title: Mucosal gene signatures to predict response to infliximab in patients with ulcerative colitis

status: Public on Jan 07 2010

city: Leuven

first: Ingrid

last: Arijs

address: Herestraat 49

department: Clinical and Experimental Medicine

country: Belgium

institute: KULeuven

summary:
Infliximab, an anti-TNF-alpha monoclonal antibody, is an effective treatment for ulcerative colitis (UC) with over 60% of patients responding to treatment and up to 30% reaching remission. The mechanism of resistance to anti-TNF-alpha is unknown. This study used colonic mucosal gene expression to provide a predictive response signature for infliximab treatment in UC.

Keywords: drug response

overall_design: Twenty-four patients with active UC, refractory to corticosteroids and/or immunosuppression, underwent colonoscopy with biopsies from diseased colon within a week prior to the first intravenous infusion of 5 mg infliximab per kg body weight. Response to infliximab was defined as endoscopic and histologic healing at 4-6 weeks after first infliximab treatment. Six control patients with normal colonoscopy were included. Total RNA was isolated from colonic mucosal biopsies, labelled and hybridized to Affymetrix Human Genome U133 Plus 2.0 Arrays.

first: Leentje

last: Van Lommel

first: Kristel

last: Van Steen

first: Gert

last: De Hertogh

first: Karel

last: Geboes

first: Frans

last: Schuit

first: Paul

last: Rutgeerts


title: Expression data of 3 prostate cancer stem cell primary lines comparing spheres and parental/adherent culture

status: Public on Jan 01 2010

city: Frederick

first: Maria

middle: Ana

last: Duhagon

state: MD

address: 1050 Boyles St.

department: Laboratory of Cancer Prevention

country: USA

institute: NCI-Frederick

summary:
Transcriptional profile of PCSC spheres in SCM-1% KO (stem-like cells) vs adherent cultures in PCSC-Celprogen medium (differentiated-like cells)
Two-condition experiment: Sphere vs. Parental/adherent cells. Biological replicates: 2 sphere replicates , 2 adherent replicates.

overall_design: Early passaged tumor cells were expanded in adherent conditions and then plated in sphere forming conditions (SCM-1KO% medium at low density) to isolate sphere growing cells.

first: M

middle: A

last: Duhagon Serrat

first: J

middle: R

last: Sotelo-Silveira


title: Comparison of human embroynic stem cell derived vascular cells to mature human vascular and hematopoietic cells

status: Public on Jan 05 2010

city: New York

first: Shahin

last: Rafii

state: NY

address: 1300 York Avenue

institute: Weill Cornell Medical College

summary: The pathways involved in hierarchical differentiation of human embryonic stem cells (hESC) into abundant and durable endothelial cells (EC) are unknown. We employed an EC-specific VE-cadherin promoter driving GFP (hVPr-GFP) to screen for factors that augmented yields of vascular-committed ECs from hESCs. In phase 1 of our approach, inhibition of TGFb, precisely at day 7 of hESC differentiation, enhanced emergence of hVPr-GFP+ ECs by 10-fold. In the second phase, TGFb-inhibition preserved proliferation and vascular identity of purified ECs, resulting in net 36-fold expansion of homogenous EC-monolayers, and allowing transcriptional profiling that revealed a unique angiogenic signature defined by the VEGFR2highId1highVE-cadherin+EphrinB2+CD133+HoxA9- phenotype. Using an Id1-YFP hESC reporter line, we showed that TGFb-inhibition sustained Id1 expression in hESC-derived ECs, which was required for increased proliferation and preservation of EC commitment. These data provide a multiphasic method for serum-free differentiation and long-term maintenance of authentic hESC-derived ECs, establishing clinical-scale generation of transplantable human ECs.

overall_design: The experiment compared 6 sets of biological duplicates which included human embryonic stem cell derived and mature vascular cell types.

first: Daylon

last: James

first: Gabsang

last: Lee

first: Hyung-song

last: Nam

first: David

last: Lyden

first: Marco

last: Seandel

first: Robert

last: Benezra

first: Daniel

last: Nolan

first: Nikica

last: Zaninovic

first: Tyler

last: Janovitz

first: Zev

last: Rosenwaks

first: Lorenz

last: Studer

first: Mark

last: Tomishima

first: Sina

middle: Y

last: Rabbany


title: siRNA-mediated knockdown of MITF and PAX3 in metastatic melanoma cell lines

status: Public on Jan 02 2010

city: Dunedin

first: Aaron

last: Jeffs

address: PO Box 56

country: New Zealand

institute: University of Otago

summary:
The transcription factors PAX3 and MITF are required for the development of the neural crest and melanocyte lineage, and both proteins play important roles in melanoma cell growth and survival.  PAX3 transcriptionally activates MITF expression during neural crest development, but the relationship between these transcription factors during melanocyte development and in melanoma cells is currently poorly understood. This study aimed to further our understanding of the interaction between transcriptional networks controlled by PAX3 and MITF by assessing the effect of siRNA-mediated knockdown of PAX3 and MITF in metastatic melanoma cell lines. The goals of this study were to determine (i) if PAX3 is required for maintaining expression of MITF in melanoma and melanocyte cell lines; (ii) whether PAX3 and MITF independently, or redundantly, influence growth and survival in melanoma cell lines; and (iii) to investigate the respective roles of PAX3 and MITF expression in melanoma cell differentiation.
Microarrays were used to measure global changes in transcript expression in response to siRNA-mediated knockdown of PAX3 or MITF compared to non-targeting controls in two metastatic melanoma cells lines.

overall_design: RNA was isolated from two different metastatic melanoma cell lines 30 hours after one of four different treaments: (i) transfection with siRNA targeting PAX3; or (ii)   transfection with siRNA targeting MITF; or (iii) or transfection with siRNA targeting luciferase (non-targeting negative control); or (iv) treatment with media only (control). Therefore, eight samples were used for gene expression profiling by using GeneChip arrays, with one replicate per cell line per treatment.

first: Mike

last: Eccles

first: Shujie

last: He


title: Let-7c and miR-294 target identification in mouse ES cells

city: San Francisco

last: Blelloch

state: CA

address: 513 Parnassus Avenue, Campus Box #0525

institute: University of California, San Francisco

summary:
let-7c and miR-294 were transfected into Dgcr8 -/- miRNA deficient ES cells and RNA was harvested after 12 hours
the goal of this study was to identify direct and indirect targets of the let-7c and miR-294 miRNAs, we chose to harvest RNA early at 12 hours to mimize secondary effects due to ES cell differentiation, prior to performing the array experiment we found that at this time point candidate miRNA targets were maximally downregulated by qPCR

overall_design: 9 samples were analyzed, 3 biological replicates each of mock transfected, let-7c transfected, and miR-294 transfected

first: Collin

last: Melton

middle: H


title: Gene exprssion profile classification predicts clinical outcome in juvenile myelomonocytic leukemia

city: Padova

first: Andrea

last: Zangrando

address: Via Giustiniani, 3

department: Woman and Child's Health

country: Italy

institute: University of Padova

summary:
Gene expression analysis identified a specific signature of differentially expressed genes discriminating good and poor responders in JMML patients.
Gene expression signatures were analyzed on two EWOG patient cohorts of pediatric JMML patients.

Keywords: Expression data

overall_design: Class comparison between AML-like vs non-AML-like signatures in JMML patients.

first: Silvia

last: Bresolin

first: Geertruy

last: te Kronnie


title: Patients affected with autosomal dominant monocytopenia with increased susceptibility to mycobacterial infection

city: Hamilton

first: Addie

last: Whitney

state: MT

address: 903 S 4th St

department: LHBP

institute: NIH/NIAID/RML

summary:
We identified 18 patients with the distinct clinical phenotype of disseminated nontuberculous mycobacterial infections, viral infections, especially with human papillomaviruses, and fungal infections, primarily histoplasmosis and molds. This syndrome typically had its onset in adulthood and was characterized by profound circulating monocytopenia, B lymphocytopenia, and NK lymphocytopenia. T lymphocytes were variably affected. Despite these peripheral cytopenias, all patients had macrophages and plasma cells at sites of inflammation and normal immunoglobulin levels.  This novel clinical syndrome links mycobacterial, viral, and fungal susceptibility with malignancy and is transmitted in an autosomal dominant pattern.
In order to elucidate the possible genetic defect that results in this novel clinical syndrome, we performed microarray expression analysis on polymorphonuclear leukocytes (PMNs) isolated from affected patients and healthy controls.

Keywords: healthy donor vs affected patient

overall_design:
Gene expression data for polymorphonuclear leukocytes (PMNs) isolated from the blood of affected patients and healthy donors.  There are two separate data sets:
For the first data set, there are 7 healthy controls and 3 affected patients [Samples GSM400913-GSM400922].
For the second data set, there are 5 healthy controls and 5 affected patients [GSM400923-GSM400932].

first: D

middle: C

last: Vinh

first: S

last: Patel

first: G

last: Uzel

first: V

middle: L

last: Anderson

first: A

middle: F

last: Freeman

first: K

middle: N

last: Olivier

first: C

last: Spalding

last: Hughes

last: Pittaluga

first: M

last: Raffeld

first: L

last: Sorbara

first: H

middle: Z

last: Elloumi

middle: B

last: Kuhns

last: Turner

first: E

middle: W

last: Cowen

last: Fink

last: Long-Priel

first: AP

last: Hsu

last: Ding

last: Paulson

middle: P

last: Sampaio

middle: M

last: Frucht

first: F

last: DeLeo

last: Holland


title: DHA supplementation suppresses LDLR and OLR1 gene expression in blood cells from hypertriglyceridemic men

status: Public on Jan 30 2010

city: Davis

first: Kevin

last: Dawson

address: 2795 Second Street, Suite 400

department: CCM

institute: UC Davis

summary: Previously published results from our double-blind, placebo-controlled parallel study with docosahexaenoic acid (DHA) supplementation (3 g/d, 90 d) to hypertriglyceridemic men (39-66yr) showed that DHA reduced several risk factors for cardiovascular disease (CVD), including the plasma concentration of inflammatory markers. To determine the effect of DHA supplementation on the global gene expression pattern, we performed Affymetrix GeneChip microarray analysis of blood cells (treated with lipopolysaccharide (LPS) or vehicle) drawn before and after the supplementation from the hyperlipidemic men who participated in the previous study. Genes that were significantly differentially regulated by the LPS treatment and DHA supplementation were identified. Differential regulation of 18 genes was then confirmed by quantitative RT-PCR. Both microarray and qRT-PCR data showed that the expression of LDL receptor (LDLR), oxidized LDL receptor (OLR1), and cathepsin L1 (CTSL) was significantly suppressed by DHA supplementation; however, LPS stimulated the expression of LDLR and CTSL but not that of OLR1. LPS up-regulated and DHA suppressed the expression of prostaglandin E synthase (PTGES), PPAR delta, and various chemokines. Enrichment with Gene Ontology categories demonstrated that the genes related to transcription factor activity, immune responses, host defense responses, inflammatory responses, and apoptosis were inversely regulated by LPS and DHA. These results provide supporting evidence for the anti-inflammatory effects of DHA supplementation, and reveal previously unrecognized genes that are regulated by DHA, and are associated with risk factors of cardiovascular diseases.

overall_design: Double-blind, placebo-controlled parallel study with DHA supplementation to hypertriglyceridemic men. Gene expression detected in LPS-stimulated (LPS) and unstimulated (vehicle) white blood cells. 3-4 replicates per group.

first: Ling

last: Zhao

first: Yuriko

last: Adkins

first: Madhuri

last: Vemuri

first: Raymond

last: Rodriguez

first: Darshan

middle: S

last: Kelley

first: Daniel

last: Hwang


title: CAL-51 breast cancer side population cells

status: Public on Dec 31 2009

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

summary:
Human solid tumors contain rare cancer side population (SP) cells, which expel the fluorescencent dye H33342 and display cancer stem cell characteristics. Transcriptional profiling of cancer SP cells isolated by H33342 fluorescence analysis is a newly emerging approach to discover cancer stem cell markers and aberrant differentiation pathways. Using Affymetrix expression microarrays this study investigated differential gene expression between SP and non-SP (NSP) cells isolated from the CAL-51 human mammary carcinoma cell line.

