title: TCEAL7 Inhibition of c-Myc Activity in Alternative Lengthening of Telomeres Regulates hTERT Expression

status: Public on May 04 2010

city: Glasgow

first: W.

middle: Nicol

last: Keith

state: Lanarkshire

address: Center for Oncology and Applied Pharmacology, University of Glasgow, CRUK Beatson Laboratories, Garscube Estate, Switchback Road

institute: The University of Glasgow

summary:
Replicative senescence forms a major barrier to tumor progression. Cancer cells bypass this by using one of the two known telomere maintenance mechanisms: telomerase or the recombination-based alternative lengthening of telomeres (ALT) mechanism. The molecular details of ALT are currently poorly understood. We have previously shown that telomerase is actively repressed through complex networks of kinase, gene expression, and chromatin
regulation. In this study, we aimed to gain further understanding of the role of kinases in the regulation of telomerase expression in ALT cells. Using a whole human kinome siRNA screen, we highlighted 106 kinases whose expression is linked to hTERT promoter activity. Network modeling of transcriptional regulation implicated c-Myc as a key regulator of the 106 kinase hits. Given our previous observations of lower c-Myc activity in ALT cells, we further
explored its potential to regulate telomerase expression in ALT. We found increased c-Myc binding at the hTERT promoter in telomerase-positive compared with ALT cells, although no expression differences in c-Myc, Mad, or Max were observed between ALT and telomerase-positive cells that could explain decreased c-Myc activity in ALT. Instead, we found increased expression of the c-Myc competitive inhibitor TCEAL7 in ALT cells and tumors and that alteration of TCEAL7 expression levels in ALT and telomerase-positive cells affects hTERT expression. Lower c-Myc activity in ALT may therefore be obtained through TCEAL7 regulation. Thus, TCEAL7 may present an interesting novel target for cancer therapy, which warrants further investigation.

overall_design: Each tumour sample performed once except S767, S758, S904R, S1451, MP28, MP31, MP33 which were performed in duplicate.

first: Kyle

last: Lafferty-Whyte

first: Alan

last: Bilsland

first: Stacey

last: Hoare

first: Sharon

last: Burns

first: Nadia

last: Zaffaroni

first: Claire

last: Cairney

first: W

middle: N


title: Translatome and transcriptome profiling of EGF response in HeLa cells

status: Public on May 09 2010

city: Povo

first: Toma

last: Tebaldi

state: Trento

address: via Sommarive n. 9

department: Centre for Integrative Biology

country: Italy

institute: University of Trento

summary:
Translatome analysis by sucrose gradient centrifugation of cell lysates followed by microarray profiling of the polysomal and subpolysomal RNA fractions represents a way of both studying translational control networks and better approximating the proteomic representation of cells. It is an established notion that translational control takes place essentially at the translation initiation level, therefore the variation in abundance of a given mRNA species on polysomes can be directly related to the variation in abundance of the corresponding protein. Comparison of  translatome profile changes with corresponding transcriptome profile changes can provide a measure of the degree of concordance between cellular controls affecting mRNA abundance and cellular controls affecting mRNA availability to translation. To provide a direct experimental evaluation of the phenomenon, we decided to study a classical example of transcriptional reprogramming of gene expression: Epidermal Growth Factor (EGF) treatment. This stimulus triggers a well known chain of intracellular transduction events, ultimately resulting in a multifaceted phenotypic spectrum of changes with prevalent induction of cell growth and proliferation. We subjected HeLa cells to serum starvation for 12h and then we added EGF at final concentration of 1 μg/ml, profiling before and after 40 minutes of treatment the transcriptome, the translatome, coming from the polysomal pool of mRNAs after sucrose gradient separation, and also the mRNA content of the subpolysomal pool, expected not to be actively translated.

Keywords: translatome profiling, polysomal profiling, polysomal RNA, translational control, translational profiling, polysome profiling, post-transcriptional regulation, EGF starvation release.

overall_design: The comparison between transcriptional and polysomal profiling  was used for the discovery of general and mRNA-specific changes in the translation state of the serum starved HeLa cells transcriptome in response to EGF stimulus. To identify translationally regulated mRNA molecules, gene expression signals derived from the polysomal and subpolysomal RNA populations were compared by microarrays analysis to those obtained from unfractionated total RNAs. Polysomal RNA, subpolysomal RNA and total RNA were isolated from HeLa cells serum starved and treated with EGF. Cells lysates were collected before (t = 0 min) and after (t = 40 min) EGF treatment. All experiments were run in triplicates.

first: Gabriella

last: Viero

first: Ilaria

last: Pegoretti

first: Valentina

last: Adami

first: Angela

last: Re

first: Alessandro

last: Quattrone


title: Functional genomics of human bronchial epithelial cells directly interacting with conidiospores of Aspergillus fumigatus

status: Public on Jun 04 2010

city: Vancouver

first: Scott

last: Tebbutt

state: BC

address: St. Paul's Hospital - Rm 166 - 1081 Burrard St.

country: Canada

institute: UBC - iCAPTURE Centre

summary: The cells of the airway epithelium play critical roles in host defense to inhaled irritants, and in asthma pathogenesis. These cells are constantly exposed to conidiospores of the ubiquitous mould Aspergillus fumigatus, which are small enough to reach the alveoli. This exposure is asymptomatic in most individuals but can be associated with a spectrum of diseases ranging from asthma and allergic bronchopulmonary aspergillosis to aspergilloma and invasive aspergillosis. Airway epithelial cells have been shown to internalize A. fumigatus conidiospores in vitro, but the implications of this process for pathogenesis remain unclear. We have developed a cell culture model for this interaction using the 16HBE cell line and a transgenic A. fumigatus strain expressing green fluorescent protein. Using fluorescence-activated cell sorting (FACS), cells directly interacting with conidiospores and cells not associated with any conidiospores were sorted into separate samples. Transcriptional profiling of these samples using Agilent Whole Human Genome microarrays revealed significant changes in gene expression in response to interaction with conidiospores. The identification of biologically relevant responses validates this methodology, and motivates further work to characterize the interactions between A. fumigatus conidiospores and primary airway epithelial cells of normal and asthmatic origins.

overall_design: Four independent samples of 16HBE cells incubated with GFP-expressing Aspergillus fumigatus conidiospores for 6 hours were analyzed by flow cytometry and divided into negative and positive samples based on the presence of a GFP signal, representing cells with no direct contact with conidiospores and cells directly interacting with conidiospores, respectively. Gene expression was analyzed in these 8 samples using Agilent Whole Human Genome microarrays, with a one-colour experiemntal design.

first: Pol

last: Gomez

first: Tillie

middle: L

last: Hackett

first: Margo

middle: M

last: Moore

first: Darryl

middle: A

last: Knight

middle: J


city: Beijing

first: Kaitai

last: Zhang

address: Pan jia yuan nan li #17

country: China

institute: Cancer Institute (Hospital), Peking Union Medical College and Chinese Academy of Medical Sciences

summary: Gene expression for NCI-H1299 cell line transfected with human DENND2D and vector (pcDNA3.1/V5-His TOPO TA vector) respectively.

overall_design: The microarray experiment was designed to perform four replicates for each H1299-DENND2D and H1299-vector sample. cRNA used in replication 1 and 2 was from the same label reaction to perform the hybridization replicates.

first: Lin

last: Feng

first: Yu

last: Liu

first: Hang

first: Zhike

last: Lu

first: Guangwu

last: Guo

first: Yanning

last: Gao

first: Shujun

last: Cheng

first: Yong


title: Expression data from C57BL/6J and MRL/MpJ hearts following acute myocardial infarction

status: Public on May 01 2010

city: La Jolla

first: Darlene

last: Hunt

state: CA

address: 9500 Gilman Drive #0412

department: Bioengineering

country: USA

institute: UC San Diego

summary:
The Murphy Roth Large (MRL) mouse, a strain capable of regenerating right ventricular myocardium, has a high post-myocardial infarction (MI) survival rate compared with C57BL6/J (C57) mice. The biological processes responsible for this survival advantage are unknown.
We compared acute post-MI gene expression in C57 and MRL hearts using microarrays and identified promising candidate biological processes underlying increased survival in the MRL.

overall_design: Hearts from both strains were excised at different time points before or after MI for RNA extraction and hybridization to MOE430A arrays. Baseline hearts were excised from healthy mice that had not undergone the MI procedure (day 0). Infarct tissue in this case means tissue taken from the anterior-apical region that would be the infarct region in a post-MI heart. Non-infarct covers the remainder of the LV. Post-MI hearts were excised either 1 or 5 days after MI. We had successful hybridizations for 3 replicates each of C57 day 0 infarct and non-infarct tissue (6 arrays), 4 MRL day 0 infarct and non-infarct tissue (8 arrays), 4 C57 day 1 infarct and non-infarct tissue (8 arrays), 4 MRL day 1 infarct and non-infarct tissue (8 arrays), 4 C57 day 5 infarct and non-infarct tissue (8 arrays), and 4 MRL day 5 infarct and non-infarct tissue (8 arrays).

first: Patrick

middle: H

last: Campbell

first: Alexander

middle: C

last: Zambon

first: Karen

last: Vranizan

first: Sylvia

last: Evans

first: Hai-Chien

last: Kuo

first: Ken

middle: D

last: Yamaguchi

first: Jeffrey

last: Omens

first: Andrew

last: McCulloch


title: Radial Migration Assay and Analysis

status: Public on Apr 29 2010

city: grand rapids

first: brian

last: haab

state: MI

address: 333 bostwick avenue NE

department: lab of cancer immunodiagnostics

institute: van andel institute

summary: When either Panc-1 or MiaPaCa-2 were plated as a discrete clump of cells in the middle of a plate, two morphologically distinct populations could be created. The cells on the periphery of the cell cluster migrated away from the region of high cell density and took on a classical mesenchymal phenotype with spindle like projections and loss of cell to cell adhesion. Cells that remained in the highly populated center showed greater intercellular adhesion and were more rounded in appearance. This model was included to provide information about whether glyco-gene expression changes observed in models of the epithelial to mesenchymal transition also are involved in migration.

overall_design: Radial Migration Assay comparing two populations (Migrating vs. Non Migrating) in two pancreatic cancer cell lines (Panc-1 and MiaPaCa-2)

first: Julianna

last: Ross

first: Nhan

last: Tran


title: Knockdown of PHF8 in HeLa S3 cells

status: Public on Apr 27 2010

city: Barcelona

first: Klaus

last: Fortschegger

address: C/ Dr. Aiguader 88

department: Gene Regulation

country: Spain

institute: Center for Genomic Regulation

summary:
PHF8 is an H3K9me2 demethylase, interacts with H3K4me3 and RNA Polymerase II, is enriched at thousands of transcription start sites and can act as a transcriptional co-activator.
In the following experiment we wanted to analyze the impact of PHF8-knockdown on transcript levels in HeLa cells.

overall_design:
Three independent replicate knockdown experiments with PHF8-shA and control NT-sh were performed (6 samples in total).
The two samples of each replicate experiment were hybridized in two color dye swap experiments (6 arrays in total).

