title: Global expression analysis of HNF4alpha and HNFgamma-mediated transcriptional control

city: Meguro

first: Kenji

last: Daigo

state: Tokyo

department: Research Center for Advanced Science and Technology

institute: University of Tokyo

summary: Hepatocyte nuclear factor-4α (HNF4α, NR2A1) is a nuclear receptor which has a critical role in hepatocyte differentiation and the maintenance of homeostasis in the adult liver. However, a detailed understanding of native HNF4α in the steady state remains to be elucidated. Here we report the native HNF4α isoforms, phosphorylation status and complexes in the steady state, as shown by shotgun proteomics in HepG2 hepatocarcinoma cells. Shotgun proteomic analysis revealed the complexity of native HNF4α, including multiple phosphorylation sites and inter-isoform heterodimerization. The associating complexes identified by label-free semi-quantitative proteomic analysis include the following: the DNA-dependent protein kinase catalytic subunit, histone acetyltransferase complexes, mRNA splicing complex, other nuclear receptor coactivator complexes, the chromatin remodeling complex, and the nucleosome remodeling and histone deacetylation complex. Among the associating proteins, GRB10 interacting GYF protein 2 (GIGYF2, PERQ2) is a new candidate cofactor in metabolic regulation. Moreover, an unexpected heterodimerization of HNF4α and Hepatocyte nuclear factor-4γ was found. A biochemical and genome-wide analysis of transcriptional regulation showed that this heterodimerization activates gene transcription. The genes thus transcribed include the cell death-inducing DEF45-like effector b (CIDEB) gene, which is an important regulator of lipid metabolism in the liver. This suggests that the analysis of the distinctive stoichiometric balance of native HNF4α and its cofactor complexes described here is important for an accurate understanding of transcriptional regulation.

overall_design: siRNA-mediated HNF4alpha and HNF4gamma double knockdown in HepG2 cells were analysed by using the Affymetrix GeneChip system in tripricate.

first: Takeshi

last: Kawamura

first: Yoshihiro

last: Ohta

first: Riuko

last: Ohashi

first: Satoshi

last: Katayose

first: Toshiya

last: Tanaka

first: Hiroyuki

last: Aburatani

first: Makoto

last: Naito

first: Tatsuhiko

last: Kodama

first: Sigeo

last: Ihara

first: Takao

last: Hamakubo


title: Gene expression profiling of spleen marginal zone B cells and spleen follicular B cells in IRF8 conditional KO mice

status: Public on Dec 20 2010

city: Seoul

first: Dong-Mi

last: Shin

address: 1 gwanak-ro

country: South Korea

institute: seoul national university

summary:
Conditional IRF8 KO mice (mice with a conditional allele of Irf8 crossed with CD19-Cre mice) showed increased numbers of both Gene expression data spleen marginal zone (MZ) and Gene expression data spleen follicular (FO) B cells compared to control mice.
To evaluate gene expression patterns that distinguished FO or MZ B cells derived from conditional KO and control mice, we used Affymetrix GeneChip® Mouse gene 1.0 ST Array.

overall_design: FACS-sorted MZ and FO B cells from individual mouse were used for RNA extraction and Affyarray hybridization. There were six independent biological replications in each group - six cases of MZ B cells and FO cells in IRF8 conditional KO mice and six cases of MZ B cells and FO cells in control WT mice.

first: Jianxun

last: Feng

first: Hongsheng

last: Wang

first: Marek

last: Masiuk

first: Chen-Feng

last: Qi

first: Herbert

middle: C

last: Morse


title: Comparison of CD4+ T cells from human fetal and adult donors

status: Public on Dec 17 2010

city: San Francisco

first: Jeff

middle: E.

last: Mold

state: CA

address: UCSF Box 1234, SFGH Bldg 3

department: Division of Experimental Medicine

country: USA

institute: University of California San Francisco

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

overall_design: Refer to individual Series


title: Transcriptional Profiling of CD133+ Cells in Coronary Artery Disease and Effects of Exercise on Gene Expression

city: Bethesda

first: Delong

last: Liu

state: MD

address: 10 Center Drive

institute: NHLBI/NIH

summary: Bone marrow-derived progenitor cells are under investigation for cardiovascular repair, but may be altered by disease. We identified 82 differentially expressed genes in CD133+ cells from patients with coronary artery disease (CAD) versus controls, of which 59 were found to be up-regulated and 23 down-regulated. These genes were found to be involved in carbohydrate metabolism, cellular development and signaling, molecular transport and cell differentiation. Following completion of an exercise program, gene expression patterns resembled those of controls in 7 of 10 patients.

overall_design: Blood sampled from 4 healthy subjects (H), and from 10 patients with coronary artery disease at baseline (A) and after 3 months (B) of exercise.

first: Richard

last: Cannon Jr.


title: Comparison of gene expression profiles by CD3+CD4+ thymocytes derived from fetal and adult hematopoietic stem cells

summary: Human fetal and adult hematopoietic stem cells (HSC) were obtained from fetal liver, fetal bone marrow (BM), and adult BM. These were injected into human fetal thymic implants in SCID-hu Thy/Liv mice (4-6 separate mice per HSC donor) and allowed to mature into single positive CD4+ (SP4) thymocytes over the course of 7-8 weeks. SP4 thymocytes from injected stem cells were subsequently sort-purified from thymic implants and gene expression was performed.

overall_design: HSC from fetal (age 18-22 gestational weeks) and adult (age: 19-43 year old) HLA-A2+ donors were obtained from different tissues. After injection into human fetal thymic implants (SCID-hu Thy/Liv HLA-A2-) the cells were allowed to mature into thymocytes and sorted on the basis of HLA-A2+ expression and CD3+CD4+ (SP4) expression. 3 separate thymic implants were analyzed for each group.

middle: E

first: Cheryl

middle: A

last: Stoddart

first: Shivkumar

last: Venkatasubrahmanyam

first: Trevor

middle: D

last: Burt

first: Jakob

last: Michaelsson

first: Jose

middle: M

last: Rivera

first: Sofiya

last: Galkina

first: Joseph

last: McCune

first: Kenneth

last: Weinberg


title: Human Fetal and Adult Peripheral Naïve CD4+ T cells and CD4+CD25+ Treg cells

summary: We compared differences in fetal and adult T cells by performing whole genome profiling on sort-purified T cells (naïve CD4+ and Treg cells) from human fetal specimens (18-22 gestational weeks) and adult specimens (age 25-40 years old). Fetal and Adult Naïve CD4+ T cells phenotype: CD3+CD4+CD45RA+CCR7+CD27+, Fetal and Adult CD4+CD25+ Treg phenotype: CD3+CD4+CD25bright

overall_design: Four different groups were analyzed: Fetal Naïve CD4+ T cells, Adult Naïve CD4+ T cells, Fetal Treg cells, Adult Treg cells.  For each group three independent donors were analyzed.


title: Expression data from human umbilical vein endothelial cells (HUVECs) as a function of cell adhesion and VEGF exposure

status: Public on Dec 15 2010

city: Philadelphia

first: Colette

last: Shen

state: PA

address: 210 S. 33rd St., 510 Skirkanich Hall

institute: University of Pennsylvania

summary:
Angiogenesis is tightly regulated by both soluble growth factors and cellular interactions with the extracellular matrix (ECM).  While cell adhesion via integrins has been shown to be required for growth factor signaling and downstream angiogenesis, the effects of quantitative changes in cell adhesion and spreading against the ECM remain less clear.
Examining changes in global gene expression in limited versus high adhesion contexts in human umbilical vein endothelial cells, we demonstrated a VEGF-induced upregulation of genes associated with vascular invasion and remodeling when cell adhesion was restricted, whereas cells on highly adhesive surfaces upregulated genes associated with a proliferative response.

overall_design: HUVECs were cultured on micropatterned islands of fibronectin or allowed to spread fully for 2 hrs and then stimulated with 50ng/ml VEGF or no growth factor for 18 hrs in starve media.  Sample RNA from three biological replicates was extracted and prepared for hybridization on Affymetrix microarrays.

middle: J

first: Srivatsan

last: Raghavan

first: Christopher

middle: S

last: Chen


title: Expression Data from Uveal Melanoma primary tumors.

status: Public on Dec 14 2010

city: Paris Cedex 05

first: Cecile

last: Laurent

address: 26 rue d'ulm

country: France

institute: Institut Curie

summary:
A high percentage of uveal melanoma patients develop metastatic tumors that predominately occur in the liver. To identify genes associated with metastasis in this pathology, we studied 63 molecular profiles derived from gene expression microarrays performed from enuceated primary tumors.
Metastasis free survival analysis was performed to obtain clinical and genomic variables associated to metastasis occurrence. We also compared within the 57 tumors with at least 36 months follow-up, 28 uveal melanoma from patients who developed liver metastases (meta1 group) with 29 tumors arising from patients without metastases (or later metastases, i.e. after 36 months) (meta0 group).

overall_design: The transcriptome of 63 uveal melanoma from enucleation of untreated patients were analyzed using Affymetrix U133plus2 Arrays.

first: Cécile

first: Fabien

last: Valet

first: Nathalie

last: Planque

first: Licia

last: Silveri

first: Selma

last: Maacha

first: Océane

last: Anezo

first: Philippe

last: Hupé

first: Corine

last: Plancher

last: Reyes

first: Benoit

last: Albaud

first: Audrey

last: Rapinat

first: David

last: Gentien

first: Jérôme

last: Couturier

first: Xavier

last: Sastre-Garau

first: Laurence

last: Desjardins

first: Jean-Paul

last: Thiery

first: Sergio

last: Roman-Roman

first: Sophie

last: Piperno-Neumann

first: Bernard

last: Asselain

first: Emmanuel

last: Barillot

first: Simon

last: Saule


title: Gene expression profiling of Hodgkin lymphoma cell line KMH2: Comparison of CIITA-BX648577 knockdown cultures with non-silencing controls

status: Public on Dec 11 2010

city: Vancouver

first: Christian

last: Steidl

state: BC

address: 675 West 10th Avenue

department: Pathology

country: Canada

institute: BC Cancer Agency

summary: Description of differentially expressed genes between KMH2 CIITA-BX648577 knockdown cultures and non-silencing controls

overall_design: To determine the change in gene expression after siRNA interference with the fusion transcript CIITA-BX 648577 identified in KMH2 cells.


title: Premature progesterone rise

status: Public on Dec 21 2010

city: Brussel

first: Inge

last: Van Vaerenbergh

address: Laarbeeklaan 103

department: EXPA

country: Belgium

institute: Vrije Universiteit Brussel

summary:
Premature progesterone (P) rise during GnRH antagonist cycles for IVF is a frequent phenomenon and has been associated with lower pregnancy and implantation rates. Different thresholds of progesterone have been used so far to define its premature rise during the follicular phase of an IVF stimulated cycle. In this study, we evaluated endometrial gene expression on the day of oocyte retrieval according to the level of serum progesterone on the day of hCG administration in GnRH antagonist cycles.Endometrial biopsies from eleven patients were taken with a Pipelle de Cornier (Prodimed, Neuilly-en-Thelle, France) on the day of oocyte retrieval in a GnRH antagonist/rec-FSH stimulated IVF cycle with fresh embryo transfer. Biopsies were analysed for gene expression with Affymetrix Human Genome (HG) U133 Plus 2.0 Arrays and GCOS software (Affymetrix, Santa Clara, CA, USA). Patients were divided into three different groups according to their progesterone serum concentration on the day of hCG administration (A) P <= 0.9 ng/mL, (B) 1 < P < 1.5 ng/mL, and (C) P > 1.5 ng/mL. Serum P was measured with the automated Elecsys immunoanalyser (Roche Diagnostics, Mannheim, Germany). Selected differentially expressed genes were validated with quantitative real-time PCR (QPCR) with TaqMan Gene Expression Assays (Applied Biosystems, Foster City, CA, USA).

