title: Transcriptional analysis of cervical epithelial cell responses to HIV-1

city: Lincoln

first: Andrew

last: Block

state: Nebraska

address: 4240 Fair Street

department: Department of Biology

institute: University of Nebraska - Lincoln

summary: HIV-1 infections of women are mainly acquired through female reproductive tract where cervical and vaginal epithelial cells are the first line of defense. Although HIV-1 does not directly infect epithelial cells, HIV-1 obligatorily interacts with and crosses over epithelial layer to infect susceptible target cells, mainly CD4+ T cells, in the lamina propria to initiate an infection. However, the mechanism and ramification of the interaction of HIV-1 and epithelial cells in vaginal transmission of HIV-1 remain to be elucidated. We hypothesized that cervical epithelial cells are not a passive barrier, but actively respond to HIV-1 to change  mucosal milieu and facilitate HIV-1 transmission. We tested this hypothesis by studying the responses of cervical epithelial cells to HIV-1 through profiling genome-wide transcription. We found 1) cervical epithelial cells actively respond to HIV-1. Five hundred forty-three transcripts/genes in cervical epithelial cells were significantly altered in expression at four hours post exposure to HIV-1, of which many relate to important signaling pathways, such as innate immune responses, pattern recognition receptors, apoptosis, biosynthesis, and energy production, 2) HIV-1 increases the expression of CXC Chemokines (IL-8, CXCL1 and CXCL3) in cervical epithelial cells. IL-8 and CXCL1 are potent chemotactic for multinuclear neutrophils (MNP), monocytes and a minority of lymphocytes, and CXCL3 is predominant chemotactic for monocytes, 3) HIV-1 increases the expression of key inflammatory enzymes-COX-1 and COX-2.  COX-1 is responsible for the production of prostaglandins that are important for homeostatic functions, and COX-2 is a key enzyme to convert arachidonic acid to prostaglandins, key inflammatory mediators, and 4) the increased expression of IL-8 and COX-2 revealed using microarray analysis was mapped into the endocervical epithelial cells of macaques inoculated with inactivated SIV in vivo. Our date lead to a role model of epithelial cells in HIV-1 vaginal transmission, that is the axis of HIV-1, epithelial cells, proinflammatory molecules (IL-8, CXCL1, CXCL3, COX-1 and COX-2), cell recruitment (MNP, monocytes and T cells), and inflammation. This model implies that moderating epithelial proinflammatory response to HIV-1 may be utilized in prevention of HIV vaginal transmission.

overall_design: Human endocervical epithelial cell line, CRL-2615, was inoculated with HIV-1 ME1 and collected 4hrs post exposure. Biologically duplicated mRNAs were prepared after exposure.

first: Qingsheng


title: Klf5 controls bone marrow homing of stem cells and progenitors through Rab5-mediated membrane Beta1/Beta2-integrin expression

status: Public on Jan 30 2013

city: Cincinnati

first: Jose

last: Cancelas

state: OH

address: 3333 Burnet Ave,  ML 7013

department: Experimental Hematology

country: USA

institute: CCHMC

summary: The Kruppel-like factor 5 (Klf5) regulates pluripotent stem cell self-renewal but its role in somatic stem cells is unknown. Klf5 deficient hematopoietic stem cells and progenitors (HSC/P) fail to engraft after transplantation. This HSC/P defect was associated with impaired bone marrow (BM) homing and lodging and decreased retention in BM. The Klf5Δ/Δ HSC/P homing defect associated with decreased adhesion to fibronectin and expression of membrane-bound β1/β2-integrins. In vivo inducible gain-of-function of Klf5 in HSC translated into increased HSC/P adhesion. The expression of Rab5 family members, mediators of β1/β2-integrin recycling in the early endosome, was decreased in Klf5Δ/Δ HSC/P. Klf5 binds directly to the promoter of Rab5a/b and overexpression of Rab5b rescued the expression of activated β1/β2-integrins, adhesion and BM homing of Klf5Δ/Δ HSC/P. Altogether, these data indicate that Klf5 is indispensable for adhesion, homing, lodging and retention of HSC/P in the BM through Rab5-dependent post-translational regulation of Beta1/Beta2 integrins.

overall_design: Differential gene expression analyses was performed with Affymetrix GeneChip Mouse 1.0 ST assay. LSK cells from KLF-/- (n=4) and wt (n=5), bred on a C57BL/6 background, was analyzed for differential gene expression using GeneSpring GX11 using student's T-test.

first: E

middle: T

last: Ishikawa

first: K

middle: H

last: Chang

first: R

last: Nayak

first: H

middle: A

last: Olsson

first: A

last: Ficker

first: S

middle: K

last: Dunn

first: M

last: Madhu

last: Sengupta

first: J

last: Whitsett

middle: L

last: Grimes


title: Comparative transcriptome analysis of Th22 and Th17 cells

status: Public on Jan 29 2013

city: Birmingham

first: CASEY

last: WEAVER

state: Alabama

address: 845 19th Street South

department: Pathology

institute: University of Alabama at Birmingham

summary: Microarray was used to delineate the global gene expression profile underlying the specific developmental program of two divergent antigen-specific T helper subsets (Th22 versus Th17) by identifying upregulation or downregulation of key lineage-determining transcription factors, cytokines, chemokines and other genes that govern their functional attributes.

overall_design: To identify factors that might distinguish the Th22 and Th17 developmental programs, comparative global transcriptome analysis between these 2 subsets was performed. Naïve splenic CD4+ T cells from OT-II-transgenic mice were isolated and grown in vitro under T-helper lineage-specific conditions in the presence of cognate antigen (ovalbumin) to identify their distinctive global gene-regulation profiles.

first: Rajatava

last: Basu

first: Casey

last: Weaver

first: David

last: Crossman


title: Intrinsic glioma subtypes in EORTC 26951

status: Public on Feb 01 2013

city: Rotterdam

first: Pim

last: French

address: Dr Molewaterplein 50

department: Neurology

country: Netherlands

institute: Erasmus MC

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

overall_design: Refer to individual Series


title: Identification of anaplastic lymphoma kinase as a candidate of new therapeutic target for BCC

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

summary: Background; Basal cell carcinoma (BCC) is the most common cancer in humans.  The pathogenesis of BCC is associated with the sonic hedgehog (SHH) signaling pathway.  Vismodegib, a smoothened inhibitor, that targets this pathway is now in clinical use for advanced BCC patients, but its efficacy is limited.  Therefore, new therapeutic options for this cancer are required.  Methods; We studied gene expression profiling of BCC tumour tissue coupled with laser capture microdissection to identify tumor specific receptor tyrosine kinase expression that can be targeted by small molecule inhibitors.  The expression of selected molecules was confirmed by quantitative RT-PCR (qRT-PCR) and by immunohistochemistry.  The action of kinase inhibitors was examined on primary normal human epidermal keratinocytes.  Results; We found a >250 fold change increase (false discovery rate <10-4) of the   oncogene, anaplastic lymphoma kinase (ALK) as well as its ligands, pleiotrophin and midkine in BCC compared to microdissected normal epidermis.  qRT-PCR confirmed increased expression of ALK (p<0.05).  Stronger staining of phosphorylated ALK in BCC tumour nests than normal skin was observed by immunohistochemistry.  Additionally, Crizotinib, an FDA-approved ALK inhibitor, reduced keratinocyte proliferation in culture, whereas a c-Met, another receptor tyrosine kinase, inhibitor did not.  Crizotinib significantly reduced the expression of GLI1 and CCND2 mRNA by approximately 60% and 20%, respectively (p<0.05).  Conclusions; Our data suggest that ALK may increase GLI1 expression in parallel with the conventional SHH-pathway and promotes keratinocyte proliferation.  Furthermore, an ALK inhibitor alone or in combination with targeting SHH-pathway molecules may be a potential treatment for BCC patients.

overall_design: Laser capture microdissection was performed on 5 cases of nodular/superficial BCC, 5 cases of infiltrative BCC.

first: Hiroshi

last: Mitsui

first: Hanna

last: Ning

last: Suárez-Fariñas

first: James

middle: G

last: Krueger


title: Prediction of sensitivity of rectal cancer cells in response to preoperative chemoradiotherapy by DNA microarray analysis of gene expression profiles.

city: Bunkyo-ku

first: Toshiaki

last: Watanabe

state: Tokyo

department: Department of Surgical Oncology

country: Japan

institute: University of Tokyo

summary: Samples were prospectively collected during colonoscopic examination from 46 rectal cancer patients before starting preoperative chemoradiotherapy. The expression profiles were determined using Affymetrix Human Genome U133 Plus 2.0 arrays. Comparison between the sample groups allow to identify a set of discriminating genes that can be used for prediction of the response to radiotherapy in rectal cancer.

overall_design: Specimens from 46 rectal cancer patients who approved to receive preoperative chemoradiotherapy were studied. We prospectively collected biopsy specimens during colonoscopic examination from rectal cancer before starting preoperative chemoradiotherapy. Specimens from tumors were snap-frozen in liquid nitrogen and stored at -80 C until use. Paralleled tumor specimens were formalin fixed and paraffin embedded for histologic examination and other specimens were used for RNA extraction.  RNA was extracted from tumor tissue using frozen samples. The patients provided written, informed consent to the collection of specimens, and the local Ethics Committee approved the study protocol. All patients received a total dose of 50.4 Gy of radiation, UFT(300-500mg/day) and LV (75mg/day) and underwent standardized curative resection, following an interval of 4 weeks after chemoradiotherapy.

first: Takashi

last: Kobunai

first: Eriko

last: Hashimoto


title: Gene expression profiling in psoriatic lesional and non-lesional skin [Set 2]

status: Public on Jan 28 2013

city: Seattle

first: Jeannette

last: Bigler

state: WA

address: 3200 NE 92nd Street

institute: BJ Group, LLC

summary: To explore the psoriasis phenotype and pathways involved in psoriasis, we characterized gene expression in lesional and non-lesional skin from psoriasis patients.

overall_design: From each of the 24 psoriasis patients, we obtained two biopsies, one from a lesion and the other from non-lesional skin in the same general body geography. Total RNA was extracted from 6mm punch biopsies that were split in half. A total of 48 samples were run on Affymetrix HU133 Plus 2.0 microarrays.

first: Marty

last: Timour

first: Keith

last: Kerkof

first: Christopher

middle: B

last: Russell


title: Re-analysis by microarray using cDNA target of samples from psoriasis patients enrolled in an etanercept trial

summary: cDNA and cRNA hybridization technologies have different, probe-specific sensitivities. We used samples from an etanercept trial (GSE11903) to explore in a real-life setting the uniqueness of each platform.

overall_design: We obtained total RNA for a subset of the samples in GSE11903 from Jim Krueger and generated expression profiles using labeled cDNA target. From 14 patients, available base-line lesional and non-lesional skin biopsy pairs as well as post-dose samples were analyzed. All the samples were run on Affymetrix HU133 Plus 2.0 microarrays.


title: Comparison of Gene Expression in Psoriatic Skin from Different Sources


title: Transcriptional profiles of TIMP-2 and Ala+TIMP-2 A549 overexpressing cells and in tumor xenografts.

