title: HDL suppresses the type I interferon response

city: Seattle

first: James

last: MacDonald

address: 4225 Roosevelt Way NE

institute: University of Washington

summary: Background: High density lipoprotein (HDL) protects the artery wall by removing cholesterol from lipid-laden macrophages. However, recent evidence suggests that it might also inhibit atherogenesis by combating inflammation. Methods and Results: To identify potential anti-inflammatory mechanisms, we challenged macrophages with lipopolysaccharide (LPS), an inflammatory microbial ligand for Toll-like receptor 4 (TLR4). HDL inhibited the expression of 33% (301 of 911) of the genes normally induced by LPS, microarray analysis revealed. One of its major targets was the type I interferon response pathway, a family of potent viral immunoregulators controlled by TLR4 and the TRAM/TRIF signaling pathway. Unexpectedly, HDL’s ability to inhibit gene expression was independent of cellular cholesterol stores. Moreover, it was unaffected by downregulation of two ATP-binding cassette transporters, ABCA1 and ABCG1, that promote cholesterol efflux. To examine the pathway’s potential in vivo relevance, we used mice deficient in apolipoprotein (apo) A-I, HDL’s major protein. After infection with Salmonella (a Gram-negative bacterium that expresses LPS), apoA-I–deficient mice had 6-fold higher plasma levels of interferon-beta-a key regulator of the type I interferon response than did wild-type mice. Conclusions: HDL inhibits a subset of LPS-stimulated macrophage genes that regulate the type I interferon response, and its action is independent of sterol metabolism. These findings raise the possibility that regulation of macrophage genes by HDL might link innate immunity and cardioprotection.

overall_design: 12 arrays, 3 experimental groups, mMncN (no treatment), mMncL (LPS treated, exposed for 4 h to serum-free medium or serum-free medium supplemented with 100 ng/mL of LPS), and mMwtL (HDL treated, Macrophages were treated for 4 h with serum-free medium or serum-free medium supplemented with 50 mg/mL of HDL, washed twice with PBS).

first: Richard

middle: P

last: Beyer

first: Masashi

last: Suzuki

first: David

last: Pritchard

first: Lev

last: Becker

first: Andrew

middle: N

last: Hoofnagle

first: Theo

last: Bammler

first: Roger

last: Bumgarner

first: Tomas

last: Vaisar

first: Maria

middle: C

last: de Beer

first: Frederick

first: John

middle: F

last: Oram

first: Jay

last: Heinecke


title: microRNA and mRNA expression profiles of human pancreatic islet-like cell clusters

status: Public on Sep 30 2010

city: Taipei

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

summary: Type 1 diabetes is an autoimmune destruction of pancreatic islet beta cell disease, and it is important to find new alternative source of the islet beta cells to replace the damaged cells. Human embryonic stem (hES) cells possess unlimited self-renewal and pluripotency and thus have the potential to provide an unlimited supply of different cell types for tissue replacement. The hES-T3 cells with normal female karyotype were first differentiated into embryoid bodies and then induced to generate the pancreatic islet-like cell clusters, which expressed pancreatic islet cell-specific markers of insulin, glucagon and somatostatin. The expression profiles of microRNAs and mRNAs from the pancreatic islet-like cell clusters were further analyzed and compared with those of undifferentiated hES-T3 cells and differentiated embryoid bodies. MicroRNAs negatively regulate the expression of protein-coding mRNAs. The pancreatic islet-like cell clusters were found to exhibit very high expression of microRNAs miR-186, miR-199a and miR-339, which down-regulated the expression of LIN28, PRDM1, CALB1, GCNT2, RBM47, PLEKHH1, RBPMS2 and PAK6. Therefore, these microRNAs are very likely to play important regulatory roles in the differentiation of pancreatic islet cells and early embryonic development.

overall_design:
In this investigation, both miRNA and mRNA expression profiles from the pancreatic islet-like cell clusters differentiated from hES-T3 cells (T3pi) were quantitatively determined and compared with those of undifferentiated hES-T3 cells grown on mouse embryonic fibroblast (MEF) feeder (T3ES) and embryoid bodies differentiated from hES-T3 cells (T3EB). Several target genes of pancreatic islet cell-specific miRNAs were identified.

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

first: Bo-Zhi

last: Chen

first: Sher

last: Singh

first: Steven

middle: S

last: Li


title: Homo sapiens immortalized MSCs: 3A6

status: Public on Sep 25 2010

first: Chih

middle: Chien

last: Tsai

address: No. 201, Sec. 2, Shih-Pai Road, Taipei 112, Taiwan

institute: Taipei Vaterans General Hospital

summary: Gene expression profiling of immortalized human mesenchymal stem cells with hTERT/E6/E7 transfected MSCs. hTERT may change gene expression in MSCs. Goal was to determine the gene expressions of immortalized MSCs.

overall_design: One-condition experment, gene expression of 3A6

first: Chih-Chien

first: Chun-Li

first: Shih-Chieh

last: Hung


title: Elucidation of the Mechanisms by which the Progesterone Receptor Inhibits Inflammatory Responses in Cellular Models of Breast Cancer

status: Public on Oct 01 2010

city: Palo Alto

first: Dmitri

middle: A

last: Kazmin

state: CA

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

country: USA

institute: Stanford University

summary: Both pro- and anti-mitogenic activities have been ascribed to progesterone receptor (PR) agonists and antagonists in breast cancer cells, however, the transcriptional responses that underlie these paradoxical functions are not apparent. Using non-transformed, normal human mammary epithelial cells (hMECs) engineered to express PR, and standard microarray technology, we defined 2,370 genes that were significantly regulated by the PR agonist R5020. Gene Ontology (GO) analysis revealed that GO-terms involved in inflammation and NF-κB signaling were among the most significantly regulated. Interestingly, on those NF-κB responsive genes that were inhibited by agonist-activated PR, antagonists either (a) mimicked the actions of agonists or (b) reversed the inhibitory actions of agonists.  This difference in pharmacological response could be attributed to the fact that although agonist and antagonist-activated PR is recruited to the promoters of NF-κB responsive promoters, the physical presence of PR tethered to the promoter of some genes is sufficient for transcriptional inhibition whereas on others an agonist-activated PR conformation is required for inhibition of NF-κB signaling.  Importantly, the actions of PR on the latter class of genes were reversed by an AF-2 inhibiting, LXXLL-containing peptide. Consideration of the relative activities of these distinct anti-inflammatory pathways in breast cancer may be instructive with respect to the likely therapeutic activity of PR agonists or antagonists in the treatment of breast cancer.

overall_design: Human mammary epithelial cells treated with R5020 or vehicle.

first: Sakiko

last: Kobayashi

first: Donald

last: McDonnell


title: Lactic acidosis triggers starvation response with distinct metabolic profiles

status: Public on Sep 27 2010

city: Durham

first: Julia

middle: Ling-Yu

state: NC

address: CIEMAS Rm.2141, 101 Science Dr.

institute: Duke university

summary:
[1] Lactic acidosis time course: MCF7 cells were exposed to lactic acidosis for different length of time. We used microarrays to examine the genomic programs of cells incubated under lactic acidosis for different length of time

[2] Metabolic profiling: MCF7 cells were exposed to control condition, 25mM lactic acidosis, glucose deprivation (zero glucose) and hypoxia (1% oxygen level).

[3] Mouse study: Lactic acidosis triggers starvation response with paradoxical induction of TXNIP through MondoA. Wild-type mouse embryo fibroblasts (MEFs) and TXNIP-null MEFs were exposed to Ctrl versus lactic acidosis conditions for 24hrs and the RNAs from cells were extracted with MiRVana kit (Ambion) and applied to Affymetrix 430A mouse chips

We used microarrays to examine the genomic programs of cells incubated under different microenvironmental stresses.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
[1] Lactic acidosis time course: MCF7 cells were exposed to lactic acidosis for 1, 4, 12 and 24 hours.
[2] Metabolic profiling: MCF7 cells were exposed to lactic acidosis, glucose deprivation and hypoxia for 4hours.
[3] wild-type mouse embryo fibroblasts (MEFs) and TXNIP-null MEFs were exposed to Ctrl versus lactic acidosis conditions for 24hrs.

middle: L

first: J-T

last: Chi


title: Gene expression analysis of human lung cancer and control samples

city: Granada

first: Mª Esther

last: Farez-Vidal

address: Avda Dr. Oloriz s/n

country: Spain

institute: Hospital Universitario San Cecilio

summary:
PURPOSE
The development of reliable gene expression profiling technology is having an increasing impact on our understanding of lung cancer biology. The present study aims to determine whether the phenotypic heterogeneity and genetic diversity of lung cancer are correlated.
PATIENTS AND METHODS
In this study, microarray analysis was performed in a set of 91 non-small cell lung cancer (NSCLC) samples in order to: establish gene signatures in primary adenocarcinomas and squamous-cell carcinomas; determine differentially expressed gene sequences at different stages of the disease; and identify sequences with biological significance for tumor progression. After microarray analysis, the expression level of 92 selected genes was validated by qPCR in an independent set of 70 samples.
RESULTS
Gene sequences were differentially expressed as a function of tumor type, stage, and differentiation grade. High upregulation was observed for KRT15 and PKP1, which may be good markers to distinguish squamous cell carcinoma samples. High downregulation was observed for DSG3 in stage IA adenocarcinomas.
CONCLUSION
Expression signatures in NSCLC distinguish tumor type, stage, and differentiation grade.

Keywords: Tumor vs control comparative genomics study

overall_design: 91 samples studied, 46 tumors and 45 controls. All samples are paired except three.

first: Abel

last: Ramos

first: Mercedes

middle: G

last: Morales

first: Jose

last: Gomez-Capilla

first: Vicente

last: Muriel

first: Mª

middle: E


title: Expression data for PAR-1-positive and -negative melanoma cell lines

status: Public on Sep 22 2010

city: Houston

first: Gabriel

middle: J

last: Villares

state: TX

address: 1515 Holcombe Blvd

institute: University of Texas, MD Anderson Cancer Center

summary: PAR-1 is known to be involved in the transition from non-metastatic to metastatic melanoma. We sought to determine the downstream target genes regulated by PAR-1 to determine how PAR-1 is contributing to the metastatic melanoma phenotype.

overall_design: The A375SM metastatic melanoma cell line was subjected to stable transduction of lentiviral-delivered small hairpin RNA (shRNA) targeting PAR-1. As a control, a non-targeting shRNA sequence (no homology to any human gene) was also transduced into A375SM cells.


title: Identification of genes up-regulated by the overexpression of HSF1 in human HeLa cells

city: Ube

first: Akira

last: Nakai

state: Yamaguchi Prefecture

address: Minami-Kogushi 1-1-1

department: Graduate School of Medicine

country: Japan

institute: Yamaguchi University

summary: To analyze target genes of human heat shock transcription factor 1 (HSF1), we first generated two independent HeLa clones (RDT1 and RDT2) expressing an actively mutated hHSF1 (hHSF1ΔRDT), which lacks the regulatory domain that masks its activation domain and possesses a glutamic acid at amino acid 395 instead of a leucine in the suppression domain of the trimerization domain (Fujimoto et al., J. Biol. Chem. 280, 34908-34916, 2005). We also generated a HeLa clone expressing chicken HSF1 (HeLa/cHSF1) to compare its profile of gene expression with those of RDT1 and RDT2 cells (Nakai and Morimoto, Mol. Cell. Biol. 13, 1983-1997, 1993). We then carried out DNA microarray analysis using total RNA isolated from HeLa, HeLa/cHSF1, RDT1, and RDT2 cells grown under normal growth conditions.

