-expressing human embryonic stem cells (hESCs). Differentiation and functional studies as well as clonal analyses and gene expression profiling reveal that expression of MLL-AF4 in hESCs has a phenotypic, functional and gene expression impact. It enhances the specification of hemogenic precursors from hESCs and impairs further hematopoietic commitment of these precursors in favour of the endothelial cell fate. Similar to that reported in cord blood CD34+ hematopoietic stem/progenitor cells (HSPCs), MLL-AF4 expression is not sufficient to transform hESC-derived hematopoietic cells in vitro or in vivo, indicating that additional events may be required to initiate leukemogenesis or that embryonic hematopoiesis is not the appropriate human cellular target for MLL-AF4-mediated leukemogenesis. This work illustrates how hESCs can provide unique insights into human  development and further our understanding of how leukemic fusion genes known to arise pre-natally regulate human embryonic hematopoietic specification.

overall_design: MLL is involved in transcriptional regulation and most MLL translocations appear to result in increased expression of Hox genes and hematopoietic genes. We therefore assessed the impact of MLL-AF4 expression on the transcriptome of hESCs. Gene expression profiling performed in MLL-AF4 hESCs revealed that MLL-AF4 preferentially activates transcription. 1826 out of the 3001 genes (61%) expressed were up-regulated in MLL-AF4 hESCs. Human ESC samples were collected during the exponential cell growth phase and stabilized in RNA later. 500 ng of each total RNA sample was labelled with Cy3 using the Quick-Amp Labelling kit and hybridized with the Gene Expression Hybridization kit to a Whole Human Genome Oligo Microarray (Agilent Technologies) following the Manufacturer’s instructions. Each cell line was analyzed as independent duplicates. NEO-expressing (empty lentivector) hESC line was used as the baseline.

first: Clara

last: Bueno

first: Rosa

last: Montes

first: Verónica

last: Ramos-Mejia

first: Pedro

last: Real

last: Ayllón

first: Laura

last: Sanchez

first: Gertrudis

last: Ligero

first: Iván

last: Gutierrez-Aranda

first: Agustín

middle: F

last: Fernández

first: Mario

last: Fraga

first: Inmaculada

last: Moreno-Gimeno

first: Deborah

last: Burks

first: María

last: del Carmen Plaza-Calonge

first: Mel

last: Greaves

first: Juan

last: Rodríguez-Manzaneque

first: Pablo

last: Menendez


title: Transcriptional profiling after bile duct ligation identifies PAI-1 as a contributor to cholestatic injury in mice.

city: St Louis

first: Rekha

last: Meyer

state: MO

address: 4320 Forest Park Av

institute: Washington University School of Medicine

summary:
Extrahepatic cholestasis leads to complex injury and repair processes that result in bile infarct formation, neutrophil infiltration, cholangiocyte and hepatocyte proliferation, extracellular matrix remodeling, and fibrosis. To identify early molecular mechanisms of injury and repair after bile duct obstruction, microarray analysis was performed on liver tissue 24 hours after bile duct ligation (BDL) or sham surgery. The most upregulated gene identified encodes plasminogen activator inhibitor 1 (PAI-1, Serpine 1), a protease inhibitor that blocks urokinase plasminogen activator (uPA) and tissue-type plasminogen activator (tPA) activity.
Because PAI-1, uPA, and tPA influence growth factor and cytokine processing as well as extracellular matrix remodeling, we evaluated the role of PAI-1 in cholestatic liver injury by comparing the injury and repair processes in wild-type (WT) and PAI-1-deficient (PAI-1-/-) mice after BDL. PAI-1-/- mice had fewer and smaller bile infarcts, less neutrophil infiltration, and higher levels of cholangiocyte and hepatocyte proliferation than WT animals after BDL. Furthermore, PAI-1-/- mice had higher levels of tPA activation and mature hepatocyte growth factor (HGF) after BDL than WT mice, suggesting that PAI-1 effects on HGF activation critically influence cholestatic liver injury. This was further supported by elevated levels of c-Met and Akt phosphorylation in PAI-1-/- mice after BDL. In conclusion, PAI-1 deficiency reduces liver injury after BDL in mice. These data suggest that inhibiting PAI-1 might attenuate liver injury in cholestatic liver diseases.

overall_design:
Total RNA isolated using TRI Reagent (Sigma, St. Louis, MO) was purified with an RNeasy mini kit (Qiagen, Valencia, CA). Twenty micrograms cRNA was hybridized to a mouse GeneChip (U74Av2, Affymetrix, Santa Clara, CA) at the Siteman Cancer Center GeneChip facility as described by the manufacturer. Analyses used one mouse per chip. Gene expression changes were analyzed using Affymetrix MicroArray Suite 4.0 and GeneChip 3.1 Expression Analysis and Statistical Algorithms (Affymetrix). The complete methodology and full data sets for all 6 analyzed chips are available at http://bioinformatics.wustl.edu.beckerproxy.wustl.edu

This study compares the injury and repair processed in wild-type mice after BDL.

first: H

last: Wang

first: B

middle: P

last: Vohra

first: Y

last: Zhang

first: R

middle: O

last: Heuckeroth


title: Systematic Bias in Genomic Classification Due to Contaminating Normal Tissue in Breast Tumor Samples

status: Public on Jul 19 2011

city: Chapel Hill

first: Melissa

last: Troester

state: NC

address: 135 Dauer Drive, CB 7435

department: Epidemiology

institute: University of North Carolina at Chapel Hill

summary:
Results: Normal tissue contamination caused misclassification of tumors in all predictors, but different breast cancer predictors showed different susceptibility to normal tissue bias. Sensitivity and negative predictive value (NPV) of the PAM50 assay was improved by accounting for normal tissue.

Conclusions: Normal tissue sampled concurrently with tumor tissue is an important source of bias in genomic predictors.  Adjustments for normal tissue contamination could improve the application of breast cancer genomic predictors in both research and in clinical settings.

overall_design: Reference x breast tumor samples.

first: Fathi

last: Elloumi


title: CPG stimulation for Gene Expression of unmutated B-CLL

status: Public on Jun 30 2011

city: Aviano

first: daniela

last: marconi

address: Via franco Gallini 2

country: Italy

institute: CRO AVIANO

summary: The aim is to identify the differential gene expression profile of unmutated B-CLL stimulated with CPG.

overall_design: Two-condition experiment, CPG-stimulated B-CLL unmutated vs. Unstimulated B-CLL unmutated . Biological replicates: 9 unstimulated replicates, 9 CPG-stimulated replicates. Reference design;

first: Riccardo

last: Bomben

first: Daniela

last: Marconi

first: Dimitar

last: Efremov

first: Stefano

last: Volinia

first: Valter

last: Gattei


title: Fungal allergen extracts-induced gene expression in airway epithelial cells (NCI-H292)

status: Public on Jul 07 2011

city: Shinjuku-ku

first: TSUYOSHI

last: OGUMA

state: Tokyo

address: 35 Shinanomachi

department: Department of Medicine

institute: Keio University School of Medicine

summary: We compared the gene expression stimulated with fungal extracts from Aspergillus (A.) fumigatus, Alternaria (A.) alternata, or Penicillium (P.) notatum in NCI-H292 (a human bronchial epithelial cell line) to search Allergic bronchopulmonary mycosis (ABPM)-related genes. We identified a mucin-related MUC5AC gene, the expression of which was selectively induced by A. fumigatus.

overall_design: Total RNA from NCI-H292 cells stimulated for 24 h with the A. fumigatus, A. alternata, or P. notatum fungi extracts was extracted and subjected to microarray analysis. Each experiments were perfomed once for each stimulus.

first: Tsuyoshi

last: Oguma

first: Koichiro

last: Asano


title: The MALAT-1 noncoding RNA Regulates Cell Mobility by Modulating Gene Expressions

status: Public on Jun 02 2011

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

institute: University of Tsukuba

summary: MALAT-1, originally identified as a metastasis associated long noncoding transcript in lung adenocarcinoma, is localized to nuclear speckles. However, functional role of MALAT-1 in metastatic characters in cancer cells has not been elucidated. Our current research has revealed that suppression of MALAT-1 expression in lung adenocarcinoma cell line by RNA interference significantly inhibited cellular mobility both in wound healing assay and in migration assay using Boyden's chamber. Moreover, we have identified metastasis/mobility-associated genes among down-regulated genes in the MALAT-1 knockdown cells by DNA microarray analysis. Quantitative analysis of pre-mRNAs has shown that the pre-mRNAs of some genes were suppressed in MALAT-1 knockdown cells but the others were not suppressed even though their matured mRNAs were found to be down-regulated. Our results suggest that MALAT-1 facilitates cell mobility by modulating the expression of metastasis/mobility-associated genes at the transcriptional and post-transcriptional stages.