Keywords: gene expression analysis, premature progesterone rise

overall_design: Endometrial biopsies from fourteen patients were taken on the day of oocyte retrieval in a GnRH/rec-FSH stimulated IVF cycle with fresh embryo transfer and analyzed with microarrays. Patients were divided into three groups according to their progesterone serum concentration on day of hCG: A <=0.9ng/ml; B 1-1.5 ng/ml; C > 1.5ng/ml

first: Human

last: Fatemi

first: Christophe

last: Blockeel

first: Leentje

last: Van Lommel

first: Peter

last: In't Veld

first: Frans

last: Schuit

first: E

last: Kolibianakis

first: Paul

last: Devroey

first: Claire

last: Bourgain


title: Gene expression of LMPC cells of infratentorial ependymomas when compared to LMPC ependymal cells

status: Public on Dec 10 2010

city: Muenster

first: Björn

last: Koos

address: Domagkstr. 19

country: Germany

institute: Institute of Neuropathology, Muenster

summary: Ependymomas are glial tumors that share morphologic similarities with ependymal cells. Here we laser microdissected ependymoma cells of 15 infratentorial tumors and generated gene expression profiles. These profiles were compared to those of 7 laser microdissected ependymal tissues.

overall_design: 10 000 laser microdissected cells of each of the 15 different infratentorial ependymomas and seven ependymal autopsy tissues were lysed and gene expression profiles were generated. Expression profiles of ependymomas were compared to those of ependymal cells.

first: Martin

last: Hasselblatt


title: Gene expression profiling of cell lines derived from classical Hodgkin lymphoma

summary: Hodgkin lymphoma is derived from germinal center / post-germinal center B cells.

overall_design: To determine differentially expressed genes between Hodgkin Reed Sternberg cells and their presumed cell of origin we investigated the expression profiles of 5 commonly used Hodgkin lymphoma cell lines as compared to reactive germinal centers.


title: Expression genes induced by intermittent mechanical stress (MS) in human periodontal ligament (PDL) cells

city: Fukuoka

first: Hiroshi

last: Kajiya

address: 2-15-1 Tamura, Sawara-ku

department: Physiological Science and Molecular Biology

country: Japan

institute: Fukuoka Dental College

summary: Excessive MS is known to result in disappearance of the alveolar hard line, enlargement of thePDL space, and destruction of alveolar bone, leading to occlusal traumatism. The regulatory role of MS is believed to play a critical role in the process of alveolar bone remodeling. However, little is known about the effect of excessive MS on expression of osteoclastogenesis-related genes in human PDL cells.

overall_design: Human PDL cells were cultured in silicon chambers, which was attached to a stretching apparatus (STB-140; Strex Co. Ltd., Osaka, Japan) The cells were allowed to attach to the chamber base for 48 hours, after which uniaxial sinusoidal stretching (conditions: 60 sec/returns, resting time; 29 sec, stretch length; 1.6 mm, stretch ratio; 105%) was applied at 37°C, 5% CO2. We compared to the genes expression between 0 and 48 hours after MS stimulation.

first: Tetsuomi

last: Nemoto


title: CD133- HCC cells infected with miR-130b vs. empty vector control

city: Hong Kong

first: Stephanie

last: Ma

address: Rm 47, 1/F, Lab Block, Faculty of Medicine Bldg, 21 Sassoon Rd, Pok Fu Lam

department: School of Biomedical Sciences

country: Hong Kong

institute: The University of Hong Kong

summary: To identify candidate downstream mRNA target for hsa-miR-130b

overall_design: miR-130b or empty vector control was overexpressed in PLC8024 CD133- HCC cells using lentivirus


title: Antagonistic regulation of motility and other cellular functions by RpoN and RpoS in Escherichia coli

status: Public on Dec 04 2010

city: Hamilton

first: Herb

last: Schellhorn

state: ON

address: 1280 Main St. W.,

department: Biology

institute: McMaster University

summary: Bacteria generally possess multiple σ factors that, based on structural and functional similarity, divide into two families: σD and σN. Among the seven σ factors in Escherichia coli, six belongs to the σD family. Each σ factor recognizes a group of promoters, providing effective control of differential gene expression. Many studies have shown that σ factors of the σD family compete with each other for function. In contrast, the competition between σN and σD families has yet to be fully explored. Here we report a global antagonistic effect on gene expression between two alternative σ factors, σN (RpoN) and σS (RpoS), a σD family protein. Mutations in rpoS and rpoN inversely affected a number of cellular traits, such as expression of flagellar genes, σN-controlled growth on poor nitrogen sources, and σS-directed expression of acid phosphatase AppA. Transcriptome analysis reveals that 40% of genes in the RpoN regulon were under reciprocal RpoS control. Furthermore, loss of RpoN led to increased levels of RpoS, while RpoN levels were unaffected by rpoS mutations. Expression of the flagellar σF factor (FliA), another σD family protein, was controlled positively by RpoN but negatively by RpoS. These findings unveil a complex regulatory interaction among σN, σS and σF, and underscore the need to employ systems biology approaches to assess the effect of such interaction of σ factors on cellular functions, including motility, nutrient utilization, and stress response.

overall_design: Precise deletion mutants of rpoS or rpoN of MG1655 were constructed and employed in this study. Cultures were inoculated in triplicate in M9 minimal media (0.2% glucose) at a starting OD of 0.0001 and grown aerobically at 37C. Cultures were harvested at OD600 = 0.3 in exponential phase. For RNA extraction, cultures were mixed directly with a boiling lysis buffer containing SDS and EDTA followed by acidic hot phenol to minimize RNA degradation. RNA samples were hybridized to Affymetrix E. coli Genome 2.0 Array according to Affymetrix's standard protocols.

first: Tao

last: Dong

first: Rosemary

last: Yu


title: Expression data from the comparison between CD8 single positive (SP) thymocytes of CIITAtgpIV-/- mouse and B6 WT mouse

status: Public on Dec 18 2010

first: Hye Sook

last: Min

address: Chongnogu Yongondong 28

institute: Seoul National University College of Medicine

summary:
Thymocyte-thymocyte interaction can be very efficiently occur in CIITAtgpIV-/- mouse. We analyzed the gene expression profile between CD8+ T cells generated in CIITAtgpIV-/- mouse, and compared it to that of CD8+ T cells from B6 WT mouse.
In this dataset, we include the expression data obtained from  CD8 single positive thymocytes generated in CIITAtgpIV-/- mouse and B6 WT mouse. These data are used to obtain 279 genes that showed differentially increased expression in CIITAtgpIV-/- mouse.

overall_design: Total 1 sample from 2-4 CIITAtgpIV-/- mice and B6 WT mice were analyzed. We compared these using Affymetrix Expression console1.1, R affy-package(2.9.2), DAVID. Genes with an FDR≤10% and a fold-change ≥2 were selected.

first: B

middle: H

last: Kang

first: Y

last: Lee


title: Gene expression changes in NFAT5/TonEBP under isotonic and hypertonic conditions

first: Todd

last: Lamitina

address: 3700 Hamilton Walk, A702

department: Physiology

summary: TonEBP is a transcription factor that promotes cellular accumulation of organic osmolytes in the hypertonic renal medulla by stimulating expression of its target genes. Genetically modified animals with deficient TonEBP activity in the kidney suffer from severe medullary atrophy in association with cell death, demonstrating that TonEBP is essential for the survival of the renal medullary cells. Using both TonEBP knockout cells and RNA interference of TonEBP, we found that TonEBP promoted cellular adaptation to hypertonic stress. Microarray analyses revealed that genetic response to hypertonicity was dominated by TonEBP in that expression of totally different sets of genes was increased by hypertonicity in those cells with TonEBP vs. those without TonEBP activity. Out of over 100 potentially new TonEBP regulated genes, we selected 7 for further analyses and found that their expression was all dependent on TonEBP. RNA interference experiments showed that some of these genes – asporin, insulin-like growth factor-binding protein 5 and 7, and an extracellular lysophosphlipase D – plus Hsp70, a known TonEBP target gene, contributed to the adaptation to hypertonicity without promoting organic osmolyte accumulation. We conclude that TonEBP stimulates multiple cellular pathways for adaptation to hypertonic stress in addition to organic osmolyte accumulation.

overall_design: Quadruplicate samples were collected for each condition and then pooled into a single sample for hybridization to microarrays.

first: Samuel

middle: T

first: Sang

first: Soo

middle: Y

last: Choi

first: Sun

middle: W

last: Lim

first: Steffan

middle: N

last: Ho

first: Willian

last: Go

first: H

last: Kwon


title: Cranberry derived proanthocyanidins induce a state of iron-limitation in uropathogenic Escherichia coli CFT073 as revealed by microarray analysis

status: Public on Dec 02 2010

city: Montreal

first: Gabriela

last: Hidalgo

state: Quebec

address: 3610 University St

department: Chemical Engineering

institute: McGill University

summary: Transcriptional profiles of uropathogenic Escherichia coli CFT073 exposed to cranberry-derived proanthocyanidins (PACs) were determined. Our results indicate that bacteria grown on media supplemented with PACs were iron-deprived. To our knowledge, this is the first time that PACs have been shown to induce a state of iron-limitation in this bacterium.

overall_design: Cultures of E. coli CFT073 were streaked onto LB agar plates and incubated (37°C, 24 h).  A single colony was inoculated into 150 mL of LB broth.  Three inoculated flasks contained LB broth alone (controls), and three inoculated flasks were supplemented with cranberry PACs (100 µg/mL).  After incubation (37°C, 5 h, 200 rpm to mid-log growth phase), bacteria were harvested for RNA extraction.

first: André

last: Ponton

first: Julien

last: Fatisson

first: Che

last: O’May

first: Bahareh

last: Asadishad

first: Tim

last: Schinner

first: Nathalie

last: Tufenkji


title: Expression data from IL-10+ and IL-10- CD8 T cells

status: Public on Dec 07 2010

city: Iowa City

first: Stanley

last: Perlman

state: IA

address: 51 Newton Road

department: Department of Microbiology

institute: University of Iowa

summary:
IL-10 is an anti-inflammatory cytokine that has been shown to be produced by antigen-specific CD8 T cells at the peak of viral encephalitis. We found that IL-10+CD8 T cells are more activated and cytolytic than IL-10-CD8 T cells.
We used microarrays to detect gene expression changes in directly ex vivo sorted CNS IL-10+ and IL-10- CD8 T cells from a neurotropic J2.2-V-1-infected mouse.

overall_design: C57Bl/6 Vert-X (IL-10-eGFP) mice were infected intracranially with 500 PFU J2.2-V-1 virus and seven days later their brain lymphocytes from three mice were pooled and then isolated and negatively selected for CD8 T cells. The CD8 pooled brain lymphocytes were then sorted for IL-10+ and IL-10- CD8 T lymphocytes using GFP as a marker from the same samples. This was performed three times to obtain six samples total. RNA was extracted and hybridized to GeneChip Mouse GENE 1.0 ST arrays (Affymetrix).