overall_design: mRNA levels in human HeLa, RDT1, RDT2, and HeLa/cHSF1 were analyzed by DNA microarray analysis using GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix).

first: Mitsuaki

last: Fujimoto

first: Naoki

last: Hayashida

first: Hitoshi

last: Ichikawa


title: Investigation of over-expressing Annexin receptor cell line with and without agonists

status: Public on Sep 28 2010

city: London

first: Trinidad

last: Montero

address: Charterhouse Square

department: Biochemical Pharmacology

country: United Kingdom

institute: Whilliam Harvey Research Institute, Bart's and The London School of Medicine; Queen Mary University of London

summary: The therapeutic potential of pro-resolution factors in determining the outcome of inflammatory events has gained ground over the past decade. However, the attention has been focused on the non-genomic effects of these endogenous, anti-inflammatory substances. In this study, we have focused our attention on identifying specific annexin 1 (AnxA1) protein/ALX receptor mediated gene activation, in an effort to identify down-stream genomic targets of this well-known, glucocorticoid induced, pro-resolution factor.

overall_design: In this study, we used four different types of samples (with 2 replicates each):1)cells transfected with the empty pGEX-4T-327 vector and vehicle (PBS) treated; 2)cells transfected with the annexin receptor ALXR (also known as FPR2) and vehicle (PBS) treated; 3)cells transfected with the annexin receptor ALXR and treated with 10uM Ac-26 peptide for 4 hours; 4) cells transfected with the annexin receptor ALXR and treated with 0.5uM Annexin 1 for 4 hours. After the treatments, cells were collected for RNA extraction.

first: Derek

last: Renshaw

first: Mauro

last: Perretti


title: Analysis of genome-wide methylation and gene expression induced by decitabine treatment in HL60 leukemia cell line

status: Public on Sep 21 2010

city: Rome

first: Emiliano

last: Fabiani

address: L.go A. Gemelli 10

department: Hematology

country: Italy

institute: Università Cattolica del Sacro Cuore

type: Methylation profiling by genome tiling array

summary: Epigenetic changes play a role in the pathogenesis of myeloid malignancies and hypomethylating agents have shown efficacy in these diseases. We studied the apoptotic effect, the genome-wide methylation and gene expression profiles in HL60 cells following decitabine treatment, using micro-array technologies. Decitabine treatment resulted in a decrease in global DNA methylation, corresponding to 4876 probeset IDs with significantly reduced methylation levels, while expression of 2583 IDs was induced. The integrated analysis identified 160 genes demethylated and upregulated by decitabine, mainly including development and differentiation pathways genes. Genes target of polycomb group protein regulation were overrepresented in this group. Apoptosis was induced by decitabine and apoptosis-specific PCR arrays more precisely indicated decitabine-induced upregulation of 13 apoptosis-related genes, in particular Dap-kinase 1 and Bcl2L10. Correspondingly, in primary patient samples, BCL2L10 was hypermethylated in 45% of AML, 43% of therapy-related myeloid neoplasms, 12% of MDS and in none of the controls.

overall_design: In this work, we were interested in the identification of key pathways involved in the global methylation and gene expression changes induced by decitabine in a myeloid cell line model. The human acute myeloid leukemia cell line HL60 was treated with 1 µM decitabine or the same volume of vehicle (mock sample) for 3 days. At the end of treatment DNA and total RNA were extracted for methylation and gene expression studies, to identify genes hypermethylated in HL60 cells and that could be targets of hypomethylating treatment. Methylation profiling was performed by the Methylated DNA Immunoprecipitation (MeDIP) using an anti-5-Methylcytidine Antibody (GeneTex Inc). Methylation-enriched DNA and total DNA  were labeled and hybridized on the Affymetrix GeneChip Human Promoter 1.0R Tiling Arrays (Affymetrix, USA). Gene expression profiling (GEP) was performed using the Affymetrix  U133 Plus 2.0 expression array. All hybridization reactions were performed using GeneChip Fluidics Station 450, and GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 (Affymetrix, USA). The MeDIP.CEL files for biological triplicates of HL60 mock and decitabine-treated were log2 transformed, normalized and imported into the Partek Genomic Suite software (PGS). The differences between treated and control samples were performed using a t-Test (p-value 0.05). Significantly enriched regions were obtained by the MAT algorithm (Model-based Analysis of Tiling arrays). The expression array .CEL files for HL60 mock and decitabine-treated cells were imported in PGS using the Gene Expression Workflow tool, after GC-RMA normalization and log2 transformation. Significantly over and under-expressed genes were detected using the 1-way ANOVA tool at p<0.01 and +/- 2 fold enrichment. The integration between significantly demethylated and induced genes upon decitabine treatment was performed using the VENN diagram tool in PGS.

first: Manuela

last: Giachelia

first: Francesco

last: D'Alò

first: Maria-Teresa

last: Voso


title: Expression profiling of p53 wildtype inducible DLD-1 cells

city: Leipzig

first: Levin

last: Böhlig

address: Semmelweisstr. 14

country: Germany

institute: University of Leipzig

summary: This is an initial experiment which was performed in order to identify novel transcriptional targets of the tumor suppressor p53

overall_design: One Microarray was run per RNA, respectively. We included control DLD-1 cells and cells which were induced for p53 expression for 9h.


title: Expression data from human brain samples

status: Public on Sep 24 2010

city: Barcelona

first: Sophie

last: Domingues

address: Pg Vall d’Hebron 119-129

department: Department of Neurology

institute: Institut de Recerca Hospital Vall d’Hebron

summary:
Spontaneous intracerebral hemorrhage (ICH) represents about 15% of all strokes and is associated with high mortality rates. Our aim was to identify the gene expression changes and biological pathways altered in the brain following ICH.
Twelve brain samples were obtained from four deceased patients who suffered an ICH including perihematomal tissue (PH) and the corresponding contralateral white (CW) and grey (CG) matter.

overall_design: Brain samples from 4 deceased patients who had a supratentorial intracerebral hemorrhage within the previous 4 days were included in the microarray study. This study group included 2 women and 2 men with a median age of 79 (68-92). On autopsy and during macroscopic exam, perihematomal areas suspected to present edema were identified by an experienced neuropathologist using last available neuroradiology images. Samples from perihematomal areas (PH), contralateral grey matter (CG) and contralateral white matter (CW) were obtained within the first 5 h after death and snap frozen in liquid nitrogen and stored at -80ºC until RNA isolation.

first: Anna

last: Rosell

last: Vilalta

first: Teresa

last: García-Berrocoso

first: Israel

last: Fernández-Cadenas

last: Domingues-Montanari

first: Eloy

last: Cuadrado

first: Pilar

last: Delgado

first: Marc

last: Ribó

first: Elena

last: Martínez-Sáez

first: Arantxa

last: Ortega-Aznar

first: Joan

last: Montaner


title: ChIP-chip of MoCRZ1

status: Public on Sep 17 2010

city: Columbus

first: Soonok

last: Kim

state: OH

address: 2021 Coffey Rd.

department: Plant Pathology

institute: The Ohio State University

type: Genome binding/occupancy profiling by array

summary: CRZ1 (Calcineurin Responsive Zinc finger 1) is a conserved transcription factor that relays Ca2+/calcineurin signals within the cell. To catalog genome wide locations that MoCRZ1 binds to, we have conducted chromatin immunoprecipitation coupled with microarray (ChIP-chip) in the rice blast fungus, Magnaporthe oryzae. Fungal mycelia were treated with 200mM CaCl2 to activate translocation of MoCRZ1 to the nucleus, thereby binding to the promoter regions of downstream genes, and CaCl2 together with 10ug/ml FK506 to block these phenomena. Using ChIP-chip, we were able to identify over 100 direct targets of MoCRZ1 which include well known downstream genes as well as previously unknown genes.

overall_design: Fungal mycelia expressing MoCRZ1::GFP under its native promoter were treated with 200mM CaCl2. MoCRZ1 bound DNA fragments which were immunoprecipitated with antiGFP-antibody were compared with 30% input DNA. Mycelia treated with 200mM CaCl2 and 10ug/ml FK506 were processed as the same way and used as negative control treatment.

first: Thomas

last: Mitchell


title: Expression data from SPARKS CHARMS JIA cohort

first: Lucy

middle: R

last: Wedderburn

address: 30 Guilford Street

department: Rheumatology

institute: Institute of Child Health, UCL

summary: Gene expression on peripheral blood mononuclear cells (PBMC) from SPARKS CHARMS juvenile idiopathic arthritis (JIA) cohort pre and post methotrexate therapy. This is the first study to our knowledge, to evaluate gene expression profiles in children with JIA before and after MTX, and to analyze genetic variation in differentially expressed genes. We have identified a gene, which may contribute to genetic variability in MTX response in JIA.

overall_design: PBMC were isolated from blood samples taken from 11 patients with JIA pre methotrexate therapy  and at 6 months into therapy

first: H

last: Moncrieffe


title: Ca2+/calcineurin/CRZ1 dependent gene expression in Magnaporthe oryzae

summary: The Ca2+/calcineurin signaling pathway is a central conduit regulating growth, development, and virulence of fungal pathogens infecting plants and human. We have analyzed global gene expression profiles during Ca2+ treatment in the rice blast fungus, Magnaporthe oryzae. An immunosuppressive drug, FK506, and the knock-out mutant of a transcription factor, MoCRZ1, were included to analyze calcineurin- and/or CRZ1-dependent gene expression, respectively. About 1,400 genes were up or down regulated by Ca2+ treatment, while about 200 genes seemed to be up-regulated in a calcineurin/CRZ1-dependent manner.

overall_design: This study analyzes global gene expression dynamics during Ca2+ treatment in the rice blast fungus. We have used Agilent M. grisea 2.0 4×44K Microarrays using a single channel hybridization design. An immunosuppressive drug, FK506, and the knock out mutant of a transcription factor, MoCRZ1, were included to analyze calcineurin- and/or CRZ1-dependent gene expression, respectively. To know the time point at which the gene expression fluctuates most significantly, we treated mycelia with CaCl2 for 0, 15, 30, and 60 min. PMC1 expression level was checked by RT-PCR with the highest expression at 30 min time point. Four biological replicates of wild type and mutant mycelia were harvested after 30 min treatment with chemicals. Pairwise comparisons between Ca2+ treated vs. control and Ca2+ vs. Ca2+/FK506 in wild type (WT), and Ca2+ treated in WT vs. in mutant were conducted.