overall_design: Comparison between control (A549) and knockdown (MALAT-1) cells was performed. Two biological replicates were used, and each replicate was dye-swaped.

first: Ryu

last: Miyagawa

first: Rie

last: Mizuno

first: Yo

last: Nakamura

first: Ijiri

last: Kenichi

first: Randeep

last: Rakwal

first: Junko

last: Shibaot

first: Yoshinori

last: Masuo

first: Tetsuro

last: Hirose

first: Nobuyoshi

last: Akimitsu


title: Respiratory chain protein analysis and gene expression profiles of fibroblast cell lines from 9 patients with SURF1 gene mutations

status: Public on Jun 01 2011

city: Prague

first: Viktor

last: Stranecky

address: Ke Karlovu 2

department: 1st Faculty of Medicine

country: Czech Republic

institute: Charles University

summary: Upregulation of  CI, CIII and CV  at a protein but not mRNA level in LSCOX cell with COX deficiency due to SURF1 mutations compared to control – evidence for posttranscriptional compensatory mechanism.

overall_design: Two-condition experiment, patients vs. controls cells. Biological replicates: 3 controls and 9 patients, independently grown and harvested.

first: Nikola

last: Kovarova

first: Alena

last: Cizkova Vrbacka

first: Petr

last: Pecina

first: Ewa

last: Pronicka

first: Stanislav

last: Kmoch

first: Josef

last: Houstek


title: Hey3Met2 human ovarian cancer cells overexpressing wild type or catalytically-dead mutant RNASET2

city: Ispra (VA)

first: marco

last: fabbri

address: Via E. Fermi, 2749

department: Institute for Health and Consumer Protection

institute: European Commission - Joint Research Centre

summary: Hey3Met2 cells were stably transfected with plasmids encoding either wild-type RNASET2 or a catalytically dead form (whose cDNA has been previously mutagenized in the two CAS catalytic sites) or with the empty vector as a control. The control of ovarian tumorigenesis by RNASET2 occurs through modification of the cellular microenvironment and involvement of immunocompetent cells, thus providing evidence for specific modulations of cellular responses induced by RNASET2 that might underlay ovarian tumorigenesis. In order to get more inside on the effect of RNASET2 on the modulation of other genes, a whole genome expression has been run on Hey3Met2 cell transfected with wildtype or mutated RNASET2.

overall_design: Hey3Met2 human ovarian cancer cells were  transfected with espression vectors encoding either wild type or catalitycally dead mutant RNASET2. Clones transfected with the empty vectors were used as negative controls. Three independent clones were used for the each type of transfected plasmid.

first: Maria

middle: G

last: Sacco

first: Marco

last: Fabbri

first: Laura

last: Gribaldo

last: Monti

first: Marta

last: Lualdi

first: Raffaella

last: Cinquetti

first: Solange

last: Roumengous

first: Francesco

last: Acquati

first: Roberto

last: Taramelli


title: miRNA and mRNA expression profile of CLL cells

first: daniela

last: marconi

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

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

overall_design: Refer to individual Series

first: Riccardo

last: Bomben

first: Daniela

last: Marconi

first: Dimitar

last: Efremov

first: Valter

last: Gattei


title: Gene expression profiles of PNT1a prostate cells expressing FGFR-4 Arg388 or Gly388.

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary:
We have shown that in PNT1a cells expressing exogenous FGFR4 Arg388 or Gly388 under the control of the EF1 promoter almost all FGFR signaling can be attributed to the transfected receptor, and the two FGFR-4 isoforms are expressed at equivalent levels in the two cell lines. Furthermore, we have shown that serum contains abundant FGFs capable of activating FGFR-4 so these initial experiments were carried out in serum to mimic physiological conditions. In such conditions the Arg388 expressing PNT1a cells display increased invasiveness and motility compared to Gly388 expressing cells. FGFR-4 Arg388 allele shows increased receptor stability and sustained receptor activation following ligand binding when compared to the Gly388 allele. However, the impact of this sustained signaling on cellular signal transduction pathways is unknown. We therefore analyzed the effect of FGFR-4 Arg388 expression on signal transduction in prostatic epithelial cells. We have found that expression of the FGFR-4 Arg388 allele leads to increased activity of the MAPK pathway, increased activity of serum response factor and AP1 and transcription of multiple genes which are correlated with aggressive clinical behavior in prostate cancer.

Keywords: two group comparison

overall_design: To further understand the underlying molecular mechanisms of increased cell motility and invasiveness in Arg388 expressing cells, microarray studies of biological duplicates were performed on FGFR4 Arg388 and Gly388 expressing PNT1a cells using Agilent 44k whole genome expression microarrays to identify the effector genes that may be responsible for phenotypic differences between the two variants.

first: Michael

last: Ittmann

first: Olga

last: Dakhova

first: Wendong

last: Yu


title: Gene Expression Profiling of Tuberculous Meningitis

city: Bangalore

first: Akhilesh

last: Pandey

email: pandey@jhmi.edu, arivusudar@ibioinformatics.org, sameerkumar.iob@gmail.com, microarray@ibioinformatics.org

state: Karnataka

address: UnitI, Discoverer building, ITPL

country: India

institute: Institute of Bioinformatics

summary: Tuberculous meningitis is one of the fatal forms of extra pulmonary disease associated with high mortality and severe neurological defects in affected individuals.  We have carried out transcriptome level analysis using whole human genome microarrays to identify differential expression of genes between tuberculous meningitis and normals.  In our gene expression analysis, we found 2,434 genes that were differentially erexpressed with 2 or more than 2 fold changes between tuberculous meningitis compared to normal cases. Most of the genes encoded many of the proteins, which involves metabolism, energy pathways, cell growth and/or maintenance, transport and cell communication and signal transduction. We have performed immunohistochemistry for the validation of some of the novel candidates identified in our microarray studies.!Series_overall_design = Present study carried out mRNA expression profiling of five samples from patients diagnosed with tuberculous meningitis and four head injury cases were used as controls. We have used 4X44K arrays from agilent plaform. To validate our microarray results, we have done Immunohistochemistry on 15 TBM cases with control groups.

overall_design: Present study carried out mRNA expression profiling of five samples from patients diagnosed with tuberculous meningitis and four head injury cases were used as controls. We have used 4X44K arrays from agilent plaform. To validate our microarray results, we have done Immunohistochemistry on 15 TBM cases with control groups.!Series_type = Expression profiling by array


title: Genes Differentially Expressed as a result of Candida albicans SC5314 exposure to 10b

status: Public on May 11 2011

city: Shanghai

first: Liang

last: Rong-mei

address: Guohe road 325

country: China

institute: smmu

summary: Azole resistance and varying degrees of cross-resistance to other members of the azole family in clinical isolates have been documented, which has necessitated additional and prolonged use of the antifungal agents available. 2-Amino-Nonyl-6-Methoxyl-Tetralin Muriate (10b), a novel chemical structural aminotetralin derivate, is synthesized as an antifungal agent and exibited strong antifungal activity. To further investigated the action mechanism, we used microarray analysis to investigate the genes expression profiles of C. albicans cells treated or untreated with 10b and found 957 genes were differentially expressed. Of them,457 showed a decrease in expression and 500 showed an increase in expression. 33 down-regulated genes were involved in glycolysis (e.g., PFK1, CDC19 and HXK2), fermentation (e.g., PDC11, ALD5 and ADH1) and respiratory electron transport chain (e.g., CBP3, COR1 and QCR8). 30 differentially expressed genes were found to relate to biofilm formation, filamentous or hyphal growth. It was noticed that striking up-regulation of SFL1 and marked down-regulation of YWP1 directly related to prevent C. albicans from changing its morphology from the yeast form to the hyphal. Two genes related to specifically hydrolyzing beta-1, 3 glucan (e.g., XOG1) and chitin (e.g., CHT1) were significantly increased. 40 overexpressed genes and 15 down-regulated genes were related to the lipid metabolic process. Of them, Eight were directly linked to ergosterol biosynthesis, including ERG2, ERG6 and ERG11. 99 genes related to translation were down-regulated following exposure to 10b, which account for 21.66% in down-regulated genes. This suggested that translation might be lower in SC5314 cells exposed to 10b than in control.

overall_design: Total RNA from the control SC5314 cells and 10b-treated SC5314 cells were used to generate target cDNA, and then hybridized to 8k Candida albicans Genome Array Genechips, representing about 7925 characterized Candida albicans genes. Two independent experiments were conducted. Reference strain was control SC5314 cells and test strain was SC5314 cells treated with 10b.

