title: Innate immune repsonses to TREM-1 activation

city: Cambridge

first: Scott

last: Jelinsky

state: MA

address: 610 Main Street

department: Inflammation and Immunology

institute: Pfizer

summary:
TREM-1 is an orphan immunoreceptor expressed on monocytes, macrophages, and neutrophils. TREM-1 associates with and signals via the adapter protein DAP12/TYROBP, which contains an immunoreceptor tyrosine-based activation motif (ITAM). TREM-1 activation by receptor cross-linking is pro-inflammatory, and can amplify cellular responses to Toll-like receptor (TLR) ligands such as bacterial lipopolysaccharide (LPS). To investigate the cellular consequences of TREM-1 activation, we have characterized global gene expression changes in human monocytes in response to TREM-1 cross-linking in comparison to and combined with LPS. Both TREM-1 activation and LPS up-regulate chemokines, cytokines, matrix metalloproteases, and PTGS/COX2, consistent with a core inflammatory response. However, other immunomodulatory factors are selectively induced, including SPP1 and CSF1 (i.e., M-CSF) by TREM-1 activation and IL-23 and CSF3 (i.e., G-CSF) by LPS. Additionally, cross-talk between TREM-1 activation and LPS occurs on multiple levels. While synergy in GM-CSF protein production is reflected in commensurate mRNA abundance, comparable synergy in IL-1b protein production is not. TREM-1 activation also attenuates the induction of some LPS target genes, including those that encode IL-12 cytokine family subunits. Whereas positive TREM-1 outputs are abolished by the PI3K inhibitor wortmannin, this attenuation is largely PI3K-independent. These experiments provide a detailed analysis of the cellular consequences of TREM-1 activation, and highlight some of the complexity in signal integration between ITAM- and TLR-mediated signaling.
Keywords: Stress response

overall_design: 11 anonymous donors were treated with Vehicle, isotype control antibody, TREM1 antibody, LPS, isotype control antibody plus LPS and TREM1 antibody plus LPS

first: Ken

last: Dower


title: Search for New Biomarkers for the Monitoring of the Minimal Residual Disease of the Acute Lymphoblastic Leukemia.

status: Public on Mar 15 2008

city: Monterrey

first: Angel

last: Lugo-Trampe

state: Nuevo León

address: Av. Madero y Dr. Eduardo Aguirre Pequeño

department: Bioquímica

country: Mexico

institute: Universidad Autónoma de Nuevo León

summary:
The main goal of the research was to find some new biomarkers for the monitoring of the Minimal Residual Disease in Acute Lymphoblastic Leukemia patients.
Keywords: Search for new Biomarkers

overall_design: Lymphocytes from the Periferical Blood Samples of 11 patients with Acute Lymphoblastic Leukemia were purified according to lineage defined by the immunofenotype. The total RNA from the 11 samples were processed according to manufacturer’s instructions (Affymetrix, Inc., Santa Clara, CA). The batch .CEL files generated by GeneChip Operating Software (GCOS) were analyzed into R software with the affy module from the Bioconductor consortium. Samples with technical replicates were normalized applying the Quantile Normalization method. Then all the data were globally normalized applying the Loess Normalization Altorithm. Finally the gene expression differences were calculated.

first: Rocio

last: Ortiz-López

first: José

middle: C

last: Jaime-Pérez

first: Augusto

last: Rojas-Martínez

first: David

last: Gómez-Almaguer

first: Herminia

middle: G

last: Martínez-Rodríguez

first: Gerardo

last: Jiménez-Sanchez

first: Irma

last: Silva-Zolezzi

first: Claudia

last: Rangel-Escareño

first: Oscar

last: González-Llano

first: César

middle: H

last: Gutierrez-Aguirre

first: Nereida

last: Méndez-Ramírez

first: Rosario

last: Salazar-Riojas

first: Odra

middle: L

last: Martínez-González

first: Laura

middle: E

last: Martínez-Garza

first: Rosa

last: De la Rosa-Alvarado

first: Berenice

last: Pérez-Cavazos

first: Karla

last: Haces-Gil

first: Idalia

last: Garza-Veloz


title: Cryptosporidium infection of human intestinal tissues causes increased expression of Osteoprotegerin

status: Public on Mar 14 2008

city: Houston

first: Alejandro

last: Castellanos

state: TX

address: One Baylor Plaza

department: Medicine-Infectious Diseases

country: USA

institute: Baylor College of Medicine

summary:
Cryptosporidium hominis and parvum primarily infect intestinal epithelial cells, which, in turn, play a key role in activating and communicating with the host immune system. To determinate which genes are regulated during early infection of non-transformed human epithelial cells, human ileal mucosa was removed (from surgical specimens), placed on collagen membranes, and cultured as explants. Explant cultures were infected with C. parvum, C. hominis, or control culture medium. After 24 hrs, RNA was extracted and analyzed using Affmetrix GeneChip microarrays. Among the more prominent genes with regulated expression was Osteoprotegerin (OPG), which was increased in all of the explants at 24 hrs and further up-regulated 1.58 fold by C. parvum and 2.54 fold by C. hominis infection compared with uninfected explants. Using real time PCR, we confirmed a 3.14 and 3.79 fold increase in OPG mRNA after infection with C. parvum and C. hominis respectively.
Keywords: gene expression analysis via microarray

overall_design: Ileal tissue, which would otherwise have been discarded, was obtained from 3 individuals undergoing bowel resections. The mucosa was removed mechanically and cutured as explants in medium CMRL-1066 and incubated 3 hrs prior to ex vivo infection. Specimens from each individual were divided into 4 parts. A base lane specimen was preserved in RNAse inhibitor directly. The other 3 specimens were infected with 106 oocysts of C. parvum, C hominis or excystation solution. After 24h, the tissues were place in RNAse inhibitor. Subsequently, RNA was extracted with RNAeasy Mini Kit Quiagen and submitted to Baylor College of Medicine microarray facility. The samples were analyzed for gene expression profiles using the Affymetrix Human Genome U133 2.0 array.

first: A

last: Castellanos-Gonzalez

first: L

last: Yancey

first: H

last: Wang

first: B

last: Pantenburg

first: K

last: Liscum

last: White


title: Expression data from transplanted intestine bifor signs of rejection, and when their was signs of rejection

status: Public on Mar 12 2008

city: worcester

first: Georg

last: Elias

address: 377 plantation St/ Biotech 4

department: Surgery/ Transplant

institute: UMASSMED

summary:
Acute cellular rejection (ACR) is the major cause of intestinal graft loss. Little is known about the genetic response occurring in small bowel transplantation (SBTx) during ACR. We report the case of a 44 year-old female with short gut syndrome following multiple surgeries for familial adenomatous polyposis that underwent living-related SBTx. We obtained for the first time a gene expression profile of the intestinal graft during ACR. Microarray analysis revealed increased transcript levels for genes that match identically to an IFN? signature reported for activated plasmacytoid dendritic cells and T-cell chemotaxis and cytolysis correlating with the diagnosis of ACR.
Keywords: disease state analysis

overall_design:
sam1, sam2, sam3 (without signs of rejection)

sam4, sam5, sam6 (with signs and symptoms of rejection , histology showed increasing lymphocyte infiltration in the lamina propria and epithelium)

first: Sean

middle: P

last: Bradley

middle: M

first: Melissa

last: Brown

first: Mohan

last: Pahari

first: Barbara

last: Bannar

first: Cristiana

last: Rastellini

first: Luca

last: Cicalese


title: Human induced pluripotent stem (iPS) cells from neonatal skin derived cells

status: Public on Mar 16 2008

city: Chuo-ku

first: Tetsuya

last: Ishikawa

state: Tokyo

address: 1-1, Tsukiji 5-chome

department: Research Institute

country: Japan

institute: Japanease National Cancer Center

summary:
Induction of germline-competent pluripotent stem cells from mouse fibroblasts has been achieved by the ectopic expression of four genes (Oct3/4, Sox2, c-Myc and Klf4). If this method can be applied to humans for the generation of personalized human pluripotent stem cells, it would greatly facilitate the therapeutic application of stem cells by avoiding the problem of immune rejection by the recipient associated with allograft transplants. Here we show that the ectopic expression of the same four genes in human neonatal skin derived cells is sufficient to induce pluripotent stem cells indistinguishable from human embryonic stem cells in morphology, gene expression, DNA methylation, teratoma formation and long term self-renewal ability. Extensive analysis of colonies generated by ectopic expression of these four genes indicates the presence of considerable heterogeneity in the induced colonies. These results provide a new finding to generate human induced pluripotent stem cells from postnatal somatic tissues.
Keywords: Cell type comparison

overall_design: The microarray study was carried out using Affymetrix Human Genome U133 Plus 2.0 gene expression arrays or Agilent Whole Human Genome Oligo microarrays. Total RNA was extracted from cells with RNeasy (Qiagen). For Affymetrix array, biotin-labelled cRNA was reverse transcribed from 1 µg of total RNA according to Affymetrix technical protocols. Fifteen micrograms of cRNA was fragmented and hybridized to Affymetrix U133 plus 2 GeneChip arrays at 45C for 16 h and then washed and stained using Affimetrix Fluidics. The arrays were scanned using an Affimetrix GCS3000 scanner, and the images obtained were processed to data using the GCOS software. For Agilent array (G4112A), Total RNA was labeled with Cy3. Samples were hybridized with Agilent Gene Expression Hybridization kit according to the one color protocol. Arrays were scanned with a Agilent Microarray Scanner System and processed to data with Feature Extraction Software (v.9.5.3). Data from this experiment and the GEO database were analysed with the GeneSpring 7.3.1. software.

first: Hideki

last: Masaki

first: Shunichi

last: Takahashi

first: Kazuhiro

last: Sakurada


title: H522 lung cancer cells' TGFbeta response was restored by putting back BRG1 and TGFbRII

status: Public on Mar 18 2008

city: New York

first: Qiaoran

last: Xi

state: NY

address: 1275, York ave.

department: Cancer biology and genetics

institute: MSKCC

summary:
The transcription factors Smad2 and Smad3 mediate a large set of genes responses induced by the cytokine TGFβ, but the extent to which their function depends on chromatin remodeling remains to be defined. We observed interactions between these two Smads and BRG1, BAF250b, BAF170 and BAF155, which are core components of the SWI/SNF chromatin-remodeling complex. Smad2 and Smad3 have a similar affinity for these components in vitro, and their interactions are primarily mediated by BRG1. In vivo, however, BRG1 predominantly interacts with Smad3, and this interaction is enhanced by TGFβ stimulation. Our results suggest that BRG1 is incorporated into transcriptional complexes that are formed by activated Smads in the nucleus, on target promoters. Using BRG1-deficient cell systems(H522 lung cancer cells), we defined the BRG1 dependence of the TGFβ transcriptional program genome-wide. Most TGFβ gene responses in human epithelial cells are dependent on BRG1 function. Remarkably, BRG1 is not required for the TGFβ-mediated induction of SMAD7 and SNON, which encode key mediators of negative feedback in this pathway. Our results provide a genome-wide scope of the participation of BRG1 in TGFβ action and suggest a widespread yet differential involvement of BRG1 SWI/SNF remodeler in the transcriptional response of many genes to this cytokine.
Keywords: comparative genomic hybridization

overall_design: NCI-H522 cells that were transduced with BRG1, TβR-II, or both vectors combined were incubated with TGFβ and subjected to transcriptomic analysis. Totally 6 samples.

first: Wei

last: He

first: Xiang

last: Zhang

first: Joan

last: Massague


title: Acute myeloid leukemia samples of samples =< 60yrs on HG-U133 plus 2

first: Roel

last: Verhaak

address: 1400 Pressler St

department: Bioinformatics and Comp Bio

institute: MD Anderson Cancer Center

summary:
The pretreatment karyotype of leukemic blasts is currently the key determinant in therapy decision-making in acute myeloid leukemia (AML). However, approximately fifty percent of AML patients, often carrying a normal karyotype, are currently unclassifiable based these established methods. Gene expression profiling has proven to be valuable for risk stratification of AML.