first: Yeonyee

last: Oh

first: Yong-Hwan

last: Lee

first: Ralph

last: Dean

middle: K


city: Fort Collins

first: Andrey

last: Ptitsyn

state: CO

address: 1682 Canpus Delivery

department: Center for Bioinformatics

institute: Colorado State University

summary: Adipose-derived stromal/stem cells (ASC) capable of multipotential differentiation can be isolated with high yield from human subcutaneous lipoaspirates.  This study reports our recent experience isolating and immunophenotypically characterizing ASCs from >60 human subjects

overall_design: Total RNA was isolated from ASCs obtained from three individual donors and maintained under uninduced or adipogenic induced culture conditions for 9 days following confluence.   The RNA was assessed by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA), cDNA synthesized using a Superscript cDNA Synthesis kit (Invitrogen, Carlsbad, CA) and a T7-(dT)24 primer.  Biotinylated cRNA was transcribed in vitro using a GeneChip IVT Labeling kit (Affymetrix, Santa Clara, CA), purified using a GeneChip Sample Cleanup Module, incubated in fragmentation buffer (200 mM Tris-acetate pH 8.1, 500 mM potassium acetate, 150 mM magnesium acetate) at 94oC for 35 min, chilled on ice, and hybridized to a Human U133 Plus 2.0 Array of ~47,400 transcripts and variants, including 38,500 well-characterized genes.  Arrays were incubated at 45oC for 16 hrs rotating at 60 rpm, washed, stained at 25oC for 10 min with 10 μg/ml streptavidin R phycoerythrin (Vector Laboratories, Burlingame, CA), stained at 25oC for 10 min (X2) with 3 μg/ml biotinylated goat anti-streptavidin antibody (Vector Laboratories), washed, and scanned using a GeneChip Scanner 3000.  Pixel intensities were measured, expression signals were globally scaled to a target intensity value of 2500, and features extracted using GeneChip Operating Software v1.2 (Affymetrix).  Data mining and statistical analyses  were performed with Data Mining Tool v.3 (Affymetrix) algorithms.  The absolute call (present, marginal, absent) of each gene expression, the direction of change, and the fold change were identified with the above software.

first: Gang

last: Yu

first: Xiying

last: Wu

first: Marilyn

last: Dietrich

first: Elizabeth

last: Floyd

first: Paula

last: Polk

first: Keith

last: Scott

first: Jeffrey

middle: M

last: Gimble


title: Stable Set8 effect on gene expression in U2OS cells

status: Public on Sep 18 2010

city: Charlottesville

first: Anindya

last: Dutta

state: VA

address: 1300 Jefferson Park Ave

department: Biochemistry & Molecular Genetics

institute: University Of Virginia

summary: Ubiquitin-mediated proteolysis play a significant role in various biological processes including transcription, DNA repair and cell cycle progression. The identification of Set8 and Set8b (a splice isoform) histone H4K20 methyl transferase as a substrate for the cullin-based ubiquitin ligase (CRL4-Cdt2) demonstrate that this pathway plays a significant role in promoting cell cycle progression, specifically promoting G2 progression. This study investigate the effect of failure to degrade Set8 in S-phase of the cell cycle via CRL4-Cdt2 on gene expression.

overall_design:
We used microarrays to detail the effect of the expression of stable form of Set8b H4K20 mono-methyl transferase (Set8b_deltaPIP2) on gene expression
Human osteosarcoma-derived human cells were transduced with retroviruses encoding either wt-Set8b or a mutant of Setb8 which is resistant to degradation via CRL4-Cdt2 ubiquitin ligase complex (Set8b_deltaPIP2) or with an a control pMSCV empty virus. 5 days after transduction, cells were harvested and the RNA was extracted by Trizol (Invitrogen) and hybridized to the affymetrix chips array.

first: Tarek

last: Abbas

first: Etsuko

last: Shibata

first: Jonghoon

last: Park

first: Sudhakar

last: Jha

first: Neerja

last: Karnani


title: Adult human liver tissue expression (Affymetrix)

city: shanghai

first: yao

last: yu

address: yueyang road 320, room 123

country: China

institute: sibs

summary:
The human liver plays a vital role in meeting the body's metabolic needs and maintaining homeostasis. To address the molecular mechanisms of liver function, we integrated multiple gene expression datasets from microarray, MPSS, SAGE and EST platforms to generate a transcriptome atlas of the normal human liver. The integrated liver transcriptome data should provide a valuable resource for the in-depth understanding of human liver biology and liver disease.
Microarray is one of these platforms. In this part, adult human liver tissues from 10 adult human were surgically resected due to hemangioma in the liver. The gene expression of normal human liver was detected by Microarray platform.

overall_design:
The samples were obtained from the portion unaffected by the hemangioma and were immediately frozen in liquid nitrogen. All procedures and risks were explained verbally, and patients provided written consent. The samples were sectioned and confirmed to be histologically normal. All laboratory data assessing hepatic function were within normal ranges, including serum alanine aminotransferase, aspartate aminotransferase, gamma-glutamyl transpeptidase, alkaline phosphatase, total bilirubin, albumin, prothrombin activity, glucose, cholesterol, and triglycerides (data not shown). Serological tests for hepatitis B surface antigen, hepatitis C virus antibodies, and human immunodeficiency virus antibodies also proved negative. Neither heavy alcohol consumption nor the intake of prescription or other drugs was observed before surgical resection. Total RNA was extracted according to the manufacturer’s instructions, and RNase-free DNase I was used to remove DNA contamination. Nucleic acid concentration and purity were assessed at 260 nm using a spectrophotometer (DU 530, Beckman-Coulter Inc., Fullerton, CA), and the quality was assessed using an Agilent 2100 Bioanalyzer. In order to address gene expression polymorphism, the total RNA from 10 livers was pooled.

***This submission represents the Affymetrix component of the study only***

first: Yao

first: Jie

last: Ping

first: Hui

last: Chen

first: Longxian

last: Jiao

first: Siyuan

last: Zheng

first: Ze-Guang

last: Huang

first: Pei

last: Hao

first: Jian


title: Sera-induced transcriptional signatures in human leukemia cell lines

status: Public on Sep 16 2010

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

summary:
Inflammation is common to many disorders and responsible for tissue and organ damage. However, the associated peripheral cytokine milieu is frequently dilute and difficult to measure, necessitating development of more sensitive and informative biomarkers for mechanistic studies, earlier diagnosis, and monitoring therapeutic interventions. Previously, we have shown that sera from type 1 diabetes (T1D) patients induces a unique disease-specific pro-inflammatory transcriptional profile in fresh peripheral blood mononuclear cells (PBMCs) compared to sera of healthy controls.
To address the potential variance introduced by heterogeneity in responsiveness of PBMCs from different donors, we evaluated human leukemia cell lines as surrogates for fresh PBMCs.  Expression signatures of 7 different cell lines were 1) tested in their power to differentiate sera of T1D patients from healthy controls; and 2) compared to the signature obtained with fresh PBMCs.

overall_design: For each of the 7 cell lines, we assayed 6 individual samples (three stimulated with recent-onset (RO) T1D sera and three stimulated with healthy control sera). Hence, a total of 42 samples were analyzed in this study.

first: Parthav

last: Jailwala

first: Shuang

last: Jia

first: Mary

last: Kaldunski

first: Rhonda

last: Geoffrey

first: Joanna

last: Kramer

first: Xujing

last: Wang


title: ChIP-chip and gene expression model of the MoCRZ1 mediated circuit for Ca2+/calcineurin signaling in rice blast fungus

first: Soonok

last: Kim

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

overall_design: Refer to individual Series


title: Low dose hCG pregnant vs non-pregnant

status: Public on Sep 07 2010

city: Brussel

first: Inge

last: Van Vaerenbergh

address: Laarbeeklaan 103

department: EXPA

country: Belgium

institute: Vrije Universiteit Brussel

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

overall_design: In total 6 samples were analyzed for gene expression analysis with microarrays, 3 pregnant and 3 non-pregnant patients were compared.

first: Christophe

last: Blockeel

first: Leentje

last: Van Lommel

first: Vanessa

last: Ghislain

first: Peter

last: In't Veld

first: Frans

last: Schuit

first: Human

last: Fatemi

first: Paul

last: Devroey

first: Claire

last: Bourgain


title: Differentiation of Mammary Tumors by SKI-606 (bostutinib) (illumina)

status: Public on Sep 15 2010

city: La Jolla

first: Roy

last: Williams

address: 3030 Science Park Road

department: Regenerative Medicine

institute: The Scripps Research Institute

summary: While c-Src is infrequently mutated in human cancers, it mediates oncogenic signals of many activated growth factor receptors and thus remains a key potential target of cancer therapy. However, the widespread function of Src in many cell types and processes requires evaluation of Src-targeted therapeutics within a normal developmental and immune competent environment. In an effort to direct clinical use of Src inhibitors, we tested the effectiveness of one of the four Src inhibitors in clinical testing, SKI-606 (bosutinib), in the MMTV-PyVmT transgenic mouse model of breast cancer. Tumor formation in this model is dependent on the presence of Src, but the necessity of Src kinase activity for tumor formation has not been determined. Furthermore, Src inhibitors have not been examined in an autochthonous tumor model. Here we show that oral administration of the Src inhibitor SKI-606 inhibited the phosphorylation of Src in mammary tumors, and caused a rapid decrease in the Ezh2 Polycomb group histone H3K27 methyltransferase and an increase in epithelial organization.  SKI-606 prevented the appearance of palpable tumors in more than half of the animals treated from puberty and stopped tumor growth in older animals with preexisting tumors.  These antitumor effects were accompanied by decreased cellular proliferation, altered tumor blood vessel organization and dramatically increased differentiation to lactational and epidermal cell fates. SKI-606 controls the development of mammary tumors in this model by inducing differentiation.

first: Robert

last: Oshima

first: Lionel

last: Hebbard


title: The Monocyte Advantage

status: Public on Sep 09 2010

city: St. Louis

first: J

middle: Perren

last: Cobb

state: MO

address: Campus Box 8109, 660 South Euclid Avenue

institute: Washington University in St. Louis

summary:
INTRO: The ongoing challenge of accurately diagnosing infection in the ICU motivates a search for novel molecular diagnostics. In the current study, we tested the hypothesis that the informational content of circulating leukocytes differs, thereby allowing one to rank leukocyte populations on their potential to contribute to RNA diagnostics for pneumonia.
METHODS: Sixteen patients (10 male, 6 female) at risk for VAP were entered into our IRB-approved study that collects blood and clinical data every 48 hours for up to 21 days. Four of the sixteen patients developed VAP as diagnosed and treated by the attending ICU physician. Previously reported blood protocols were used to isolate buffy coat, enriched neutrophil, and enriched monocyte populations by using negative selection. Cellular purity was assessed by FACS for one of the 4 VAP patients. Genome-wide expression analysis was performed on RMA-normalized signal from Affymetrix U133 2.0 Plus GeneChips. EDGE software (FDR=0.10) was used to determine changes in mRNA abundance over time for each cell population.
RESULTS: During the 5-day window in which each of the four patients (all males) developed VAP, significant changes in gene expression were observed (Table 2), but the information content (number of genes altered) varied across leukocyte populations. These differences were not due to signal variance (coefficient of variation, CV) or differences in the number of samples available for analysis. Moreover, only 0.6% of the monocyte gene list overlaps with the neutrophil list, arguing that neutrophil contamination of monocyte populations is insufficient to explain the 40-fold difference in gene number.
CONCLUSIONS: Enriched monocyte populations from circulating blood provide far more genes for study of the host response to VAP than the other 2 cell populations studied. This information should be considered when designing blood gene expression profiling experiments in patients at risk for sepsis.