first: Ramin

last: Shiekhattar


title: Mutations in the SHANK2 synaptic scaffolding gene in autism spectrum disorder and mental retardation

city: Tuebingen

first: Michael

last: Bonin

state: BW

address: CAlwerstr. 7

department: Medical Genetics

country: Germany

institute: University Tuebingen

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

summary: Autism spectrum disorder (ASD) and mental retardation (MR) represent clinically distinct neurodevelopmental disorders with a complex genetic etiology. Using microarrays we identified de novo copy number variations in the SHANK2 synaptic scaffolding gene in two unrelated ASD and MR patients; DNA sequencing of SHANK2 revealed additional variants including a de novo nonsense mutation and 7 rare inherited changes. Our findings further link common genes between ASD and intellectual disability.

overall_design: We analyzed a patients with autism spectrum disorder and mental retardation (with their related parents) using whole genome SNP arrays.

first: Simone

last: Berkel

first: Christian

middle: R

last: Marshall

first: Birgit

last: Weiss

first: Jennifer

last: Howe

first: Ralph

last: Roeth

first: Volker

last: Endris

first: Wendy

last: Roberts

first: Peter

last: Szatmari

first: Pinto

last: Dalila

first: Angelika

last: Riess

first: Hartmut

last: Engels

first: Sprengel

last: Rolf

first: Ute

last: Moog

first: Stephen

middle: W

last: Scherer

first: Gudrun

last: Rappold


title: Identification of genes differentially regulated upon infection of Thp-1 cells with H37Rv

city: New Delhi

first: Aanchal

last: Chopra

address: Aruna Asaf Ali Marg

country: India

institute: International Centre for Genetic Engineering and Biotechnology(ICGEB)

summary: Perturbation of host physiology by intracellular Mycobacterium tuberculosis (H37Rv) can be reflected by changes in gene expression pattern of host genes. Total RNA was isolated from PMA differentiated uninfected cells or cells infected with H37Rv for 16, 48 or 90 hours and gene expression profile was obtained.

overall_design: There are in all 8 samples, two replcates of each 4. Two samples, namely 1D,1E (replicates of one) are control (PMA differentiated Thp-1 cells Uninfected controls). Cells were infected with H37Rv at an MOI of 1:10 and samples were collected at 16 hours, 48 hours and 90 hours post-infection.

first: Dhiraj

last: Kumar

first: Lekha

last: Nath

first: Azhar

last: Kamal

first: Ankur

last: Varshney

first: Avinash

last: Jain

first: Sarman

last: Singh

first: Kanury

middle: V

last: Rao


title: HORMAD1 mutation disrupts synaptonemal complex formation and chromosomal segregation in fertilized eggs

city: Pittsburgh

first: Aleksandar

last: Rajkovic

state: PA

address: 204 Craft Ave. Suite A230

department: Dept. of Obstetrics, Gynecology & Reproductive Sciences

institute: Magee-Womens Research Institute

summary: Hormad1 encodes a protein that contains a HORMA domain, and unlike Mad2, Hormad1 expression is germ cell specific. We discovered that both male and female are infertile, and HORMAD1 has important function in synaptonemal complex formation, sex chromosome inactivation during spermatogenesis and chromosome segregation in meiosis.

overall_design: RNA isolated from wild-type and Hormad1-/- 2-week-old testes was used for performing Illumina BeadChip MouseWG-6 2.0 arrays. Three replicates per genotype were performed.

first: Yonghyun

last: Shin

first: HoyWon

last: Ahn


title: Regulation of human skin pigmentation in situ by repetitive UV exposure - Molecular characterization of responses to UVA, UVB and SSR

status: Public on Apr 22 2010

city: Bethesda

first: Vincent

last: Hearing

state: MD

address: Bldg 37  Rm 2132

department: National Cancer Institute

institute: National Institutes of Health

summary: To test the hypothesis that different mechanisms and/or factors might be involved in physiological pigmentary responses of the skin to different types of UV, we used whole human genome microarrays and immunohistochemical analyses to characterize human skin in situ to examine how melanocyte-specific proteins and paracrine melanogenic factors are regulated by repetitive exposure to suberythemal doses of different types of UV (UVA, UVB or SSR).

overall_design: Six volunteers with skin type II-III were irradiated with SSR, UVA or UVB radiation for 2 weeks (5 times per week, 10 times total) after preliminary determination of their MEDs. Biopsies were taken 3 days after the last irradiation.

first: Wonseon

last: Choi


title: A Hierarchy of Self-Renewing Tumor-Initiating Cell Types in Glioblastoma

city: South San Francisco

first: Anthony

middle: Steve

last: Guerrero

address: 1 DNA Way

department: Bioinformatics

institute: Genentech

type: Genome binding/occupancy profiling by SNP array

type: Genome variation profiling by genome tiling array

summary:
The neural stem cell marker CD133 is reported to identify cells within glioblastoma (GBM) that can initiate neurosphere growth and tumor formation, however, instances of CD133- cells exhibiting similar properties have also been reported.  Here, we show that some PTEN-deficient GBM tumors produce a series of CD133+ and CD133- self-renewing tumor-initiating cell types and provide evidence that these cell types constitute a lineage hierarchy.  Our results show that the capacities for self-renewal and tumor initiation in GBM need not be restricted to a uniform population of stem-like cells, but can be shared by a lineage of self-renewing cell types expressing a range of markers of forebrain lineage.

Keywords: Expression and copy number analysis of glioblastomas and neurosphere forming derivative cell lines of same.

overall_design: DNA analysis and Expression profiling: DNA from patient tumor mincates was profiled for copy number changes on Affymetrix 500k chips and sequenced for mutations in exons 4-8 of p53 and exons 5&6 of PTEN.  For determination of amplification, samples with mean relative copy number estimates of >3 for SNPs residing within the locus were scored as amplified.  Copy number losses were determined using data from 30 SNPs within or immediately flanking the locus of interest.  Relative copy number losses that were statistically significant at the p<.001 level were scored as losses regardless of the magnitude of the alteration.  DNA from neurosphere lines was analyzed for copy number alterations by profiling on Agilent 244K arrays. Relative copy number estimates were determined using the GLAD segmentation algorithm.  For expression profiling, RNA was extracted as previously described (Phillips et al., 2006) and profiled on Agilent WHG (for patient samples) or WHG 4x44 chips (for neurosphere lines and grafts) according to the manufacturer's (Agilent technologies, Palo Alto CA)  protocol.


title: Mouse mammary epithelial cell subpopulations from pregnant and virgin mice

status: Public on Apr 10 2010

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: To study the effect of pregnancy on mouse mammary epithelial subpopulations, epthelial cells derived from virgin or pregnant (12.5 day pregnant) mice were isolated using fluorescence-activated cell sorting.  After elimination of haematopoietic and endothelial cells, two distinct epithelial subpopulations were sorted using antibodies against CD29 and CD24. Based on the immunohistochemical phenotype, and in vivo and in vitro functional assays, these subpopulations were identified as mammary stem cell enriched (CD29hiCD24+) and luminal (CD29loCD24+) respectively (ref: Shackleton et al, Nature 2006). Microarray profiling was used to compare gene expression profiles of the two subpopulations in 12.5 day pregnant and virgin mice.

overall_design: For each biological replicate, mammary gland from virgin or 12.5 day pregnant FVB/NJ mice were collected and digested to obtain a single cell suspension. CD45-CD31-TER119- cells were then sorted based on the expression of cell surface markers CD24 and CD29. There were 4 pools of pregant mice and 3 pools of virgin mice.

first: Di

last: Wu

first: Marie-Liesse

last: Asselin-Labat

first: Geoffrey

last: Lindeman

first: Jane

middle: E

last: Visvader


title: Mammary epithelial cell subpopulations from control and ovariectomized mice

summary: To study the effect of pregnancy on mouse mammary epithelial subpopulations, epthelial cells derived from control or ovariectomized adult mice were isolated using fluorescence-activated cell sorting. After elimination of haematopoietic and endothelial cells, two distinct epithelial subpopulations were sorted using antibodies against CD29 and CD24. Based on the immunohistochemical phenotype, and in vivo and in vitro functional assays, these subpopulations were identified as mammary stem cell enriched (CD29hiCD24+) and luminal (CD29loCD24+) respectively (ref: Shackleton et al, Nature 2006). Microarray profiling was used to compare gene expression profiles of the two subpopulations isolated from ovariectomized and control mice.

overall_design: For each of two biological replicates, 6 FVB/NJ mice were ovariectomized at 8 weeks of age. 4 weeks after ovariectomy (Ovx) mammary gland from control or Ovx animals were collected and digested to obtain a single cell suspension. CD45-CD31-TER119- cells were then sorted based on the expression of cell surface markers CD24 and CD29. Similarly for two pools of control mice. There were also 4 technical replicates, to make 12 BeadChips in total.


title: Screening of genes involved in chromosome segregation in meiosis I

status: Public on Mar 31 2010

city: Toyoake

first: Hiroshi

last: Kogo

state: Aichi

address: 1-98, Dengakugakubo, Kutsukake

department: ICMS

country: Japan

institute: Fujita Health University

summary: Prophase I of male meiosis involves dynamic chromosome segregation processes during early spermatogenesis, including synapsis, meiotic recombination, and cohesion. Genetic defects in genes participating in these processes consistently cause reproduction failure in mice. To identify candidate genes responsible for infertility in humans, we performed expression profiling of mouse spermatogenic cells undergoing meiotic prophase I.

overall_design: Cell fractions enriched in spermatogonia, leptotene/zygotene spermatocytes, or pachytene spermatocytes were separately isolated from mouse testes for RNA extraction. To minimize the contamination of other cell types, we fractionated the testicular cells undergoing the first round of spermatogenesis using Percoll gradient procedure.  The cell fractions were characterized by morphological analysis by phase contrast microscopy and Nomarski interference microscopy, and then expression of cell lineage- and spermatogenesis stage-specific genes were examined by RT-PCR. The most enriched fractions for spermatogonia (fraction2 from day8), leptotene/zygotene spermatocytes (fraction5 from day12), and pachytene spermatocytes (fraction8 from day15) were subjected to hybridization on Affymetrix microarrays.

first: Hiroe

last: Kowa

first: Kouji

last: Yamada

first: Hasbaira

last: Bolor

first: Makiko

last: Tsutsumi

first: Tamae

last: Ohye

first: Hidehito

last: Inagaki

first: Mariko

last: Taniguchi

first: Tatsushi

last: Toda

first: Hiroki

last: Kurahashi


title: Genome-wide analysis of USF1-associated differential gene expression in mouse liver

city: Los Angeles

first: Sulin

address: 675 Charles Young E. Dr,

department: Human Genetics

institute: UCLA

summary: Analysis of adenovirus-mediated USF1 overexpression in liver at gene expression level. Results provide important information of the response of mouse liver to USF1 overexpression, such as specific USF1-induced, suppressed, up- or down-regulated genes invovled in metabolism and immune responses.

overall_design: Total RNA isolated from whole mouse liver 5 days post tail vein injection of adenovirus carrying either hUSF1 cDNA or eGFP alone as control vector.