first: Kathryn

last: Trandem


title: Expression profiles of amniotic fluid from human fetuses with Trisomy 18 and euploid controls

status: Public on Dec 03 2010

city: Medford

first: Donna

middle: K

last: Slonim

state: MA

address: 161 College Ave.

department: Computer Science

institute: Tufts University

summary:
To understand the molecular mechanisms underlying the congenital anomalies observed in patients with Trisomy 18, we compared gene expression in uncultured amniotic fluid supernatant samples from second trimester fetuses with Trisomy 18 and from euploid controls.
Analysis of differential expression using both individual-gene and gene-set or pathway methods indicated disrupted function in ion transport, MHCII/T-cell mediated immunity, DNA repair, G-protein mediated signaling, kinases, and glycosylation. Significant down-regulation of genes involved in adrenal development was also identified in the trisomic fetuses, possibly explaining both the abnormal maternal serum estriols and the pre- and postnatal growth restriction found in this condition.

overall_design: We compared expression in five female fetuses with confirmed metaphase karotypes 47, XX, +18 and six female controls (46, XX).  The gestational ages of the samples ranged from 17 5/7 to 20 6/7 weeks.

first: Keiko

last: Koide

first: Kirby

middle: L

last: Johnson

first: Umadevi

last: Tantravahi

first: Janet

last: Cowan

first: Diana

last: Bianchi


title: Expression data from melanoma cell lines

status: Public on Dec 01 2010

city: Los Angeles

first: Ali

last: Jazirehi

address: 10833 LeConte Ave, CHS 54-140

institute: UCLA, Department of Surgery

summary: Differential gene expression analysis of parental and sub-lines of melanoma cell line resistant to F5 CTL lymphocyte

overall_design: parental melanoma cell line and CTL resistant sub-line


title: Porcine intramuscular fat content and composition are regulated by quantitative trait loci with muscle-specific effects

city: lleida

first: angela

last: canovas

state: lleida

address: 191, rovira roure

country: Spain

institute: irta

summary: Intramuscular fat (IMF) storage is a biological process with strong impact on nutritional and technological properties of meat, and also with relevant consequences on human health. The genetic architecture of IMF content and composition phenotypes has been thoroughly studied in pigs through the identification of quantitative trait loci (QTL) and the estimation of genetic parameters. A question that has not been elucidated yet is if the genetic determinants of IMF-related phenotypes are muscle specific or, conversely, they have broad effects on the whole skeletal muscle compartment. We have addressed this question by generating lipid QTL maps for two muscles with a high commercial value, gluteus medius (GM) and longissimus thoracis et lumborum (LTL), in a Duroc commercial population (N=350). As a complementary approach, we have analysed the mRNA expression pattern of both muscles at a whole genome scale. The lack of concordance between the GM and LTL QTL maps evidenced that the effects of polymorphisms influencing IMF, cholesterol and fatty acids contents are modulated to some extent by complex spatial factors related with muscle location, metabolism and function. This interpretation was supported by our finding that genes influencing cell differentiation, muscle development and function and lipid metabolism are differentially expressed between muscles. These results have important implications on the implementation of genomic selection schemes aimed to improve the lipid profile of swine meat. Moreover, they confirm pigs as a valuable model to dissect the genetic basis of muscle lipid phenotypes of clinical interest in human.

overall_design: Longissimus thoracis et lumborum muscle tissue from 10 high and 9 low fattening Duroc pigs were compared in this study.

first: R

last: Quintanilla

last: Pena

first: D

last: Gallardo

first: A

last: Cánovas

first: O

last: Ramírez

first: I

last: Díaz

first: J

last: Reixach

last: Noguera

first: M

last: Amills


title: Skeletal muscle gene expression in response to resistance exercise: sex specific regulation

status: Public on Dec 06 2010

city: Ann Arbor

first: GORDON

last: PAUL

state: MI

address: 325 E Eisenhower

institute: University of Michigan

summary: The molecular mechanisms underlying the sex differences in human muscle morphology and function remain to be elucidated. The purpose of the study was to detect the sex differences in the skeletal muscle transcriptome in both the resting state and following anabolic stimuli, resistance exericse.

overall_design: We used microarrays to profile the transcriptome of the biceps brachii of young men and women who underwent an acute unilateral RE session following 12 weeks of progressive training. Bilateral muscle biopsies were obtained either at an early (4h post-exercise) or late recovery (24h post-exercise) time point. Muscle transcription profiles were compared in the resting state between men (n=6) and women (n=8), and in response to acute RE in trained exercised vs. untrained non-exercised control muscle for each sex and time point separately (4h post-exercise, n=3 males, n=4 females; 24h post-exercise, n=3 males, n=4 females). A logistic regression-based method (LRpath), following Bayesian moderated t-statistic (IMBT), was used to test gene functional groups and biological pathways enriched with differentially expressed genes.

first: Dongmei

last: Liu

first: Maureen

last: Sartor

first: Gustavo

last: Nader

first: Laurie

last: Gutmann

first: Mary

last: Treutelaar

first: Emidio

last: Pistilli

first: Heidi

middle: B

last: IglayReger

first: Charles

middle: F

last: Burant

first: Eric

middle: P

last: Hoffman

first: Paul

last: Gordon


title: The effects of terbutaline or GW9508 on TNF-alpha and IFN gamma (TNF-alpha + IFN gamma) stimulation by HaCaT

city: Kyoto

first: Tomoko

last: Fujita

address: Yoshida Konoe-Cho

department: Medicine

institute: Kyoto University

summary:
G-protein coupled receptors (GPCRs) have diverse roles in physiological processes, including immunity. Gs-coupled GPCRs increase  while Gi-coupled ones decrease intracellular cAMP. Previous studies suggest that, in epithelial cells, Gs-coupled GPCRs enhance whereas Gi-coupled GPCRs suppress pro-inflammatory immune responses. In order to examine the issue, we chose beta2 adrenergic receptor and GPR40 as representatives of Gs- and Gi- coupled GPCRs, respectively, and examined their effects on TNF-alpha and IFN-gamma-(TNF-alpha + IFN-gamma) induced gene expression by HaCaT.
We used microarrays to detail the global changes of gene expression induced by a beta2 adrenergic receptor agonist terbutaline or GPR40 agonist GW9508 pre-treatment in TNF-alpha + IFN-gamma - stimulated HaCaT cells.

overall_design: HaCaT cells were pre-treated with terbutaline or GW9508, TNF-alpha + IFN-gamma were then added, and cultured for another 24 h. Cells were then used for RNA extraction and hybridization on Affymetrix microarrays. We sought to clarify changes in gene expression after 1) TNF-alpha + IFN-gamma, 2) TNF-alpha + IFN-gamma + terbutaline, and 3) TNF-alpha + IFN-gamma + GW9508 treatment. To this end, we set 4 groups of samples; 1) unstimulated group, 2)  TNF-alpha + IFN-gamma-stimulated group, 3) TNF-alpha + IFN-gamma + terbutaline-stimulated group, and 4) TNF-alpha + IFN-gamma + GW9508-stimulated group. In each group, HaCaT cells were stimulated in triplicate wells (n=3).

first: Shuh

last: Narumiya


title: Expression data from HPV(-) and HPV(+) squamous cell carcinoma cell lines

first: Jung

last: Kim

address: 1420 Washington Heights

summary: Oncogenic human papillomaviruses (HPVs) are associated with nearly all carcinomas of the uterine cervix and have also become an increasingly important factor in the etiology of a subset of oropharyngeal tumors.  HPV-associated head and neck cancers (HNSCCs) have a distinct risk profile and appreciate a prognostic advantage compared to HPV-negative HNSCC. We analyzed the genome-wide expression patterns in two HPV(+) and two HPV(-) squamous cell carcinoma (SCC) cell lines.

overall_design: The Affymetrix Human Genome U133 Plus 2.0 Array platform was used to assess genome-wide expression differences between the HPV(+) and HPV(-) cell lines utilizing the RMA normalization package available for R.  Cell lines analyzed: UM-SCC-4, UM-SCC-47, UM-SCC-74A, and CaSki.

first: Dana

middle: C

last: Dolinoy

first: Thomas

last: Carey

first: Tamara

last: Jones

first: Justin

last: Colacino

first: Laura

last: Rozek


title: Genotypic and phenotypic characterization of the side population of gastric cancer cell lines

city: Berlin

first: Rosa

last: Schmuck

state: Berlin

address: Cariteplatz 1

department: Institute of Pathology

institute: Charite university medicine

summary: To sum up our results, we managed to isolate a reproducible SP cell fraction of human gastric carcinoma cell lines for the first time. Those cells differed from the rest of the population regarding morphology and biological behaviour. They had the ability to build a population resembling the basic tumor population and therefore performed differenziation and asymmetric cell division. SP cells expressed potential stem cell markers like musashi 1 and Cd133 and also showed a high expression of genes that encode for stem cell properties. The so identified phenotypic and genetic factors showed a variable expression in tumor samples of patient series and might be applicable as prognostic factors in the diagnosis of gastric carcinoma.

overall_design:
Aims: The side population (SP) of tumor cell lines shares characteristics with tumor stem cells. In this study we phenotypically and genotypically characterized the SP of gastric cancer cell lines.
Methods: The SP was obtained from MKN45- and AGS-gastric cancer cells using Hoechst 33342 staining and fluorescence-activated cell sorting (FACS). SP cells were subsequently studied morphologically (cytology, immunocytochemistry), on the transcriptional level (gene array) and in cell culture (recultivation assays). Genes differentially expressed in the SP cells were finally searched by immunohistochemistry in neoplastic and non-neoplastic gastric tissue from gastric cancer patients.
Results: The SP was reproducibly obtained from gastric cancer cell lines. The SP cells were smaller and rounder then non-SP cells. SP cells self-renewed in re-cultivation experiments and differentiated into SP- and non-SP cells. Re-cultivated SP- and non-SP cells showed distinct phenotypes in culture regarding cell shape and colony-formation. SP cells had increased levels of the stem cell markers CD133 and Musashi 1. Transcriptional analyses demonstrated that SP cells express genes that encode for stem cell properties like FZD7, HEY1, SMO and ADAM17. Finally we detected the transcripts of these genes in tissue samples from patients with gastric cancer.
Conclusions: Human gastric cancer cell lines enclose a phenotypically and genotypically distinct cell population with tumor stem cell features. Phenotypical characteristics of this distinct cell population are also present in gastric cancer tissue.

first: Christoph

last: Röcken


title: Expression data from hyperplastic polyps and normal colonic mucosa from patients with familial and sporadic HPPS

city: Lisboa

first: Cristina

last: Albuquerque

address: Rua Professor Lima Basto

department: Centro de Investigação de Patobiologia Molecular (CIPM)

country: Portugal

institute: Instituto Português de Oncologia de Lisboa Francisco Gentil, EPE

summary:
Expression data from hyperplastic polyps and normal colonic mucosa from patients with familial and sporadic hyperplastic polyposis syndrome (HPPS).
We aim to characterize at a molecular level a cohort of hyperplastic lesions from HPPS patients with and without family history.

overall_design: RNA from hyperplastic polyps and normal colonic mucosa (proximal and distal) from patients with familial and sporadic HPPS were included in this study. Total RNA was isolated from each tissue sample, quantified and its quality evaluated. cRNA preparation, hybridization and analysis of results was performed according to Affymetrix recommendations. cRNA was hybridised in the  GeneChip array (Human Genome U133 Plus 2.0, Affymetrix), and the intensity was measured.

