title: Expression data from parietal cortex of G114V genetic Creutzfeldt-Jakob disease patient

city: Beijing

first: chan

last: tian

address: Changbai Road, Changping district

institute: Chinese Center for Disease Control and Prevention, China CDC

summary: The familial or genetic Creutzfeldt-Jakob disease (fCJD or gCJD) is the inherent form of human prion diseases, which accounts for approximately 10-15% of human prion diseases that are caused by mutations of the prion protein gene (PRNP). In this study, the global expression patterns of the parietal cortex from a patient with G114V gCJD were comparatively analyzed with the normal controls by using a commercial human genome expression chip. Totally 8774 genes showed differential expression, among them 2769 genes were upregulated and 6005 ones were downregulated. The reliability of the results was confirmed by the real-time RT-PCR assays for several specific genes. The most differentially expressed genes involved in the functions of regulation of transcription, ion transport, transcription, cell adhesion, signal transduction. The gene associated with gliosis was upregulated and the genes marked for neurons were downregulated, while the transcription of PRNP gene maintained unchanged. 169 different pathways showed significantly changed in the brain of G114V gCJD. The most significantly regulated pathways included that of Alzheimer’s and Parkinson’s disease, oxidative phosphorylation, regulation of actin cytoskeleton, MAPK signaling pathway and proteasome, which were described in prion diseases previously. In addition, some rarely addressed pathways in prion diseases, such as axon guidance, gap junction and purine metabolism, were also significantly changed in G114V gCJD. The transcriptional situations of the most genes in the top ten changed pathways were down-regulated. The extensive reductions of gene expressions in G114V gCJD showed the comparable profiles with sporadic CJD. The data here raised the useful clues for understanding the pathogenesis of the disease and selecting the potential biomarkers for diagnostic and therapeutic tools.

overall_design: Brain tissues of parietal cortex from a definitely diagnosed G114V gCJD were enrolled into this study. The patient was a 47-year-old Han-Chinese woman at the onset. Neuropathological assays of ten different brain regions revealed typical sCJD-like abnormality and PrPSc deposits. Meanwhile, a commercial normal human parietal cortex total RNA (Clontech) pooled from four male/female aged 35-89 was utilized as control.

first: Chan

last: Tian

first: Xiaoping

last: Dong

first: Di

last: Liu


title: Expression data for Cediranib in Metastatic ASPS

status: Public on Jul 01 2013

city: Bethesda

first: Eric

middle: C

last: Polley

state: MD

address: 9609 Medical Center Drive, Rm 5W118

department: Biometric Research Branch

country: USA

institute: National Cancer Institute

summary: Gene expression from pre- and post- Cediranib treated patients with metastatic Alveolar Soft Part Sarcoma (ASPS)

overall_design: Paired tumor biopsies from 6 patients were collected. Samples were collected at baseline and 3 to 5 days following treatment. The patients are all enrolled in the replicate cohort of a National Cancer Institute (NCI)-sponsered investigational new drug application with institutional review board approval, and all participants provided written informed consent. ClinicalTrials.gov number, NCT00942877. The timing of the tumor biopsies was based on clinical observations of increased tumor pain associated with an inflammatory-like response in peripheral tumor lesions, usually within the second week of treatment.  Tumor biopsies were obtained in the first week of treatment before the development of clinical signs and symptoms to evaluate gene expression changes. The time points are labeled "pre" and "post" to denote their relationship to treatment.

first: Shivaani

last: Kummar

first: Agnes

last: Strassberger

first: Anne

last: Monks

first: Curtis

middle: D

last: Hose

first: S

middle: P

last: Ivy

first: Ismail

middle: B

last: Turkbey

first: Peter

last: Choyke

first: Seth

middle: M

last: Steinberg

first: Robert

middle: J

last: Kinders

first: Richard

last: Simon

first: James

middle: H

last: Doroshow

first: Lee

last: Helman


title: Diverse stresses dramatically alter genome-wide p53 binding and transactivation landscape in human cancer cells (Affymetrix)