The gene expression profiles of AML samples of two independent cohorts (n=247 and n=214) were determined using Affymetrix U133Plus2.0 GeneChips: all Samples below 4000 are in the training cohort; all Samples higher than 4000 are in the validation cohort.

Data analyses were carried out to discover and predict  prognostically relevant subtypes in AML (<60 years) based on their gene expression signatures. Statistical analyses were performed to determine the prognostic significance of cases of AML with specific molecular signatures. Unsupervised cluster analyses of the gene expression signatures of both independent cohorts of AML patients confirmed that chromosomal lesions and mutations, often resulting in aberrant transcription factors, induce discriminatory patterns of gene expression. In contrast, however, mutations in signalling molecules do not establish strong molecular signatures. Consequently, prognostically important subtypes, which express mutated trancription factors were predicted with high accuracy using minimal sets of genes. We identified several novel clusters, some consisting of patients with normal karyotypes. Gene expression profiling allows classification of AML subtypes characterized by the expression of abnormal transcription factors, however, prediction of clinically relevant mutations affecting signalling molecules is impossible and thus still requires addition molecular methods.

Keywords: acute myeloid leukemia, patient blood or bone marrow samples

overall_design: 461 blood or bone marrow samples of acute myeloid leukemia patients were hybridized to Affymetrix HG-U133 plus 2 GeneChips. 76 additonal samples added on 7/28/2011.

first: Bas

middle: J

last: Wouters

first: Claudia

middle: A

last: Erpelinck

first: Saman

last: Abbas

first: Berna

last: Beverlo

first: Sanne

last: Lugthart

first: Bob

last: Löwenberg

first: Ruud

last: Delwel

first: Peter

last: Valk


title: Time course of NHBE cells exposed to whole cigarette smoke

status: Public on Mar 04 2008

first: Ellen

last: Jorgensen

address: 712 Fifth Avenue

institute: Vector Research Ltd.

summary:
Gene expression patterns were assessed in normal human bronchial epithelial (NHBE) cells exposed to cigarette smoke from a reference cigarette (2R4F, University of Kentucky) and a typical American brand of "light" cigarettes ("Lights") in order to develop a better understanding of the genomic impact of tobacco exposure, which can ultimately define biomarkers that discriminate tobacco-related effects and outcomes in a clinical setting.  NHBE cells were treated with whole cigarette smoke for 15 minutes and alterations to the transcriptome assessed at 2, 4, 8 and 24 hours post-exposure using high-density oligonucleotide microarrays.
Keywords: time course, cigarette smoke exposure

overall_design: 4 replicate Petri dishes of cells were exposed in a custom-built smoke exposure chamber. Cigarettes were smoked as per FTC protocols, and the smoke diluted such that the cells were at least 50% viable as compared to mock (air)-exposed controls after 24h. RNA from each replicate dish was analyzed using a separate array. Four replicates of an incubator (untreated with either smoke or air) are included also.

middle: D

first: Anthony

last: Albino


title: A case of primary hyperparathyroidism and undetectable serum PTH due to a truncating PTH gene mutation

status: Public on Mar 01 2008

city: St Leonards

first: Roderick

last: Clifton-Bligh

state: NSW

address: Pacific Hwy

country: Australia

institute: Kolling Institute of Medical Research

summary:
A investigation of the gene expression of one parathyroid tumour compared to its adjacent normal tissue
Keywords: differentially expressed gene profile

overall_design: Affymetrix Human Gene Expression Chip (Human Genome U133 plus 2.0 Array. One sample compared directly to the other to find genes that are differentially expressed and that are significant to the tumour. Univariate analysis was applied.

first: Amy

middle: Y

last: Au

first: Kerrie

last: McDonald

last: Gill

first: Margaret

last: Wilkinson

first: Hee-Chang

last: Mun

first: Terrence

last: Diamond

first: Liza

last: Nery

first: Mark

last: Sywak

first: Arthur

last: Conigrave


title: Expression analysis in A431_wt vs A431_GR cells

status: Public on Mar 05 2008

city: Nashville

first: Shizhen Emily

last: Wang

state: TN

address: 2220 Pierce AVE, PRB-771

department: Cancer Biology

institute: Vanderbilt University

summary:
A431 wild-type (wt) cancer cell line is sensitive to treatment with EGFR tyrosine kinase inhibitors (TKIs). By culturing it chronically under gefitinib, it eventually becomes resistant (A431_GR cell). We know of a few proteins involved in this mechanism of drug resistance, but a cDNA exprssion array would add information to other genes that might be involved in this resistance mechanism.
We used microarrays to identify the differences in the global gene expression between A431_wt (wild-type) cells and A431_GR cells.
Keywords: comparison of two cell lines

overall_design: Total RNA was isolated from parental (wild-type) and GR (gefitinib-resistant) A431 cells using TRIzol reagent (Invitrogen, Carlsbad, CA), followed by RNeasy Mini Kit column purification (Qiagen, Valencia, CA) including an in column DNAse clean-up using RNAse-free DNAse Set (Qiagen). Synthesis of cRNA target, its hybridization to Human Genome U133 Plus 2.0 microarrays and scanning of those arrays was performed using Affymetrix GeneChip products and reagents in accordance with the manufacturer’s recommendations at the Vanderbilt Microarray Shared Resource.

first: Marta

last: Guix

first: Emily

first: Carlos

last: Arteaga


title: Expression data from decoy receptor 3-treated monocyte-derived macrophages

city: Taipei

first: Yung-Chi

last: Chang

address: 155, Sec. 2, Li-Nong St.

department: Microbiology and Immunology

country: Taiwan

institute: National Yang-Ming University

summary:
Decoy receptor 3 (DcR3) is a member of the TNF receptor superfamily and is up-regulated in tumors that originate from a diversity of lineages. DcR3 is capable of promoting angiogenesis, inducing dendritic cell apoptosis, and modulating macrophage differentiation. Since tumor-associated macrophages (TAMs) are the major infiltrating leukocytes in most malignant tumors, we used microarray technology to investigate whether DcR3 contributes to the development of TAMs. Among the DcR3-modulated genes expressed by TAMs, those that encode proteins involved in MHC class II (MHC-II)-dependent antigen presentation were down-regulated substantially, together with the master regulator of MHC-II expression (the class II transactivator, CIITA). The ERK- and JNK-induced deacetylation of histones associated with the CIITA promoters was responsible for DcR3-mediated down-regulation of MHC-II expression. Furthermore, the expression level of DcR3 in cancer cells correlated inversely with HLA-DR levels on TAMs and with the overall survival time of pancreatic cancer patients. The role of DcR3 in the development of TAMs was further confirmed using transgenic mice over-expressing DcR3. This elucidates the molecular mechanism of impaired MHC-II-mediated antigen presentation by TAMs, and raises the possibility that subversion of TAM-induced immunosuppression via inhibition of DcR3 expression might represent a target for the design of new therapeutics.
Keywords: time-dose response

overall_design: Freshly isolated human monocytes were cultured with DcR3 or control hIgG1 in the presence of M-CSF for 2 days. Data were collected from two independent donors

first: Tse-Ching

last: Chen

first: Chun-Ting

last: Lee

first: Chih-Ya

last: Yang

first: Hsei-Wei

first: Chao-Ching

first: Shie-Liang

last: Hsieh


title: Time course of NHBE cells exposed to whole cigarette smoke (full flavor)

first: Ellen

last: Jorgensen

summary:
Gene expression patterns were assessed in normal human bronchial epithelial (NHBE) cells exposed to cigarette smoke (CS) from a typical "full flavor" American brand of cigarettes in order to develop a better understanding of the genomic impact of tobacco exposure, which can ultimately define biomarkers that discriminate tobacco-related effects and outcomes in a clinical setting.  NHBE cells were treated with CS for 15 minutes and alterations to the transcriptome assessed at 1,2,4 and 24 hours post-CS-exposure using high-density oligonucleotide microarrays.
Keywords: Time course

overall_design: Cells were exposed to smoke or air (“mock-exposed”) for 15 min, after which they were refed with fresh media and allowed to incubate for 1h, 2h, 4h or 24h.  Smoke and mock samples were compared at each time point.

first: Anthony

last: Albino


title: Expression Profiles of Monozygotic Twin

status: Public on Mar 30 2008

city: Brisbane

first: Nicholas

last: Matigian

state: Queensland

address: 170 Kessels Rd, Nathan

institute: National Adult Stem Cell Centre

summary:
The expression level for 15 887 transcripts in lymphoblastoid cell lines from 19 monozygotic twin pairs (10 male, 9 female) were analysed for the effects of genotype and sex. On an average, the effect of twin pairs explained 31% of the variance in normalized gene expression levels, consistent with previous broad sense heritability estimates. The effect of sex on gene expression levels was most noticeable on the X chromosome, which contained 15 of the 20 significantly differentially expressed genes. A high concordance was observed between the sex difference test statistics and surveys of genes escaping X chromosome inactivation. Notably, several autosomal genes showed significant differences in gene expression between the sexes despite much of the cellular environment differences being effectively removed in the cell lines. A publicly available gene expression data set from the CEPH families was used to validate the results. The heritability of gene expression levels as estimated from the two data sets showed a highly significant positive correlation, particularly when both estimates were close to one and thus had the smallest standard error. There was a large concordance between the genes significantly differentially expressed between the sexes in the two data sets. Analysis of the variability of probe binding intensities within a probe set indicated that results are robust to the possible presence of polymorphisms in the target sequences.
Keywords: Monozygotic twin pair Expression Profiles

overall_design: Genome-wide gene expression in lymphoblastoid cell lines was determined using microarrays derived from 15 monozygotic (MZ) twin  pairs (10 male, 9 female).  10 twin pair are discordant, 4 are concordant for a disease phenotype and their are 5 controls which have no disease phenotype.  This data set was analyzed  to interrupt replicated effects of sex and genotype, not disease characteristics.  Subsets of these samples have been analyzed separately for disease characteristics, (GSE7036 – 3 MZ twins discordant for bipolar disorder) and (GSE7486 - 5 discordant and 4 concordant MZ twin pairs with idiopathic absence epilepsies and 5 unaffected MZ twin pairs).

first: Allan

middle: F

last: McRae

first: Lata

last: Vadlamudi

first: John

last: Mulley

first: Bryan

last: Mowry

last: Martin

first: Sam

last: Berkovic

middle: K

last: Hayward

first: Peter

last: Visscher


title: Expression profile of 5 ovarian tumour samples (two different cell types from each sample profiles)

city: Melbourne

first: Prof David

last: Bowtell PhD.