first: Joana

last: Dinis

first: Patrícia

last: Silva


title: Transcriptome drift of FADU after expression of HIF-1a, Twist1 or Bmi1

city: Taipei

first: Muh-Hwa

last: Yang

address: No.155, Sec.2, Li-Nong Street

department: Institute of Clinical Medicine

country: Taiwan

institute: National Yang-Ming University

summary: Expression of HIF-1a or Twist1 or Bmi1 in human hypopharyngeal cancer cell line FADU results in the drift of transcriptome profile from an epithelial cell-like signature to a mesenchymal stem cell-like signature.

overall_design: Stable transfection of pHA-HIF1a(dODD), pFLAG-Twist1 or pcDNA3-Bmi1 in FADU cell and analyzed the transcriptome by cDNA microarray. FADU transfected with pcDNA3.1 empty vector was used as a control of experiment.

first: Hsei-Wei

last: Wang

first: Wei-Lun

last: Huang


title: Expression and methylation analyses of HPV(-) and HPV(+) squamous cell carcinoma cell lines

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: PGC-1 alpha Mediates Differentiation of Mesenchymal Stem Cells toward Brown Adipose Cells

first: Shih-Hwa

last: Chiou

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

institute: Vghtpe

summary: Mesenchymal stem cells (MSCs) are a multipotent cell type that can differentiate into non-hematopoietic cells, such as adipocytes. Adipocyte tissue is central to regulate energy balance. PGC-1 alpha controls several aspects of mitochondrial biogenesis. However, roles of PGC-1 alpha in brown fat differentiation of MSCs remain uncertain. To investigate roles of PGC-1 alpha in brown fat differentiation immortalized human MSCs were used for all experiments. The changes in genetic profiling between MSCs and PGC-1 alpha-expressing MSCs were analyzed by microarray analysis. The genetic profiling of PGC-1 alpha-expressing MSCs shows the significant increase of genes related to mitochondrial functions and lipid metabolism compared to that of MSCs. When expressed in MSCs, PGC-1 alpha activates a robust mitochondrial biogenesis and respiration. The expression of thermogenic markers, such as cytochrome C and complex II, was significantly increased in MSCs with treatment of adenovirus expressing PGC-1 alpha. Our microarray results also indicate that genetic pattern of PGC-1 alpha-expressing MSCs is very closed to that of adipose tissues.

overall_design: Bone marrow-derived MSCs were infected with Ad-GFP, or Ad-PGC-1α at a multiplicity of infection (m.o.i.) of 500 overnight.

first: Lung-Kuo

last: Tai

first: Li-Shin

last: Chen

first: Chung-Lan

last: Kao

first: Kai-Hsi

last: Lu

first: Shih-Chie

last: Hung


title: DUSP1/MKP1 promotes angiogenesis, invasion and metastasis in non-small cell lung cancer

status: Public on Dec 09 2010

city: Pamplona

first: Eva

last: Bandres

address: Avda Pio XII, 55

department: Cancer Research Program

institute: Center for Applied Medical Research (CIMA), University of Navarra

summary:
DUSP1 is involved in different cellular pathways including cancer cell proliferation, angiogenesis, invasion and resistance to chemotherapy. To understand more about the cellular responses regulated by DUSP1 in NSCLC cells, we interfered DUSP1 expression in the NSCLC cell line H460 and studied the changes in gene expression differentially regulated by this phosphatase.

Keywords: Expression profiling by array in cells with genetic modification

overall_design: The human non small lung cancer cell line H460 used in this study was from ATCC (American Type Culture Collection). The cell line was maintained in RPMI (Gibco, Invitrogen) supplemented with 10% bovine serum and transfected by Lipofectamine Plus Reagent from Life Technologies as directed by the manufacturer. The DUSP1 pSuperRetro-derived vectors were constructed as described (Chattoppadhyay et al., 2006). Clones expressing siRNA for DUSP1 were selected for their ability to grow in the presence of puromycin  and kept for selection. Stable transfection was confirmed by Western blotting. RNA was extracted and quality control was checked before hybridization on Affymetrix microarrays.

first: Veronica

last: Moncho-Amor

first: Inmaculada

last: Ibanez deCaceres

first: Beatriz

last: Martinez-Poveda

first: José

last: Luis Orgaz

first: Isabel

last: Sanchez-Pérez

first: Sandra

last: Zazo

first: Ana

last: Rovira

first: Joan

last: Albanell

first: Benilde

last: Jimenez-Cuenca

first: Federico

last: Rojo

first: Jesús

last: Garcia-Foncillas

first: Rosario

last: Perona


title: Effect of insulin on the stromal and adipocyte cells within hMSC derived adipocytes

status: Public on Nov 30 2010

city: Groton

first: Shelley

last: des Etages

state: CT

address: Eastern Point Road

institute: Pfizer Inc.

summary: There are an estimated 21million diabetics in the United States and 150 million diabetics worldwide.  The World Health Organization anticipates that these numbers will double in the next 20 years. Metabolic syndrome is a well recognized set of symptoms that increases a patient’s risk of developing diabetes.  Insulin resistance is a factor in both metabolic syndrome and Type 2 diabetes. It is characterized by decreased insulin stimulated glucose uptake in peripheral tissues, decreased adiponectin levels, increased adipocyte  FFA and cytokine production, and increased insulin and hepatic glucose output.  Prevention or reversal of insulin resistance should serve as an important strategy in addressing the growing health concerns posed by the Diabetes epidemic. While increased adiposity is associated with insulin resistance, the role of the cell types present within adipose (adipocytes, pre-adipocytes, endothelial cells, macrophages, fibroblasts, leukocytes and smooth muscle cells) in insulin resistance is unclear.  In an effort to begin dissection of this question, we examined the transcriptional response of the buoyant and non-buoyant fractions isolated from insulin sensitive or TNF induced insulin resistant hMSC derived adipocytes before and after treatment with insulin.

overall_design: hMSC derived adipocytes were treated with 0 or 10ng/ml TNF for 24 hours to induce insulin resistance and subsequently serum starved for 5 h followed by treatment with 0 or 20nM insulin for 2 hours. At the end of the incubation period, cells were harvested as is (mixed) or subjected to fractionation to separate the adipocytes (buoyant fraction) and the stromal cells (non-buoyant fraction). These isolated cells were resuspended in RLT buffer to prepare lysates for total RNA isolation using the Qiagen RNeasy kit. Total RNA was submitted to GeneLogic for cRNA preparation using the Affymetrix GenChip  IVT kit and hybridization to Affymetrix U133 Plus 2.0 arrays.

middle: G

last: desEtages

first: Lisa

last: Hayes

first: Andrew

last: Kuhn

first: Amy

last: Baumann

first: Mark

last: Thiede

first: Mary

last: Bauchmann


status: Public on Nov 29 2010

city: Maastricht

first: Florence

last: van Tienen

address: Universiteitssingel 50

department: Genetics and Cell biology

country: Netherlands

institute: Maastricht University

summary:
Skeletal muscle mitochondrial dysfunction is secondary to T2DM and can be improved by long-term regular exercise training

Mitochondrial dysfunction has long been implicated to play a causative role in development of type 2 diabetes (T2DM). However, a growing number of recent studies provide data that mitochondrial dysfunction is a consequence of T2DM development. The aim of our study is to clarify in further detail the causal role of mitochondrial dysfunction in T2DM by a comprehensive ex vivo analysis of mitochondrial function combined with global gene expression analysis in muscle of pre-diabetic newly diagnosed untreated T2DM subjects and long-standing insulin treated T2DM subjects compared with age- and BMI-matched controls. In addition, we assessed the impact of long-term interval exercise training on physical activity performance, mitochondrial function and glycemic control in long-standing insulin-treated T2DM subjects.  Ex vivo mitochondrial density, quality and functioning was comparable between pre-diabetic subjects and matched controls, however, gene expression analysis showed a switch from carbohydrate toward lipids as energy source in pre-diabetes subjects. In contrast, long-term insulin treated T2DM subjects had slightly decreased mitochondrial density and ex vivo function. Expression of Krebs cycle and OXPHOS related genes were decreased, indicating a decreased capacity to use lipids as an energy source. The insulin-treated T2DM subjects had a lower physical activity level than pre-diabetic and normoglycemic subjects. A 52 weeks exercise training of these subjects increased submaximal oxidative efficiency, increased in vivo PCr recovery rate, as well as mildly increased in vitro mitochondrial function. Gene expression of β-oxidation, Krebs cycle and OXPHOS-related genes was increased.  Our data demonstrate that mitochondrial dysfunction is rather a consequence than a causative factor in T2DM development as it was only detected in overt diabetes and not in early diabetes. Regular exercise training stabilized exogenous insulin requirement and improved mitochondrial functioning, fatty acid oxidation and general physical work load capacity in long-standing insulin-treated T2DM subjects. As such, the present study shows for the first time that long-term exercise interventions are beneficial in this group of complex diabetes patient and may prevent further metabolic deterioration.

overall_design: Insulin-treated T2DM subjects before and after 52 weeks of exercise training (T2DM_0 and T2DM_52), normoglycemic controls (NGT) and pre-diabetes subjects (IGT) and were selected. RNA was extracted from skeletal muscle biopsies and hybridized on Affymetrix microarrays.

first: Stephan

last: Praet

first: Henk

last: de Feyter

first: Nicole

last: van den Broek

first: Patrick

last: Lindsey

first: Kees

last: Schoenderwoerd

first: Irineus

last: de Coo

first: Klaas

last: Nicolay

first: Janine

last: Prompers

first: Hubert

last: Smeets

first: Luc

last: van Loon


title: Genomic landscape of meningiomas: gene expression

first: Stanley

last: Nelson

address: 695 Charles E. Young Drive South, Bldg Gonda, Rm 5554

department: Human Genetics

summary:
Meningiomas are one of the most common adult brain tumors.  For most patients, surgical excision is curative.  However, up to 20% recur.  Currently, the molecular determinants predicting recurrence and malignant transformation are lacking.  We performed global genetic and genomic analysis of 85 meningioma samples of various grades.
Copy number alterations were assessed by 100K SNP arrays and correlated with gene expression, proliferation indices, and clinical outcome.  In addition to chromosome 22q loss, which was detected in the majority of clinical samples, chromosome 18q and 6q loss significantly predicted recurrence and was associated with anaplastic histology.  Five classes of meningiomas were detected by gene expression analysis that correlated with copy number alterations, recurrence risk, and malignant histology.  These classes more accurately predicted tumor recurrence than Ki-67 index, the gold standard for determining risk of recurrence, and highlight substantial expression heterogeneity between meningiomas. These data offer the most complete description of the genomic landscape of meningiomas and provide a set of tools that could be used to more accurately stratify meningioma patients into prognostic risk groups.

overall_design: Tumor biopsies from 43 female and 25 male subjects with sporadic meningioma were identified from the UCLA Neuro-oncology Program Tissue Bank through institutional review board approved protocols.  43 tumors were designated "benign" WHO I, 19 tumors were "atypical" WHO II, and 6 were "anaplastic" WHO III. Gene expression analysis was performed on the 68 tumor biopsies.