first: Thomas

last: Drake


title: Gene expression profiles of normal mouse mammary cell subpopulations FACS sorted based on expression of biomarkers

status: Public on Mar 21 2010

state: Victoria

address: 1G Royal Parade

department: Victorian Breast Cancer Research Consortium

institute: The Walter and Eliza Hall Institute of Medical Research

summary: To delineate epithelial subpopulations in mouse mammary tissue, hematopoietic and endothelial cells were depleted from freshly isolated cell suspensions derived from mammary glands using fluorescence-activated cell sorting. The resultant Lin- population was fractionated into four distinct subpopulations using antibodies against CD29, CD24 and CD61. Based on the immunohistochemical phenotype, and in vivo and in vitro functional assays, these subpopulations were identified as fibroblast-containing stromal (CD29loCD24-), mammary stem cell (MaSC)-enriched (CD29hiCD24+CD61+), luminal progenitor (CD29loCD24+CD61+),  and mature luminal (CD29loCD24+CD61-) cell subpopulations. Microarray profiling was used to derive gene expression signatures of these 4 subpopulations. The four mammary cell subpopulations were found to have distinct gene expression profiles.

overall_design: Four mammary cell subpopulations from 3-5 pooled mouse tissues were analysed. MS is for the MaSC-enriched cell subpopulation. LP is for the Luminal Progenitor subpopulation. ML is for the Mature Luminal subpopulation.

first: Gordon

first: Elgene

last: Lim


title: Prediction of progression-free survival in patients with advanced-stage serous ovarian cancer

status: Public on Mar 22 2010

city: Niigata

first: Kosuke

last: Yoshihara

address: 1-757 Asahimachi-dori

department: Obstetrics and Gynecology

institute: Niigata University

summary:
To identify and evaluate the prognostic ability of progression-free survival-related profile for advanced-stage ovarian cancer, advanced-stage serous ovarian cancer tissues from 110 patients who received primary surgery and a platinum/taxane-based chemotherapy were profiled using oligonucleotide microarrays of more than 40,000 transcripts. We first selected 88 genes by a univariate Cox proportional hazard analysis (p<0.01) and next optimized regression coefficients by ridge regression model using 10-fold cross-validation. The prognostic index was independently associated with PFS time compared to other clinical factors in
multivariate analysis [hazard ratio (HR), 3.72; 95% confidence interval (CI), 2.66–5.43; p,0.0001]. In an external dataset,
multivariate analysis revealed that this prognostic index was significantly correlated with PFS time (HR, 1.54; 95% CI, 1.20–1.98; p = 0.0008). Furthermore, the correlation between the prognostic index and overall survival time was confirmed in the two independent external datasets (log rank test, p = 0.0010 and 0.0008).  In multivariable analysis, our prognostic index was independently associated with progression-free survival times compared to other clinical factors (p<0.001). Furthermore, the prognostic ability of our prognostic index was validated in external, publicly available dataset (n = 87), and was proved in multivariate analysis (p = 0.0032). These results suggest that disease progression or recurrence of advanced-stage serous ovarian cancer can be predicted by gene expression profile. The prognostic ability of our index based on the 88-gene expression profile in ridge regression Cox hazard model was shown to be independent of other clinical factors in predicting cancer prognosis across two distinct datasets. Further study will be necessary to improve predictive accuracy of the prognostic index toward clinical application for evaluation of the risk of recurrence in patients with advanced-stage serous ovarian cancer.

overall_design: One hundred ten patients who were diagnosed as advanced-stage serous ovarian cancer were recruited in this study.

first: Atsushi

last: Tajima

first: Tetsuro

last: Yahata

first: Tadashi

last: Yamamoto

first: Shoji

last: Kodama

first: Hiroyuki

last: Fujiwara

first: Mitsuaki

last: Suzuki

first: Yoshitaka

last: Onishi

first: Masayuki

last: Hatae

first: Kazunobu

last: Sueyoshi

first: Hisaya

first: Yoshiki

last: Kudo

first: Kohei

last: Kotera

first: Hideaki

last: Masuzaki

first: Hironori

last: Tashiro

first: Hidetaka

last: Katabuchi

first: Ituro

last: Inoue

first: Kenichi

last: Tanaka


title: Gene expression profiling of CD45+/Sca1+ cells isolated from the bone marrow and the muscle

status: Public on Apr 06 2010

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

institute: Centre for Regenerative Medicine

summary:
The BM-derived CD45+/Sca1+ cells are haematopoietic stem/progenitor cells that have the ability to circulate and migrate and engraft to the muscle tissue, and therefore they are of particular interest. Notably, these cells retain their haematopoietic potential, as revealed both by in vitro and in vivo assays; but they also acquire myogenic potential, as shown by their ability to participate in muscle regeneration. Whether, this latter remarkable ability is the result of the reprogramming of the BM-CD45+/Sca1+ cells and the activation of a myogenic molecular program within these cells, remains controversial. This study aims to clarify this aspect of the process, investigating the role of the muscle microenviroment and key myogenic transcription factors.

Keywords: CD45+/Sca1+ cells, BM, muscle

overall_design: CD45+/Sca1+ cells isolated from the BM or the muscle were processed fresh and their RNA was extracted. Moreover, CD45+/Sca1+ cells isolated from the muscle of BM transplanted or untransplanted mice after injury with Cardiotoxin were processed fresh and their RNA was extracted.

first: Alexandros

last: Xynos

first: Paola

last: Corbella

first: Nathalie

last: Belmonte

first: Ahmed

last: Mansouri

first: Roberta

last: Zini

last: Manfradini

first: Giuliana

last: Ferrari


title: Expression of HCT116 cells transfected with CD44 siRNAs relative to that of HCT116 cells transfected with a control siRNA

status: Public on Mar 19 2010

city: Tokyo

first: Osamu

last: Nagano

state: DDS PhD

address: ３５　Shinanomachi

department: Institute for Advanced Medical Research

institute: Keio University School of Medicine

summary: To examine whether depletion of CD44 might affect antioxidant gene expression in cancer cells, HCT116 cells were transfected with CD44 or control siRNAs and subjected to cDNA microarray analysis. Although the CD44 siRNA was found to deplete the cells of CD44 mRNA, the expression of antioxidant genes was largely unaffected.

overall_design: HCT116 cells were transfected with CD44 or control siRNAs and subjected to cDNA microarray analysis. Two replicates per siRNA.

first: T

last: Ishimoto

first: O

first: H

last: Saya


title: Transcriptome analysis of myelid cell types (normal and leukemic)

city: Regensburg

first: Michael

last: Rehli

address: F.-J.-Strauss-Allee 11

department: Internal Med III

institute: University Hospital Regensburg

summary:
Transcriptome analysis of freshly sorted human CD34+ hematopoietic progenitor cells, human CD14+ peripheral blood monocytes and the human cell line U937

Keywords: one-color based gene expression

overall_design: Cells used for this study included freshly sorted human CD34+ hematopoietic progenitor cells from two independent healthy male donors, human CD14+ peripheral blood monocytes from three independent healthy male donors and the human cell line U937. Each sample was analysed seperately.

first: Maja

last: Klug

first: Claudia

last: Gebhard


title: Expression profiling of nasopharyngeal carcinoma cell lines

status: Public on Mar 09 2010

city: Zhunan Miaoli County

first: Chia

middle: Huei

last: Lee

address: 35, Keyan Rd.

department: National Institute of Cancer Research

country: Taiwan

institute: Taiwan National Health Research Institute

summary:
To identify the deregulated genes which may involved in the carcinogenesis of nasopharyngeal carcinoma (NPC).
To identify potential tumor suppressor genes / oncogenes of NPC, we have employed whole genome microarray expression profiling as a discovery platform to analyze two NPC cell lines, TW01 and HONE1. For the purpose to filter out differential genes may not related to carcinogenesis of NPC, a gene expression database for premalignant nasopharyngeal epithelial cells was obtained from NP460hTert cells, and we used the commercial universal human RNA (stratagene) as common reference for all microarray experiments. A total of 1272 genes were commonly up-regulated (fold change > 2)  and 1810 genes were commonly down-regulated (fold change < 0.5) in TW01 and HONE1 cell lines, whereas not deregulated in NP460hTert cells.

overall_design: Four samples including two NPC cell lines (TW01 and HONE1), an immortalized premalignant epithelial cell line NP460hTert, and the commercial universal human RNA (common reference) were analyzed. Differential genes found in NP460hTert were not considered as NPC-related.  Biological replicate experiments were performed for each sample.

first: C

last: Chen


title: Nasopharyngeal carcinoma cell lines TW01 and HONE1: transcriptomic and genomic analyses

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

overall_design: Refer to individual Series


title: Gene expression profiling of a mouse model of dilated cardiomyopathy

city: Detroit

first: Margot

last: LaPointe

address: 2799 W. Grand Blvd.

department: Internal Medicine

institute: Henry Ford Hospital

summary:
Analysis of the effects of aging on the development of dilated cardiomyopathy by characterizing both changes in ejection fraction (EF) and gene expression profile in 3 groups of male mice: Control (Cont or WT, n=11)  and transgenic (Tg or KO) mice with either high EF (KO-H or Tg-H, n=7) or low EF (KO-L or Tg-L, n=6).
We previously produced a line of transgenic mice (Tg) on a mixed genetic background where cardiac-specific overexpression of Cre recombinase reduced expression of the EP4 receptor gene. There were no obvious phenotypes in 10-12-week-old male Tg mice. To determine if a cardiac phenotype developed in aged mice, we assessed cardiac structure and function by echocardiography, histology and gene expression in 23-33-week-old male Tg and littermates (Cont). After echocardiography, hearts were removed to assess hypertrophy (MCSA), fibrosis (ICF) and macrophage infiltration by histological methods and for extraction of total RNA and protein. Cont mice had a normal EF of 80±0.6% (n=70), whereas Tg mice had a lower EF (60±2.7%, n=55, p<0.001) coupled with left ventricular dilatation. The distribution of EFs in the Tg mice was large, ranging from normal to below 30%.  MCSA and infiltrating macrophages were not different between groups, but ICF increased by 35% in Tg mice. Cre protein levels in heart lysates did not correlate with either age or EF. In contrast to male Tg mice, female Tg mice had no cardiac dysfunction assessed by echocardiography from 12 to 28 weeks of age. To understand gene expression differences between Cont and Tg mice, whole genome gene expression profiling (Illumina BeadChips) on hearts of 30-32 week old male mice was done. Data indicated that 595 genes were overexpressed in the Tg hearts, 156 of which changed more than 2-fold, including genes involved in remodeling, inflammation, and oxidative stress. 512 genes were downregulated in the Cont hearts, 79 of which changed more than 2-fold, including genes involved with calcium handling, K+ channels, and fatty acid transport and metabolism. In conclusion, Cre overexpression and EP4 knock down in cardiac myocytes in aged male but not female Tg mice are in part associated with increased fibrosis, reduced EF and dilated cardiomyopathy; however, Cre protein itself does not seem to be responsible for the cardiomyopathy. The absence of cardiac dysfunction in female mice suggests a sexual dimorphism in the phenotype.
Creation of the cardiac-myocyte specific EP4 KO mouse and littermate controls was described in JY Qian et al, Hypertension 2008: 51(pt 2):560-566.

overall_design: Total RNA extracted from left ventricle of control (Cont or WT, n =11) and cardiac-specific EP4 KO (Tg or KO, n=13) male mice (mean age 31 weeks).