state: VIC

address: Locked Bag 1 A' Beckett St

department: Research Division

institute: PeterMacCallum Cancer Centre

summary:
We used microarrays to profile the expression levels of 5 tumour samples
Keywords: expression difference of cell types in tumour samples

overall_design: Expression profiles of stroma and epithelial cells from 5 matched tumour samples

first: Richard

last: Tothill

first: Anna

last: Tinker

first: Joshy

last: George

first: Robert

last: Brown

first: Stephen

last: Fox

first: Daryl

last: Johnson

first: Melanie

last: Trivett

first: Dariush

last: Etemadmogadham

first: Bianca

last: Locandro

first: Nadia

last: Traficante

first: Sian

last: Fereday

first: Jillian

last: Hung

first: Yoke-Eng

last: Chiew

first: Izhak

last: Haviv

first: Dorota

last: Gertig

last: deFazio

first: David

last: Bowtell


title: Comparative gene expression in the limbus of the vervet monkey

city: Los Angeles

first: Sophie

last: deng

state: CA

address: 100 Stein plaza

institute: Jules Stein Eye Institute-UCLA

summary:
The limbus is a unique anatomic structure that is highly innervated and vascularized yet sets the boundary for the avascularized cornea. The corneal epithelial stem cells are believed to reside at the limbus. The intrinsic and external molecular signals that modulate the differentiation and proliferation of the limbal stems cells are still largely unidentified because of a lack of known specific markers. In this study, we used microarray technology to identify the unique gene expression profile in the limbus by comparing directly to that of its immediate adjacent structures, the cornea and conjunctiva, in the vervet monkey (Chlorocebus aethiops sabaeus).  Many new genes were found to be preferentially expressed in the limbus, and two new biological pathways, melanin metabolism and apoptosis, were among other previously known processes identified in the limbus. These findings may shed light on the molecular components of limbal stem cells and their niche.
Keywords: transcription profiling, gene expression

overall_design: The study consisted of gene expression profile comparisons across three anatomical structures of the eye. The parts of the eye compared included the cornea, the conjunctiva, and the limbus.

first: Zhenhua

last: Ding

first: Jun

last: Dong

first: Jason

last: Liu

middle: X

last: Deng


title: Longitudinal Analysis of Progression to Androgen Independence

status: Public on Feb 29 2008

city: Pittsburgh

first: Beth

middle: R.

last: Pflug

state: PA

address: 5200 Centre Ave

department: Urology

institute: University of Pittsburgh

summary:
Following androgen ablation therapy (AAT), the vast majority of prostate cancer patients develop treatment resistance with a median time of 18-24 months to disease progression. To identify molecular targets that aid in prostate cancer cell survival and contribute to the androgen independent phenotype, we evaluated changes in LNCaP cell gene expression during 12 months of androgen deprivation. At time points reflecting critical growth and phenotypic changes, we performed Affymetrix expression array analysis to examine the effects of androgen deprivation during the acute response, during the period of apparent quiescence, and during the emergence of highly proliferative, androgen-independent prostate cancer cells (LNCaP-AI). We discovered alterations in gene expression for a host of molecules associated with promoting prostate cancer cell growth and survival, regulating cell cycle progression, apoptosis and adrenal androgen metabolism, in addition to AR co-regulators and markers of neuroendocrine disease. These findings illustrate the complexity and unpredictable nature of cancer cell biology and contribute greatly to our understanding of how prostate cancer cells likely survive AAT. The value of this longitudinal approach lies in the ability to examine gene expression changes throughout the cellular response to androgen deprivation; it provides a more dynamic illustration of those genes which contribute to disease progression in addition to specific genes which constitute a malignant androgen-independent phenotype. In conclusion, it is of great importance that we employ new approaches, such as the one proposed here, to continue exploring the cellular mechanisms of therapy resistance and identify promising targets to improve cancer therapeutics.
Keywords: Time Course

last: D'Antonio

first: Changqing

last: Ma

first: Federico

last: Monzon

middle: R


title: the recurrent SET-NUP214 fusion as a new HOXA activation mechanism in pediatric T-ALL

status: Public on Feb 23 2008

city: Utrecht

first: Jules

last: Meijerink

address: Uppsalalaan 8

country: Netherlands

institute: Princess Máxima Center for Pediatric Oncology

summary:
T-cell acute lymphoblastic leukemia (T-ALL) is mostly characterized by specific chromosomal abnormalities, some occurring in a mutually exclusive manner possibly delineating specific T-ALL subgroups. One subgroup, including MLL-rearranged, CALM-AF10 or inv(7)(p15q34) cases, is characterized by elevated expression of HOXA genes. Using a gene expression based clustering analysis of 67 T-ALL cases with recurrent molecular genetic abnormalities and 25 samples lacking apparent aberrations, we identified 5 new cases with elevated HOXA levels. Using array-CGH, a cryptic and recurrent deletion, del(9)(q34.11q34.13), was exclusively identified in 3 of these 5 cases. This deletion results in a conserved SET-NUP214 fusion product, that was also identified in the T-ALL cell line LOUCY. SET-NUP214 binds in the promoter regions of specific HOXA genes, where it may interact with CRM1 and DOT1L leading to the transcriptional activation of HOXA genes. Targeted inhibition of SET-NUP214 by siRNA abolished expression of HOXA genes, inhibited proliferation and induced differentiation in LOUCY but not in other T-ALL lines. We conclude that SET-NUP214 may contribute to the pathogenesis of T-ALL by enforcing T-cell differentiation arrest.
We combined gene expression profiling and array-CGH analysis to detect a new and recurrent molecular cytogenetic abnormality in T-ALL patients that co-clustered with 5 well-defined HOXA-activated T-ALL samples. We describe the cloning of a recurrent SET-NUP214 fusion product in these samples, and identified a potential mechanism by which SET-NUP214 may activate the HOXA gene cluster as potential leukemogenic event in T-ALL.
Keywords: cluster analysis

overall_design: For 67 T-ALL patients having one of the major molecular cytogenetic abnormalities (i.e. TAL1 (n=24), LMO2 (n=9), HOXA (n=5), HOX11/TLX1 (n=7), and HOX11L2/TLX3 (n=22)), differentially expressed probesets were calculated from Affymetrix U133plus2.0 data based upon a Wilcoxon analysis and corrected for multiple testing for each probeset. Significant and differentially expressed probesets were obtained for the TAL1, HOX11 and HOX11L2 subgroups. No significant probesets were obtained for the HOXA subgroup or the LMO2 subgroup . As TAL1 and LMO2 both participate in the same transcriptional complex, activation of these genes may both lead to a highly similar expression profile. Combined analysis of TAL1 and LMO2 rearranged cases revealed significant and differentially expressed probesets that, as expected, almost entirely overlapped with the gene signature obtained for the TAL1-subgroup only. Next, we clustered 92 T-ALL cases, that besides the 67 cases as described above further included 25 T-ALL that lacked any of these recurrent abnormalities. Cluster analysis was performed based upon the top 25, 50 or 100 most significant probesets for the TAL1, TAL1/LMO2, HOX11 and HOX11L2 subgroups combined with 15 HOXA probesets identified by Soulier et al (2005)

first: Pieter

middle: V

last: Vlierberghe

first: Martine

last: Grotel

first: Rob

last: Pieters


title: Expression profile of 285 ovarian tumour samples

first: Prof David

last: Bowtell PhD.

summary:
We used microarrays to profile the expression levels of 285 ovarian samples in order to identify molecular subtypes of the tumour
Keywords: disease state analysis

overall_design: Randomly selected samples from the AOCS ( Australian Ovarian Cancer Study) was expression profiled on the affymetrix U133_plus2 platform to identify novel subtypes of ovarian tumour

first: Richard

last: Tothill

first: Anna

last: Tinker

first: Joshy

last: George

first: Robert

last: Brown

first: Stephen

last: Fox

first: Daryl

last: Johnson

first: Melanie

last: Trivett

first: Dariush

last: Etemadmogadham

first: Bianca

last: Locandro

first: Nadia

last: Traficante

first: Sian

last: Fereday

last: Hung

last: Chiew

last: Haviv


title: Interaction of bone marrow stroma and monocytes

city: Seattle

first: Lynn

last: Graf

state: WA

address: 1100 Fairview Ave. N. D1-100

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

summary:
The bone marrow microenvironment is a complex mixture of cells that function in concert to regulate hematopoiesis. Cellular components include fixed nonhematopoietic stromal elements as well as monocytes and resident macrophages, which are derived from the hematopoietic stem cells. Although these monocyte-lineage cells are reported to modify stromal cell function, the reverse also occurs.  Given the secretory capability of the monocyte/macrophage and their various potential functions, it is not surprising that stromal cells contained within a particular niche can modify monocyte gene expression and functional  maturation.
Keywords: cellular response to cell contact and secreted factors

overall_design: Monocytes were isolated from peripheral blood mononuclear cells from 2 different normal donors and cultured for 48h in conditioned medium (CM). The CM was collected from each of two functionally distinct human bone marrow stromal cell lines (HS5 and HS27a) representing different compartments of the bone marrow microenvironment (Roecklein BA, Torok-Storb B. Blood. 1995;85:997-1005). Four samples were analyzed, with two biological replicates for each CM.

first: Beverly

last: Torok-Storb

first: Mineo

last: Iwata


title: Gene expression analysis in absence epilepsy using a monozygotic twin design

status: Public on Feb 28 2008

first: Nicholas

last: Matigian

summary:
Objective:
To identify genes involved in idiopathic absence epilepsies by analysing gene expression using a monozygotic (MZ) twin design.
Methods:
Genome-wide gene expression in lymphoblastoid cell lines was determined using microarrays derived from five discordant and four concordant MZ twin pairs with idiopathic absence epilepsies and five unaffected MZ twin pairs.  Gene expression was analysed using three strategies: discordant MZ twins were compared as matched pairs, MZ twins concordant for epilepsy were compared to control MZ twins, and a singleton design of affected versus unaffected MZ twin individuals was used irrespective of twin pairing.  An overlapping gene list was generated from these analyses.  Dysregulation of genes recognised from the microarray experiment were validated using quantitative real time PCR (qRT-PCR) in the twin sample and in an independent sample of 18 sporadic absence cases and 24 healthy controls.
Results:
Sixty-five probe sets were identified from the microarray analysis strategies.  Sixteen genes were chosen for validation and nine of these genes confirmed by qRT-PCR in the twin sample.  Differential expression of the immediate early gene EGR1 and RCN2, coding for the calcium-binding protein Reticulocalbin 2, was re-confirmed by qRT-PCR in the independent sample.
Interpretation:
Using a unique sample of discordant MZ twins, our study identified genes with altered expression, which suggest novel mechanisms in idiopathic absence epilepsy.  Dysregulation of EGR1 and RCN2 might represent common transcriptional alterations in idiopathic absence epilepsy.
Keywords: Childhood Absence Epilepsy, Juvenile Absence Epilepsy, Idiopathic Generalised Epilepsy, gene expression, twin study, monozygotic twins

first: Ingo

last: Helbig

first: Lata

last: Vadlamudi

first: Kate

last: Lawrence

first: Marta

last: Zielinski

first: Sharon

last: Bain

first: Dileepa

last: Diyagama

first: Ingrid

last: Scheffer

first: John

middle: C

last: Mulley

first: Andrew

last: Holloway

first: Leanne

last: Dibbens

first: Samuel

last: Berkovic

last: Hayward


title: Transcriptome analyses in normal prostate epithelial cells following exposure to low-dose cadmium

city: Cincinnati

first: Xiang

last: Zhang

state: OH

address: Kettering labs PO box 670056, 3223 Eden Ave

department: Environmental Health

institute: University of Cincinnati

summary:
BACKGROUND: Cadmium is implicated in prostate carcinogenesis, but its oncogenic action remains unclear.
OBJECTIVES: In this study we aimed to decipher changes in cell growth and the transcriptome in an immortalized human normal prostate epithelial cell line (NPrEC) following exposure to low-dose Cd.
METHODS: Synchronized NPrEC cells were exposed to different doses of Cd and assayed for cell viability and cell-cycle progression. We investigated changes in transcriptome by global profiling and used Ingenuity Pathways Analysis software to develop propositions about functional connections among differentially expressed genes. A neutralizing antibody was used to negate the effect of Cd-induced up-regulation of tumor necrosis factor (TNF) in NPrEC cells.
RESULTS: Exposure of NPrEC to 2.5 μM Cd enhanced cell viability and accelerated cell-cycle progression. Global expression profiling identified 48 genes that exhibited ≥ 1.5-fold changes in expression after 4, 8, 16, and 32 hr of Cd treatment. Pathway analyses inferred a functional connection among 35 of these genes in one major network, with TNF as the most prominent node. Fourteen of the 35 genes are related to TNF, and 11 exhibited an average of > 2-fold changes in gene expression. Real-time reverse transcriptase-polymerase chain reaction confirmed the up-regulation of 7 of the 11 genes (ADAM8, EDN1, IL8, IL24, IL13RA2, COX2/PTGS2, and SERPINB2) and uncovered a 28-fold transient increase in TNF expression in Cd-treated NPrEC cells. A TNF-neutralizing antibody effectively blocked Cd-induced elevations in the expression of these genes.
CONCLUSIONS: Noncytotoxic, low-dose Cd has growth-promoting effects on NPrEC cells and induces transient overexpression of TNF, leading to up-regulation of genes with oncogenic and immunomodulation functions.
KEY WORDS: carcinogenesis, cytokine, global expression profiling, heavy metals, immune response, inflammation, Ingenuity Pathway Analysis, knowledge-based analysis, prostate cancer.

