title: Effects of EVI1 mild expression in HeLa cells

summary:
We studied the variations of mRNA amounts after Flag-EVI1 or Flag expression in HeLa cells.
Despites EVI1 discovery in 1988, its recognized role as a dominant oncogene in myeloid leukemia and more recently in epithelial cancers, only a few target genes were known and it was not clear why EVI1 was involved in cancer progression. Here we obtained the genomic binding occupancy and expression data for EVI1 in human cells. We identified numerous EVI1 target cancer genes and genes controlling cell migration and adhesion. Moreover, we characterized a transcriptional cooperation between AP1 and EVI1 that regulated proliferation and adhesion through a feed-forward loop. Furthermore, this study provides human genome-wide mapping and downstream analyses for EVI1 that will be useful for the research community.

overall_design: 8 samples were collected. Each condition was done in 4 replicates, collected 24 hours after transfection (for mild expression of EVI1). Transfections with Flag-expressing vector were used as controls.


title: Estrogen receptors in breast cancer stem cells

status: Public on Jan 12 2012

city: Stockholm

first: Johan

last: Hartman

department: Dept of Oncology and Pathology

country: Sweden

institute: Karolinska Institute

summary:
Breast cancer stem cells are considered estrogen receptor negative and estrogen insensitive. However, estrogens potentiate growth of the vast majority of breast tumors. In this study, we characterize the expression of estrogen receptors in breast cancer stem cells.
We used microarrays to characterize the global gene expression underlying estrogen receptor activation versus inhibition in breast cancer cells from invasive breast cancers.

overall_design: Cancer cells from invasive breast carcinomas are treated with D (DPN), T (4OHT) or untreated (vehicle control).

first: Linda

last: Lindström


title: Primary TNBC tumor in the presence or absence of SHP2

status: Public on Jan 16 2012

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

summary: The first bona fide PTP proto-oncogene was the Src-homology 2 domain-containing phosphatase SHP2 (encoded by PTPN11), an ubiquitously expressed PTP that transduces mitogenic, pro-survival, cell fate and/or pro-migratory signals from numerous growth factor-, cytokine- and extracellular matrix receptors. In malignancies, SHP2 is hyperactivated either downstream of oncoproteins or by mutations.We provide analysis of a primary triple-negative breast tumor grown as xenografts in the presence or absence of SHP2 for 30 days.

overall_design: A primary triple-negative breast tumor (BT8) was transduced with a doxycycline-inducible lentiviral vector expressing a CTRL miR or SHP2 miR1 or SHP2 miR2. Cells from each group were injected in imuunodeficient mice and after tumor development, the knockdown of SHP2 was induced for 30 days in vivo. At day 30, tumors were dissected and RNA isolated for gene expression analysis.

first: Nicola

last: Aceto

first: Stephane

last: Thiry

first: Mohamed

last: Bentires-Alj


title: Paired whole blood human transcription profiles from children with severe malaria and mild malaria

status: Public on Jan 11 2012

city: Bronx

first: Johanna

middle: Patricia

last: Daily

state: NY

address: 1301 Morris Park Avenue, Price Center

department: Medicine (Infectious Disease)

country: USA

institute: Albert Einstein College of Medicine

summary:
Whole blood transcriptomes from a longitudinal study of  5 Malawian children who first present with severe Plasmodium falciparum malaria, and return in one month with mild malaria
We used microarrays to identify transcripts that were associated with each clinical presentation.

overall_design: A blood sample was taken upon presentation during the severe and mild malaria episodes in 5 Malawian children (total n=5 pairs)  followed by RNA extraction and hybridization on Affymetrix GeneChip Human Gene 1.0 ST Array, using a paired analysis

middle: P


title: Expression data from knockdown of G9a in MDA-MB231 cells

status: Public on Jan 07 2012

city: Lexington

first: Binhua

last: Zhou

state: KY

address: 789 South Limestone

department: Markey Cancer Center/Biochemistry

institute: University of Kentucky School of Medicine

summary: G9a is an H3K9m2 methyltransferase, which is critical in controlling gene suppression and DNA methylation. We used microarray analysis to identify the target genes that are regulated by G9a in MDA-MB231 cells, in which E-cadherin is silenced.

overall_design: G9a expression was stably knocked-down in MDA-MB231 cells. RNA from this clone and parental (control) cells were purified for microarray analysis.

first: Dong

last: Chenfang


title: Cell cycle expression profiles in HeLa cells

status: Public on Jan 25 2012

city: Boston

first: Subhashini

last: Sadasivam

state: MA

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana Farber Cancer Insitute

summary: Periodic expression of cell cycle genes highlights the importance of precise temporal control of transcription in regulating cell cycle events. We used HeLa cells enriched for different phases of the cell cycle to identify genes that are expressed in a periodic fashion in specific cell cycle phases. These data were generated for comparison with ChIP-Sequencing data obtained for two subunits of the B-Myb-MuvB complex, B-Myb and LIN9, in HeLa cells.

overall_design: HeLa cells were synchronized at the beginning of S phase by double thymidine block and then released into the cell cycle by washing out the thymidine resulting in tight synchrony at S, G2 and M phases of the cell cycle. Most cells entered mitosis at 8 hours after release as determined by visual inspection. Three independent replicas of double thymidine block and release experiments were performed. RNA was isolated at specific times after release from the thymidine block (0, 2, 4, 6, 8 and 12 hours) and used for generating expression profiles.

first: James

middle: A

last: DeCaprio


title: Genome-wide binding map of FoxO1 and Pax5 in pre-B cells

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Genome-wide analysis of FoxO1 and Pax5 binding in pre-B cells following attenuation of IL-7 signaling. Transcription factor FoxO1 has been shown to be an essential factor for Ig light chain rearrangement. Results demonstrate that FoxO1 and Pax5 co-target genes that are activated during pre-B cell differentiation.

overall_design: Examination of FoxO1 and/or Pax5 binding under withdrawal of IL-7R signaling.

first: Kyoko

last: Ochiai

first: Aaron

middle: R

last: Dinner

first: Harinder

last: Singh


title: Investigating the impact of heterologous expression of the Micrococcus luteus FabH on global transcription in Escherichia coli

status: Public on Jan 26 2012

city: Emeryville

first: Ee-Been

last: Goh

state: CA

address: 5885 Hollis St, 4th Floor

department: Fuels Synthesis Division

institute: Joint BioEnergy Institute

summary:
Investigation of whole genome gene expression level changes in a E. coli fatty acid overproducing strain with or without heterologous expression of the M. luteus FabH.  The strain expressing M. luteus FabH produces more methyl ketones.
This study will be further described in Goh, E.B.,  E.E.K. Baidoo, J.D. Keasling, and H.R. Beller. Engineering of bacterial methyl ketone synthesis for biofuels.

overall_design: A 11 microarray study using total RNA recovered from six separate control cultures of Escherichia coli K-12 DH1 fatty acid overproducing strain with empty vector and five separate cultures of test strain, Escherichia coli K-12 DH1 fatty acid overproducing strain with vector overexpressing M. luteus FabH.  Each chip measures the expression level of 4,254 genes from Escherichia coli K-12  with eight 60-mer probe pairs (PM/MM) per gene, with 2-fold technical redundancy.

first: Harry

last: Beller


title: Distinct epithelial gene expression phenotypes in childhood respiratory allergy

status: Public on Jan 05 2012

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

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

overall_design: Refer to individual Series


title: Nasal epithelium gene expression profiling in child respiratory allergic disease

summary:
Background: In asthma, airway epithelium remodeling can already be detected during childhood, and epithelial cells are more susceptible to virus and oxidative stress. Their exact role in natural history and severity of children allergic respiratory disease remains however surprisingly unexplored.

Aim: To analyze dysfunctions of epithelium in dust mite allergic respiratory disease (rhinitis ± asthma) in children.

Methods: Expression profilings of nasal epithelial cells collected by brushing were performed on Affymetrix Hugene 1.0 ST arrays. All allergic patients were sensitized to dust mite. 19 patients had an isolated allergic rhinitis (AR). 14 patients had AR associated with asthma. Patients were compared to 12 controls, their severity and control being assessed according to NAEPP and ARIA criteria. Infections by respiratory viruses were excluded by real-time PCR measurements.

Results: 61 probes were able to distinguish allergic rhinitis children from healthy controls. A majority of these probes was under the control of Th2 cytokines, as evidenced by parallel experiments performed on primary cultures of nasal epithelial cells. In uncontrolled asthmatic patients, we observed not only an enhanced expression of these Th2-responsive transcripts, but also a down-regulation of interferon-responsive genes.

Conclusion: Our study identifies a Th2 driven epithelial phenotype common to all dust mite allergic children. Besides, it suggests that epithelium is involved in the severity of the disease. Expression profiles observed in uncontrolled asthmatic patients suggest that severity of asthma is linked at the same time to atopy and to impaired viral response.

Nasal epithelium gene expression profiling of dust mite allergic children with isolated rhinitis, rhinitis associated with asthma and controls.

overall_design: 38 samples classified in 4 categories : 14 isolated rhinitis (R), 6 rhinitis with uncontrolled asthma (UA), 7 rhinitis with controlled asthma (CA) and 11 healthy subjects (C )

first: Lisa

last: Giovannini-Chami

first: Chimène

last: Moreilhon

first: Kévin

last: Le Brigand

first: Pascal

last: Barbry


title: Gene expression profiling of differentiated HNECs stimulated by IL4, IL13, IFNalpha, IFNbeta, IFNgamma and controls

summary:
Background: In asthma, airway epithelium remodeling can already be detected during childhood, and epithelial cells are more susceptible to virus and oxidative stress. Their exact role in natural history and severity of children allergic respiratory disease remains however surprisingly unexplored.

Aim: To analyze dysfunctions of epithelium in dust mite allergic respiratory disease (rhinitis ± asthma) in children.

Methods: Expression profilings of nasal epithelial cells collected by brushing were performed on Affymetrix Hugene 1.0 ST arrays. All allergic patients were sensitized to dust mite. 19 patients had an isolated allergic rhinitis (AR). 14 patients had AR associated with asthma. Patients were compared to 12 controls, their severity and control being assessed according to NAEPP and ARIA criteria. Infections by respiratory viruses were excluded by real-time PCR measurements.

Results: 61 probes were able to distinguish allergic rhinitis children from healthy controls. A majority of these probes was under the control of Th2 cytokines, as evidenced by parallel experiments performed on primary cultures of nasal epithelial cells. In uncontrolled asthmatic patients, we observed not only an enhanced expression of these Th2-responsive transcripts, but also a down-regulation of interferon-responsive genes.

Conclusion: Our study identifies a Th2 driven epithelial phenotype common to all dust mite allergic children. Besides, it suggests that epithelium is involved in the severity of the disease. Expression profiles observed in uncontrolled asthmatic patients suggest that severity of asthma is linked at the same time to atopy and to impaired viral response.