Keywords: time course

overall_design: Four patients over several timepoints measured three different cell types for VAP signal

first: William

last: Schierding

first: David

last: Dixon

first: Jianhua

last: Ruan

first: Douglas

last: Oppedal

first: Sandra

last: MacMillan

first: Buddy

last: Brownstein

first: Weixiong

last: Zhang


title: Expression data from human soft tissue sarcomas with complex genomics

city: Paris

first: Laure

last: Gibault

address: 26 rue d'Ulm

country: France

institute: Curie Institute

summary: Differentially expressed genes between 171 human soft tissue sarcomas with complex genomics

overall_design:
RNA extraction was performed on frozen samples of tumors and hybridized on U133 Plus 2.0 Affymetrix microarrays, for which we had performed Comparative Genomic Hybridization profiling.

This submission represents the gene expression component of the study.

first: Alain

last: Aurias


title: COX-2 network as predictive molecular marker for clinical pregnancy in IVF

first: Inge

last: Van Vaerenbergh

summary:
CONTEXT Nowadays, the molecular mechanisms involved in endometrial receptivity and implantation are still not clear.

OBJECTIVE The gene expression of human endometrium of patients undergoing an IVF treatment with GnRH antagonists/rec-FSH was studied.

CONCLUSIONS COX-2 has been extensively studied as a crucial fertility element in both knock-out mice and human. It appears that increased expression of COX-2 and/or SCGB1D2 on the day of oocyte retrieval in GnRH antagonist/rec-FSH stimulated cycles coincides with a lower probability of achieving a clinical pregnancy in this cycle.

Keywords: gene expression analysis, clinical pregnancy in IVF stimulated cycles

overall_design: Endometrial biopsies taken from patients on day of oocyte retrieval in stimulated IVF cycles with 1 or 2 embryos replaced in the same cycle. Gene expression of pregnant patients (n=4) was compared with matched non-pregnant patients (n=4)

first: Leentje

last: Van Lommel

first: Vanessa

last: Ghislain

first: Peter

last: In't Veld

first: Frans

last: Schuit


title: Evaluation of the Affymetrix Brassica Exon 1.0 ST array

status: Public on Sep 10 2010

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

summary: The aim of the experiment was to evaluate the performance of the Affymetrix Brassica Exon 1.0 ST array. Root and leaf samples from Brassica rapa line R-O-18 were compared. The same RNA samples were hybridised to the Agilent Brassica array, to compare the performance of the two arrays.

platform_organism:
Brassica
Brassica rapa

overall_design: 6 samples were hybridised to each array. Triplicate samples of 11-day-old roots and 2 semi-expanded leaves from 23-day-old Brassica rapoa R-O-18 plants.

first: Chris

last: Love

first: Neil

last: Graham

first: Seosamh

middle: O

last: Lochlainn

first: Sean

middle: T

last: May

first: Helen

last: Bowen

first: Philip

last: White

first: Martin

last: Broadley

first: John

last: Hammond

first: Graham

last: King


title: Genes regulated by miR-145

city: Singapore

first: George

middle: W

last: Yip

address: 4 Medical Drive, Block MD10

country: Singapore

institute: National University of Singapore

summary: We used Affymetrix HG U133 Plus 2.0 GeneChips to compare the transcriptome of miR-145-overexpressing MDA-MB-231 cells against negative control miRNA precursor-transfected cells.

overall_design: MDA-MB-231 cells were transfected with pre-miR-145 or a negative control pre-miRNA, and subsequently total RNA was collected and processed for analysis using Affymetrix microarrays. Three independent replicates were prepared for each comparison group.

last: Götte


title: Expression data from Gambian children with and without the clinical signs of active trachoma: U133 Plus2.0 array

status: Public on Sep 03 2010

middle: James

last: Holland

address: Keppel Street

department: Infectious and Tropical Diseases

institute: London School of Hygiene and Tropical Medicine

summary: Conjunctival samples from 60 individuals with and without the clinical signs of active trachoma were analysed on the U133 Plus 2.0 arrays.  Global transcriptional changes characteristic of disease and infection phenotypes were identified. Two analysis methods found large numbers of differentially regulated genes and the existence of networks of co-expressed genes. There were signatures characteristic of the host defence response with evidence supporting infiltration of various types of leukocytes and activation of innate responses of epithelial cells. Two separate methods could classify disease and infection phenotype based on transcription signatures with 70% accuracy.  These results provide an insight into the complexity of the acute response in trachoma but are able to partly explain the biology of trachoma through the identification of pathways and gene expression sets useful to future studies on chlamydial immunopathogenesis.

overall_design: Conjunctival samples from 60 participants were tested on U133 plus 2.0 arrays (40 participants with clinical signs of active trachoma and 20 controls with normal conjunctivas as before). Samples were further sub-divided based on the detection and quantification of ocular Chlamydia trachomatis load by PCR tests. Gene expression was then assessed using differential expression and construction of co-expression networks. The content of the constructed gene lists which were identified as part of a network or differentially expressed were then tested for enrichment using publically available analysis tools to identify biological pathways expressed in the conjunctiva during C. trachomatis infection and disease episodes.

first: Angels

last: Natividad

first: Tom

middle: C

last: Freeman

first: David

last: Jeffries

first: Matthew

last: Burton

last: Mabey

first: Robin

last: Bailey


title: Pathogenesis of hepatitis E and hepatitis C in chimpanzees: Similarities and differences

city: Bethesda

first: Claro

last: Yu

email: clyu@niaid.nih.gov, boond@mail.nih.gov

state: MD

address: 50 South Drive

department: Hepatitis Viruses Section

institute: NIAID

summary: The chimpanzee is the only model other than man for investigating the pathogenesis of viral hepatitis types A through E. Studies of the host response, including microarray analyses, have relied on the close relationship between these two primate species: chimpanzee samples are commonly tested with human-based reagents. In this study, the host response to two dissimilar viruses, hepatitis E virus (HEV) and hepatitis C virus (HCV), was compared in multiple experimentally-infected chimpanzees. Affymetrix U133+2.0 human microarray chips were used to assess the entire transcriptome in serial liver biopsies obtained over the course of the infections. The comparison utilized a permutational t-test-based analysis of selected time points. More specifically, baseline samples were compared with post-inoculation samples that were strategically chosen based on their relationship to viremia, and probe sequences were aligned to the human and chimpanzee genome sequences to assess their relative sensitivity for detecting differentially expressed genes. Regardless of the viral infection, the alignment of differentially expressed genes to the human genome sequence resulted in a larger number of genes being identified when compared with alignment to the chimpanzee genome sequence. This probably reflects the lesser refinement of gene annotation for chimpanzees. In general, the two viruses demonstrated very distinct temporal changes in host response genes, although both RNA viruses induced genes that were involved in many of the same biological systems, including interferon-induced genes. The host response to HCV infection was more robust than the response to HEV infection.

overall_design:
Three chimpanzees were inoculated intravenously with the hepatitis C virus: chimp 1628 was infected with < 100 infectious doses (ID) of the H77 strain (genotype 1a) (30); chimp 1417 was infected with an unknown titer, in serum, of the HC-J6 strain (genotype 2a) (31); chimp 1422 was infected with an unknown titer, in serum, of the T.N. strain (genotype 1a) (35). Four chimpanzees (CH1616, CH1618, CH1374 and CH1375) were inoculated intravenously with 0.5 ml of the HEV SAR55 strain (genotype 1) at approximately 10^6 ID. Grouping of the biological replicates was based on viremia: groups consisted of the first positive week (and the second positive week for HCV), the peak positive week, the last positive week, the first negative week and the fourth negative week. There were 3 biological replicates for HCV. The 4 replicates for HEV were both biological and technical. For chimp 1417, 7 samples were taken between weeks 0 and 17. For chimp 1422, 8 samples were taken between weeks 0 and 13. For chimp 1628, 8 samples were taken between weeks 0 and 19. For chimp 1374, 6 samples were taken between weeks 0 and 8. For chimp 1375, 4 samples were taken between weeks 0 and 8. For chimp 1616, 5 samples were taken between weeks 0 and 7. For chimp 1618, 6 samples were taken between weeks 0 and 8.

Normalized probe set level data not provided for individual Sample records. Processed data is available on Series record.


title: Evaluation of gene expression data generated from expired Affymetrix GeneChip® microarrays using MAQC reference RNA samples

status: Public on Sep 02 2010

city: Shanghai

first: Leming

last: Shi

address: 2005 Songhu Road

department: School of Life Sciences

institute: Fudan University

summary:
The Affymetrix GeneChip® system is a commonly used platform for microarray analysis but the technology is inherently expensive. Unfortunately, changes in experimental planning and execution, such as the unavailability of previously anticipated samples or a shift in research focus, may render significant numbers of pre-purchased GeneChip® microarrays unprocessed before their manufacturer’s expiration dates. Researchers and microarray core facilities wonder whether expired microarrays are still useful for gene expression analysis.
Our results demonstrated that microarray data generated using U133A microarrays, which were more than four years past the manufacturer’s expiration date, were highly specific and consistent with those from unexpired microarrays in identifying DEGs despite some appreciable fold change compression and decrease in sensitivity. Our data also suggested that the MAQC reference RNA samples, stored at -80°C, were stable over a time frame of at least four years.

overall_design: The new gene expression data were generated with 12 microarrays (2 types of microarrays × 2 samples × 3 replicates). Three replicates for each of the two MAQC samples (A = Stratagene’s Universal Human Reference RNA; B = Ambion’s Human Brain Reference RNA) were profiled in 2009 by using both the expired U133A microarrays (expired in 2004) and the unexpired U133Plus2 microarrays. In addition, gene expression data generated with unexpired U133Plus2 microarrays (AFX), other microarray platforms, and TaqMan® assays by the MAQC project in 2005 were used as references to assess the stability of the MAQC samples stored at -80°C for four years by comparing new microarray data with those obtained four years ago. The MAQC reference data also allowed for further evaluation of the usefulness of the data generated with expired U133A microarrays.

first: Zhining

last: Wen

first: Charles

last: Wang

first: Quan

first: Ying

last: Huang

first: Zhenqiang

last: Su

first: Huixiao

last: Hong

first: Weida

last: Tong


title: Prdm16 newborn mouse (ventricular zone) VZ cells microarray

city: Ann Arbor

first: Sean

last: Morrison

state: MI

address: 210 Washtenaw Ave

department: HHMI/Department of Internal Medicine

institute: Center for Stem Cell Biology, 5435 Life Sciences Institute University of Michigan

summary:
As Prdm16 deficiency reduces self-renewal potential and depletes neural stem cells in culture we decided to investigate the underlying molecular mechanisms of the neural stem cells depletion in the Prdm16 deficient animals. For the experiment we used Prdm16Gt(OST67423)Lex (Prdm16LacZ) genetrap mice obtained from the NIH Mutant Mouse Regional Resource Center (http://www.mmrrc.org/).
We compared the gene expression profiles of uncultured ventricular zone cells from newborn Prdm16LacZ/LacZ (KO), Prdm16LacZ/+(HET), and Prdm16+/+ (WT) mice.