first: Yohan

last: Lee


title: Gene expression profiles of granulin- and control-treated normal human mammary fibroblasts

status: Public on Nov 27 2010

city: Lund

first: Björn

last: Nilsson

address: BMC

department: Hematology and Transfusion Medicine

country: Sweden

institute: Lund University

summary: To examine the effects of recombinant granulin on human mammary stromal fibroblasts, we cultured normal human mammary fibroblasts in the presence of recombinant human granulin (1ug/ml) or PBS every 24h for 6 days.

overall_design: We cultured normal human mammary fibroblasts in the presence human granulin (1ug/ml) or PBS control every 24h for 6 days.  The analysis showen are for 3 control (control) and 3 granulin-treated (PGRN) fibrobast cultures.

first: Christina

last: Scheel

first: Bjorn

first: Sandra

last: McAllister


title: Quantitative Gene Expression Profiling in Formalin-Fixed Paraffin-Embedded Samples by Affymetrix Microarrays

status: Public on Nov 25 2010

city: San Diego

first: Elai

last: Davicioni

state: California

address: 9725 Lusk Blvd

institute: Veracyte, Inc

summary:
Background: To date, few studies have systematically characterized microarray gene expression signal performance with degraded RNA from formalin-fixed paraffin-embedded (FFPE) specimens in comparison to intact RNA from unfixed fresh-frozen (FF) specimens.
Methodology: RNA was extracted and isolated from paired tumor and normal samples from both FFPE and FF kidney, lung and colon tissue specimens. Microarray signal dynamics on both the raw probe and probeset level were evaluated. A contrast metric was developed to directly compare microarray signal derived from RNA extracted from matched FFPE and FF specimens. Gene-level summaries were then compared to determine the degree of overlap in expression profiles.
Results: RNA extracted from FFPE material was more degraded and fragmented than FF, resulting in reduced dynamic range of expression signal. It was found that probe performance is not affected uniformly and declines sharply toward 5’ end of genes. The most significant differences in FFPE vs. FF signal were consistent across three tissue types and enriched with ribosomal genes.
Significance: Our results show that archived FFPE samples can be used to profile for expression signatures and assess differential expression similar to unfixed tissue sources. This study provides guidelines for application of these methods in the discovery, validation, and clinical application of microarray expression profiling with FFPE material.

overall_design: 53 samples: 16 FF colon, 7 FFPE colon, 6 FF lung, 8 FFPE lung, 8 FF kidney, and 8 FFPE kidney specimens. Samples are paired tumor and normal tissue. 1-4 biological replicates.

first: Diana

last: Abdueva

first: Michele

last: Wing

first: Betty

last: Schaub

first: Timothy

last: Triche


title: t(11;18)-positive vs. t(11;18)-negative MALT lymphoma

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

institute: VIB

summary: Comparison of t(11;18)-positive MALT lymphoma to t(11;18)-negative MALT lymphoma, with a special focus on the NF-KB pathway and it's targets

overall_design: 8 t(11;18)-negative and 6 t(11;18)-positive cases of MALT lymphoma, as well as six spleen control samples (1 mix of spleens and 5 singular spleen samples)

first: Xavier

last: Sagaert

first: Peter

last: Van Loo

first: Mathijs

last: Baens


title: Sorted B cells from mice treated with MPL and/or R837

city: SÃO PAULO

first: Helder

middle: I.

last: Nakaya

state: SÃO PAULO

address: AVENIDA PROFESSOR LINEU PRESTES, 580, Block 17

country: Brazil

institute: Universidade de São Paulo

summary: Many successful vaccines induce persistent antibody responses that can last a lifetime. The mechanisms by which they do so remain unclear, but emerging evidence suggests that activate dendritic cells (DCs) via Toll-like receptors (TLRs). For example, the yellow fever vaccine YF-17D,  one of the most successful empiric vaccines ever developed, activates DCs via multiple TLRs to stimulate pro-inflammatory cytokines. Triggering specific combinations of TLRs in DCs can induce synergistic production of cytokines, which results in enhanced T cell responses, but its impact on antibody responses remain unknown. Learning the critical parameters of innate immunity that programs such antibody responses remains a major challenge in vaccinology. We demonstrated that immunization of mice with synthetic nanoparticles containing antigens plus Toll-like receptor (TLR) ligands 4 (MPL) + 7 (R837) induces synergistic increases in antigen-specific, neutralizing antibodies compared to immunization with a single TLR ligand. To determine whether there was any early programming of B cells, we isolated isotype switched, TCRbeta-CD11b-CD19+IgD-IgG+ B cells by FACS at 7 days post immunization with nanoparticles containing various adjuvants plus OVA, and performed microarray analyses to assess their molecular signatures.

overall_design: Two independent sets of samples at day 7 post-treatment were used in our analyses. Each set is comprised by B-cells from mice treated with MPL + R837 or from those treated with either individual MPL or R837 alone.

first: Sudhir

last: Kasturi

first: Ioanna

last: Skountzou

middle: I

first: Bali

last: Pulendran


title: Genomic landscape of meningiomas

first: Stanley

last: Nelson

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


title: Profiling of promoter occupancy by PPARα in human hepatoma cells via ChIP-chip analysis

status: Public on Nov 23 2010

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary: The transcription factor Peroxisome Proliferator-Activated Receptor α (PPARα) is an important regulator of hepatic lipid metabolism. While PPARα is known to activate transcription of numerous genes, no comprehensive picture of PPARα binding to endogenous genes has yet been reported. To fill this gap, we performed ChIP-chip in combination with transcriptional profiling on HepG2 human hepatoma cells treated with the PPARα agonist GW7647. We found that GW7647 increased PPARα binding to 4220 binding regions. GW7647-induced binding regions showed a bias around the transcription start site and most contained a predicted PPAR binding motif. Several genes known to be regulated by PPARα, such as ACOX1, SULT2A1, ACADL, CD36, IGFBP1 and G0S2, showed GW7647-induced PPARα binding to their promoter. A GW7647-induced PPARα-binding region was also assigned to SREBP-targets HMGCS1, HMGCR, FDFT1, SC4MOL, and LPIN1, expression of which was induced by GW7647, suggesting cross-talk between PPARα and SREBP signaling. Our data furthermore demonstrate interaction between PPARα and STAT transcription factors in PPARα-mediated transcriptional repression, and suggest interaction between PPARα and TBP and C/EBPα in PPARα-mediated transcriptional activation. Overall, our analysis leads to important new insights into the mechanisms and impact of transcriptional regulation by PPARα in human liver and highlight the importance of cross-talk with other transcription factors.

overall_design:
HepG2 cells were grown in phenol red-free Dulbecco’s modified medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin. Cells were split the day before experiments. Cells were kept at 37 °C and 5% CO2. The following day, cells were treated with either 100 nM of the PPARα agonist GW7647 or control vehicle (DMSO). Cells used for gene expression analysis were harvested after 6 h or 24 h of GW7647 treatment.

This submission represents the gene expression component of the study.

first: David

last: van der Meer

first: Tatjana

last: Degenhardt

first: Sami

last: Väisänen

first: Philip

last: de Groot

first: Merja

last: Heinäniemi

first: Sacco

last: de Vries

first: Michael

last: Müller

first: Carsten

last: Carlberg

first: Sander

last: Kersten


title: Circadian transcriptional profiling of peritoneal macrophages

status: Public on Nov 24 2010

first: Bert

last: Maier

address: Hessische Straße 3-4

department: Institute for Medical Immunology

institute: Charité Universitätsmedizin

summary: In the immune system various parameters and immune functions are controlled by the circadian system. To investigate molecular mechanisms that link the circadian clock and the immune system we analyzed the transcriptom of peritoneal macrophages from mice collected in a time course for two consecutive days. We found that more than 8% of expressed genes are under circadian control including many important regulators in pathogen recognition, signal transduction and cytokine secretion.

overall_design: Peritoneal macrophages from mice kept in constant conditions were isolated in 4 h intervalls over a period of 48 h. RNA of CD11b sorted cells was extracted, pooled from 3 mice per time point and used for microarray analysis.

first: Jeannine

last: Mazuch

first: Achim

last: Kramer


title: Gene expression profiling of four subpopulations in GBM

status: Public on Nov 21 2010

city: new york

first: Viviane

last: Tabar

state: NY

address: 411 east 67th street

department: neurosurgery

institute: MSKCC

summary: GBM is a heterogenous brain tumor with hyperproliferation of endothelial cells. In order to understand the cellular mechanism of vasculogenesis in GBM, four fractions of cells are seperated. Microarray assays was performed to examine the potential lineage relationship and the signal pathways involved in determining the cell identity and function.

overall_design: Four subpopulation of cells were seperated from two independent GBM dissociates by FCAS assay based on the expression of membrane marker CD133 and CD144. Total RNA was extracted from freshly sorted cells without any culture.


title: Testis developmental gene expression in cryptorchid boys at risk of azoospermia

city: Basel

first: Edward

middle: James

last: Oakeley

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

summary:
Despite timely and successful surgery, 32% of patients with bilateral and 10% with unilateral cryptorchidism will develop azoospermia. Cryptorchid boys at risk of azoospermia display a typical testicular histology of impaired mini-puberty at the time of the orchidopexy.
During mini-puberty increased gonadotropin and testosterone secretion stimulate transformation of gonocytes into Ad spermatogonia. In azoospermia risk group this transformation is to a great extent impaired. This study aimed to analyze data on whole genome expression signatures of undescended testes at risk of developing azoospermia.

overall_design: Twenty-three testicular biopsies from 22 boys were analyzed (19 testes from 18 boys with cryptorchidism) and 4 contralateral descended testes from patients with testicular agenesis. Expression profiling identified 483 genes not or under-expressed in the azoospermia risk group compared with the control and LAZR groups. Annotated loci were associated with spermatogenesis. Other significant genes were cellular defense response genes and hormone controlled loci involved in spermatogenesis. Some genes transcribed in normal adult meiotic and post-meiotic germ cells are activated in healthy juvenile Ad spermatogonia. Thus, molecular events initiating the testicular expression program at the onset of puberty and maintaining it during adulthood occur very early in prepubertal testes. This molecular event is to a great extent impaired in HAZR group lacking Ad spermatogonia (stem cells for spermatozoa) indicating impaired mini puberty.

first: F

last: Hadziselimovic

first: N

middle: O

first: P

last: Demougin

first: E


title: The ERAD inhibitor Eeyarestatin I is a bifunctional compound with an ER localizing domain and a p97/VCP inhibitory group

city: Bethesda

first: WeiPing

last: Chen

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

summary:
Protein homeostasis in the endoplasmic reticulum (ER) has recently emerged as a therapeutic target for cancer treatment. Disruption of ER homeostasis results in ER stress, which is a major cause of cell death for cells exposed to the proteasome inhibitor Bortezomib, an anti-cancer drug approved for treatment of multiple myeloma and Mantle cell lymphoma. We recently reported that the ERAD inhibitor Eeyarestatin I (EerI) also disturbs ER homeostasis and has anti-cancer activities resembling that of Bortezomib.
Our findings reveal a class of bifunctional chemical agents that can preferentially inhibit membrane-bound p97 to disrupt ER homeostasis and induce tumor cell death. These results also suggest that the AAA ATPase p97 may be a potential drug target for cancer therapy.