Differentiated HNECs gene expression profiling in context of Th2 and IFN cytokine stimulation

overall_design: Each condition was performed in triplicates: total of 21 samples


title: Effects of Ars2 or DGCR8 siRNA on gene and microRNA expression

status: Public on Feb 01 2012

city: New York

first: Scott

middle: H

last: Olejniczak

address: 417 E68th St

institute: Memorial Sloan Kettering Cancer Center

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

platform_organism:
Homo sapiens
synthetic construct


title: Expression data from MDA-MB-231 cell line treated with Zoledronate, or Fluvastatin, or mock-treated control cells.

status: Public on Jan 01 2012

city: Paris

first: Nadejda

last: Vintonenko

address: 1 Avenue Claude Vellefaux

institute: Inserm

summary: Statins and bisphosponates (BPs) are two distinct classes of isoprenoid pathway inhibitors targeting HMG-CoA reductase (upstream enzyme) and Farnesyl-pyrophospate synthase (downstream enzyme) respectively. Here we conducted a comparative study of two representatives of these classes, fluvastatin (Fluva) and Zoledronate (Zol), to assess the differences in their in vivo metastatic potentials and pharmacogenomic profiles. Both drugs, being administered after emergence of detectable metastases, appeared to be potent metastasis inhibitors in MDA-MB-231 breast cancer metastasis model. We observed a reduced number of metastatic sites under Fluva, but not Zol treatment. Combinatorial in vivo treatment by Fluva and Zol showed no synergy for these drugs, as reported earlier on the basis of in vitro studies (Budman DR, Oncology 2006), staying in line with similarity of their transcriptomic profiles. Comparison of Zol and Fluva transcriptomic profiles revealed similar patterns of affected genes (describe involved genes functions) through different kinetics (when treated with IC50 determined for 72h treatment, the majority of changes were observed after 24h incubation with Fluva , and only after 48h incubation with Zol at 72h-IC50 or after 24h treatment with its 3 times higher dose). We demonstrated here that targeting different enzymes of the same pathway neither necessarily leads to distinct changes in gene profiles, nor to synergy for in vivo anti-metastatic potential.

overall_design: Subconfluent MDA-MB-321 cells were treated with 2 µM Fluvastatine or 30 µM Zoledronate (concentrations corresponding to IC50 at 72h treatment) for 12h and 24h , or treated with Zoledronate for longer time (48h at 30 µM) or  with higher concentration (24h at 100 µM of Zoledronate ).  Mock-treated (control) cells were obtained in parallel for each time point. Four independent replicates were used for each condition. Total of 40 samples were analyzed (10 conditions with 4 replicates for each). To determine differentially expressed genes, differences between treated cells versus corresponding mock-treated control were calculated using R-Bioconductor statistical environment. Pairing was made to remove source of variation due to the day of measurement in the comparison between the two conditions.

first: Jean-Philippe

last: Jais

first: Melanie

last: Di Benedetto


title: Substitutions in the KRas oncogene determine protein behavior: Implications for signaling and clinical outcome.

city: Houston

first: Pierre

last: Saintigny

address: 1515 Holcombe

department: Thoracic / Head and Neck Medical Oncology

institute: The University of Texas M.D. Anderson Cancer Center

summary:
Mutant KRAS (mut-KRAS) is present in 30% of all human cancers and plays a critical role in cancer cell growth and resistance to therapy. There is evidence from colon cancer that mut-KRAS is a poor prognostic factor and negative predictor of patient response to molecularly targeted therapy.  However, evidence for such a relationship in non small cell lung cancer (NSCLC) is conflicting.  KRAS mutations are primarily found at codons 12 and 13, where different base changes lead to alternate amino acid substitutions that lock the protein in an active state. The patterns of mut-KRas amino acid substitutions in colon cancer and NSCLC are quite different, with aspartate (D) predominating in colon cancer (50%) and cysteine (C) in NSCLC (47%).
Through an analysis of a recently completed biopsy biomarker-driven, molecularly targeted multi-arm trial of 215 evaluable patients with refractory NSCLC we show that mut-KRas-G12C/V but not total mut-KRAS predicts progression free survival for the overall group, and for the sorafenib and vandetanib treatment arms. Transcriptome microarray data shows differential expression of cell cycle genes between mut-KRas-G12C/V and G12D patient tumors.  A panel of NSCLC cell lines with known mut-KRas amino acid substitutions was used to identify pathways activated by the different mut-KRas, showing that mut-KRas-G12D activates both PI-3-K and MEK signaling, while mut-KRas G12C does not, and alternatively activates RAL signaling. This finding was confirmed using immortalized human bronchial epithelial cells stably transfected with wt-KRAS and different forms of mut-KRAS.  Molecular modeling studies show that the different conformation imposed by mut-KRas-G12C could lead to altered association with downstream signaling transducers compared to wild type and mut-KRas-G12D. The significance of the findings for developing mut-KRAS therapies is profound, since it suggests that not all mut-KRas amino acid substitutions signal to effectors in a similar way, and may require different therapeutic interventions.

overall_design: Gene expression profiles were measured in 22 core biopsies from patients with refractory non-small cell lung cancer included in the  Biomarker-integrated Approaches of Targeted Therapy for Lung Cancer Elimination (BATTLE). All tumors were KRAS mutants, but with different patterns of amino acid substitutions. Supervised analysis of transcriptome profiling was performed to compare cysteine or valine KRAS mutants with other KRAS mutants.

first: Ignacio

middle: I

last: Wistuba

first: John

middle: V

last: Heymach

first: Edward

middle: S

last: Kim

middle: M

last: Lippman

first: Roy

last: Herbst

first: Waun

middle: K

last: Hong

first: J

middle: J

last: Lee

last: Coombes

first: Li

last: Mao


title: Gene expression in Ewing tumor cell lines after STEAP1 silencing

city: Heidelberg

first: Thomas

middle: Georg Philipp

last: Grunewald

address: Im Neuenheimer Feld 280

department: Division of Translational Pediatric Sarcoma Research

country: Germany

institute: German Cancer Research Center (DKFZ)

summary:
Goal: identification of differentially expressed genes after STEAP1 silencing.
Ewing tumors (ET) are characterized by oncogenic EWS/ETS translocations and early metastasis. STEAP1 is a membrane-bound channel protein of unkown function. While overexpressed in many cancers, STEAP1 expression is strongly restricted to mesenchymal stem cells, prostate and urothelium among benign tissues. Here we show that STEAP1 is a direct transcriptional target of EWS/FLI1 and critical for ET malignancy. We demonstrate that STEAP1 is most prominently expressed in ET among sarcomas and provide further evidence for the concept of STEAP1 as a universal diagnostic marker for carcinomas. Using RNA interference we determined that STEAP1 promotes cellular invasiveness and anchorage-independent growth in vitro and accelerates tumor growth and metastasis in vivo. Transcriptome and proteome analyses as well as functional studies reveal that STEAP1 contributes to the generation of reactive oxygen species that in turn regulate the levels of redox-sensitive signaling molecules and pro-metatstatic genes. In synopsis, these data illuminate the hitherto unkown oncogenic function of STEAP1 as a redox-modulator in ET and point to a potential role of STEAP1 as universal drug target for anti-cancer therapy.

overall_design: 6 samples (3x A673 cells; 3x SK-N-MC cells); for each cell line one sample was transfected with control non silencing siRNA and two samples with different STEAP1 siRNAs (siSTEAP1_2 and siSTEAP1_3).

middle: G

first: Olivia

last: Prazeres-daCosta

first: Stefan

last: Burdach

first: Guenther

last: Richter


title: MCF10A-HER2/3 cells grown in 3D cultures in the presence or absence of SHP2

status: Public on Dec 20 2011

first: Tim

last: Roloff

summary: The first bona fide PTP proto-oncogene was the Src-homology 2 domain-containing phosphatase SHP2 (encoded by PTPN11), an ubiquitously expressed PTP that transduces mitogenic, pro-survival, cell fate and/or pro-migratory signals from numerous growth factor-, cytokine- and extracellular matrix receptors. In malignancies, SHP2 is hyperactivated either downstream of oncoproteins or by mutations.We provide analysis of the mammary epithelial cells MCF10A overexpressing human HER2 and HER3 and grown in 3D cultures for 15 days in the presence or absence of SHP2.

overall_design: The human mammary epithelial cells MCF10A were transduced with a doxycycline-inducible lentiviral vector expressing a CTRL miR or SHP2 miR1 or SHP2 miR2. Cells from each group were grown in 3D cultures, and the knockdown of SHP2 was induced for 15 days. RNA was extracted for gene expression analysis.

first: Nicola

last: Aceto

first: Stephane

last: Thiry

first: Mohamed

last: Bentires-Alj


title: Time-course expression: hiPSC differentiation toward cardiomyocytes

status: Public on Dec 31 2011

city: Baltimore

first: Hideki

last: Uosaki

state: MD

address: 720 Rutland Ave, Ross 954

department: Division of Cardiology

institute: Johns Hopkins University

summary: Human embryonic and induced pluripotent stem cells (hESCs/iPSCs) are promising cell sources for cardiac regenerative medicine. To realize hESC/iPSC-based cardiac cell therapy, efficient induction, purification, and transplantation methods for cardiomyocytes should be required. Though marker gene transduction or fluorescent-based purification methods were reported, fast, efficient and scalable purification methods with no genetic modification are essential for clinical purposes but have not been established yet. In this study, we used microarrays to detail the global gene program during cardiac differentiation and to identify cardiac-specific cell surface markers. hiPSCs (201B6) were differentiated toward cardiomyocytes using a modified-directed differentiation protocol (high density culture in RPMI+B27-insulin, sequential administration of Activin A 100ng/mL 1 day, BMP4 10ng/mL+bFGF 10ng/mL 4 days, and Dkk1 100ng/mL 2 days). Beating clusters were first observed at day 8-9 and spread by day 11 after Activin A administration. Cardiac troponin-T (cTnT)-positive cells appeared at day 7-8 after induction and were observed in 30-70% of cells at day 11. qPCR and genome-wide analysis reflected differentiation processes from the undifferentiated state to cardiomyocytes. Rapid downregulation of pluripotent stem cell markers such as NANOG and POU5F1 was observed within 2 days of differentiation. Early and cardiac mesodermal genes (T, MESP1, KDR, ISL1) were expressed during day 2-5, and cardiac genes (NKX2-5, MYH6, MYH7, MYL2, and MYL7) were expressed after day 7. We identified VCAM1 as a cardiac-specific cell surface marker by microarray and flow cytometry.

overall_design: Human induced pluripotent stem cells (iPSCs; 201B6) were differentiated toward cardiomyocytes (RPMI+B27 medium supplemented d0-1 Activin A, d1-5 BMP4+bFGF, d5-7 Dkk1). RNA was extracted from cells at day 0, day 2, day 5, day 7, day 9, and day 11. Cardiomyocytes appeared after day 7 and reached about 50% of total cells at day 11.

first: Hiroyuki

last: Fukushima

first: Ayako

last: Takeuchi

first: Satoshi

last: Matsuoka

first: Norio

last: Nakatsuji

first: Shinya

last: Yamanaka

first: Jun

last: Yamashita


title: BT474 tumors in the presence or absence of SHP2

summary: The first bona fide PTP proto-oncogene was the Src-homology 2 domain-containing phosphatase SHP2 (encoded by PTPN11), an ubiquitously expressed PTP that transduces mitogenic, pro-survival, cell fate and/or pro-migratory signals from numerous growth factor-, cytokine- and extracellular matrix receptors. In malignancies, SHP2 is hyperactivated either downstream of oncoproteins or by mutations.We provide analysis of the breast cancer cells BT474 grown as xenografts in the presence or absence of SHP2 for 30 days.