first: Rong-mei

last: Liang


title: Dissection of human fibroblast populations by lung regions: genomic differences and functional pathway analysis

city: Pittsburgh

first: XIUXIA

last: ZHOU

address: 3459 fifth ave

institute: University of Pittsburgh

summary: ABSTRACT  Background: Primary human distal lung/parenchymal fibroblasts (DLF) exhibit a different phenotype from airway fibroblasts (AF), including the expression of high levels of alpha-SMA. The scope of the differences and the mechanisms driving them are unknown. We hypothesized that the distinct fibroblast characteristics based on lung region predicted a broad range of genomic differences which contribute to distinctly different functional pathway activation in AF and DLF. Methods and Findings: To investigate whether comprehensive gene expression patterns vary between AF and DLF, we compared global gene expression profiles of 3 matched pairs of primary human fibroblasts isolated from proximal and distal lung. 194 transcripts were upregulated in AF, and 290 transcripts upregulated in DLF. Quantitative real-time PCR (qRT-PCR) from both asthmatic and normal subjects confirmed the validity of microarray data (n = 8). Further analysis identified distinct pathway activation patterns, including the identification of the TGF-β receptor/SMAD3 signaling pathway as critical to the phenotypic differences in AF and DLF. The functional impact of these molecular differences on AF and DLF was then analyzed using Western blot, qRT-PCR, ELISA and gene knock-down approaches. TGF-β receptor/SMAD2-3 pathway analysis confirmed the contribution of higher TGF-β1 expression and accompanying SMAD3 and JNK activation to the increased alpha-SMA level seen in DLF. There are two limitations associated with our work. First, the microarray sample size was small. Second, for ethical reasons, a large majority of our data were from asthmatic subjects, only one pair of airway and distal lung tissues from a subject without knowing preexisting lung disease matched for age and smoking status was available. In this single normal subject, the same pattern of differences existed, supporting the concept that these genomic differences are regional, rather than disease-related.   Conclusions: These findings demonstrated marked molecular and functional differences for these two lung regional fibroblast populations. These results suggest that airway and parenchymal fibroblasts differ in their responses to injury, repair, and remodeling in the lungs. There are likely profound implications of these observations for understanding mechanisms of development of fibrotic lung diseases as well as approaching therapy.

overall_design: In order to identify the underlying molecular differences between airway- and distal lung fibroblasts, microarray analysis was performed on 3 different matched pairs of fibroblasts.

first: Xiuxia

last: Zhou

first: Wei

last: Wu

first: Haizhen

last: Hu

first: Jadaranka

last: Milosevic

first: Kazuhisa

last: Konishi

first: Naftali

last: Kaminski

first: Sally

last: Wenzel


title: Interactions with Fibroblasts are Distinct in Basal-like and Luminal Breast Cancers

status: Public on May 27 2011

first: Melissa

last: Troester

summary: Basal-like breast cancers have several well-characterized distinguishing molecular features, but most of these are features of the cancer cells themselves. The unique stromal-epithelial interactions, and more generally, microenvironmental features of basal-like breast cancers, have not been well characterized. To identify characteristic microenvironment features of basal-like breast cancer, we performed cocultures of several basal-like breast cancer cell lines with fibroblasts (reduction mammoplasty-derived fibroblast line; RMF) and compared these to cocultures of luminal breast cancer cell lines with fibroblasts. Interactions between basal-like cancer cells and fibroblasts induced expression of numerous interleukins and chemokines, including IL-6, IL-8, CXCL1, CXCL3, and TGFbeta. Under the influence of fibroblasts, basal-like breast cancer cell lines also showed increased migration in vitro. Migration was less pronounced for luminal lines, but these lines were more likely to have altered proliferation. These differences were relevant to tumor biology in vivo, as the gene set that distinguished luminal and basal-like stromal interactions in coculture also distinguishes basal-like from luminal tumors with 98% accuracy in 10-fold CV and 100% accuracy in an independent test set. However, comparisons between cocultures where cells were in direct contact and cocultures where interaction was solely through soluble factors suggest that there is an important impact of direct cell-to-cell contact. The phenotypes and gene expression changes invoked by cancer cell interactions with fibroblasts support the microenvironment and cell-cell interactions as intrinsic features of breast cancer subtypes.

overall_design: 99 samples were hybridized with Stratagene common reference and profiled on Agilent microarrays.

first: JT

last: Camp


title: miR-142-3p over-expression in the Raji B-cell line

status: Public on May 30 2011

city: Nantes

first: Richard

last: Danger

address: 30 Boulevard Jean Monnet

country: France

institute: CHU Nantes - INSERM- Nantes Universite

summary: miR-142-3p is highly expressed in peripheral blood mononuclear cells (PBMCs) and has been described as a hematopoietic-restricted lineage, suggesting immune functions (Chen, Li et al. 2004; Landgraf, Rusu et al. 2007; Merkerova, Belickova et al. 2008). In order to determine the roles of miR-142-3p in B lymphocytes, we over-expressed this miRNA in the Raji B-cell line using a synthetic mimic of miR-142-3p and analyzed gene expression 24 hours after the transfection.

overall_design: Four replicates each of miR-142-3p-mimic transfection and apparied control mimic.

first: Sophie

last: Brouard


title: Gene expression profiles of MCF7 with CARM1 knocked down

city: Madison

last: Xu

state: WI

address: 1400 University Ave

institute: UW-Madison

summary:
The goal of this study is to identify ERalpha-target genes affected by knocking down of the histone arginine methyltransferase CARM1 in MCF7 breast cancer cells. The roles of CARM1 in ERalpha+ breast cancer was not well characterized. Therefore, we created a Dox inducible CARM1 knockingdown MCF7 cell line where CARM1 is decreased to 20% of endogeneous level to determine the
created a Dox-inducible CARM1shRNA overexpressing MCF7 cells for evaluation of the global effects of CARM1 on ERalpha-target gene expression.

overall_design: MCF7-tet-on-CARM1shRNA clone 1 were treated under 4 conditions: DMSO; Dox; E2 (10nM); Dox+E2. In Dox+E2 condition, cells were pre-treated with Dox for 5 days before treating with E2 for 4 hours. 3 biological replicates were included and total of 12 samples were analyzed.

first: Yuerong

last: Zhu

first: Jiacai

first: Sujun

last: Hua

first: Kevin

last: White


title: Differentially expressed genes in metallopanstimulin-1 knockdown cells

status: Public on Apr 27 2011

first: Zhongyin

last: Yang

address: NO.197 Ruijin er road

department: Department of Surgery

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

summary: To identify the differentially expressed genes in metallopanstimulin-1 (MPS-1) knockdown gastric cancer cells compared with negative control ones, we employed the microarray profiling analysis. MPS-1 was knockdown by retroviral interfering system in human gastric adenocarcinoma originated cell SGC7901 and the transfectants named P4, while the negative control named NC. Genes with greater than 1.5-fold change and P-value ＜0.05 were identified as differentially expressed genes between NC and P4 cells. Among those, apoptotic related gene (Gadd45β, cIAP2, Bcl2, CAD, Bid, etc) and adhesive related genes (integrin beta 4, ECM2, etc) were quantified by real-time PCR as well as western blotting.

overall_design: The two groups of negative control (NC) and MPS-1 knockdown gastric cancer cells (P4) were harvested after puromycin screening. Three independent experiments were performed for each group.

first: Qinlong

last: Gu


title: Comparison between Gene expression in stroma and glands of the transitional and peripheral zone of the prostate

status: Public on May 06 2011

city: Bonn

first: Andreas

last: Lindstrot

address: Sigmund-Freud-Str. 25

department: Molekular Patholoy

country: Germany

institute: University of Bonn

summary: To investigate the gene expression differences between the stroma and glands in the transitional and peripheral zones of the prostate

overall_design: Laser microdissection of prostate cancer tissues to separate glands from stroma followed by RNA extraction from the glands and whole Genome Microarray. We have pooled normal glands and stroma out of the transitional and peripheral zones from 10 patients after radical prostatectomy

first: Zaki

last: Shaikibrahim

first: Reinhard

last: Büttner

first: Nicolas

last: Wernert


title: DNA Methylation Profiling of Glioblastoma: Impact on Gene Expression and Clinical Outcome

status: Public on Jun 29 2011

city: Rennes

first: Amandine

last: Etcheverry

address: 2 rue Henri Le Guilloux

institute: CNRS UMR 6290 - IGDR

type:
Expression profiling by array
Methylation profiling by array


title: Human glioma cells: Control (GFP) vs PDGF-A expressing

status: Public on Apr 21 2011

city: PITTSBURGH

first: HAIZHONG

last: FENG

address: 5117 CENTRE AVE

institute: UNIVERSITY OF PITTSBURGH

summary: Transcriptional profiling of human glioma cells comparing control GFP expressing cells with glioma cells transfected with a human PDGF-A gene. The isogenic cell lines were used to study the impact on glioma tumorigenesis and invasion. Goal was to determine the effects of PDGF-A gene transfection on global ES gene expression.