overall_design: Cells were treated with EerI, CBU-028, or 5-NA each at 10uM in duplicates for 10h

first: Qiuyan

last: Wang

first: Bidhan

middle: A

last: Shinkre

first: Jin-gu

last: Lee

first: Marc

last: Weniger

first: Yanfen

last: Liu

first: Weiping

first: Adrian

last: Wiestner

first: William

last: Trenkle

first: Yihong

last: Ye


title: KLF13 regulate memory-like CD8 T cells

first: Dazhi

last: Lai

address: 10 Center Dr, 7B20A

department: NHLBI

institute: NIH

summary: “Memory-like T cells” are a subset of thymic cells that acquire effector function through the maturation process rather than interaction with specific antigen. Disruption of genes encoding T cell signaling proteins or transcription factors have provided insights into the differentiation of such cells. We show here that in BALB/c but not C57BL/6 mice, a large portion of thymic CD4-CD8+ T cells exhibit a memory-like phenotype. In BALB/c mice, IL-4 secreted by invariant natural killer T (iNKT) cells is both essential and sufficient for the generation of memory-like T cells. In C57BL/6 mice, iNKT cells are less abundant, producing IL-4 that is insufficient to induce thymic memory-like CD8+ T cells. BALB/c mice deficient in the transcription factor Kruppel-like factor (KLF) 13 have comparable numbers of iNKT cells to C57BL/6 mice and extremely low levels of thymic memory-like CD8+ T cells.  This work documents the dramatic impact of a small number of KLF13-dependent iNKT cells.

overall_design: FACS-sorted naive splenic CD8 T cells from wild type and KLF13 ko mice were compared.

first: Carol

last: Clayberger

first: Alan

last: Krensky


title: Expression profiling of mouse ing2 -/- mice with spermatogenic arrest and infertility

status: Public on Nov 19 2010

first: Ana

last: Robles

address: 37 Convent Dr 37/3060D

institute: National Cancer Institute/NIH

summary: Expression profiling of mouse ing2 -/- testis vs WT reveals gene expression differences consistent with spermatogenic arrest and infertility. Ing2 is indispensable for male germ cell development in mice. While mice deficient for Ing2 were born and grew without apparent abnormalities, male, but not female, were infertile, consistent with the highest expression of Ing2 in testes in wild-type mice and in humans. Histological and DNA content analyses in Ing2-/- testes revealed a spermatogenesis arrest at meiotic phase and enhanced apoptosis associated with increased p53, resulting in a  decline in mature spermatozoa, which became more severe in older age. HDAC1 accumulation and core histone deacetylation at pachytene stage were impaired in Ing2-/- testes, suggesting that the recruitment of HDAC1 by Ing2 plays a critical role in spermatogenesis. This study establishes Ing2 as a novel mammalian regulator of spermatocyte differentiation, which coordinates spermatogenesis stage-specific histone modifications. This study has implications in understanding human male infertility.

overall_design: Testis from WT and Ing2 KO mice at 2-3 months of age where analyzed for differences in gene expression.

first: Motonobu

last: Saito

first: Kensuke

last: Kumamoto

first: Izumi

last: Horikawa

first: Curtis

last: Harris


title: Expression data from human alternatively activated macrophages

status: Public on Nov 18 2010

city: Boston

first: Attila

last: Szanto

address: 185 Cambridge St.

department: Molecular Biology

institute: Massachusetts General Hospital

summary: Human CD14 positive monocytes were purified from healthy volunteers’ blood and cultured in vitro for 6 hours. While culturing, macrophages were activated alternatively with interleukin-4 (IL-4 100 ng/ml). Simultaneously, macrophages were also treated with vehicle (DMSO:ethanol) or 1uM synthetic PPARg agonist, Rosiglitazone. We used Affymetrix microarrays (U133Plus 2.0) to analyze activation and PPARg-induced gene expression changes.

overall_design: Monocytes from 2 donors were used and treated as indicated in Summary. Technical replicates were generated from each sample.

first: Laszlo

last: Nagy


title: Gene expression analysis of Hodgkin and non-Hodgkin lymphoma cell lines

status: Public on Nov 17 2010

first: Karl

last: Koechert

address: Robert-Roessle-Str. 10

institute: Max-Delbrueck-Centre for Molecular Medicine

summary: Genomewide gene expression analysis of lymphoid cell lines of Hodgkin, non-Hodgkin and acute leukemia origin

overall_design: Affymetrix U133 Plus 2.0 oligonucleotide arrays were hybridized to determine the gene expression profile of Hodgkin (L428, L1236, KM-H2, HDLM-2, L540, L540Cy), non-Hodgkin (Namalwa, SU-DHL-4) and acute lymphoblastic leukemia (Reh) cell lines; all hybridizations were done in biological duplicates (except L540, L50Cy, SU-DHL-4).

first: Martin

last: Janz

first: Stephan

last: Mathas

last: Köchert


title: Gene expression in endometrial cancer cells treated with metastin-10 (kp10)

first: Tsukasa

last: Baba

address: 54 Shogoin Kawahara-cho, Sakyo-ku

department: Department of Gynecology and Obstetrics

institute: Kyoto University Graduate School of Medicine

summary: Invasion into deep myometrium and/or lymphovascular space is a well-known risk factor for endometrial cancer metastasis, resulting in poor prognosis. It is therefore clinically important to identify novel molecules that suppress tumor invasion. Reduced expression of the metastasis suppressor, KISS1 (kisspeptin), and its endogenous receptor, GPR54, has been reported in several cancers, but the significance of the KISS1/GPR54 axis in endometrial cancer metastasis has not been clarified. Metastin-10 is the minimal bioactive sequence of genetic products of KISS1. Clinicopathological analysis of 92 endometrial cancers revealed overall survival is improved in cancers with high expression of GPR54. Through RNAi and mousemodel analyses, metastin-10 was predicted to suppress invasion and metastasis of GPR54-expressing endometrial cancers. These data suggest that metastin-10 may induce genetic changes in the metastatic character of endometrial cancers.

overall_design:
We used microarrays to clarify the changes of gene expression along with metastin-10 treatment and to confirm whether the changes were derived via the metastin-GPR54 axis.
Gene expression microarray data (Affymetrix U133 Plus 2.0) for Ishikawa cells treated with or without 10μM metastin-10 and/or GPR54 siRNA were generated in triplicate and RMA-normalized.

first: Hyun

middle: S

last: Kang

first: Masaki

last: Mandai

first: Noriomi

last: Matsumura

first: Junzo

last: Hamanishi

first: Budiman

last: Kharma

first: Eiji

last: Kondoh

first: Yumiko

last: Yoshioka

first: Shinya

last: Oishi

first: Nobutaka

last: Fujii

first: Susan

last: Murphy

first: Ikuo

last: Konishi


title: Licensing of PPARg-regulated gene expression by IL-4-induced alternative macrophage activation

first: Attila

last: Szanto

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Expression data from human blood samples

city: Barcelona

first: Sophie

last: Domingues

address: Pg Vall d’Hebron 119-129

department: Department of Neurology

institute: Institut de Recerca Hospital Vall d’Hebron

summary:
Genetic factors contribute to the development of ischemic stroke but their identity remains largely unknown. We tested the association with ischemic stroke of 210 single nucleotide polymorphisms (SNPs) associated with pathways functionally related to stroke. We observed an association between the rs7956957 SNP in LRP1 and next performed microarrays analysis in healthy individuals to investigate possible associations of LRP genotypes with the expression of other genes.
Twelve blood samples were obtained from twelve different healthy subjects carrying different genotypes for the rs7956957 SNP of the LRP1 gene (GG, CG or CC).

overall_design: Blood was extracted from 12 subjects. EDTA tubes were centrifuged at 3500rpm for 15 min to obtain the white blood cell fraction and the samples were stored at -80ºC until RNA isolation. RiboPureTM -Blood kit from Ambion (Ambion, Woodward st. Austin, USA) was used to extract total RNA following manufacturer’s instructions. Globin RNA from erythrocytes that causes interference was extracted using the Globin-Clear kit (Ambion, Woodward st. Austin, USA).

last: Domingues-Montanari

first: Israel

last: Fernández-Cadenas

first: Alberto

last: del Río-Espinola

first: Maite

last: Mendioroz

first: Anna

last: Penalba

first: Marc

last: Ribo

first: Dolors

last: Giralt

first: Manolo

last: Quintana

first: Marta

last: Rubiera

first: Jessica

last: Fernandez-Morales

first: José

last: Alvarez-Sabin

first: Joan

last: Montaner


title: Transcriptome in alveolar epithelial progenitor cells isolated from adult human lung

status: Public on Nov 16 2010

city: Sendai

first: Hiroshi

last: Kubo

address: 2-1 Seiryoumachi, Aobaku

department: Advanced Preventive Medicine for Infectious Disease

institute: Tohoku University Graduate School of Medicine

summary: Resident stem/progenitor cells in the lung are important for tissue homeostasis and repair. However, a progenitor population for alveolar type II (ATII) cells in adult human lungs have not been identified. Here we isolated alveolar epithelial progenitor cells (AEPCs) from adult human lungs. AEPCs showed mesenchymal stem cell (MSC)-like characteristics combined with ATII cell-phenotypes. AEPCs had the capability for self-renewal and the potential to generate ATII cells in vitro. Furthermore, cells expressing similar markers were present within alveolar walls in normal lungs and these cells were significantly increased in ATII cell hyperplasias. These results suggest that adult human lungs contain a progenitor population for ATII cells.

overall_design: We isolated AEPCs from tissue samples obtained from patients who underwent lung resection at the Department of Thoracic Surgery at Tohoku University Hospital. We profiled the gene expression in three different batches of the AEPCs. We extracted total RNA from the confluent cells at passage 4. This study was approved by the Ethics Committee at Tohoku University School of Medicine. All subjects gave informed consent.

first: Naoya

last: Fujino


title: Gene expression profiles of primary cultured ovarian cells in the presence and absence of a DNA methyltransferase inhibitor

city: Durham

first: Susan

middle: K.

last: Murphy

state: NC

address: B226 LSRC B Wing, Research Drive, Box 91012

department: Obstetrics and Gynecology

institute: Duke University Medical Center

summary: Epithelial ovarian cancer is the leading cause of death among gynecologic malignancies.  Diagnosis usually occurs after metastatic spread, largely reflecting vague symptoms of early disease combined with lack of an effective screening strategy.  Epigenetic mechanisms of gene regulation, including DNA methylation, are fundamental to normal cellular function and also play a major role in carcinogenesis. To elucidate the biological and clinical relevance of DNA methylation in ovarian cancer, we conducted expression microarray analysis of 39 cell lines and 17 primary culture specimens grown in the presence or absence of DNA methyltransferase (DNMT) inhibitors. Two parameters, induction of expression and standard deviation among untreated samples, identified 378 candidate methylated genes, many relevant to TGF-beta signaling. We analyzed 43 of these genes and they all exhibited methylation.  Treatment with DNMT inhibitors increased TGF-beta pathway activity. Hierarchical clustering of ovarian cancers using the 378 genes reproducibly generated a distinct gene cluster strongly correlated with TGF-beta pathway activity that discriminates patients based on age. These data suggest that accumulation of age-related epigenetic modifications leads to suppression of TGF-beta signaling and contributes to ovarian carcinogenesis.

overall_design: Seventeen primary cultures of ovarian cells (two pooled normal ovarian surface epithelium, two serous borderline tumors, one endometrioid and twelve serous epithelial ovarian cancers) were mock treated or  treated with 5 µM 5-AzaC for 72 hours, followed by gene expression microarray analysis to enable identification of genes differentially expressed as a result of inhibition of DNA methyltransferase activity.