Keywords: cell type comparison

overall_design: To characterize differential gene expression between CAL-51 breast cancer SP and NSP cells, three consecutive cell culture passages of CAL-51 were independently subjected to H33342 labeling and dual wavelength fluorescence analysis and were then flow cytometrically sorted into SP and NSP cell fractions. Subsequently, each of the six cell preparations was subjected to global transcriptional profiling using Affymetrix HG U133 Plus 2.0 expression microarrays.

first: R

last: Christgen


title: Gene expression profile of ascites cell samples from patients with advanced ovarian cancer

city: London

first: Hagen

last: Kulbe

address: Charterhouse Square

department: Centre for Cancer and Inflammation

country: United Kingdom

institute: Institute of Cancer and the CR-UK Clinical Centre, Barts and The London School of Medicine and Dentistry

summary:
We present evidence for an autocrine cytokine network in human ovarian cancer that has paracrine actions on the tumour microenvironment. In experiments using bioinformatics analysis of large gene expression array datasets and ovarian cancer biopsies, we found that the inflammatory cytokines TNF-α and IL-6, the chemokine receptor CXCR4 and its ligand CXCL12, are co-regulated in malignant cells. We named this co-regulation the TNF network.
We had access to a unique set of ascites cell samples from patients with advanced ovarian cancer treated with the therapeutic anti-human TNF-α antibody infliximab. Serial samples pre and during treatment were obtained during paracentesis (drainage of ascites fluid for symptomatic relief). In nine of these patients there was sufficient mRNA available for gene expression profile analysis before treatment.

overall_design: The Affymetrix GeneChip Human Genome U133Plus 2.0 arrays were used to define gene expression profiles in each of the ascites cell samples.

first: Kellie

last: Charles


title: EXPRESSION SIGNATURE TO PREDICT MAJOR CYTOGENETIC RESPONSE IN CHRONIC PHASE CML PATIENTS TREATED WITH IMATINIB

city: Portland

first: Michael

last: Deininger

state: OR

address: 3181 SW Sam Jackson Park Rd

institute: OHSU

summary:
Newly diagnosed chronic phase chronic myeloid leukemia (CML) patients with a major cytogenetic response (MCyR) after 12 months of imatinib therapy have an excellent long-term outcome, while patients without MCyR have a high progression risk. Since patients with primary cytogenetic resistance may benefit from more intensive therapy up-front, we sought to identify biomarkers to predict MCyR.

Keywords: Two group comparison to identify trasncriptomic signature that predicts response to therapy

overall_design: CD34+ cells were isolated from cryopreserved mononuclear cells of chronic phase CML patients with a complete cytogenetic response (CCyR) or >65% Ph-positive metaphases after 12 months of imatinib therapy (training set N=36). Gene expression profiles generated on amplified RNA using Affymetrix HG-U133 Plus 2.0 arrays were compared between responders and non-responders, using the criteria ANOVA p<0.1 and fold difference >I1.5I. A minimal response classifier derived from the comparison was used to predict response in a prospectively collected validation set using same criteria for responders/nonresponders (N=23).

first: Shannon

middle: K

last: McWeeney


title: Gene expression profile of human ovarian cancer cell lines in vitro

summary:
We have previously described how TNF-α, IL-6, CXCR4 and the CXCR4 ligand CXCL12 are expressed by human ovarian cancer cells in vitro. By comparing four ovarian cancer cell lines with varying levels of constitutive TNF-α production we found that CXCR4, CXCL12, TNF-α and IL-6 were linked in an autocrine network in malignant cells that had an effect on tumour growth and angiogenesis in one xenograft model of ovarian cancer.
Using Affymetrix microarrays we compared in vitro gene expression in parental IGROV-1 and TOV21 cells (high  CXCR4 expression) with TOV112D and SKOV-3 cells (low CXCR4 expression). Gene Set Enrichment Analysis (GSEA) of those genes which were differentially expressed between cell lines with high versus low CXCR4 expression revealed evidence for a cell autonomous signaling network involving CXCR4, TNF-a, IL6 and Notch pathways in ovarian cancer cells.

overall_design: The Affymetrix GeneChip Human Genome U133Plus 2.0 arrays were used to define gene expression profiles in each cell line.


title: Expression data from Foxl2 wild-type and mutant ovaries and testes

city: Heidelberg

first: Henriette

last: Uhlenhaut

address: Meyerhofstrasse 1

department: Developmental Biology Unit

institute: EMBL

summary:
Foxl2 is a forkhead transcription factor expressed only in the female, but not in the male gonad. We have created mice homozygous mutant for the Foxl2 gene (KO) as well as mice carrying a conditional mutant Foxl2 allele (floxed).
The expression profiles of conventional Foxl2 knockout and wildtype ovaries were compared at P3, using the Affy Mouse Genome 430 2.0 Array. Adult wildtype and conditional mutant (Foxl2 floxed x RosaCre-EBD treated with tamoxifen) ovaries were compared to adult wildtype testes using the Affymetrix Mouse Gene 1.0 ST Array. Both experiments (KO/WT P3 and Mutant/WT/Testis Adult were also compared to each other.)

overall_design: Ovaries from newborn (postnatal day 3) and adult (8 week old) mice were excised from the animal and RNA was prepared from whole ovaries (Adult testes were excised and RNA was isolated from 1/4 testis).


title: Smad signaling is required for maintenance of epigenetic gene silencing during breast cancer progression

first: steve

last: shen

address: 545 First Ave

department: Biochemistry

institute: New York University

summary:
In this study, we took advantage of a previously established breast cancer progression cell line model system, which consists of a parental MCF10A (MI) spontaneously immortalized mammary epithelial cell line and two of its derivatives: 1) MCF10ATk.cl2 (MII), a MCF10A H-Ras transformed cell line and 3) MCF10CA1h (MIII), derived from a xenograft of the MII cells in nude mice that progressed to carcinoma (1, 2). These cell lines were previously reported to exhibit distinct tumorigenic properties when re-implanted in nude mice; MI is non-tumorigenic, MII forms benign hyperplastic lesions and MIII forms low-grade, well differentiated carcinomas (2, 3). The advantage of this system is that these cell lines were derived from a common genetic background (MCF10A) and accumulated distinct genetic/epigenetic alterations in vivo enabling them to acquire a range of non-tumorigenic to carcinogenic properties. Our initial studies showed that MIII cells, but not MI or MII, exhibit an EMT phenotype, promoter DNA hypermethylation of epithelial genes and highly invasive properties in vitro.
To investigate the role of TGFβ  pathway in these processes, we disrupted the TGFβ downstream signaling events in MIII, by stably overexpressing the inhibitory Smad7, and analyzed the gene expression profiles of MII, MIII and MIIISmad7 cells using microarray analysis.    Total RNA was isolated from three biological replicates corresponding to MIIpB, MIIIpB and MIIIpB-Smad7 cells using Trizol (Invitrogen) according to the manufacturer’s protocol, and the RNeasy mini-kit (Qiagen) was used to clean-up the RNA. Labeled cRNA fragments derived from the samples were hybridized onto human genome U133 plus 2.0 arrays (Affymetrix). Gene-expression estimates and a measure of sequence-specificity of the hybridization intensities were both determined using standard settings in MAS5 (Affymetrix). Probesets that did not exhibit sequence-specific hybridization in any sample were excluded from subsequent analysis.  Differential expression between MIIpB and MIIIpB as well as between MIIIpB and MIIIpBSmad7 was assessed using Student’s t-test. Genes with a false discovery rate (FDR) < 0.05 and a greater than 2-fold difference in expression between the two cell lines were considered to be differentially expressed.

first: Papageorgis

last: Panagiotis

first: Thiagalingam

last: Sam


title: Ovarian Cancer gene expression profiling identifies the surface of the ovary as a stem cell niche

city: Atlanta

first: Nathan

middle: J.

last: Bowen

state: GA

address: 223 James P Brawley Drive

department: Center for Cancer Research and Therapeutic Development

institute: Clark Atlanta University

summary: In contrast to epithelial derived carcinomas that arise in most human organs, ovarian surface epithelial cells become more rather than less differentiated as the malignancy progresses. To test the hypothesis that ovarian surface epithelial cells retain properties of relatively uncommitted pluripotent cells until undergoing neoplastic transformation, we conducted gene expression profiling analysis (Affymetrix, U133 Plus 2.0) of 12 ovarian surface epithelial cells and 12 laser capture microdissected serous papillary ovarian cances. We find that over 2000 genes are significantly differentially expressed between the surface epithelial and cancer samples. Network analysis implicates key signaling pathways and pathway interactions in ovarian cancer development. Genes previously associated with adult stem cell maintenance are expressed in ovarian surface epithelial cells and significantly down-regulated in ovarian cancer cells. Our results indicate that the surface of the ovary is an adult stem cell niche and that deregulation of genes involved in maintaining the quiescence of ovarian surface epithelial cells is instrumental in the initiation and development of ovarian cancer.

overall_design: Twelve healthy ovarian surface epithelia samples (OSE) were compared to twelve laser capture microdissected serous ovarian cancer epithelia samples (CEPI) via Affymetrix 3' expression array.

middle: J

first: Lila

middle: D

last: Walker

first: Lilya

middle: V

last: Matyunina

first: Kimbery

last: Totten

first: Benedict

last: Benigno

first: John

last: McDonald


title: Epigenotyping by quantitative DNA methylation analysis revealed three epigenotypes in colorectal cancer

city: Meguro-ku

first: Atsushi

last: Kaneda

state: Tokyo

address: 4-6-1 Komaba

department: RCAST

country: Japan

institute: The University of Tokyo

type: Methylation profiling by genome tiling array

summary: Aberrant DNA methylation, one of the major epigenetic alterations in cancer, has been reported to accumulate in a subset of colorectal cancer (CRC), so-called CpG island methylator phenotype (CIMP), which was known to correlate with microsatellite instability (MSI)-high CRC. To select new methylation markers genome-widely and epigenotype CRC by DNA methylation comprehensively, we performed methylated DNA immunoprecipitation-on-chip analysis using MSI-high CRC cell line HCT116 and microsatellite-stable SW480, and re-expression array analysis by 5-aza-2-deoxycytidine/Trichostatin A. Methylation levels of 44 new markers selected and 16 previously reported markers were analyzed quantitatively in 149 clinical CRC samples using MALDI-TOF mass spectrometry. By unsupervised two-way hierarchical clustering, CRC was clustered into high-, intermediate-, and low-methylation epigenotypes. Methylation markers were clustered into two groups: Group-1 showing methylation in high-methylation epigenotype and including all the 11 CIMP-related markers except NEUROG1, and Group-2 showing methylation in high- and intermediate-methylation epigenotypes. Marker panel deciding methylation epigenotypes with the highest accuracy was developed: 1st-Panel consisting of Group-1 genes (CACNA1G, LOX, SLC30A10) to extract high-methylation epigenotype, and 2nd-Panel consisting of Group-2 genes (ELMO1, FBN2, THBD, HAND1) and SLC30A10 again to divide the remains into intermediate- and low-methylation epigenotypes.  High-methylation epigenotype correlated significantly with BRAF mutation, MSI, proximal tumor location, and mucinous component, in concordance with reported CIMP. Intermediate- and low-methylation epigenotypes significantly correlated with KRAS-mutation(+) and KRAS-mutation(-), respectively. KRAS-mutation(+) intermediate-methylation epigenotype showed worse prognosis than KRAS-mutation(-)  low-methylation epigenotype (p=0.030). These three epigenotypes with different genetic characteristics suggested different molecular CRC genesis, and the markers might be useful to predict prognosis.