overall_design: The uncultured ventricular zone cells from newborn Prdm16LacZ/LacZ, Prdm16LacZ/+, and Prdm16+/+ mice were dissected from the brains and placed into the Trizol reagent. Purified RNA was reverse transcribed and amplified using the WT-Ovation™ Applause WT/Amp RNA amplification system (NuGEN Technologies,) following the manufacturer’s instructions. Sense strand cDNA was fragmented and labeled using the FL-Ovation™ cDNA Biotin Module V2 (NuGEN). 2.5µg of labeled cDNA were hybridized to Affymetrix Mouse Gene ST 1.0 microarrays.

first: Sergei

last: Chuikov

first: Boaz

middle: P

last: Levi


title: Expression data from an Avian pathogenic Escherichia coli strain

city: Campinas

first: Fernanda

last: Pace

address: Av. Marechal Cândido Rondom

country: Brazil

institute: Universidade Estadual de Campinas

summary: Avian pathogenic Escherichia coli strains frequently cause extra-intestinal infections and are responsible for significant economic losses in the poultry industry worldwide. APEC isolates are closely related to human extraintestinal pathogenic E.coli strains and may also act as pathogens for humans. In this work, three type VI secretion systems were deleted to analyze which pathogenicity characteristics would change in the mutants, compared to wild type strain (SEPT 362).

overall_design: Four Avian Pathogenic Escherichia coli strains (one wild type and three deleted mutants) were grown at 37°C in Dulbecco´s Modified Eagle´s Media (DMEM) media until reach O.D 600 = 0.8, for RNA extraction and hybridization on Affymatrix microarrays.

first: Vanessa

last: Sperandio

first: Wanderley

last: Dias da Silveira


title: QseA regulation of virulence factors in EHEC

city: Baltimore

first: David

last: Rasko

address: 801 W. Baltimore Street, Room 619

department: Istitute for Genome Sciences/Microbiology and Immunology

institute: University of Maryland School of Medicine

summary: Enterohemorrhagic E. coli (EHEC) colonizes the large intestine and causes attaching and effacing lesions (AE). Most of the genes involved in the formation of AE lesions are encoded within a chromosomal pathogenicity island termed the Locus of Enterocyte Effacement (LEE). The LysR-like transcriptional factor QseA regulates the LEE by binding directly to the regulatory region of ler. Here, we performed transcriptome analyses comparing WT EHEC and the isogenic qseA mutant in order to elucidate the extent of QseA’s role in gene regulation in EHEC. The following results compare genes that were up-regulated and down-regulated ! 2-fold in the qseA mutant strain compared to the WT strain. At mid-exponential growth, 222 genes were up-regulated and 1874 were downregulated. At late-exponential growth, a total of 55 genes were up-regulated and 605 genes were down-regulated. During mid-exponential growth, QseA represses its own transcription, whereas during late-logarithmic growth, QseA activates expression of the LEE genes as well as non-LEE encoded effector proteins. During both growth phases, several genes carried in O-islands, were activated by QseA, whereas genes involved in cell metabolism were repressed. We also performed electrophoretic mobility shift assays, competition experiments, and DNAseI footprints, and the results suggested that QseA directly binds both the ler proximal and distal promoters, its own promoter, as well as promoters of genes encoded in EHEC-specific O-islands. Additionally, we mapped the transcriptional start site of qseA, leading to the identification of two promoter sequences. Taken together, these results indicate that QseA acts as a global regulator in EHEC, coordinating expression of virulence genes.

overall_design: Design of the study was to make the knockout of the qseA gene and compare the transcriptional response to that and the wild type.

first: Melissa

last: Kendall


title: Quality Control in Microarray Assessment of Gene Expression in Human Airway Epithelium

status: Public on Sep 20 2010

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

summary:
Microarray technology provides a powerful tool for defining gene expression profiles of airway epithelium that lend insight into the pathogenesis of human airway disorders. The focus of this study was to establish rigorous quality control parameters to ensure that microarray assessment of the airway epithelium is not confounded by experimental artifact. Samples (total n=223) of trachea, large and small airway epithelium were collected by fiberoptic bronchoscopy of 144 individuals (42 healthy non-smokers, 49 healthy smokers, 11 symptomatic smokers, 22 smokers with lone emphysema with normal spirometry, and 20 smokers with COPD) were processed and hybridized to Affymetrix HG-U133 2.0 Plus microarrays. The pre- and post-chip quality control (QC) criteria established, included: (1) RNA quality, assessed by RNA Integrity Number (RIN) ≥7.0 using Agilent 2100 Bioanalyzer software; (2) cRNA transcript integrity, assessed by signal intensity ratio of GAPDH 3' to 5' probe sets ≤3.0; and (3) the multi-chip normalization scaling factor ≤10.0
Of the 223 samples, 213 (95.5%) passed the QC criteria. In a data set of 34 arrays (10 samples failing QC criteria, 24 randomly chosen samples passing QC criteria), correlation coefficients for pairwise comparisons of expression levels for 100 housekeeping genes in which at least one array failed the QC criteria were significantly lower (average Pearson r = 0.90 ± 0.04) and more broadly dispersed than correlation coefficients for pairwise comparisons between any two arrays that passed the QC criteria (average Pearson r = 0.97 ± 0.01). By using the QC cutoff criteria, the inter-array variability, as assessed by the coefficient of variation in the expression levels for 100 housekeeping genes, was reduced from 35.7% to 21.7%.  Based on the aberrant housekeeping gene data generated from samples failing the established QC criteria, we propose that the QC criteria outlined in this study can accurately distinguish high quality from low quality data and can be used to delete poor quality microarray samples before proceeding to higher-order biological analyses and interpretation.

overall_design: Affymetrix arrays were used to assess the quality of gene expression data in trachea, large airway and small airway epithelium obtained by fiberoptic bronchoscopy of 42 healthy non-smokers, 49 healthy smokers, 11 symptomatic smokers, 22 smokers with lone emphysema with normal spirometry, and 20 smokers with COPD.

first: Tina

last: Raman

first: Timothy

last: O'Connor

first: Neil

last: Hackett

first: Wei

first: Ben-Gary

last: Harvey

first: Marc

last: Attiyeh

last: Dang

first: Matthew

last: Teater

first: Ronald

last: Crystal


title: Expression data from TGF-beta treated Panc-1 pancreatic adenocarcinoma cell line

city: grand rapids

first: brian

last: haab

address: 333 bostwick avenue NE

department: lab of cancer immunodiagnostics

institute: van andel institute

summary:
TGF-beta treatment of Panc-1 pancreatic adenocarcinoma cell line on Affymetrix HG_U133_plus_2 arrays; triplicate experiments.
The goal of the experiment is to profile temporal gene expression changes during TGF-beta-induced epithelial-mesenchymal transition (EMT). During EMT cancer cells lose their epithelial specifc proteins and gain mesenchymal proteins to acquire migratory and invasive phenotype essential for metastasis. Human Panc-1 pancreatic adenocarcinoma cell line was treated with 5 ng/mL TGF-beta for 48 h to induce EMT. The experiment was repeated 3 times. Samples were assayed using Affymetrix HG_U133_plus_2 arrays with 54675 probe-sets, using standard techniques.

overall_design: Human Panc-1 pancreatic adenocarcinoma cell line was treated with 5 ng/mL TGF-beta for 48 h. The experiment was repeated 3 times. Samples were assayed using Affymetrix HG_U133_plus_2 arrays with 54675 probe-sets, using standard techniques.

first: Maureen

last: Sartor

first: Vasudeva

last: Mahavisno

first: Venkateshwar

last: Keshamouni

first: James

last: Cavalcoli

first: Zachary

last: Wright

first: Alla

last: Karnovsky

first: Rork

last: Kuick

first: HV

last: Jagadish

first: Barbara

last: Mirel

first: Terry

last: Weymouth

first: Brian

last: Athey

first: Gilbert

middle: S

last: Omenn


title: Transcriptome profiling of genes regulated by RXR and its partners in monocyte-derived dendritic cells

status: Public on Sep 01 2010

city: DEBRECEN

first: LAJOS

last: SZELES

address: Egyetem tér

country: Hungary

institute: UNIVERSITY OF DEBRECEN

summary:
CD14+ human monocytes differentiating into DCs in the presence of IL4 and GM-CSF were treated with agonists for RXR and its partners or vehicle 18 hours after plating (experiment with RXR and permissive partners, donor 1-3) or 14 hours after plating (experiment with nonpermissive partners, donor 4-6). Cells were harvested 12 hours thereafter. Experiments were performed in biological triplicates representing samples from three different donors.
In this study all probable RXR-signaling pathways induced by agonists for RXR, LXRs, PPARs, RAR and VDR were identified in differentiating human monocyte-derived dendritic cells.

overall_design:
In the experiments, differentiating dendritic cells were treated for 12 hours with one of the following compounds (ligands):
vehicle (DMS:EtOH 1:1)
LG268 (RXR agonist)
9-cis retinoic acid (9cisRA, agonist of RAR and RXR)
GW3965 (LXRalpha/beta panagonist)
rosiglitazone (RSG, PPARgamma agonist)
GW1516 (PPARdelta agonist)
AM580 (RARalpha agonist)
1,25-dihydroxyvitamin D3 (VDR agonist)

first: Lajos

last: Szeles

first: Laszlo

last: Nagy


title: A cryptic sensor for HIV-1 activates antiviral innate immunity in dendritic cells

first: Dan

last: Littman

address: 540 1st ave

institute: NYU Medical Center

summary: Dendritic cells (DC) serve a key function in host defense, linking innate detection of microbes to the activation of pathogen-specific adaptive immune responses. Whether there is cell-intrinsic recognition of HIV-1 by host innate pattern-recognition receptors and subsequent coupling to antiviral T cell responses is not yet known. DC are largely resistant to infection with HIV-1, but facilitate infection of co-cultured T-helper cells through a process of trans-enhancement. We show here that, when DC resistance to infection is circumvented, HIV-1 induces DC maturation, an antiviral type I interferon response and activation of T cells. This innate response is dependent on the interaction of newly-synthesized HIV-1 capsid (CA) with cellular cyclophilin A (CypA) and the subsequent activation of the transcription factor IRF3. Because the peptidyl-prolyl isomerase CypA also interacts with CA to promote HIV-1 infectivity, our results suggest that CA conformation has evolved under opposing selective pressures for infectivity versus furtiveness. Thus, a cell intrinsic sensor for HIV-1 exists in DC and mediates an antiviral immune response, but it is not typically engaged due to absence of DC infection. The virulence of HIV-1 may be related to evasion of this response, whose manipulation may be necessary to generate an effective HIV-1 vaccine.

overall_design: We analyzed the gene expression profiles of uninfected human monocyte-derived dendritic cells (MDDCs) and MDDCs infected with an envelope-defective GFP-encoding VSV-G-pseudotyped HIV-1 vector (HIVGFP(G)) and with VSV-G pseudotyped virus-like particles derived from SIVmac to deliver Vpx (SIVVLP(G)), alone or in combination. Cells were infected at day 4 of differentiation and cells were harvested 48 hours later. RNA was extracted with TRIzol. RNA was labeled and hybridized to Human Genome U133A 2.0 arrays arrays following the Affymetrix protocols. Data were analyzed in R and Bioconductor.