title: Expression data from human macrophages

last: Szanto

summary: Human CD14 positive monocytes were purified from healthy volunteers’ blood and cultured in vitro for 4, 12, 24, 72 hours. While culturing, macrophages were activated alternatively with interleukin-4 (IL-4 100 ng/ml) or classically with interferon-gamma (IFNg 100 ng/ml)+tumor necrosis factor (TNF 50 ng/ml) or left without activation. Simultaneously, macrophages were also treated with vehicle (DMSO:ethanol) or 1mM synthetic PPARg agonist, Rosiglitazone. We used Affymetrix microarrays (U133Plus 2.0) to analyze activation and PPARg-induced gene expression changes.

overall_design: Monocytes from 3 donors were used and treated as indicated in Summary.

first: Laszlo

last: Nagy


title: Hodgkin lymphoma

status: Public on Dec 11 2010

city: Vancouver

first: Christian

last: Steidl

address: 675 West 10th Avenue

department: Pathology

institute: BC Cancer Agency

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

overall_design:
Refer to individual Series

*** This submission represents the microarray gene expression and microarray copy number components of the study


title: Restoring miR-200c to aggressive endometrial cancer cell line

city: Aurora

first: Erin

middle: N.

last: Howe

state: CO

address: UCD AMC, Mail Stop 8104 PO Box 6511

institute: University of Colorado at Denver, Anschutz Medical Campus

summary: Using a mimic miR-200c was restored to an aggressive, Type 2 endometrial cancer cell line, Hec50

overall_design: We sought to identify genes regulated by miR-200c in an aggressive cancer.

first: Dawn

middle: R

last: Cochrane

first: Jennifer

last: Richer


title: Expression data from breast tumors and reduction mammoplasty explants

city: Pittsburgh

first: Jean

middle: Johanna

last: Latimer

state: Pennsylvania

address: 5150 Centre Avenue

institute: University of Pittsburgh

summary:
Breast tumorigenesis involves modulation of gene expression.
We used microarrays to detail the global program of gene expression underlying breast tumorigenesis.

overall_design: Three examples of stage I breast tumor and 3 samples of breast reduction mammoplasty tissue were expanded as explant cultures for RNA extraction and hybridization to Affymetrix microarrays.

middle: J

first: Stephen

last: Grant


title: Expression data from hepatocellular carcinoma and adjacent normal liver tissue

status: Public on Nov 14 2010

city: Philadelphia

first: Hojun

last: Li

address: 3501 Civic Center Boulevard

department: Hematology

institute: Children's Hospital of Philadelphia

summary: Assay of gene expression pattern differences between liver cancer tissue and normal liver tissue from the same mouse by microarray in 4 separate mice injected with recombinant adeno-associated viral (AAV) vector

overall_design: 4 Mice (M24, M48, M50, M60) were necropsied at 18 months post-injection of AAV-vector, and livers removed.  Tumor tissue and adjacent normal tissue were identified and dissected for RNA extraction.

first: Katherine

last: High


title: Effects of TX527, a hypocalcemic vitamin D analog on human activated T lymphocytes

status: Public on Nov 15 2010

first: Femke

last: Baeke

address: O&N1, Herestraat 49 box 902

department: Experimental Medicine

institute: Katholieke Universiteit Leuven

summary:
Hypocalcemic vitamin D analogs are appealing molecules to exploit the immunomodulatory actions of active vitamin D in vivo. The functional modulation of dendritic cells is regarded as the key mechanism underlying their ability to regulate T cell responses. In contrast, the direct actions of vitamin D and structural analogs on T lymphocytes remain less well characterized.
Microarray analysis was performed to gain insight into the direct immunomodulatory actions of TX527, a hypocalcemic vitamin D analog, on human T lymphocytes. Gene expression analysis revealed that TX527 regulated a wide variety of genes involved in different aspects of T cell function, including cellular growth and proliferation, cell death, cellular development, cellular movement and cell-to-cell signalling and interaction.

overall_design: Human CD3+ T cells, isolated from peripheral blood from healthy donors, were activated by anti-CD3/anti-CD28 and cultured in the presence of TX527 (10-8M) or vehicle (ethanol) for 10 days. Expression profiles of TX527-treated and vehicle-treated T cells were compared using Affymetrix Human Genome U133 Plus 2.0 Arrays.

first: Hannelie

last: Korf

first: Lut

last: Overbergh

first: Annemieke

last: Verstuyf

first: Lieven

last: Thorrez

first: Leentje

last: Van Lommel

first: Mark

last: Waer

first: Frans

last: Schuit

first: Conny

last: Gysemans

first: Chantal

last: Mathieu


title: Effect of PDE4 inhibition on host gene expression of Mtb-infected mouse lungs.

status: Public on Nov 13 2010

city: Newark

first: Mi-Sun

last: Koo

state: NJ

address: 225 Warren Street, W250Q

department: Public Health Research Institute

institute: University of Medicine and Dentistry of New Jersey

summary: Global gene expressions of Mtb-infected mouse lungs were compared between with and without PDE4 inhibitor treatment.  A lot of host genes are differentially expressed 21d and 28d post-Mtb infection.  PDE4 inhibitor, however, downregulate 10% of genes among those and genes differentially regulated by PDE4 inhibitor are mainly involved immune response.

overall_design: Total RNA was isolated from Mtb-infected mouse lungs with or without CC-3052 (25 mg/kg/day) using Trizol reagent and gene profile was analyed using Affymetrix mouse ST 1.0

first: Hong

last: Guo

first: Gilla

last: Kaplan


title: Direct Conversion of Trophoblast Stem Cells into Pluripotent Stem Cells by Oct4

status: Public on Nov 12 2010

city: Beijing

first: Tong

last: Wu

address: No. 7, Science Park Road, Zhongguancun Life Science Park, Beijing

country: China

institute: National Institute of Biological Sciences, Beijing

summary: Embryonic stem (ES) cells and trophoblast stem (TS) cells are both derived from early embryos, yet these cells have distinct differentiation properties. ES cells can differentiate into all three germ layer cell types, whereas TS cells can only differentiate into placental cells. It has not been determined whether TS cells can be converted into ES-like pluripotent stem (PS) cells. Here we report that overexpression of a single transcription factor, Oct4, in TS cells is sufficient to convert TS cells into a pluripotent state. These Oct4 induced pluripotent stem (OiPS) cells have the epigenetic characteristics of ES cells, including X chromosome reactivation and elevated H3K27 me3 modifications. The gene expression profile of OiPS cells and ES cells was very similar. Moreover, OiPS cells can differentiate into the three germ layer cell types in vitro and in vivo. More importantly, chimeric mice with germline transmission could be efficiently produced from OiPS cells. To our knowledge, this is the first evidence showing that only one single transcription factor could convert the non-embryonic TS cells into pluripotent stem cells with pluripotency.

overall_design: Gene expression profile of iPS cells and trophoblast stem cells were generated by Affymetrix Mouse Gene 1.0 ST Array. The Gene expression profile of  ES cell R1 in GSE17004 was used as control. Three biological repeats were included for each line.


title: Novel mediators of eicosanoid and epithelial nitric oxide production in asthma

status: Public on Nov 10 2010

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary: Asthma is a heterogeneous disease. Exercise-induced bronchoconstriction (EIB) is a distinct syndrome that occurs in 30-50% of asthmatics and is characterized by high levels of pro-inflammatory eicosanoids. We identified genes differentially expressed in the airways of asthmatics with EIB relative to asthmatics without EIB. Genes related to epithelial repair and mast cell infiltration including beta-tryptase and carboxypeptidase A3 were upregulated by exercise challenge in the asthma group with EIB. We confirmed that two novel mediators trefoil factor 3 (TFF3) and transglutaminase 2 (TGM2) have increased expression in airways cells and secreted product in the airways. In vitro studies indicate that 1) TFF3 induces nitric oxide synthase in airway epithelial cells from asthmatics and 2) TGM2 augments the enzymatic activity of secreted phospholipase A2 (sPLA2) group X, an enzyme recently been implicated in asthma pathogenesis. Since PLA2 serves as the first rate-limiting step leading to eicosanoid generation, these results suggest that TGM2 may be a key initiator of the airway inflammatory cascade in asthma.

overall_design: EIB positive and EIB negative subjects sampled pre- and post-exercise

first: Richard

last: Beyer

first: Teal

last: Hallstrand

middle: M

last: Wurfel

first: Ying

last: Lai

first: Zhanglin

last: Ni

first: Michael

middle: H

last: Gelb

first: William

last: Altemeier

first: Moira

middle: L

last: Aitken

last: Henderson


title: Expression data from BAP1 depleted cells

status: Public on Nov 05 2010

city: Montreal

first: El Bachir

last: Affar

address: 5415 boul. De l'Assomption

institute: Maisonneuve-Rosemont Hospital, University of Montreal

summary:
The deubiquitinase BAP1 is a candidate tumor suppressor regulating cell proliferation in human and is required for development in Drosophila. BAP1 is assembled into high molecular weight transcriptional multi-protein complexes.
In order to identify potential BAP1 target genes, global mRNA expression profiling using microarrays was conducted.

overall_design: U2OS cells, transfected with a non-target control shRNA or shRNAs targeting BAP1, were selected with puromycin containing medium and then synchronized at the G1/S border to allow comparative analysis of gene expression.

first: Helen

last: Yu

first: El-Bachir


title: Effect of von Willebrand factor on gene expression in HUVECs

city: Stony Brook

first: Sergey

middle: V.

last: Doronin

address: Nicolls Rd

department: Physiology&Biophysics

institute: Stony Brook University

summary:
Von Willebrand factor is a paracrine/autocrine  regulator of human mesenchymal stem cell adhesion to distressed/apoptotic endothelial cells.
This data set examines effect of vWF on gene expression in HUVECs.

overall_design: HUVECs were maintained in EGM2 media and treated with vWF in Hank's buffered salt solution (HBSS).

first: Irina

last: Potapova


title: An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer: gene expression

first: Raj

last: Chari

state: BC

department: Cancer Genetics and Developmental Biology

institute: BC Cancer Research Centre

type:
Expression profiling by array
Third-party reanalysis

summary: 10 Breast cancer cell lines profiled on the Affymetrix U133 Plus 2.0 platform used in conjunction with matched DNA copy number and DNA methylation data for integrative analysis.

overall_design: In total, 10 samples were used. The MCF10A profile used as normal was obtained from GSM254525 and the remaining 2 cell lines were obtained from caBIG. Full RMA normalized expression profile is attached.


title: Gene Expression profiles of human iPS cells from CBC

status: Public on Nov 03 2010

city: Kobe

first: Shin

last: Kawamata

state: Hyogo

department: The Basic Reserch Group for Regenerative Medicine

institute: Foundation for Biomedical and Innovation

summary: We investigated that gene expression profile of generated human iPS cells from cord blood cells using temperature sensitive sendai-virus vector.

overall_design: three samples

first: Naoki

last: Nishishita


title: Human Trophoblast Responses to P. gingivalis Infection

status: Public on Nov 02 2010

city: Louisville

last: Lamont

state: KY

address: 570 South Preston Street

department: Oral Biology

institute: University of Louisville

summary: Porphyromonas gingivalis is a periodontal pathogen that is also associated with preterm low birth weight delivery.  We investigated the transcriptional responses of human extravillous trophoblasts (HTR-8) to infection with P. gingivalis.  Over 2000 genes were differentially regulated in HTR-8 cells by P. gingivalis.  In ontology analyses of regulated genes, overpopulated biological pathways included MAP kinase signaling and cytokine production.  Immunoblots confirmed over expression of the MAP kinase pathway components MEK3, p38 and Max.  Furthermore, P. gingivalis infection induced phosphorylation and activation of MEK3 and p38.  Increased production of IL-1β and IL-8 by HTR-8 cells was demonstrated phenotypically by ELISA of HTR-8 cell lysates and culture supernatants.  Thus infection of trophoblasts by P. gingivalis can impact signal transduction pathways and modulate cytokine expression, outcomes that could disrupt the maintenance of pregnancy.