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: The effects of diverse stresses on promoter selectivity and transcription regulation by the tumor suppressor p53 are poorly understood. We have taken a comprehensive approach to characterizing the human p53 network that includes p53 levels, binding, expression and chromatin changes under diverse stresses. Human osteosarcoma U2OS cells treated with anti-cancer drugs Doxorubicin or Nutlin-3 led to strikingly different p53 gene binding patterns based on ChIP-seq experiments. While two contiguous RRRCWWGYYY decamers is the consensus binding motif, p53 can bind a single decamer and function in vivo. Although the number of sites bound by p53 was 6-times greater for Nutlin-3 than Doxorubicin, expression changes induced by Nutlin-3 were much less dramatic compared to Doxorubicin. Unexpectedly, the solvent DMSO alone induced p53 binding to many sites common to Doxorubicin; however, this binding had no effect on target gene expression. Together, these data imply a two-stage mechanism for p53 transactivation where p53 binding only constitutes the first stage. Furthermore, both p53 binding and transactivation were associated with increased active histone modification H3K4me3. We discovered 149 putative new p53 target genes including several that are relevant to tumor suppression, revealing potential new targets for cancer therapy and expanding our understanding of the p53 regulatory network.

overall_design: Gene expression analysis (using Affymetrix Human Genome U133 Plus 2.0 GeneChip® arrays) of the p53 response in U2OS cells treated with either Doxorubicin or Nutlin-3, relative to their controls No Treatment and DMSO, respectively.

first: Daniel

last: Menendez

first: Thuy-Ai

middle: T

last: Nguyen

first: Johannes

last: Freudenberg

first: Viju

last: Mathew

first: Carl

middle: W

last: Anderson

first: Raja

last: Jothi

first: Michael

middle: A

last: Resnick


title: Orchestrated intron retention regulates normal granulocyte differentiation [Affymetrix arrays]

status: Public on Jun 27 2013

city: Camperdown

first: william

last: ritchie

state: NSW

address: Building 93

country: Australia

institute: centenary institute

summary: Using mRNA-seq, we determined intron retaining genes that were differentially regulated in FACS purified cells at three progressive stages of mouse granulopoiesis; CD34+Kit+Gr-1low promyelocytes, CD34-Kit-Gr-1mid myelocytes and CD34-Kit-Gr-1high granulocytes. We found that IR affects 86 genes, including those specific to granulocyte (Lyz2 and MMP8) and nuclear architecture (Lmnb1 and Lbr). IR was associated with the decrease in protein levels measured by mass spectrometry (P=0.0015, binomial test). Inhibition of NMD in granulocytes resulted in marked accumulation of 39/86 intron retaining mRNAs (P<0.05, RUV procedure with Holm-Bonferroni correction), indicating that IR triggers NMD to downregulate mRNA and protein expression.

overall_design: We used Affymetrix's Mouse Gene 1.0 ST array to determine accumulation of RNA-transcripts following inhibition of nonsense-mediated decay in primary mouse granulocytes using caffeine.

first: William

last: Ritchie

first: Justin

last: Wong


title: Runx1/Cbfb deficiency effect on MLL-AF9 cells

status: Public on Jun 30 2013

city: Cincinnati

first: Susumu

last: Goyama

state: Ohio

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

summary: To identify the target genes of Runx1/Cbfb in MLL fusion leukemia, we performed microarray analysis using control and Runx1/Cbfb-deleted MLL-AF9 cells.

overall_design: c-Kit(+) bone marrow cells derived from Runx1/Cbfb double floxed mice were transduced with MLL-AF9 and CreERT2 (coexpressing Puromycin).  After several rounds of replating with Puromycin, EtOH (control) or 4OHT was added to induce gene deletion. Two independent experiments with 2 independent clones were performed, and gene-expression was compared using the 4 sets of samples 24 hours after 4OHT addition.