city: BETHESDA

first: DIMITRA

last: BOURBOULIA

state: MD

address: 8717 GROVEMONT CIRCLE

department: RADIATION ONCOLOGY BRANCH

institute: NIH

summary: TIMP-2 is an endogenous angiogenesis inhibitor, i.e. inhibits endothelial cell proliferation and tumor angiogenesis. As a result, TIMP-2 inhibits tumor growth and progression to metastasis. Understanding, therefore, the mechanisms of TIMP-2-mediated tumor growth inhibition would provide further support on the use of TIMP-2 as a novel biological agent for cancer therapy. We used microarray analysis to determine the TIMP-2 and Ala+TIMP-2 transcriptional profiles of A549 cancer cells in order to understand how TIMP-2 inhibits tumor growth and angiogenesis.

overall_design: We overexpressed TIMP-2 and its mutant (does not inhibit MMP) in A549 human lung cancer cells and determined TIMP-2 and Ala+TIMP-2 transcriptional profiles, groups of genes and associated biological functions. We then injected the cells in NOD-SCID mice and RNA from tumors were isolated for further analysis to identify genes that are associated with tumor growth inhibition.

first: Dimitra

last: Bourboulia

first: Biju

last: Isaac


title: Attenuation of Global Transcript Changes Induced by Elastase with Symplostatin 5 Cotreatment

city: Gainesville

first: Lilibeth

last: Salvador

state: Fl

address: 1600 SW Archer Road

department: Medicinal Chemistry

institute: University of Florida

summary:
Microarray profiling using the Affymetrix GeneChip Human Genome U133 plus 2.0 arrays was performed to comprehensively determine global changes in transcript levels in bronchial epithelial cells following elastase treatment. Elastase caused a significant change in expression (P < 0.05, fold change 1.5) of 364 transcripts corresponding to 348 genes. Elastase affected the expression of signaling molecules including chemokines, cytokines, and receptors, as well as components of the spliceosome, transcription machinery, cell cycle and ubiquitin-mediated proteolysis.
Importantly, the transcriptional response to elastase was attenuated by co-administration of 10 µM symplostatin 5. Comparison of the global heatmap of significantly modulated transcripts indicated that symplostatin 5 potently prevented the global effects of elastase. Symplostatin 5 caused a 20–68 % reduction in transcript levels of elastase-inducible genes including those involved in NOD- and MAPK- signaling pathways which are relevant to inflammation.

overall_design: Four samples were analyzed in biological duplicates. Transcriptome profile of elastase, elastase+symplostatin 5 were compared to control.

first: Kanchan

last: Taori

first: Jason

middle: S

last: Biggs

first: Jean

last: Jakoncic

last: Ostrov

first: Valerie

middle: J

last: Paul

first: Hendrik

last: Luesch


title: Identification of genes responsive to mild hyperthermia in human cervical squamous cell carcinoma HeLa cells

status: Public on Jan 24 2013

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

institute: University of Toyama

summary:
Hyperthermia (HT) is widely used to treat patients with various cancers. In general, HT elicits a wide spectrum of stress responses such as induction of heat shock proteins, protein aggregation and cell death in mammalian cells. Although many biological processes are affected by HT, the overall responses to HT in mammalian cells remain unknown.
The effects of heat stress at 41°C for 30 min (mild hyperthermia) on the gene expression in human cervical squamous cell carcinoma HeLa cells were investigated using an Affymetrix GeneChip system.

overall_design: Human cervical squamous cell carcinoma HeLa cells were treated with heat stress (41°C for 30 min) and followed by incubation for 0, 1, or 3 h at 37°C. Non-treated cells were served as control. Total RNA samples were prepared from the cells, and quality of the RNA was analyzed using a Bioanalyzer 2100. Gene expression was monitored by an Affymetrix GeneChip® system with a Human Genome U133-plus 2.0 array. Sample preparation for array hybridization was carried out as described in the manufacturer’s instructions.

first: Ayako

last: Kariya

first: Tatsuya

last: Yunoki


title: Transcriptional analysis of type 1 diabetes reveals an interferon signature that precedes T cell activation

city: St. Louis

first: Javier

last: Carrero

state: MO

address: 660 S Euclid Ave Box 8118

department: Pathology and Immunology

institute: Washington University School of Medicine

summary: Type 1 diabetes (T1D) is an autoimmune disease triggered by T cell reactivity to protein antigens produced by the β-cells. Here we present a chronological compendium of transcriptional profiles from islets of Langerhans isolated from non-obese diabetic (NOD) mice ranging from 2 wks up to diabetes and compared to controls. Parallel analysis was made of cellular components of the islets. Myeloid cells populated the islets early during development in all mouse strains. This was followed by a type I interferon signature detectable at 4-6 wks of age only in diabetes susceptible mice. Concurrently, CD4 T cells were found within islets, many in contact with intra-islet antigen presenting cells. Early cellular signs of islet reactivity were detected by six wks. By 8 wks, NOD islets contained all major leukocytes populations and an inflammatory gene signature. This work establishes the natural transcriptional signature of T1D and provides a resource for future research.

overall_design: 57 RNA samples isolated from the pancreatic islets of langerhans of experimental mice: 2-18 wk old non-obese diabetic (NOD) and newly diabetic NOD were compared to controls: NOD.RAG-/-, B6.g7 and C57BL/6. There were 3 or 6 biological replicates per condition. All mice were female. All data was normalized using RMA in Arraystar.  Data table includes normalized probe intensity for every  probe.


title: CXCL12 Production by Early Mesenchymal Progenitors is Required for Hematopoietic Stem Cell Maintenance

status: Public on Jan 31 2013

first: Yen-Michael

last: Hsu

address: 660 S. Euclid Avenue

institute: Washington University

summary:
Hematopoietic stem cells (HSCs) primarily reside in the bone marrow where signals generated by stromal cells regulate their self-renewal, proliferation, and trafficking.  Endosteal osteoblasts and perivascular stromal cells including endothelial cells3, CXCL12-abundant reticular (CAR) cells, leptin-receptor positive stromal cells, and nestin-GFP positive mesenchymal progenitors have all been implicated in HSC maintenance.  However, it is unclear if specific hematopoietic progenitor cell (HPC) subsets reside in distinct niches defined by the surrounding stromal cells and the regulatory molecules they produce. CXCL12 (stromal-derived factor-1, SDF-1) regulates both HSCs and lymphoid progenitors and is expressed by all of these stromal cell populations.
Here, we selectively deleted Cxcl12 from candidate niche stromal cell populations and characterized the effect on HPCs. Deletion of Cxcl12 from mineralizing osteoblasts has no effect on HSCs or lymphoid progenitors.  Deletion of Cxcl12 from osterix-expressing stromal cells, which includes CAR cells and osteoblasts, results in constitutive HPC mobilization and a loss of B lymphoid progenitors, but HSC function is normal. Cxcl12 deletion in endothelial cells results in a modest loss of long-term repopulating activity.  Strikingly, deletion of Cxcl12 in nestin-negative mesenchymal progenitors using Prx1-Cre is associated with a marked loss of HSCs, long-term repopulating activity, HSC quiescence, and common lymphoid progenitors.  These data suggest that osterix-expressing stromal cells comprise a distinct niche that supports B lymphoid progenitors and retains HPC in the bone marrow, while expression of CXCL12 from stromal cells in the perivascular region, including endothelial cells and mesenchymal progenitors, support HSCs.

overall_design: Total of three samples of two groups analyzed. Replica samples of CXCL12-abundant reticular (CAR) cells from two CXCL12-GFP knock-in mice and a combined sample of PDGFRa+ Sca+ CD45- lineage- cells from three Prx1-Cre Rosa26Ai9/+ Cxcl12gfp/+ mice were used and analyzed.

first: Daniel

middle: C

last: Link


title: Gene expression profiling in psoriatic lesional and non-lesional skin [Set 1]

first: Jeannette

last: Bigler

summary: To explore the psoriasis phenotype, we characterize gene expression in lesional and non-lesional skin from psoriasis patients.

overall_design: We extracted total RNA from 5mm punch biopsies taken from 14 psoriatic patients. From each patient, we obtained two biopsies, one from a lesion and the other from non-lesional skin in the same general body geography. A total of 28 samples were run on Affymetrix HU133 Plus 2.0 microarrays.

first: Marty

last: Timour

first: Keith

last: Kerkof

last: Russell


title: MicroRNA regulate immunological pathways in T-cells in immune thrombocytopenia (ITP)  [mRNA]

status: Public on Jan 22 2013

city: Little Rock

first: Intawat

last: Nookaew

address: 4301 W Markham St

department: Department of Biomedical Informatics

institute: University of Arkansas for Medical Sciences

summary: MicroRNA are small non-coding RNA molecules that regulate gene expression. To investigate the role of microRNA in ITP, we performed genome-wide expression analyses of mRNA and microRNA in T-cells from ITP patients and controls. We identified 1,915 regulated genes and 22 regulated microRNA that differed between ITP patients and controls. Seventeen of the 22 regulated microRNA were linked to changes in target gene expression; 57 of these target genes were associated with the immune system, e.g. T-cell activation and regulation of immunoglobulin production. CXCL13 and IL-21 were two microRNA target genes significantly increased in ITP. We could demonstrate increased plasma levels of CXCL13 and others have reported increased plasma levels of IL-21 in ITP. Thus, regulated microRNA were significantly associated with both gene and protein expression of molecules in immunological pathways. We suggest that microRNA may be important regulatory molecules involved in the loss of tolerance in ITP.

overall_design: Microarray expression analysis of mRNA and miRNA in peripheral blood T-cell of control and ITP patients.

first: Margareta

last: Jernås

first: Hans

last: Wadenvik

first: Bob

last: Olsson


title: MicroRNA regulate immunological pathways in T-cells in immune thrombocytopenia (ITP)

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

platform_organism:
Homo sapiens
synthetic construct


title: Sequential waves of gene expression in patients with clinically defined Dengue illnesses reveal subtle disease phases and predict disease severity.

status: Public on Jan 26 2013

city: silver spring

first: peifang

last: sun

address: 503 robert grant ave

institute: Naval Medical Research Center

summary:
Background: Dengue virus (DENV) infection often leads to acute illness lasting 2-7 days with severity ranging from dengue fever (DF) to hemorrhagic fever (DHF) and fatal dengue shock syndrome (DSS). The dynamic changes of host responses on the gene transcription level that accompany DENV infection and differences between DF and DHF cases have been poorly understood, particularly for South American population.

Methodology/Principal Findings:  Supported by a longitudinal active surveillance program for dengue transmission in Maracay, Venezuela, we conducted a prospective study to investigate host responses in dengue patients. Blood specimens and clinical information were collected on a daily basis from febrile cases confirmed with DENV infection from their first day of enrollment to early defervescence together with one convalescent sample. A total of 49 and 13 study participants were defined as DF and DHF cases respectively based on their clinical and hematological information. Using convalescent specimens as baseline, day-to-day gene expression was evaluated ex vivo in peripheral blood mononuclear cells of the study participants.  Two waves of gene expression were detected: the first wave peaked at day 1 from the onset of fever (day 0) then declined at days 3-4; the second wave emerged from day 4 and peaked around day 5-6. Genes associated with innate immune process, including type I interferon signaling, cytokine-mediated signaling, chemotaxis, and antiviral responses, dominated the first wave; whereas genes involved in cell cycle processes, including cell division, mitosis, DNA replication, chromosome, and spindle organization dominated the second wave. Measureable genomic markers predicted early acute, late acute and convalescent phases with 91% accuracy. Gene signatures expressed in early acute phase predicted disease severity (DF vs DHF) with 96% accuracy.