first: James

last: Yang


title: Identification and analysis of miRNA target genes in a cell system

status: Public on Mar 12 2010

city: New York

first: Thomas

last: Templin

state: NY

address: 630 West 168th Street

institute: Columbia University Medical Center

summary: MicroRNAs are instructions used by the genetic programs of a cell to fine-regulate protein expression levels. In order to gain insight into the full spectrum of miRNA regulation in a particular cellular context, we have exploited the idea that doubling the quantity of the endogenous miRNAs by transfection would enhance downregulation of the normally targeted transcripts. To this end, we isolated the small RNA fraction from cells in culture and transfected it into an identical culture in an amount corresponding to that of the endogenous miRNAs. A comparative gene expression analysis between transfected and mock-transfected cells revealed a large number of modestly downregulated genes. In silico analysis using TargetScan 5 revealed that a very high number of the expressed genes are predicted targets of the endogenous miRNAs, which we identified by deep-sequencing the small RNA fraction. Network analysis of the downregulated genes showed that miRNAs are involved in the simultaneous regulation of many pathways by targeting key molecules that interact with multiple pathways, suggesting a role of miRNAs in the synchronization of the activities of different pathways. Interestingly, we found a very high percentage of the genes regulated by miRNAs to be related to genetic disorders. This suggests that miRNAs might play a key role in maintaining homeostasis in processes that result in disease states when disregulated. Such a crucial role for miRNA regulation further underlines its importance for cell and organism survival. These results also confirm the important experimental value of our methodology as a high-throughput tool for the identification of genes endogenously regulated by miRNAs.

overall_design: miRNA-induced gene expression was measured by doubling cellular miRNA content by transfecting the endogenous small RNA fraction (< 200 bp) into cells of the same cell type (AG01522 normal human fibroblasts). Total RNA was isolated for gene expression analysis 38 h after transfection, when the cells were actively cycling. Five biological repeats were used for the transfected and mock-transfected cells.

first: Sally

last: Amundson

first: Shanaz

last: Ghandhi

first: Guangming

last: Zhou

first: Lubomir

middle: B

last: Smilenov


title: Genome-wide Identification of Targets & Function of Individual MicroRNAs in Mouse Embryonic Stem Cells

status: Public on Feb 27 2010

city: Cambridge

first: Sophie

middle: Alexandra

last: Hanina

state: Cambridgeshire

address: Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: University of Cambridge

summary: Mouse Embryonic Stem (ES) cells express a unique set of microRNAs (miRNAs), the miR-290-295 cluster. To elucidate the role of these miRNAs and how they integrate into the ES cell regulatory network requires identification of their direct regulatory targets. The difficulty, however, arises from the limited complementarity of metazoan miRNAs to their targets, with the interaction requiring as few as six nucleotides of the miRNA seed sequence. To identify miR-294 targets, we used Dicer1-null ES cells, which lack all endogenous mature miRNAs, and introduced just miR-294 into these ES cells. We then employed two approaches to discover miR-294 targets in mouse ES cells: transcriptome profiling using microarrays, and a biochemical approach to isolate mRNA targets associated with the Argonaute2 (Ago2) protein of the RISC (RNA Induced Silencing Complex) effector, followed by RNA-Sequencing. In the absence of Dicer1, the RISC complexes are largely devoid of mature miRNAs, and should therefore contain only transfected miR-294 and its base-paired targets. Our data suggest that miR-294 may promote pluripotency by regulating a subset of c-Myc target genes, and upregulating pluripotency-associated genes such as Lin28.

overall_design: Cells were co-transfected (Amaxa nucleofection) with 300pmol of microRNA and 1 microgram of pEGFP-1, which served as a control for transfection efficiency. GFP-positive cells were sorted 24 hours after transfection. We profiled the transcriptome of Dicer1-null mouse ES cells transfected with miR-294 or a control microRNA (cel-239b), using the Illumina WG-6 v2.0 platform.

first: William

last: Mifsud

first: M

last: Surani


title: HuR differentially regulates unique subsets of mRNAs in estrogen receptor negative and positive breast cancer

status: Public on Feb 15 2010

city: North Chicago

first: J

middle: Wade

last: Davis

state: IL

address: 1 N Waukegan Rd

institute: AbbVie

summary: Analysis of RNA immunoprecipitation of HuR, a RNA binding protein (RBP), in breast cancer cell lines. This approach, utilizing RNA immunoprecipitation hybridized to microarray (RIP-Chip), provides global identification of putative endogenous mRNA targets of different RBPs.  HuR is an RBP that binds to the AU-rich (ARE) regions of labile mRNAs, such as proto-oncogenes, facilitating their translation into protein. HuR has been shown to play a role in cancer progression and elevated levels of cytoplasmic HuR directly correlate with increased invasiveness and poor prognosis for many cancers, including those of the breast.  We used HuR RIP-Chip as a comprehensive and systematic method to survey breast cancer target genes in both MCF-7 (estrogen receptor positive, ER+) and MDA-MB-231 (estrogen receptor negative, ER-) breast cancer cell lines. We identified unique subsets of HuR associated mRNAs found individually or in both cell types. Two novel HuR targets, CD-9 and CALM-2, were identified and validated by quantitative RT-PCR and biotin pulldown analysis. Our findings reveal that the differential regulation of these two cancer-related genes by HuR was contingent upon the cellular environment.

overall_design: RNA immunoprecipitation of the HuR RNA binding protein by 3A2 antibody and IgG (control) from two human breast cancer cell lines, MCF-7 and MDA-MB-231 .

first: Ulus

last: Atasoy

first: Robert

last: Calaluce

first: Matt

last: Grubin

first: Joseph

last: Magee

first: Yuki

last: Kuwano

last: Gorospe


title: Effect of glucocorticoid chemical structure and receptor potency on human trabecular meshwork cells

city: Irvine

first: Alissar

last: Nehme

address: 2525 Dupont Drive

institute: Allergan Inc.

summary: Glucocorticoids with different chemical structures but similar glucocorticoid receptor potency regulate subsets of common and unique genes in human trabecular meshwork cells. Gene expression changes of human trabecular meshwork cells, TM 86 and TM 93, due to treatment with dexamethasone (Dex), fluocinolone acetonide (FA), and triamcinolone acetonide (TA).

overall_design: Agilent Human Whole Genome Expression oligonucleotide microarray. Changes of genome-wide mRNA transcription levels were determined by treating cultured TM 86 and TM 93 cells with 1 uM of either Dex, FA, and TA for 24 hours versus DMSO vehicle controls. This was followed by total RNA extraction, labeling of RNA with Cy3, and hybridization of Cy3-labeled cRNA to the Agilent Human Whole Genome microarray for 17 hours. The microarray experiment was repeated three times.

first: Edward

last: Lobenhofer


title: Minicircle-derived iPS cells - Agilent Data

status: Public on Feb 01 2010

city: Stanford

first: Kitchener

middle: D.

last: Wilson

address: S140 Grant Bldg

institute: Stanford University

summary: Owing to the risk of insertional mutagenesis, viral transduction has been increasingly replaced by nonviral methods to generate induced pluripotent stem (iPS) cells. We report the use of ‘minicircle’ DNA, a vector type that is free of bacterial DNA and capable of high expression in cells. Here we use a single minicircle vector to generate transgene-free iPSCs from adult human adipose stem cells.  (Note: Our Nature Methods publication included analysis of array data from GSM374067 and GSM374068 in conjunction with this series).

overall_design: Total RNA from H7 hESCs (n = 2) and minicircle-derived human iPS cells (n = 2 subclones from adipose tissue of two individual patients) was hybridized to four Agilent Whole Human Genome microarrays. A pooled reference sample was used that contained total RNA from H9 hESCs, H9 embryoid bodies, cardiac and endothelial cells derived from H9 hESCs, cardiac fetal tissue, and human umbilical vein endothelial cells (HUVECs).

first: Fangjun

last: Jia


title: The transcriptional network for mesenchymal transformation of brain tumours

status: Public on Feb 12 2010

first: Mariano

middle: Javier

last: Alvarez

address: 1130 St. Nicholas ave.

department: Systems Biology

institute: Columbia University

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Genome-wide analysis of gene expression profiles in ITNK

status: Public on Mar 23 2010

city: Frederick

first: Jack

last: Chen

address: SAIC-Frederick Miller Dr

institute: NIH

summary: Analysis of gene expression profiles in Induced T-to-Natural Killer (ITNK), compared to DN3 parental T cells and IL-2-expanded NK cells (LAK). The hypothesis tested in the present study was that gene expression profiles of ITNK that were derived from DN3 T cells after deletion of Bcl11b were more similar to LAK, rather than DN3 T cells. Results provide important information of the ITNKs, such as canditate genes regulated by Bcl11b, up-regulated important genes expressed in NK cells, and down-regulated T cell genes.

overall_design: Total RNA obtained from DN3-derived ITNKs in vitro compared to DN3 parental T cells and LAKs.

first: Pentao

last: Liu

first: Peng

last: Li

first: Xiongfong


title: Gene Expression Profile in kidneys from Cldn16 +/+, +/-, -/- female mice

city: Berlin

first: Constanze

last: Will

address: Hessische Str. 3 - 4

department: CCR

institute: Charité

summary: Claudin-16 deficiency leads to renal salt wasting in humans and mice. Analysis of renal gene expression in Claudin-16 deficient mice, compared to heterozygous and wild type littermates, was performed to gain insights into molecular mechanisms compensating salt loss. Our results indicate the upregulation of known and putative genes for renal transcellular transporters. Furthermore, we could identify a transcript so far not associated with renal salt metabolism, which will provide a first link to a human electrolyte disorder disease.

overall_design: Female Cldn16 +/+, +/-, -/- mice were sacrificed at the age of 8 weeks for kidney dissection, removal of kidney poles and preparation of total RNA for expression analysis.

first: Dominik

last: Müller

first: Marchel

last: Stuiver


title: Profiling of genes deregulated in CD4+ T cells expressing constitutively full-length or first-exon Tat protein of HIV-1

status: Public on Jan 29 2010

city: Madrid

first: Sergio

last: Callejas

address: Melchor Fernández Almagro, 3

department: Genomics Unit

institute: Centro Nacional de Investigaciones Cardiovasculares (CNIC)

summary:
Background: The role of HIV-1 Tat protein in gene expression deregulation and functional biology of CD4+ T lymphocytes was analyzed, as well as the function of Tat second exon for the complete activity of this protein. Gene expression deregulation profiles of triplicate samples from Jurkat cells expressing intracellular full-length Tat (1-101aa) in comparison with a truncated form lacking the second exon (1-72aa) was evaluated by bioinformatics using whole human genome microarrays. Results: More than 1000 genes were deregulated in Jurkat Tat101 cells, whereas less than 300 genes were deregulated in Jurkat Tat72 cells (q-value<5%; fold change >2 or <-2). Ontological analysis indicated that several functions were impaired mainly in Jurkat Tat101 as cellular movement, growth and proliferation, cell-to-cell signaling, molecular transport, cell death, cell morphology, and T-cell activation. In accordance, biological and functional analyses proved that Tat101 intracellular expression induced changes in cell size and complexity, cytoskeletal rearrangements and chemotaxis impairment, higher resistance to apoptosis, decrease in the surface expression of adhesion molecules and receptors, and higher basal transcriptional activation. These alterations were attenuated or absent in Jurkat Tat72 cells. Furthermore, computational modeling showed that the absence of second exon severely reduced the C-terminus of Tat72 with notable decrease of positive charging. Conclusion: Full-length Tat intracellular expression induced dramatic structural changes and impaired essential functions in CD4+ T cells, whereas Tat72 was less aggressive. Consequently, although Tat first exon is transcriptionally autonomous, second exon should be indispensable for triggering HIV-1 pathogenic events induced by Tat protein.