overall_design: Two set of glioma cell lines, LN444 vs LN444/PDGF-A and LN443 vs LN443/PDGF-A. Biological replicates: 2 control replicates, 2 transfected replicates.

first: Feng

last: Haizhong

first: Bo

last: Hu

first: Kun-Wei

last: Liu

first: Xinghua

last: Lu

first: Jia-Jean

last: Yiin

first: Songjian

first: Susan

last: Keezer

first: Tim

last: Fenton

first: Frank

middle: B

last: Furnari

first: Ronald

middle: L

last: Hamilton

first: Kristiina

last: Vuori

first: Motoo

last: Nagane

first: Ryo

last: Nishikawa

first: Webster

last: Cavenee

first: Shi-Yuan

last: Cheng


title: Inflammatory activation of airway epithelial cells by pyocyanin

city: Rockville

first: Balazs

last: Rada

address: 12441 Parklawn Drive

department: NIAID

institute: NIH

summary: Despite the appreciated in vivo role of the redox-active Pseudomonas virulence factor pyocyanin in Pseudomonas airway infections and the recognized importance of airway epithelial cells in combating bacterial pathogens, little is known about pyocyanin’s effect on airway epithelial cells. We find that exposure of bronchiolar epithelial cells to pyocyanin results in MUC2/MUC5AC induction and mucin secretion mediated by reactive oxygen species production, activation of the epidermal growth factor receptor pathway and release of inflammatory cytokines (IL-1b, IL-6, TGFa, TNFa). Microarray analysis identified 286 pyocyanin-induced genes in airway epithelial cells, including many of the inflammatory mediators elevated in cystic fibrosis airways (G-CSF, GM-CSF, CXCL1, SAA). We also found several novel pyocyanin-responsive genes of potential importance in the infection process (IL-24, CXCL2, CXCL3, CCL20, SOD2). This comprehensive study uncovers numerous details of pyocyanin’s proinflammatory action and establishes airway epithelial cells as key responders following exposure to this microbial toxin.

overall_design: H292 cells were treated with or without 8 uM pyocyanin for 48 hrs in serum-free RPMI medium. RNA was isolated in four independent experiments, collected, processed and subjected to microarray analysis simultaneously (biological repeats).


title: Comparison of gene expression pattern of THP-1 cell treated with ATRA and RAD001

status: Public on Apr 25 2011

city: Kyoto

first: Toshihiko

last: Imamura

address: 465 Kajiichou Hirokouji Kawaramachi Sakyo-ku

department: Pediatrics

institute: Kyoto Prefectural University of Medicine

summary: To explore the mechanism related to the induction of monocytic differentiation in AML combination of ATRA and RAD001, gene expression patterns of THP-1 cells  were analyzed using  the Agilent Whole Human Genome Expression Array.

overall_design: Gene expression patterns of THP-1 cell cultured under four different conditions were analyzed. The conditions were as follows; 1, untreated. 2,  treated with ATRA (1mM) and RAD001 (2.5nM). Total RNA was extracted at 5 days after starting treatment.

first: Hideki

last: Yoshida


title: Agilent expression analysis of prostate cancer tissue samples

status: Public on May 03 2011

city: Ann Arbor

first: Jung

last: Kim

address: 1400 E. Medical Center Drive

institute: University of Michigan

summary: Beginning with precursor lesions, aberrant DNA methylation marks the entire spectrum of prostate cancer progression. We mapped the global DNA methylation patterns in selected prostate tissues and cell lines using Methylplex-Next Generation Sequencing (M-NGS). Hidden Markov Model based next generation sequence analysis identified ~68,000 methylated regions per sample. While global CpG Island (CGI) methylation was not differential between benign adjacent and cancer samples, overall promoter CGI methylation increased from ~12.6% in benign samples to 19.3% and 21.8% in localized and metastatic cancer tissues, respectively. We found distinct patterns of promoter methylation around transcription start sites, where methylation occurred not only on the CGIs, but also on flanking regions and CGI sparse promoters. Among the 6,691 methylated promoters in prostate tissues, 2481 differentially methylated regions (DMRs) are cancer specific, including numerous novel DMRs. A novel cancer specific DMR in WFDC2 promoter showed heavy methylation in cancer (17/22 tissues, 6/6 cell lines), but not in the benign tissues (0/10) and normal PrEC cells. Integration of LNCaP DNA methylation and H3K4me3 data suggested an epigenetic mechanism for alternate transcription start site utilization and these modifications segregated into distinct regions when present on the same promoter. Finally, we observed differences in repeat element methylation, particularly LINE-1, between ERG gene fusion positive and negative cancers. This comprehensive methylome map will further our understanding of epigenetic regulation in prostate cancer progression.  In this submission, Agilent expression array data used for Gene Set Enrichment Analysis (GSEA) for enrichment analysis for gene repression is provided.

overall_design: A total of 13 prostate tissue samples are hybridized against a benign prostate tissue sample pool obtained form a commercial source (Clontech Laboratories, Mountain View, CA) on Agilent Human GE 44k miroarray platform. The fold change between the average expression value from normal/benign (n = 4) and cancer samples (n = 9) was calculated and pre-ranked (representing 27,928 unique probes). This list was uploaded to GSEA, and enrichment analysis is performed using methylation target gene lists in tumor samples.

first: Xuhong

last: Cao

first: Xiaojun

last: Jing

first: Saravana

middle: M

last: Dhanasekaran

first: Arul

last: Chinnaiyan


title: Comparisson between tumour and healthy prostate glands

status: Public on Apr 15 2011

first: Andreas

last: Lindstrot

summary: To investigate the gene expression differences between the normal peripheral zone glands compared to the moderatly and poorly differentiated tumor glands of the prostate.

overall_design: Laser microdissection of prostate cancer tissues to separate glands from stroma followed by RNA extraction from the glands and whole Genome Microarray. We have pooled normal glands from 10 patients, moderately differentiated tumor from 5 patients and poorly differentiated tumors from 4 patients with prostate carcinomas.

first: Zaki

last: Shaikibrahim

first: Reinhard

last: Büttner

first: Nicolas

last: Wernert


title: Transcriptomic and proteomic profiling of KEAP1 disrupted and sulforaphane treated human breast epithelial cells

status: Public on Apr 22 2011

city: Baltimore

first: Abena

last: Agyeman

address: 615 N Wolfe St

department: Biochemistry and Molecular Biology

institute: Johns Hopkins School of Public Health

summary: Sulforaphane (SFN), an isothiocyanate found in cruciferous vegetables, is a potent inhibitor of experimental mammary carcinogenesis and may be an effective, safe chemopreventive agent for use in humans. SFN acts in part on the Keap1/Nrf2 pathway to regulate a battery of cytoprotective genes. In this study transcriptomic and proteomic changes in the estrogen receptor negative, non tumorigenic human breast epithelial MCF10A cell line were analyzed following SFN treatment or KEAP1 knockdown with siRNA using microarray and stable isotopic labeling with amino acids in culture (SILAC), respectively. Changes in selected transcripts and proteins were confirmed by PCR and Western blot in MCF10A and MCF12A cells. There was strong correlation between the transcriptomic and proteomic responses in both the SFN treatment (R=0.679, P<0.05) and KEAP1 knockdown (R=0.853, P<0.05) experiments. Common pathways for SFN treatment and KEAP1 knockdown were xenobiotic metabolism and antioxidants, glutathione metabolism, carbohydrate metabolism and NADH/NADPH regeneration. Moreover, these pathways were most prominent in both the transcriptomic and proteomic analyses. The aldo-keto reductase family members, AKR1B10, AKR1C1, AKR1C2 and AKR1C3, as well as NQO1 and ALDH3A1, were highly upregulated at both the transcriptomic and proteomic level.  Collectively, these studies served to identify potential biomarkers that can be used in clinical trials to investigate the initial pharmacodynamic action of SFN in the breast.

overall_design: MCF10A cells were treated with SFN or had KEAP1 knocked down by siRNA.

middle: S


title: FACS-array profiling in retinal endothelial cells from living mouse retinas

status: Public on Apr 17 2011

city: Kobe

first: Sentaro

last: Kusuhara

state: Hyogo

address: 7-5-2 Kusunoki-cho, Chuo-ku

institute: Kobe University Graduate School of Medicine

summary: Deregulated retinal angiogenesis directly cause vision loss in many ocular diseases, such as diabetic retinopathy and retinopathy of prematurity. To identify endothelial-specific genes expressed in angiogenic retinal vessels, we purified genetically labeled endothelial cells from Tie2-GFP transgenic mice and performed gene expression profiling using DNA microarray. To find out genes associated with angiogenesis, comparisons of microarray data were carried out between GFP-negative non-endothelial retinal cells and GFP-positive retinal endothelial cells in angiogenic P8 retina.