first: Janet

last: Schibler

first: Shawn

last: Smith

first: Gang

last: Huang

last: Mulloy


title: Host directed activity of Pyrazinamide in Mycobacterium tuberculosis infection

status: Public on Jun 28 2013

city: Newark

first: Selvakumar

last: Subbian

state: NJ

address: 225 Warren Street

department: Medicine

institute: PHRI, NJMS, Rutgers the State University of NJ

summary: Pyrazinamide (PZA) is one of the first line antibiotics used for the treatment of tuberculosis (TB).  we have used human monocyte and a mouse model of pulmonary TB to investigate whether treatment with PZA, in addition to its known anti-mycobacterial properties, modulate the host immune response during Mycobacterium tuberculosis (Mtb) infection.

overall_design: Mice were infected with Mtb and treatment with PZA was started at 28 days post-infection.  At 42 days and 63 days post-infection, group of animals were euthanized and lung tissue was collected to isolate total RNA and used in microarray experiments.  Mtb-infected, untreated animals served as controls.

first: MiSun

last: Koo

first: Gilla

last: Kaplan


title: Differential expression in Wn5a and vector transduced 4T1 cells. [Affymetrix microarray data]

status: Public on Jun 26 2013

city: Birmingham

first: Rosa

last: Serra

state: AL

address: 1918 University Blvd. 660 MCLM

department: Cell Biology

institute: University of Alabama at Birmingham

summary: A highly metastatic breast cancer cell line, 4T1, was used to generate stable Wnt5a expressing and vector only control cells.  Cells were generated using lentivirus infection and selection with blasticidin. Expression of Wnt5a was confirmed using western blot.  Cell behaviour was characterized. Wnt5a expressing cells exhibited reduced migration in a transwell assay and reduced metastasis in a tail vein injection assay. Growth was not significantly affected.

overall_design: Four total samples.  Two biological replicates of the Wnt5a expressing cells and two biological replicates of the vector only control cells. RNA was isolated from cells close to confluence (70%).


title: Vitamin C induces Tet-dependent DNA demethylation in ES cells to promote a blastocyst-like methylome [Affymetrix]

city: Vancouver

first: Martin

last: Hirst

state: BC

address: 675 West 10th Avenue

department: Epigenomics

country: Canada

institute: BCCA Genome Sciences Centre

summary: DNA methylation is a heritable epigenetic modification involved in gene silencing, imprinting, and the suppression of retrotransposons. Global DNA demethylation occurs in the early embryo and the germline and may be mediated by Tet (ten-eleven-translocation) enzymes, which convert 5-methylcytosine (mC) to 5-hydroxymethylcytosine (hmC). Tet enzymes have been extensively studied in mouse embryonic stem (ES) cells, which are generally cultured in the absence of Vitamin C, a potential co-factor for Fe(II) 2-oxoglutarate dioxygenase enzymes like Tets. Here we report that addition of Vitamin C to ES cells promotes Tet activity leading to a rapid and global increase in hmC. This is followed by DNA demethylation of numerous gene promoters and up-regulation of demethylated germline genes. Tet1 binding is enriched near the transcription start site (TSS) of genes affected by Vitamin C treatment. Importantly, Vitamin C, but not other antioxidants, enhances the activity of recombinant human Tet1 in a biochemical assay and the Vitamin C-induced changes in hmC and mC are entirely suppressed in Tet1/2 double knockout (Tet DKO) ES cells. Vitamin C has the strongest effects on regions that gain methylation in cultured ES cells compared to blastocysts and in vivo are methylated only after implantation. In contrast, imprinted regions and intracisternal A-particle (IAP) elements, which are resistant to demethylation in the early embryo, are resistant to Vitamin C-induced DNA demethylation. Collectively, this study establishes that Vitamin C is a direct regulator of Tet activity and DNA methylation fidelity in ES cells.

overall_design: Oct4-GiP mouse embryonic stem (ES) cells were cultured in the presence or absence of Vitamin C (L-ascorbic acid 2-phosphate, 200 μg/ml) for 72 hours.  RNA was harvested from biological triplicates for each condition and hybridized to Affymetrix microarrays.  Cells were maintained in N2B27 medium supplemented with LIF (1000 U/ml), MEK inhibitor PD0325901 (1 μM), and GSK3β inhibitor CHIR99021 (3 μM).