overall_design: The HER2-postive breast cancer cell line BT474 was transduced with a doxycycline-inducible lentiviral vector expressing a CTRL miR or SHP2 miR1 or SHP2 miR2. Cells from each group were injected in imuunodeficinet mice and after tumor development, the knockdown of SHP2 was induced for 30 days in vivo. At day 30, tumors were dissected and RNA isolated for gene expression analysis.


title: BT474 tumors, primary TN tumors and MCF10A-HER2/3 cells in the presence or absence of SHP2


title: Expression data of ITK deficient, HVS transformed CD4+ T cells

city: Duesseldorf

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

institute: University of Duesseldorf

summary:
We analyzed gene expression profiles of unstimulated Herpesvirus Saimiri (HVS) transformed T cells (CD4+) of patients harboring a homozygous R335W mutation in the IL-2 inducible T cell kinase (ITK) compared to healthy control HVS cells.
We identified a set of 1927 Affymetrix probe sets showing significant misregulation in the ITK deficient cells (Welch's T-test, p<0.05).

overall_design: HVS T cell lines (ITK wt or ITK R335W, each CD4+) from three independent culturing time points were used for RNA extraction and hybridization on Affymetrix microarrays.

first: Rene

last: Linka

last: Deenen

last: Köhrer

first: Arndt

last: Borkhardt


title: Carboplatin-treated human retinal endothelial cells

status: Public on Dec 13 2011

city: Memphis

first: Jena

last: Steinle

state: TN

address: 930 Madison Ave, Suite 768

department: Ophthalmology

institute: University of Tennessee Health Science Center

summary: Super-selective intra-ophthalmic artery chemotherapy (SSIOAC) is an organ-specific drug-delivery strategy to treat retinoblastoma, the most common primary ocular malignancy in children. Unfortunately, recent clinical reports associate adverse vascular toxicities with SSIOAC using melphalan, the most commonly used chemotherapeutic. To explore the reason for the unexpected vascular toxicities, we have developed in vitro studies with human retinal endothelial cells to test the effects of the chemotherapeutics and a non-human primate model to monitor the SSIOAC treatment in real-time and post-treatment. Melphalan and carboplatin (another chemotherapeutic used to treat retinoblastoma via SSIOAC) triggered migration, proliferation, and apoptosis when used to treat human retinal endothelial cells. Melphalan was associated with increased adhesion of leukocytes to human retinal endothelial cells, and tended to increase with increased cell expression of adhesion proteins (ICAM-1) and soluble chemotactic factors (IL-8). Histopathology post-SSIOAC indicated vessel wall sloughing, leukostasis, and vessel occlusion. We have established an in vitro human cell culture model and a non-human primate model to evaluate strategies designed to obviate vascular side effects, and optimize the efficacy of SSIAOC and the drug preparations used in SSIOAC.

overall_design: 4 non-treated (CNT) vs. 4 carboplatin-treated primary human retinal endothelial cells (RECs).


title: Melphalan-treated human retinal endothelial cells

overall_design: 4 non-treated (MNT) vs. 4 melphalan-treated primary human retinal endothelial cells (RECs).


title: Virus-induced inflammatory gene networks underlying asthma exacerbations in vivo

status: Public on Dec 11 2011

city: Subiaco

first: Anthony

last: Bosco

state: WA

address: 100 Roberts Road

country: Australia

institute: Telethon Kids Institute

summary:
Global patterns of gene expression was profiled in nasal lavage samples obtained from asthmatic children during an acute Picornavirus-induced exacerbation and 7-14 days later.
Gene coexpression network analysis and prior knowledge was employed to reconstruct the wiring diagram of the underlying gene networks.

overall_design: The study design consisted of paired samples obtained during the acute exacerbation and 7-14 days later from 16 asthmatic children.

first: Samira

last: Ehteshami

first: Sujatha

last: Panyala

first: Fernando

middle: D

last: Martinez


title: Microarrays analysis of anti-Enterovirus 71 activity of Heparin

status: Public on Dec 10 2011

city: Mashhad

first: Hamid

middle: Reza

last: Pourianfar

state: Khorasan Razavi

address: Azadi Square

country: Iran

institute: Current Address: Iranian Academic Centre for Education, Culture and Research, Mashhad Branch

summary:
We have previously shown that Heparin (Hep) significantly inhibited Enterovirus 71 (EV71) infection and binding in both Vero and a human neural cell line, SK-N-SH, in vitro. Therefore, in this study we intended to gain insight into the cellular and molecular mechanisms of action of Hep against clinical EV71 infection in neural cells.  Instead of stating a long list of gene functions and pathways, we tried to select for EV71-induced genes that were exclusively affected by antiviral activity of Hep through a multi-level comparison and characterization.
Overall, the findings of this study suggest several molecular targets by which Hep might exert its antiviral activity against clinical EV71 infection in neural cells.  Mostly, Hep appeared to modulate induction effect of EV71 on several genes in a way that may benefit the host cell and inhibit the viral infection.  The most important genes where expression patterns were significantly changed by Hep include genes related to; (i) cell growth, (ii) DNA repair and replication, (iii) cytoplasmic microfilaments and related apoptosis, (iv) regulation of energy metabolism and mitochondrion-related apoptosis, (v) cytoplasmic viral transport, (vi) transmembrane proteins and the related signaling pathways, (vii) phosphoribosyltransferase, (viii) transcription factors, (ix) G protein-coupled receptors and G protein-coupled receptors-interacting proteins, (x) remodeling actin filament assembly, (xi) chemokin receptors, and (xii) immunosuppression.  In addition, Hep sometimes appeared to be harmful for cells, like the case in that Hep likely suppresses regulation of Metallothionein 1E.  Furthermore, it should not be ignored that the Hep-caused affects seen in this microarray analysis may partially be attributed to a significant inhibitory effect of Hep on EV71 entry into the cells.
In conclusion, we propose that our microarray findings may suggest new directions for further studies on molecular targets of anti-EV71 activity of Hep.  EV71 is a neurovirological virus that can cause severe and fatal CNS complications in infected patients.  There is no approved drug for prophylaxis of EV71-casued disease and discovering a molecular drug target(s) for EV71 infection would be beneficial.  The microarray analysis reported here was a large-scale microarray pilot study and thus further confirmatory experiments such as real time RT PCR and Western blotting would be warranted in order to confirm the mode of action of Hep implied here.

overall_design: SK-N-SH cells were infected with a clinical EV71 isolate followed by treatment with 125 µg/mL of Hep.  At 72 hours post infection, antiviral activity and cytotoxicity of Hep at 125 µg/mL in 12-well plates were carried out at the same time as RNA extraction.  This way, we could ensure that we would assess transcript profiles of the host cells under the same condition and time as assessment of antiviral activity and cytotoxicity for the same replicates.  Changes in expression profiles of the host cells were comparatively assessed under four conditions: cell control (neither infection nor treatment, designated CC), treated only with Hep (compound control, designated Cyto), EV71-infected cells treated with Hep (treatment, designated H), and infected with EV71 without treatment with Hep (virus control, designated V). All experiments were applied in triplicate, and totally twelve GeneChip® Human Gene 1.0 ST arrays were purchased from Affymetrix and processed. Then, the following five contrasts were made: Hep vs. CC; VC vs. CC; Cyto vs CC; Hep vs. VC; and Hep vs. Cyto.  For each contrast, only samples from the two target groups were included.  The statistical parameters of ANOVAs, p values, multiple test corrections, and fold changes were calculated within each contrast.  Then, a multi-level selection and analysis procedure was employed in order to attribute changes in the gene transcription level to antiviral activity of Hep.

first: Lara

last: Grollo


title: Cell leukostasis during organ-targeted chemotherapy in human retinal endothelial cells and rhesus macaques endothelial cells


title: Expression profile of human natural killer cells co-cultured with P. falciparum infected erythrocytes

status: Public on Dec 01 2011

city: Tuebingen

first: Michael

last: Bonin

state: BW

address: CAlwerstr. 7

department: Medical Genetics

institute: University Tuebingen

summary: In order to identify an expression signature that might characterize the impact of Plasmodium parasites on NK cells, we have used Affymetrix oligonucleotide microarrays to examin the global gene expression profile of primary NK cells that have been co-incubated with P. falciparum infected red blood cells and have compared it to the expression pattern of NK genes induced by cytokine treatment.

overall_design: PBMCs were isolated from 3 healthy donors and were incubated with iRBCs, uRBCs, IL12 plus IL18 and without any stimulus. After 24 hours at 37ºC and 5%CO2, Natural killer cells were isolated by negative selection, checked for purity by flow cytometry and processed for RNA extraction and analysis with the Human Gene 1.0 Affymetrix array. The experiment was repeated 3 times (1-2 weeks apart) for each one of the 3 donors.

first: Elisandra

last: de Carvalho

first: Jürgen

middle: F

last: Kun


title: miRNA profiling in osteosarcoma: a cell line based approach with correlation to gene expression

status: Public on Nov 30 2011

city: Neuherberg

first: Jan

last: Smida

address: Ingolstaedter Land 1

department: CCg Osteosarcoma

institute: HelmholtzZentrum

summary:
We found various genes involved in differentiation (RGMB, LRRC17), cell cycle control (Cyclin E1) and apoptosis (LIMA1, CAMK2N1) were found to be deregulated in osteosarcoma cell lines, most likely due to altered miRNA expression patterns.
Our findings indicate a crucial impact of deregulated miRNAs with consecutive changes in gene expression in osteosarcomas that strongly suggests pathogenetic and potentially therapeutic implications.

overall_design:
We investigated seven well-established osteosarcoma cell lines for genome wide miRNA expression (miRBase version 15.0) and integrated our findings with gene expression
--------------------------
This represents the mRNA component of the study

first: Daniel

last: Baumhoer

first: Stephanie

last: Zillmer

first: Kristian

last: Unger

last: Rosemann

last: Atkinson

first: Martin

last: Irmler

first: Johannes

last: Beckers

first: Heide

last: Siggelkow

first: Irene

last: von Luettichau

first: Gernot

last: Jundt

first: Michaela

last: Nathrath


title: Expression profiles of CD24-/CD44+/ESA+ population in MDA-MB-231 and its highly metastatic variants.

city: Springfield

first: Hiroshi

last: Okuda

address: 825 N. Rutledge

department: Med. Microbiol. Immunol. & Cell Biol.

institute: Southern Illinois University School of Medicine

summary: Breast cancer is a curable disease if it is diagnosed at an early stage.  However, only little options are left once the tumor is metastasized to distant organs, and more than 90% of breast cancer death is attributed to metastatic disease.  The process of metastasis is highly complex and involves many steps for successful colonization of tumor cells at a target organ.  According to the cancer stem cell (CSC) theory, which still remains a hypothesis, these metastatic cells must have stem cell-like capability for their self-renewal in addition to their invasive ability. Therefore, it has been predicted that a “metastatic stem cell”, which is distinct from a cancer stem cell, must exist in the primary tumor mass. To identify genes that are involved in metastasis of CSCs, we isolated CSC populations from a well-established model cell line of breast cancer, MDA-MB231, and that of highly metastatic variants, 231BoM-1833 and 231BrM-2a, using CD24, CD44 and EpCAM (ESA), which have been identified as surface markers for CSCs in breast cancers. Overall yield of CSCs from these cells ranged from 2% to 4%. We then performed global expression profile analysis for these CSCs using the Affymetrix Human Gene 1.0ST array.