overall_design: Eighteen arrays are included. Utilizing fluorescence-activated cell sorting (FACS), we isolated endothelial cells as GFP-positive cells from P8 retina in homozygous Tie2-GFP transgenic mice. GFP-negative cells were served as non-endothelial control. RNA extracts from sorted cells were amplified and then hybridized to Affymetrix MGU74v2 series arrays in triplicate.

first: Lars

last: Jakt


title: Human Hair follicles: Control Vs. 0.5 µM spermidine treatment

status: Public on Apr 16 2011

city: Jerusalem

first: Yuval

last: Ramot

address: Kiryat Hadassah, p.o.b 12000

country: Israel

institute: Hadassah - Hebrew University Medical Center

summary: To compare the effects of spermidine, key polyamine, on the gene expression profile of organ cultured human hair follicles

overall_design: Vehicle treated Vs. 0.5 µM spermidine treatment. Two control samples, two spermidine treated samples

first: Ralf

last: Paus


title: cDNA microarray analysis of miR-1 transfected HeLa and NPC-TW01 cells

status: Public on Apr 13 2011

city: Taipei

first: Chin-Tarng

last: Lin

address: No. 7 Chung-Shan S. Rd

department: Pathology

country: Taiwan

institute: National Taiwan University

summary: To investigate the mechanisms of miR-1 inducing apoptosis, we performed cDNA expression microarray analysis to identify the candidate miR-1 regulating genes that are involved in apoptosis.

overall_design:
NPC-TW01 cells were transfected with miR-1 or miR-negative control for 40 hours, their total RNA were isolated from the cells and hybridized to an Agilent human whole genome oligo 4 x 44 K microarray.
HeLa cells were transfected with miR-1 or miR-negative control for 40 hours, their total RNA were isolated from the cells and hybridized to an Agilent human whole genome oligo 4 x 44 K microarray.

first: Cheng-Der

last: Wu

first: Yuan-Sung

last: Kuo

first: Han


title: Expression data from LSK mice that overpexpress Ezh2 versus LSK Control

status: Public on Apr 05 2011

city: Madrid

first: Antonio

middle: Herrera

last: Merchan

address: Melchor Fernández Almagro, 3

department: Regenerative Cardiology

institute: CNIC

summary:
Ezh2 is a protein member of PRC2 and has described like a functional repressor gene. We are investigating the role of Ezh2 in hematopoietic stem cell, aging and leukemia.
In the present study, we generated mouse models that allow gain-of-function of Ezh2 in the hematopoietic system. Activation of Ezh2 expression specifically in self-renewing HSCs alters gene expression programs and severely compromises hematopoietic function, leading to the development of myeloproliferative disease.

overall_design:
We used microarrays to detail the global programme of gene expression in LSK that has relationship with the overexpression of Ezh2.
LSK were marked and isolated by Fluorescence-activated cell sorting in Trizol.

first: Susana

last: González

last: Herrera-Merchan


title: Comparison of gene expression profiles of A549 cell treated with NRF2 siRNA and control siRNA

status: Public on Apr 01 2011

city: Sendai

first: Hozumi

last: Motohashi

state: Miyagi

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

department: Center for Radioisotope Science

institute: Tohoku University Graduate School of Medicine

summary:
To examine the role of NRF2 in accelerating cell proliferation and to identify the target genes responsible for this function, transcriptome analysis was performed using A549 cells, in which NRF2 is constitutively activated.
NRF2 was knocked down by siRNA against NRF2, and the gene expression profile was compared with that of A549 cells treated with control siRNA.  To exclude off-target effects, three different siRNAs against NRF2 was independently applied.

overall_design: NRF2 siRNA or control siRNA was transfected into A549 cells.  Cells were harvested 24 hours after transfection, and total RNA was purified.

first: Y

last: Mitsuishi

first: M

last: Yamamoto

first: H


title: Expression profiling of KSR1-/- MEFs expressing KSR1 and/or H-RasV12

status: Public on Apr 02 2011

city: Omaha

first: Robert

last: Lewis

state: NE

address: 12706 Lied Transplant Center

institute: Univ. of Nebraska Medical Center

summary: We engineered KSR1-/- mouse embryonic fibroblasts (MEFs) to express GFP alone, KSR1 or RasV12 and GFP, or KSR1, H-RasV12 and GFP, and performed gene expression profiling on all 4 cell lines.

overall_design:
Each cell line was measured in triplicate:
1. GFP alone
2. H-RasV12 and GFP
3. KSR1 and GFP
4. KSR1, H-RasV12, and GFP

first: Kurt

middle: W

last: Fisher


title: Identification of novel target genes of nerve growth factor (NGF) in human mastocytoma cell line (HMC-1 (V560G c-Kit)) by transcriptome analysis

status: Public on Mar 22 2011

city: Hannover

first: Oliver

last: Dittrich-Breiholz

address: Carl-Neuberg-Str. 1

department: Research Core Unit Genomics

institute: Medical School Hannover

summary: Nerve growth factor (NGF) pays a role in neuronal differentiation and may also play a  role in hematopoietic differentiation as shown by synergistic action for the colony formation of CD34 positive hematopoietic progenitor cells treated with M-CSF or SCF. However, the exact role of NGF in hematopoietic system is unclear. It is also not clear whether NGF mediated signals in hematopoietic cells are identical to those in neuronal cells. To study the signal transduction pathways induced by NGF treatment in hematopoietic cells, we utilized the mastocytoma cell line HMC-1 (V560G c-Kit) which expresses the NGF receptor, TrkA, as well as the constitutively activated SCF receptor, V560G c-Kit, which can be inhibited by treatment with tyrosine kinase inhibitor imatinib mesylate. NGF rescues HMC-1 (V560G c-Kit) from imatinib induced cell death and promotes proliferation. To examine the NGF mediated proliferation and survival in these cells, we compared the NGF mediated upregulated genes (30 and 120 min after stimulation) to the downregulated genes by imatinib treatment (downregulation of c-Kit activity for 4 h) by transcriptome analysis. The following conclusions can be drawn from the microarray data: Firstly, gene expression profiling reaveals 50% overlap of genes induced by NGF-TrkA with genes expressed downstream of V560G c-Kit. Secondly, NGF treatment does not enhance expression of genes involved in immune related functions that were down modulated by imatinib. Thirdly, more than 55% of common upregulated genes are involved in cell proliferation and survival. Forthly, we found KLF2 and SMAD7 as the NGF mediated novel down stream genes in hematopoietic cells that may play a role in NGF mediated survival signal in HMC-1 (V560G c-Kit) cells. Keywords: Transcriptome analysis - comparison of TrkA and V560G c-Kit downstream genes in HMC-1 (V560G c-Kit) cells

overall_design: In total, 4 samples were analyzed, one of which served as a common reference (HMC1 17h SerumStarv 4h Imatinib). This sample was labeled with Cy3. All additional samples were labeled with Cy5 and were cohybridized against the common reference. The first hybridization (M2370) represents a self-self-hybridization using the common reference.

first: Priyanka

last: Dutta

first: Alexandra

last: Koch

first: Bjoern

last: Breyer

first: Heike

last: Schneider

first: Michael

last: Kracht

first: Teruko

last: Tamura


title: Gene Re-expression in Calu6 Tumors Following Epigenetic Therapy

city: Albuquerque

first: Steven

middle: A

last: Belinsky

state: NM

address: 2425 Ridgecrest Dr SE

department: Lung Cancer Program

institute: Lovelace Respiratory Research Institute

summary: Transciptional profiling of Calu6 tumors comparing 4 pooled untreated tumors to 5-azacytodine or 5-azacytodine + MS-275 (combined therapy) treated tumors

overall_design: Three-condition experiment, untreated vs. 5-Azacytodine tumors, and untreated vs. 5-azacytodine + MS-275 tumors: 4 pooled untreated tumors; 4 5-Azacytodine treated, 4 5-Azacytodine + MS-275 treated.  Study used a loop design with dye-swap.