Keywords: Microarray Genome-wide expression analysis. Comparison of genetically modified cells

overall_design: Total RNA was obtained from Jurkat cell lines that express constitutively intracellular HIV-1 Tat101 or Tat72. Gene expression profiles were obtained for each sample and compared with a parental Jurkat cell line that does not express Tat.

first: MR

last: López-Huertas

first: S

first: D

last: Abia

first: A

last: Dopazo

first: J

last: Alcamí

first: M

last: Coiras


title: Transcriptional Characterization of Human Embryonic Stem Cell-Derived Endothelial Cells

status: Public on Jan 28 2010

first: Kitchener

summary: Differentiation of human embryonic stem cells into endothelial cells (hESC-ECs) has the potential to provide an unlimited source of cells for novel transplantation therapies of ischemic diseases by supporting angiogenesis and vasculogenesis. In this study, we developed an extracellular matrix culture system for increasing endothelial differentiation and free from contaminating animal cells. We investigated the transcriptional changes that occur during endothelial differentiation of hESCs using whole genome microarray, and compared to human umbilical vein endothelial cells (HUVECs). (Note: Please see our publication, PMID 20046878, which includes analysis of array data from GSM348001-GSM348004 in conjunction with this series).

overall_design: Total RNA from Day 12 Embryoid Bodies that were differentiated from H9 human embryonic stem cells (EB, n = 4), endothelial cells differentiated from H9 human embryonic stem cells  (hESC-EC, n = 4), and human umbilical vein endothelial cells (HUVECs, n = 4) was hybridized to four Agilent Whole Human Genome microarrays. A pooled reference sample was used that contained total RNA from H9 hESCs, H9 embryoid bodies, cardiac and endothelial cells derived from H9 hESCs, cardiac fetal tissue, and human umbilical vein endothelial cells (HUVECs).

first: Zongjin


title: Gene expression profile of myeloma cells treated with IGF-1

status: Public on Feb 28 2010

city: Leuven

first: Lieven

last: Thorrez

address: Kasteelpark Arenberg 10

country: Belgium

institute: Katholieke Universiteit Leuven

summary: Objective of this study was to find changes in gene expression of mouse multiple myeloma cells upon treatment with IGF-1

overall_design: Murine multiple myeloma cells were incubated in serum free medium for 12 hours in the absence (3 replicates) or presence (3 replicates) of 100 ng/ml IGF-1

first: Elke

last: De Bruyne

first: Karin

last: Vanderkerken

first: Leentje

last: Van Lommel

first: Frans

last: Schuit


title: Effects of sanguinarine on murine myocyte gene expression

city: Houston

first: David

middle: S

last: Loose

state: TX

address: 6431 Fannin St, MSB 4.130

department: Integrative Biology & Pharm

institute: University of Texas

summary:
Sanguinarine (13-methyl[1,3]benzodioxolo[5,6-c]-1.3-dioxolo[4,5-i]phenanthridinium) is derived from the root of Sanguinaria canadensis L. (blood root), Chelidonium majus L. (Greater Celandine) and other poppy-fumaria species.  Sanguinarine belongs to the benzophenanthridine alkaloid group, which are biosynthesized from phenylalanine in plants of the papaveraceae.  This alkaloid has been reported to display a wide spectrum of biological effects, such as antifungal, antimicrobial, analgesic and moreover, anti-cancer properties via the induction of cell death.

Utilizing dose-response studies with sanguinarine, we have shown that at two different concentrations sanguinarine induced over 95% apoptosis and oncosis respectively, in several cancer cell lines Also, the fact that oncosis and apoptosis are both induced in the same cell line under similar conditions and time points (with the sole exception being the concentration used) makes it a highly attractive model, because it facilitates easy and accurate comparison of both forms of cell death. These qualities make sanguinarine an ideal tool to study and compare oncosis with apoptosis. We are not aware of any other cell model system used to study oncosis that has all the above advantages.The objective of this study was to provide insight into the pathogenetic mechanisms of oncosis and apoptosis  in cardiac myocytes in ischemic/reperfusion injury so that appropriate interventions could be designed to minimize injury and preserve myocardial function. We have shown here that primary cardiomyocytes, when exposed to sanguinarine at concentrations of 1.5 µg/ml (low dose) and 25 µg/ml (high dose) for 1 hour, displayed the classic biphasic pattern of apoptosis and oncosis. Using Illumina whole-genome expression microarrays, we have identified over  488 probes that were differentially expressed at p < 0.001 in cardiac myocytes between  the low dose and high dose of sanguinarine after 1 hour of treatment; 78 of these changed more than 2-fold. Thus far, oncosis/necrosis has been thought of as uncontrolled and accidental, and lacking the features of apoptosis and autophagy. However, our findings and that of others reported in the literature indicate that this occurrence is not accidental but a tightly regulated physiological process. To our knowledge, this is the first report to present a model for the comparative study of apoptosis vs. oncosis in primary cardiomyocytes.

overall_design: Cultured murine myocytes were cultured under standard conditions and treated for 1 hour with either vehicle (EtOH), 1.5 ug/ml, or 25 ug/ml sanguinarine. 3 separate experiments were done for a total of 7 biological replicates for control, 4 for 1.5 ug/ml dose and 8 for the 25 ug/ml dose. Total RNA was extracted and processed using standard Illumina protocols.

first: Priya

last: Weerarsinghe


title: RNA Expression Profiling of Lung Tissue Identifies Mutually Distinct Molecular Signatures in PAH and PH Secondary to IPF

status: Public on Jan 22 2010

city: Iowa City

first: Ferhaan

last: Ahmad

state: IA

address: 100 Newton Road, 1191D ML

institute: University of Iowa

summary:
Idiopathic pulmonary arterial hypertension (PAH) is a life-threatening condition characterized by pulmonary arteriolar remodeling, and is frequently associated with right heart failure. This study identifies significant novel biological changes in eight genes and several genetic pathways, that were likely to contribute to the pathogenesis of PAH. We also demonstrate that PAH and PH secondary to idiopathic pulmonary fibrosis (IPF) are characterized by distinct gene expression signatures, implying distinct pathophysiological mechanisms.
Keywords: disease versus control

Keywords: Expression profiling by array

overall_design:
Fresh frozen lung tissue specimens from PAH subjects (n=18), IPF subjects with secondary PH (n=8), and normal controls (n=13) were obtained from the University of Pittsburgh Health Sciences Tissue Bank following approval by the University of Pittsburgh Institutional Review Board.
Total RNA was isolated from lung tissue using Trizol (Invitrogen) and purified using the RNeasy Mini kit (Qiagen). RNA quantity and quality was assessed using Agilent Nanodrop and Agilent 2100 Bioanalyzer, respectively. 500 ng of total RNA meeting was Cy3 labeled using the Agilent Low RNA Input Linear Amplification Kit PLUS (One-Color). After purification and fragmentation, aliquots of each sample were hybridized to an Agilent Whole Human Genome 4 X 44K microarray, sequentially washed, and scanned on an Agilent DNA microarray scanner.

first: Revathi

last: Rajkumar

first: Kazuhisa

last: Konishi

last: Ishizawar

first: Andrew

last: Wiechert

first: Thomas

last: Richards

first: Naftali

last: Kaminski


title: Genome-wide analysis of gene expression during differentiation in C2C12 cells

status: Public on Jan 27 2010

city: Seatttle

first: Yi

last: Cao

state: WA

address: 1100 Fairview Ave. N

department: Human Biology

institute: Fred Hutchinson CRC

summary: Investigate the genome-wide gene expression profiles of 50% and 95% confluent C2C12 myoblasts and C2C12 myotubes differentiated for 24 and 48 hours.

overall_design: Triplicate total RNA samples were obtained from 50% and 95% confluent C2C12 myoblasts, and C2C12 myotubes differentiated for 24 and 48 hours.

first: Zizhen

last: Yao


title: Global Gene Expression Analysis Reveals Differences in Cellular Responses to Hydroxyl- and Superoxide Anion Radical-...

status: Public on Jan 12 2010

city: Maastricht

first: Jacob

middle: Jan

last: Briede

address: PO Box 616

department: Health Risk Analysis and Toxicology

country: Netherlands

institute: Maastricht University

summary:
Global Gene Expression Analysis Reveals Differences in Cellular Responses to Hydroxyl- and Superoxide-induced Oxidative Stress in Caco-2 Cells.
Reactive oxygen species-induced oxidative stress in the colon is involved in inflammatory bowel diseases and is suggested to be associated with colorectal cancer risk. However, our insight in molecular responses to different oxygen radicals is still fragmentary. Therefore, we studied global gene expression by an extensive time serie (0.08, 0.25, 0.5, 1, 2, 4, 8, 16, or 24 hours ) analyses in human colon cancer (Caco-2) cells after exposure to H2O2 or menadione, leading to the formation of HO. or O2.- radicals respectively. Next to gene expression, induction of pathways and correlations with related phenotypic markers (oxidative DNA damage, cell cycle arrest) was investigated. Gene expression analysis resulted in 1404 differentially expressed genes upon H2O2 challenge and 979 genes after menadione treatment. Time-dependent co-regulated genes immediately showed a pulse-like response to HO. formation while the O2.--induced expression is not restored over 24 hours. Pathway analyses demonstrated that the difference in the modulation of gene expression is also reflected in regulation of pathways by HO. and O2.-: H2O2 immediately influences pathways involved in the immune function, while menadione constantly regulated cell cycle-related pathways. Altogether, this study offers a novel and detailed insight in differential time-dependent oxidative stress response, but most importantly, shows that effects of HO. and O2.- can also be discriminated regarding their modulation of particular carcinogenesis-related mechanisms.

Keywords: Comparison of genome-wide gene expression between different time points for H2O2 and menadione.

overall_design: The study investigated differential gene expression in Caco-2 cell line mRNA at 9 timepoints (t=0.08, 0.25, 0.5, 1, 2, 4, 8, 16, or 24h)  within 24 hours of exposure to H2O2 or manadione . Two biological replicates per time point. One compound per array, hybridized against time-matched control. Dye-swap include for all biological replicates.

middle: J

last: Briedé

first: Joost

middle: M

last: van Delft

first: Jos

last: Kleinjans

first: Theo

last: de Kok


title: Genes regulated by miR-181c

status: Public on Jan 20 2010

city: Yushima, Bunkyo-ku

first: Yutaka

last: Hashimoto

state: Tokyo

department: Molecular Oncology

institute: Tokyo Medical and Dental University Graduate School

summary:
We found frequently down-regulation of microRNA-181c in human gastric cancer cases. To identify the potential target of miR-181c, we introduced miR-181c into a gastric cancer cell line KATO-III　and analyzed significant changes of gene expression which was induced after introducing miR-181c.
Keywords: dose response

overall_design: KATO-III cells were transfected with Precursor Molecule mimicking miR-181c (Ambion) or mock.  Precursor Molecules were gave a final concentration of 100 nmol/L by using MicroPorator MP-100 (Digital BioTechnology, Seoul, Korea), according to the manufacturer’s instructions. At 24 h after transfection, cells were harvested for cDNA microarray analysis.