Conclusions/Significance: Our study established a dynamic pattern of detailed host immune responses to DENV infection and revealed genomic signatures valuable for diagnostics purposes.

overall_design:
Total 64 subjects representing 51 DF (dengue fever) and 13 DHF (dengue hemorrhagic fever) cases were used to study gene expression during the course of dengue acute illness. Sample information regarding Patient No., Infecting serotype, fever status (fever days or defervescent (df) days), and disease severity (DF vs DHF) were provided. The date for a sample for gene chip hybridization and image scanning was marked as Scan date.   Samples from study subjects were collected once a patient was enrolled. Over 200 samples were collected. Two genechip platforms were used, the HG-focus and HG-U133plus2. A total of 168 samples were assayed on the HG-focus platform, 2 were excluded for further analysis as they failed on quality control (i.e. VFP-0003_G7_DF, VFP-0029_G1_DF samples). A total of 101 samples were assayed on the HG-U133plus2 platform, 4 were excluded for further analysis as they failed on quality control (i.e. VFP_0186_G4_DF, VFP-0213_G3_DF, VFP_0213_G5_DF, VFP_0220_G3_DHF). Data generated by HG-focus platform were used to explore significantly expressed genes in individual Gs, phases, and for prediction analysis for disease phases. Whereas data generated by HG-U133plus2 were first used to assess the reproducibility of results generated by the HG-focus platform. Secondarily, they were used to perform prediction analysis for disease severity.
Samples were grouped into stages (G) based on the timepoint when they were collected: G0=day0 (on the day of fever onset); G1=day 1 (one day after fever onset); G2=day2 (two days after fever onset)…until G5; G6=day6-10 (6-10 days after fever onset); G7= convalescent time point (around day 28 after the first sample). Samples were also grouped into early acute (G0-G3), late acute (G4-G6) and convalescent phases (G7).
References for the protocols; PMID 12803996 and 20078211

first: Sun

last: Peifang

first: Josefina

last: García

first: Guillermo

last: Comach

first: Maryanne

last: Vahey

first: Zhining

last: Wang

first: Isabel

last: Bazan

first: Thomas

middle: W

last: Scott

first: Christian

middle: F

last: Ockenhouse

first: Gloria

last: Sierra

first: Stalin

last: Vilcarromero

first: Patrick

last: Blair

first: Brett

middle: M

last: Forshey

first: Claudio

last: Rocha

first: Daria

middle: E

last: Camacho

first: Amy

last: Morrison

first: Eric

last: Halsey

first: Tadeusz

last: Kochel


title: Mammalian TRIM71 as repressor of mRNAs that inhibits translation and affects mRNA stability

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Expression data from mouse embryonic stem cells upon TRIM71 KD and parental ctrl cells

summary: We identify mammalian TRIM71 as repressor of mRNAs that inhibits translation and affects mRNA stability. In this data set we compare the expression profile of mouse ES upon Trim71 KD versus that of the parental cells.

overall_design: Experiment was performed in triplicate.

first: I

last: Loedige

first: T

first: S

last: Thiry

first: W

last: Filipowicz


title: Gene expression changes in subclones of a Burkitt lymphoma cell line with different patterns of EBV latent infection

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

country: United Kingdom

institute: Durham University

summary: In this study we have investigated the gene expression profiles of three different types of subclone all generated by single cell cloning of the same parental EBV positive Burkitt lymphoma cell line Awia-BL. These included  EBV negative clones which have lost the virus episome, EBV positive clones with a conventional Latency I form of infection and EBV positive clones with an atypical Wp-restricted form of infection.

overall_design: Gene expression was compared between two different EBV negative clones (both performed in biological duplicate), four different Latency I clones and four different Wp-restricted clones using HG U133 Plus 2.0 gene chip arrays.

first: Gemma

last: Kelly

first: Julianna

last: Stylianou

first: Jane

last: Rasaiyaah

first: Wendy

last: Thomas

first: Debbie

last: Croom-Carter

last: Kohler

first: Rainer

last: Spang

first: Ciaran

last: Woodman

first: Paul

last: Kellam

first: Alan

last: Rickinson

first: Andrew

middle: I

last: Bell


title: Pediatric rhabdoid tumors of kidney and brain show many differences in gene expression but share dysregulation of cell cycle and epigenetic effector genes

status: Public on Jan 21 2013

city: Aurora

first: Diane

last: Birks

state: CO

department: Neurosurgery

institute: University of Colorado, Denver - Anschutz Medical Campus

summary: Rhabdoid tumors (RTs) are aggressive tumors of early childhood that occur most often in brain (AT/RTs) or kidney (KRTs). Regardless of location, they are characterized by loss of functional SMARCB1 protein, a component of the SWI/SNF chromatin remodeling complex. The aim of this study was to determine genes and biological process dysregulated in common to both AT/RTs and KRTs. Gene expression for AT/RTs was compared to that of other brain tumors and normal brain using microarray data from our lab. Similar analysis was performed for KRTs and other kidney tumors and normal kidney using data from GEO. Dysregulated genes common to both analyses were analyzed for functional significance. Unsupervised hierarchical clustering of RTs identified 3 major subsets: 2 comprised of AT/RTs, and 1 of KRTs. Compared to other tumors, 1187, 663 and 539 genes were dysregulated in each subset, respectively. Only 14 dysregulated genes were common to all 3 subsets. Compared to normal tissue, 5209, 4275 and 2841 genes were dysregulated in each subset, with an overlap of 610 dysregulated genes. Among these genes, processes associated with cell proliferation, MYC activation, and epigenetic dysregulation were common to all 3 RT subsets. The low overlap of dysregulated genes in AT/RTs and KRTs suggests that factors in addition to SMARCB1 loss play a role in determining subsequent gene expression. Drugs which target cell cycle or epigenetic genes may be useful in all RTs. Additionally, targeted therapies tailored to specific RT subset molecular profiles should be considered.

overall_design:
Molecular profiling of 20 ATRTs, 42 other pediatric CNS WHO Grade IV tumor samples and 9 pediatric normal brain samples was performed using Affymetrix U133 Plus2 GeneChips. Data were background corrected and normalized using gcRMA (as implemented in Bioconductor). ANOVA was used to identify differentially expressed genes for AT/RTs compared to other brain tumor types. Various analyses, including bioinformatics tools DAVID, Gene Set Enrichment (GSEA), and Ingenuity Pathways Analysis,  were used to identify biological processes and genes of particular interest among the  differentially expressed genes. Similar analysis of publicly available KRT and pediatric kidney tumor  and normal kidney data was also performed by us. The overlaps between the results were examined to determine genes and processes dysregulated in common to both ATRTs and KRTs.

This study includes a re-analysis of samples from other studies (AT/RT: GSE28026;  glioblastoma: GSE33331).

last: Donson

first: Purvi

middle: R

last: Patel

first: Alexandra

last: Sufit

first: Elizabeth

last: Algar

first: Christopher

last: Dunham

first: Bette

last: Kleinschmidt-DeMasters

first: Michael

last: Handler

first: Rajeev

last: Vibhakar

first: Nicholas

last: Foreman


title: Generation and maintenance of hiPSCs on PCM-DM

status: Public on Jan 20 2013

city: Osaka

first: Yonehiro

last: Kanemura

address: 2-1-14 Hoenzaka, Chuo-ku

department: Division of Regenerative Medicine Institute for Clinical Research

institute: National Hospital Organization Osaka National Hospital

summary:
Human ES cells (hESCs) and human induced pluripotent stem cells (hiPSCs) are usually generated and maintained on living feeder cells like mouse embryonic fibroblasts or on a cell-free substrate like Matrigel. For clinical applications, a quality-controlled, xenobiotic-free culture system is required to minimize risks from contaminating animal-derived pathogens and immunogens. We previously reported that the pericellular matrix of decidua-derived mesenchymal cells (PCM-DM) is an ideal human-derived substrate on which to maintain hiPSCs/hESCs. In this study, we examined whether PCM-DM could be used for the generation and long-term stable maintenance of hiPSCs. Decidua-derived mesenchymal cells (DMCs) were reprogrammed by the retroviral transduction of four factors (OCT4, SOX2, KLF4, c-MYC) and cultured on PCM-DM. The established hiPSC clones expressed alkaline phosphatase, hESC-specific genes and cell-surface markers, and differentiated into three germ layers in vitro and in vivo. At over 20 passages, the hiPSCs cultured on PCM-DM held the same cellular properties with genome integrity as those at early passages. Global gene expression analysis showed that the GDF3, FGF4, UTF1, and XIST expression levels varied during culture, and GATA6 was highly expressed under our culture conditions; however, these gene expressions did not affect the cells’ pluripotency. PCM-DM can be conveniently prepared from DMCs, which have a high proliferative potential. Our findings indicate that PCM-DM is a versatile and practical human-derived substrate that can be used for the feeder-cell-free generation and long-term stable maintenance of hiPSCs.
Keywords: Induced pluripotent stem cells; Extracellular matrix; Decidua; Mesenchymal cells

overall_design: The microarray study was carried out using Affymetrix Human Genome U133 Plus 2.0 gene expression arrays. Total RNA was extracted from cells with RNeasy (Qiagen), and 100ng of total RNA was used to synthesize aRNA using the 3’ IVT Express Kit, according to the manufacturer’s instructions (Affymetrix Inc., Santa Clara, CA). After aRNA purification, 15 μg of aRNA was fragmented and hybridized with a pre-equilibrated GeneChip array (Human Genome U133 Plus 2.0 gene expression array, Affymetrix) at 45°C for 16 hours. The GeneChip array was then washed, stained, and scanned according to the manufacturer’s instructions. The gene expression data were extracted using Affymetrix Expression Console software.

first: Hayato

last: Fukusumi

first: Tomoko

last: Shofuda

first: Yoshiki

last: Sasai


title: Gene expression profile of HCT116 exposed to chronic hypoxia

status: Public on Jan 18 2013

city: Frederick

first: Nicole

last: Fer

address: PO Box B

institute: Frederick National Laboratory for Cancer Research

summary: To identify genes involved in survival to prolonged hypoxia we exposed HCT116 to hypoxia for 3 days. Control cells were exposed to normoxic conditions.

overall_design: HCT116 colon cancer cells were serum starved and exposed to hypoxia (1%O2) or normoxia (21%O2) for 3 days.