first: Maria

last: Picchi

first: Hugh

last: Mitchell


title: Gene expression changes upon knockdown or over-expression of the ETS gene ETV4 in prostate cancer cell lines

status: Public on Mar 25 2011

city: Bloomington

first: Peter

last: Hollenhorst

state: IN

address: 1001 E Third St, Jordan Hall 104

institute: Indiana University

summary: Chromosomal abnormalities that give rise to elevated expression levels of the ETS genes ETV1, ETV4, ETV5, or ERG are prevalent in prostate cancer, but the function of these transcription factors in carcinogenesis is not clear. Previous work implicates ERG, ETV1, and ETV5 as regulators of invasive growth but not transformation in cell lines. Here we show that the PC3 prostate cancer cell line provides a model system to study the over-expression of ETV4. Anchorage independent growth assays and microarray analysis indicate that high ETV4 expression is critical for the transformation phenotype of PC3 cells. However, genes up-regulated upon ETV4 over-expression were very similar to genes up-regulated by ETV1 over-expression in the RWPE-1 normal prostate cell line. Together these data indicate that the ETV4 dependent transformation phenotype observed in PC3 cells is due to the genetic background of the cell line, rather than a distinct characteristic of ETV4. Furthermore, these findings suggest that the function of ETS genes in prostate cancer may differ based on other genetic alterations in a tumor.

overall_design: Two sets of two color experiments. First is PC3 cells expressing one of two independent ETV4 shRNAs versus PC3 cells expressing a control shRNA (luciferase). Second is RWPE-1 cells expressing 3xFlag tagged ETV4 versus RWPE-1 cells with a control (empty) vector.

first: Barbara

middle: J

last: Graves

first: Litty

last: Paul


title: Mutated KRAS induces overexpression of DUSP4, a MAP-kinase phosphatase, and SMYD3, a histone methyltransferase, in rectal carcinomas

status: Public on Mar 11 2011

city: Goettingen

first: Marian

last: Grade

address: Robert-Koch-Str. 40

department: Surgery

institute: University Medical Center Goettingen, Georg-August-University

summary: Mutations of the KRAS oncogene are predictive for resistance to treatment with antibodies against the epithelial growth factor receptor in patients with colorectal cancer. Overcoming this therapeutic dilemma could potentially be achieved by the introduction of drugs that inhibit signaling pathways that are activated by KRAS mutations. To comprehensively identify such signaling pathways we profiled pretreatment biopsies from 65 patients with locally advanced rectal cancer – 30 of which carried mutated KRAS - using global gene expression microarrays. By comparing all tumor tissues exclusively to matched normal mucosa, we could improve assay sensitivity, and identified a total of 22,297 features that were differentially expressed (adjusted p-value p<0.05) between normal mucosa and cancer, including several novel potential rectal cancer genes. We then used this comprehensive description of the rectal cancer transcriptome as the baseline for identifying KRAS-dependent alterations.  The presence of activating KRAS mutations resulted in significant upregulation of 13 genes (adjusted p-value < 0.05), among them DUSP4, a MAP-kinase phosphatase, and SMYD3, a histone methyltransferase. Inhibition of the expression of both genes has been achieved therapeutically with the MEK1-inhibitor PD98059 and the antibacterial compound Novobiocin, respectively, suggesting a potential approach to overcome resistance to treatment with antibodies against the epithelial growth factor receptor in patients with KRAS-mutant rectal carcinomas.

overall_design: Paired samples of tumor and mucosa from a total of 65 patients, i.e. 130 arrays

first: Jochen

last: Gaedcke

first: Klaus

last: Jung

first: Jordi

last: Camps

last: Jo

first: Georg

last: Emons

first: Anastasia

last: Gehoff

first: Ulrich

last: Sax

first: Markus

last: Schirmer

first: Heinz

last: Becker

first: Tim

last: Beissbarth

first: Thomas

last: Ried

last: Ghadimi


title: Identification of differentially expressed miRNAs in BM+ vs. BM- lung cancer samples

status: Public on Feb 16 2011

city: Phoenix

first: Julianna

last: Ross

state: AZ

department: Cancer and Cell Biology

institute: Translational Genomics Research Institute

summary: Brain metastasis (BM) can affect up to 25% of non-small cell lung cancer (NSCLC) patients during their lifetime. Efforts to characterize patients that will develop BM have been fairly disappointing. Small non-coding microRNAs (miRNAs) regulate the expression of target mRNAs by repressing their translation or regulating their sequence-specific degradation.  miRNAs play a role in regulating a variety of targets and, consequently, multiple pathways, which makes them a powerful tool to be exploited for early detection of disease, risk assessment, and prognosis.  In this study, we investigated miRNAs that may serve as biomarkers to differentiate between NSCLC patients with and without BM.   miRNA microarray profiling was performed on samples from clinically matched NSCLC from patients with BM (BM+) and without BM (BM-).  miR-328 and miR-330-3p were able to correctly classify BM+ vs. BM- patients.  Gene expression analysis comparing NSCLC parental and stably transfected miR-328 cells identified several significantly differentially-expressed genes, whose expression may be directly or indirectly regulated by miR-328.

overall_design:
NSCLC Cell Line A549 analysis: Two-condition experiment, A549 GFP Control vs. A549 miR-328 cells. Biological replicates: 2 control replicates, 2 miR-328 replicates.

miRNA microarray analysis was performed on RNA extracted from formalin-fixed paraffin-embedded (FFPE) NSCLC tumor specimens from 7 BM+ patients and 5 BM- patients.

middle: T

first: Shilpi

last: Arora


title: Deficiency of CXCR2, but Not Other Chemokine Receptors, Attenuates Autoantibody-Mediated Arthritis in a Murine Model

status: Public on Feb 24 2011

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: To examine patterns of gene expression in ankle synovial fluid cells and peripheral blood leukocytes during serum transferred arthritis.

overall_design: A time-course microarray analysis of serum-transferred arthritis was performed, examining ankle tissue, synovial fluid, and peripheral blood leukocytes.

first: Jonathan

last: Jacobs

first: Adriana

last: Ortiz-Lopez

first: James

last: Campbell

first: Craig

last: Gerard

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Human SV80 Cells: Control vs. Caspase-8 knock down

status: Public on Feb 07 2011

city: Rehovot

first: Akhil

last: Rajput

address: 1, Herzl

department: Biological Chemistry

institute: The Weizmann Institute

summary: Excessive responses to pattern-recognition receptors are prevented by regulatory mechanisms that affect the amounts, conformation, and associative properties of their signaling proteins. We report that signaling by the ribonucleic acid sensor RIG-I is restricted, in addition, by caspase-mediated cleavage that results in conversion of a signaling enhancer to a signaling inhibitor. RIP1 and caspase-8, two proteins known to mediate effects of receptors of the TNF/NGF family, are recruited to the RIG-I complex following viral infection, and serve in a coordinated manner antagonistic regulatory roles: conjugation of a ubiquitin chain to Lys-377 in RIP1 facilitates assembly of the RIG-I complex, but it also renders RIP1 susceptible to caspase-8-mediated cleavage, yielding an inhibitory RIP1 fragment. The dependence of RIP1 cleavage on the same molecular change as the one that facilitates RIG-I signaling allows for RIG-I signaling to be restricted in its duration without compromising its initial activation.

overall_design:
Transcriptional profiling of human SV80 cells comparing cells infected with control lenti virus to cells infected with caspase-8 siRNA expressing lenti virus. Goal was to determine the effects of caspase-8 knock down on global gene expression.
Two-condition experiment, Control lenti Vs caspase-8 siRNA expressing lenti. Biological replicates: 4 control, 4 caspase-8 siRNA infected

first: David

last: Wallach


title: Whole Blood Cell Gene Expression Profiling in Patients with Coronary Artery Disease from the PREDICT Trial

status: Public on Mar 01 2011

city: CA

middle: A.

last: Wingrove

state: CA

address: 2500 Faber Place

institute: CardioDx, Inc.

summary:
Expression profiling of whole blood cells isolated from patients piror to undergoing cardiac catheterization.
PREDICT is a prospective, multi-center coronary catheter-lab trial being run in the US for the purpose of identifying biomarkers associated with coronary disease.  A summary of the trial can be found at http://clinicaltrials.gov (identifier # NCT00500617).

overall_design: 2 condition, paired experiment: Cases (1) are patients with  ≥50% stenosis in >= 1 major vessel by quantitative coronary angiography (QCA), Controls (0) have luminal stenosis of < 50% by QCA.  Samples were paired based on case/control status, age, and gender.