overall_design: CSC populations (CD24-/CD44+/ESA+) from MDA-MB231, 231BoM-1833 and 231BrM-2a were isolated by magnetic-activated cell sorting (MACS) using specific antibodies to these surface markers. The total RNA was isolated from the CSC populations using the RNeasy RNA isolation kit (Qiagen). The RNA was then converted to cDNA and they were hybridized to the Human Gene 1.0ST chip (Affymetrix). The data was normalized using the RMA algorithm of the Expression Console software (Affymetrix). A comparison of transcriptional profiles was then performed in CSCs of highly metastatic cell lines (231BoM-1833 and 231BrM-2a) compared to the CSCs of MDA-MB-231.

first: Kounosuke

last: Watabe


title: Methylation data from normal thymocytes, 24 day pre-tumor Dnmt3b-deficient thymocytes, Wild-Type Tumors, and Dnmt3b-deficient Tumors

status: Public on Nov 21 2011

city: Omaha

first: Ryan

last: Hlady

state: Nebraska

department: Eppley

institute: UNMC

type: Methylation profiling by high throughput sequencing

summary: Dnmt3b is a DNA methytransferase which is an enzyme that methylated genomic DNA which contributes to genomic stability and transcriptional regulation.

overall_design: We genetically inactivated Dnmt3b in the hematopoeitic compartment in the context of MYC overexpression and analysed the resulting thymic lymphomas.

first: Rene

last: Opavsky

first: Jana

last: Opavska

first: Slavomira

last: Novakova

first: David

last: Klinkebiel


title: Expression data for HIF1alpha-regulated genes in clear cell renal carcinoma cells (ccRCC)

status: Public on Dec 02 2011

city: Boston

first: Chuan

last: Shen

address: 44 Binney Street

institute: Dana-Farber Cancer Institute

summary: Gene expression profiling was performed in ccRCC cells, which either express both HIF1alpha and HIF2alpha (either naturally or by virtue of induced expression of HIF1alpha) or express HIF2alpha alone (either naturally or by virtue of a HIF1alpha shRNA), to identify genes regulated by HIF1alpha in ccRCC cells.

overall_design: Three H2 cell lines 769P, A498, and SLR24 were stably infected with retrovirus encoding doxycycline-inducible Luciferase (control) or HIF1alpha, and two H1H2 cell lines Caki-2 and SLR25 were stably infected with retroviruses encoding scrambled (control) or HIF1alpha shRNA. Duplicated samples were used for each condition.

first: Kaelin

last: William

first: Shen

last: Chuan


title: Expression data of NCI-H441 cells stably expressing hsa-mir-365-2 vs empty vector

status: Public on Nov 15 2011

city: Hershey

last: Mu

state: PA

address: 500 University Dr H083

institute: Penn State Universitiy College of Medicine

summary:
Hsa-mir-365-2 is one of the two precursors that give rise to miR-365. We discovered that miR-365 directly regulates a lung cancer and developmental gene termed thyroid transcription factor 1 (TTF-1 or NKX2-1).
Hsa-mir-365-2 was transfected into NCI-H441 cells via retrovirus-mediated gene transfer. Arrays hybridized: Affymetrix GeneChip Human Gene 1.0 ST Array.

overall_design: A total of 4 samples were analyzed. The first two were H441 cells expressing hsa-mir-365-2 and the other two were H441 transfected with empty vector. The class comparison function (significant cutoff, 0.001) of BRB Array Tool (4.1.0 beta_3 release) was used to analyze for differentially expressed genes as a result of enforced expression of hsa-mir-365-2.

first: Ji

last: Qi


title: mRNA-Seq reveals complex patterns of gene regulation and expression in the mouse skeletal muscle transcriptome associated with calorie restriction

status: Public on Nov 22 2011

city: Elk Grove

first: joseph

last: dhahbi

state: ca

address: 9700 West Taron Drive

department: Medical Education

institute: California Northstate University College of Medicine

type: Expression profiling by high throughput sequencing

summary: Sarcopenia is an age-associated loss of skeletal muscle mass and strength that increases the risk of disability. Calorie restriction (CR), the consumption of fewer calories while maintaining adequate nutrition, mitigates sarcopenia and many other age-related diseases. To identify potential mechanisms by which CR preserves skeletal muscle integrity during aging, we used mRNA-Seq for deep characterization of gene regulation and mRNA abundance in skeletal muscle of old mice compared with old mice subjected to CR. mRNA-Seq revealed complex CR-associated changes in expression of mRNA isoforms, many of which occur without a change in total message abundance and thus would not be detected by methods other than mRNA-Seq. Functional annotation of differentially expressed genes reveals CR-associated upregulation of pathways involved in energy metabolism and lipid biosynthesis, and downregulation of pathways mediating protein breakdown and oxidative stress, consistent with earlier microarray-based studies. CR-associated changes not noted in previous studies involved downregulation of genes controlling actin cytoskeletal structures and muscle development. These CR-associated changes reflect generally healthier muscle, consistent with CR’s mitigation of sarcopenia. mRNA-Seq generates a rich picture of the changes in gene expression associated with CR, and may facilitate identification of genes that are primary mediators of CR’s effects.

overall_design: Comprehensive survey of mRNA from skeletal muscle of mice subjected to calorie restricted or control diets using deep sequencing

first: Joseph

last: Dhahbi


title: Perivascular Human Endometrial Mesenchymal Stem Cells Express Pathways Relevant to Self-Renewal, Lineage Specification, and Functional Phenotype

status: Public on Nov 14 2011

city: San Francisco

first: Linda

last: Giudice

address: 513 Parnassus Ave. HSE 1619

department: OBGYN and RS

institute: University of California, San Francisco

summary:
A population of endometrial cells displaying key properties of mesenchymal stem cells (eMSC) has been identified in human endometrium.  eMSC co-express CD146 and PDGFRB surface markers, have a perivascular location, and likely represent the reservoir of progenitors giving rise to the endometrial stromal fibroblast lineage. Endometrial stromal cells isolated from 16 oocyte donors and 3 benign gynecologic surgery subjects were FACS sorted into four populations: CD146+/PDGFRB+ (eMSC); CD146+/PDGFRB- (endothelial cells); CD146-/PDGFRB+ (stromal fibroblasts); CD146-/PDGFRB- (mixed population) then subjected to gene expression analysis on Affymetrix Human Gene 1.0 ST arrays, and differentially expressed genes compared between eMSC, stromal fibroblast, and endothelial cell populations. Ninety-two genes were validated by multiplex quantitative RT-PCR on seventy of these sorted cell populations. Immunohistochemistry was used to verify the perivascular location of eMSCs.Principal component analysis and hierarchical clustering showed eMSC clustering discretely near stromal fibroblasts and separately from endothelial cells.  eMSC expressed pericyte markers and genes involved hypoxia response, inflammation, proteolysis, and angiogenesis/vasculogenesis – all relevant to endometrial tissue breakdown and regeneration. Additionally, eMSC displayed distinct gene profiles for cell-cell communication and regulation of gene expression. Overall, the phenotype of the eMSC is that of a multipotent pericyte responsive to hypoxic, proteolytic, and inflammatory stimuli, able to induce angiogenesis, migrate and differentiate into lineage cells, and potentially respond to estradiol and progesterone. Identifying the pathways and gene families described herein in the context of the endometrial niche, will be valuable in understanding normal and abnormal endometrial development in utero and differentiation in adult uterus.
The multipotent, perivascular endometrial mesenchymal stem cell has a “niche phenotype” of high Notch, TGFB, IGF, and Hedgehog and low canonical/non-canonical Wnt and EGF signaling.

overall_design: Oocyte donors with no known uterine pathology underwent endometrial biopsy at the time of oocyte retrieval, following comparable GnHR agonist downregulated ovarian stimulation protocols. Tissue was digested and stromal cells isolated and sorted based on expression of CD146 and PDGFRB. RNA was extracted and hybridized on Affymetrix microarrays. Resulting data were compared between sorted isolated cell populations.

first: Trimble

middle: L

last: Spitzer

first: Zara

last: Zelenko

first: Lusine

last: Aghajanova

first: Angela

last: Rojas

last: Erikson

first: Fatima

last: Barragan

first: Amy

middle: E

last: Hamilton

first: Michelle

last: Meyer

first: Juan

middle: C

last: Irwin


title: Comparison of two hepatocellular cancer cell lines with distinct properties regarding epithelial-mesenchymal transition

city: Vienna

first: Martin

last: Bilban

country: Austria

institute: Medical University of Vienna

summary: The epithelial to mesenchymal transition (EMT) of malignant hepatocytes is a crucial event in hepatocellular carcinoma (HCC) progression and recurrence. We aimed to establish a human model of EMT to examine drug efficacy and specificity in HCC progression. Human HCC cell populations were characterized by immunofluorescence analysis, migration and invasion assays, array comparative genomic hybridization, whole-genome expression profiling and promoter methylation. Therapeutic agents clinically used against HCC were examined for efficacy by determination of IC50 values. Liver cancer cell lines showed either an epithelial or mesenchymal phenotype of which latter showed strong migratory and invasive abilities in vitro. The common cellular origin of both cell types indicated that mesenchymal HCC cells have been derived from epithelial hepatocytes through EMT in the HCC patient. Drug exposure of mesenchymal HCC cells showed higher resistance to the targeted therapeutic agents sorafenib and erlotinib as compared to epithelial HCC cells, which were slightly more resistant to cytostatic drugs. Most remarkably, combined treatment with doxorubicin and sorafenib caused increased susceptibility of both HCC cell types resulting in enhanced drug efficacy. Taken together, this novel model of human HCC allows to monitor the differential effect of liver cancer progression on drug efficacy in pre-clinical studies.