overall_design: A total of 19 samples were analyzed, each experimental condition having two biological replicates, except Cadmium 4hr which has only 1 sample.  Cadmium-treated and control samples were taken at 0, 4, 8, 16, and 32 hours.

first: Shlomo

last: Bakshi

first: Sonia

last: Godoy-Tundidor

first: Robert

last: Cheng

first: Maureen

last: Sartor

first: Mario

last: Medvedovic

first: Shuk-Mei

last: Ho


title: E. coli BW25113 yncC vs wt biofilm cells in LB 15h 37C and  MG1655 yncC vs wt colony cells in LB plates 15h 37C

status: Public on Feb 22 2008

city: State College

first: Thomas

middle: K.

last: Wood

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

institute: Pennsylvania State University

summary:
E. coli K-12 BW25113 mutant strain yncC expression in biofilm cells relative to E. coli wild-type strain expression in biofilm cells. All samples were cultured in LB with glasswool at 37C for 15 hours and E. coli K-12 MG1655 mutant yncC colony cells vs wild type colony cells in LB plates 15h 37C.

Quorum-sensing signal autoinducer 2 (AI-2) stimulates Escherichia coli biofilm formation through the motility regulator MqsR that induces expression of the putative transcription factor encoded by yncC. Here we show YncC increases biofilm formation by decreasing mucoidy (corroborated by decreased exopolysaccharide production and increased sensitivity to bacteriophage P1 infection).  Differential gene expression and gel shift assays demonstrated that YncC is a repressor of the predicted periplasmic protein-encoding gene ybiM which was corroborated by the isogenic yncC ybiM double mutation which repressed the yncC phenotypes (biofilm formation, mucoidy, and bacteriophage resistance). Through nickel-enrichment microarrays and additional gel shift assays, we found that the putative transcription factor B3023 (directly upstream of mqsR) binds the yncC promoter.  Overexpressing MqsR, AI-2 import regulators LsrR/LsrK, and AI-2 exporter TqsA induced yncC transcription whereas the AI-2 synthase LuxS and B3023 repressed yncC.  MqsR has a toxic effect on E. coli bacterial growth which is partially reduced by the b3023 mutation. Therefore, AI-2 quorum-sensing control of biofilm formation is mediated through regulator MqsR that induces expression of the transcription factor YncC which serves to inhibit the expression of periplasmic YbiM; this inhibition of YbiM prevents it from overexpressing exopolysaccharide (causing mucoidy) and prevents YbiM from inhibiting biofilm formation.
Keywords: biofilm gene expression and colony gene expression

platform_organism:
Escherichia coli
Escherichia coli K-12

overall_design:
Strains: E. coli K-12 BW25113 wild-type, mutant yncC
and E. coli K-12 MG1655 wild-type, mutant yncC
Medium: LB
Biofilm grown on glasswool or colony cells growth in LB plates
Time: 15 hours
Temperature: 37C
Cell type: biofilm or colony

For the biofilm arrays in BW25113 background:

Overnight cultures (16 h, 2.5 mL) of wild type E. coli BW25113 and BW25113 yncC in LB and LB with kanamycin (50 μg/mL), respectively, were used to inoculate 250 mL LB with 10 g of glass wool (Corning Glass Works, Corning, NY) for forming biofilm.  After incubating at 37°C for 15 h with shaking (250 rpm), biofilm cells were prepared by rinsing and sonicating the glass wool in sterile 0.85% NaCl solution at 0°C as described before.  The total RNA was isolated from biofilm cells as described previously.
	The E. coli Genechip antisense genome array (P/N 900381, Affymetrix, Santa Clara, CA) containing probes for more than 4200 open reading frames (ORFs) was used to analyze the complete E. coli transcriptome as described previously. Hybridizations were performed for 16 h and the total cell intensity was scaled automatically in the software to an average value of 630. The Gene Expression Technical Manual (Affymetrix) was followed for the procedures of DNA microarrays, and the GeneChip operating software (Affymetrix) was applied to analyze data of DNA microarrays. The data quality was assessed following the manufacturer's guidelines (GeneChip Expression Analysis: Data Analysis Fundamentals; Affymetrix) and also was based on the expected signals of E. coli BW25113 and the yncC mutant genotypes (e.g., signals of the deleted genes, araA and rhaA, were low for both BW25113 and BW25113 yncC, while the signal of yncC was low for the yncC mutant). A gene was identified as differentially-expressed when the P value based on the False Discovery Rate Method was less than 0.05 and the expression ratio was greater than threefold since the standard deviation for the expression ratio for all of genes was 2.

for the colony arrays in MG1655 background:

For the agar biofilm, fresh single colonies of wild-type E. coli MG1655 and MG1655 yncC were re-streaked on LB agar plates, incubated, and about 0.05 g of the colony cultures on LB plate were quickly transferred to 2-mL collection tubes. The total RNA was isolated from these colony cells as described previously. The E. coli GeneChip Genome 2.0 Array (Affymetrix, P/N 900551, Santa Clara, CA) containing 10,208 probe sets for open reading frames, rRNA, tRNA, and intergenic regions for four E. coli strains: MG1655, CFT073, O157:H7-Sakai, and O157:H7-EDL933, was used to analyze the complete E. coli transcriptome. A gene was identified as differentially-expressed when the P value based on the False Discovery Rate Method (Benjamini & Hochberg, 1995) was less than 0.05 and the expression ratio was greater than threefold since the standard deviation for the expression ratio for all of MG1655 genes (except the deleted yncC gene) was 2.

first: Xue-Song

first: Rodolfo

last: Garcia-Contreras


title: Expression data from recent-onset T1D patients and controls

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

summary:
Naturally occurring FoxP3+CD4+CD25+high regulatory T cells (Tregs) play an important role in dominant tolerance, suppressing auto-reactive CD4+CD25- T cell activity. Although Tregs from T1D subjects are functionally deficient, there is little knowledge of the molecular mechanisms that orchestrate this loss of Treg function. We observed increased apoptosis (by a novel YOPRO-1/7AAD dual staining protocol) and decreased suppression in polyclonal Tregs in the periphery from high at-risk and T1D subjects. We hypothesize that prior to and during the onset of disease, Tregs lack pro-survival signals and are caught up in a relatively deficient cytokine milieu whose effects may be detectable in the periphery.
Microarray analysis was performed on un-stimulated Tregs from 12 subjects with newly diagnosed T1D and 15 healthy controls.
Keywords: disease-state analysis

overall_design: Recent-onset T1D subjects were T1D patients diagnosed within 1 year. At the time of each visit, the following clinical measurements were taken: HbA1c, glucose level, height, weight and BMI.  The presence of auto-antibodies was measured from peripheral blood. Peripheral blood mononuclear cells (PBMCs) were collected and Tregs were isolated using FACS isolation. RNA was isolated, amplified and cRNA was fragmented and hybridized to Affymetrix whole genome U133Plus2.0 arrays having 54675 probe-sets. Bayesian Hierarchical analysis (BGX) was used to analyze the data.

first: Parthav

last: Jailwala

first: Jill

last: Waukau

first: Sanja

last: Glisic-Milosavljevic

first: Srikanta

last: Jana

first: Sarah

last: Ehlenbach

first: Marilyn

last: Koppen

first: Matthew

last: Klinker

first: Marty

first: Jennie

last: Schiller

first: Ramin

last: Alemzadeh

first: William

last: Hagopian

first: Shigemi

last: Matsuyama

first: Xujing

last: Wang

first: Prakash

last: Laud

first: Soumitra

last: Ghosh


title: Migratory chondrogenic progenitor cells from repair tissue during the later stages of human osteoarthritis

status: Public on Feb 21 2008

city: Göttingen

first: Nicolai

last: Miosge

address: Robert-Koch-Str. 40

department: Prothetik, Oral biology and Tissue regeneration

country: Germany

institute: University Göttingen

summary:
The regeneration of diseased hyaline cartilage remains a great challenge, mainly because degeneration activities after major injury or due to age-related processes overwhelm the self-renewal capacity of the tissue. We show that repair tissue from human articular cartilage of late stages of osteoarthritis harbor a unique progenitor cell population, termed chondrogenic progenitor cells exhibiting stem cell characteristics, such as multipotency, lack of immune system activation and, in particular, migratory activity. The isolated CPC exhibit a high chondrogenic potential and were able to populate diseased tissue in vivo. Moreover, down-regulation of the osteogenic transcription factor runx-2 enhanced the expression of the chondrogenic transcription factor sox-9 and consequently the matrix synthesis potential of chondrogenic progenitor cells. Our results, while offering new insight into the biology of progenitor cells from diseased cartilage tissue, might assist future strategies to treat late stages of osteoarthritis.
Keywords: cell type comparison

overall_design: Characterization chondrogenic progenitor cells in P1 of 3 male and 3 female patients with late-stage OA in comparison to healthy chondrocytes in P1


title: Activation of Sez-4 cell line with IL-2, IL-15 or IL-21.

status: Public on Feb 19 2008

city: Philadelphia

first: Mariusz

last: Wasik

address: 3620 Hamilton Walk

department: Pathology

institute: University of Pennsylvania

summary:
In this study we compared the effects of IL-2, IL-15, and IL-21 on the gene expression, activation of cell signaling pathways, and functional properties of cells derived from the CD4+ cutaneous T-cell lymphoma (CTCL). Whereas both IL-2 and IL-15 that signal through receptors that share the common gamma chain and the beta chain modulated the expression of >1,000 genes, IL-21 that signals via the receptor also containing gamma chain up-regulated <40 genes. All three cytokines induced tyrosine phosphorylation of Jak1 and Jak3. However, only IL-2 and IL-15 strongly activated STAT5, PI3K/Akt, and MEK/ERK signaling pathways. In contrast, IL-21 selectively activated STAT3. Whereas all three cytokines protected CTCL cells from apoptosis, only IL-2 and IL-15 promoted their proliferation. The effects of the cytokine stimulation were Jak3- and Jak1-kinase dependent. These findings document the vastly different impact of IL-2 and IL-15 vs. IL-21 on malignant CD4+ T cells. They also suggest two novel therapeutic approaches to CTCL and, possibly, other CD4+ T cell lymphomas: inhibition of the Jak1/Jak3 kinase complex and, given the known strong immunostimulatory properties of IL-21 on CD8+ T, NK, and B cells, application of this cytokine to boost an immune response against malignant CD4+ T cells.
Keywords: 3 replicates in each of 4 conditions

overall_design: Sez-4 cell line was starved of IL2 for 16h, washed twice and placed into 6-well plates in 10ml RPMI (10% FBS) for 2 h followed by addition of IL-2 (200U), IL-15 (20ng/mL), or IL-21 (100 ng/ml) or medium alone for 4 h.