overall_design: To epigenotype (=classify using epigenetic information) colorectal cancer, comprehensive approach, e.g. hierarchial clustering using quantitative methylation data by a single detection method using genome-widely selected markers, was required to be performed. We selected new methylation markers through genome-wide methylation and expression analyses, and examined their methylation levels quantitatively by MALDI-TOF mass spectrometry in clinical colorectal cancer samples, in addition to previously reported genes/markers.

first: Koichi

last: Yagi

first: Hiroshi

last: Hayashi

first: Genta

last: Nagae

first: Shingo

last: Tsuji

first: Takayuki

last: Isagawa

first: Hiroyuki

last: Aburatani


title: Expression profiles in PCARNEQ ncRNA depletion in prostate cancer cells

city: Tokyo

first: Hidewaki

last: Nakaagwa

address: 4-6-1 Shirokanedai, Minato-ku,

department: Institute of Medical Science

summary: To globally address the function of a novel ncRNA PCARNEQ located in chromosome 8q24, microarray analysis was performed on RNA isolated from prostate cancer  cell line LNCaP cells treated with siRNA to PCARNEQ and the control siRNA to EGFP (siEGFP).

overall_design: LNCaP cells were treated with siRNA to PCARNEQ or the control siRNA to EGFP and total RNA from each experiment was analyzed in triplicate by microarray.

last: Nakagawa

first: Suyoun

last: Chung

first: Tatsuhiko

last: Tsunoda

first: Michiaki

last: Kubo

first: Yusuke

last: Nakamura


title: An expression profile that predicts the therapeutic response of the basal-like breast cancer to neoadjuvant chemotherapy

status: Public on Dec 30 2009

city: St Louis

first: Rekha

last: Meyer

state: MO

address: 4320 Forest Park Av

institute: Washington University School of Medicine

summary:
A gene expression signature characterizes expression data from breast cancer samples of patients with pathological complete response (pCR) or residual disease (RD) following the neoadjuvant trial.
Several gene expression profiles have been reported to predict breast cancer response to neoadjuvant chemotherapy. These studies often consider breast cancer as a homogeneous entity, although higher rates of pathologic complete response (pCR) are known to occur within the basal-like subclass. We postulated that profiles with higher predictive accuracy could be derived from a subset analysis of basal-like tumors in isolation. Using a previously described ‘‘intrinsic’’ signature to differentiate breast tumor subclasses, we identified 50 basal-like tumors from two independent clinical trials associated with gene expression profile data. 24 tumor data sets (included in this GEO submission) were derived from a 119-patient neoadjuvant trial at our institution and an additional 26 tumor data sets were identified from a published data set (Hess et al. J Clin Oncol 24:4236–4244, 2006). The combined 50 basal-like tumors were partitioned to form a 37 sample training set with 13 sequestered for validation. Clinical surveillance occurred for a mean of 26 months. We identified a 23-gene profile which predicted pCR in basal-like breast cancers with 92% predictive accuracy in the sequestered validation data set. Furthermore, distinct cluster of patients with high rates of cancer recurrence was observed based on cluster analysis with the 23-gene signature. Disease-free survival analysis of these three clusters revealed significantly reduced survival in the patients of this high recurrence cluster. We identified a 23- gene signature which predicts response of basal-like breast cancer to neoadjuvant chemotherapy as well as disease-free survival. This signature is independent of tissue collection method and chemotherapeutic regimen.

Keywords: Disease state analysis

overall_design: Core biopsies were obtained from 86 patients prior to neoadjuvant therapy out of which 70 fulfilled the requirements to undergo expression analysis (24 of these 70 were used in the published analysis). pCR was defined as no residual invasive disease in the breast or lymph nodes. Residual in situ carcinoma was also considered as pCR. RNA was extracted from snap frozen 14-gauge core samples obtained from pre-treatment tumors. Specimens containing more than 40% of tumor on histological examination were analyzed.

first: Yiing

last: Lin

first: Shin

first: Mark

last: Watson

first: Kathryn

last: Trinkaus

first: Sacha

last: Kuo

first: Michael

last: Naughton

first: Katherine

last: Weilbaecher

first: Timothy

last: Fleming

first: Rebecca

last: Aft


title: Transcriptional response of normal human lung WI-38 fibroblasts to benzo[a]pyrene diol epoxide: a dose-response study

city: Stockholm

first: Kristian

last: Dreij

address: Nobels väg 13

department: Environmental Medicine

country: Sweden

institute: Karolinska Institutet

summary: Cellular responses to carcinogens are typically studied in transformed cell lines, which do not reflect the physiological status of normal tissues. To address this question, we have characterized the transcriptional program and cellular responses of normal human lung WI-38 fibroblasts upon exposure to the ultimate carcinogen benzo[a]pyrene diol epoxide (BPDE). Exposure to BPDE induces a strong inflammatory response in WI-38 primary fibroblasts. Whole-genome microarray analysis shows induction of several genes related to the production of inflammatory factors, including those that encode interleukins (ILs), growth factors, and enzymes related to prostaglandin synthesis and signaling. This is the first demonstration that a strong inflammatory response is triggered in primary fibroblasts in response to a reactive diol epoxide derived from a polycyclic aromatic hydrocarbon.

overall_design: Normal human lung WI-38 fibroblasts were exposed to vehicle control (DMSO) and increasing doses (0.1, 0.5 and 1 uM) of anti-BPDE, respectively. The genome wide transcriptional response of the three treatments were compared to that of the control, respectively, in quadruplicates (Control and 1 uM) and triplicates (0.1 and 0.5 uM).

first: Kahn

last: Rhrissorrakrai

first: Kristin

last: Gunsalus

first: Nicholas

middle: E

last: Geacintov

first: David

middle: A

last: Scicchitano


title: SOCS-3 in muscle

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary:
Aims/hypothesis Due to their ability to regulate various signalling pathways (cytokines, hormones, growth factors), the suppressor of cytokine signalling (SOCS) proteins are thought to be promising therapeutic targets for metabolic and inflammatory disorders. Hence, their role in vivo has to be precisely determined.
Methods We generated transgenic mice constitutively expressing SOCS-3 in skeletal muscle to define whether the sole expression of SOCS-3 is sufficient to induce metabolic disorders and whether SOCS-3 is implicated in physiological roles distinct from metabolism.
Results We demonstrate here that chronic expression of SOCS-3 in skeletal muscle leads to overweight in mice and worsening of high-fat diet-induced systemic insulin resistance. Counter intuitively, insulin sensitivity in muscle of transgenic mice appears to be unaltered. However, following constitutive SOCS-3 expression, several genes had deregulated expression, among them other members of the SOCS family. This could maintain the insulin signal into skeletal muscle. Interestingly, we found that SOCS-3 interacts with calcineurin, which has been implicated in muscle contractility. In SOCS-3 transgenic muscle, this leads to delocalisation of calcineurin to the fibre periphery. Relevant to this finding, SOCS-3 transgenic animals had dilatation of the sarcoplasmic reticulum associated with swollen mitochondria and  decreased voluntary activity.
Conclusions/interpretation Our results show that constitutive SOCS-3 expression in skeletal muscle is not in itself sufficient to induce the establishment of metabolic disorders such as diabetes. In contrast, we reveal a novel role of SOCS-3, which appears to be important for muscle integrity and locomotor activity.
(Patricia Lebrun et al, Diabetologia, 2009)

overall_design: Expression profile established on a MoGene platform (Affymetrix), using three replicate for the wild type (WT), and three replicates for the transgene (TG).

first: Patricia

last: Lebrun

first: Chimène

last: Moreilhon

first: Pascal

last: Barbry

first: Emmanuel

last: Van Obberghen


title: Age-related expression data from composite bone marrow from healthy humans

city: Oslo

last: Jensen

address: Kirkeveien 166

department: Department of Clinical Chemistry

country: Norway

institute: Ullevål University Hospital

summary:
Human bone marrow is a complex, diversified and well-organized hematopoietic network changing composition with age. The purpose of this study was to analyze variations in relative precursor B cell abundance in bone marrow with age by means of global gene expression profiling. RNA was isolated from composite bone marrow from 25 healthy children, adolescents and adults age 2 months to 28 years. As reference transcript for precursor B cells we used recombination activating gene RAG1 exploring the data for other transcripts showing the same profile as RAG1 with age. We identified 54 genes with correlated expression profiles to RAG1 (r ≥ 0.9, p = 0), characterized by high expression at 3 - 20 months followed by a fast decline to lower signal levels maintained until early adulthood. Immunophenotyping from a similar healthy age-matched cohort (n = 37) showed a comparable decrease of precursor B cells. Of the 54 genes 15 were characteristically B cell associated representing cell surface molecules (CD19, CD72, CD79A, CD79B, CD180, IGL@, IGLL1, VPREB1, VPREB3), a signal transduction molecule (BLNK) and transcription factors (DNTT, EBF1, PAX5, POU2AF1, RAG2). Of the remaining transcripts some may represent novel B cell transcripts or genes involved in control of B cells.
Bone marrow was obtained from healthy children eligible for elective minor surgery and voluntary health care workers. The bone marrow samples (2.5ml) were immediately after aspiration transferred to PAXgene tubes for mRNA stabilization before RNA extraction and hybridization on Affymetrix microarrays. To that end, the study presents a picture of the total marrow activity with minimal manipulation that would otherwise influence gene expression results.

overall_design: We used microarrays to determine age-related changes in precursor B cell transcripts in bone marrow from 25 healthy children and adults and searched for other transcripts showing the same expression profile with age.