overall_design: hepatocellular carcinoma cell lines HCC-1.2 and HCC-1.1 cells, referred to as 3p and 3sp cells, respectively, were isolated from one HCC patient as described ( Sagmeister S, Eisenbauer M, Pirker C, et al. New cellular tools reveal complex epithelial-mesenchymal interactions in hepatocarcinogenesis. Br J Cancer 2008;99(1):151-9.). 3p cells of passages 10 to 12 and 3sp cells of passages 7 to 13 are termed 3p early and 3sp early, respectively. 3p cells between passage 71 and 76 and 3sp from passage 72 to 87 were termed 3p late and 3sp late, respectively

first: Franziska

last: van Zijl

first: Wolfgang

last: Mikulits


title: Seminal fluid induces cytokine and chemokine mRNA expression in the human cervix after coitus

status: Public on Nov 17 2011

city: Adelaide

first: Sarah

middle: Anne

last: Robertson

state: SA

address: Frome Rd

department: paediatrics and Reproductive Health

institute: University of Adelaide

summary:
In mice, seminal fluid elicits an inflammation-like response in the female genital tract that activates immune adaptations to advance the likelihood of conception and pregnancy. Here we examined whether similar changes in leukocyte and cytokine parameters occur in the human cervix in response to the male partner’s seminal fluid. After a period of abstinence in proven-fertile women, duplicate sets of biopsies were taken from the ectocervix in the peri-ovulatory period and again 48 h later, 12 h after unprotected vaginal coitus, vaginal coitus with use of a condom, or no coitus. One pair of first biopsy and second biopsy RNA samples from each treatment group were reverse transcribed into cDNA and hybridized to Affymetrix Human Gene 1.0 ST arrays. A total of 713 probe sets were identified as differentially expressed (fold change >2) between first and second biopsies after unprotected coitus, with 436 genes upregulated and 277 genes downregulated. Ingenuity Pathway Analysis revealed that gene pathways including inflammatory response, immune response, immune cell trafficking, cellular movement and antigen presentation were significantly affected by seminal fluid exposure. Amongst these were genes encoding several chemokines which target granulocytes, monocyte/macrophages, dendritic cells and lymphocytes, proinflammatory cytokines and regulators of cytokine synthesis, prostaglandin pathway gene including PTGS2; COX-2) and several matrix metalloproteinases (MMPs). Of these genes, no change or a substantially smaller change was seen between first and second biopsies obtained after coitus with condom use, or abstinence. An increase in CSF2, IL6, IL8 and IL1A expression was confirmed by qRT-PCR in larger sets of duplicate biopsies (n=6-7 per group). We conclude that seminal fluid introduced at intercourse elicits expression of pro-inflammatory cytokines and chemokines which underpins the accompanying recruitment of macrophages, dendritic cells and memory T cells. The leukocyte and cytokine environment induced in the cervix by seminal fluid appears competent to initiate adaptations in the female immune response that promote fertility. This response is also relevant to transmission of sexually transmitted pathogens, and potentially susceptibility to cervical metaplasia.
Women aged 18-40 years, with regular menstrual cycles and a current sexual relationship with a proven fertile regular partner, volunteered for the study. All women had previously undergone tubal ligation and none of the women used steroidal contraceptives or an intrauterine device for a minimum of three months preceding the study. Subjects were screened to exclude bacterial or viral infection. A negative test result was a prerequisite for inclusion in the study. The study was approved by the local ethics committee of Karolinska University Hospital, Stockholm, Sweden.

overall_design: RNA from each of six cervical biopsies was analysed. The six tissues comprised three pairs of cervical biopsies (a ‘first’ and a ‘second’ biopsy); one pair from each of three women assigned to three different treatment protocols. Treatments were (1) no coitus (control); (2) coitus with a condom (condom), or (3) unprotected coitus (coitus). To synchronise the timing of the biopsies, all subjects determined their LH peak in urine samples taken twice daily from approximately day 10 after the onset of menstruation to the time at which an LH increase was detected (LH0-LH+1), using a rapid self-test (Clearplan, Searle Unipath Ltd., Bedford, UK).  The first biopsy was recovered during the peri-ovulatory stage of the menstrual cycle (at 0900 h - 1200 h on day LH0 to LH+1), and the second biopsy was recovered 48 h later (at 0900 h - 1200 h on day LH+2 to LH+3). Small needle biopsies (approximately 50-100 mg tissue) were taken from the ectocervix, approximately 1 cm from the transformation zone. Women then abstained from intercourse for 36 hours to enable haemostasis and healing of the biopsy site. Women allocated to groups (1) and (2) had intercourse, without or with condom use respectively, on one occasion approximately 36 hours after the first biopsy and 12 hours prior to the second biopsy. The abstinent woman did not have intercourse between the two biopsies. Before all biopsies, the cervix was washed with 10 ml of saline solution to clear mucous and debris. All cervical washings were collected and examined microscopically for the presence of sperm to confirm compliance.

middle: A

first: David

last: Sharkey

first: Anne

last: Macpherson


title: Gene expression profile of DAP12 knockdown THP-1 cells following exposure to phorbol 12-myristate 13-acetate

city: Tokyo

first: Jun-ichi

last: Satoh

address: 2-522-1 Noshio, Kiyose

department: Bioinformatics

country: Japan

institute: Meiji Pharmaceutical University

summary: Nasu-Hakola disease (NHD), also designated polycystic lipomembranous osteodysplasia with sclerosing leukoencephalopathy (PLOSL), is a rare autosomal recessive disorder characterized by progressive presenile dementia and formation of multifocal bone cysts, caused by a loss-of-function mutation of DAP12 or TREM2. TREM2 and DAP12 constitute a receptor/adaptor complex expressed on osteoclasts, dendritic cells, macrophages, monocytes, and microglia. At present, the precise molecular mechanisms underlying development of leukoencephalopathy and bone cysts in NHD remain largely unknown. We established THP-1 human monocyte clones that stably express small interfering RNA (siRNA) targeting DAP12 for serving as a cellular model of NHD. Genome-wide transcriptome analysis identified a set of 22 genes consistently downregulated in DAP12 knockdown cells. They constituted the molecular network closely related to the network defined by cell-to-cell signaling and interaction, hematological system development and function, and inflammatory response, where NF-kappaB acts as a central regulator. These results suggest that a molecular defect of DAP12 in human monocytes deregulates the gene network pivotal for maintenance of myeloid cell function in NHD. We found that both DAP12 knockdown and control clones were capable of equally responding to phorbol 12-myristate 13-acetate (PMA), a known inducer of morphological differentiation of THP-1 cells, by exhibiting almost similar gene expression profiles between both, following a 24-hour exposure to 50 nM PMA.

overall_design:
The siRNA vector construct targeting the DAP12 sequence (SI) and the control vector construct targeting the scrambled sequence (SCR) were generated by using GeneClip U1 Hairpin cloning system (Promega). The vectors were transfected in THP-1 cells by using Lipofectamine LTX reagent. The stable cell lines were selected by incubating them for approximately two months in the feeding medium with inclusion of 200 microgram/ml Hygromycin B. Then, two SI clones named SI5 and SI17, in addition to two SCR clones named SCR1 and SCR4, were selected by limiting dilution of the cells in a manner of a single cell per well plated in a 96-well cell culture plate.
Microarray data for clones SCR4 and SI17 submitted in this Series.

first: Yoshihiro

last: Shimamura

first: Hiroko

last: Tabunoki


title: Expression data from severe asthmatics, mild asthmatics and healthy controls

city: Stockholm

first: Christina

last: Orsmark Pietras

address: Hälsovägen 7-9

institute: Karolinska Institutet

summary: Background: Around 5% of children with asthma suffer from chronic symptoms and/or severe exacerbations despite extensive treatment. The causes of severe therapy-resistant childhood asthma are poorly understood. Objectives: To define global patterns of gene expression in severe therapy-resistant vs. controlled asthma and healthy controls. Methods: Children with severe, therapy-resistant (SA, n=20) and controlled asthma (CA, n=20) were identified from a Swedish nation-wide study including extensive clinical and immunological characterisation. In addition, healthy controls were recruited (Ctrl, n=19). White blood cells were isolated and the global transcriptome profile was characterised using the Affymetrix Human Gene ST 1.0 chip. Results: 1378 genes were differentially expressed in one or several of the CA vs. Ctrl, SA vs. CA or SA vs. Ctrl contrasts. A large number could uniquely differentiate the SA group from the CA (n=351 genes) and Ctrl (n=315) groups, whereas fewer genes differentiated the CA from the Ctrl group (n=149). Several non-coding RNAs were found up-regulated in SA compared to CA or Ctrl. Three significantly enriched KEGG pathways were represented; bitter taste transduction, TAS2Rs (up-regulated mostly in SA), natural killer cell mediated cytotoxicity (up-regulated in CA) and N-Glycan biosynthesis (down-regulated in SA). An unsupervised hierarchical clustering of the 1378 genes could crudely separate the SA, CA and Ctrl individuals. Conclusion: Our data indicate a separation in gene expression patterns between children with severe, therapy-resistant asthma and controlled persistent asthma, and suggest novel pathways characterizing the severe therapy-resistant asthma phenotype.

overall_design: The transcriptomes of 59 subjects were assayed on the Affymetrix Human Gene ST 1.0 expression array. All samples passed pre-hybridisation quality control. After pre-processing and quality control of the post-hybridised arrays, five samples were regarded as outliers and removed (ctrl 510, MA 248, SA 141, SA 261, SA 41). The remaining sample set of 17 severe asthmatics (SA), 19 mild asthmatics (MA) and 18 controls (ctrl) were used for down-stream analysis.

middle: O

last: Pietras

first: Erik

last: Melén


title: Gene expression profile of THP-1 monocytes following knockdown of DAP12, a causative gene for Nasu-Hakola disease

summary: Nasu-Hakola disease (NHD), also designated polycystic lipomembranous osteodysplasia with sclerosing leukoencephalopathy (PLOSL), is a rare autosomal recessive disorder characterized by progressive presenile dementia and formation of multifocal bone cysts, caused by a loss-of-function mutation of DAP12 or TREM2. TREM2 and DAP12 constitute a receptor/adaptor complex expressed on osteoclasts, dendritic cells, macrophages, monocytes, and microglia. At present, the precise molecular mechanisms underlying development of leukoencephalopathy and bone cysts in NHD remain largely unknown. We established THP-1 human monocyte clones that stably express small interfering RNA (siRNA) targeting DAP12 for serving as a cellular model of NHD. Genome-wide transcriptome analysis identified a set of 22 genes consistently downregulated in DAP12 knockdown cells. They constituted the molecular network closely related to the network defined by cell-to-cell signaling and interaction, hematological system development and function, and inflammatory response, where NF-kappaB acts as a central regulator. These results suggest that a molecular defect of DAP12 in human monocytes deregulates the gene network pivotal for maintenance of myeloid cell function in NHD.

overall_design: The siRNA vector construct targeting the DAP12 sequence (SI) and the control vector construct targeting the scrambled sequence (SCR) were generated by using GeneClip U1 Hairpin cloning system (Promega). The vectors were transfected in THP-1 cells by using Lipofectamine LTX reagent. The stable cell lines were selected by incubating them for approximately two months in the feeding medium with inclusion of 200 microgram/ml Hygromycin B. Then, two SI clones named SI5 and SI17, in addition to two SCR clones named SCR1 and SCR4, were selected by limiting dilution of the cells in a manner of a single cell per well plated in a 96-well cell culture plate.


title: Microarray analysis of gene expression profiles in response to tomato leaves extract treatment in MCF-7 breast cancer cells

status: Public on Nov 05 2011

city: Gombak

first: Amid

last: Azura

state: Selangor

address: Jalan Gombak

department: Biotechnology Engineering

country: Malaysia

institute: IIUM,Gombak

summary:
Microarray analysis was performed to evaluate the global gene expression profiles of MCF-7 breast cancer cells treated with tomato leaves extract (TLE) in 1 hr and 48 hrs of treatment.
Several of genes with p < 0.05 and fold-change cut-off <2.00 from human genome had significantly changed after the treatments. Its showed the greatest roles in cancer cells growth and were found either to be down-regulated or up-regulated in cells after the treatment.TLE gave significant expression effects towards several genes such as CRYAB, PIM1, BTG1, CYR61, HIF1A, CEBP-beta, TXNIP, THBS1, HMG1L1 and HIST2H3D genes. These results demonstrate the potent activity of TLE as an anti-cancer agent.