first: Kathryn

last: Blaschke

first: Kevin

last: Ebata

first: Mohammed

last: Karimi

first: Matthew

last: Lorincz

first: Miguel

last: Ramalho-Santos


title: Reprogramming of mouse somatic cells into pluripotent stem cells using a combination of small molecules

status: Public on Jun 29 2013

city: Seoul

first: Seungkwon

last: You

address: Anam-dong Sungbuk-go

country: South Korea

institute: Korea University

summary: Somatic cells can be reprogrammed to generate induced pluripotent stem cells (iPSCs) by overexpression of four transcription factors, Oct4, Klf4, Sox2, and c-Myc. Bmi1  is responsible for conversion of adult mouse astrocytes and fibroblasts into neural stem cell-like cells and conversion of fibroblasts into iPSCs under enforced expression of Oct4. Here, in the first step of generating iPSCs, stable intermediate cells were generated from mouse astrocytes by Bmi1 in the absence of other transcription factors. These cells [called induced epiblast stem cell (EpiSC)-like cells (iEpiSCLCs)] are similar to EpiSCs in terms of expression of specific markers, epigenetic state, and ability to differentiate into three germ layers. Treatment with MEK/ERK and GSK3 pathway inhibitors in the presence of leukemia inhibitory factor resulted in conversion of iEpiSCLCs into iPSCs that were similar to mouse embryonic stem cells (mESCs), suggesting that Bmi1 is sufficient to reprogram astrocytes to pluripotency. Next, Bmi1 function was replaced with Shh activators (oxysterol and purmorphamine), which demonstrated that specific combinations of small molecules alone can reprogram mouse fibroblasts into iPSCs. These iPSCs resembled mESCs in terms of global gene expression profile, epigenetic status, and developmental potential, demonstrating that combinations of small molecules can compensate for reprogramming factors and are sufficient to directly reprogram mouse somatic cells into iPSCs.

overall_design: 4 Affymetrix and 4 Agilent samples


title: Re-activation of EWS-FLI1 suppressed FOXO1 expression as a novel therapeutic strategy for Ewing´s sarcoma

city: Vienna

first: Maximilian

last: Kauer

address: Zimmermannplatz 10

department: Molecular Biology

country: Austria

institute: CCRI, St.Anna Children Cancer Research Institute

summary: Transient transfection of a Ewing's Sarcoma cell line expressing type I EWS-FLI1 fusion and doxycycline-inducible short hairpin RNA against EWS-FLI1 (A673sh)

overall_design: In total, 7 samples were analysed: empty vector control and two nuclear directed AKT- and CDK2- phosphorylation resistant FOXO1 versions as well as  sh-scrambled and sh-FOXO1, either in the presence (w.o. Doxy.) or absence of EWS-FLI1 (+ Doxy.) each 2 replicates

first: Stephan

last: Niedan

first: Udo

last: Kontny

first: Raphaela

last: Schwentner

first: Reinhard

last: Kofler

first: Heinrich

last: Kovar


title: Changes in gene expression induced by CDK9 inhibition alone and in combination with fludarabine

status: Public on Jun 25 2013

city: Cardiff

first: Chris

last: Pepper

address: Heath Park

country: United Kingdom

institute: Cardiff University

summary:
Using a transcriptomics approach we explored the mechanism(s) of synergy observed between CDKI-73 and fludarabine in primary CLL cells. The cytotoxic effects of CDKI-73 were associated with transcriptional inhibition of cdk9 target genes including MCL1 and XIAP. In contrast, fludarabine induced the transcription of these genes, an effect that was reversed by the combination of CDKI-73 and fludarabine.
We used microarrays to explore the cytoxic synergy observed in primary CLL cells when we combined a novel CDK9 inhibitor with the purine nucleoside analogue fludarabine

overall_design: Primary CLL cells were inclubated with 0.1 μM CDKI-73, 10 μM fludarabine or the two drugs in combination for 4h.