first: Lana

last: Schaffer

first: Ole

last: Olstad

first: Anne

middle: G

last: Bechensteen

first: Marit

last: Hellebostad

first: Geir

last: Tjønnfjord

first: Peter

last: Kierulf

first: Kaare

last: Gautvik

first: Liv

middle: T

last: Osnes


title: QK-knockdown Hs683 transduced with miR-20a or a scrambled non-targeting microRNA (miR-NT)

city: Boston

first: Hailei

last: Zhang

state: MA

address: 44 Binney Street

institute: Dana-Farber Cancer Institute

summary: Identify potential miR-20a regulated mRNAs and linked pathways in the setting of QK knockdown by comparing the transcriptional profiles of shQK-transduced human Hs683 cells together with miR-20a or a scrambled miRNA control (miR-NT)

first: An-Jou

last: Chen


title: QK-knockdown U87 transduced with miR-20a or a scrambled non-targeting microRNA (miR-NT)

summary: Identify potential miR-20a regulated mRNAs and linked pathways in the setting of QK knockdown by comparing the transcriptional profiles of shQK-transduced human U87 cells together with miR-20a or a scrambled miRNA control (miR-NT)

overall_design: QK-knockdown U87 transduced with miR-20a and a scrambled non-targeting microRNA (miR-NT)


title: Fine-tuning of human dendritic cells regulation revealed by translational profiling

city: Marseille

first: Philippe

last: Pierre

address: Campus Luminy - case 906

institute: CIML - CNRS - INSERM

summary: Dendritic cells (DCs) are the sentinels of the mammalian immune system and they undergo a complex maturation process mediated by activation upon pathogen detection. Recent studies described the analysis of activated DCs by transcriptional profiling, but translation regulation was never taken in account. Therefore, the nature of the mRNAs being translated at various stages of DC activation was determined with the help of translational profiling, which is the sucrose gradient fractionation of polysomal-bound mRNAs combined to microarrays analysis. Total and polysomal-bound mRNA populations were compared in immature (0h) and LPS-stimulated (4h and 16h) human monocyte-derived DCs  with the help of Affymetrix microarrays. Biostatistical analysis indicated that 296 mRNA molecules are translationally regulated during DC-activation. The most abundant biological process among the regulated mRNAs was protein biosynthesis, indicating the existence of a negative feedback loop regulating translation. Interestingly, a cluster of 17 ribosomal proteins were part of the regulated mRNAs, indicating that translation may be fine-tuned by particular components of the translational machinery. Our observations highlight the importance of translation regulation during the immune response, and may favour the identification of novel gene clusters or protein networks relevant for immunity. Our study also provides information on the possible absence of correlation between gene expression and real protein production in DCs.

overall_design: To identify translationally regulated mRNA molecules, gene expression derived from the polysome-bound mRNAs was compared by Affymetrix microarrays analysis to the gene expression derived from unfractionated total mRNAs derived from whole-cell lysates, as recently described on several reports (Johannes 1999, Rajasekhar 2003, Bushell 2006, Lü 2006, Parent 2008). Polysomal RNA (P) and total RNA (T) were isolated from MoDCs generated from four different blood donors. Since three timepoints (0h, 4h and 16h) were chosen for each blood donor and RNA type, twenty-four RNA samples were totally analyzed by microarrays.

first: Maurizio

last: Ceppi

first: Damien

last: Chaussabel

first: Jacques

last: Banchereau

first: Derek

last: Blankenship


title: Hepatic gene expression before and during interferon and ribavirin combination therapy

city: Kanazawa

first: Masao

last: Honda

address: Takara-Machi 13-1

department: Gastroenterology

institute: Kanazawa University

summary: Patients who cleared HCV viremia early during therapy tended to show favorable outcomes, whereas patients who needed a longer period to clear HCV had poorer outcomes. We explored the mechanisms of treatment resistance by comparing hepatic gene expression before and during treatment

overall_design: We explored the mechanisms of treatment resistance by comparing hepatic gene expression before and during treatment. Liver biopsy was performed in 30 patients before and one week after starting combination therapy with IFN + Rib. Hepatocytes and liver-infiltrating lymphocytes (LILs) were obtained from 12 patients using laser capture micro dissection (LCM).

first: Mikiko

last: Nakamura

first: Makoto

last: Tateno

first: Akito

last: Sakai

first: Tetsuro

last: Shimakami

first: Takayoshi

last: Shirasaki

first: Tatsuya

last: Yamashita

first: Kuniaki

last: Arai

first: Taro

first: Yoshio

first: Shuichi

last: Kaneko


title: Reprogramming of anaerobic metabolism by the FnrS Small RNA

city: Bethesda

first: Sylvain

last: Durand

address: 5000 Rockville Pike

institute: NICHD

summary: Small RNAs (sRNA) that act by base pairing with trans-encoded mRNAs modulate metabolism in response to a variety of environmental stimuli.  Here, we describe an Hfq-binding sRNA (FnrS) whose expression is induced upon a shift from aerobic to anaerobic conditions and which acts to down regulate the levels of a variety of mRNAs encoding metabolic enzymes.  Anaerobic induction in minimal medium depends strongly on FNR but is also affected by ArcA and CRP.  Whole genome expression analysis showed that the levels of at least 32 mRNAs are down regulated upon FnrS overexpression, 15 of which are predicted to base pair with FnrS by TargetRNA.  The sRNA is highly conserved across its entire length in numerous enterobacteria, and mutation analysis revealed that two separate regions of FnrS base pair with different sets of target mRNAs.  The majority of the target genes previously reported to be down regulated in an FNR-dependent manner lack recognizable FNR binding sites.  We thus suggest that FnrS extends the FNR regulon and increases the efficiency of anaerobic metabolism by repressing the synthesis of enzymes that are not needed under these conditions.

overall_design: MG1655 carrying either pFnrS or the control vector pAZ3 was used in all experiments.  Overnight bacterial cultures grown with shaking at 37˚C in LB media with ampicillin at a final concentration of 50 ug/mL were diluted 1000-fold into 10 ml of LB-ampicillin media and grown with shaking at 37˚C.  When cultures reached an O.D.600 of 0.5, arabinose was added at a final concentration of 0.2%. Total RNA was extracted from cells at the indicated times using the hot phenol procedure.

first: Gisela

last: Storz


title: Global gene expression profile of primary human leukemic blasts

status: Public on Dec 29 2009

city: Frankfurt

first: Jan-Henning

last: Klusmann

address: Theodor-Stern-Kai 7

department: Pediatric Hematology and Oncology

institute: Goehte University Frankfurt

summary:
The goal of this study is to define the global gene expression profile of primary leukemic blasts from patients with different forms of myeloid leukemia and different FAB subtypes.
Here we report the global gene expression profile of 2 patients with AML FAB M5, 2 patients with AML FAB M7, 3 patients with Down syndrome AML FAB M7 and 3 patients with Down syndrome transient leukemia.

overall_design: Leukemic blasts were FACS sorted by their immunophenotype and expression profiles were generated by microarray.

first: Zhe

last: Li

first: Dirk

last: Reinhardt

first: Stuart

last: Orkin


title: Identification of miR-125b-2 target genes

summary:
The goal of this study is to define miR-125b-2 target genes in the hematopoietic system by genetic alteration of miR-125b expression levels.
Here we report the identification of miR-125b-2 targets in the hematopoietic system by repressing miR125b in megakaryoblastic leukemia (AMKL) cell lines and overexpressing miR-125b-2 in hematopoietic stem and progenitor cells (CD34+-HSPCs)

overall_design: M07 and CMK cells were transfected with Cy3-labelled non-silencing olignucleotides or anti-miR-125b and sorted (two experiments). HSPCs were retrovirally transduced and sorted for GFP positive cells. We generated their expression profiles by microarray.


first: Hailei

last: Zhang

summary: Identify potential QK-regulated mRNAs and linked pathways by comparing the transcriptional profiles of shGFP- and shQK-transduced human Hs683 cells

overall_design: Hs683 cells infected with shQk-2, shQk-5 and Hs683 cells infected with shGFP as control

first: An-Jou

last: Chen

first: Yonghong

last: Xiao


title: Expression profile of early stage druing induced pluripotency regulated by BMP/FBS

status: Public on Dec 23 2009

city: Guangzhou

first: Duanqing

last: Pei

state: Guangdong

address: Room 301, International Business Incubator, Guangzhou science park

department: Center for Molecular Medicine

country: China

institute: Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences(GIBH.CAS)

summary:
FBS and BMP influence the somatic reprogramming induced by Oct4/Sox2/Klf4/c-Myc similarly. Bone morphogenetic proteins (BMPs) are abundant in serum and activate Smad1/5/8 to regulated target genes.
BMPs play a important role in ES self-renewal, neurogenesis, osteogenesis, angiogenesis. We performed this experiment for identify what targets are regulated by BMPs and FBS.

overall_design: We performed a expression profile analysis at D3 after reprogramming factor transduction in various media.  The media include standard medium for ES culture (mES), serum free medium for iPS (iPS-SF1), iPS-SF1 supplemented with BMP4, iPS-SF1 supplemented with FBS, iPS-SF1 supplemented with BMP4 and Noggin. Three biological repeats were perfromed.

first: Jiekai

first: Wenzhi

last: He


title: STAR RNA-binding protein, Quaking, suppresses cancer via regulation of microRNA

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

summary:
MicroRNAs have emerged as major genetic elements in the genesis and suppression of cancer.  Here, multi-dimensional cancer genome analysis and validation has defined a novel Glioblastoma Multiforme (GBM) tumor suppressor pathway and mechanism of action centered on Quaking (QK), a member of the STAR family of RNA-binding proteins.  Combined functional, biochemical and computational studies establish that p53 directly regulates QK gene expression, QK protein binds and stabilizes miR-20a of the cancer-relevant miR-17-92 cluster, and miR-20a in turn functions to regulate TGFβR2 and the TGFβ signaling network. Linkage of these pathway components is supported by their genome and expression status across GBM specimens and by their gain- and loss-of-function interactions in in vitro and in vivo complementation studies. This p53-QK-miR-20a axis expands our understanding of the p53 tumor suppression network in cancer and reveals a novel tumor suppression mechanism involving regulation of specific cancer-relevant microRNAs.

This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Homo sapiens
Mus musculus

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

overall_design: Refer to individual Series.


title: Influenza virus infected HUVEC

city: Hannover

first: Dorothee

last: Viemann

state: Deutschland

address: Carl-Neuberg-Straße 1

department: Department of Pediatric Pulmonology, Allergy and Neonatology

institute: Hannover Medical School

summary: To delineate specific patterns of signaling networks activated by H5N1 we used a comparative systems biology approach analyzing gene expression in endothelial cells infected with three different human and avian influenza strains of high and low pathogenicity.

overall_design: HUVECs were infected with either PR8, FPV or H5N1 virus. We used wildtype HUVEC or HUVEC transfected with a dominant negative mutant of IKK2 (block of the NF-kB signaling pathway). In case of FPV infections we also blocked p38 MAP kinase with an SB-inhibitor.

first: Mirco

last: Schmolke

first: Aloys

last: Lueken

first: Yvonne

last: Boergeling

first: Judith

last: Friesenhagen

first: Helmut

last: Wittkowski

first: Stephan

last: Ludwig

first: Johannes

last: Roth


title: Expression array analysis of the effects of vitamin D3 and mutp53

city: Rehovot

first: Perry

last: Stambolsky

address: Herzel 200

department: MCB

country: Israel

institute: Weizmann institute of science

summary:
We wanted to examine the effect of vitamin D3 and endogenous mutant p53 expressed in SKBR3 cells on gene expression paterns.
Expression microarray analysis was performed on SKBR3 cells without or with endogenous mutp53 knockdown, with or without 1a25-vitamin D3 treatment.

overall_design: SKBR3 cells expressing p53R175H, transfected either with siRNA for p53 (p53i) or with control LacZ siRNA, 48h after transfection, three samples of each transfection were treated with 1a25(OH)2D3 (D3;100nM) for different time points; 8 houres, 20 hours and 50 hours. Cells were subjected to RNA extraction and hybridization on Affymetrix microarrays.

first: Yuval

last: Tabach


title: mRNA profiling reveals divergent roles of PPARa and PPARß/d in regulating mouse liver gene expression (PPARb/d samples)

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary:
Little is known about the role of the transcription factor PPARß/d in liver. Here we set out to better elucidate the function of PPARß/d in liver by comparing the effect of PPARa and PPARß/d deletion using whole genome transcriptional profiling and analysis of plasma and liver metabolites. In fed state, the number of genes altered by PPARa and PPARß/d deletion was similar, whereas in fasted state the effect of PPARa deletion was much more pronounced, consistent with the pattern of gene expression of PPARa and PPARß/d. Minor overlap was found between PPARa- and PPARß/d-dependent gene regulation in liver. Pathways upregulated by PPARß/d deletion were connected to innate immunity. Pathways downregulated by PPARß/d deletion included lipoprotein metabolism and various pathways related to glucose utilization, which correlated with elevated plasma glucose and triglycerides and reduced plasma cholesterol in PPARß/d-/- mice. Downregulated genes that may underlie these metabolic alterations included Pklr, Fbp1, Apoa4, Vldlr, Lipg, and Pcsk9, which may represent novel PPARß/d target genes. In contrast to PPARa-/- mice, no changes in plasma FFA, plasma ß-hydroxybutyrate, liver triglycerides and liver glycogen were observed in PPARß/d-/- mice. Our data indicate a role for PPARß/d in hepatic glucose utilization and lipoprotein metabolism but not in the adaptive response to fasting.