overall_design: We analyzed untreated (0 hr) and treated MCF-7 breast cancer cells (after 1 hr and 48hrs) using the Affymetrix Human Exon 1.0 ST platform. Chip array was scanned by Affymetrix Microarray Suite/GCOS. Experiment were performed in triplicates. Raw data was processed by GeneSpringGX v7.2 (Agilent Technology, USA).

first: Azura

last: Amid

first: Dalila

middle: W

last: Chik


title: Vaginal epithelial gene expression in postmenopausal women suffering from vaginal dryness

status: Public on Nov 12 2011

city: London

first: Jordan

middle: Eduard

last: Bisanz

state: Ontario

address: 268 Grosvenor Street, Room F2-116

country: Canada

institute: Lawson Health Research Institute

summary:
The onset of menopause is accompanied by a dramatic increase in reported symptoms of vaginal dryness, soreness, irritation or itching, pain with intercourse and bleeding after intercourse. Collectively these affect 25-50% of women of post-menopausal age and significantly impact their quality of life. To examine how gene expression differs between these groups, surface vaginal epithelial cells were collected from postmenopausal women suffering from vaginal dryness and appropriate controls not suffering from dryness.
Affymetrix GeneChip Human 1.0 ST microarrays were performed on RNA isolated from ten participants.

overall_design: Suitable RNA was extracted from ten participants which were classified into two groups, the dryness and control groups, based on diagnosis of dryness by a nurse during gynecoligical examination.

first: Gregor

last: Reid


title: Effect of iron chelators on global gene expression pattern in SW480 cells

status: Public on Oct 16 2011

city: Toronto

first: Liliana

last: Attisano

address: 160 College Street

department: Biochemistry

institute: University of Toronto

summary: Gene expression analysis of SW480 cells treated with inhibitor compounds for 6 hours. Results provide insights into the role of iron in Wnt signalling and demonstrate that iron depletion is the primary mode of actions of these compounds on Wnt pathway.

overall_design: SW480 cells were incubated with 10 mM of compounds (OICR623), control (DMSO) and two known iron chelators (DFO and Deferasirox) for 6 hours. RNA was extracted and cDNA samples isolated from 2-4 independent experiments were hybridized to the Affymetrix GeneChip® Human Gene 1.0 ST array.

first: Wrana

last: Jeff


title: Gene expression in primate postnatal brain through lifespan - prefrontal cortex

status: Public on Dec 09 2011

city: Leipzig

first: Mehmet

last: Somel

address: Deutscher Platz 6

department: Evolutionary Genetics

institute: Max Planck Institute for Evolutionary Anthropology

summary:
We investigated molecular changes during human, chimpanzee, and rhesus macaque postnatal brain development at the transcriptome, proteome, and metabolome levels in two brain regions: the prefrontal cortex (PFC) that is involved in several human-specific cognitive processes, and the cerebellar cortex (CBC) that may be functionally more conserved. We find a nearly three-fold excess of human-specific gene expression changes in PFC compared to CBC. The most prominent human-specific mRNA expression pattern in the PFC is a developmental delay of approximately 5 years in the expression of genes associated with learning and memory, such as synaptic transmission and long-term potentiation. This pattern is supported by correlated changes in concentrations of proteins and the respective neurotransmitters and its magnitude is beyond the shift expected from the life-histories of the species. Mechanistically, it might be driven by change in timing of expression of four or more transcription factors. We speculate that delayed synaptic maturation in PFC may play a role in the emergence of human-specific cognitive abilities.

Keywords: Age series

sample_organism:
Macaca mulatta
Pan troglodytes
Homo sapiens

overall_design:
Human, chimpanzee and rhesus macaque post-mortem brain samples from the superior frontal gyrus region of the prefrontal cortex were collected. The age ranges of the individuals in all three species covered the respective species' postnatal maturation period from infancy to old adulthood. RNA extracted from the dissected tissue was hybridized to Affymetrix® Human Gene 1.0 ST arrays.

PFC samples.

first: Xiling

last: Liu

first: Lin

last: Tang

first: Yan

last: Zheng

first: Song

last: Guo

first: Philipp

last: Khaitovich


title: Renal medulla expression differences between hypertensive and normotensive patients

status: Public on Oct 15 2011

city: Sydney

last: Morris

state: NSW

address: Anderson Stuart Building, room N452, University of Sydney

department: Physiology

institute: University of Sydney

summary: Identification of renal medulla genes whose expression differs between male individuals with high blood pressure and normal blood pressure using Affymetrix GeneChip Human Gene 1.0 ST Arrays.

overall_design: The Silesian Renal Tissue Bank, a collection of tissue which aimed to investigate candidate genes in human cardiovascular disease, was used to analyze the gene expression in hypertensive and normotensive patients. Approximately 1 cm3 of tissue from the healthy (unaffected by cancer) pole of the kidney was obtained immediately after surgery and transferred into containers with RNAlater (Ambion) and preserved at 70°C before mRNA extraction, which used a commercially available assay (RNeasy, Qiagen). Medulla and cortex were separated and individual RNA was obtained for each of them.  No pooling was performed. After extraction of RNA, cRNA was prepared and arrays performed using Affymetrix GeneChip Human Gene 1.0 ST Arrays performed at the Ramaciotti Gene Function Analysis facility, University of New South Wales in Sydney, Australia.

first: Francine

middle: Z

last: Marques

first: Anna

last: Campain

first: Maciej

last: Tomaszewski

first: Ewa

last: Zukowska-Szczechowska

first: Yee

middle: H

last: Yang

first: Brian

first: Fadi

last: Charchar


title: Transcriptional effect of an off-target shRNA targeting nucleostemin in human glioblastoma-derived cancer stem cells

status: Public on Oct 21 2011

city: Madrid

first: Jon

last: Gil-Ranedo

state: Madrid

address: C/ Nicolás Cabrera nº1, CBMSO, lab 224

country: Spain

institute: CBMSO

summary: Glioblastomas (GBM) may contain a variable proportion of active cancer stem cells (CSCs) capable of self-renewal, of aggregating into CD133+ neurospheres, and to develop intracranial tumors that phenocopy the original ones. We hypothesized that nucleostemin may contribute to cancer stem cell biology as these cells share characteristics with normal stem cells. Here we report that nucleostemin is expressed in GBM-CSCs isolated from patient samples. The significance of its expression was addressed by targeting the corresponding mRNA using lentivirally transduced short hairpin RNA (shRNA). We found that an off-target nucleostemin RNAi (shRNA22) abolishes proliferation and induces apoptosis in GBM-CSCs. Furthermore, in the presence of shRNA22, GBM-CSCs failed to form neurospheres in vitro or grow on soft agar. When these cells are xenotransplanted into the brains of nude rats, tumor development is severely compromised. Attempts were made to identify the primary target of shRNA22, suggesting a transcription factor involved in one of the MAP-kinases signaling-pathways. The use of this shRNA may offer a new therapeutic approach for this incurable type of brain tumors.

overall_design: The transcriptional profile of neurosphere cultures infected with lentiviral particles containing shRNA22 was compared with the profile of neurosphere cultures infected with lentiviral particles containing control shRNA. Experiments were done in triplicate.

first: Marta

last: Izquierdo Rojo


title: Renal cortex expression differences between hypertensive and normotensive patients

summary: Identification of renal cortex genes whose expression differs between male individuals with high blood pressure and normal blood pressure using Affymetrix GeneChip Human Gene 1.0 ST Arrays.


title: Time kinetics of gene expression in NK92 cells after Plasmodium falciparum-iRBC encounter

city: Tuebingen

first: Evelyn

last: Boettger

address: Wilhelmstrasse 27

institute: Institute of Tropical Medicine

summary: To study the effect of Plasmodium falciparum-infected erythrocytes on gene expression in NK92 cells, microarray analysis after 6, 12 and 24 hours of co-culture with either uRBC or iRBC was performed. The aim was to identify pathways in NK92 cells that are switched on after iRBC encounter in a time-dependent manner that will help to understand the mechanisms in innate immune defenses against Plasmodium falciparum infection.

overall_design: Variation in gene expression of NK92 cells was determined after 6, 12, and 24 hours of co-culture with either infected or uninfected RBC compared to timepoint 0 (start of co-culture, untreated control). All experiments were done in triplicate, that means that samples were collected in 3 different experiments (A, B, and C) each time after 0, 6, 12 and 24 hours of co-culture.


title: Expression data from Caco-2 cells expressing TLR4 and associated mutants

status: Public on Oct 11 2011

city: Essen

first: Elke

last: Cario

state: NRW

address: Virchowstr. 171

department: Division of Gastroenterology and Hepatology

institute: University of Duisburg-Essen, University Hospital of Essen

summary:
Common missense mutations (D299G, T399I) have been recently identified in the human TLR4 gene. The aim of this study was to determine how TLR4 and associated mutants affect gene expression in Caco-2 cells.
We used microarrays to asses gene expression profiles in Caco-2 stably overexpressing TLR4-WT, TLR4-D299G, TLR4-T399I or untransfected.

overall_design: Caco-2 clones stably overexpressing HA-tagged wildtype TLR4-WT, mutant TLR4-D299G or TLR4-T399I were generated. Prior to analysis, cell clones were cultured for 8 days in all experiments. RNA (triplicate) was extracted and hybridized on Affymetrix microarrays.

first: Annette

last: Eyking


title: Expression profiling of cisplatin resistant cells derived from H460 lung cell line.

status: Public on Sep 27 2011

city: Nashville

first: Bo

last: Lu

address: 1301 22nd Avenue South

department: Radiation Oncology

institute: Vanderbilt University Medical Center

summary: Combination of platinum-based chemotherapy and radiation is currently the standard treatment for locally advanced lung cancer patients. However, therapeutic resistance to these therapies may arise from the presence of cancer stem cells (CSCs). To investigate the CSCs hypothesis of chemo-radiation resistance, we used microarray assay to profile CSCs-like cisplatin-resistant lung cancer cells (CDDP-R) versus its parental cells.  CDDP-R cells were established by exposing H460 lung cancer cells to 3µM cisplatin for 7 days, followed by 0.8% methylcellulose selection over 14 consecutive days. We found that CDDP-R cells expressed higher levels of stem cell markers, including CD133 and ALDH. They are more resistant to cisplatin- and etoposide-induced apoptosis and to high radiation dose (20Gy). Clonogenic assays suggest that CDDP-R cells were more resistant to radiation than parental H460 cells (DER=1.21, p<0.01). Xenograft studies suggest that CDDP-R cells were more tumorigenic (p<0.001). Microarray and comprehensive protein interaction networks analyses revealed IGFBP3 as a highly ranked hub protein which plays an important role in the mechanism of cisplatin resistance. We found reduced level of IGFBP3 and enhanced IGFR-1 activation upon IGF stimulation in CDDP-R cells. The specific targeting of IGF-1R using siRNA resulted in significant sensitization of CDDP-cells (DER=1.17, p<0.05) to radiation compared with the parental H460 cells. Our findings suggest that CDDP-R cells have the characteristics of CSCs and constitute a “suitable” model to study lung CSCs. Profiling of CSCs-like H460 cells led to the identification of IGF as an important pathway for chemo- and radiotherapy resistance in lung cancer.