first: Shudong

last: Wang


title: Expression data comparing dp53R-shSCR and dp53R-shARF mouse embryonic fibroblasts

city: Saint Louis

first: Jason

middle: Dean

last: Weber

state: MO

address: 660 South Euclid Avenue

department: Internal Medicine

institute: Washington University

summary: Mouse embryonic fibroblasts deficient for p53 and expressing mutant RasV12 were infected with lentiviral constructs carrying short hairpin RNAs targeting ARF or a scrambled control.  Four days post infection, cells were harvested for microarray analysis.

overall_design: 6 Total samples were analyzed. Arrays were downloaded from Washington University bioinformatics web site and processed in Affymetrix Expression Console (Affymetrix, Version) using RMA (Robust Multi-chip Average)algorithm. Only core probesets were used for the analysis. Control probesets as well as those interrogating probesets that are absent across all 12 arrays were filtered out. We considered those probesets as 'Present' while their signal intensity exceeded Mean (negative control signal intensity) +2 X Standard deviations (negative control signal intensity).Hierarchical cluster map was plotted using Partek Genomic suite to visualize the sample quality and differential expression analysis was performed using Significant Analysis of Microarrays (SAM) and list of differentially expressed genes were generated.

last: Forys


title: Identification of Adaptive mutations in the influenza A virus non-structural 1 gene that increase cytoplasmic localization and differentially regulate host gene expression

status: Public on Jun 22 2013

city: Ottawa

first: Earl

middle: Garnet

last: Brown

state: Ontario

address: 451 Smyth Rd

department: Biochemistry Microbiology and Immunology

institute: University of Ottawa

summary: The NS1 protein of influenza A virus (IAV) is a multifunctional virulence factor. Mouse adaptive mutations in the NS1 protein of the human isolate A/Hong Kong/1/1968(H3N2) (HK) have been previously reported to increase virulence, viral fitness, and interferon antagonism, but differ in binding to post-transcriptional processing factor CPSF30. Because nuclear trafficking is a major genetic determinant of influenza virus host adaptation, we assessed subcellular localization and host gene expression of NS1 adaptive mutations. Recombinant HK viruses with adaptive mutations in the NS1 gene were assessed for NS1 protein subcellular localization in mouse and human cells using confocal microscopy and cellular fractionation.  HK-wt virus NS1 partitioned equivalently between the cytoplasm and nucleus in human cells but was defective in cytoplasmic localization in mouse cells. The adaptive mutations either increased the proportion or abundance of NS1 in the cytoplasm, and/or the nucleus. NS1 mutations that increased cytoplasmic distribution identified a putative second nuclear export signal (NES) spanning aa positions 98-106 LSEDWFMLM, (mutation sites in bold); with the strongest effect seen for mutation M106I. The putative NES in the NS3 protein was associated with cytoplasmic localization.  The host gene expression profile of the adaptive mutants was determined by microarray analysis of infected mouse cells to show either high or low gene regulation (HGR or LGR) phenotypes that mapped to the amino-terminal and the carboxy-terminal regions respectively. The HGR and LGR mutations were predominantly down regulating versus up regulating respectively. The greatest effect on host gene expression in the HGR group correlated with the ability of the NS1 protein to bind CPSF30. To our knowledge this is the first report of roles of adaptive NS1 mutations that affect intracellular localization and regulation of host gene expression.

overall_design:
biological triplicates of mock infected mouse M1 cells; cells infected with A/HK/1/1968(H3N2) wt and NS1 mtuatn with mutaions, D2N, V23A, L98S, L98S + M106I, F103L, M106V, M106V + M124I, D125G, V180A, V226I, M106I, and R227K.
Cells were infected at a multiplicty of infection of 2 and cels were incubated for 8 hr at 37 C for 8 hrs before RNA extraction and analysis relative to mock PBS infected cells.

middle: G

last: Pelchat

first: Nicole

last: Forbes


title: The gene expression profiles of WT and NML-KO livers

first: Shohei

last: Oie

address: 1-1-1 tennodai

country: Japan

institute: Tsukuba university

summary: To examine whether energy starvation caused by the increase in rRNA transcription affects liver metabolism, we compared the gene expression profiles of WT and NML-KO livers using Affymetrix microarray technology.