first: Michal

last: Marzec

first: Krzysztof

last: Halasa

first: Monika

last: Kasprzycka

first: Maria

last: Wysocka

first: Xiaobin

last: Liu

first: John

middle: W

last: Tobias

first: Donald

last: Baldwin

first: Qian

last: Zhang

first: Niels

last: Odum

first: Alain

middle: H

last: Rook


title: Inhibition of activation of Sez-4 cell line with IL-2 by Jak kinase inhibitors.

overall_design: Sez-4 cell line was starved of IL-2 for 16h, washed twice and placed into 6-well plates in 10ml RPMI (10% FBS) for 2h followed by pre-treating for 30’ with pan-Jak inhibitor (300 nM), Jak3 inhibitor (300 nM), or drig solvent and cultured with IL-2 (200U) or medium alone for 4 h.


title: Treatment of primary acute myelogenous leukemia (AML) specimens with parthenolide (PTL)

status: Public on Feb 27 2008

first: Duane

last: Hassane

address: 1305 York Avenue, Box 140

institute: Weill Cornell Medical College

summary:
The effects of 7.5 micromolar parthenolide (PTL) were assessed on primary CD34+ acute myelogenous leukemia specimens obtained from 12 patients.
Keywords: drug response, gene expression search agent

overall_design: Acute myelogenous leukemia (AML) specimens were obtained from 12 patients and CD34+ cells were isolated.  For each patient, cells were cultured in vitro and exposed to either 7.5 micromolar parthenolide (PTL) or left untreated (UT) for 6 h.  Total RNA was then harvested for global gene expression analysis.

first: Monica

middle: L

last: Guzman

first: Xiaojie

last: Li

first: Cheryl

last: Corbett

first: Ramzi

last: Abboud

first: Fay

last: Young

first: Jane

last: Liesveld

first: Martin

last: Carroll

first: Craig

middle: T

last: Jordan


title: Early Response and Outcome in High-Risk Childhood Acute Lymphoblastic Leukemia: A Children’s Oncology Group Study

status: Public on Feb 15 2008

first: Deepa

last: Bhojwani

address: Smilow Research Building 1206-B, 522 First Avenue

department: Pediatric Hematology Oncology

institute: New York University School of Medicine

summary:
The cure rate for childhood ALL has improved considerably in part because therapy is routinely tailored to the predicted risk of relapse. Various clinical and laboratory variables are used in current risk-stratification schemes, but many children who fail therapy lack adverse prognostic factors at initial diagnosis. Using gene expression analysis, we have identified genes and pathways in a NCI high-risk childhood B-precursor ALL cohort at diagnosis that may play a role in early blast regression as correlated with the Day 7 marrow status. We have also identified a 47-probeset signature (representing 41 unique genes) that was predictive of long term outcome in our dataset as well as three large independent datasets of childhood ALL treated on different protocols.
Keywords: ordered, case-control

overall_design: Diagnostic marrow samples from 99 children with NCI high risk B-precursor ALL  treated on the protocol COG 1961 were analyzed. To study genetic profiles associated with early response to therapy, 82 of the total 99 patients were analyzed: 42 patients with a M1 marrow at day 7 of therapy were compared to 40 patients with a M3 marrow at day 7. To study the genes associated with long-term outcome, expression profiles of 59 (of the total 99) patients were analyzed: 28 patients who remained in complete continuous remission (CCR) for at least 4 years and 31 patients who suffered a bone marrow relapse within the first 3 years of initial diagnosis. Forty-two patients were common in both the early response and outcome analyses.

first: William


title: Interaction of bone marrow stroma and monocytes: bone marrow stromal cell lines cultured with monocytes

first: Lynn

last: Graf

summary:
The hematopoietic microenvironment consists of  non-hematopoietic derived stromal elements and hematopoietic derived monocytes and macrophages which interact and function together to control the proliferation and differentiation of early blood-forming cells. Two human stromal cell lines (HS-5 and HS-27a) representing distinct functional components of this microenvironment have been extensively characterized and shown to influence monocyte gene expression. This series of gene expression profiles is intended to extend the previous studies and identify which gene expression changes may require cell-cell contact or occur in the stromal cells as a result of monocyte influence;or in the monocytes as a result of stormal influences.
Keywords: cellular response to cell contact and secreted factors

overall_design:
Two human bone marrow stromal cell lines (HS5 and HS27a) were cultured with and without monocytes (CD14+ cells) from 2 different donors.
culture condition: stroma no monocytes: HS5-1, HS5-2, HS27a-1, HS27a-2
culture condition: stroma with monocytes: HS5-MO-1, HS5-MO-2, HS27a-MO-1, HS27a-MO-2
donor: donor 3: HS5-MO-1, HS27a-MO-1
donor: donor 4: HS5-MO-2, HS27a-MO-2
cell line: HS5: HS5-1, HS5-2,  HS5-MO-1, HS5-MO-2
cell line: HS27a: HS27a-1, HS27a-2, HS27a-MO-1, HS27a-MO-2

first: Beverly

last: Torok-Storb

first: Mineo

last: Iwata

first: Aravind

last: Ramakrishnan


title: Chronic CD4+ T cell Activation & Depletion in HIV-1 Infection: Type I Interferon-Mediated Disruption of T Cell Dynamics

city: Baltimore

first: Ahmad

last: Sedaghat

state: MD

address: 733 North Broadway

department: School of Medicine

institute: The Johns Hopkins University

summary:
The mechanism of CD4(+) T cell depletion during chronic human immunodeficiency virus type 1 (HIV-1) infection remains unknown. Many studies suggest a significant role for chronic CD4(+) T cell activation. We assumed that the pathogenic process of excessive CD4(+) T cell activation would be reflected in the transcriptional profiles of activated CD4(+) T cells. Here we demonstrate that the transcriptional programs of in vivo activated CD4(+) T cells from untreated HIV(+) individuals are clearly different from those activated CD4(+) T cells from HIV(-) individuals. We observed a dramatic up-regulation of cell cycle-associated and interferon-stimulated transcripts in activated CD4(+) T cells of untreated HIV(+) individuals. Furthermore, we find an enrichment of proliferative and Type I interferon-responsive transcription factor binding sites in the promoters of genes that are differentially expressed in activated CD4(+) T cells of untreated HIV(+) individuals compared to HIV(-) individuals. We confirm these findings by examination of in vivo activated CD4(+) T cells. Taken together, these results suggest that activated CD4(+) T cells from untreated HIV(+) individuals are in a hyper-proliferative state that is modulated by Type I interferons. From these results, we propose a new model for CD4(+) T cell depletion during chronic HIV-1 infection.
Keywords: disease state analysis

overall_design:
This experiment compares the expression of CD4+ T-cells obtained from 11 HIV+ individuals with that from comparable 9 HIV- control individuals.  Each individual's cells were analyzed on separate single-color chips, and the average values of both biological replicate groups were analyzed for statistical significance.

The biological significance of up- and down-regulated probesets/genes was analyzed using the Gene Ontology annotation dataset.

first: Jennifer

last: German

first: Tanya

middle: M

last: Teslovich

first: Joseph

last: Cofrancesco Jr

first: Chunfa

last: Jie

first: Conover

last: Talbot Jr

first: Robert

last: Siliciano


title: Expression profile of ovarian tumour samples

first: Prof David

last: Bowtell PhD.

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

overall_design: Refer to individual Series


title: Expression data from MCF7 xenografts

status: Public on Feb 14 2008

city: Houston

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary:
In order to help determine the genes involved in resistance of breast cancer to endocrine therapy, we compared global gene expression profiles of tamoxifen-resistant MCF-7 WT xenograft tumors with E2-supplemented tumors.
Keywords: two group comparison

overall_design: MCF7 xenografts were established in ovariectomized five to six week-old nu/nu athymic nude mice supplemented with 0.25 mg 21 day release estrogen pellets by inoculating subcutaneously (s.c.) 5E-6 cells. When tumors reached the size of 150-200 mm3 (3-5 weeks), the animals were randomly allocated to continued estrogen (E2) and estrogen withdrawal plus tamoxifen citrate.  Tumors were harvested for molecular studies when they became resistant to treatment and reached the size of 1000 mm3 (n=7).

first: Suleiman

last: Massarweh

first: Rachel

last: Schiff


title: Transcriptomic Dissection of Tongue Squamous Cell Carcinoma

status: Public on Feb 12 2008

city: Atlanta

first: Tianwei

last: Yu

state: GA

address: 1518 Clifton Rd NE

department: Biostatistics

institute: Emory University

summary:
The head and neck / oral squamous cell carcinoma (HNOSCC) is a diverse group of cancers, which develop from many different anatomic sites and are associated with different risk factors and genetic characteristics. The oral tongue squamous cell carcinoma (OTSCC) is one of the most common types of HNOSCC. It is significantly more aggressive than other forms of HNOSCC, in terms of local invasion and spread. In this study, we aim to identify specific transcriptomic signatures that associated with OTSCC.
Keywords: Disease/Control analysis

overall_design: 26 OTSCC samples and 12 control samples were analyzed using Affymetrix U133 Plus 2.0 array.

first: Xiaofeng

last: Zhou

first: Hui

last: Ye

first: Zugen

last: Chen

first: David

last: Wong


title: Functional interaction between a PIP2 novel polyA polymerase and type 1 PIPKIalpha

status: Public on Feb 25 2008

city: Madison

first: Christy

last: Barlow

address: 1300 University Ave

department: Pharmacology

institute: University of Wisconsin

summary:
A loss of StarPap would be predicted to result in a decrease in cellular levels of mRNAs which it polyadenylates.  Moreover, if PIPKIalpha has a function relationship with StarPap, knockdown of PIPKIalpha should cause a decrease in a pool of target mRNAs which require both StarPap and PIPKIalpha for their maturation.  To test this, we independently knocked down StarPap and PIPKIalpha, and performed microarray analysis of total polyadenylated mRNAs from each group.
Keywords: Gene expression after siRNA knockdown

overall_design: HEK293 cells were transfected with siRNA specific for StarPap or PIPKIalpha or control siRNA.  N=3


title: Transcriptome analysis of HTLV-1 Tax-transformed T cell line Tesi in absence and presence of Tax

city: Erlangen

first: Ralph

last: Grassmann

address: Schlossgarten 4

department: Institute of Clinical and Molecular Virology

institute: Universität Erlangen Nürnberg

summary:
The Tesi system allows analysis of HTLV-1 Tax's impact on the transcriptome of a human CD4+ T-cell which is not derived from leukemia but directly from normal human lymphocytes. By comparing cells with and without Tax, one can specifically filter for celluar genes that are either activated or repressed in the presence of Tax.
Keywords: cell type comparison, Tax

overall_design: Tesi cells were kept in RPMI 1640 with 50% Panserin, 20% FCS, 0.35g/l glutamine, streptomycin as antibiotic and 40U/ml interleukin-2. To repress Tax expression, 1µg/ml tetracycline was added for ten days. Subsequently, total cellular RNA was extracted from samples and subjected to Affymetrix microarray analysis. For each state (with Tax and without Tax) a biological replicate was generated. Mean values of replicated samples were then compared.