overall_design: gene expression comparison of two groups

first: Yunguang

last: Sun

first: Siyuan

first: Zhongming

last: Zhao


title: Methylation specifies distinct estrogen-induced binding site repertoires of CBP to chromatin (mRNA)

status: Public on Oct 07 2011

city: Illkirch; Strasbourg

first: Marco Antonio

last: Mendoza-Parra

address: 1, rue Laurent Fries

institute: IGBMC

summary: Multiple signaling pathways ultimately modulate the epigenetic information embedded in the chromatin of gene promoters by recruiting epigenetic enzymes. We found that, in estrogen-regulated gene programming, the acetyltransferase CREB-binding protein (CBP) is specifically and exclusively methylated by the coactivator-associated arginine methyltransferase (CARM1) in vivo. CARM1-dependent CBP methylation and p160 coactivators were required for estrogen-induced recruitment to chromatin targets. Notably, methylation increased the histone acetyltransferase (HAT) activity of CBP and stimulated its autoacetylation. Comparative genome-wide chromatin immunoprecipitation sequencing (ChIP-seq) studies revealed a variety of patterns by which p160, CBP, and methyl-CBP (meCBP) are recruited (or not) by estrogen to chromatin targets. Moreover, significant target gene-specific variation in the recruitment of (1) the p160 RAC3 protein, (2) the fraction of a given meCBP species within the total CBP, and (3) the relative recruitment of different meCBP species suggests the existence of a target gene-specific “fingerprint” for coregulator recruitment. Crossing ChIP-seq and transcriptomics profiles revealed the existence of meCBP “hubs” within the network of estrogen-regulated genes. Together, our data provide evidence for an unprecedented mechanism by which CARM1-dependent CBP methylation results in gene-selective association of estrogen-recruited meCBP species with different HAT activities and specifies distinct target gene hubs, thus diversifying estrogen receptor programming.

overall_design: Examination of estrogen-induced transcription in H3396 cells

first: Danilo

last: Ceschin

first: Mannu

last: Walia

first: Sandra

middle: S

last: Wenk

first: Carine

last: Duboé

first: Claudine

last: Gaudon

first: Yu

last: Xiao

first: Lucas

last: Fauquier

first: Martial

last: Sankar

first: Laurence

last: Vandel

first: Hinrich

last: Gronemeyer


title: Renal cortex and medulla microRNA and mRNA expression differences between hypertensive and normotensive patients

middle: J

last: Morris

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

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

overall_design: Refer to individual Series


title: ENCODE SUNY RNA Binding Protein GeneST Data for H1ESC

status: Public on Sep 19 2011

city: Albany

first: Frank

last: Doyle

state: NY

address: 257 Fuller Rd

department: Nanobiology

institute: UAlbany CNSE

summary:
RNA Binding Protein immunoprecipitation study for multiple target proteins in H1ESC cell line as part of the ENCODE consortium.  Analyzed data tracks available for view on UCSC Genome browser.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: Three sample replicates per sample type.  Total input RNA and Negative target RIP (antibody for bacteriophage coat protein) are provided as controls.  Individual samples reflect biological replicates defined as separate RIP runs (as opposed to technical replicate defined as multiple arrays run with same RIP sample as starting material)

first: Scott

last: Tenenbaum

first: Francis

first: Sabarinath

last: Jayaseelan

first: Sridar

middle: V

last: Chittur


title: ENCODE SUNY RNA Binding Protein GeneST Data for HeLaS3

summary:
RNA Binding Protein immunoprecipitation study for multiple target proteins in HeLaS3 cell line as part of the ENCODE consortium.  Analyzed data tracks available for view on UCSC Genome browser.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf


title: ENCODE SUNY RNA Binding Protein GeneST Data for K562

summary:
RNA Binding Protein immunoprecipitation study for multiple target proteins in K562 cell line as part of the ENCODE consortium.  Analyzed data tracks available for view on UCSC Genome browser.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf


title: ENCODE SUNY RNA Binding Protein GeneST Data for various cell lines

status: Public on Sep 20 2011

summary:
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

This SuperSeries is composed of the SubSeries listed below.

relation:
SuperSeries of: GSE31716
SuperSeries of: GSE31717
SuperSeries of: GSE31719
SuperSeries of: GSE31720
SuperSeries of: GSE31721


title: ENCODE SUNY RNA Binding Protein GeneST Data for GM12878

summary:
RNA Binding Protein immunoprecipitation study for multiple target proteins in GM12878 cell line as part of the ENCODE consortium.  Analyzed data tracks available for view on UCSC Genome browser.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

first: Luiz

last: Penalva


title: Expression data from peripheral blood - blood draws at Pre and Post time points of Methacholine (MCh) inhalation challenge

status: Public on Sep 18 2011

city: Vancouver

last: Tebbutt

state: BC

address: Room 166, 1081 Burrard Street

department: Medicine

institute: University of British Columbia

summary:
Evaluate the effect of methacholine-induced bronchoconstriction on the peripheral whole-blood transcriptome, post-challenge compared to pre-challenge.
Blood was collected immediately prior to, and two hours after challenge.

overall_design: 28 total blood samples (14 Pre- and 14 Post-challenge) were analyzed. Robust regression in the Linear Models for MicroArrays (LIMMA) was used to compaire gene expression between Pre and Post time points. No pre-filtering of probe sets was performed prior to statistical analyses. In addtion, and FDR of 10% was used to deteremine signifance of genes.

first: Jianquing

last: He

first: Casey

last: Shannnon

first: Amritpal

last: Singh

first: Chris

last: Charlsten


title: ENCODE SUNY RNA Binding Protein GeneST Data for HepG2

summary:
RNA Binding Protein immunoprecipitation study for multiple target proteins in HepG2 cell line as part of the ENCODE consortium.  Analyzed data tracks available for view on UCSC Genome browser.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf


title: Expression data from macrophage maturation and polarization c-Myc in alternative macrophage activation experiments

status: Public on Sep 16 2011

city: Rozzano

first: Massimo

last: Locati

state: MILAN

address: Via Manzoni, 113

department: Department of Translational Medicine of the University of Milan Faculty of Medicine, IRCCS Istituto Clinico Humanitas

country: Italy

institute: Istituto Clinico Humanitas

summary:
In response to microenvironmental signals macrophages undergo different activation, indicated as classic/M1 and alternative/M2 polarization. C-Myc transcription factor could be an essential player in M2 polarization.
Functional relevance of c-Myc in M2 macrophage biology is investigated by evaluating the effect of 100-58F4, on the transcriptional profile induced on human macrophages by IL-4.

overall_design: Human monocytes were obtained from normal donor buffy coats by two-step gradient centrifugation using Ficoll (Biochrom) and Percoll (Amersham). Non-adherent cells were discarded, and the purified monocytes were incubated for 7 days in RPMI 1640 (Biochom) supplemented with 10% FCS (HyClone) and 100 ng/mL M-CSF to obtain resting macrophages. Macrophage polarization was obtained by removing the culture medium and culturing cells in RPMI 1640 supplemented with 10% FCS and 100 ng/mL LPS plus 20 ng/mL IFN-gamma (M1 polarization) or 20 ng/mL IL-4 (M2 polarization) for 24 h. When needed, chemical inhibitors were added with IL-4.

first: Oscar

middle: M

last: Pello


title: Genomic profiling of enzastaurin-treated B cell lymphoma RL cells

status: Public on Sep 15 2011

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

institute: IRCCS Istituto Nazionale dei Tumori

summary: Follicular lymphoma (FL) is an indolent lymphoma associated with follicular center B cells, and typically contains the Bcl-2 chromosomal translocation t(14;18), which leads to overexpression of the anti-apoptotic intracellular protein Bcl-2. FLs are sensitive to chemotherapy; however, patient relapses occur and response duration becomes progressively shorter, with the majority of patients eventually dying from the disease. Enzastaurin (LY317615), an acyclic bisindolylmaleimide, was initially developed as an ATP-competitive selective inhibitor of PKC. We found, in agreement with recent reports, that enzastaurin inhibits cell proliferation and induces apoptosis. These results are consistent with decreased phosphorylation of the Akt pathway and its downstream targets. To provide new insights into the anti-tumor action of enzastaurin on non-Hodgkin lymphoma, we investigated its effects on gene expression profiles of the B cell lymphoma RL cell line by oligonucleotide microarray analysis. We identified a set of 41 differentially expressed genes, mainly involved in cellular adhesion, apoptosis, inflammation, and immune and defense responses. These observations provide new insights into the mechanisms involved in the induction of apoptosis by enzastaurin in B cell lymphoma cell lines, and identify possible pathways that may contribute to the induction of apoptosis.

overall_design: This series of microarray experiments contains the gene expression profiles of independent replicates of the B lymphoma RL cell line carrying t(14;18) before and after LY317615 treatment. 100 nanograms of total RNA were processed and fragmented. Biotin-labelled single-stranded DNA target was hybridized to the GeneChip® Gene 1.0 ST array following the Affymetrix  manufacturer's instructions.

first: Stefano

last: Sacchi

first: Monica

last: Civallero

first: Maria

last: Cosenza

first: Katia

last: Todoerti

first: Antonino

last: Neri


title: Expression data of human trophectoderm cells

status: Public on Sep 09 2011

city: San Francisco

first: Linda

last: Giudice

state: CA

address: 513 Parnassus Ave. HSE 1619

institute: University of California, San Francisco

summary:
The implantation process begins with attachment of the trophectoderm (TE) of the blastocyst to the maternal endometrial epithelium. Herein we have investigated the transcriptome of mural TE cells from 13 human blastocysts and compared these with those of human embryonic stem cell (hESC)-derived-TE (hESCtroph).  The transcriptomes of hESFtroph at days 8, 10, and 12 had the greatest consistency with TE. Among genes coding for secreted proteins of the TE of human blastocysts and of hESCtroph are several molecules known to be involved in the implantation process as well as novel ones, such as CXCL12, HBEGF, inhibin A, DKK3, Wnt 5A, follistatin. The similarities between the two lineages underscore some of the known mechanisms and offer discovery of new mechanisms and players in the process of the very early stages of human implantation.  We propose that the hESCtroph is a viable functional model of human trophoblasts to study trophoblast-endometrial interactions. Furthermore, the data derived herein offer the promise of novel diagnostics and therapeutics aimed at practical challenges in human infertility and pregnancy disorders associated with abnormal embryonic implantation.
Transcriptome analyses suggest human embryonic stem cell-derived-trophoblast as a viable functional model of human trophoblast to study trophoblast-endometrial interactions.

overall_design:
Five pools of trophectoderm cells were subjected to RNA isolation and microarray. The resulting data were compared to the transcriptomes of H7 human embryonic stem cells differentiated to the trophoblast lineage after 0, 2, 4, 6, 8, 10 and 12 days of induction with BMP-4.