overall_design: We analyzed 5 livers of WT mice and 5 livers of NML-KO mice.

first: Naoya

last: Iwasaki


title: Innate and antigen-specific cytotoxic cells and Paradoxical HIV-associated Tuberculosis Immune reconstitution inflammatory syndrome (TB-IRIS)

status: Public on Jun 24 2013

city: Cape Town

first: Mark

last: Nicol

address: Anzio Road, Observatory,

country: South Africa

institute: University of Cape Town

summary:
Tuberculosis Immune Reconstitution Inflammatory Syndrome (TB-IRIS) frequently complicates combined anti-retroviral therapy (ART) and anti-tubercular therapy in HIV-1 co-infected tuberculosis (TB) patients. The immunopathological mechanism underlying TB-IRIS is incompletely defined.
Differential transcript abundance in PBMC from IRIS and control patients stimulated with heat killed H37Rv was determined by microarray

overall_design: Blood samples were collected during longitudinal observational studies of TB-IRIS patients and controls (both groups HIV-infected patients placed on antiretroviral treatment). PBMC were stimulated with heat killed H37Rv and RNA extracted.

first: Katalin

last: Wilkinson

first: Naomi

middle: F

last: Walker

first: Graeme

last: Meintjes

first: Keira

last: Skolimowska

first: Kerryn

last: Matthews

first: Rebecca

last: Tadokera

first: Ronnett

last: Seldon

first: Gary

last: Maartens

first: Molebogeng

middle: X

last: Rangaka

first: Gurdyal

middle: S

last: Besra

first: Robert


title: Molecular Signature of Pregnancy Associated Breast Cancer (PABC)

city: Cleveland

first: Jihye

last: Kim

address: 9500 Euclid Ave.

department: Quantitative Health Sciences

institute: Cleveland Clinic

summary:
Malignant epithelia and tumor-associated stroma of PABC and Non-PABC were isolated by laser capture microdissection and gene expression profiled. Additionally, normal breast epithelia and stroma adjacent to the two tumor types were profiled.
Lastly, subsets of previously identified E- and P-regulated genes were defined in all tissues.

overall_design: Breast cancers have been obtained from women whose tumors arose while they were pregnant or within 1 year of delivery and from age-matched controls who had never been pregnant. Malignant epithelial cells were separated by laser capture microdissection (LCM) of frozen sections. RNA was isolated and analyzed by expression profiling using Affymetrix U133 2plus Human Gene Chips

first: Djuana

last: Harvell


title: Preimplantation Factor Effect on Endometrial and Decidual Cells

status: Public on Jun 21 2013

city: New Haven

first: Christina

middle: Maria

last: Duzyj

state: CT

address: 333 Cedar St

department: Ob/Gyn: Maternal Fetal Medicine

institute: Yale University

summary:
Embryos secrete preimplantation factor (PIF), a peptide present in maternal circulation during viable pregnancy.  We compared downstream synthetic PIF effect on gene expression in non-pregnant Human
Endometrial Stromal Cell (HESC) and First Trimester Decidual cell (FTDC) culture to mimic the maternal intrauterine environment during embryo implantation and trophoblast invasion.

overall_design: Cells were cultured in triplicate with and without synthetic PIF for 24 hours. Cultured cells were then pooled for chip analysis. Altered gene expression relative to controls was assessed by Affymetrix microarray

first: Michael

last: Paidas

first: Lellean

last: Jebailey

first: Jack

last: Annunziato

last: Romano

first: S

last: Huang

first: Eytan

middle: R

last: Barnea


title: DNA methylation in Early Onset Preeclamptic placentas

first: Wendy

last: Robinson

address: 950 W 28th Ave

department: Medical Genetics

institute: University of British Columbia

type: Methylation profiling by genome tiling array

summary: We investigated the DNA methylation and gene expression of 20 chorionic villi samples from early onset preeclampsia placentas to 20 gestational age matched controls. From this we were able to see a widespread disregulation in DNA methylation across a subset of genes in the genome. This may help to elucidate the underlying biological problems that lead to early onset preeclampsia. We noted that there were DNA methylation changes in many genes of importance as well as in different genomic elements such as enhancers.