first: Klemens

last: Pichler

first: Andrea

last: Kress

first: Juliane

last: Gentzsch


title: Comparisons of Affymetrix Whole-Transcript Human Gene 1.0 ST array with standard 3' expression arrays

status: Public on Feb 01 2008

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

country: Switzerland

institute: UNI Lausanne

summary:
The recently released Affymetrix Human Gene 1.0 ST array has two major differences compared with standard 3'™ based arrays: (1) it interrogates the entire mRNA transcript, and (2) it uses cDNA targets. To assess the impact of these differences on array performance, we performed series of comparative hybridizations between the Human Gene 1.0 ST and the Affymetrix HG-U133 Plus 2.0 and the Illumina HumanRef-8 BeadChip arrays. Additionally, both cRNA and cDNA targets were probed on the HG-U133 Plus 2.0 array. The results show that the overall reproducibility is best using the Gene 1.0 ST array. When looking only at the high intensity probes, the reproducibility of the Gene 1.0 ST array and the Illumina BeadChip array is equally good. Concordance of array results was assessed using different inter-platform mappings. The Gene 1.0 ST is most concordant with the HG-U133 array hybridized with cDNA targets, thus showing the impact of the target type. Agreements are better between platforms with designs which choose probes from the 3' end of the gene. Overall, the high degree of correspondence provides strong evidence for the reliability of the Gene 1.0 ST array.
Keywords: Cross-platform comparison

overall_design: Expression data from two distinct reference RNA samples: Stratagene Universal Human Reference RNA (Catalog #740000) and Ambion Human Brain Reference RNA (Catalog #6050) were generated using different labeling protocols and technology platforms. We compared the results from 4 different technical protocols: Affymetrix HG-U133 Plus 2.0 array with Message Amp from Ambion labeling (protocol A), Affymetrix HG-U133 Plus 2.0 array with Ovation from NuGen labeling (protocol N), Affymetrix Gene 1.0 ST array (protocol G) and Illumina HumanRef-8 BeadChip (protocol I) with their respective labeling methods. Samples labeling and hybridization were repeated 2 times on different days with each time 2 technical replicates for a total of 4 technical replicates per condition.

first: Keith

last: Harshmann

first: Otto

last: Hagenbüchle

first: Alexandra

last: Paillusson

first: Johann

last: Weber

first: Jérôme

last: Thomas


title: Triazole Antifungal Toxicogenomics: human_primary_hepatocytes_CellzDirect

status: Public on Feb 07 2008

city: Research Triangle Park

last: Dix

state: NC

address: 109 TW Alexander Drive

department: ORD/NCCT

institute: US EPA

summary:
The triazole antifungals myclobutanil (MYC), propiconazole (PPZ) and triadimefon (TDF) [Propiconazole CASNR 60207-90-1; Triadimefon CASNR 43121-43-3; Myclobutanil CASNR 88671-89-0] all disrupt steroid hormone homeostasis and cause varying degrees of hepatic toxicity. To identify biological pathways consistently activated across various study designs, gene expression profiling was conducted on livers from rats following acute, repeated dose, or prenatal to adult exposures. To explore conservation of responses across species, gene expression from these rat in vivo studies were also compared to in vitro data from rat and human primary hepatocytes exposed to MYC, PPZ, or TDF. Pathway and gene level analyses across time of exposure, dose, and species identified patterns of expression common to all three triazoles, which were also conserved between rodents and humans. Pathways affected included androgen and estrogen metabolism, xenobiotic metabolism signaling through CAR and PXR, and CYP mediated metabolism.  Many of the differentially expressed genes are regulated by the nuclear receptors CAR, PPAR alpha and PXR, including ABC transporter genes (Abcb1 and MDR1), genes significant to xenobiotic, fatty acid, sterol and steroid metabolism (Cyp2b2 and CYP2B6; Cyp3a1 and CYP3A4; Cyp4a22 and CYP4A11) and xxx (Ugt1a1 and UGT1A1). Modulation of hepatic sterol and steroid metabolism is a plausible mechanism for triazole induced increases in serum testosterone. The gene expression changes caused by all three triazoles appear to focus on pathways regulating lipid and testosterone homeostasis, identifying potential common mechanisms of triazole hepatotoxicity that are conserved between rodents and humans.
Keywords: dose response, time course, comparative toxicogenomics

overall_design: A total of 43 samples were analyzed.  Four biological replicates for the controls (DMSO 0.1%), 2 biological replicates for positive control Rifampicin CASNR 13292-46-1, 4 biological replicates for positive control Phenobarbital sodium CASNR 57-30-7, 3 biological replicates for low dose myclobutanil, 3 biological replicates for mid dose myclobutanil, 4 biological replicates for high dose myclobutanil.  Four biological replicates each for low, mid, and high dose propiconazole, and 4, 4, and 3 biological replicates each for low, mid, and high dose triadimefon, respectively.

middle: J

first: Amber

last: Goetz


title: MCF7 HRG stimulation

status: Public on Feb 08 2008

city: Yokohama

first: Mariko

last: Okada

address: W518, 1-7-22, Suehiro-cho, Tsurumi-ku

institute: RIKEN RCAI

summary:
Heregulin beta-1 (HRG) is an extracellular ligand that activates mitogen-activated protein kinase (MAPK) and phosphatidylinositol-3-OH kinase (PI3K)/Akt signaling pathways through ErbB receptors. MAPK and Akt have been shown to phosphorylate the estrogen receptor (ER) at Ser-118 and Ser-167, respectively, thereby mimicking the effects of estrogenic activity such as estrogen responsive element (ERE)-dependent transcription. In the current study, integrative analysis was performed using two tiling array platforms, comprising histone H3 lysine 9 (H3K9) acetylation and RNA mapping, together with  array comparative genomic hybridization (CGH) analysis in an effort to identify HRG-regulated genes in ER-positive MCF-7 breast cancer cells. Through application of various threshold settings, 333 (326 up-regulated and 7 down-regulated) HRG-regulated genes were detected. Prediction of upstream transcription factors (TFs) and pathway analysis indicated that 21% of HRG-induced gene regulation may be controlled by the MAPK cascade, while only 0.6% of the gene expression is controlled by ERE. A comparison with previously reported estrogen (E2)-regulated gene expression data revealed that only 12 common genes were identified between the 333 HRG-regulated (3.6%) and 239 E2-regulated (5.0%) gene groups. However, with respect to enriched upstream TFs, 4 common TFs were identified in the 14 HRG-regulated (28.6%) and 13 E2-regulated (30.8%) gene groups. These results indicated that while E2 and HRG may induce common TFs, the regulatory mechanisms that govern HRG- and E2-induced gene expression differ.
Keywords: growth hormone response

overall_design: MCF-7 human breast cancer cells were incubated 2hour after administration of 10nM of the growth hormones (heregulin (HRG)). Control was set as growth hormone non-treated cells.


title: Multipotent mesenchymal stromal cells: identification of pathways common to TGFβ3/BMP2-induced chondrogenesis

status: Public on Jan 30 2008

city: Berlin

first: Thomas

last: Häupl

address: Charitéplatz 1

department: Rheumatology

institute: Charité

summary:
Human mesenchymal stem cells (MSC) display a high potential for the development of novel treatment strategies for cartilage repair. However, the pathways involved in their differentiation to functional and non hypertrophic chondrocytes remain largely unknown, despite the work on embryologic development and the identification of key growth factors including members of the TGFβ, Hh, Wnt and FGF families. In this study, we asked if we could identify specific biological networks independently from the growth factor used (TGFβ-3 or BMP-2). To address this question, we used DNA microarrays and performed large-scale expression profiling of MSC at different time points during their chondral differentiation. By comparing these data with those obtained during their differentiation into osteoblasts and adipocytes, we identified 318 genes specific for chondrogenesis. We distributed the selected genes in 5 classes according to their kinetic of expression and used the Ingenuity software in order to identify new biological networks. We could reconstruct 3 phases for chondral differentiation, characterized by functional pathways. The first phase corresponds to cell attachment and apoptosis prevention with the up-regulation of α5 integrins, BCL6, NFIL3, RGS2 and down-regulation of CTGF and CYR61. The second phase is characterized by a proliferation/differentiation step with the continuous expression of MAF, PGF, HGMA1 or NOTCH3, CHI3L1, WNT5A, LEPR. Finally, the last step of differentiation/hypertrophy is characterized by expression of DKK1, APOD/E, SERPINF1 and TIMP4. These data propose new pathways to understand the complexity of MSC differentiation to chondrocytes and new potential targets for cell therapy applied to cartilage repair.
Keywords: dose response

overall_design: To identify genes involved in TGFβ3/BMP2-induced chondrogenesis, MSC were isolated from human bone marrow aspirates by adherence to culture dishes and cultivated to passage 3. After induction of chondrogenic differentiation with BMP2 or TGFβ3, gene expression was determined by microarray hybridization after 1, 3, 7 and 21 days and compared to the undifferentiated MSC.

first: Dominique

last: Mrugala

first: Nadège

last: Dossat

first: Jochen

last: Ringe

first: Bruno

last: Delorme

first: Amandine

last: Coffy

first: Claire

last: Bony

first: Pierre

last: Charbord

first: Jean-Pierre

last: Daures

first: Danièle

last: Noël

first: Christian

last: Jorgensen


title: Human ES cell-derived neural rosettes reveal a functionally distinct early neural stem cell stage

city: New York

first: Agnes

last: Viale

address: 1275 York Avenue

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

summary:
All data are derived from the same batch of human ES cells (line H9, WA-09). With the exception of the “UD” file all files represent neural cell types derived from the undifferentiated hESCs. Following mechanical isolation, rosettes were maintained for various passages in the presence of defined growth factors and morphogen factors as indicated below at the R-NSC stage. Cells at the NSCFGF/EGF stage were derived from mechanically isolated neural rosettes that were purified and long-term expanded as attached monolayer cultures in serum free medium in the presence of FGF2/EGF.
Keywords: differentiation of human ES cells (line H9, WA-09).

first: Yechiel

last: Elkabetz

first: Lorenz

last: Studer


title: Transcriptome profile of Trypanosoma cruzi-infected cells

status: Public on Feb 06 2008

city: Tokyo

first: Takako

last: Shigihara

address: 2-1-1, Hongo, Bunkyo-ku

department: Biomedical Research Center

institute: Juntendo University Graduate School of Medicine

summary:
As Trypanosoma cruzi, the etiological agent of Chagas disease, multiplies in the cytoplasm of nucleated host cells, infection with this parasite is highly likely to affect host cells. We performed an exhaustive transcriptome analysis of T. cruzi-infected HeLa cells using an oligonucleotide microarray containing probes for greater than 47,000 human gene transcripts. In comparison with uninfected cells, those infected with T. cruzi showed greater than threefold up-regulation of 41 genes and greater than threefold down-regulation of 23 genes. Real-time reverse transcriptase-polymerase chain reaction (RT-PCR) of selected, differentially expressed genes confirmed the microarray data. Many of these up- and down-regulated genes were related to cellular proliferation, including seven up-regulated genes encoding proliferation inhibitors and three down-regulated genes encoding proliferation promoters, strongly suggesting that T. cruzi infection inhibits host cell proliferation, which may allow more time for T. cruzi to replicate and produce its intracellular nests. These findings provide new insight into the molecular mechanisms by which intracellular T. cruzi infection influences the host cell, leading to pathogenicity.
Keywords: infection response

sample_organism:
Trypanosoma cruzi
Homo sapiens

overall_design: Three replicates of infected and uninfected HeLa cell were analyzed. To examine the extent of cross hybridization between T. cruzi cRNA and Human chip, trypomastigote cRNA was hybridized with the same chip.

first: Muneaki

last: Hashimoto

first: Noriko

last: Shindo

first: Takashi

last: Aoki


title: Identification of YAP target genes in MCF10A cells

status: Public on Jan 31 2008

city: Charlestown

first: Daniel

last: Haber

state: MA

address: Rm.7119, Bldg.149, 13th Street

department: Cancer Center

institute: Massachusetts General Hospital

summary:
YAP is an oncogene and an inducer of Epithelial-to-Mesenchymal Transition (EMT).
We used microarrays to detail the global program of gene expression to identify YAP target genes.