first: Nicolas

last: Manel

first: Brandon

last: Hogstad

first: Yaming

last: Wang

first: Derya

last: Unutmaz

first: David

last: Levy


title: Expression data from Merm1/Wbscr22 knock-down tumor cells

city: Ariake, Koto-ward

first: Youya

last: Nakazawa

state: Tokyo

department: Cancer Chemotherapy Center

institute: Japanese Foundation for Cancer Research

summary: Merm1/Wbscr22 is one of genes in chromosomal region deleted in Williams-Beuren syndrome, a multisystem developmental disorder. Wbscr22 contains a nuclear localization signal and an S-adenosyl-L-methionine-dependent methyltransferase fold, but its real function is completely unknown.　In this study, to examine the function, we compared the gene expression profiles between control and Merm1/Wbscr22 knock-downed tumor cells.

overall_design: Four established cell lines were selected for RNA extraction and hybridization on Affymetrix microarrays: (1) control LM8 cells, designated as LM8/control, (2) Merm1/Wbscr22 knock-downed LM8 cells, designated as LM8/shRNA, (3) control A375M cells, designated as A375M/control, and (4) Merm1/Wbscr22 knock-downed A375M cells, designated as A375M/shRNA.

first: Naoya

last: Fujita


title: Increased expression of Bcl11b in human transformed T cell lines leads to chemoresistance accompanied by G1 accumulation.

city: Greifswald

first: Maren

last: Depke

address: F.-L.-Jahn-Str. 15a

department: Department of Functional Genomics

institute: Ernst-Moritz-Arndt-University Greifswald, Interfaculty Institute of Genetics and Functional Genomics

summary:
ABSTRACT
Background: The expression of BCL11B has been reported in normal and transformed cells derived from T-lymphocytes, neurons, keratinocytes and recently in a subset of squamous cell carcinomas. Despite the rapidly accumulating knowledge concerning Bcl11b biology, the contribution of this protein to normal or transformed cell homeostasis remains open.
Methodology/Principal Findings: Here, by employing an overexpression strategy and cells endogenously expressing BCL11B we revealed formerly unidentified features of Bcl11b which shed some light on the potential involvement of the protein in tumor maintenance. Two different T cell lines were forced to overexpress BCL11B which resulted in markedly increased resistance to radiomimetic drugs while no influence on death-receptor apoptotic pathway was observed. Apoptosis resistance triggered by BCL11B overexpression was accompanied by a cell cycle delay caused by accumulation of cells at G1. This cell cycle restriction was associated with upregulation of CDKN1C (p57) and CDKN2C (p18) cyclin dependent kinase inhibitors. Moreover, p27 and p130 proteins accumulated and the SKP2 gene encoding a protein of the ubiquitin-binding complex responsible for their degradation was repressed. Furthermore, the expression of the MYCN oncogene was silenced which resulted in significant depletion of the protein in cells expressing high BCL11B levels. Both cell cycle restriction and resistance to DNA-damage-induced apoptosis coincided and required the histone deacetylase binding N-terminal domain of Bcl11b. The sensitivity to genotoxic stress could be restored by the histone deacetylase inhibitor trichostatine A.
Conclusions: The data presented here suggest a potential role of BCL11B in tumor survival and encourage developing Bcl11b-inhibitory approaches as a potential tool to specifically target chemoresistant tumor cells.

overall_design: Using a retroviral-vector-based system in Jurkat cells BCL11B overexpression was compared to controls transfected with the empty vector. Of each group one biological replicate was analyzed on one array.

first: Piotr

last: Grabarczyk

first: Christian

middle: A

last: Schmidt

first: Uwe

last: Völker


title: Effect of loss of Gfi1b on hematopietic stem cells

city: Essen

first: Cyrus

last: Khandanpour

address: Hufelandstr. 55

department: Hematology

institute: University Hospital Essen

summary: Using Gfi1b conditional mice, deletion of gfi1b in the hematopietic system was induced by injecting MxCre tg Gfi1bfl/fl mice with pIpC. 30 days after injection, Cd150 pos, Cd 48 neg, Lin neg Sca and c-kit pos stem cells were sortrted from Gfi1bfl/fl and Mxcre tg Gfi1bfl/fl mice and analysed. We used the mouse Affymetrix Gene ST Array.

overall_design: The study should determine whether loss of Gfi1 alters the gene expression pattern in the hematopietic stem cells.

first: Lothar

last: Vassen

first: Tarik

last: Moroy


title: microRNA and mRNA expression profiles of human embryonic stem cells treated with activin A

city: Taipei

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

institute: National Taiwan University

summary: Human embryonic stem (hES) cells have the capacities to propagate for extended periods and to differentiate into cell types from all three germ layers both in vitro and in vivo. These characteristics of self-renewal and pluripotency enable hES cells having the potential to provide an unlimited supply of different cell types for tissue replacement, drug screening, and functional genomics studies. The hES-T3 cells with normal female karyotype cultured on either mouse embryonic fibroblasts (MEF) in hES medium (containing 4 ng/ml bFGF) (T3MF) or feeder-free Matrigel in MEF-conditioned medium (supplemented with additional 4 ng/ml bFGF) (T3CM) were found to express very similar profiles of mRNAs and microRNAs, indicating that the unlimited self-renewal and pluripotency of hES cells can be maintained by continuing culture on these two conditions. However, the expression profiles, especially microRNAs, of the hES-T3 cells cultured on Matrigel in hES medium supplemented with 4 ng/ml bFGF and 5 ng/ml activin A (T3BA) were found to be different from those of T3MF and T3CM cells. In T3BA cells, four hES cell-specific microRNAs miR-372, miR-302d, miR-367 and miR-200c, as well as three other microRNAs miR-199a, miR-19a and miR-217, were found to be up-regulated, whereas five miRNAs miR-19b, miR-221, miR-222, let-7b and let-7c were down-regulated by activin A. Thirteen abundantly differentially expressed mRNAs, including NR4A2, ERBB4, CXCR4, PCDH9, TMEFF2, CD24 and COX6A1 genes, targeted by seven over-expressed miRNAs were identified by inverse expression levels of these seven microRNAs to their target mRNAs in T3BA and T3CM cells. The NR4A2, ERBB4 and CXCR4 target genes were further found to be regulated by EGF and/or TNF. The 50 abundantly differentially expressed genes targeted by five under-expressed miRNAs were also identified. The abundantly expressed mRNAs in T3BA and T3CM cells were also analyzed for the network and signaling pathways, and roles of activin A in cell proliferation and differentiation were found. These findings will help elucidate the complex signaling network which maintains the self-renewal and pluripotency of hES cells.

overall_design:
In this investigation, both miRNA and mRNA expression profiles from human embryonic stem cells grown on MEF feeder (T3MF), feeder-free Matrigel in MEF-conditioned medium (T3CM) and in hES medium (containing 4 ng/ml bFGF) supplemented with 5 ng/ml activin A (T3BA) were quantitatively determined. Several target genes of T3BA and T3CM cells-specific miRNAs were identified.

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

first: Zong-Yun

last: Tsai

first: Sher

last: Singh

first: Steven

last: Li


title: Dynamic changes during adaptation to estrogen deprivation in MCF7 cell line

city: Barcelona

first: Miguel Angel

last: Pujana

address: Gran Via 199

institute: Institut Catala d'Oncologia IDIBELL

summary: Endocrine therapies targeting the proliferative effect of 17β-estradiol (17βE2) through estrogen receptor α (ERα) are the most effective systemic treatment of ERα-positive breast cancer. However, most breast tumors initially responsive to these therapies develop resistance through a molecular mechanism that is not yet fully understood. The long-term estrogen-deprived (LTED) MCF7 cell model has been proposed to recapitulate acquired resistance to aromatase inhibitors (AIs) in postmenopausal women. To elucidate this resistance, genomic, transcriptomic and molecular data were integrated into the time course of MCF7-LTED adaptation. Dynamic and widespread genomic changes were observed, including amplification of the ESR1 locus consequently linked to an increase in ERα. Dynamic transcriptomic profiles were also observed that correlated significantly with genomic changes and were influenced by transcription factors known to be involved in acquired resistance or cell proliferation (e.g. IRF1 and E2F1, respectively) but, notably, not by canonical ERα transcriptional function. Consistently, at the molecular level, activation of growth factor signaling pathways by EGFR/ERBB/AKT and a switch from phospho-Ser118 (pS118)- to pS167-ERα were observed during MCF7-LTED adaptation. Evaluation of relevant clinical settings identified significant associations between MCF7-LTED and breast tumor transcriptome profiles that characterize ERα-negative status, early response to letrozole and recurrence after tamoxifen treatment. This study proposes a mechanism for acquired resistance to estrogen deprivation that is coordinated across biological levels and independent of canonical ERα function.

overall_design: LTED (long term estrogen deprived) cell line was generated from MCF-7 cells by long-term culture under estrogen deprivated conditions. And RNA samples were obtained after 3, 15, 30, 90, 120, 150 and 180 days.


title: Expression data from tamoxifen treated and control injection treated Tg(αMHC-MerCreMer) and wild type mus musculus.

city: Oslo

first: Karina

last: Hougen

address: Kirkeveien 166

country: Norway

institute: University of Oslo

summary:
α-myosin heavy chain promoter controlled MerCreMer expression enables conditional, cardiomyocyte specific and tamoxifen dependent gene inactivation of floxed genes. Administration of tamoxifen has been linked to development of acute and transient cardiomyopathy. The mechanism for this is unknown.
We used microarrays to sort out factors relevant for adverse effects following tamoxifen dependent gene inactivation, to develop a protocol with minimal adverse effects, and to identify the most proper control animals.

overall_design: Mus musculus Tg(αMHC-MerCreMer) and wild type were sacrificed 4 days after 1 or 4 consecutive days of 40 mg/kg tamoxifen injected intraperitoneally, or after corresponding control injection treatment.

first: Ståle

last: Nygård

first: Ivar

last: Sjaastad


title: Effect of Protease-resistant PML-RARα on the leukemogenic potential in a mouse model of Acute Promyelocytic Leukemia

city: St Louis

first: Rekha

last: Meyer

address: 4320 Forest Park Av

institute: Washington University School of Medicine

summary:
Previous studies in our laboratory demonstrated that the azurophil granule protease neutrophil elastase (NE) cleaves PML-RARA (PR), the fusion protein that initiates acute promyelocytic leukemia (APL). Further, NE deficiency reduces the penetrance of APL in a murine model of this disease. We therefore predicted that NE-mediated PR cleavage might be important for its ability to initiate APL. To test this hypothesis, we generated a mouse expressing NE-resistant PR. These mice developed APL indistinguishable from wild type PR, but with significantly reduced latency (median leukemia-free survival of 274 days versus 473 days for wild type PR, p<0.001).  Resistance to proteolysis may increase the abundance of full length PR protein in early myeloid cells, and our previous data suggested that non-cleaved PR may be less toxic to early myeloid cells. Together, these effects appear to increase the leukemogenicity of NE-resistant PR, contrary to our previous prediction. We conclude that NE deficiency may reduce APL penetrance via indirect mechanisms that are still NE dependent.