first: Michael

middle: R

last: Elashoff

first: Philip

last: Beineke

first: Susan

middle: E

last: Daniels


title: Gene expression signatures for human iPS cell lines

status: Public on Mar 07 2011

city: Tsukuba

first: Makoto

last: Asashima

address: 1-1-1 Higashi

department: Tsukuba Central 4

institute: National Institute of Advanced Industrial Science Technology (AIST)

summary: The reprogramming of human fibroblasts to generate induced pluripotent stem cells (hiPSCs) has been achieved through the expression of only a few exotic factors1-8, which is morphologically and molecularly verified in outer cellular states by characteristic markers, due to the remodeling of the somatic cell transcription programs in inner cellular states to the ES-like condition. Transcription factor-induced reprogramming to self-renewal and pluripotency raises the question as to how the exotic factors act to bring about these changes in the two cellular states9-11. Here, we applied RNA profiling to uncover gene expression changes and glycan profiling12 to survey structural changes in glycans, to compare hiPSCs and parental somatic cells, in total 51 cells, which were originally cultured and established, and the changes were analyzed by the combination of standard statistical techniques and a network approach13. We fist found a gene expression signature of 2502 genes with significant difference between iPSCs and SCs, and by the following network analysis by considering the expression signature, we found a network signature of 28 regulatory networks of 76 genes, which were related to the glycan biosynthetic pathways including 3 glycosyltransferase, in addition to well known signal pathways and cell-cell interaction pathways. Concomitantly, we found a glycan signature of six glycan structures characterized 16 lectins on lectin microarray by the correspondence with 12 glycosyltransferases in expression signature. In particular, the correspondence detected between the three expression signatures revealed 14 candidate glycosyltransferase, which are responsible for glycan transfer related to known epitopes for the differentiation such as SSEA epitope family in glycan biosynthesis pathway, based on characteristic changes in the cellular surface states of the hiPSCs. This sheds new light on a possible linkage between the inner and outer cellular states for reprogramming to self-renewal and pluripotency in hiPSC.

overall_design: Gene expressions in human induced pluripotent stem (iPS) cells and the provenance somatic cells . iPS cells were induced from four different somatic cells by infection of the retroviral vectors pMXs encoding OCT3/4, SOX2, KLF4 and c-MYC, simultaneously.

first: Yasuko

last: Onuma

first: Yuzuru

last: Ito


title: A Gene Expression Signature for Chemoradiosensitivity of Colorectal Cancer Cells

status: Public on Feb 10 2011

first: Melanie

last: Spitzner

department: Department of General and Visceral Surgery

institute: Georg-August-University Goettingen

summary: In this study, we use cancer cell lines to investigate the molecular differences between resistant and responsive colorectal cancer cells.  Since the treatment of patients with locally advanced rectal cancers involves chemoradiotherapy (CT/RT), we specifically implemented an in vitro protocol that mimics this clinical setting.  We anticipate that this analysis will unveil relevant pathways underlying the resistance of rectal cancers to CT/RT, and enable the identification of novel therapeutic target genes.

overall_design: 12 colorectal cancer (CRC) cell lines were obtained from the ATCC, and cultured in the respective tissue culture medium as recommended by the ATCC: Caco-2, HT-29, LS411N, LS513, LS1034, SW403, SW480, SW620, SW837, SW1116, SW1463, and WiDr.  For each cell line, RNA was independently isolated at three different passages, and hybridized to a gene expression array.  Accordingly, there are three biological triplicates per cell line.  Additionally, SW480 (triplicate), SW837 (triplicate), and Caco-2 (duplicate) were cultured in RPMI.

first: Georg

last: Emons

first: Frank

last: Kramer

first: Jochen

last: Gaedcke

first: Margret

last: Rave-Fränk

first: Jens-Gerd

last: Scharf

first: Peter

last: Burfeind

first: Heinz

last: Becker

first: Tim

last: Beissbarth

last: Ghadimi

first: Thomas

last: Ried

first: Marian

last: Grade


title: Whole Blood Cell Gene Expression Profiling in Patients with Coronary Artery Disease from the Cathgen Registry

first: James

last: Wingrove

summary:
Expression profiling of whole blood cells isolated from patients piror to undergoing cardiac catheterization.
The Cathgen Registry is a single-center coronary catheter-lab cohort being run at Duke University for the purpose of identifying biomarkers associated with coronary disease.

overall_design: 3 condition experiment: Cases (2) are patients with  ≥70% stenosis in >1 major vessel or ≥50% stenosis in >2 arteries; intermediates (1) are patients with luminal stenosis >25% but less than 50%;  controls (0) have luminal stenosis of <=25%

first: Michael

last: Elashoff

last: Beineke


title: Whole Blood Cell Gene Expression Profiling in Patients with Coronary Artery Disease (Homo sapiens)

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

overall_design: Refer to individual Series


title: GATA6 Activates Wnt Signaling in Pancreatic Cancer by Negatively Regulating the Wnt Antagonist Dickkopf-1

first: Christine

last: Iacobuzio Donahue

state: MD

address: 1550 Orleans Street, CRB2 Rm 343

institute: Johns Hopkins

summary: Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal disease characterized by late diagnosis and treatment resistance.  Recurrent genetic alterations in defined genes in association with perturbations of developmental cell signaling pathways have been associated with PDAC development and progression. Here, we show that GATA6 contributes to pancreatic carcinogenesis during the temporal progression of pancreatic intraepithelial neoplasia by virtue of Wnt pathway activation.  GATA6 is recurrently amplified by both quantitative-PCR and fluorescent in-situ hybridization in human pancreatic intraepithelial neoplasia and in PDAC tissues, and GATA6 copy number is significantly correlated with overall patient survival.  Forced overexpression of GATA6 in cancer cell lines enhanced cell proliferation and colony formation in soft agar in vitro and growth in vivo, as well as increased Wnt signaling. By contrast siRNA mediated knockdown of GATA6 led to corresponding decreases in these same parameters. The effects of GATA6 were found to be due to its ability to bind DNA, as forced overexpression of a DNA-binding mutant of GATA6 had no effects on cell growth in vitro or in vivo, nor did they affect Wnt signaling levels in these same cells. A microarray analysis revealed the Wnt antagonist Dickopf-1 (DKK1) as a dysregulated gene in association with GATA6 knockdown, and direct binding of GATA6 to the DKK1 promoter was confirmed by chromatin immunoprecipitation and electrophoretic mobility shift assays. Transient transfection of GATA6, but not mutant GATA6, into cancer cell lines led to decreased DKK1 mRNA expression and secretion of DKK1 protein into culture media.  Forced overexpression of DKK1 antagonized the effects of GATA6 on Wnt signaling in pancreatic cancer cells.  These findings illustrate that one mechanism by which GATA6 promotes pancreatic intraepithelial neoplasia is by virtue of its activation of canonical Wnt signaling via regulation of DKK1.

overall_design: AsPC1 and A13A cells were stably transfected with a lentivirus expressing mock shRNA or shRNA to GATA6. Each control/shRNA pair (total 4 samples) was analyzed by two-color microarray and the genes commonly dysregulated in both cell lines identified.

last: Iacobuzio-Donahue


title: Acute high dose X-irradiation-induced genomic changes in a lung tumor cell line

status: Public on Feb 04 2011

city: Berlin

first: Artur

last: Muradyan

address: Ihnestr. 73

institute: Max Planck Institute for Molecular Genetics

type: Genome variation profiling by genome tiling array

summary: Accidents with ionizing radiation (IR) often involve acute high dose exposures that can lead to acute radiation syndrome and late effects. IR can induce genomic lesions, cell death or carcinogenesis. Here, we investigated acute IR-induced cellular genomic signatures at the genome wide level. After exposing  the adenocarcinoma cell line A549 to an acute 6 Gy 240 kV X-Ray dose, four surviving clonogenic cells were recovered by minimal dilution and further expanded and analyzed by cytogenetics, chromosome painting and tiling-path array CGH, with the non-irradiated clone0 serving as control. It was found that acute X-ray exposure induced changes in modal chromosome number and specific translocations in the four irradiation surviving clones. Furthermore, clone4 displayed an increased radiosensitivity at D > 5 Gy. Array CGH disclosed unique and recurrent genomic changes, predominantly gains, and disclosed fragile sites FRA3B and FRA16D as preferential regions of genomic alterations in all irradiated clones, which likely relates to irradiation-induced genomic stress. Gene expression analysis revealed a specific profile of 364 genes in clone4, of which p53 pathway genes may contribute to its increased radiosensitivity. IR-induced genomic changes AND  fragile site expression highlight the capacity of a single acute radiation exposure to resculpture the genome of tumor cells by inflicting genomic stress.

overall_design: Gene expression and array-CGH in A549 cell line was analysed after exposure to 6Gy X-rays at a dose rate of 1Gy/min.