PUBLICATION ABSTRACT:
The Hippo pathway defines a novel signaling cascade regulating cell proliferation and survival in Drosophila, which involves the negative regulation of the transcriptional coactivator Yorkie by the kinases Hippo and Warts. We have recently shown that the human ortholog of Yorkie, YAP, maps to a minimal amplification locus in mouse and human cancers, and that it mediates dramatic transforming activity in MCF10A primary mammary epithelial cells. Here we show that LATS proteins (mammalian orthologs of Warts) interact directly with YAP in mammalian cells and that ectopic expression of LATS1, but not LATS2, effectively suppresses the YAP phenotypes. Furthermore, shRNA-mediated knockdown of LATS1 phenocopies YAP overexpression. Since this effect can be suppressed by simultaneous YAP knockdown, it suggests that YAP is the primary target of LATS1 in mammalian cells. Expression profiling of genes induced by ectopic expression of YAP or by knockdown of LATS1 reveals a subset of potential Hippo pathway targets implicated in epithelial-to-mesenchymal transition (EMT), suggesting that this is a key feature of YAP signaling in mammalian cells.
Keywords: vector vs. YAP comparison

overall_design: MCF10A cells were infected with retrovirus constructs (vector or YAP) and puromycin was used to select for transduced cells. Cells were split and grown to ~60-75%% confluency at which point they were harvested for RNA. Vector vs. YAP comparison was done in duplicate.

first: Gromoslaw

middle: A

last: Smolen

first: Jianmin

last: Zhang


title: Non-Classical Functions of Human Topoisomerase I: Genome-wide and Pharmacological Analyses

city: gaithersburg

first: audrey

middle: n

last: player

address: 8717 grovemont circle

department: microarray facility

institute: national cancer institute

summary:
The biological functions of nuclear topoisomerase I (Top1) have been difficult to study because knocking out TOP1 is lethal in metazoans. To reveal the functions of human Top1, we have generated stable Top1siRNA cell lines from colon and breast carcinomas (HCT116-siTop1 and MCF-7-siTop1, respectively). In those cells, Top2 compensates for Top1 deficiency. A prominent feature of the siTop1 cells is genomic instability, with chromosomal aberrations and histone gamma-H2AX foci associated with replication. siTop1 cells also show rDNA and nucleolar alterations, and increased nuclear volume. Genome-wide transcription profiling revealed 55 genes with consistent changes in siTop1 cells. Among them, asparagine synthetase (ASNS) was reduced in siTop1 cells, as it also was in cells with transient Top1 downregulation. Conversely, Top1 complementation increased ASNS, indicating a causal link between Top1 and ASNS expression. Correspondingly, pharmacological profiling showed l-asparaginase hypersensitivity in the siTop1 cells. Resistance to camptothecin, aphidicolin, hydroxyurea and staurosporine, and hypersensitivity to etoposide and actinomycin D demonstrated that Top1, in addition to being the target of camptothecins, also regulates DNA replication, rDNA stability and apoptosis. Overall, our studies demonstrate the pleiotropic nature of human Top1 activities. In addition to its classical DNA nicking-closing functions, Top1 plays critical non-classical roles in genomic stability, gene-specific transcription, and response to various anticancer agents.
Keywords: genetic modification design

overall_design: We are using Affymetrix whole genome array U133 Plus 2, which is a single color microarray platform. For colon experiments, we analyzed 2 different samples as 4 replicates. For breast experiments, we analyzed 2 samples as replicates.


title: Gene Expression in MCF10A cells through Differentiation on Transwells

city: Cincinnati

first: Nelson

middle: D

last: Horseman

address: 231 Albert Sabin Way; MSB 3160

department: Molec & Cell Physiology

institute: University of Cincinnati

summary:
To further understand the differences occurring in MCF10A cells as they polarize and differentiate in the Transwell® model, we performed gene expression profiling with Affymetrix Human Genome U133 Plus 2.0 Arrays.  Four experimental time points, were sampled:  conventional cultures of MCF10A cells grown on plastic (Monolayer) and MCF10A cells plated on Transwells® sampled at three TEER values, 200-300 Ω cm2 (Base), 1400-1600 Ω cm2 (Midpoint), and 3000-3200 Ω cm2 (Plateau).
Keywords: Mammary Epithelial Cell Differentiation

overall_design: Cells are grown in monolayer to 90-95% confluency, trypsinized and counted for seeding onto permeable supports (Transwell®, 0.4 µm pores, polyester) in normal growth medium.  MCF10A cells are seeded on 12-well Transwells® (Corning) at 105 cells/cm2.  Both chambers of media were changed strictly on a 24-hour schedule.  Transepithelial electrical resistance (TEER) is measured daily with Epithelial Volt-Ohm Meter (EVOM; World Precision Instruments), prior to media change.  Total RNA was isolated at the indicated TEER listed above.  Canonical monolayer MCF10A cells served as a control comparison.  Each time point was performed on triplicate arrays except for Plateau (n=4).

first: Aaron

last: Marshall

first: Vaibhav

middle: P

last: Pai

first: Maureen

last: Sartor

first: Danielle

last: Halbleib


title: Cohesin mediates transcriptional insulation by CCCTC-binding factor

city: Bunkyo-ku

first: Katsuhiko

last: Shirahige

address: 1-1-1 Yayoi

department: Research Center for Epigenetic Disease

institute: The University of Tokyo

type: Genome binding/occupancy profiling by genome tiling array

summary:
Chromosome segregation in mitosis and meiosis depends on sister chromatid cohesion mediated by cohesin complexes. Mutation of cohesin and other cohesion proteins causes transcriptional and developmental defects in animals and humans, but the molecular cause of these phenotypes is unknown. Here we describe 8811 cohesin binding sites in the human genome and show that the CCCTC-binding factor (CTCF) is associated with 88% of these. CTCF is dispensable for loading of cohesin onto DNA but is required for enrichment of cohesin at its binding sites. We provide evidence that cohesin is required for the role of CTCF sites in insulating promoters from distant enhancers. Like CTCF, cohesin is located on the maternal but not on the paternal allele of the H19 imprinting control region (ICR) and is required for imprinting of the H19-Igf2 locus. We find that cohesin is widely expressed in mammalian tissues, consistent with a cohesionindependent role in regulating gene expression. We propose that cohesin functions as a transcriptional insulator and speculate that subtle deficiencies in this function may be the cause of "cohesinopathies" such as Cornelia de Lange and Roberts syndrome.
Keywords: ChIP-chip analysis

overall_design: This series contains two sets of whole genome ChIP-chip data, 16 sets of ENCODE array ChIP-chip data, and four sets of transcriptional analyses data, involving the cohesin subunits Scc1, Smc3, and SA2.

first: Kerstin

middle: S

last: Wendt

first: Keisuke

last: Yoshida

first: Takehiko

last: Itoh

first: Masashige

last: Bando

first: Birgit

last: Koch

first: Erika

last: Schirghuber

first: Kazuhiro

last: Maeshima

first: Hiroyuki

last: Aburatani

first: Jan-Michael

last: Peters


title: gene expression levels in long-term cultures of human dental pulp stem cells

city: Gifu City

first: Ken-ichi

last: Tezuka

state: Gifu

address: 1-1 Yanagido

department: Gifu University Graduate School of Medicine

summary:
In previous studies, human dental pulp stem cells (hDPSCs) were mainly isolated from adults. In this manuscript, we tried characterization of hDPSCs isolated from an earlier developmental stage to evaluate potential usage of these cells for tissue regenerative therapy. hDPSCs isolated at the crown-completed stage showed a higher proliferation rate than those isolated at the later stage. When the cells from either group were cultured in medium promoting differentiation towards cells of the osteo/odontoblastic lineage, both became alkaline phosphatase positive, produced calcified matrix, and were also capable of forming dentin-like matrix on scaffolds in vivo. However, during long-term passage, these cells underwent a change in morphology and lost their differentiation ability. The results of a DNA array experiment showed that the expression of a number of genes, such as WNT16, was markedly changed with increasing number of passages, which might have caused the loss of their characteristics as hDPSCs.
Keywords: gene expression study, long-term cultures

overall_design: To identify genes modulated by passage, we performed cDNA microarray analysis on 3 independent samples at the crown-completed stage (DP2, 28, and 31) that had undergone P4 or P10. Human gene expression was examined by using a Human Genome U133 Plus 2.0 probe array (GeneChip; Affymetrix, Santa Clara, CA, USA), and a Hewlett-Packard Gene Array Scanner (Palo Alto, CA, USA). Each sample was analyzed once. The fluorescence intensity of each probe was quantified by GeneChip Analysis Suite 5.0 (Affymetrix). The level of gene expression was determined as the average difference, obtained by using the GeneChip software.

first: Tomoko

last: Takeda

first: Yoko

first: Machiko

last: Horiuchi

last: Hosono

first: Kazuki

last: Iida

first: Daijiro

last: Hatakeyama

first: Shigeru

last: Miyaki

first: Takahiro

last: Kunusada

first: Toshiyuki

last: Shibata


title: Expression data from human plasmacytoid dendritic cells treated with p17 or CpG

city: Brescia

first: Simona

last: Fiorentini

address: piazzale Spedali Civili 1

department: Experimental and Applied Medicine

country: Italy

institute: University of Brescia

summary:
We used microarrays to detail the global program of gene expression underlying the effect of p17 on human plasmacytoid dendritic cells and was compared to CpG profile.
Keywords: gene expression study

overall_design: Human plasmacytoid dendritic cells were purified from two donors and cultured in the presence of p17 or CpG for 18 h.