Keywords: Analysis of target gene regulation by using microarrays

overall_design: PPARβ/δ knockout mice on a mixed background (Sv129/C57Bl/6) and corresponding wildtype mice were used. Male mice (n=4-5 per group) were either fed or fasted for 24 hours. At the end of the experiment, mice were anaesthetized with a mixture of isofluorane (1.5%), nitrous oxide (70%) and oxygen (30%). Blood was collected by orbital puncture, after which the mice were sacrificed by cervical dislocation. Livers were dissected, snap frozen in liquid nitrogen and kept at -80ºC until further analysis. For RNA analyses, tissue from the same part of the liver lobe was used.

first: Linda

last: Sanderson

first: Mark

last: Boekschoten

first: Beatrice

last: Desvergne

first: Michael

last: Müller

first: Sander

last: Kersten


title: Time course of 1,25(OH)2D treated RWPE1 cells.

status: Public on Dec 18 2009

city: West Lafayette

first: Pavlo

last: Kovalenko

state: IN

address: 700 W State st

department: Foods and Nutrition

institute: Purdue University

summary:
Background:  Prostate cancer is the second leading cause of cancer mortality among US men.  Epidemiological evidence suggests that high vitamin D status protects men from prostate cancer and the active form of vitamin D, 1α,25 dihydroxyvitamin D3 (1,25(OH)2D) has anti-cancer effects in cultured prostate cells. Still, the molecular mechanisms and the gene targets for vitamin D-mediated prostate cancer prevention are unknown.
Results: We examined the effect of 1,25(OH)2D (+/- 100 nM, 6, 24, 48 h) on the transcript profile of proliferating RWPE1 cells, an immortalized, non-tumorigenic prostate epithelial cell line that is growth arrested by 1,25(OH)2D (Affymetrix U133 Plus 2.0, n=4/treatment per time and dose). Our analysis revealed many transcript level changes at a 5% false detection rate: 6 h, 1571 (61% up), 24 h, 1816 (60 % up), 48 h, 3566 (38 % up). 288 transcripts were regulated similarly at all time points (182 up, 80 down) and many of the promoters for these transcripts contained putative vitamin D response elements.  Functional analysis by pathway or Gene Set Analysis revealed early suppression of WNT, Notch, NF-kB, and IGF1 signaling.  Transcripts related to inflammation were suppressed at 6 h (e.g. IL-1 pathway) and suppression of proinflammatory pathways continued at later time points (e.g. IL-17 and IL-6 pathways).  There was also evidence for induction of anti-angiogenic pathways and induction of transcripts for protection from oxidative stress or maintenance of cell redox homeostasis at 6 h.
Conclusions: Our data reveal of large number of potential new, direct vitamin D target genes relevant to prostate cancer prevention.  In addition, our data suggests that rather than having a single strong regulatory effect, vitamin D orchestrates a pattern of changes within prostate epithelial cells that limit or slow carcinogenesis.

overall_design: RWPE1 cells were treated with medium containing 100 nM of 1,25(OH)2D or vehicle (0.1% ethanol) for 6, 24 or 48 hours (n=4 per treatment, 24 total samples). The transcripts levels in each sample were measured by using the Affymetrix HU133 plus 2.0 GeneChip (Affymetrix, Santa Clara, CA).

first: James

middle: C

last: Fleet

middle: L

first: Steven

last: Clinton


title: Determining direct targets of the bHLH MIST1

status: Public on Dec 17 2009

city: Houston.

first: Jason

last: Mills

state: T

address: One Baylor Plaza

department: Gastroenterology, Medicine

institute: Baylor College of Medicine

summary: The transcription factor MIST1 is required for final maturation of secretory cells of diverse tissues, including gastric digestive-enzyme secreting zymogenic (chief) cells (ZCs). Here, we show that MIST1 directly activates RAB26, RAB3D and several other genes.

overall_design: We used microarrays to determine genes upregulated following transient MIST1 transfection. Two gastric cell lines were used: HGC-27 and AGS. Three chips were generated from each cell line: parental (untransfected), GFP+empty vector (a control for effects of transfection), and GFP+MIST1. The latter two chips were generated from cells flow sorted based on GFP fluorescence to isolate cells with high levels of transfection. Chips were analyzed by dChip to identify genes expressed in both MIST1-transfected cell populations relative to their respective controls in multiple Boolean 'AND' comparisons.


title: Bacterial Correlates of Gingival Gene Expression

status: Public on Dec 22 2009

city: New York

first: Ryan

last: Demmer

department: Epidemiology

institute: Columbia University

summary: We investigated the association between subgingival bacterial profiles and gene expression patterns in gingival tissues of patients with periodontitis.

overall_design: A total of 120 patients undergoing periodontal surgery contributed with a minimum of two interproximal gingival papillae (range 2-4) from a maxillary posterior. Prior to tissue harvesting, subgingival plaque samples were collected from the mesial and distal aspects of each papilla. Gingival tissue RNA was extracted, reverse-transcribed, labeled, and hybridized with whole-genome microarrays (310 in total)

first: Panos

middle: N

last: Papapanou

first: Paul

last: Pavlidis


title: Gene expression profiling of YAP wild-type or mutants overexpressing MCF10A cells

status: Public on Dec 16 2009

city: Ja Jolla

first: Bin

last: Zhao

address: 3855 Health Sciences Dr.

institute: University of California, San Diego

summary: This study compares gene expression change upon expression of Yes-associated protein (YAP) wild-type or mutants in order to establish the importance of TEAD binding and WW domains in the gene-induction function of YAP. The results indicate that gene-induction is seriously comprised in YAP-S94A (TEAD binding domain mutant) expressing cells. And mutantion of WW domains (YAP-W1W2) also affect a fraction of YAP induced genes. Therefore both TEAD binding domain and WW domains are required for the full function of YAP in gene-induction.

overall_design: Four samples are included: 1. pQCXIH vector control; 2 YAP-WT expression; 3. YAP-S94A expression; 4. YAP-W1W2 expression. Gene expression profiles of YAP wild-type or mutants expressing cells were compared to that of vector control. Experiments were done in MCF10A mammary epithelial cells.

first: Jindan

last: Yu

first: Kun-liang

last: Guan


title: Transcriptional profiling reveals divergent roles of PPARa and PPARß/d in regulation of gene expression in mouse liver

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

overall_design: Refer to individual Series


title: Gene expression data from AP-2γ silenced MCF-7 cells

status: Public on Dec 14 2009

city: London

first: Helen

last: Hurst

address: Charterhouse Square

department: Centre for Tumour Biology

institute: Institute of Cancer

summary:
Overexpression of the AP-2γ  transcription factor in breast tumours has been identified as an independent predictor of poor outcome and failure of hormone therapy, even in ER positive, ErbB2 negative tumours; markers of a more favourable prognosis. To understand further the role of AP-2γ in breast carcinoma, we have used an RNA interference and gene expression profiling strategy using the MCF-7 cell line as a model for ER positive, ErbB2 negative tumours with AP-2γ overexpression.
Gene expression changes between control and silenced cells implicate AP-2γ  in the control of cell cycle progression and developmental signalling.

Keywords: RNA interference

overall_design: We compared the expression profiles of MCF-7 cells separately transfected with three independent AP-2γ targeting sequences with those from control cells treated with transfection reagent alone or a non-silencing control siRNA on Affymetrix arrays; each condition was examined in triplicate.

first: Christopher

last: Williams


title: Expression array analysis in patients with neuroaxonal injury in cerebral palsy

status: Public on Dec 11 2009

city: Rotterdam

first: J.

last: Verkerk

address: Molewaterplein 50

department: Bioinformatics

institute: Erasmus Medical Center

summary:
We have analysed a family with an autosomal recessive type of tetraplegic cerebral palsy with mental retardation, reduction of cerebral white matter, and atrophy of the cerebellum in an inbred sibship.
Homozygosity mapping using SNPs was performed to identify the chromosomal locus for the disease. In the 14 Mb candidate region on chromosome 7q22, RNA expression profiling was used to select among the 203 genes in the area.

overall_design: In order to select putative candidate genes from the linkage region in patients, mRNA expression arrays were used to study the transcripts in fibroblasts of probands (IV-1,3,4,5,6) and controls (IV-2,9 plus two independent controls (male and female)).

first: Sigrid

last: Swagemakers

first: Rachel

last: Schot

first: Annemieke

first: Peter

last: van der Spek

first: Grazia

last: Mancini


title: Global Gene Expression of Human Hepatoma Cells After Amino Acid Limitation

status: Public on Dec 20 2009

city: Gainesville

first: jixiu

last: shan

state: FL

address: 1600 SW Archer Road

department: Biochemistry and Molecular Biology

institute: University of Florida

summary: 1507 known genes have been identified differentially regulated during HisOH treatment by more than 2 fold. This includes 250 down-regulated genes and 1257 up-regulated genes.

overall_design: Two conditions were used, 8 arrays, 4 for each condition, M-basal condition, H-HisOH treatment.