first: Yoshimitsu

last: Akiyama

first: Takeshi

last: Otsubo

first: Shu

last: Shimada

first: Yasuhito

last: Yuasa


title: Novel IL-21 signaling pathway upregulates c-Myc and induces apoptosis of diffuse large B-cell lymphomas

status: Public on Jan 01 2010

city: Miami

first: Kristopher

middle: A

last: Sarosiek

state: FL

address: 1580 NW 10th Ave

institute: University of Miami

summary: Diffuse large B cell lymphoma is a heterogenous malignancy that is diagnosed in over 60,000 patients each year.  Interleukin-21 has been shown to induce apoptosis in certain B cells originating from mice. Diffuse large B cell lyphomas express the Interleukin-21 Receptor yet the effects of Interleukin-21 on this malignancy are uknown.  Identified genes responsive to IL-21 treatment in diffuse large B cell lymphoma.

overall_design: RC-K8 is a diffuse large B cell lymphoma cell line that responds to IL-21 stimulation with apoptosis.  By chronically treating RC-K8 cells with IL-21 with increasing doses for 10 weeks we were able to generate a resistant RC-K8 cell line that will be referred to as RC-K8-R.  Both RC-K8 and RC-K8-R cells were treated with IL-21 at 100ng/mL.  After 6 hours of treatment cells were lysed and total mRNA was collected.  Arrays were performed on Agilent Oligo microarrays.  We used microarrays to detail the changes in gene expression upon Interleukin-21 treatment in diffuse large B cell lymphoma cell lines and observed distinct up-regulated and down-regulated genes.  Replicates are not included.  Human Reference RNA was used as reference.

first: Raquel

last: Malumbres

first: Hovav

last: Nechushtan

last: Gentles

first: Eli

last: Avisar

first: Izidore

last: Lossos


title: Characterization of the mid-foregut transcriptome identifies genes regulated during lung bud induction.

status: Public on Jan 14 2010

city: Boston

first: Maria

middle: Isabel

last: Ramirez

state: MA

address: 72 E. Concord St. E603

department: Medicine

institute: Boston University School of Medicine

summary: To identify genes expressed during initiation of lung organogenesis, we generated transcriptional profiles of the prospective lung region of the mouse foregut (mid-foregut) microdissected from embryos at three developmental stages between embryonic day 8.5 (E8.5) and E9.5. This period spans from lung specification of foregut cells to the emergence of the primary lung buds. We identified a number of known and novel genes that are temporally regulated as the lung bud forms. Genes that regulate transcription, including DNA binding factors, co-factors, and chromatin remodeling genes, are the main functional groups that change during lung bud formation. Members of key developmental transcription and growth factor families, not previously described to participate in lung organogenesis, are expressed in the mid-foregut during lung bud induction. These studies also show early expression in the mid-foregut of genes that participate in later stages of lung development. This characterization of the mid-foregut transcriptome provides new insights into molecular events leading to lung organogenesis.

overall_design: Three samples (developmental stages), three biological replicates (5-10 pooled mid-foreguts)

first: Guetchyn

last: Millien

first: Jennifer

last: Beane

first: Marc

last: Lenburg

first: Po-Nien

last: Tsao

first: Jining

last: Lu

first: Avrum

last: Spira

middle: I


title: LNCaP prostate cancer cell line spheres (S) vs. adherent (A)

status: Public on Dec 31 2009

middle: Ana

last: Duhagon

address: 1050 Boyles St.

department: Laboratory of Cancer Prevention

institute: NCI-Frederick

summary: Transcriptional profile of LNCaP spheres in SCM-1% KO (stem-like cells) vs adherent cultures in RPMI-1640-10% FBS (differentiated-like cells)

overall_design: Two-condition experiment, S vs. A cells. Biological replicates: 3 sphere replicates, 3 adherent replicates.

first: M

last: Duhagon Serrat

first: J

middle: R

last: Sotelo-Silveira


title: mRNA expression in islets isolated from wild type and SHPKO mice fed chow or western diet

status: Public on Feb 24 2010

city: Rootstown

first: Yoonkwang

last: Lee

address: 4209 State Route 44

department: Integrative Medical Sciences

institute: Northeast Ohio Medical University

summary: SHP (small heterodimer partner; NR0B2) belongs to the nuclear hormone receptor superfamily, which regulates numerous developmental and metabolic cellular functions. To study physiological function of SHP, we generated congenic SHP-/- mice on C57Bl/6 background. When the congenic SHP-/- mice were challenged with a western diet (high fat, hgih sucrose, high cholesterol) for 20 weeks, they were resistant to diet induced obesity but severely glucose intolerant compared to wild type control mice. However, their overall peripheral tissue insulin sensitivity was normal when assessed by insulin tolerance test. Next, we examined the glucose stimulated insulin secretion (GSIS) in isolated islets from these animals. Islets from SHP-/- mice showed strongly impaired GSIS especially fed the western diet, which is believed to be a major factor causing the whole body glucose intolerance in SHP-/- mice. Therefore, we explored gene expression in islets using illumina beadchip array to understand mechanisms underneath the impaired GSIS.

overall_design: Islets were isolated from C57Bl/6 wild type and C57Bl/6 SHP-/- mice fed chow or western diet. The same amount of total RNA obtained from these islets was pooled from 5-9 mice each group and subjected to illumina beadchip gene expression profiling in triplicates.

first: Yoon

middle: K

first: David

middle: D

last: Moore


title: Expression data from RAW 264.7 macrophage

city: Davis

first: Kimberly

middle: E

last: Barnholt

state: CA

address: 451 E. Health Sciences Drive

institute: University of California, Davis

summary:
IFNg is a pro-inflammatory and pro-atherogenic cytokine that leads to macrophage activation. Adenosine has well-documented anti-inflammatory properties. We used microarrays to compare the global gene expression profile in mouse macrophages stimulated with IFNg alone and those cells treated with IFNg and adenosine.
We determined that adenosine suppressed the expression of many IFNg-regulated pro-inflammatory cytokines, chemokines, and other pro-atherogenic genes.

Keywords: treatment response

overall_design: RAW 264.7 cells were treated for 4 hours with either IFNg or IFNg plus adenosine. Following treatment, total RNA was extracted and treatment groups were pooled from 2 separate experiments for hybridization of Affymetrix microarrays.

first: John

middle: C

last: Rutledge


title: miR-193b represses cell proliferation and regulates cyclin D1 in melanoma

status: Public on Dec 20 2009

city: Kingston

first: Harriet

last: Feilotter

state: Ontario

address: 88 Stuart St

department: Pathology and molecular department

institute: Queen's University

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

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

overall_design: Refer to individual Series


title: miR-193b represses cell proliferation and regulates cyclin D1 in melanoma: Malme-3M

summary: Cutaneous melanoma is an increasingly common form of skin cancer. The molecular mechanisms regulating melanoma progression are not completely understood. We speculated that specific miRNAs may be involved in melanoma development. We compared the miRNA expression profiles of benign nevi and metastatic melanomas. Unsupervised hierarchical clustering demonstrated a distinct miRNA expression pattern in metastatic melanomas compared to nevi. We identified miRNAs that were differentially expressed in melanoma. Notably, miR-193b was significantly down-regulated in the melanoma tissue examined. Using functional studies we demonstrated that over-expression of miR-193b significantly reduced melanoma cell proliferation, and arrested cell at G1 phase. Further gene expression analysis revealed that miR-193b regulated targets involved in cell cycle. Cyclin D1 was down-regulated by miR-193b at both  the mRNA and protein level. This is the first study to show that the miR-193b may reduce cell proliferation by directly repressing cyclin D1. Overall, our study suggests that miRNAs are dysregulated in metastatic melanoma, and that miR-193b may play an important role in melanoma.

overall_design: Malme-3M cells were transfected with miRNA precursors (either miR-193b or negative control) for 24 h. Two independent experiments with a total of 4 samples.

first: Jiamin

last: Chen

first: Xiao

last: Zhang

first: Victor

last: Tron


title: Microarray analysis of transcriptional regulations in IL-17-producing hybridoma

city: Fukuoka

first: Kensuke

last: Shibata

address: 3-1-1, Maidashi, Higashi-ku

department: Medical Institute of Bioregulation

institute: Kyushu University

summary: Identification of molecules which regulate the IL-17-producing function

overall_design: Total RNAs between IL-17-producing and IL-17-non-producing hybridoma were compared.


title: The Snf1-Related Kinase, Hunk, Is Essential for Mammary Tumor Metastasis

city: Philadelphia

first: Lewis

middle: A.

last: Chodosh

state: PA

address: 421 curie blvd, BRB II/III 616

department: Cancer Biology

institute: University of Pennsylvania

summary: We previously identified a novel SNF1/AMPK-related protein kinase, Hunk, from a mammary tumor arising in an MMTV-neu transgenic mouse. The function of this kinase is unknown. Using targeted deletion in mice, we now demonstrate that Hunk is required for the metastasis of c-myc-induced mammary tumors, but is dispensable for normal development. Reconstitution experiments revealed that Hunk is sufficient to restore the metastatic potential of Hunk-deficient tumor cells, as well as defects in migration and invasion, and does so in a manner that requires its kinase activity. Consistent with a role for Hunk in the progression of human cancers, the human homologue of Hunk is overexpressed in aggressive subsets of carcinomas of the ovary, colon, and breast. In addition, a murine gene expression signature that distinguishes Hunk-wild type from Hunk-deficient mammary tumors predicts clinical outcome in women with breast cancer. Together, these findings establish a role for Hunk in metastasis and an in vivo function for this kinase.

overall_design: Hunk-deficient animals were crossed to mice harboring an MMTV-c-myc transgene (Leder et al., 1986).  Hunk heterozygous, MMTV-c-myc mice were backcrossed to Hunk heterozygous animals.  MMTV-c-myc female animals of each Hunk genotype were mated twice, then monitored twice weekly for mammary tumors.  Mice possessing tumors with a maximum diameter of 20 mm were sacrificed and organs were examined at necropsy.  Tumor nodules were identified by examination of organs through a Leica Wild MZ8 dissection microscope.

first: Gerald

middle: B

last: Wertheim

first: Thomas

middle: W

last: Yang

first: Tien-chi

last: Pan

first: Anna

last: Ramne

first: Zhandong

last: Liu

first: Heather

middle: P

last: Gardner

first: Katherine

last: Dugan

first: Petra

last: Kristel

first: Bas

last: Kreike

last: Van De Vijver

first: Robert

last: Cardiff

first: Carol

last: Reynolds


title: Comparative Analysis of Extraembryonic Endoderm Cells with Cardiac Inducing Ability

status: Public on Dec 19 2009

city: New York

first: Ann

last: Foley

address: 510 E70th Street

institute: Weill Cornell Medical College

summary: Comparative analysis of Endodermal-like cell lines with demonstrated ability to support myocardial differentiation

overall_design: Total RNA was isolated in triplicate from each of the three heart-inducing cell lines.