title: Bisphenol A induces a profile of tumor aggressiveness in high-risk cells of breast cancer patients

status: Public on Jan 26 2008

city: Stanford

first: Junhee

last: Seok

address: 318 Campus Drive W310 - Davis Lab

institute: Stanford University

summary:
Breast cancer outcome is highly variable. Whether inadvertent exposure to environmental xenobiotics evokes a biological response promoting cancer aggressiveness and a higher probability of tumor recurrence remains unknown. To determine specific molecular alterations, which arise in high-risk breast tissue in the presence of the ubiquitous xenoestrogen, bisphenol A (BPA), we employed non-malignant random periareolar fine needle aspirates (RPFNA) in a novel functional assay. Early events induced by BPA in epithelial-stromal cocultures derived from the contralateral tissue of breast cancer patients included gene expression patterns, which facilitate apoptosis evasion, endurance of microenvironmental stress, and cell cycle deregulation without a detectable increase in cell number. This BPA response profile was significantly associated with breast tumors characterized by high histologic grade (p<0.001), and large tumor size (p=0.002), resulting in decreased recurrence-free patient survival (p<0.001). Our assays demonstrate a biological “fingerprint” of probable prior exposure to endocrine disrupting agents, and suggest a scenario in which their presence in the microenvironmental milieu of high-risk breast tissue could play a deterministic role in establishing and maintaining tumor aggressiveness and poor patient outcome.
Keywords: Gene expression, Epithelial, Breast cancer

overall_design: The study included twelve patients undergoing breast biopsy or surgery for breast cancer. Random periareolar fine needle aspirates (RPFNA) were collected from the unaffected contralateral breast of these patients. Control and hormone treated RPFNA cell cultures were analyzed using Affymetrix GeneChip(TM) arrays


title: Systematic Assessment of Human Osteoblast Transcriptome in Resting and Induced Primary Cells

city: Montreal

first: Elin

last: Grundberg

address: 740 Dr Penfield Avenue

country: Canada

institute: McGill University and Genome Quebec Innovation Centre

summary:
Osteoblasts are key players in bone remodeling. The accessibility of human primary osteoblast-like cells (HOb) from bone explants render them a lucrative model for studying molecular physiology of bone turnover, discovery of novel anabolic therapeutics and mesenchymal cell biology in general. Relatively little is known about resting and dynamic expression profiles of HObs and no studies have been conducted to date to systematically assess the osteoblast transcriptome. The aim of this study was to characterize HObs and investigate signaling cascades and gene networks using genomewide expression profiling in resting and Bone Morphogenic Protein (BMP)-2 and Dexamethasone induced cells.
Our data showed a vast number of genes and networks expressed predominantly in HObs as compared to closely related cells such as fibroblasts or chondrocytes. For instance,  genes in the insulin-like growth factor (IGF) signaling pathway were enriched in HObs (p=0.003) and included the binding proteins (IGFBP1, 2, 5) and IGF-2 and its receptor. Another HOb specific expression pattern included leptin and its receptor (p<10-8). Furthermore, after stimulating HObs with Dexamethasone or BMP-2, the expression of several interesting genes and pathways were observed where data supported the role of peripheral leptin signaling in bone cell function.
In conclusion, we provide the landscape of tissue-specific and dynamic gene expression in HObs, a resource, which will allow utilization of osteoblasts as a model to study specific gene networks and gene families related to human bone physiology and diseases.
Keywords: cell type comparison

overall_design:
Human trabecular bone from the proximal femoral shaft was collected from two male patients, both undergoing total hip replacement. The bone chips were minced thoroughly and washed with PBS and cultured in three biological replicates in cell medium containing α-MEM supplemented with 2 mmol/l L-Glutamine, 100U/mL penicillin, 100mg/mL streptomycin, and 10% fetal bovine serum and grown at 37°C with 5% CO2 until confluence. At 70-80% confluence, each replicate was trypsinized and sub-cultured in 6-well plates (100 000 cells/well) for 12 days. Prior to treatment, the cells were starved for 20h by adding complete cell medium containing 0.5% fetal bovine serum. The cells were then incubated for 2h and 24h with 10-7 M of dexamethasone and 10-4 mg/ml of rhBMP-2 with the same concentration of vehicle, respectively.
At the two time points, the cell medium was removed and the cells were harvested stored in -70°C until RNA extraction.

RNA was isolated from the cell lysates using the RNeasy® Mini Kit and
expression studies were performed in triplicate (biological replicates) using the Affymetrix Human Genome U133 plus 2.0 Array (Affymetrix, Santa Clara, CA, USA). One microgram of RNA was reverse transcribed into cDNA and in vitro transcription was performed to generate biotin-labeled cRNA for subsequent hybridization. Hybridized target cRNA was then stained with streptavidin phycoerythrin, and arrays were scanned using a GeneArray Scanner at an excitation wavelength of 488nm.

first: Helena

last: Brändstöm

first: Kevin

last: Lam

first: Scott

last: Gurd

first: Bing

last: Ge

first: Eef

last: Harmsen

first: Andreas

last: Kindmark

first: A

last: Ljunggren

first: Hans

last: Mallmin

first: Olle

last: Nilsson

first: Tomi

last: Pastinen


title: Gene expression of diesel exhaust inhalation in peripheral blood mononuclear cells from healthy human volunteers

status: Public on Jan 03 2008

city: Seattle

first: James

middle: William

last: MacDonald

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary:
Background: Diesel exhaust (DE) is the primary source of urban fine particulate matter, which has been associated with cardiovascular disease in epidemiological studies. These effects may be related to oxidative stress and systemic inflammation with resulting perturbation of vascular homeostasis. Peripheral leukocytes are involved in both inflammation and control of vascular homeostasis.  Objectives: We conducted an exploratory study using microarray techniques to analyze whether global gene expression in peripheral blood mononuclear cells (PBMCs) can inform on potential mechanisms of effect of DE inhalation. Methods: In a double-blind, crossover, controlled exposure study, healthy adult volunteers were exposed in randomized order to filtered air (FA) and diluted DE in two-hour sessions. We isolated RNA (Trizol/Qiagen method) form PBMCs before, and two times after each exposure. RNA samples were arrayed using the Affymetrix® platform (GeneChip® Human Genome U133 Plus 2.0 Array). Results: Microarray analyses were conducted on five subjects with available RNA sample form exposures to FA and to the highest DE inhalation (200 µg/m³ of fine particulate matter). Following data normalization and statistical analysis, a total of 1290 out of 54,675 probe sets with significant evidence for differential expression (more than 1.5-fold up or down regulated with p < 0.05) were identified. These include genes involved in inflammatory response (e.g., IL8RA, TNFAIP6, FOS), oxidative stress (e.g., HMOX1, BAX, PRDX1,), and in biochemical pathways like mitogen-activated protein kinases (MAPK) and tight junction pathways. Conclusions: These data suggest that DE may exert time-dependent changes in gene expression in PBMCs in healthy individuals. Genes that may be affected by DE inhalation are involved in inflammatory and oxidative stress processes.
Keywords: time course

overall_design: We conducted a crossover, double-blind experiment, randomized to order of DE and filtered-air (FA) exposure with each participant exposed on four different days to each of four conditions: FA and DE calibrated to 50µg/m3 (DE50), 100µg/m3 (DE100), and 200µg/m3 (DE200) of fine particulate matter (PM2.5- particles with aerodynamic diameter 2.5µm or less). Exposure sessions were conducted at least 2 weeks apart.

first: Alon

last: Peretz

first: Erin

last: Peck

first: Theo

middle: K

last: Bammler

first: Richard

last: Beyer

first: Jeffrey

last: Sullivan

first: Carol

last: Trenga

first: Sengkeo

last: Srinouanprachnah

first: Federico

last: Farin

first: Joel

last: Kaufman


title: IP Staufen2

status: Public on Jan 18 2008

city: Montréal

first: Luc

last: DesGroseillers

state: Québec

address: 2900 Edouard Montpetit

department: Biochimie

institute: Université de Montréal

summary:
In human cells, Staufen2 is a double-stranded RNA-binding protein involved in several cellular functions. Although 51% identical to Staufen1, these proteins are nevertheless found in different RNA particles. In addition, differential splicing events generate Staufen2 isoforms that only differ at their N-terminal extremities. We used a genome wide approach to identify and compare the mRNA targets of mammalian Staufen2 isoforms. The mRNA content of Staufen mRNPs was identified by probing DNA microarrays with probes derived from mRNAs isolated from immunopurified Staufen2-containing complexes following transfection of HEK293T cells with Stau2-HA (59kDa) or Stau2-HA (62kDa) expressors. Our results indicate that 11% of the cellular RNAs expressed in HEK293T cells are found in Stau2-containing mRNPs. There is a predominance of mRNAs involved in cell metabolism, transport, transcription, regulation of cell processes and catalytic activity.
Keywords: Immunoprecipitation, Staufen, microarray

overall_design: HEK293 cells were transiantly transfected with plasmids coding for Staufen2-HA isoforms. Cell extracts were immunoprecipitated using anti-HA antibodies and co-immunoprecipitated mRNAs were purified and used to hybridize microarrays. As control, cell extract from mock transfected cells were used.

last: Furic

first: Marjolaine

last: Maher-Laporte


title: Aberrant expression of Fra-2 promotes CCR4 expression and cell proliferation in adult T-cell leukemia

status: Public on Jan 16 2008

city: Osaka

first: Tokuzo

last: Arao

address: 377-2 Ohno-Higashi, Osaka-Sayama

department: Department of Genome Biology

institute: Kinki University School of Medicine

summary:
The 4　Fra2-targeting siRNA and 4 control-siRNA samples were used for analysis.
Keywords: siRNA

overall_design: A microarray procedure was performed according to the Affymetrix protocols (Santa Clara, CA). In brief, total RNA extracted from the tumor samples was analyzed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany) and cRNA was synthesized with the GeneChip® 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (Affymetrix). The labeled cRNAs were then purified and used for probes. Hybridization was performed on the Affymetrix GeneChip HG-U133 Plus2.0 array for 16 hours at 45 ºC. Signal intensity was measured by a GeneChip®Scanner3000 (Affymetrix) and converted to numerical data with GeneChip Operating Software, Ver.1 (Affymetrix).

first: Takashi

last: Nakayama

first: Kazuto

last: Nishio


title: Activation of aryl hydrocarbon receptor

city: Vienna

first: Moritz

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

summary:
VAF347 is a low molecular weight compound which inhibits allergic lung inflammation in vivo. This effect is likely due to a block of dendritic cell (DC) function to generate pro-inflammatory T-helper (Th) cells since VAF347 inhibits IL-6, CD86 and HLA-DR expression by human monocyte derived DC, three relevant molecules for Th-cell generation. Here we demonstrate that VAF347 interacts with the aryl hydrocarbon receptor (AhR) protein resulting in activation of the AhR signaling pathway. Functional AhR is responsible for the biological activity of VAF347 since, i) other AhR agonists display an identical activity profile in vitro, ii) gene silencing of wild type AhR expression or forced over-expression of a trans-dominant negative AhR ablates VAF347 activity to inhibit cytokine induced IL-6 expression in a human monocytic cell line and iii) AhR deficient mice are resistant to the compound’s ability to block allergic lung inflammation in vivo. These data identify the AhR protein as key molecular target of VAF347 and its essential role for mediating the anti-inflammatory effects of the compound in vitro and in vivo.
Keywords: effect of compound

overall_design: Immature monocyte-derived DC were activated with anti-CD40 antibodies for 8 hours in the absence or presence of VAF347. Two donors (D1,D2) were used, resulting in four data sets: D1_ctrl, D2_ctrl (ctrl=no treatment),  D1_VAF347, D2_VAF347.

first: B

last: Lawrence

first: Michael

last: Denison

first: Hermann

last: Novak

first: Beth

last: Vorderstrasse

first: Nathalie

last: Harrer

first: Wolfgang

last: Neruda

first: Claudia

last: Reichel

first: Maximilian

last: Woisetschläger


title: ChIP-chip from HCT116 cells with UbH2B and H3K4me2 coupled to expression analysis

first: Neri

last: Minsky

address: 1230 York Avenue

institute: Rockefeller University

summary:
Histone H2B monoubiquitylation has been implicated in transcription. We generated anti-UbH2B antibodies and applied these antibodies in ChIP-chip experiments revealing preferential association of ubiquitylated H2B with the transcribed regions of highly expressed genes.
Unlike dimethylated H3K4, UbH2B was not associated with distal promoter regions.
Keywords: Chip-chip, Expression analysis

overall_design: ChIP from HCT116 cells using anti-UbH2B and anti-H3K4me2 (Control antibody used as well), and expression analysis.

first: Efrat

last: Shema

first: Yair

last: Field

first: Meromit

last: Schuster

first: Eran

last: Segal

first: Moshe

last: Oren