first: Jixiu

last: Shan

first: Michael

last: Kilberg


title: Human primary subcutaneous preadipocytes treated with glucocorticoids prior to the initiation of differentiation

status: Public on Dec 10 2009

city: Calgary

first: Robert

last: Haché

state: Alberta

address: 2500 University Drive NW

country: Canada

institute: University of Calgary

summary:
Full title: Expression data from human primary subcutaneous preadipocytes treated with glucocorticoids prior to the initiation of differentiation.
Preadipocytes are continuously exposed to glucocorticoids in situ due to both steroid present in the circulatory system as well as adipose tissue specific 11βHSD1 activity.  While the effects of glucocorticoids during differentiation are well studied, the effect of exposure of preadipocytes to glucocorticoids prior to differentiation is unknown.  We therefore treated confluent human primary preadipocytes drived from subcutaneous adipose tissue with the synthetic glucocorticoid dexamethasone for 48 hours prior to the initiation of differentiation and assessed what effect this had on their subsequent potential to differentiate.  We found that pretreatment with glucocorticoids had a priming effect and resulted in increased differentiation of these preadipocytes.  Furthermore, this treatment was additive to the effects of glucocorticoids during the initial phase of adipogenesis.  Microarray analysis performed subsequent to the pretreatment with glucocorticoids (at the time point at which preadipocytes would have been induced to differentiate) identified glucocorticoid-responsive, candidate genes whose altered expression could mediate these effects.
keywords: glucocorticoids, glucocorticoid receptor, preadipocytes, adipogenesis, human primary preadipocytes, subcutaneous, adipose tissue

overall_design: Human subcutaneous primary preadipocytes were purchased from Zen-Bio Inc.  Preadipocytes from 5 female donors (average BMI 22.5±0.2kg/m2) were pooled prior to the initial seeding in T75 flasks.  Cells were maintained at 5% CO2 in DMEM with 1.0g/L glucose, 20% calf serum, 100U/ml penicillin, 100mg/ml streptomycin and 50U/ml nystatin.  Cells were expanded once prior to seeding in Nunc-brand 12-well dishes.  Upon reaching confluence (24 h post-splitting), preadipocytes were stimulated with vehicle or 1uM dex for 48 hours in growth media containing 3% calf serum. Microarray analysis was performed on duplicate samples.

first: Julianna

last: Tomlinson

first: Dongmei

last: Wu

first: Adèle

last: Boudreau

first: Alan

last: Mears


title: HepaRG cells as a model of the primary human hepatocyte transcriptome

city: Kansas City

first: Steven

last: Hart

state: KS

address: 3901 Rainbow Blvd

department: Pharmacology, Toxicology & Therapeutics

institute: University of Kansas Medical Center

summary: The aim of this experiment is to determine the similarities and differences between gene expression profiles in HepaRG cells versus primary human hepatocytes, human liver, and the commonly used HepG2 cell.

overall_design: We compared the gene expression profiles from replicate triplicate biological samples of human liver, primary human hepatocytes, HepG2 cells, and HepaRG at differing levels of maturity (differentiated and undifferentiated).

first: Xiaobo

last: Zhong


title: Expression analysis for nasopharyngeal carcinoma cell lines 5-8F

first: Zhong-Xi

last: Huang

address: Tonghe

department: Cancer Institute

institute: Southern Medical University

summary: High metastatic nasopharyngeal carcinoma cell line 5-8F expression patterns.

overall_design: This study was done to detect genes expressed in NPC cell line 5-8F. The microarray analyses were done in a same batch. cells are cultured and harvested at two different time points.

first: Jia

last: Li

first: Ying

last: Fan

first: Jing

last: Chen

first: Kai-Tai

last: Yao


title: Expression data from E. coli cells overexpressing GraL for short and long periods of time

status: Public on Dec 09 2009

first: Katarzyna

last: Potrykus

address: 6 Center Drive, 6B rm 316

department: NICHD

institute: NIH


title: Expression analysis for nasopharyngeal carcinoma cell lines (5-8F and 6-10B)

summary: High metastatic nasopharyngeal carcinoma cell line 5-8F expression patterns against low metastatic nasopharyngeal carcinoma cell line 6-10B.

overall_design: This study was done to screen genes related with metastasis in NPC. The microarray analyses were done in a same batch. 6-10B cells are cultured and harvested at three different time points.


title: Activation of phosphatidylcholine-cycle enzymes in human epithelial ovarian cancer cells

status: Public on Dec 08 2009

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

summary: Altered phosphatidylcholine (PC) metabolism in epithelial ovarian cancer (EOC) can provide choline-based imaging approaches as powerful tools to improve diagnosis and identify new therapeutic targets. Biochemical, protein and mRNA expression analyses demonstrated that the increase in the major choline-containing metabolite phosphocholine (PCho) in EOC compared with normal and non-tumoral immortalized counterparts (EONT) mainly rely upon: 1) ChoK activation, consistent with higher protein content and increased ChoKalpha mRNA expression levels; 2) PC-plc activation, consistent with higher, previously reported, protein expression. More limited and variable sources of PCho could derive, in some EOC cells, from activation of Phospholipase D or GPC-pd. Phospholipase A2 activity and isoforms’ expression levels were lower or unchanged in EOC compared with EONT cells. Increased ChoKalpha mRNA, as well as ChoK and PC-plc protein expression, were also detected in surgical specimens isolated from EOC patients. Overall, we demonstrated that the elevated PCho pool detected in EOC cells primarily resulted from the upregulation/activation of ChoK and PC-plc involved in the biosynthetic and in a degradative pathway of the PC-cycle, respectively.

overall_design: 20 EOC frozen surgical specimens, 8 EOC cell lines and Ovarian Surface Epithelial (OSE) cells (4 different preparations, 3 of them pooled in one sample).

first: L

first: D

last: Mezzanzanica

first: M

last: Bagnoli

first: S

last: Canevari


title: Human Cytomegalovirus Infection Causes Premature and Abnormal Differentiation of Human Neural Progenitor Cells

city: Orange

first: Philip

middle: Hitchins

last: Schwartz

address: 455 South Main Street

department: Research Institute

institute: Children's Hospital of Orange County

summary:
Our results suggest that HCMV infection disrupts the self-renewal capacity of NPCs and influences their differentiation.
Whole genome expression analysis revealed many changes in cellular gene expression, including downregulation of genes pertinent to the neuronal lineage.

overall_design: For gene expression analysis, cells were either mock- or virus-infected. Mock-infected cells were harvested at 12 hpi, virus infected cells were harvested at 4, 12 and 24 hpi. Virus- and mock-infections were performed in duplicate, with each individual sample harvested separately, thereby acting as biological replicates for analysis.

middle: H

first: Elizabeth

last: Fortunato


title: Expression data from E. coli cells overexpressing GraL for short periods of time

city: Bethesda

summary:
While studying greA expression, we noted presence of an intrinsic terminator in the leader region of greA mRNA transcript. We found this terminator to be quite efficient both in vivo and in vitro. This region seems to be conserved among many enteric bacteria. Judging from fitness experiments, the resulting short RNAs (50-59nt long) exert biological effects. This lead us to propose that greA leader region encodes a novel small non-coding RNA that we collectively call GraL.
We used microarrays to detail the effects of GraL after short and longterm overproduction of GraL.

overall_design: E. coli cells harbouring plasmids overexpressing GraL or vector control, were monitored in an effort to elucidate a longterm (constitutive overexpression) or short term (15 min induction with IPTG) effects. This was done in two backgrounds- either in wt E. coli cells, or ppGpp0 cells (delta relA, delta spoT).

first: Helen

last: Murphy

first: Xiongfong

first: Jonathan

last: Epstein

first: Michael

last: Cashel


title: Comparison of gene expression profiles between human and mouse monocyte subsets [human data]

status: Public on Dec 07 2009

city: Gauting

first: Loems

last: Ziegler-Heitbrock

address: Robert-Koch Allee 29

department: Asklepios-Fachklinik and Helmholtz Zentrum München

institute: German Research Center for Environmental Health

summary:
Human and mouse blood each contain two monocyte subsets. Here, we investigated the extent of their similarity using a microarray approach. Approximately 300 genes in human and 550 genes in mouse were differentially expressed between subsets. More than 130 of these gene expression differences were conserved between mouse and human monocyte subsets. We confirmed numerous differences at the cell surface protein level. Despite overall conservation, some molecules were conversely expressed between the two species’ subsets, including CD36, CD9, and TREM-1. Furthermore, other differences existed, including a prominent PPARγ signature in mouse monocytes absent in human. Overall, human and mouse monocyte subsets are far more broadly conserved than currently recognized. Thus, studies in mice may indeed yield relevant information regarding the biology of human monocyte subsets. However, differences between the species deserve consideration in models of human disease studied in the mouse.

Keywords: Expression profiling by array

overall_design: The two major subsets of monocytes (Ly-6C+ and Ly-6Clo) from 12-week old C57Bl/6 mice were sorted and the RNA extracted and hybridized to Affymetrix GeneChip® 430 2.0 arrays. We pooled leukocytes from 5 mice for each sort and sorted 4 separate times for 4 biological replicates. The two major monocyte subsets (CD16- and CD16+) were isolated from venous heparinized blood from apparently healthy human volunteers using MACS technology with all reagents and tools from Miltenyi Biotec. Three separate donors were hybridized three different times to Affymetrix U133 Plus 2.0 array.


title: NK-cell associated receptors expression in EBV-positive gamma-delta T cell lines.

city: Tokyo

first: Junko

last: Ohyashiki

address: 6-7-1, Nishishinjuku, Shinjuku-ku

department: Intractable Immune System Diseases Research Center

institute: Tokyo Medical University

summary: The contribution of chronic antigen stimulation to the occurrence of lymphoproliferative disorder (LPD) with the gamma-delta T-cell lineage is unclear, despite the fact that Epstein-Barr virus (EBV) positive T-cell LPD is derived from antigen-stimulated cytotoxic T-cells. Given the possible association of antigen stimulation with the development of cytotoxic T-cell LPD, we compared gene expression patterns in Epstein-Barr virus (EBV)-positive gamma-delta T-cell lines derived from patients with nasal T-cell lymphoma and chronic active EBV infection and those in gamma-delta T-cells from healthy volunteers. Three EBV-positive gamma-delta T-cells lines, SNT cells (SNT-8, SNT-13 and SNT-15), were used in this study. SNT-8 was established from patients with nasal T-cell lymphoma and SNT-13, -15 were established from patients with chronic active EBV infection (Zhang Y, et al., Br J Cancer 94:599-608, 2006). All the SNT cells exhibits common rearrangement of Vgamma9-JgammaP and Jdelta3 genes. The gamma-delta T-cells obtained from healthy volunteers were expanded ex vivo by 1 microM of zoledronate (ZOL) plus IL-2 for 14 days incubation.

overall_design: We compared gene expression profiling in 3 EBV-positive positive gamma-delta T-cells lines with those in gamma-delta T cells obtaied from a healthy volunteer.  Global gene expression was analyzed using the Affymetrix Human Genome U133 2.0 Plus GeneChip Set. Analysis of variance (ANOVA) was done using GeneSifter® (VizXLabs). Values of P<0.05 were considered to be a statistically significant difference.

first: Yu

last: Zhang

first: Norio

last: Shimizu

first: Kazuma


title: Global gene expression analysis in Stat3deltaIEC APCMin/+ mice

status: Public on Dec 01 2009

city: Vienna

first: Martin

last: Bilban

country: Austria

institute: Medical University of Vienna

summary:
Background and aims: The transcription factor Stat3 has been considered to promote progression and metastasis of intestinal cancers.
Methods: We investigated the role of Stat3 in intestinal tumors using mice with conditional ablation of Stat3 in intestinal epithelial cells (Stat3deltaIEC).
Results: In the APCmin mouse model of intestinal cancer, genetic ablation of Stat3 reduced the multiplicity of early adenomas. However, loss of Stat3 promoted tumor progression at later stages leading to formation of invasive carcinomas which significantly shortened the lifespan of Stat3deltaIEC APCmin/+ mice. Interestingly, loss of Stat3 in tumors of APCmin/+ mice had no significant impact on cell survival and angiogenesis but promoted cell proliferation. A genome-wide expression analysis of Stat3-deficient tumors suggested that Stat3 negatively regulates intestinal cancer progression via the cell adhesion molecule Ceacam1.
Conclusions: Our data suggest that Stat3 impairs progression of intestinal tumors. Therefore, detrimental effects on tumor progression have to be considered upon therapeutic targeting of the Stat3 signaling pathway in intestinal cancer.