first: Barbara

last: Onnis

first: Giovanni

last: Melillo


title: Cultured Cyto and Syncytio-trophoblast samples exposed to varying degrees of hypoxia (methylation)

city: Vancouver

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

country: Canada

institute: University of British Columbia

summary: The mechanisms by which the placenta adapts to exogenous stimuli to create a stable and healthy environment for the growing fetus are not well known. Low oxygen tension and sub-optimal vitamin D levels influence placental function and both are associated with preeclampsia, a condition associated with altered development of placental trophoblast. We hypothesized that oxygen tension, vitamin D levels, or both affect villous trophoblast by modulation of gene expression through DNA methylation. To test this we used the Illumina Infinium Human Methylation 450 BeadChip array to compare the DNA methylation profile of primary cultures of human cytotrophoblasts and syncytiotrophoblasts under three oxygen tensions and three vitamin D levels. We found no effect on global DNA methylation by either treatment, but a limited set of loci became hypermethylated in cytotrophoblasts exposed for 24 hours to 1% oxygen, as compared to the same cells exposed to 8% or 20% oxygen. Vitamin D levels had no detectable effect on methylation profiles in either trophoblast type. Hypermethylation with low oxygen tension was independently confirmed by bisulfite-pyrosequencing in a subset of functionally important genes including CP, ITGA5, SOD2, XDH and ZNF2. Intriguingly, 70 out of the 147 hypoxia-associated CpGs, overlapped with CpG sites that become hypomethylated upon differentiation of cytotrophoblasts into syncytiotrophoblasts. Furthermore, the preponderance of altered sites was located at AP-1 binding sites. We suggest that AP-1 expression is triggered by hypoxia and interacts with DNA methyltransferases (DNMTs) to target methylation at specific sites in the genome, thus causing suppression of the associated genes that are responsible for differentiation of villous cytotrophoblast to syncytiotrophoblast.

overall_design: DNA from 2 cell types from 5 placentas exposed to 3 different conditions of hypoxia (1%,8%,20%) and treated with 3 levels of vitamin D were bisulfite converted and run on the Illumina HumanMethylation450 BeadChip

first: Ryan

last: Yuen

first: Baosheng

last: Chen

first: John

middle: D

last: Blair

middle: P

first: D

last: Nelson


title: Notch Pathway Activation Targets AML Cell Homeostasis and Differentiation: THP1 cell line

city: Paris

first: Camille

last: Lobry

address: 16 rue de la Grange aux Belles

department: IRSL Inserm U944 / CNRS UMR7212

country: France

institute: Inserm

summary: Expression data from untreated or Dll4-Fc treated THP1 cell line.  We used Dll4-Fc stimulation of AML cells to study whether Notch activation has an impact on AML. We analyzed THP1 cell line in vitro treated with Dll4-Fc or vehicle control to determine genes affected by Notch activation.

overall_design: THP1 cell line was cultured on plate coated with 30 nM Dll4-Fc or vehicle for 48 hours prior to RNA extraction and hybridization to Human Genome U133 Plus 2.0 Affymetrix arrays.

first: Iannis

last: Aifantis


title: Expression data from bone marrow of primary multiple myeloma patients

city: salt lake city

first: fenghuang

last: zhan

state: UT

institute: university of utah

summary: Drug resistance is a major obstacle in cancer therapy. The molecular mechanisms of drug resistance still remain largely elusive. Microarray analyses on paired primary myeloma samples at baseline and after therapy or at relapse showed that NEK2 was one of the most up-regulated genes in myeloma cells after high-dose chemotherapy or at relapse. By analyzing the published (> 2,500) microarrays and clinical datasets, we found that NEK2 expression is increased in many malignancies, and that high expression of NEK2 was associated with a shorter event-free and overall survival. Moreover, NEK2 expression was typically increased in tumors with aggressive subtype and advanced TNM stage. Our studies indicate that over-expressing NEK2 in cancer cells resulted in enhanced cell proliferation and drug resistance, whereas knockdown of NEK2 induced significant cancer cell death and growth inhibition. We found that NEK2 over-expression activates cell cycle progression and cell division through the stimulation of cell cycling genes CDC2/CCNB1 and PBK. Interestingly, NEK2-overexpression also activated the Wnt/β-catenin signaling pathway. We conclude that NEK2 represents a predictor for drug resistance and poor prognosis in cancers and could be a potential target for cancer therapy.

overall_design: Myeloma tumor cells from bone marrow aspirates were collected at baseline and after chemotherapy (pre-1st and pre-2nd bone marrow transplant, and pre-consolidation)  for RNA extraction and hybridization on Affymetrix microarrays. We sought to define genes related to chemotheraputic resistance.


title: Microarray analysis of wildtype, Klf8gt/gt, Klf3-/- and Klf3-/- Klf8gt/gt TER119+ E13.5 fetal liver cells

status: Public on Jan 17 2013

city: University of NSW

first: Alister

last: Funnell

address: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of NSW

summary:
The aim of this experiment was to investigate the regulation of gene expression by KLF3 and KLF8 in fetal erythroid cells by analyzing single and double mutant mouse models.
Affymetrix microarrays were performed on RNA from TER119+ fetal liver cells from E13.5 wildtype, Klf8gt/gt, Klf3-/- and Klf3-/- Klf8gt/gt mice.

overall_design: Four wildtype replicates, four Klf8gt/gt replicates, three Klf3-/- replicates and four Klf3-/- Klf8gt/gt replicates of E13.5 TER119+ fetal liver cell samples, litter-matched where possible.

first: Ka

last: Mak

first: Merlin

last: Crossley


title: Cultured Cyto and Syncytio-trophoblast samples exposed to varying degrees of hypoxia

type:
Expression profiling by array
Methylation profiling by array

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

overall_design: Refer to individual Series

first: David


title: Notch Pathway Activation Targets AML Cell Homeostasis and Differentiation


title: Expression data from fibroblasts treated with TGF-Beta

city: Barcelona

first: Alexandre

last: CALON

address: Dr. Aiguader, 88

country: Spain

institute: Hospital del Mar Medical Research Institute (IMIM)

summary:
The survival of isolated metastatic cells and expansion into macroscopic tumour has been recognized as a limiting step for metastasis formation in several cancer types yet the determinants of this process remain largely uncharacterized. In colorectal cancer (CRC), we identify a transcriptional programme in tumour-associated stromal cells, which is intimately linked to a high risk of developing recurrent disease after therapy. A large proportion of CRCs display mutational inactivation of the TGF-beta pathway but paradoxically they are characterized by high TGF-beta production. In these tumours, TGF-beta instructs a transcriptional programme in stromal cells, which confers a high risk of developing metastatic disease.
We quantified the association of TGF-beta-activated fibroblasts with disease progression. To this end, we used as surrogates the gene expression programme upregulated by addition of TGF-beta to normal colon mucosa-derived fibroblasts (CCD-Co-18) in culture.

overall_design: CCD-Co-18 were seeded at 60% confluence and treated with TGF-β1. Gene expression profiles were measured in duplicate using HG-U133 plus 2.0. We used RMA background correction, quantile normalization and RMA summarization (Gautier et al., 2004). A TGF-β response signature was obtained by selecting genes with limma P-value < 0.05 and at least two fold up-regulation in TGF-β treated fibroblasts.

last: Calon

first: Elisa

last: Espinet

first: Eduard

last: Batlle


title: An Expression Atlas of Human Primary Cells: Inference of Gene Function from Coexpression Networks

status: Public on Aug 16 2013

city: Edinburgh

first: Tom

last: Freeman

state: Midlothian

address: Easter Bush

department: The Roslin Institute

institute: Univeristy of Edinburgh

type:
Expression profiling by array
Third-party reanalysis

summary: The specialisation of mammalian cells in time and space requires genes associated with specific pathways and functions to be co-ordinately expressed.  Here we have combined a large number  of publically available microarray datasets (745 samples, from over 100 separate studies) derived from human primary cells and analysed on the Affymetrix U133plus2.0 array.  Using the network analysis tool BioLayout Express3D  we have constructed and clustered large correlation graphs of these data in order to identify robust co-associations of genes expressed in a wide variety of cell lineages.  We discuss the biological significance of a number of these associations, in particular the coexpression of key transcription factors with the genes that they are likely to control.  We consider the regulation of genes in human primary cells and specifically in the human mononuclear phagocyte system.  Of particular note is the fact that these data do not support the identity of putative markers of antigen-presenting dendritic cells, nor classification of M1 and M2 activation states, a current subject of debate within immunological field. We have provided this data resource on the BioGPS web site (www.biogps.org) and on macrophages.com (www.macrophages.com).

overall_design: Meta-analysis of publically available human primary cell data run on the Affymetrix U133plus2.0 array.


title: Identification of Prognosis-Relevant Subgroups in Patients with Chemoresistant Triple Negative Breast Cancer

status: Public on Jan 15 2013

city: Houston

first: Keda

last: Yu

address: 6565 Fannin Street

institute: The Methodist Hospital Cancer Center, Houston, Texas

summary: Triple-negative breast cancer (TNBC) patients with residual disease after neoadjuvant chemotherapy generally have worse outcome; however, some patients with residual tumor after neoadjuvant chemotherapy do not relapse. We hypothesize that there are subgroups of chemoresistant TNBC patients with different prognosis. In this study, 25 chemoresistant samples from 47 neoadjuvant chemotherapy-treated TNBC (The Methodist Hospital) are chosen for study

overall_design: We used gene expression data of TNBC patients with residual disease and different prognosis to molecularly define the clinically relevant subgroups, and developed a 7-gene prognostic signature for chemoresistant TNBCs

first: Jenny

last: Chang


title: A data-driven approach to preprocessing Illumina 450K methylation array data

city: London

first: Chloe

last: Wong

state: Select a State or Province

address: MRC SGDP Centre, Institute of Psychiatry,

institute: King's College London

summary:
Background: As the most stable and experimentally accessible epigenetic mark, DNA methylation is of great interest to the research community. The landscape of DNA methylation across tissues, through development and in disease pathogenesis is not yet well characterised. Thus there is a need for rapid and cost effective methods for assessing genome-wide levels of DNA methylation. The Illumina Infinium HumanMethylation450 (450K) BeadChip is a very useful addition to the available methods but its complex design, incorporating two different assay methods, requires careful consideration. Accordingly, several normalization schemes have been published. We have taken advantage of known DNA methylation patterns associated with genomic imprinting and X-chromosome inactivation (XCI), in addition to the performance of SNP genotyping assays present on the array, to derive three independent metrics which we use to test alternative schemes of correction and normalization. These metrics also have potential utility as quality scores for datasets.
Results: The standard index of DNA methylation at any specific CpG site is β = M/(M + U + 100) where M and U are methylated and unmethylated signal intensities. Betas calculated from raw signal intensities (the default GenomeStudio behaviour) perform well, but using 11 methylomic datasets we demonstrate that quantile normalization methods produce marked improvement, even in highly consistent data, by all three metrics. The commonly used procedure of normalizing betas is inferior to the separate normalization of M and U, and it is also advantageous to normalize Type I and Type II assays separately. More elaborate manipulation of quantiles proves to be counterproductive.
Conclusions: Careful selection of preprocessing steps can minimise variance and thus improve statistical power, especially for the detection of the small absolute DNA methylation changes likely associated with complex disease phenotypes. For the convenience of the research community we have created an R software package called wateRmelon, compatible with the existing methylumi, minfi and IMA packages, that allows others to utilise the same normalization methods and data quality tests on 450K data.