first: Kemar

last: Brown

first: Jerome

last: Artus

first: Michael

middle: X

last: Doss

first: Stephanie

last: Legros

first: Raya

last: Khanin

first: Anna-Katerina

last: Hadjantonakis


title: Transcriptomic analysis of TLR4 pathways in a murine model of chronic pulmonary inflammation and carcinogenesis

status: Public on Dec 12 2009

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary:
Toll like receptor 4 (TLR4), an innate immunity gene, is involved in responses to several pulmonary agonists including endotoxin (LPS; Poltorak et al.,1998), ozone (O3 ,Kleeberger et. al., 2001), Pseudomonas aeruginosa (Faure et al, 2004), and hyperoxia (Zhang et al, 2005). TLR4 appears to partially mediate the response to LPS- and O3-induced lung injury, however, TLR4 is protective for prevention of injury in Pseudomonas aeruginosa infection and against acute lung injury (hyperoxia). The mechanism behind this protection is unclear. We previously demonstrated that TLR4 was also protective against BHT-induced chronic inflammation and tumor promotion (Bauer et al, 2005).  C.C3H-Tlr4Lps-d (BALBLps-d) mice, congenic for a 10 cM region of C3H/HeJ chromosome 4 that contains Tlr4 (Vogel et al, 1994), have a missence mutation that renders TLR4 dysfunctional.   The Tlr4 mutation likely abrogates signaling by disrupting a direct point of contact with other signaling molecules (Akira S, Takeda K. Toll-like receptor signalling. Nat Rev Immunol 2004;4(7):499-511.).  Bronchoalveolar lavage fluid (BALF) alveolar macrophages, lymphocytes, and total protein content were significantly elevated in BALBLps-d mice compared to BALB/c (BALB; Tlr4 sufficient) mice following chronic BHT (Bauer et al., 2005).   BALBLps-d mice also had a significant increase in tumor multiplicity (60%) over that of BALB mice in response to an MCA/BHT tumor promotion protocol.   While this was the first model to demonstrate a protective role for TLR4 in chronic lung inflammation and tumorigenesis, the downstream mechanism regulating this protective response remains unknown.  Using Affymetrix microarray analysis followed by GeneSpring and Ingenuity pathway analyses, we herein identified known and novel downstream pathways and their interactions that may be involved in the protective mechanism elicited by TLR4.  We therefore hypothesize that these pathways and interactions amongst the genes identified during the tumor promotion/chronic inflammation stage are in part influencing the differential strain response observed during tumorigenesis.
Keywords: time course, tumor study

overall_design:
Protocol 1 - 3 biological replicates after chronic dosing in each mouse strain
Protocol 2 - multiple replicates after MCA/BHT tumor progression model used

first: Alison

last: Bauer

first: Laura

last: Degraff

first: Jennifer

last: Fostel

first: Christopher

last: Walker

first: Sherry

middle: F

last: Grissom

first: Julie

first: Steven

last: Kleeberger

first: Elizabeth

last: Rondini


title: A transcriptional module initiates and maintains mesenchymal transformation in brain tumors [mouse data]

first: Mariano

middle: Javier

last: Alvarez

address: 1130 St. Nicholas ave.

institute: Columbia University

summary: Using a novel combination of cellular-network reverse-engineering algorithms and experimental validation assays, we identified a transcriptional module, including six transcription factors that synergistically regulates the mesenchymal signature of malignant glioma. This is a poorly understood molecular phenotype, never observed in normal neural tissue. It represents the hallmark of tumor aggressiveness in high-grade glioma, and its upstream regulation is so far unknown. Overall, the newly discovered transcriptional module regulates >74% of the signature genes, while two of its transcription factors (C/EBPβ and Stat3) display features of initiators and master regulators of mesenchymal transformation. Ectopic co-expression of C/EBPβ and Stat3 is sufficient to reprogram neural stem cells along the aberrant mesenchymal lineage, while simultaneously suppressing differentiation along the default neural lineages (neuronal and glial). Conversely, silencing the two transcription factors in human glioma cell lines and glioblastoma-derived tumor initiating cells leads to collapse of the mesenchymal signature with corresponding loss of tumor aggressiveness in vitro and in immunodeficient mice after intracranial injection. In human tumor samples, combined expression of C/EBPβ and Stat3 correlates with mesenchymal differentiation of primary glioma and is a predictor of poor clinical outcome. Taken together, these results reveal that activation of a small regulatory module, inferred from the accurate reconstruction of transcriptional networks, is necessary and sufficient to initiate and maintain an aberrant phenotypic state in eukaryotic cells.

overall_design: C17.2 murine stem cells and primary murine stem cells were transduced with STAT3 and CEBPB retrovirus.

first: Maria

middle: S

last: Carro

first: Wei

last: Lim

middle: J

first: Robert

last: Bollo

first: Xudong

last: Zhao

first: Evan

middle: Y

last: Snyder

first: Erik

last: Sulman

first: Sandrine

middle: L

last: Anne

first: Fiona

last: Doetsch

first: Howard

last: Colman

first: Anna

last: Lasorella

first: Ken

last: Aldape

first: Andrea

last: Califano

first: Antonio

last: Iavarone


title: Dynamic response of annexin A11-associated gene expression to cisplatin treatment

status: Public on Dec 01 2009

city: Baltimore

first: Jin

last: Song

state: MD

address: 419 N. Caroline Str.

department: Pathology

institute: Johns Hopkins Medical Institutions

summary:
Based on a time-course study of cisplatin response in ovarian cancer cells with/without suppression of annexin A11 expression using whole genome oligonucleotide microarrays, we identified a set of differentially expressed genes associated with annexin A11 expression and patterns of gene expressions in response to cisplatin exposure.

Keywords: human ovarian cancer cell lines

overall_design: 2008 cells (one ovarian cancer cell line) were transfected with ANXA11_RNAi or control_RNAi for 2 days and then treated with 10 µM cisplatin (Sigma) for 0, 8, 16, 24 hours. Total RNA of 8 samples were prepared for gene expression profiling using the Agilent 44K whole genome oligonucleotide microarrays.

first: Zhang

last: Zhen

first: Song

last: Jin


title: Genome-wide comparison of EpiSC lines derived from fertilized (FT) and somatic cell nuclear transfer (NT) embryos

status: Public on Feb 05 2010

city: JOUY EN JOSAS

first: Julien

last: MARUOTTI

address: Domaine de Vilvert

country: France

institute: INRA

summary:
Genome wide comparison of gene expression between EpiSC lines derived from fertilized (FT) embryos and somatic cell nuclear transfer (NT) embryos.
EpiSC lines were derived from fertilized and somatic cell nuclear transfer embryos and cultured until 15 to 20 passages. RNA was then extracted in order to compare transcriptomic profiles.

overall_design: Total RNA was extracted from 3 FT-EpiSC lines, and 3 NT-EpiSC lines. For each line, there were 3 biological repeat.

last: Maruotti

first: XiangPeng

last: Dai

first: Vincent

last: Brochard

first: Luc

last: Jouneau

first: Jun

last: Liu

first: Ludovic

last: Vallier

first: Gabrielle

last: Brons

first: Roger

last: Pedersen

first: Qi

last: Zhou

first: Jean-Paul

last: Renard

first: Alice

first: Amélie

last: Bonnet-Garnier

first: Hélène

last: Jammes


title: Transcriptional profiling of luteinising hormone receptor deficient mice before and after testosterone treatment

status: Public on Dec 14 2009

city: Canterbury

first: Peter

middle: James

last: Ellis

state: Kent

address: Stacey Building

department: School of Biosciences

institute: University of Kent

summary: Luteinising hormone (LH) is a key regulator of male fertility through its effects on testosterone secretion by Leydig cells.  Mice in which the LH receptor is knocked out (LuRKO) show reduced testicular size, reduced testosterone, elevated serum LH, and a spermatogenic arrest that can be rescued by administration of testosterone.  This study examines the onset of spermatogenic arrest in LuRKO males using transcriptional profiling of developing mutant and control testes.  We also examine the initial stages of testosterone rescue of the phenotype, in order to identify key upstream regulators of testosterone-dependent spermatogenesis.

overall_design: Three experimental series were obtained: (a) a developmental time course examining LuRKO and wild-type litter-mate testes at postpartum days 3, 8, 13, 19 and 27, taking birth as day 1; (b) a “rescue” time course following the testicular response to testosterone propionate treatment (2.5mg) at 2, 4, 8, 12, 24, and 48 hours post injection; (c) a second “rescue” time course examining the dose sensitivity of the androgen response at 24hrs post injection, using varying doses of testosterone propionate (vehicle only control, 250ng, 2.5µg, 25µg and 2.5mg).  For each experimental sample, two biological replicates were obtained.  Each individual replicate comprised pooled testis tissue from two animals.

first: Darren

last: Griffin

first: Ben

last: Dunmore

last: Bauer

first: Margaret

middle: H

last: Abel

first: Nabeel

middle: A

last: Affara


title: Whole genome transcription profile of antigen receptor activated B cells

status: Public on Nov 25 2009

city: Umeå

first: Thomas

last: Grundström

address: Analysvägen 1

department: Department of Molecular Biology

country: Sweden

institute: Umeå University

summary: To search for rapid changes in gene expression following BCR activation, we performed DNA microarray analysis of activated splenic B cells with and without anti-IgM treatment for 3 hour. The expression of a remarkably large set of genes differed significantly.

overall_design: Primary B-lymphocytes were purified from mouse spleens and stimulated with IL-4 (Pepro-Tech) and CD40L (R&D Systems) as indicated at 5 ng/ml and 200 ng/ml, respectively. The BCR of stimulated cells was activated by incubation with goat F(ab’)2 anti-mouse IgM (Southern Biotechnologies) at 2.5 μg/ml for 3 hour.

first: Jiyoti

last: Verma-Gaur


title: Transcriptomic profile indicative of immunotoxic exposure; in vitro studies in peripheral blood mononuclear cells

status: Public on Nov 19 2009

first: Kevin

last: Hochstenbach

address: Universiteitssingel 50

institute: Maastricht University

summary:
Investigating the immunotoxic effects of exposure to chemicals usually comprises evaluation of weight and histopathology of lymphoid tissues, various lymphocyte parameters in the circulation and immune function. Immunotoxicity assessment is time consuming in humans or requires a high number of animals, making it expensive. Furthermore, reducing the use of animals in research is an important ethical and political issue. Immunotoxicogenomics represents a novel approach to investigate immunotoxicity able of overcoming these limitations. The current research, embedded in the EU project NewGeneris, aimed to retrieve gene expression profiles that are indicative of exposure to immunotoxicants. To this end, whole genome gene expression was investigated in human peripheral blood mononuclear cells (PBMC) in response to in vitro exposure to a range of immunotoxic chemicals (4-hydroxy-2-nonenal, aflatoxin B1, benzo[a]pyrene, deoxynivalenol, ethanol, malondialdehyde, polychlorinated biphenyl 153, 2,3,7,8-tetrachlorodibenzo-p-dioxin) and non-immunotoxic chemicals (acrylamide, dimethylnitrosamine, 2-amino-3-methyl-3H-imidazo[4,5-F]quinoline, 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine). Using Agilent oligonucleotide microarrays, whole genome gene expression profiles were generated, which were analysed using Genedata’s Expressionist® software. Using Recursive Feature Elimination and Support Vector Machine, a set of 48 genes was identified that distinguishes the immunotoxic from the non-immunotoxic compounds. Analysis for enrichment of biological processes showed the gene set to be highly biologically and immunologically relevant. We conclude that we have identified a transcriptomic profile indicative of immunotoxic exposure.