Keywords: Time course

overall_design: U937 cells were transfected with one of three tagged constructs GFP,GFP-PR,GFP-PR-2VR sorted for GFP positivity at the indicated time points and harvested for RNA.

first: Geoffrey

last: Uy

first: Timothy

last: Ley


title: Gene expression profile of poorly differentiated synovial sarcoma

city: Tokyo

first: Hitoshi

last: Ichikawa

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

institute: National Cancer Center Research Institute

summary: Poorly differentiated type synovial sarcoma (PDSS) is a variant of synovial sarcoma characterized by predominantly round or short-spindled cells. Although accumulating evidence from clinicopathological studies suggests a strong association between this variant of synovial sarcoma and poor prognosis, little has been reported on the molecular basis of PDSS. To gain insight into the mechanism(s) that underlie the emergence of PDSS, we analyzed the gene expression profiles of 34 synovial sarcoma clinical samples, including 5 cases of PDSS, using an oligonucleotide microarray. In an unsupervised analysis, the 34 samples fell into 3 groups that correlated highly with histological subtype, namely, monophasic, biphasic, and poorly differentiated types. PDSS was characterized by down-regulation of genes associated with neuronal and skeletal development and cell adhesion, and up-regulation of genes on a specific chromosomal locus, 8q21.11. This locus-specific transcriptional activation in PDSS was confirmed by reverse transcriptase (RT)-PCR analysis of 9 additional synovial sarcoma samples. Our results indicate that PDSS tumors constitute a distinct genetic group based on expression profiles.

overall_design: 34 SYT-SSX fusion transcript-positive SS samples, consisting of 21 MSS, 8 BSS and 5 PDSS cases, were analyzed using an oligonucleotide microarray using a GeneChip Human Genome U133 plus 2.0 array (Affymetrix).

first: Robert

last: Nakayama


title: Genome Wide Expression Analysis of Middle Eastern Colorectal Cancer Reveals FOXM1 as a Novel Target for Cancer Therapy

status: Public on Aug 31 2010

city: RIYADH 11211

first: ABDUL

middle: KHALID

last: SIRAJ

state: KSA

department: HUMAN CANCER GENOMIC

country: Saudi Arabia

institute: KING FAISAL SPECIALIST HOSPITAL & RESEARCH CENTER

summary:
In order to identify potential genes that may play an important role in progression of colorectal carcinoma, we screened and validated the global gene expression using cDNA expression array on 36 CRC tissues and compared with 24 non-cancerous colorectal tissue.
We investigated the differential expression levels using cDNA microarray technique in a series of 35 CRC and 24 normal samples. FoxM1 was identified as one of the dysregulated genes and was  significantly overexpressed in the tumor samples in comparison to the normal samples.

overall_design: 35 colorectal cancer samples versus 24 normal samples.

first: Shahab

last: Uddin

first: Maqbool

last: Ahmed

first: Azhar

last: Hussain

first: Jehad

last: Abubaker

first: Nasser

last: Al-Sanea

first: Alaa

last: Abdul Jabbar

first: Luai

middle: H

last: Ashari

first: Samar

last: Alhomoud

first: Fouad

last: Al-Dayel

first: Zeenath

last: Jehan

first: Prashant

last: Bavi

first: Abdul

last: Siraj

first: Khawla

last: Al-Kuraya


title: Staging of biliary atresia at diagnosis by molecular profiling of the liver

city: Cincinnati

first: Jorge

last: Bezerra

address: 3333 Burnet Ave.

department: Gastroenterology, Hepatology & Nutrition

institute: Cincinnati Children's Hospital Medical Center

summary: BACKGROUND: Young age at portoenterostomy has been linked to improved outcome in biliary atresia, but pre-existing biological factors may influence the rate of disease progression. In this study, we aimed to determine whether molecular profiling of the liver identifies stages of disease at diagnosis. METHODS: We examined liver biopsies from 47 infants with biliary atresia enrolled in a prospective observational study. Biopsies were scored for inflammation and fibrosis, used for gene expression profiles, and tested for association with indicators of disease severity, response to surgery, and survival at 2 years. RESULTS: Fourteen of 47 livers displayed prominent features of inflammation (N=9) or fibrosis (N=5), with the remainder showing similar levels of both simultaneously. Differential profiling of gene expression of the 14 livers displayed a unique molecular signature containing 150 gene probes. Applying prediction analysis models, the probes classified 29 of the remaining 33 livers into inflammation or fibrosis. Molecular classification into the two groups was validated by the findings of increased hepatic population of lymphocyte subsets or tissue accumulation of matrix substrates. The groups had no association with traditional markers of liver injury or function, response to surgery, or complications of cirrhosis. However, infants with an inflammation signature were younger, while those with a fibrosis signature had decreased transplant-free survival. CONCLUSION: Molecular profiling at diagnosis of biliary atresia uncovers a signature of inflammation or fibrosis in most livers. This signature may relate to staging of disease at diagnosis and has implications to clinical outcomes.

overall_design: Clinical and laboratory data and liver biopies were obtained from 47 infants at diagnosis of biliary atresia and every 3-6 month intervals until 2 years of age as part of a prospective, observational study of the Biliary Atresia Research Consortium. Liver biopsies underwent histological scoring and those specimens classified as inflammation or fibrosis were used to generate a group-specific gene expression profile. The profile was used to assign a molecular stages of inflammation or fibrosis to the entire cohort. Molecular groups were tested for biological plausibility using immunostaining to quantify hepatic inflammatory cells, and quantitative PCR to reproduce the expression of gene groups and the expression of collagen genes. They were also tested for clinical relevance by testing of association with indicators of liver function, complications of disease, and clinical outcome.

first: Katie

last: Moyer

first: Vivek

last: Kaimal

first: Cristina

last: Pacheco

first: Reena

last: Mourya

first: Huan

last: Xu

first: Pranavkumar

last: Shivakumar

first: Ranajit

last: Chakraborty

first: Marepalli

last: Rao

first: John

last: Magee

first: Kevin

last: Bove

first: Anil

last: Jegga


title: Gene expression signature and the prediction of lymph node metastases

city: Bunkyo-ku

first: Toshiaki

last: Watanabe

department: Department of Surgical Oncology

institute: University of Tokyo

summary:
Samples were taken from colorectal cancers in surgically resected specimens in 89 colorectal cancer patients. The expression profiles were determined using Affymetrix Human Genome U133 Plus 2.0 arrays. Comparison between the sample groups allow to identify a set of discriminating genes that can be used for molecular markers for predicting lymph node metastases.
Keywords: disease state analysis

overall_design: Eighty-nine colorectal cancer patients were studied. Samples from 89 patients were divided into a training set (69 samples) and a testing set (20 samples).

first: Takashi

last: Kobunai

first: Etsuko

last: Toda

first: Toshinori

last: Oka


title: Altered immune phenotype in peripheral blood cells of patients with scleroderma-associated pulmonary hypertension

status: Public on Aug 30 2010

city: Aurora

first: Christopher

middle: D

last: Coldren

address: 12700 East 17th Place

department: Medicine

institute: University of Colorado School of Medicine

summary:
Rationale:  Pulmonary arterial hypertension is a common and potentially fatal complication of scleroderma that may involve inflammatory and autoimmune mechanisms.  Alterations in the gene expression of peripheral blood mononuclear cells have been previously described in patients with pulmonary arterial hypertension.  The ability to identify patients at risk for developing pulmonary hypertension would be clinically beneficial.
Objective:  To identify genes that are differentially expressed in peripheral blood mononuclear cells in scleroderma patients with and without pulmonary hypertension which could be used as biomarkers of disease for early diagnosis and provide insight into pathogenesis of pulmonary hypertension in at-risk populations.
Methods and Results:  Gene expression analysis was performed on a carefully characterized Microarray Cohort of scleroderma patients with (n=10) and without (n=10) pulmonary hypertension.  Differentially expressed genes were confirmed in the Microarray Cohort and validated in a separate Validation Cohort of scleroderma patients with (n=15) and without (n=19) pulmonary hypertension by RT-qPCR.  We identified inflammatory and immune-related genes including interleukin-7 receptor (IL-7R) and chemokine receptor 7 (CCR7) as differentially expressed in patients with scleroderma-associated pulmonary hypertension.  Flow cytometry confirmed decreased expression of IL-7R on circulating CD4+ T cells from scleroderma patients with pulmonary hypertension.
Conclusions:  Differences exist in the expression of inflammatory and immune-related genes  in peripheral blood cells derived from patients with scleroderma-related pulmonary hypertension compared to those with normal pulmonary artery pressures.  These findings may have implications as biomarkers to screen at-risk populations to facilitate early diagnosis and provide insight into inflammatory and autoimmune mechanisms of scleroderma-related pulmonary hypertension.

overall_design: Gene expression analysis was performed on a carefully characterized Microarray Cohort of scleroderma patients with (n=10) and without (n=10) pulmonary hypertension.  Differentially expressed genes were confirmed in the Microarray Cohort by RT-qPCR.

first: Michael

middle: G

last: Risbano

first: Christina

last: Meadows

last: Edwards

first: David

last: Collier

first: Wendy

last: Huber

first: Douglas

last: Mack

first: Andrew

last: Fontenot

first: Mark

last: Geraci

first: Todd

last: Bull


title: Gene expression profiles of HCT116 colorectal carcinoma cells treated with HDAC inhibitors

status: Public on Aug 28 2010

city: Gainesville

first: yanxia

last: liu

state: FL

address: 1600 SW Archer Rd

department: Medicinal Chemistry

institute: University of Florida

summary:
Histone deacetylases (HDACs) regulate gene expression. Inhibition of class I HDACs has been shown to inhibit cancer cell growth. Largazole, a new potent HDAC inhibitor, shows strong antitumor activity, presumably by modulating transcription of cancer relevant genes.
We used microarray analysis of human HCT116 colorectal carcinoma cell line to determine the gene expression profile after largazole treatment in comparison with other HDAC inhibitors (FK228 and SAHA). The goal was to identify regulated genes that can be linked to the antiproliferative effects of these HDAC inhibitors in HCT116 cells.

overall_design: To characterize the genes regulated by Largazole, SAHA and FK228, genome-wide gene expression analysis was carried out. Human HCT116 colorectal carcinoma cells (400,000) were seeded per well (6-well dish) and one day later treated with Largazole, SAHA, FK228 and vehicle control. 10 h later, total RNA was extracted and processed for hybridization to an Affymetrix Human Genome U133 2.0 GeneChip. Global alterations in transcript levels upon Largazole, SAHA and FK228 treatment were determined through comparison with data derived from cells treated with vehicle control. The experiment was carried out in duplicate.