overall_design: Bisulfite converted DNA from the 11 cohorts (N=695, including 36 technical replicates) were hybridised to the Illumina Infinium 450k Human Methylation Beadchip v1.2

first: Ruth

last: Pidsley

first: Manuela

last: Volta

first: Katie

last: Lunnon

first: Jonathan

last: Mill

first: Leonard

last: Schalkwyk


title: Human subcutaneous adipose tissue and perithyroid adipose tissue gene expression

city: Gothenburg

first: Per-Arne

last: Svensson

department: Department of molecular and clinical medicine

country: Sweden

institute: institute of medicine

summary: Different human adipose tissue depots may have functional differences. Subcutaneous human adipose tissue has been extensively studied, but less is known about other depots. Perithyroid (PT) adipose tissue contains not only white adipocytes but also brown adipocytes. The aim of this study was to compare the expression of brown adipocyte containing perithyroid adipose tissue with s.c. adipose tissue.role in the development of obesity. Expression profiling of adipose tissue may give insights into mechanisms contributing to obesity and obesity-related disorders.

overall_design: Expression analysis of paired biopsies from s.c and perithyriod (PT) adipose tissue from nine subjects undergoing surgery in the thyroid region.

first: Margareta

last: Jernås

first: Bengt

last: Nilsson

first: Lena

last: Carlsson


title: Transcriptome analysis on whole kidney of Usp2 knockout mice

status: Public on Jan 16 2013

city: Lausanne

first: Daniel

last: Pouly

address: Rue du Bugnon 27

department: Department of Pharmacology and Toxicology

institute: University of Lausanne

summary: Ubiquitylation plays an important role in the control of Na+ homeostasis by the kidney. It is well established that the epithelial Na+ channel ENaC is regulated by the ubiquitin-protein ligase NEDD4-2, limiting ENaC cell surface expression and activity. Ubiquitylation can be reversed by the action of deubiquitylating enzymes (DUBs). One such DUB, USP2-45, was identified previously as an aldosterone-induced protein in the kidney, and is also a circadian output gene. In heterologous expression systems USP2-45 binds to ENaC, deubiquitylates it and enhances channel density and activity at the cell surface. Because the role of USP2-45 in renal Na+ transport had not been studied in vivo, we investigated here the effect of Usp2 gene inactivation in this process. We demonstrate first that the USP2-45 protein has a rhythmic expression with a peak at ZT12. Usp2-KO  mice did not show any differences to wild-type littermates with respect to the diurnal control of Na+ or K+ urinary excretion and plasma levels neither on standard diet, nor after acute and chronic changes to low and high Na+ diets, respectively. Moreover, they had similar aldosterone levels either at low or high Na+ diet. Blood pressure measurements using telemetry did not reveal variations as compared to control mice. Usp2-KO did neither display alternations in ENaC or Na+,Cl--cotransporter (NCC) expression, nor were there any changes in regulatory protein levels, as evidenced by immunoblotting and transcriptome analysis. We conclude that USP2-45 is not crucial for the regulation of Na+ balance or maintenance of blood pressure in vivo.

overall_design: We compared gene expression in kidneys from Usp2 Knock-Out versus Wild-Type. Six pairs of male littermates Usp2-KO and WT were combined in two pools per condition (3 animals per pool) keeping the littermate pairing between pools.

first: Sylvain

last: Pradervand

first: Olivier

last: Staub


title: Expression data from endometrial carcinoma cells

status: Public on Jan 23 2013

city: seoul

first: hyunhee

last: cho

address: seochogu banpodong

country: South Korea

institute: catholic university medical colleage

summary:
some genes associated with cell growth, cell differentiation, meiosis, migration, and apoptosis are regulated in ECC-1 after DEHP exposure.
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.

overall_design: ECC-1 (human endometrial cancer) cell lines were subjected to DEHP for 48 h with 50 μM DEHP and total RNA was extracted. Quantified spectro-photometrically, and RNA quality was verified via agarose-gel electrophoresis. Gene expression changes were analyzed using oligonucleotide microarray hybridization by comparing the treated and control groups (two-fold change, P<0.05).


title: Gene expression in mouse pre-B cells transduced with Ikaros.

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

institute: MRC London Institute of Medical Sciences

summary: Ikaros family DNA binding proteins are critical regulators of B cell development. To identify Ikaros-regulated genes in pre-B cells we performed gene expression studies at enhanced temporal resolution.

overall_design: We used retroviral gene transfer to express Ikaros proteins in the pre-B cell line B3. Total RNA from 2 biological replicates of B3 cells transduced with wild type Ikaros (HA-Ikaros-IRES-GFP) and DNA binding-deficient Ikaros mutant 159A (HA-159A Ikaros-IRES-GFP) was isolated 48h after infection. To increase the temporal resolution of Ikaros-regulated gene expression we transduced B3 cells with inducible Ikaros (HA-Ikaros-ERt2-IRES-GFP) and isolated  total RNA from 3 biological replicates after 2 h and 6 h of exposure to 4-hydroxytamoxifen. Vector transduced B3 cells (ERt2-IRES-GFP)  treated with 4-hydroxytamoxifen were used as controls.

first: Isabel

last: Vidal

first: Tom

last: Carroll

first: Matthias

last: Merkenschlager


title: Gene expression in mouse primary pre-B cells transduced with Ikaros

summary: Ikaros family DNA binding proteins are critical regulators of B cell development. To identify Ikaros-regulated genes in primary pre-B cells we performed gene expression microarrays.

overall_design: We used retroviral gene transfer to express Ikaros proteins. Total RNA from 3 biological replicates of primary pre-B cells transduced with wild type Ikaros (HA-Ikaros-IRES-GFP) and control vector (IRES-GFP) was isolated 48h after infection.


title: JAG1 is an Invasion and Metastasis promoting genes of Lung cancer

status: Public on Jan 12 2013

city: Taipei

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

summary: Background: JAG-1 is a ligand of Notch signaling and can regulate cell differentiation and proliferation in cancers. Recent studies indicated that JAG1 is a gene associated with cancer progression. Therefore, we investigated the role of JAG1 in lung cancer progression. Methods: The expression of JAG1 was manipulated by overexpression or RNA silencing in several human lung cell lines. The effect of JAG1 on tumorigenesis and invasion was assessed by the cell anchorage-independent growth, cell proliferation, cell migration and invasion assays in vitro as well as metastasis in vivo. The potential downstream genes of JAG1 were identified by oligonucleotide microarrays and quantitative reverse transcription¡Vpolymerase chain reaction (RT-PCR). We further measured JAG1 expression in lung cancer specimens by RT-PCR. Correlation between JAG1 expression and overall survival of lung cancer patients was determined by using the log-rank test and multivariable Cox proportional hazards regression analysis. All statistical tests were two-sided. Results: JAG1 enhanced anchorage-independent growth, cell migration, invasion in the lower invasive cells, CL1-0. JAG1 also increased the capability of migration and invasion in the other two lung cancer cell lines (A549 and NCI-H226). The silencing of JAG1 inhibited migration and invasion activities of the higher invasive cells, CL1-5, by siRNA technology. The invasion-promoting activity of JAG1 was also demonstrated in vivo by using a mouse metastasis model. By microarray analysis, we found that the expression of heat shock 70kDa protein 2 (HSPA2) was activated by JAG1 overexpression and eliminated by JAG1 silencing. Moreover, lung cancer patients with high JAG1 expressing tumors had shorter overall survival than those with low-expressing tumors. Conclusion: JAG1 might be an oncogene which promotes colonogenesis and metastasis, and high JAG1 expression is associated with shorten survival in lung cancer.

overall_design: In this investigation, we used a lung cancer invasion cell model to identify the genes involved in cancer progression. JAG1 is a potential oncogene whose expression is correlated to the survival of patients with breast, prostate and liver cancers. However, the role of JAG1 in lung caner progression has not been reported, particularly in metastasis. Here, JAG1 was ectopically expressed in lower invasive lung cancer cell line its impact on colonogenesis, migration and invasiveness was assessed. The underlying mechanism was explored by JAG1-expressed transfectants and microarrays and the clinical relevance was evaluated by quantitative RT-PCR.

first: Chien-Hung

last: Yeh


title: Expression data from laser captured gastric neck cells and zymogenic cell from wild type and MIST1 knockout mice

city: Houston.

first: Jason

last: Mills

state: T

address: One Baylor Plaza

department: Gastroenterology, Medicine

institute: Baylor College of Medicine

summary: MIST1 is a bHLH transcription factor that is necessary for the maturation of gastric zymogenic cells as they differentiate from their precursor mucous neck cells. In this experiment, mucous neck cells and zymogenic cells of normal, adult C57BL/6 and MIST1 knockout mice were laser-capture microdissected in order to determine MIST1-dependent, zymogenic cell specific gene expression.

overall_design: Stomachs were excised immediately following sacrifice, quickly flushed with room-temperature PBS, inflated by duodenal injection of OCT compound, frozen in Cytocool II, and cut into serial 7-μm-thick cryosections, which were mounted on Superfrost slides, fixed in 70% EtOH, rehydrated in nuclease-free water, and then incubated in Alexa Fluor 488-conjugated Griffonia simplicifolia GS-II (diluted 1:500 in nuclease-free water) for 15 min. Sections were washed in nuclease-free water and dehydrated in graded ethanol followed by xylene. ZCs were identified as corpus cells that were basal to GS-II labeling and which did not show the dark silhouettes and characteristic shape of parietal cells following xylene dehydration. Four wild-type mice and 5 Mist1−/− mice were used for dissection (PixCell II LCM apparatus [7.5-μm spot diameter] and CapSure HS LCM caps) to generate two caps per mouse. RNA was purified by PicoPure kit, and RNA integrity was confirmed by an Agilent 2100 Bioanalyzer. All RNA from each cap was treated with DNase I and then reverse transcribed using the SuperScript III (Invitrogen) standard protocol (most cDNA syntheses started with 10 ng of total RNA). Biotinylated cRNA probes were hybridized to the GeneChips. Gene chip arrays used in these experiments were Affymetrix Mouse Gene 1.0ST arrays. Chip quality control and GeneChip to GeneChip comparisons to generate expression profiles were performed using dChip.

first: Benjamin

last: Capoccia

first: Ramon

middle: U

last: Jin


title: Genome-wide DNA methylation profiling of Progeria and Werner syndrome patients

status: Public on Jan 14 2013

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

institute: IDIBELL

summary: DNA methylation gradiently changes with age and is likely to be involved in aging-related processes resulting in phenotype changes and increased susceptibility to certain diseases. The Hutchinson-Gilford Progeria Syndrome (HGP) and Werner Syndrome are two premature aging diseases showing features of common aging. Mutations in LMNA and WRN genes were associated to disease onset; however for a subset of patients the underlying causative mechanisms remain elusive. We aimed to evaluate the role of epigenetic alteration on premature aging diseases by performing genome-wide DNA methylation profiling of HGP and WS patients.