first: Stephanie

last: Stabentheiner

first: Susan

last: Klause

first: Hannelore

last: Madle

first: Viktor

last: Meineke

first: Reinhard

last: Ullmann

first: Harry

last: Scherthan


title: Comparable mRNA expression of pluripotency-related genes in SNUhES3 cells cultured on autofeeder or xenofeeder system

status: Public on Feb 02 2011

city: seoul

first: Eun Ju

last: Lee

address: 28 yongon dong

country: South Korea

institute: seoul natonal university

summary: I developed a new culture system for hES cells; this system does not require supplementation with bFGF to obtain hES cells that are suitable for tissue engineering and regenerative medicine. This culture system employed mesenchymal stem cells derived from hES cells (hESC-MSCs) as autologous human feeder cells in the absence of bFGF. For pluripotency-related gene expression profiling, a cDNA microarray analysis was performed

overall_design: SNUhES3 cultured on the autofeeder hESC-MSCs layer maintained the undifferentiated state for 30 passages in a manner similar to the SNUhES3 cells on xenofeeder STO cell layer. To compare the pluripotency-related genes in SNUhES3 cells cultured on autofeeder or xenofeeder system, I used agilent one-color array. Two independant experiment performed.

first: Eun-Ju


title: Transcriptome Signatures of Sezary Cells from Patients and Cultured Hut 78, Hut 102 and Jurkat Cells

status: Public on Dec 31 2010

city: Vancouver

first: Youwen

last: Zhou

address: 835 W 10th Ave

country: Canada

institute: University of British Columbia

summary: Comparative transcriptome profiles of patient-derived Sezary cells and cultured Sezary cell line (Hut78) mycosis fungoides cell line (Hut 102) and non-Sezary T cell leukemia cell line (Jurkat) relative to benign CD4+ T cells from individuals with no T cell malignancy. There are three goals. The first and primary goal is to establish a list of genes with differential expression between Sezary cells and the benign CD4+ T cell counter part from individuals without Sezary syndrome.  A secondary goal is to examine if these differentially expresses genes in clinical samples of Sezary cells are preserved in Hut78 and Hut102 cells, which are the two most frequently used experimental cell models of Sezary cells in the research community. The third goal is to examine if these Sezary cell specific genes are also present in a non-Sezary T cell malignancy, such as Jurkat cells, which is derived from a non-Sezary cell T cell leukemia patient.

overall_design: Two color experiment, 6 biological replicates (6 unique patients) with Sezary syndrome, 1 Hut78 cell,1 Hut102 cell and 1 Jurkat cell lines as the experimental samples, each compared with a distinct individual with no T cell malignancy of the skin or the blood.

first: Mingwan

last: Su

first: Yang

last: Wang


title: Highly Recurrent MYD88 Mutations That Promote Human Lymphoma Cell Survival

status: Public on Dec 30 2010

city: Bethesda

first: Louis

middle: M.

last: Staudt

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

summary: The ABC subtype of diffuse large B cell lymphoma (DLBCL) remains the least curable form of this lymphoma despite recent advances in therapy. We have combined structural and functional genomics to triangulate on new oncogenic mechanisms and devise new therapeutic strategies. RNA interference screen revealed a dependence of ABC DLBCL cell lines on MYD88 and IRAK1. High throughput resequencing of RNA (RNA-Seq) revealed frequent somatic mutations in MYD88 that preferentially occurred in the ABC DLBCL subtype. Remarkably, one third of ABC DLBCL tumor samples harbored the same amino acid substitution, L265P, in the MYD88 TIR domain at an evolutionarily invariant residue in its hydrophobic core. This mutation was rare or absent in two other DLBCL subtypes, but was observed in 9% of MALT lymphomas. At a lower frequency, multiple other mutations were observed in the MYD88 TIR domain, occurring in both the ABC and GCB subtypes of DLBCL. Survival of ABC DLBCL lines bearing the L265P mutation was sustained by the mutant but not wild type MYD88 isoform, demonstrating that this MYD88 mutant is oncogenic and gain-of-function. The MYD88 L265P mutant assembled a protein complex that spontaneous triggers the phosphorylation of IRAK1, leading to NF-kB signaling, secretion of the cytokines IL-6, IL-10 and interferon-b, and JAK kinase signaling. These findings demonstrate that the MYD88 signaling pathway is integral to the pathogenesis of ABC DLBCL, providing a genetic rationale for therapeutic targeting of the MYD88 signaling pathway in this lymphoma subtype.

overall_design:
To generate a gene expression signature of MYD88 signaling in ABC DLBCL, the HBL-1 cell line was transduced with retroviral vectors expressing either shMYD88-4 or shMYD88-7. Following puromycin selection, shRNA expression was induced for 24 or 48 hours and gene expression was measured, comparing uninduced (Cy3) to induced (Cy5) cells, using genome-wide Agilent 4x44K oligonucleotide microarrays. A signature of NF-kB signaling in ABC DLBCL was generated by treating HBL-1 cells with the IkB kinase beta inhibitor MLN120B for 2h, 3h, 4h, 6h, 8h, 12h, 16h, and 24h (Cy5), and comparing their gene expression to untreated cells (Cy3). A signature of JAK signaling in ABC DLBCL was generated by treating HBL-1 cells with JAK inhibitor I (5 micromolar; Calbiochem) for 2h, 4h, 6h, and 8h (Cy5) and comparing their gene expression to vehicle-treated cells (DMSO, Cy3).

RNA-Seq data not provided.


title: Cooperative Epigenetic Modulation by Cancer Amplicon Genes

status: Public on Jan 04 2011

summary: Amplification of a ~2.5 megabase region on chromosome 9p24 is frequent in both primary mediastinal B-cell lymphoma (PMBL) and Hodgkin's lymphoma (HL). To identify the oncogenic genes in this interval, we created a RNA interference library targeting amplicon genes. A genetic screen using this library identified three genes that are essential for the proliferation and survival of PMBL and HL lines with this amplicon, which encode the kinase JAK2, the histone demethylase JMJD2C and a gene of unknown function, RANBP6. Inhibition of JAK2 and JMJD2C cooperated in killing these lymphomas and in remodeling their chromatin by globally increasing trimethylation of lysine 9 on histone H3 (H3K9me3) and heterochromatin formation. JAK2 and JMJD2C inhibition silenced MYC and its target genes, which coincided with an increase in H3K9me3 and the heterochromatin protein HP1alpha at the MYC locus. We conclude that amplification of JAK2 and JMJD2C cooperatively reprograms the PMBL and HL epigenome, sustaining their survival and proliferation.

overall_design: Signal from untreated shRNA cells or DMSO control cells (Cy3) was compared to 4 dox-treated JAK2 shRNA cells, 4 dox-treated JMJD2C shRNA cells, or 8 JAK2 inhibitor-treated cells (Cy5).


title: A critical role of microRNAs in human pulmonary arterial hypertension. miR-204: a novel therapeutic target (gene expression)

status: Public on Dec 16 2010

city: Lausanne

first: Eric

last: Paquet

state: Vaud

address: Station 15  CH - 1015

department: Life sciences

country: Switzerland

institute: EPFL

summary: Pulmonary arterial hypertension (PAH) is a vascular remodeling disease characterized by enhanced pulmonary artery smooth muscle cell (PASMC) proliferation and suppressed apoptosis. Downregulation of the BMPR2 gene along with activation of the transcription factor NFAT have been implicated in the maintenance of pro-proliferative and anti-apoptotic stages of cells. Since an increasing number of microRNAs have been implicated in the regulation of genes specifically important for cell proliferation and apoptosis, we hypothesized that microRNAs might be associated with these cellular features in the etiology of PAH. We demonstrate that downregulation of one such microRNA (miR-204) in human PAH-PASMC promotes the activation of an Src/STAT3/NFAT axis that increases PAH-PASMC proliferation and their resistance to apoptosis. Stimulation experiments using the pro-PAH factors (PDGF, endothelin-1 and angiotensin II) and time course analysis in experimental PAH show that STAT3 activation leads to miR-204 downregulation, thereby activating an Src-dependent positive feedback loop sustaining STAT3 and activating NFAT. More importantly, restoring miR-204 expression decreases proliferation and resistance to apoptosis in human and in an experimental PAH model. Taken together, our study uncovers a new STAT3-miR-204-Src/STAT3/NFAT axis that links the STAT3-dependent downregulation of BMPR2 with the NFAT-mediated pro-proliferative and anti-apoptotic phenotype observed in PAH. Our data point toward a novel potential strategy for treating patients with PAH.

overall_design: Comparative expression profiling of PAH versus healthy patients to evaluate the modulated genes in the disease. Following the demonstration of the downregulation of miR-204 in PAH we want to investigate the effect of the inhibition (using antagomir) of miR-204 expression in PASMC cells.

first: Audrey

last: Courboulin

first: Roxane

last: Paulin

first: Nellie

last: Giguère

first: Nehmé

last: Saksouk

first: Jacques

last: Côté

first: Martin

last: Simard

first: Sébastien

last: Bonnet