first: Hendrik

last: Luesch

first: Yanxia

last: Liu


title: Calmodulin controlled gene expression profiling in mouse cortical neruons

status: Public on Aug 26 2010

city: Palo Alto

first: Zhiping

last: Pang

address: 1050 Arastradero Road

department: Molecular and Cellular Physiology

institute: Stanford University School of Medicine

summary: We used wild-type neurons, and directly compared neurons that had been infected with lentiviruses expressing the CaM shRNAs either without or with a wild-type CaM rescue protein. We then analyzed the gene expression patterns in these neurons with the Affymetrix mouse gene ST_1.0 chip. We identified in two independent array studies ~250 genes whose expression was consistently up- or down-regulated by the CaM KD, as compared to the CaM KD/rescue control. As expected, multiple classes of genes were regulated by CaM. Consistent with previous studies, we found that activity-dependent genes, such as Homers, Npas2, Arc and Egr3, were down-regulated by the CaM KD. Interestingly, we observed that several synaptic trafficking proteins were either up- or downregulated by the CaM KD. Among these was a large increase in the expression of Syt2, which can serve as a Ca2+-sensor for synaptic exocytosis; thus, this upregulation of Syt2 by the CaM KD likely accounts for the rescue of the Syt1 KO phenotype. In addition, expression of Syb1 was massively increased, whereas expression of Syt4, Syt9, and syntaxin-1A was decreased. Another intriguing class of proteins whose expression was strongly regulated by CaM were cell-adhesion molecules, such as the synaptic cell-adhesion molecules Lrrtm1, Lrrtm3, and contactin-2. Moreover, we observed up-regulation of sodium channels, and a down-regulation of potassium channels, suggesting that CaM might control the activity-dependent regulation of neuronal excitability. Finally, we detected changes in multiple genes encoding transcription factors, intracellular signal transduction proteins, elements of the cytoskeleton, or metabolic enzymes. It should be noted, however, that despite these multifarious changes, more than 95% of genes showed no CaM KD-induced change, suggesting that the observed CaM KD-dependent expression changes are specific.

overall_design: Microarray analysis was performed twice (dated 11/26 and 11/30) representing two repeats. Experimental groups:  L309 samples are control infections of mouse cortical neurons, KD30 samples are calmodulin knockdowns, rCaM Samples are shRNA-rescued with shRNA resistant calmodulin knockdowns. Both test samples were compared to the L309 control samples and only ratio data are available. CEL files for the two control Samples are available on the Series record.

first: Wei

last: Xu

first: Peng

last: Cao

first: Thomas

last: Sudhof


title: Genetic ablation of Dicer in adult forebrain neurons results in abnormal tau hyperphosphorylation and neurodegeneration

city: Quebec

first: Ezequiel

middle: L

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

country: Canada

institute: CRCHUL

summary: The type III RNase Dicer is responsible for the maturation and function of microRNA (miRNA) molecules in the cell. It is now well documented that Dicer and the fine-tuning of the miRNA gene network are important for neuronal integrity. However, the underlying mechanisms involved in neuronal death, particularly in the adult brain, remain poorly defined. Here, we show that absence of Dicer in the adult forebrain is accompanied by a mixed neurodegenerative phenotype. While neuronal loss is observed in the hippocampus, cellular shrinkage is predominant in the cortex. Interestingly, neuronal degeneration coincides with the hyperphosphorylation of endogenous tau at several epitopes previously associated with neurofibrillary pathology. Transcriptome analysis of enzymes involved in tau phosphorylation identified ERK1 as one of the candidate kinases responsible for this event in vivo. We further demonstrate that miRNAs belonging to the miR-15 family are potent regulators of ERK1 expression in mouse neuronal cells and co-expressed with ERK1/2 in vivo. Last, we show that miR-15a is specifically downregulated in Alzheimer’s disease brain. In sum, these results support the hypothesis that changes in the miRNA network may contribute to a neurodegenerative phenotype by affecting tau phosphorylation.

overall_design: Dicer KO vs. control

first: S

last: Hebert

first: A

last: Papadopoulou

first: P

last: Smith

first: M

last: Galas

first: E

last: Planel

middle: N

last: Silahtaroglu

first: N

last: Sergeant

first: L

last: Buee

first: b

last: De Strooper


title: Integrative analysis of gene expression profiling and genomic copy number in Gastrointestinal Stromal Tumors

status: Public on Aug 27 2010

city: Bologna

first: Maria

middle: Abbondanza

last: Pantaleo

state: BO

address: via Massarenti 9

department: Institute of Hematology and Medical Oncology "L.A.Seragnoli"

institute: Policlinico S. Orsola-Malpighi, University of Bologna

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

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

overall_design: Refer to individual Series


title: Identification of an intermediate signature that marks the initial phases of colorectal adenoma-carcinoma transition

status: Public on Aug 29 2010

city: Kunming

first: Hui

last: Tang

state: Yunnan

address: No. 157 Jinbi Street

department: The First People’s Hospital of Yunnan Province, Kunhua Affiliated Hospital of Kunming Medical College

institute: Institute of Basic Medicine

summary: The colorectal adenoma-carcinoma sequence describes the stepwise progression from normal to dysplastic epithelium and then to carcinoma; only a small proportion of colorectal adenoma (CRA) progresses to colorectal carcinoma (CRC). Presently, endoscopic intervention is used on patients with CRAs of high grade dysplasia, diameters > 1 cm, or villous components > 25% who are at higher risk than other CRA sufferers. During the process, biopsy samples were taken for conventional histological diagnosis, but poor pathomorphological sensitivity and specificity greatly limit the diagnostic accuracy. Unfortunately, there are no reliable molecular criteria available that can predict the potential development of CRA to CRC. In present study, we use microarrays to detail the global programme of gene expression underlying the gradual progress of colorectal adenoma-carcinoma sequence.

overall_design: Gene expression profiles of normal colorectal mucosa (NOR), CRA, and different Duke’s stages of CRC biopsy specimens, which represent the gradual progress of the colorectal adenoma-carcinoma sequence, were determined by Affymetrix technology. Intersectional analysis of discriminative expression signatures of CRC vs. CRA and CRA vs. NOR allowed the identification of the intermediate signature that mark the NOR→CRA→CRC progression. This signature represents a reservoir of candidate markers for early diagnosis of higher-risk CRA during the early stage, allowing timely therapeutic intervention and more selective treatment.

first: Qiang

last: Guo

first: Chao

last: Zhang

first: Jun

last: Zhu

last: Yang

first: Yun-lian

last: Zou

first: Yan

last: Yan

first: Hong

last: Dong

first: Tao

last: Sou

first: Xin-min


title: Analysis of human in vivo irritated epidermis: differential profiles induced by sodium lauryl sulphate and nonanoic acid

status: Public on Aug 20 2010

city: Odense

first: Mads

last: Thomassen

address: Soender Boulevard 9

department: Clinical Genetics (KKA)

country: Denmark

institute: Odense University Hospital

summary: Irritant contact dermatitis (ICD) pathogenesis is not completely understood and the genes participating in the epidermal response towards chemical irritants are only partly known. It is commonly accepted that different irritants have different mechanisms of action in the development of ICD. To define the differential molecular events induced in the epidermis by different irritants, we collected sequential biopsies (½, 4 and 24 hours after a single exposure and at day 11 after repeated exposure) from human volunteers exposed to sodium lauryl sulphate (SLS) or nonanoic acid (NON). Gene expression analysis using high-density oligonucleotide microarrays revealed essentially different pathway responses ½ h after exposure: NON transiently induced the IL-6 pathway as well as a number of mitogen activated signalling cascades including ERK and growth factor receptor signalling, whereas SLS transiently downregulated cellular energy metabolism pathways. Differential expression of the cyclooxygenase-2 and matrix metalloproteinase 3 transcripts was confirmed immunohistochemically. After cumulative exposure, 883 genes were differentially expressed while 26 suggested common biomarkers were identified . In conclusion, we bring new insights into two hitherto less well elucidated phases of skin irritancy: the very initial as well as the late phase after single and cumulative exposure, respectively.

overall_design: 36 healthy volunteers were exposed to the skin irritants SLS (n=18) or NON (n=18). Samples from 18 volunteers (9 SLS and 9 NON-exposed) were selected for the microarray experiment. Samples were obtained according to elapsed time following a single cutaneous exposure: 0.5 h, 4h and 24h. Moreover, samples were obtained at day 11 coresponding to a cumulatively (10 min for 5+4 days) irritated skin site. A balanced incomplete block design was used to obtain samples from the 4 time points; however, 0h samples (controls) were obtained for all subjects. Samples from the time point 0.5 h were of special interest and therefore doubled. Thus, 24 chips were hybridized for each irritant giving a total of 48 chips in the experiment. The relative contribution of chips per timepoint for each irritant: 0h (n=9), 0.5h (n=6), 4h (n=3), 24h (n=3), day 11 (n=3).

first: Anders

last: Clemmensen


title: Gene expression data from GIST with KIT mutation

summary:
In addition to KIT and PDGFRA mutations, sequential accumulation of other genetic events is involved in the development and progression of gastrointestinal stromal tumors (GISTs). Until recently, the significance of these other alterations has not been thoroughly investigated. The combination of gene expression profiling and high-resolution genomic copy number analysis offers a detailed molecular portrait of GISTs, providing an essential comprehensive knowledge necessary to guide the discovery of novel target genes involved in tumor development and progression.
Fresh tissue specimens from 25 patients with GIST were collected and gene expression profiling was performed using Affymetrix U133Plus array.

overall_design: GIST tumor samples from mutated (KIT or PDGFRA) or Wild Type patients were labeled for hybridization on Affymetrix microarrays. Gene expression data was then analyzed.

first: Annalisa

last: Astolfi

first: Margherita

last: Nannini

first: Monica

last: Di Battista

first: Michael

last: Heinrich

first: Donatella

last: Santini

first: Fausto

last: Catena

first: Christopher

last: Corless

first: Alessandra

last: Maleddu

first: Maristella

last: Saponara

first: Cristian

last: Lolli

first: Valerio

last: Di Scioscio

first: Serena

last: Formica

first: Guido

last: Biasco


title: Gene expression profiles of fibroblasts from MCT8 patients

status: Public on Aug 23 2010

city: Rotterdam

first: W

middle: Edward

last: Visser

address: Dr Molewaterplein 50

department: Internal Medicine

country: Netherlands

institute: Erasmus Medical Center

summary:
Thyroid hormone is crucial for normal brain development. Thyroid hormone transporters control thyroid hormone homeostatis in brain. Mutations in the thyroid hormone transporter MCT8 result in a complex endocrine and neurological phenotype.
We investigated the mechanisms of disease by analyzing gene expression profiles in fibroblasts from patients with mutations in MCT8. Performing comparative transcriptome analysis, we linked the genes differentially expressed in patient fibroblasts to the human brain transcriptome.

overall_design: Skin fibroblasts of controls and patients were cultured in different thyroid states for 24 h.

first: Sigrid

middle: M

last: Swagemakers

middle: E


title: Female human iPS cells retain an inactive X-chromosome

status: Public on Aug 19 2010

city: Los Angeles

first: Kathrin

last: Plath

state: CA

address: 615 Charles E. Young Drive South

department: Biological Chemistry

country: USA

institute: UCLA

summary: Comparison of human iPSC lines, ESC and fibroblasts to determine their expression patterns.  All early passage female lines profiled expressed XIST RNA which is an indicator of an inactive X chromosome.  Genes on the X-chromosome were also analyzed for overall levels of gene expression compared to human fibroblasts.

overall_design: hiPSC lines were generated and extracted for RNA with TriZOL and hybridization on Affymetrix arrays.

first: Jason

last: Tchieu