overall_design: DNA was quantified by Quant-iT PicoGreen dsDNA Reagent (Invitrogen) and the integrity was analyzed in a 1.3% agarose gel. Bisulfite conversion of 600 ng of each sample was perform according to the manufacturer's recommendation for Illumina Infinium Assay. Effective bisulphite conversion was checked for three controls that were converted simultaneously with the samples. 4 ul of bisulfite converted DNA were used to hybridize on Infinium HumanMethylation 450 BeadChip, following Illumina Infinium HD Methylation protocol. Chip analysis was performed using Illumina HiScan SQ fluorescent scanner. The intensities of the images are extracted using GenomeStudio (2010.3) Methylation module (1.8.5) software. Methylation score of each CpG is represented as beta value. Naive B-cells and peripheral blood mononuclear cells were analyzed to correct for the epigenetic effects of the Epstein-Barr virus immortalization (lymphoblastoid cell lines) and cell composition of the samples, respectively.

first: Holger

last: Heyn


title: Gene expression data from 62 colorectal cancers

city: Macclesfield

first: Garry

last: Beran

address: Mereside, Alderley Park

department: Oncology

institute: AstraZeneca

summary: We stratified colorectal tumor samples using a new unsupervised, iterative method based on non-negative matrix factorization (NMF). The resulting five subtypes exhibited activation of specific signaling pathways, and significant differences in microsatellite status and tumor location. We could also align three CRC cell lines panels to these subtypes.

overall_design: mRNA from 62 colorectal tumor samples was hybridized to Affymetrix HGU133 Plus 2.0 expression arrays. Log2 gene expression values were calculated using RMA.

first: Andreas

last: Schlicker

first: Christine

last: Chresta

first: Gael

last: McWalter

first: Alison

last: Pritchard

first: Susie

last: Weston

first: Sarah

last: Runswick

last: Davenport

first: Kerry

last: Jackson

first: Denis

middle: A

last: Castro

first: George

last: Orphanides

first: Tim

last: French

first: Lodewyk

last: Wessels


title: Development of Transcriptomic Biomarker Signature in Human Saliva to Detect Lung Cancer

status: Public on Jan 11 2013

city: Los Angeles

first: Hua

last: Xiao

state: CA

address: 10833 Le Conte Ave

institute: UCLA

summary:
Affymetrix HG U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA) was used to profile transcriptomes and discover altered gene expression in saliva supernatant. Salivary transcriptomic biomarker discovery was performed on 10 lung cancer patients and 10 matched controls.
Seven messenger RNA biomarkers were discovered and pre-validated

overall_design: This study consisted of two phases, including a discovery phase, followed by a pre-validation phase. 10 lung cancer samples and 10 matched control samples were chosen for the biomarker discovery phase. The transscriptomic approach profiled the saliva supernatant samples from 10 lung cancer patients and 10 healthy control subjects using the Affymetrix HG U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA). Biomarkers identified from the microarray study were first verified using the discovery sample set (10 lung cancer and 10 healthy control).

first: Lei

last: Zhang


title: Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor

status: Public on Jan 08 2013

city: Sao PAulo

first: Fernanda

middle: Maria

last: Franzin

state: Sao Paulo

address: 1210 Joaquim Tavora st

department: Laboratory of Genetics

country: Brazil

institute: Butantan Institute

summary: Atypical EPEC (aEPEC) strains are part of group of pathogens capable of forming the Attaching and Effacing (A/E) lesion. This lesion is characterized by intimate adherence of bacteria to enterocytes, and microvilli destruction. The genes responsible to cause that lesion are located in a pathogenicity island called Locus of Enterocyte Effacement (LEE). Transcription of LEE genes is subjected to various levels of regulation, including quorum sensing through autoinducer 3 (AI-3) system. AI-3 is an aromatic compound with similar characteristics to the epinephrine and norepinephrine hormones. This similarity allows bacteria to use these hormones and AI-3 to perform cell – to – cell signaling processes and bacteria - host communication processes in order to modulate its virulence. AI-3, epinephrine and norepinephrine are detected by a sensor kinase named quorum sensing E.coli regulator (QseC). In order to investigate the role of QseC and epinephrine in atypical EPEC O55:H7 virulence, we constructed a QseC mutant of this strain and performed transcription and phenotypic analyses in the presence or absence of epinephrine. We have reported here, for the first time, the quorum sensing QseC regulation of virulence genes in atypical EPEC. Our results shown that QseC is a global regulator of gene expression in aEPEC and positively regulates flagellar genes, LEE and non-LEE encoded factors. We also have shown that the presence of epinephrine could be sensed by other receptor that acts as negative regulator of LEE4 and LEE5 genes.

overall_design: Comparison of transcriptional regulation of enteropathogenic E. coli serotype O55:H7 wild type and the qseC mutant in the absence or presence of epinephrine signal to identify the regulated targets

first: Alline

last: Pacheco

first: Melissa

last: Kendall

first: Vanessa

last: Sperandio

first: Marcelo

last: Sircili


title: Expression profiles of cell populations purified from human CRC (3 ways)

first: Alexandre

last: CALON

summary:
The survival of isolated metastatic cells and expansion into macroscopic tumour has been recognized as a limiting step for metastasis formation in several cancer types yet the determinants of this process remain largely uncharacterized. In colorectal cancer (CRC), we identify a transcriptional programme in tumour-associated stromal cells, which is intimately linked to a high risk of developing recurrent disease after therapy. A large proportion of CRCs display mutational inactivation of the TGF-beta pathway but paradoxically they are characterized by high TGF-beta production. In these tumours, TGF-beta instructs a transcriptional programme in stromal cells, which confers a high risk of developing metastatic disease.
We purified by FACS [CD45(+),Epcam(-)], [CD45(-) Epcam(+)] and [CD45(-) Epcam(-)]  cell populations from fresh CRC samples and assessed their gene expression profiles

overall_design: Freshly obtained tumors from CRC patients (n=8) treated at Hospital del Mar (Barcelona, Spain) were minced and incubated with 0.1% Hyaluronidase and 0.1% Collagenase 1A. Pieces were then homogenized. Enzymatic reaction was stopped by adding 10% FBS and single cells were collected by sequential filtering. Cells were resuspended in Ammonium Chloride (0.15M) to lyse erythrocytes. Cells were stained with anti-hEpcam/TROP1-APC and anti-CD45-PE conjugated antibody. Dead cells were labeled with Propidium Iodide. Fluorescence Activated Cell Sorting (FACS) was used to separate cells.

last: Calon

first: Elisa

last: Espinet

first: Eduard

last: Batlle


title: Gene expression changes induced by overexpression of EVI1 in Lin- hematopoietic cells [EVI1_ST]

city: Hannover

first: Adrian

last: Schwarzer

address: Carl-Neuberg-Str. 1

department: Experimental Hematology

country: Germany

institute: Hannover Medical School

summary: The transcription factor Evi1 is essential for the formation and maintenance of hematopoietic stem cells, and induces clonal dominance with malignant progression upon constitutive activation by chromosomal rearrangements or transgene integration events. To understand the immediate and adaptive response of primary murine hematopoietic cells to the transcriptional upregulation of Evi1, we developed an inducible lentiviral vector system with a robust expression switch. We found that Evi1 delays differentiation and promotes survival in myeloid culture conditions, orchestrating a battery of genes involved in stemness (Aldh1a1, Ly6a [Sca1], Abca1, Epcam, among others). Importantly, Evi1 suppresses Cyclins and Cyclin-dependent kinases (Cdk), while it upregulates Cdk inhibitors, inducing quiescence in various proliferation-inducing cytokine conditions and operating in a strictly dose-dependent manner. Hematopoietic cells with persisting Evi1-induction tend to adopt a relatively low expression level. We thus classify Evi1 as a dormancy-inducing oncogene, likely requiring epigenetic and genetic compensation for cell expansion and malignant progression.

overall_design: Lin- Rosa26rtTA cells were isolated, transduced either with pRRL.PPT.Tet.Evi1.IRES.EGFP.pre or with the pRRL.PPT.Tet.EGFP.pre control vector in S3F11 cytokines, induced the next day with DOX [1 μg/ml] and 20 hours later sorted for EGFP expressing cells, from which total RNA was extraced and subjected to Microarray Analysis.

first: Olga

last: Kustikova


title: Induced Pluripotent Mesenchymal Stromal Cell Clones Retain Donor-Derived Differences in DNA Methylation Profiles

status: Public on Jan 09 2013

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

type: Methylation profiling by genome tiling array

summary: Reprogramming of somatic cells into induced pluripotent stem cells (iPSC) is an epigenetic phenomenon. It has been suggested that iPSC retain some tissue-specific memory whereas little is known about inter-individual epigenetic variation of iPSC clones. In this study we have reprogrammed mesenchymal stromal cells (MSC) from human bone marrow by retrovirus-mediated overexpression of OCT-3/4, SOX2, c-MYC, and KLF4. Global DNA-methylation profiles of the initial MSC, MSC-derived iPSC (iP-MSC) and embryonic stem cells (ESC) were then compared using a high density DNA-methylation array covering more than 450,000 CpG sites. Overall, DNA-methylation patterns of iP-MSC and ESC were similar whereas some CpG sites revealed highly significant differences, which were not related to parental MSC. Furthermore, hypermethylation in iP-MSC versus ESC was particularly enriched in developmental genes as well as shore regions next to CpG islands indicating that these differences are not due to tissue-specific memory or random de novo methylation. Subsequently, we searched for CpG sites with donor-specific variation in MSC preparations. These “epigenetic fingerprints” were highly enriched in non-promoter regions and outside of CpG islands – and they were maintained upon reprogramming into iP-MSC. In conclusion, DNA methylation profiles of iP-MSC clones from the same donor were closely related despite heterogeneity of MSC. On the other hand, iP-MSC maintain donor-derived epigenetic differences. In the absence of isogenic controls for disease modeling applications, it would therefore be more appropriate to compare iPSC from different donors rather than a high number of different clones from the same patient.

overall_design: 16 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Kaifeng

last: Shao

first: Carmen

last: Koch

first: Manoj

middle: K

last: Gupta

first: Qiong

last: Lin

first: Michael

last: Lenz

first: Stephanie

last: Laufs

first: Bernd

last: Denecke

first: Manfred

last: Schmidt

first: Matthias

last: Linke

first: Hans

last: Hennies

first: Jürgen

last: Hescheler

first: Ulrich

last: Zechner

first: Tomo

last: Saric


title: Molecular markers associated with outcome and metastasis in human pancreatic cancer

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: Pancreatic ductal adenocarcinoma (PDAC) is a heterogeneous cancer in which differences in survival rates might be related to a variety in gene expression profiles. Although the molecular biology of PDAC begins to be revealed, genes or pathways that specifically drive tumour progression or metastasis are not well understood. Therefore, we performed microarray analyses on whole-tumour samples of 2 human PDAC subpopulations with similar clinicopathological features, but extremely distinct survival rates after potentially curative surgery, i.e., good outcome (OS and DFS > 50 months) versus bad outcome (OS < 19 months and DFS < 7 months). Additionally, liver- and peritoneal metastases were analysed and compared to primary cancer tissue. The integrin and ephrin receptor families were upregulated in all PDAC samples, irrespective of outcome, supporting an important role of the interaction between pancreatic cancer cells and the surrounding desmoplastic reaction in tumorigenesis and cancer progression. Moreover, some components, such as ITGB1 and EPHA2, were upregulated in PDAC samples with a poor outcome, Additionally, overexpression of the non-canonical Wnt/β-catenin pathway and EMT genes in PDAC samples with bad versus good outcome suggests their contribution to the invasiveness of pancreatic cancer, with β-catenin being also highly upregulated in metastatic tissue. Thus, we conclude that components of the integrin and ephrin pathways and EMT-related genes might serve as molecular markers in pancreatic cancer as their expression seems to be related with prognosis.