overall_design:
Stat3 has been implicated in initiation of azoxymethane/dextransulfate-induced colorectal tumors of mice and is considered to promote intestinal tumor progression in humans.
We addressed the question if Stat3 is required for intestinal tumor progression in the APCmin mouse model. we established a conditional mouse model to investigate tumor formation after ablation of Stat3. For that purpose, mice with floxed Stat3 alleles were crossed to transgenic mice expressing the Cre-recombinase under control of the Villin promoter with resulting Villin-cre Stat3flox/flox (Stat3deltaIEC) mice.For tumor induction, Stat3deltaIEC mice were bred into the tumor-prone genetic background of APCmin mice. The APCmin mutation causes aberrant activation of the Wnt signaling pathway and induces tumor formation predominantly in the small intestine23. We analysed early and late stage tumorigenesis in male and female Stat3flox/flox APCmin/+ and Stat3deltaIEC APCmin/+ mice.

first: Monica

last: Musteanu

first: Robert

last: Eferl


title: Expression data for 2 obese subjects from the SibPair cohort with a deletion on 16p11.2

status: Public on Dec 02 2009

first: Johanna

middle: Cecilia

last: Andersson

address: Burlington Danes Building, Hammersmith Hospital, Du Cane Road

department: Division of Genetics of Common Disease

institute: Imperial College London

summary: We report a highly-penetrant form of obesity, initially observed in 31 heterozygous carriers of a 593kb or larger deletion at 16p11.2 from amongst subjects ascertained for cognitive deficits. Nineteen similar deletions were identified from GWAS data in 16053 individuals from 8 European cohorts; such deletions was absent from healthy non-obese controls and accounted for 0.7% of our morbid obesity cases (p = 6.4x10-8, OR = 43). These findings highlight a promising strategy for identifying missing heritability in obesity and other complex traits, in which insights from rare extreme cases can be used to elucidate the basis for more common phenotypes.

overall_design: The expression data was analysed for 2 obese subjects carrying a deletion on 16p11.2. There are no replicates or controls.

first: Margareta

last: Jernås

first: Peter

last: Jacobson

first: Lena

last: Carlsson

first: Lars

last: Sjöström

first: Andrew

last: Walley

first: Mario

last: Falchi

first: Philippe

last: Froguel

first: Robin

last: Walters

first: Alexandra

middle: I

last: Blakemore

first: Adam

last: deSmith

first: Julia

last: El-Sayed-Mustafa

first: Jessica

last: Buxton

first: David

last: Balding

first: Sylvia

last: Richardson

first: Tim

last: Aitman


title: Genes regulated after knock-down of Pirin in U937 cells

first: Myriam

last: Alcalay

address: Via Adamello 16

department: Experimental Oncology

institute: European Institute of Oncology

summary:
Pirin (PIR) is a putative transcriptional regulator whose expression is silenced in cells bearing the AML1/ETO and PML/RAR leukemogenic fusion proteins and is significantly repressed in a large proportion of acute myeloid leukemias. PIR expression increases during in vitro myeloid differentiation of primary hematopoietic precursor cells, and ablation of PIR in the U937 myelomonocytic cell line or in murine primary hematopoietic precursor cells results in impairment of terminal myeloid differentiation.

Keywords: Transcriptional regulation, knock-down using shRNA

overall_design:
We analyzed gene expression profiles of U937 cells after knock-down of PIR using the shPIR#7 oligonucleotides cloned in the pSICO-R lentiviral vector. No residual PIR protein is detectable in U937-shPIR#7 cells by Western blotting. U937 cells containing the empty cloning vector (U937-pSICO) were used as control.

shPIR#7 oligonucleotide sequences:
Human PIR#7-for:
TGAAGCCACTTTGTCTTAATTTCAAGAGAATTAAGACAAAGTGGCTTCTTTTTTC
Human PIR#7-rev:
TCGAGAAAAAAGAAGCCACTTTGTCTTAATTCTCTTGAAATTAAGACAAAGTGGCTTCA

For each sample, an RNA pool was obtained by mixing equal quantities of total RNA from each of three independent RNA extractions. Each biotin-labeled target was hybridized to two GeneChip HG-U133 Plus v.2 arrays.


title: Transcriptome profiling of fenretinide-treated  and untreated CD34+ cells from 4 CML patients

city: Bristol

first: Hai

last: Fang

address: Woodland Road

department: Department of Computer Science

institute: University of Bristol

summary: Imatinib, as the first-line agent of chronic myeloid leukemia (CML), is ineffective in eradicating CML stem/progenitor cells, thus unable to prevent late relapse. Here we present data indicating that fenretinide preferentially targets CD34+ CML cells and enhances the efficacy of imatinib in CML. As tested by colony forming cell assays, both number and size of total colonies derived from CD34+ CML cells were significantly reduced by fenretinide, and by combining fenretinide with imatinib. In particular, colonies derived from erythroid progenitors and those derived from more primitive pluripotent progenitor cells were highly sensitive to fenretinide/fenretinide plus immtinib. Further data showed that fenretinide was able to induce apoptosis in CD34+ CML cells which were refractory to imatinib. Through transcriptome analysis and followed by molecular validation, we further showed that apoptosis induced by fenretinide in CD34+ CML cells was mediated by complex mechanisms of stress responses, probably triggered by elevated levels of intracellular reactive oxygen species. Thus, fenretinide combines with imatinib may represent a new strategy for the treatment of CML, in which fenretinide targets primitive CD34+ CML cells whereas imatinib targets leukemic blasts. This strategy may eventually reduce the risk of relapse and probably resistant as well in CML patients.

overall_design: Transcriptome profiles of CML CD34+ cells with and without fenretinide treatment were analyzed using whole genome expression arrays (Affymetrix HG-U133 Plus 2.0) in four CML patients (CML32, CML33, CML34 and CML35, see Table 1). To minimize potential data biases, both treated and untreated cell samples were maintained in culture for 48 hours before hybridization.

first: Xiao-ling

last: Pan

first: Yan-zhi

last: Du

first: Kan-kan

last: Wang

first: Ji

last: Zhang


title: The human reticulocyte transcriptome (HG-U133_Plus2.0)

first: Jeffery

middle: Lynn

last: Miller

address: 10 Center Drive

department: Molecular Medicine Branch

institute: NIH/NIDDK

summary: RNA from circulating blood reticulocytes was utilized to provide a robust description of genes transcribed at the final stages of erythroblast maturation. After depletion of leukocytes and platelets, Affymetrix HG-U133Plus 2.0 arrays were hybridized with probe from total RNA isolated from blood sampled from 6 umbilical cords and 6 healthy adult humans.

overall_design: Peripheral blood from 6 normal adults and 6 human umbilical cords were purified to obtain packed red blood cells and their purity was assessed by CELL-DYN4000. The contaminated WBC count was less than 1 out of 1 million cells. Total RNA from purified reticulocytes included in the purified red blood cells was extracted, labeled, and hybridized onto Affymetrix HG-U133Plus 2.0 arrays.

first: Sung-Ho

last: Goh


title: Immune profile and mitotic index of metastatic melanoma lesions enhance clinical staging in predicting patient survival.

first: Dusan

last: Bogunovic

address: 522 First Av. SML1307

institute: New York University Medical Center

summary:
Although remission rates for metastatic melanoma are generally very poor, some patients can survive for prolonged periods following metastasis. We used gene expression profiling, mitotic index (MI), and quantification of tumor infiltrating leukocytes (TILs) and CD3+ cells in metastatic lesions to search for a molecular basis for this observation and to develop improved methods for predicting patient survival. We identified a group of 266 genes associated with postrecurrence survival. Genes positively associated with survival were predominantly immune response related (e.g., ICOS, CD3d, ZAP70, TRAT1, TARP, GZMK, LCK, CD2, CXCL13, CCL19, CCR7, VCAM1) while genes negatively associated with survival were cell proliferation related (e.g., PDE4D, CDK2, GREF1, NUSAP1, SPC24).
Identification of genes associated with survival of metastatic melanoma

overall_design:
Survival Analysis was performed using Statistical Analysis of Microarrays
B D denotes same patient with multiple reccurences

last: O'Neill

first: Ilana

last: Belitskaya-Levy

first: Vladimir

last: Vacic

first: Yu

last: Yi-Lo

last: Adams

first: Farbod

last: Darvishian

first: Russell

last: Berman

first: Richard

last: Shapiro

first: Anna

last: Plavlick

first: Stefano

last: Lonardi

first: Jiri

last: Zavadil

first: Iman

last: Osman

first: Nina

last: Bhardwaj


title: Quercetin supplementation and CD14+ monocyte gene expression

city: Kiel

first: Frank

last: Döring

address: Heinrich-Hecht-Platz 10

department: Human Nutrition and Food Science

institute: Christian-Albrechts-University Kiel

summary:
Quercetin has been described to have a wide range of beneficial effects in humans, ranging from anti-carcinogenic properties to reduced risk of cardiovascular disease. We tested whether a daily supplementation of quercetin leads to reproducible changes in gene expression profiles of human monocytes.
Keywords: individual compound treatment

overall_design: CD14+ monocytes were isolated from three healthy volunteers before and after a 2 wk supplementation period of 150mg quercetin per day. With this design every subject served as his or her own control (baseline sample = control)

first: Inka

last: Boomgaarden


title: Gene expression in colon cancer stem cells (CSC) cultures identified by Wnt signaling levels

city: Amsterdam

first: Louis

last: Vermeulen

address: Meibergdreef 9

department: Center for Experimental Molecular Medicine

institute: Academic Medical Center Amsterdam

summary: Primary colon CSC cultures were transduced with a Wnt responsive construct (TOP-GFP) and were single cell cloned. 10% highest and lowest TOP-GFP cell fractions were FACS sorted and arrayed.

overall_design: Primary colon CSC cultures with a responsive construct (TOP-GFP): high and low TOP-GFP cell fractions. 4 samples.

first: Felipe

last: de Sousa E Melo

last: Medema


title: Gene expression profiling in the fetal cardiac tissue after folate and low dose trichloroethylene exposure

city: tucson

first: ornella

last: selmin

state: AZ

address: 1177 east 4th st

department: nutritional sciences

institute: university of arizona

summary: To identify transcriptional targets altered in the embryonic heart after exposure to TCE, and possible protective effects of folate, we used DNA microarray technology to profile gene expression in embryonic mouse hearts with maternal TCE exposure and dietary changes in maternal folate.  Results: Exposure to low doses of TCE (10ppb) caused extensive alterations in transcripts encoding proteins involved in transport, ion channel, transcription, differentiation, cytoskeleton, cell cycle and apoptosis. Exogenous folate did not offset the effects of TCE exposure on normal gene expression and both high and low levels of folate produced additional significant changes in gene expression.  Conclusions: A mechanism where TCE induces a folate deficiency does not explain altered gene expression patterns in the embryonic mouse heart.  The data further suggest that use of folate supplementation, in the presence of this toxin, may be detrimental and non-protective of the developing embryo.

overall_design:
Six sample groups (control and TCE exposed from each one of the three folate diet groups) were tested, each with two biological replicates for a total of 12 sample groups.  Total RNA from each group was processed by the University of Arizona microarray facility (Genomics Shared Service, Tucson, AZ).  RNA purity was evaluated using an Eppendorf BioPhotometer (Eppendorf North America, Westbury, NY) to obtain values of nucleotides, organics, proteins, and contaminants in the samples.  Viable RNA had 260/280 ratios between 1.8 and 2.0 or higher.  RNA integrity was confirmed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany) following the RNA 6000 Nano Chip Series II Assay protocol.  Twelve Affymetrix Mouse Gene 1.0 ST arrays (Affymetrix, Santa Clara, CA) containing over 28,000 gene-level probe sets were used for genome wide expression profiling.  The arrays were processed according to the protocol (GeneChip Whole Transcript) Sense Target Labeling Assay Manual, version 4) established by Affymetrix.  Briefly, 400ng of total RNA were reverse transcribed into double stranded cDNA using the Affymetrix WT cDNA Synthesis and Amplification kit.  The entire cDNA was then transcribed into cRNA overnight, cleaned using the Affymetrix GeneChip Sample Cleanup Module, and quantified on a NanoDrop 1000 (Thermo Scientific, Wilmington, DE).  8ug of cRNA were reverse transcribed into ssDNA, and labeled.  Aliquots of the labeled DNA were combined with the hybridization solution overnight.  The arrays were scanned using the Affymetrix GeneChip Scanner 3000 with 7G upgrade.  The image generated was analyzed using the Affymetrix GeneChip Operating Software (GCOS) were .DAT (image), .CEL (cell intensity data), .CHP (probe analysis data) files were generated.