overall_design: Bisulfite converted DNA from 20 third trimester early onset preeclampsia placentas and 20 gestational age matched controls

first: John

middle: D

last: Blair

first: Ryan

middle: K

last: Yuen

first: Peter

last: von Dadelszen


title: Genome-wide screening of temporal responsive genes induced by a low concentration of the carcinogen N-methyl-N'-nitro-N-nitrosoguanidine in a normal human cell line

city: hangzhou

first: li

last: hongjuan

address: 353 yan'an road

country: China

institute: zhejiang university

summary:
The alkylating agent N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) is a direct mutagen and carcinogen, causing DNA damage and other comprehensive alterations that lead to chromosomal aberrations, mutations, tumor initiation, and cell death. Our previous study revealed that MNNG at different concentrations could induce extensive changes in gene expression at an early stage of exposure. To further understand the dynamic cellular responses and hazardous effects caused by this environmental carcinogen, we used a whole-genome time-course screening methods to find out the gene expression changes induced by a low concentration of MNNG in human normal amnion epithelial FL cells. The cells were exposed to 1.0 µM MNNG, and differential gene expression profiles at 3, 12, and 24 h after MNNG treatment were obtained by use of  Affymetrix HG-U133 Plus 2.0 oligonucleotide microarray technology, followed by quantitative real-time RT-PCR validation. The results showed that the low-dose MNNG exposure triggered extensive but moderate changes in gene expression at these three experiment time points after exposure. The responsive genes encode important proteins, including cell cycle regulators, transcription factors and signal transducers that determine cell cycle progression, cell fate and other activities associate with pro-oncogenic potentials. The differential gene expression profiles at the three time points varied greatly, and generally reflected a cellular responsive process from initiation to progression and to recovery after MNNG exposure. These results will aid our understanding of the complicated mechanisms of MNNG-induced cellular responses.

Keywords：N-methyl-N'-nitro-N-nitrosoguanidine; Cellular response; Temporal gene expression change; Oligonucleotide microarray; Quantitative real-time RT-PCR

overall_design: Human amnion epithelial FL cells were exposed to vehicle control (dimethyl sulfoxide) and a low concentration (1.0 µM) MNNG for 2 h, respectively. The differential gene expression profiles at 3, 12 and 24 h post MNNG treatment were obtained using Affymetrix HG-U133 Plus 2.0 oligonucleotide microarrays. The transcriptomic changes at different time points post MNNG treatment would provide insight into the dynamic processes of cellular response to this genotoxic agent.

first: Hongjuan

last: Li

first: Jimin

last: Shao

first: Xiangyun

last: Lu

first: Yingnian

last: Yu


title: Expression data from ETV6-RUNX1-positive Reh leukemic cells after overexpression of miR-125b, miR-100 and miR-99a levels in different combinations

city: Rotterdam

first: Farhad

last: Akbari Moqadam

state: N/A = Not Applicable

address: dr. Molewaterplein 50

country: Netherlands

institute: ErasmusMC - department of Pediatric Oncology-Hematology

summary:
Combined overexpression of miR-125b with miR-99a and/or miR-100 induced VCR resistance in ETV6-RUNX1-positive leukemic cells Reh.
We used microarrays to detail the global changes in gene expression of Reh cells upon enforced expression of miR-125 per se compared with combination of overexpression of miR-125b, miR-100 and/or miR-99a

overall_design: MiR-99a and/or miR-100 were transiently overexpressed in stable miR-125b-expressing and stable scrambled miR-control-expressing Reh cells. Cellular resistance to VCR was determined by MTT assay after incubating the cells with 9 ng/mL VCR for 3 days. Changes in the gene expression pattern of Reh cells induced by miRNAs overexpression were measured using Affymetrix Arrays.