Keywords: Genome wide gene expression analysis, Transcriptomic profile indicative of immunotoxic exposure

overall_design: For analysis of whole genome gene expression by microarray, PBMC from five independent donors per compound were exposed for 20 hours to three concentrations, i.e. the 100% and two serial ten-fold dilutions (10% and 1%), and a DMSO or PBS vehicle control. Exposed samples were always labelled with Cy5, whereas the vehicle control samples were labelled with Cy3, and were competetively hybridized on 4x44K Agilent microarrays.

first: Danitsja

middle: M

last: van Leeuwen

first: Hans

last: Gmuender

first: Solvor

last: Stølevik

first: Unni

last: Nygaard

first: Martinus

last: Løvik

first: Berit

last: Granum

first: Ellen

last: Namork

first: Joost

last: van Delft

first: Henk

last: van Loveren


title: ERRγ Regulates Cardiac, Gastric and Renal Potassium Homeostasis

status: Public on Nov 05 2009

city: Research Triangle Park

first: Andrew

last: Billin

address: 5 Moore Drive

institute: GlaxoSmithKline

summary: Genomic analysis of expression in brain, kidney, stomach, liver, and salivary tissues of perinatal ERRγ null and wild type mice.

overall_design: Total RNA was extracted from brain, kidney, stomach, liver, and salivary tissues of perinatal ERRγ null and wild type mice and hybridized to Affymetrix MOE430A gene chips in triplicate.

first: William

last: Alaynick

first: James

last: Way

first: Stephanie

last: Wilson

middle: G

last: Benson

first: Liming

last: Pei

first: Michael

last: Downes

first: Ruth

last: Yu

first: Johan

last: Jonker

first: Jason

last: Holt

first: Deepak

middle: K

last: Rajpal

first: Hao

last: Li

first: Joan

last: Stuart

last: McPherson

first: Katja

last: Remlinger

first: Ching

last: Yi-Chang

first: Donald

last: McDonnell

first: Ronald

last: Evans

middle: N


title: Endothelial Responses to Atheroprone Flow

status: Public on Nov 16 2009

city: Snellville

first: Marcie

middle: R

last: Williams

state: GA

address: 2300 Country Walk 3427

department: Biomedical Engineering

institute: Georgia Institute of Technology

summary: In order to simulate the effects of shear stress in regions of the vasculature prone to developing atherosclerosis, we subjected human umbilical vein endothelial cells to reversing shear stress, in order to mimic hemodynamic conditions at the wall of the carotid sinus, a site of complex, reversing blood flow and commonly observed atherosclerosis.  We compared the effects of reversing shear stress (time-average 1 dyne/cm2, maximum +11 dynes/cm2, minimum -11 dynes/cm2, 1 Hz), arterial steady shear stress (15 dynes/cm2), and low steady shear stress (1 dyne/cm2) in terms of gene expression, cell proliferation, and monocyte adhesiveness.  Microarray analysis revealed most differentially expressed genes were similarly regulated by all three shear stress regimens when compared to static culture.  Comparisons of the three shear stress regimens to each other allowed identification of 138 genes regulated by low average shear stress and 22 by fluid reversal.  Functional assays indicated that low average shear stress induces increased cell proliferation as compared to high shear stress.  Reversing shear stress was the only condition that induced monocyte adhesion.  Monocyte adhesion was partially inhibited by incubation of the endothelial cells with ICAM-1 blocking antibody.  Increased surface heparin sulfate proteoglycan expression was observed in cells exposed to reversing shear stress.  When these cells were treated with heparinase III monocyte adhesion was significantly reduced.  Our results suggest that low steady shear stress is the major impetus for differential gene expression and cell proliferation, while reversing flow regulates monocyte adhesion.

overall_design: Gene expression in endothelial cells was measured after 24 hours of exposure to 15 dyne/cm2 steady shear stress, 1 dyne/cm2 steady shear stress, reversing flow, or static culture.  Three independent experiments were performed using different lots of endothelial cells each time.

first: Daniel

middle: E

last: Conway

first: Suzanne

last: Eskin

first: Larry

middle: V

last: McIntire


title: A gene expression signature classifying telomerase and ALT immortalization

status: Public on Nov 02 2009

city: Glasgow

first: W.

middle: Nicol

last: Keith

state: Lanarkshire

address: Center for Oncology and Applied Pharmacology, University of Glasgow, CRUK Beatson Laboratories, Garscube Estate, Switchback Road

institute: The University of Glasgow


title: PTEN heterozygosity promotes tumorigenesis in a Smoothened active mouse model of medulloblastoma

status: Public on Nov 21 2009

city: Atlanta

first: Benjamin

last: Barwick

address: 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37

department: Hematology and Medical Oncology

institute: Emory University

summary: Recent publications have described an important role for cross talk between PI-3 kinase and sonic hedgehog signaling pathways in the pathogenesis of medulloblastoma. Our primary objective was to determine if loss of Pten promotes medulloblastoma tumor formation. When mice expressing SmoA1 were crossed with mice heterozygous for Pten, SmoA1 +; Pten +/- mice exhibited decreased survival, an increased incidence, and a shorter time to onset of symptoms, compared to SmoA1 +; Pten +/+ mice. Tumors from SmoA1 +; Pten +/+ mice exhibited classic histology. In contrast, tumors from SmoA1 +; Pten +/- mice exhibited predominantly nodular/desmoplastic histology and evidence of neuronal differentiation. Analysis by gene expression microarray revealed a clear separation of gene signatures, with upregulation of genes such as Pik3cb, Mapk8, Frap1, and multiple genes involved in angiogenesis in SmoA1+; Pten +/- tumors. Downregulated genes included Pten, Trp53, and Rb1. Western blotting and immunohistochemical analysis revealed decreased expression of Pten and increased activation of Akt in the SmoA1+; Pten +/- tumors. Consistent with these findings, we detected strong expression of PCNA throughout the Pten +/+ tumors and focal areas of intense staining for PCNA in tumors from SmoA1 +/-; Pten +/- mice. Conversely, staining for Cleaved Caspase 3 revealed multiple punctuate foci in SmoA1 +; Pten +/+ tumors and almost no staining in SmoA1 +/-; Pten +/- tumors. These results suggest that increased signaling through PI-3 kinase pathways promotes MB tumorigenesis by driving proliferation and inhibiting apoptosis of granule neuron precursor cells in the developing cerebellum.

overall_design: Expression of medulloblastoma tumors were compared using a mouse model with constitutive active Smoothened (SmoA+) and 4 mice with  wildtype PTEN (PTEN +/+) compared to 8 mice heterozygous for PTEN (PTEN +/-)

first: Robert

middle: C

last: Castellino


title: A gene expression signature classifying telomerase and ALT immortalization I

summary:
A gene expression signature classifying telomerase and ALT immortalisation reveals an hTERT regulatory network and suggests a mesenchymal stem cell origin for ALT

Telomere length is maintained by 2 known mechanisms, activation of telomerase or alternative lengthening of telomeres (ALT).  The molecular mechanisms regulating the ALT phenotype are poorly understood and it is unknown how the decision of which pathway to activate is made at the cellular level.  We have shown previously that active repression of telomerase gene expression by chromatin remodelling of the promoters is one mechanism of regulation, however other genes and signalling networks are likely to be required to regulate telomerase and maintain the ALT phenotype.  Using gene expression profiling we have uncovered a signature of 1305 genes to distinguish telomerase positive and ALT cell lines.  By combining this with gene expression profiles of liposarcoma tissue samples we refined this signature to 297 genes significantly associated with telomere maintenance mechanism.  Network analysis of known direct interactions between genes within this signature revealed a regulatory signalling network consistent with a model of hTERT repression in ALT cell lines and liposarcomas.  This network expands on our existing knowledge of hTERT regulation and provides a platform to understand differential regulation of hTERT in different tumour types and normal tissues.  In addition we show evidence to suggest a novel mesenchymal stem cell origin for ALT immortalisation in cell lines and mesenchymal tissues.

Keywords: cell type comparison, gene expression

overall_design: Immortal cell lines, normal cell strains and hMSC samples were all performed in duplicate.

first: Kyle

last: Lafferty-Whyte

first: Claire

last: Cairney

first: Malcolm

middle: B

last: Will

first: Nedime

last: Serakinci

first: Maria-Grazia

last: Daidone

first: Nadia

last: Zaffaroni

first: Alan

last: Bilsland

first: W


title: Gene expression profiles of LEC, MLC-L, and MSC-BM

status: Public on Nov 01 2009

city: Hyderabad

first: geeta

middle: Kashyap

last: vemuganti

state: Andhrapradesh

address: Road No.2

department: C-TRACER

institute: L.V.Prasad Eye Institute

summary:
Gene expression profiles of limbal explant culture-derived epithelial (LEC) and mesenchymal-like cells (MLC-L) and bone marrow-derived mesenchymal stem cells (MSC-BM).
To confirm the stem cell signatures of cultured LEC and to establish the source, possible role of the stroma-derived MLC-L .

overall_design: Two-condition experiment, LEC vs. MLC-L cells, LEC vs. MSC-BM, MLC-L vs. MSC-BM. Biological replicates: 2 LEC replicates, 2 MLC-L replicates, 2 MSC_BM replicates.

first: Naresh

last: Polisetti

first: Prasoon

last: Agarwal

first: Imran

last: Khan

first: Paturu

last: Kondaiah

first: Geeta

last: Vemuganti


title: Genomic sensitization in response to G9a repression following repeated cocaine exposure

status: Public on Oct 28 2009

first: Ian

middle: Sutherland

last: Maze

state: NY

address: 1425 Madison Ave.

department: Neuroscience

institute: Mount Sinai School of Medicine

summary: Cocaine-induced alterations in gene expression cause changes in neuronal morphology and behavior that may underlie cocaine addiction.  We identified an essential role for histone 3 lysine 9 (H3K9) dimethylation and the lysine dimethyltransferase G9a in cocaine-induced structural and behavioral plasticity.  Repeated cocaine administration reduced global levels of H3K9 dimethylation in the nucleus accumbens.  This reduction in histone methylation was mediated through the repression of G9a in this brain region.  To identify whether changes in H3K9me2 correlated with genome-wide alterations in gene expression in the NAc, we employed microarray analyses to examine gene expression profiles induced by a challenge dose of cocaine in animals with or without a history of prior cocaine exposure.  Animals that had received repeated cocaine displayed dramatically increased gene expression 1 hour after a cocaine challenge in comparison to acutely treated animals.  This increased gene expression still occurred in response to a cocaine challenge given after 1 week of withdrawal from repeated cocaine.  These data suggest that repeated, but not acute, cocaine exposure results in persistent sensitized genomic responses to a cocaine challenge, indicating that sensitized behavioral responses to repeated cocaine are likely the result of G9a-dependent alterations in global transcriptional responses to cocaine.

overall_design: Four groups (3 independent biological replicates per group) were utilized for this microarray study, totaling 12 microarrays (see 'Treatment protocol' for cocaine treatment information).  1 hour following the last cocaine injection, animals were rapidly decapitated and brains were removed and placed on ice.  Dissections of nucleus accumbens were taken using a 15-gauge needle punch and were quickly frozen on dry ice until RNA was extracted.  Bilateral punches were pooled from four animals per replicate, totaling 12 mice per group.  RNA isolation, microarray processing, and data analysis were performed as previously described.  Briefly, RNA was isolated and purified and was checked for quality using Agilent’s Bioanalyzer.  Reverse transcription, amplification, labeling and hybridization to Illumina MouseWG-6 v2.0 arrays were performed using standard procedures.  Raw data were background subtracted and quantile normalized using Beadstudio software.  Normalized data were analyzed using GeneSpring software and genelists were generated using significance criteria of a 1.3 fold change cutoff coupled with a non-stringent p-value cutoff of p < 0.05.

middle: S

first: Eric

middle: J

last: Nestler