overall_design: Microarray analysis was performed on 'Good' and 'Bad' patient samples (samples with similar pathological characteristics were chosen based on the definition of the 2 diverse survival outcome groups and the required RIN values above 7.1), on surrounding non-tumoural pancreatic control samples, liver metastasis (LM) and peritoneal metastasis (PM). Comparisons between good vs. control, bad vs. control, good vs. bad, and primary pancreatic cancer versus metastasis were performed.

first: Anke

last: Van den broeck

first: Hugo

last: Vankelecom

first: Olivier

last: Govaere

first: Baki

last: Topal


title: Brain expression data from fetal mouse brains prenatally exposed to ethanol

first: Katarzyna

last: Janus

state: ON

address: 1151 Richmond Street

institute: University of Western Ontario

summary:
Moderate alcohol exposure during pregnancy can result in brain gene expression changes in resulting offspring.  We have developed a mouse model of FASD that involves moderate ethanol exposure in mid-gestation (trimester 2 equivalent) achieved by injections of ethanol.  We have previously shown that this model results in phenotypes relevant to FASD.  Since ethanol is known to directly affect the expression of genes in the developing brain leading to abnormal cell death, changes to cell proliferation, migration, and differentiation, and potential changes to epigenetic patterning, we hypothesize that there will be gene expression changes immediately following acute ethanol exposure in the fetal brain.
We used a microarray experiment and focused on the genes identified to evaluate the genome-wide alterations to the fetal brain transcriptome caused by prenatal ethanol exposure.

overall_design: To generate samples, female C57BL/6J mice were given ethanol injections (2.5g/kg of ethanol in saline) twice on gestational days 14 and 16 to produce acute ethanol exposure effects.  Control females were injected with the same volume of saline.  Dams were sacrified on gestational day 16, following ethanol exposure, and whole brains from fetuses were then extracted.  RNA was isolated from brain tissue and samples from three mice were pooled to reduce litter effects and the pooled samples were hybridized on Affymetrix arrays (2 control and 2 ethanol chips, total n=12 mice).

first: Shiva

last: Singh


title: Molecular Biomarker Signature for Bladder Cancer Detection

city: Orlando

first: Virginia

last: Urquidi

state: FL

address: 6900 Lake Nona Blvd

department: CRI

institute: MD Anderson Cancer Center Orlando

summary: In this study we applied differential gene expression analysis to exfoliated human urothelia obtained from patients of known bladder disease status. Selected targets from the microarray data were validated in an independent set of samples using a quantitative PCR approach.

overall_design: Total RNA was extracted from 52 samples of human urothelial cancer cells (C) and from 40 samples of human non-cancer (NC) urothelial cells. Fragmented, biotinylated cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 microarrays.

first: Steve

last: Goodison

first: Yunpeng

last: Cai

first: Yijun

last: Sun

first: Charles

last: Rosser


title: Expression profiling across mouse epithelial tissues

city: Irvine

first: Denise

last: Stephens

address: 250 Sprague Hall

department: Biological Chemistry

institute: University of California, Irvine

summary: To characterize genes, pathways, and transcriptional regulators enriched in the mouse cornea, we compared the expression profiles of whole mouse cornea, bladder, esophagus, lung, proximal small intestine, skin, stomach, and trachea.

overall_design: Total RNA was purified from esophagus, lung, proximal small intestine, skin, stomach, and trachea. Data from previous studies in the lab (cornea, GSE43155; bladder, GSE15770; and E18.5 skin, GSE15772) were utilized in the comparison.

middle: N

first: William

last: Gordon

first: Michael

middle: L

last: Salmans

first: Bogi

last: Andersen


title: Gene expression analysis of Ncor1 muscle-specific knockout and PGC-1alpha muscle-specific transgenic skeletal muscle

city: Basel

first: Joaquín

last: Pérez-Schindler

address: Klingelbergstrasse 50 / 70

department: Biozentrum

institute: University of Basel

summary: In the present study we have studied the mechanistic and functional aspects of NCoR1 function in mouse skeletal muscle. NCoR1 muscle-specific knockout mice exhibited an increased oxidative metabolism. Global gene expression analysis revealed a high overlap between the effects of NCoR1 deletion and peroxisome proliferator-activated receptor (PPAR) gamma coactivator 1alpha (PGC-1alpha) overexpression on oxidative metabolism in skeletal muscle. The repressive effect of NCoR1 on oxidative phosphorylation gene expression specifically antagonizes PGC-1alpha-mediated coactivation of ERRalpha. We therefore delineated the molecular mechanism by which a transcriptional network controlled by corepressor and coactivator proteins determines the metabolic properties of skeletal muscle, thus representing a potential therapeutic target for metabolic diseases.

overall_design: Gene expression of a total of 20 gastrocnemius samples from control (CON, n = 5), NCoR1 muscle-specific knockout (NCoR1 MKO, n = 5), wild type (WT, n = 5) and PGC-1alpha muscle-specific transgenic (PGC-1alpha mTg, n = 5) adult male mice was analyzed using GeneChip® Gene 1.0 ST Array System (Affymetrix). NCoR1 MKO and PGC-1alpha mTg samples were compared to CON and WT samples, respectively.

first: Christoph

last: Handschin


title: Distinct Transcriptional Signatures of Bone Marrow-Derived C57BL/6 and DBA/2 Dendritic Leucocytes Hosting Live Leishmania amazonensis Amastigotes

status: Public on Jan 07 2013

city: Paris

first: Thierry

last: Lang

address: 25 rue du Dr Roux

department: parasitology and Mycology

institute: Institut Pasteur

summary: To determine the modulation of gene expression of  C57BL/6 and DBA/2 BMDLs in the presence of living intracellular Leishmania amazonensis amastigotes

overall_design: A genome-wide transcriptional analysis was performed by comparing the gene expression profiles of control DLs and live amastigote-hosting DLs from both mouse strains. Dendritic Leucocytes were generated in vitro from bone marrow progenitors (C57Bl/6 and DBA/2 mice). Leishmania amazonensis amastigotes were purified from mouse cutaneous lesions and were added to DL cultures. After 24h, and following a sorting procedure, only BMDls housing living amastigotes were selected for total RNA extraction. Three Biological replicates per condition were run.

first: Emilie

last: de la Llave

first: Hervé

last: Lecoeur

first: Guillaume

last: Soubigou

first: Jean-Yves

last: Coppée

first: Geneviève

last: Milon

first: Eric

last: Prina


title: Ogt chromatin recruitment is mediated by TET proteins in mouse ES cells [expression array]

status: Public on Jan 06 2013

city: Milan

first: Sri Ganesh

last: Jammula

address: Via Adamello 16

country: Italy

institute: IFOM-IEO

summary: O-linked N-acetylglucosamine (O-GlcNAc ) transferase (OGT) activity is essential for embryonic stem (ES) cell viability and mouse development. OGT is present in both cytoplasm and nucleus of different cell types and mediates serine or threonine glycosylation. The Ogt gene locus resides on the X-chromosome and its activity is required for the viability of male ES cells. Using Ogt conditional knock out (KO) ES cells it was shown the failure of establishing stable KO ES clones further suggesting that Ogt activity is required for ES cell self-renewal and pluripotency. For understanding these changes, we performed global gene expression upon silencing of Ogt mediated by esiRNA in mouse Embryonic Stem Cells.

overall_design: Total RNA was extracted from E14 ES cells (derived from Ola129 mice) transiently transfected with Ogt specific and control esiRNA oligos 48 hrs. post-transfection.

first: Pietro

last: Vella

first: Andrea

last: Scelfo

first: Sri

middle: G

first: Diego

last: Pasini


title: Expression data from healthy and malignant (chronic lymphocytic leukemia, CLL) human B-lymphocytes after B-cell receptor stimulation

status: Public on Jan 04 2013

city: Strasbourg

first: Laurent

last: Vallat

address: 1, Place de l'Hopital

department: Immunology

institute: Strasbourg University Hospital

summary:
Three different cell populations (6 healthy B-lymphocytes, 6 leukemic CLL B-lymphocyte of indolent form and 5 leukemic CLL B-lymphocyte of aggressive form) were stimulated in vitro with an anti-IgM antibody, activating the B-cell receptor (BCR). We analyzed the gene expression at 4 time points (60, 90, 210 and 390 minutes). Each gene expression measurement is performed both in stimulated cells and in control unstimulated cells.
For one aggressive CLL case, we silenced expression of DUSP1 by transfecting DUSP1-specific RNAi and, as a control, transfected cells with a non-targeting RNAi. We then stimulated the BCR of these cells and analyzed the gene expression at the same time points in stimulated cells and in control unstimulated cells.

overall_design: B-cells were negatively selected from healthy donors and previously untreated CLL patients. BCR stimulated and unstimulated control B-cells were treated at four time points after stimulation for total RNA extraction and hybridization on Affymetrix microarrays.

first: John

last: Gribben


title: Gene expression profiling of enforced HOXA1 expression in melanoma cell line

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

summary: We recently reported an oncogenomics-guided screening approach designed to identify genetic drivers of early stage melanoma metastasis, and in this study we functionally validate the top-scoring candidate, homeobox transcription factor A1 (HOXA1), by demonstrating HOXA1‘s robust effects on melanoma cell invasion, metastasis and tumorigenicity.  Transcriptome and pathway profiling analyses of cells expressing HOXA1 reveal up-regulation of factors involved in diverse cytokine pathways that include the TGFβ signaling axis, which we further demonstrate to be required for HOXA1-mediated cell invasion.  Transcriptome profiling also informed HOXA1’s ability to potently down-regulate expression of microphthalmia-associated transcription factor (MITF) and other genes required for melanocyte differentiation, suggesting a mechanism by which HOXA1 expression de-differentiates cells into a pro-invasive precursor cell state concomitant with TGFβ activation.  Our analysis of publicly available datasets indicate that the HOXA1-induced gene signature successfully categorizes melanoma specimens based on their metastatic potential and, importantly, is capable of stratifying melanoma patient risk for metastasis based on expression in primary tumors.

overall_design: The HOXA1-induced transcription analysis was conducted using RNAs extracted from WM115 cells transduced with either control or HOXA1, followed by hybridization of labeled cDNA onto Affymetrix GeneChips (Human Genome U133Plus2.0).

first: Kenneth

last: Scott

first: Joanna

last: Wardwell-Ozgo


title: Microarray analysis of purified germ cells in mouse

city: Cincinnati

first: Satoshi

last: Namekawa

state: Ohio

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary: Microarray analysis of purified pachytene spermatocytes and round spermatids. Each stage was examined in wild type and RNF8 knockout mice in two biological replicates.