overall_design:
P. gingivalis were reacted with HTR-8 cells at an MOI of 200 for 2 hours at 370C in 5% CO2.  Co-cultures were carried out in quadruplicate.  The HIGK cells were lysed with Trizol (Invitrogen) prior to RNA extraction.  RNA isolation, cDNA synthesis, labeled cRNA synthesis and chip hybridization were conducted as previously described (Handfield et al., 2005).  Briefly, total RNA was extracted from Trizol-lysed cells, treated with DNase I, purified and quantified according to standard methods (Qiagen, Valencia, CA; and Affymetrix, Santa Clara, CA). Complementary DNA (cDNA) synthesis was performed according to the Affymetrix protocol (SuperScript double-stranded cDNA synthesis kit; Invitrogen,) with 8 µg of total cellular RNA used as a template to amplify mRNA species for detection.  Double-stranded cDNA was purified, and used as a template for labeled complementary RNA (cRNA) synthesis. In vitro transcription was performed using a BioArray high-yield RNA transcript labeling kit (T7) (Enzo Life Science, Farmingdale, NY), to incorporate biotinylated nucleotides.  cRNA was subsequently fragmented and hybridized onto Genechip Human Genome (HG) U133-A Plus 2.0 oligonucleotide arrays (Affymetrix) with proper controls.  Each sample was studied in parallel, and the samples were not pooled. The microarrays were hybridized for 16 h at 45°C, stained with phycoerythrin-conjugated streptavidin and washed according to the Affymetrix protocol (EukGE-WS2v4) using an Affymetrix fluidics station, and scanned with an Affymetrix GeneChip 3000 scanner.
Microarray data analysis was performed as previously described (Mans et al., 2006, Hasegawa et al., 2008).  Briefly, expression filters were applied to remove Affymetrix controls and probe-sets whose signal was undetected across all samples. The signal intensity values of the resulting dataset were variance-normalized, mean-centered and ranked by their coefficients of variation.  Normalization was performed to give equal weight to all probe-sets in the analysis, regardless of the order of magnitude of the raw signal intensity. To reduce the confounding effect of background signal variation on the analysis, only the half of the dataset demonstrating the most variation across samples was used to perform unsupervised hierarchical cluster analysis using Cluster software (Eisen et al., 1998). The resulting heat-map and cluster dendrograms were visualized with Treeview software Eisen  to reveal the extent of characteristic host cell responses to each infection state, defined as identical treatments clustering together.  Additional quality control data for the arrays is provided in the supplemental material.
Following initial assessment of the host cell response to each condition, supervised analysis was performed to investigate differences in gene regulation among experimental conditions. For this analysis, the raw signal intensities were log2-transformed for all probe-sets that passed the initial expression filters, and were correlated using BRB Array Tools (Simon and Peng-Lam, National Cancer Institute, Rockville, MD). In each supervised analysis, biological replicates were grouped into classes according to their infection state during co-culture experiments and probe sets significant at the p < 0.001 level between classes were identified. To test the ability of these significant probe sets to truly distinguish between the classes, leave-one-out-cross-validation (LOOCV) studies were preformed. In these LOOCV studies each array was left out in turn and a classifier was derived between the groups by selecting probe sets significant at p < 0.001. The significant probe sets were then used with several prediction models (compound covariate predictor, nearest neighbor predictor, and support vector machine predictor) to predict the class identity of the array that was left out and not included when the classification model was built. The significance (p<0.001) of the LOOCV analysis was estimated using a Monte Carlo simulation with 2,000 permutations of the dataset.
	KEGG pathways were populated using Pathway Express (Khatri et al., 2005), available at http://vortex.cs.wayne.edu/projects.htm

first: Jeffrey

last: Mans


title: Deconvoluting Early Post-Transplant Immunity Using Purified Cell Subsets Reveals Functional Networks Not Evident by Whole Blood Analysis

status: Public on Nov 01 2010

city: La Jolla

first: Sunil

last: Kurian

state: CA

address: 10550 N Torrey Pines Road

department: Molecular and Experimental Medicine

institute: The Scripps Research Institute

summary:
In this study we employed transcriptome  mRNA profiling of whole blood and purified CD4, CD8 T cells, B cells and monocytes in tandem with high-throughput flow cytometry in 10 kidney transplant patients sampled serially pre-transplant, 1, 2, 4, 8 and 12 weeks. We then mechanistically deconvoluted the early post-transplant immune response. The flow cytometry data confirms depletion of specific cell subsets in response to ATG  induction and immunosuppression with sustained decreases in CD4 as well as CD8 cell subsets. A series of T cell activation markers were expressed from Pre-Tx to 12 weeks indicating the evolution of immunity including expansion of CD45RO+CD62L- effector memory cells. Serial whole blood transcript monitoring demonstrated over 2000 differentially expressed genes, with over 80 percent down-regulated Post-Tx. However, cell subset analysis revealed a unique spectrum of subset-specific gene expression with time-dependent changes, with contrasting significant Post-Tx gene upregulation. Our results provide a unique view of the complex evolution of immune/inflammatory molecular networks marking the early post transplant immune response. A critical finding is that analysis of the constituent blood cell subsets provides an entirely new level of detail revealing the nature of this process, effectively deconvoluting the changes that are otherwise lost in the noise of cellular complexity of whole blood.

Keywords: kidney transplantation, peripheral blood, DNA microarrays, acute kidney rejection, cell subsets, flow cytometry, serial monitoring

overall_design: We employed Affymetrix HG-U133 Plus 2.0 GeneChips for mRNA profiling of whole blood and purified CD4, CD8 T cells, B cells and monocytes in tandem with high-throughput flow cytometry in 10 kidney transplant patients sampled serially pre-transplant, 1, 2, 4, 8 and 12 weeks. We then mechanistically deconvoluted the early post-transplant immune response.


title: Large intergenic non-coding RNAs as novel modulators of reprogramming: siRNA (gene expression)

city: Cambridge

first: Nataly

middle: Moran

last: Cabili

state: MA

address: 7  Cambridge Center

institute: Broad Institute ;  Harvard University

summary: lincRNA-ST8SIA3 was depleted using siRNAs and  associated gene expression changes were profiled on Affymentrix arrays

overall_design:
siRNAs targeting lincRNA-ST8SIA3 were transfected into human induced pluripotent stem cells; non-targeting siRNAs were used as controls
GPL570 ;Affymetrix Human Genome U133 Plus 2.0 Array [Affy_HG-U133_Plus_2]

first: Sabine

last: Loewer

first: George

middle: Q

last: Daley

first: John

last: Rinn


title: Effects of T350 phospho- on gene repression activity of EZH2

city: Minneapolis

first: Shuai

last: Chen

state: MN

address: MMC 806, 420 Delaware Street S.E.

department: Cancer Center

institute: University of Minnesota

summary:
The Polycomb group (PcG) protein enhancer of zeste homolog 2 (EZH2) plays an essential role in histone methylation-mediated epigenetic gene silencing. We demonstrate that under physiological conditions, cyclin-dependent kinase 1 (CDK1) and 2 (CDK2) bind to and phosphorylate EZH2 at threonine 350 (T350) in an evolutionally conserved motif.
T350 phosphorylation is required for EZH2 function in silencing of genes that promote differentiation and inhibit proliferation and migration. Blockage of T350 phosphorylation by generating a T350A mutation largely diminishes the global effect of EZH2 on gene silencing.

overall_design: Seven experiments have been designed. LNCaP cells were transfected with si-Control, si-EZH2, si-EZH2 plus RNAi resistant EZH2 plasmid, or si-EZH2 plus RNAi resistant T350A mutated EZH2 plsamid for 60 hours, or treated with DMSO, 5 uM TSA, or 10 uM Roscovitine for 24 hours. Two replicates per experiment.

first: Haojie

last: Huang


title: Large intergenic non-coding RNAs as novel modulators of reprogramming

type: Non-coding RNA profiling by genome tiling array

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

overall_design: Refer to individual Series


title: DC response to Respiratory syncytial virus from adult peripheral and cord blood

city: Nashville

first: James

last: Crowe

state: TN

address: T2219 21st Avenue South,

department: Vanderbilt Vaccine Center

institute: Vanderbilt University Medical Center

summary: Respiratory syncytial virus (RSV) is a major cause of morbidity and mortality. Previous studies have suggested that T cell responses may contribute to RSV immunopathology, which could be driven by dendritic cells (DCs). DCs are productively infected by RSV, and during RSV infections, there is an increase of DCs in the lungs with a decrease in the blood. Pediatric populations are particularly susceptible to severe RSV infections, however DC responses to RSV from pediatric populations have not been examined. In this study, primary isolated DCs from cord blood and adult peripheral blood were compared after RSV-infection. Transcriptional profiling and biological network analysis identified transforming growth factor (TGF)-b and associated signaling molecules as differentially regulated in the two age groups. TGF-b1 was decreased in RSV-infected adult blood DCs, but increased in RSV-infected cord blood DCs. Co-culture of adult RSV-infected DCs with autologous T-cells induced secretion of interferon gamma (IFNg), IL-12p70, IL-2, and tumor necrosis factor alpha (TNFa). Conversely, co-culture of cord RSV-infected DCs and autologous T-cells induced secretion of IL-4, IL-6, IL-1b, and IL-17. Addition of purified TGF-b1 to adult DC-T cell co-cultures reduced secretion of IFNg, IL-12p70, IL-2, and TNFa, which addition of a TGF-b chemical inhibitor to cord DC-T cell co-cultures increased secretion of IL-12p70. These data suggest that TGF-b acts as a major regulator of RSV DC-T cell responses, which could contribute to immunopathology during infancy.

overall_design: Three sets of adult peripheral DCs were analyzed and three sets of cord blood DCs.  The DCs from each donor were divided in half and either mock infected or infected with RSV and each (12 samples total) were used for affymetrix array analsis.  The donor-matched mock infected DC hybridyzation was used as the reference sample for the RSV infected.

first: Natalie

last: Thornburg

middle: E


title: Loss of sarcolipin  results in atrial remodeling

first: Gopal

last: Babu

address: 185 South Orange Ave

department: CELL BIOLOGY AND MOLECULAR MED

institute: University of Medicine & Dentistry of New Jersey-NJMS

summary: Sarcolipin (SLN) is a key regulator of SERCA pump in atria. To determine the role of SLN in atrial Ca2+ homeostasis, we have generated a SLN null (sln-/-) mouse model. Ablation of SLN results in increased SR Ca2+ load and Ca2+ transients in atria. Further, loss of SLN results in electrophysiological and strcutural remodeling of atria.

overall_design: The SLN knockout and C57/BL6 wildtype mice (each n=3) were selected for RNA extraction. The cRNA probes were hybridized to Affymetrix gene array.

first: Shanmugam

last: Mayilvahanan

first: Muthu

last: Periasamy

first: Ji

middle: Y

last: Park

first: Bin

last: Tian