Statistical analysis of DNA microarrays:  The Affymetrix mouse gene ST arrays were processed with a bioconductor library (http://www.bioconductor.org) designed for this array.  The arrays were then normalized using the RMA function in the oligo library of bioconductor.  In order to identify poor quality arrays, Spearman correlation coefficients between all arrays were computed.  A plot of the coefficients revealed that correlations between the arrays were 0.98 or greater, indicating that a relatively small number of genes were changing in response to the treatments.  As a further control, the distribution of values for positive and negative control probes were examined on each array and found to have the correct expected separation.  Since there were only two biological replicates due to the complexity of the sample preparation, a specific approach was used that identified probes that showed a consistent change between biological duplicates. A cutoff value for the change between treatments of 1.5 fold was chosen based on an examination of the distribution of expression values on these arrays and identified between 200-1000 probes that were varying to the greatest extent.  Probe lists were generated as described below.  Briefly, the objective was to find genes that were changing between treatments while reducing the effects of the biological variation between duplicate samples.  To compare two treatments, probe expression ratios for all 4 possible combinations of the duplicate arrays were calculated.  If 2 or more of these ratios were 1.5 fold or greater, the gene was considered to be changed.  These probe sets were annotated using Affymetrix data files and the affected genes, biological functions, and pathways were identified.  For the biochemical pathway analysis, lists of genes involved in pathways of biological interest were obtained from the KEGG database using the BIORAG resource (http://www.biorag.org ).  Genes showing expression ratios between treatments of greater than 1.5 fold were then identified. The additional processed data files are linked on the Series record.

first: Ornella

last: Selmin

first: Patricia

last: Caldwell

first: Ann

last: Manziello


title: BW25113 fhlA/pCA24N-FhlA133 vs fhlA/pCA24N-FhlA in modified-complex 20 mM formate at 37ºC

city: State College

first: Thomas

middle: K.

last: Wood

state: PA

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

institute: Pennsylvania State University

summary: Variant FhlA133 (Q11H, L14V, Y177F, K245R, M288K, and I342F) had eight- fold higher hydrogen production than FhlA wild-type under 30 min of anaerobic incubation in modified-complex 20 mM formate at 37ºC. The mechanism by which the FhlA133 mutations increase hydrogen production is by increasing the transcription of all of the genes activated by the native FhlA (FHL complex).

overall_design:
Strains: E. coli BW25113 fhlA/pCA24N-FhlA wild-type and E. coli BW25113 fhlA/pCA24N-FhlA133 (Q11H, L14V, Y177F, K245R, M288K, and I342F).
Medium: Modified-complex 20 mM formate
1 mL of overnight culture in modified - complex 20 mM formate + Cm 30 µg/mL was inoculated in 9 mL of fresh modified - complex 20 mM formate + Cm 30 µg/mL and incubated anaerobically at 37oC in 27 mL glass vials.
Time: 30 minutes
Cell type: Suspension

first: Viviana

last: Sanchez Torres

first: Toshinari

last: Maeda

middle: K


title: C/EBPa is required for pulmonary cytoprotection from hyperoxia injury

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary: We have previously demonstrated that deletion of the Cebpa gene in the developing fetal mouse lung caused death soon after birth from the failure of lung maturation.  Many of the transcriptional pathways regulating morphogenesis of the fetal lung are induced postnatally and mediate repair of the injured lung.  We hypothesized that C/EBPa plays a role in protection of the alveolar epithelium following hyperoxia injury of the mature lung.  Transgenic Cebpa∆/∆ mice in which Cebpa was conditionally deleted from Clara cells (from early gestation) and type II cells (from near-term) were developed.  Cebpa∆/∆ mice grow normally without any pulmonary abnormalities. Cebpa∆/∆ mice were highly susceptible to hyperoxia. Cebpa∆/∆ mice died within 4d after hyperoxia associated with severe lung inflammation and altered surfactant components at a time when all control mice survived.  Microarrays were analyzed on isolated type II cells at an early stage (24h) of hyperoxia exposure to detect the primary genes influenced by deletion of Cebpa.  The associated network analysis revealed the reduced expression of key genes related to surfactant lipid and protein homeostasis, such as Srebf, Scap, Lpcat1, Abca3, Sftpb, and Napsa.  Genes for the cell signaling, immune response, and protective antioxidants, including GSH and Vnn-1,3, were decreased in the Cebpa∆/∆ mice lung.  C/EBPa did not play a critical role in postnatal pulmonary function under normal conditions.  In contrast, in the absence of C/EBPa, exposure to hyperoxia caused respiratory failure, supporting the concept that C/EBPa plays an important role in enhancing epithelial cell survival, surfactant lipid homeostasis, and maturation of SP-B from pro-SP-B.

overall_design: Transgenic Cebpa delta/delta mice in which Cebpa was conditionally deleted from Clara cells (from early gestation) and type II cells (from near-term) were developed. Microarrays were analyzed on isolated type II cells at an early stage (0h, 2h, 24h) of hyperoxia exposure to detect the primary genes influenced by deletion of Cebpa.

first: Yanhua

last: Wang

first: Chika

last: Saegusa

first: Angelica

last: Schehr

first: Shawn

last: Grant

first: Jeffrey

last: Whitsett

first: Machiko

last: Ikegami


title: Expression data from E. coli cells overexpressing GraL for long periods of time

first: Katarzyna

last: Potrykus

state: MD

first: Helen

last: Murphy

first: Xiongfong

last: Chen

first: Jonathan

last: Epstein

first: Michael

last: Cashel


title: Comparing effects of mTR and mTERT deletion on gene expression and DNA damage response

city: Baltimore

first: Carol

last: Greider

address: 725 N Wolfe St

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

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

overall_design: Refer to individual Series


title: KSHV Manipulates Notch Signaling by Upregulating Dll4 and JAG1 to Alter Cell Cycle Gene Expression in LECs

city: London

first: Stephen

last: Henderson

address: Paul O'Gorman Building, Huntley Street

institute: UCL

summary: Kaposi sarcoma is the most common cancer in AIDS patients and is typified by red skin lesions. The disease is caused by the KSHV virus (HHV8) and is recognizable by its distinctive red skin lesions. The lesions are KSHV infected spindle cells, most commonly the lymphatic endothelial and blood vessel endothelial cells (LEC and BEC), plus surrounding stroma. Here we examine KSHVs modulation of Notch signaling using wild-type LEC cells co-cultured with DLL4 and JAG1 expressing LEC cells.

overall_design: There are  1) n=2 of LEC control cells co-cultured with pSIN expressing LEC, 2) n=3 of LEC co-cultured with pSIN-Dll4 expressing LEC, and 3) n=3 of LEC co-cultured with pSIN-JAG1 expressing LEC.

first: Vicky

last: Emuss

first: Chris

last: Boshoff


title: Gene Expression Data from U937T:PLZF-RARa Inducible Cells

status: Public on Nov 30 2009

city: Chicago

first: Kim

middle: Lee

last: Rice

state: IL

address: 303E Superior Street

department: Hematology/Oncology

institute: Northwestern University

summary:
The PLZF-RARa fusion oncoprotein is overexpressed in the t(11;17) subtype of acute promyelocytic leukemia. Gene expression microarrays were used to identify genes involved in leukemic transformation.
We used microarray to detect gene expression changes induced by the PLZF-RARa fusion oncoprotein in the U937 cell line

overall_design: The U937T:PLZF-RARa cell line was engineered to express PLZF-RARa upon tetracycline removal. PLZF-RARa was induced for 48hr and RNA was extracted and hybridized to Affymetrix HGU133Plus2.0 Chips

last: Licht


title: Comparing effects of mTR and mTERT deletion on gene expression and DNA damage response: liver

summary: Telomerase, the essential enzyme that maintains telomere length, contains two core components, TERT and TR. While early studies in yeast and mouse both indicated that loss of telomerase leads to phenotypes that arise after an increased number of generations, due to telomere shortening, recent studies claim additional roles for telomerase components in transcription and the response to DNA damage. To test these telomere length maintenance-independent roles of telomerase components, we examined first generation mTR-/- and mTERT-/- mice with long telomeres. We used gene expression profiling and found no genes that were expressed at significantly different levels when independent mTR-/- G1 mice were compared to mTERT-/- G1 mice and to wild-type mice. In addition, we compared the response to DNA damage in mTR-/-G1 and mTERT-/- G1 mouse embryonic fibroblasts, and found no increase in the response to DNA damage in the absence of either telomerase components compared to wild-type. We conclude that in the wild-type physiological telomere length setting, neither mTR nor mTERT act as a transcription factor or have a role in the DNA damage response.

overall_design:
Livers from age- and sex-matched telomerase wild-type and knock-out C57BL/6J mice were dissected out and processed for RNA extraction.
Telomerase null mice were first-generation (G1) mTERT KO or mTR KO.
3 independent wild-type + knock-out mice sets were examined.
In each set, wild-type + knock-out mice were littermates.

first: Sofia

last: Vidal-Cardenas

middle: W


title: Transcriptome analysis of pancreatic tumor cell invasion and angiogenesis in the PDAC-CAM model

city: Talence

first: Martin

last: Hagedorn

address: Av des Facultes

department: Biology

institute: University Bordeaux 1

summary: Human pancreatic adenocarcinoma cells were grafted on the chick chorioallantoic membrane (CAM). Human and chicken GeneChips were used simultaneously to study gene regulation during PDAC cell invasion.

sample_organism:
Gallus gallus
Homo sapiens

platform_organism:
Gallus gallus
Homo sapiens

overall_design: Pooled RNA from T1 (n=3) and T6 (n=3) CAMs were extracted using the RNeasy mini kit (Qiagen). T6 was compared to T1 on human GeneChips and in parallel, on chicken GeneChips.

first: Laurent

last: Dumartin