This submission represents the trophectoderm cells from blastocysts.

first: Lusine

last: Aghajanova

first: Shehua

last: Shen

first: Angela

last: Rojas

first: Susan

last: Fisher

first: Juan

last: Irwin


title: Menthol effect on gene expression profile in malignant prostate cancer cell lines, PC-3

status: Public on Aug 31 2011

city: Seoul

first: Ju-Hong

last: Jeon

state: Seoul

address: 28 Yongon-Dong, Chongno-Gu

department: Department of Physiology and Biomedical Sciences

country: South Korea

institute: Seoul National University College of Medicine

summary:
Menthol, a naturally occurring cooling compound of peppermint oil, induces an anti-proliferative activity in androgen-independent prostate cancer (AIPC). Previously, we found that menthol affects PC-3 cells viability through activating JNK but the mechanism is not fully clear. We thus studied that dysregulated cell cycle progression of PC-3 cells to menthol. We performed microarray experiments to obtain a global view of how menthol affects prostate cancer biology in gene expression profile.
Our study demonstrated that menthol induced G2/M arrest by dysregulating PLK1 in the AICP cell model.

overall_design: Menthol was dissolved in ethanol as a vehicle at 0.1% working concentration and treated in PC-3 cells in triplicate Vehicle-treated PC-3 cells in triplicate were used as control.

first: Su-Hwa

last: Kim

first: Sanghoon

last: Lee

first: Eun-Jung

last: Park

first: Chai-Young

last: Jung

first: Tae-Woo

first: Nam-Hyuk

last: Cho

first: In-Gyu

first: Insuk

last: So


title: Gene expression patterns in response to GATA2 (WT and mutants) in HL-60 cells

status: Public on Aug 20 2011

city: Adelaide

first: Chung

last: Kok

state: South Australia

address: North Terrace

institute: South Australia Health and Medical Research Institute

summary: GATA2 mutants were discovered in families predisposed to MDS/AML and in sporadic cases of CML-blast crisis. Promyelocytic HL-60 cells were transduced with lentiviral vectors that express GATA2 WT or T354M, 355delT or L359V mutants upon addition of 4-hydroxy tamoxifen (4HT). Microarrays were performed to identify GATA2 WT signatures and differences caused by these mutations.

overall_design: HL-60 cells transduced with GATA2 (WT, T354M, 355delT and L359V) lentiviruses were treated with 4HT for 24 hours and RNA isolated and gene expression measured on Affymetrix microarrays.

first: Christopher

middle: N

last: Hahn

first: Chan-Eng

last: Chong


title: Small-molecule inhibitor JQ1 effect on multiple myeloma cell lines

status: Public on Sep 02 2011

city: Plantagenet

first: Madeleine

middle: E.

last: Lemieux

state: ON

address: 275 Main St., Suite 252

institute: Bioinfo

summary: Pathologic activation of c-Myc plays a central role in pathogenesis of several neoplasias, including multiple myeloma. However, therapeutic targeting of c-Myc has remained elusive due to its lack of a clear ligand-binding domain. We therefore targeted c-Myc transcriptional function by another means, namely the disruption of chromatin-dependent signal transduction. Members of the bromodomain and extra-terminal (BET) subfamily of human bromodomain proteins (BRD2, BRD3 and BRD4) associate with acetylated chromatin and facilitate transcriptional activation by increasing the effective molarity of recruited transcriptional activators. Notably, BRD4 marks select M/G1 genes in mitotic chromatin for transcriptional memory and direct post-mitotic transcription, via direct interaction with the positive transcription elongation factor complex b (P-TEFb). Because c-Myc is known to regulate promoter-proximal pause release of Pol II, also through the recruitment of P-TEFb, we evaluated the selective small-molecule inhibitor of BET bromodomains, JQ1, as a chemical probe to interrogate the role of BET bromodomains in Myc-dependent transcription and to explore their role as therapeutic targets in c-Myc-driven neoplasias.

overall_design: Duplicate cultures of MM.1S, OPM1 and KMS11 human myeloma cells were treated with either DMSO alone or with JQ1 (500 nM), for 24 hours. Total RNA was extracted and hybridized to Affymetrix human Gene 1.0 ST microarrays (two arrays per treatment per cell line for a total of 12 arrays).


title: Comparison of WAT CD34+ vs LAF CD34+

status: Public on Aug 16 2011

city: Milan

first: Giuliana

last: Gregato

address: Via ripamonti 435

department: Anatomy pathology

institute: IEO

summary: A catalytic role has been proposed in neoplastic angiogenesis and cancer progression for bone marrow-derived endothelial progenitor cells (EPCs). However, in preclinical and clinical studies the quantitative role of marrow-derived EPCs in cancer vascularization was found to be extremely variable. Adipose tissue represents an attractive source of autologous adult stem cells due to its abundance and surgical accessibility. CD34+cells from Lipotransfer aspirates (LAs) of patients undergoing breast reconstruction after breast cancer surgery were compared with CD34+ cells from Leucapheresis of normal subjects.

overall_design: Two samples of  purified CD34+ cells from Lipotransfer Aspirates (LAs) were compared with two samples of CD34+ cells from Leucapheresis samples. The reference were considered the CD34+ RNA from leucapheresis

first: Paola

last: Marighetti

first: Ines

last: Martin-Padura

first: Angelica

last: Calleri

first: Patrizia

last: Mancuso

first: Chiara

last: Corsini

first: Giancarlo

last: Pruneri

first: Francesco

last: Bertolini


title: Expression data from STAG2 deficient and proficient human cancer cells

status: Public on Aug 19 2011

city: BETHESDA

first: abdel

middle: G

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

summary:
We have discovered frequent genetic inactivation of the STAG2 gene in diverse human cancers including glioblastoma, Ewing's sarcoma, and melanoma.  STAG2 encodes a subunit of the sister chromatid cohesion complex called the "cohesin complex" that is responsible for the cohesion of sister chromatids following DNA replication and is cleaved at the metaphase to anaphase transition to enable chromosome segregation into daughter cells.  Interestingly, the cohesin complex has also been implicated as a regulator of chromatin architecture and transcription.  To determine the functional significance of STAG2 inactivation in cancer pathogenesis, we used somatic cell gene targeting to correct the endogenous mutations of STAG2 in two aneuploid human glioblastoma cell lines, H4 and 42MGBA.  Similarly, somatic cell gene targeting was also used to introduce a nonsense mutation into codon 6 of the endogenous wild-type allele of STAG2 in HCT116 cells, a near-diploid human colorectal cancer cell line with stable karyotype.  Expression profiling of these three paired sets of STAG2-proficient and deficient cells demonstrated that STAG2 does not play a global role in transcriptional regulation nor does it recurrently modulate the expression of specific tumor-promoting or suppressing genes.
For further details, see Solomon et al., Mutational inactivation of STAG2 causes aneuploidy in human cancer.

overall_design: RNA was prepared from subconfluent asynchronously proliferating cells using TRIZOL and purified by RNeasy MinElute Cleanup kit (Qiagen).  Hybridization to Affymetrix GeneChip Human Gene 1.0 ST arrays was used to generate gene expression profiles of STAG2-deficient and proficient H4, 42MGBA, and HCT116 cells.

first: David

last: Solomon

first: Abdel

first: Weiwei

last: Wu


title: Expression data from different samples of a single ccRCC patient.

status: Public on Aug 06 2011

city: Lyon cedex 08

first: Pierre

last: Martinez

address: 28 rue Laennec

institute: Cancer Research Centre of Lyon

summary: We have sampled several tumour regions from a single patient before and after everolimus treatment, including both primary and metastatic site samples to investigate intra-tumour heterogeneity.

overall_design: We selected 4 primary tumour regions, including a pre-treatment biopsy, and 1 metastatic region for expression analysis using microarray data. Two samples were used per region (1 fresh frozen and 1 formalin-fixed).

first: Andrew

last: Rowan

first: Charles

last: Swanton


title: Amplified genes are not necessarily over expressed, they can be unchanged or down regulated in cervical cancer cell lines [expression array data]

status: Public on Aug 01 2011

city: Mexico City

first: Jaime

last: Berumen

address: Dr. Balmis #148 Col. Doctores

department: Departamento de Medicina Experimental

country: Mexico

institute: Universidad Nacional Autonoma de Mexico

summary: Several copy number altered regions (CNA) have been identified in the genome of cervical cancer, especially amplifications of 3q and 5p. However, the contribution of those alterations to cervical carcinogenesis is still a matter of debate, since genome-wide, there is a lack of correlation between CNAs and gene expression. In this study, we investigated whether the CNAs in cell lines (CaLo, CasKi, HeLa, SiHa), at a gene-by-gene level, are related to changes in gene expression. On average 19.2% of the whole genome of cell lines had CNA. However, only 2.4% consisted of minimal recurrent regions (MRR), common to all cell lines. Whereas 3q had just some sparse common gains (13%), 5p was entirely duplicated recurrently. Genome-wide, only 11% of genes located in CNAs changed gene expression. In contrast, the rate increased over 3 fold times in MRRs. Chr 5p was confirmed entirely amplified by FISH. In spite of this, at most 32.9% of the explored genes in 5p (n=202) were de-regulated. In 3q, the rate was just 11.8%. Even in 3q26, which had five MRRs and 38.7% of SNPs was gained recurrently, the rate rose slightly to 13.6% (10 out of 73). Interestingly, up to 16% of de-regulated genes in 5p and 80% in 3q26 were down-regulated, suggesting additional factors are involved in gene repression. The de-regulated genes in 3q and 5p were found in clusters, suggesting local chromatin factors may also influence gene expression. In regions amplified discontinuously, the rate of down-regulated genes rose steadily as the number of amplified SNPs increased (p<0.01, Spearman's correlation). This suggests partial gene amplification as a mechanism of silencing gene expression. Additional genes were identified up- or down-regulated in 5p and 3q, which could be involved in cervical carcinogenesis, especially implicated in apoptosis. Those include CLPTM1L, AHRR, PDCD6 and DAP in 5p and TNFSF10 and ECT2 in 3q. Overall, the gene expression and copy number profiles suggest other factors, like epigenetic or chromatin domains, may influence gene expression within the entirely amplified genome segments. Further studies are needed to elucidate how these mechanisms regulate gene expression.

overall_design:
We analyzed four cervical cancer cell lines and normal exocervix tissue from 10 healthy female subjects using the Affymetrix Human Exon 1.0 ST platform. Array data was processed by Affymetrix Exon Array Computational Tool. Biological replicates were performed for the cell lines.
biological replicate: Calo-a, Calo-b, Calo-c
biological replicate: Caski-a, Caski-b, Caski-c
biological replicate: Hela-a, Hela-b, Hela-c
biological replicate: Siha-a, Siha-b, Siha-c

first: Oscar

last: Vazquez-Mena


title: Amplified genes are not necessarily over expressed, they can be unchanged or down regulated in cervical cancer cell lines

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

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


title: Transcriptomic Signature of Trophoblast Differentiation in a Human Embryonic Stem Cell Model

status: Public on Sep 17 2011

city: Valencia

first: Jose

middle: Antonio

last: Martinez-Conejero

address: C/ Guadassuar 1, bajo

institute: iGenomix

summary: Identification of genes involved in trophoblast differentiation is of great interest in understanding cellular and molecular mechanisms involved in placental development and is relevant clinically to fetal development, fertility, and maternal health. To understand, on a global scale, changes in the transcriptome during the differentiation of hESCs down the trophoblast lineage, a large-scale microarray analysis was performed. This work provides an in vitro functional genomic model with which to identify genes involved in trophoblast development.

overall_design: We investigated differentiation of human embryonic stemcells (hESCs) down the trophoblast lineage by culture with bone morphogenetic protein 4 (BMP4) over a 10-day period and analyze the cell every 2-days.

first: Melanie

last: Marchand

last: Horcajadas

first: Francisco

last: Esteban

first: Sohyun

middle: L

last: McElroy

first: Susan

last: Fisher

first: Linda

last: Giudice