overall_design:
We performed microarray analysis using Affymetrix Gene 1.0 ST Arrays with purified pachytene spermatocytes and round spermatids.
Pachytene spermatocytes and round spermatids were enriched from 3 to 4 males from the WT or Rnf8-KO via BSA gravity sedimentation according to the previous publication [PMID 8231890] and >95% (PS, RS) enrichments were verified after DAPI staining under a fluorescent microscope. For microarray analysis, total RNAs from purified pachytene spermatocytes or round spermatids were examined.

first: Ho-Su

last: Sin


title: Gene expression profiles of gliomas with Affymetrix Human Genome U133 Plus 2.0 Array

status: Public on Jan 05 2013

city: Salamanca

first: MariaDolores

last: Tabernero

address: Paseo San Vicente 58-182

institute: Hospital Universitario de Salamanca y Centro del Cáncer

summary: Correlate the gene expression profiles with the most relevant patterns of chromosome abnormalities (cytogenetic subgroups of gliomas) and the histopathology.

overall_design: We analyzed the gene expression profiles (U133 Plus 2.0 Array) of 40 gliomas (35 astrocytic tumors, 3 oligodendrogliomas, and 2 mixed tumors) and their association with tumor cytogenetics and histopathology.

first: Maria

first: Alberto

last: Orfao


title: Skeletal muscle gene expression data from Down syndrome mice

city: Syracuse

first: Frank

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

summary: Persons with Down syndrome (DS) exhibit low muscle strength that significantly impairs their physical functioning. The Ts65Dn mouse model of DS also exhibits muscle weakness in vivo and may serve as a useful model to examine potential factors responsible for DS-associated muscle dysfunction. Therefore, the purpose of this experiment was to directly assess skeletal muscle function in the Ts65Dn mouse and to reveal potential mechanisms of DS-associated muscle weakness. Soleus muscles were harvested from anesthetized male Ts65Dn and wild-type (WT) colony controls.  In vitro muscle contractile experiments revealed normal force generation of unfatigued Ts65Dn soleus, but a 12% reduction in force was observed in Ts65Dn muscle during recovery following fatiguing contractions compared to WT muscle (p<0.05). Oxidative stress may contribute to DS-related pathologies, including muscle weakness, which may be the result of overexpression of chromosome 21 genes (e.g., copper-zinc superoxide dismutase (SOD1)). SOD1 expression was 25% higher (p<0.05) in Ts65Dn soleus compared to WT muscle but levels of other antioxidant proteins were unchanged. Lipid peroxidation (4-hydroxynoneal) was unaltered in Ts65Dn muscle although protein carbonyls were 20% greater compared to muscle of WT animals (p<0.05). Cytochrome c oxidase expression was reduced 22% in Ts65Dn muscle, suggesting a limitation in mitochondrial function may contribute to post-fatigue muscle weakness. Microarray analysis of Ts65Dn soleus revealed alteration of numerous cellular pathways including: proteolysis, glucose and fat metabolism, neuromuscular transmission, and ATP biosynthesis. In summary, the Ts65Dn mouse displays evidence of muscle dysfunction, and the potential role of mitochondria and oxidative stress warrants further investigation.

overall_design: We used microarrays to gain insight into potential mechanisms of DS-associated skeletal muscle weakness. Soleus muscles were obtained from four male Ts65Dn (DS) mice and four male colony control mice. Animals were apparently healthy and approximately five months old. The muscles were harvested in the basal state under anesthesia induced by sodium pentobarbital at approximately the same time of the day.

first: Keith

last: DeRuisseau

first: Patrick

last: Cowley


title: Gene Expression Analysis of native and disease-corrected motor neurons from human spinal muscular atrophy induced pluripotent stem cells free of vector and transgenic sequences

first: Stefania

last: Corti

address: via F. Sforza 35

department: Neurological Sciences

institute: University of Milan

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

overall_design: Refer to individual Series


title: Pigment Epithelium Derived Factor (PEDF) secreted from iPSC derived-RPE facilitates apoptotic causes cell death, not the differentiation, of iPSCs

status: Public on Jan 03 2013

city: Kobe

first: Shin

last: Kawamata

state: Hyogo

department: The Basic Reserch Group for Regenerative Medicine

institute: Foundation for Biomedical and Innovation

summary: We show that Retinal pigment epithelium (RPE) secreted-factor, pigment epithelium derived factor (PEDF) secreted/derived from primary or iPSC-derived retinal pigment epithelium (RPE)RPE, dramatically inhibitsed the cell growth of iPSCs. PEDF was detected abundantly in culture supernatant media of primary and iPSC-derived RPE.  We examined the gene expression in primary RPE and iPS-derived RPE.

overall_design: Two samples: RPE derived from 253G1 iPSC, Primary RPE.

first: Hoshiyo

last: Kanemura

first: Masahiko

last: Go

first: Naoki

last: Nishishita


title: Prediction of response to bevacizumab

city: Bunkyo-ku

first: Toshiaki

last: Watanabe

state: Tokyo

department: Department of Surgical Oncology

institute: University of Tokyo

summary: The patients who underwent surgery for primary lesions were examined. All patients had metastatic or recurrent CRC and received bevacizumab therapy as first line or second line treatment. Responders and nonresponders were determined based on RECIST and confirmed by CT or MRI. Gene-expression profiles of primary CRC were determined using Human Genome GeneChip arrays U133.

overall_design: Colorectal cancer patients who had undergone surgical resection of colorectal cancer were studied. To identify molecular signatures to predict response to bevacizumab, gene expression profiles were compared between Reponder and Non-responder.

first: Takashi

last: Kobunai

first: Eriko

last: Hashimoto


title: Prediction of response to FOLFOX

summary: The patients who underwent surgery for primary lesions were examined. All patients had metastatic or recurrent CRC and received modified FOLFOX6. Responders and nonresponders were determined based on the best observed response at the end of the first-line treatment, mFOLFOX6. Gene-expression profiles of primary CRC were determined using Human Genome GeneChip arrays U133.

overall_design: Colorectal cancer patients who had undergone surgical resection of colorectal cancer were studied. To identify molecular signatures to predict response to mFOLFOX6 regimen, gene expression profiles were compared between Reponder and Non-responder. Some patients are overlapped with Bevacizumab therapy.


title: A transcriptome profile of cornea over the lifetime of the mouse

status: Public on Jan 01 2013

first: Denise

last: Stephens


title: Global gene expression profiles of iPSC from SMA patient, unaffected father and iPS 19.9 compared to transcriptomic data obtained by corresponding fibroblasts

summary:
Spinal Muscular Atrophy (SMA) is an autosomal recessive motor neuron disease and is the second most common genetic disorder leading to death in childhood. Motoneurons derived from induced pluripotent stem cells (iPS cells) obtained by reprogramming SMA patient and his healthy father fibroblasts, and genetically corrected SMA-iPSC obtained converting SMN2 into SMN1 with target gene correction (TGC), were used to study gene expression and splicing events linked  to pathogenetic mechanisms.
Microarray technology was used to assess global gene expression profiles of iPSC from SMA patient, unaffected father and iPS 19.9 (Prof. J. Thomson's lab) compared to transcriptomic data obtained by corresponding fibroblasts.

overall_design: The microarray data derived from three different individuals: SMA patient, healthy father and control iPS cells (19.9). We analyzed iPSC from SMA patient (n=2), iPS- from healthy father (n=1) and iPS-19.9 from Prof. Thomson's lab  (n=3). The expression profile was compared to SMA patient's fibroblasts (n=2) and healthy father's fibroblasts  (n=1)

first: Dario

last: Ronchi

first: Giulietta

last: Riboldi


title: Expression profiling of wildtype mouse cornea in development, adult, and aging

summary: While the mouse cornea has been well characterized morphologically, the transcriptional changes have not been described in detail. To characterize the genes, pathways, and transcriptional regulators involved in mouse cornea development and aging, we isolated whole cornea from wildtype CB6 mice at several developmental timepoints and every 6 months in the adult. Corneal epithelium and stroma were isolated at one timepoint to provide insights into the genes that are unique to each tissue.

overall_design: Total RNA was purified from whole mouse cornea at 12 time points over the life of the mouse and from corneal epithelium and stroma at a single timepoint.

first: Michael

last: Salmans

first: Bogi

last: Andersen


title: Nuclear Receptor Corepressors are Required for the Histone Deacetylase Activity of HDAC3 In Vivo (Microarray)

first: Hee-Woong

last: Lim

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

summary: We report the hepatic gene expression changes in NCOR and SMRT DADm-mutated mice.

overall_design: 10-12 wk male mouse liver for RNA extraction and hybridization on Affymetrix microarrays. We sought to find differential gene changes between wt and NS-DADm mice.

first: Seo-Hee

last: You

first: Zheng

last: Sun

first: Molly

last: Broache

first: Kyoung-Jae

last: Won

first: Mitchell

last: Lazar


title: Neutrophil gene expression in response to Mycobacterium abscessus

status: Public on Jan 10 2013

city: Denver

first: Ken

last: Malcolm

address: 1400 Jackson St

institute: National Jewish Health

summary: The response of human neutrophils to the emerging pathogen Mycobacterium abscessus has not been described.  However, M. abscessus infections are frequently associated with neutrophil-rich abscesses.  To better understand the reponse of neutrophils to M. abscessus we performed gene expression analysis using Affymetrix HG-U133A Plus 2.0 microarrays.  Human neutrophils from healthy donors were stimulated with isogenic rough and smooth morphotypes of M. abscessus.  Staphylococcus aureus was used as a control.  Gene expression was compared to neutrophils left unstimulated.  Neutrophils from four individual donors were isolated on separate days and stimulated with freshly prepared bacteria.  Neutrophils (stimulated and control) were left for 2 hours before total RNA was isolated, and biotinylated cRNA was prepared by standard methods.  Analysis indicates that M. abscessus morphotypes induce a limited number of genes, when compared to S. aureus, which are enriched in genes for cytokines and chemokines, including neutrophil-specific chemokines.  These data suggest that neutrophils have a limited response to M. abscessus, which may contribute to neutrophil-rich abscess formation.!Series_overall_design = Human neutrophils from healthy donors were exposed to rough Mab (ATCC 19977T), smooth Mab (ATCC 19977T) and S. aureus (CF clinical strain) for two hours; control cells were exposed to saline.

first: Michelle

last: Nichols

first: Jerry

last: Nick


title: Gene expression profiling primary mouse mammary tumours from five different transplantable models

city: East Melbourne

first: Cameron

last: Johnstone

state: Vic

address: 2 St. Andrew's Place

department: Research Division

institute: Peter MacCallum Cancer Centre

summary:
To delineate gene expression levels in whole non-metastatic and metastatic transplantable primary mouse mammary tumour allografts
Abstract to be provided from publication

overall_design: Primary mouse mammary tumours were grown till 400-600mm3 in size.  Five different tumour models were analysed in triplicate.  Thus, 3 different tumours/mice were used per model for a total of 15 mice. Each sample was applied to a separate microarray. Total RNA was prepared from whole primary tumours using Trizol reagent. Each sample was applied to Affymetrix gene expression arrays Mouse Gene 1.0ST.

first: Allan

last: Burrows

first: Yvonne

last: Smith

first: Yuan

last: Cao

first: Jason

last: Li

first: Robin

last: Anderson