first: Monique

middle: L

last: den Boer


title: BreastPRS is a Gene Expression Assay that Stratifies Intermediate-Risk Oncotype DX Patients into High or Low-Risk for Disease Recurrence

status: Public on Jun 23 2013

city: NY

first: Wasay

last: Hussain

state: NY

address: NY

institute: Signal Genetics

summary: Molecular prognostic assays, such as Oncotype DX, are increasingly incorporated into the management of patients with invasive breast carcinoma. BreastPRS is a new molecular assay developed and validated from a meta-analysis of publically available genomic datasets. We applied the assay to matched fresh-frozen (FF) and formalin-fixed paraffin embedded (FFPE) tumor samples to translate the assay to FFPE.  A linear relationship of the BreastPRS prognostic score was observed between tissue preservation formats. BreastPRS recurrence scores were compared with Oncotype DX recurrence scores from 246 patients with invasive breast carcinoma and known Oncotype DX results. Using this series, a 120-gene linear discriminant algorithm (LDA) was trained to predict Oncotype DX risk groups and then applied to series of untreated, node-negative, estrogen receptor (ER) – positive patients from previously published studies with known clinical outcomes. Correlation of recurrence score and risk group between Oncotype DX and BreastPRS was statistically significant (P<0.0001).  59 of 260 (23%) patients from four previously published studies were classified as intermediate-risk when the 120-gene LDA was applied. BreastPRS reclassified the 59 patients into binary risk groups (high vs. low-risk). 23 (39%) patients were classified as low-risk 36 (61%) as high-risk [P=0.029, HR: 3.64, 95% CI: 1.40 to 9.50]. At 10 years from diagnosis, the low-risk group had a 90% recurrence-free survival (RFS) rate, compared to 60% for the high-risk group. BreastPRS recurrence score is comparable to Oncotype DX and can reclassify Oncotype DX intermediate-risk patients into two groups with significant differences in RFS. Further studies are needed to validate these findings.

overall_design: Expression profiles of 246 invasive breast carcinomas.

first: Timothy

middle: M

last: D'Alfonso

last: van Laar

first: Linda

last: Vahdat

first: Rachel

last: Flinchum

first: Nathan

last: Brown

last: Saint John

first: Sandra

last: Shin


title: Early-Onset Preeclampsia Placentas and Controls

last: Blair

state: British Columbia

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

overall_design: Refer to individual Series


title: Utility of HM450 BeadArray on Mouse Samples

city: Clayton

first: Nicholas

middle: C

last: Wong

state: Victoria

address: Wellington Road

department: Monash Bioinformatics Platform, Central Clinical School

institute: Monash University

summary: Illumina Infinium Human Methylation (HM) BeadChips are a widely used platform for measuring genome-scale DNA methylation, particularly in relation to epigenetic GWAS (EWAS) studies. The methylation profile of human samples can be assessed accurately and reproducibly using the HM27 BeadChip (27,578 CpG sites) or its successor, the HM450 BeadChip (485,577 CpG sites). To date no mouse equivalent has been developed greatly hindering the application of this methodology to the wide range of valuable murine models of disease and development in existence. We found 1,308 and 13,715 probes from HM27 and HM450 BeadChip uniquely matched the reference mouse genome (mm9) respectively. We demonstrate reproducible measurements of DNA methylation at these probes in a range of mouse tissue samples and in a murine cell line model of acute myeloid leukaemia. In the absence of a mouse counterpart, the Infinium HumanMethylation BeadChip arrays have utility in carrying out methylation profiling in non-human species.

sample_organism:
Homo sapiens
Mus musculus

overall_design:
GPL13534: 12 samples analysed in total. Two array replicates, two bisulfite conversion replicates and two biological replicates of mouse samples. 1 Human sample analysed in parallel.

GPL8490: 3 samples


title: Characterization of genome-methylome interactions in 22 nuclear pedigrees

status: Public on Jun 20 2013

city: La Jolla

first: Nongluk

last: Plongthongkum

state: California

address: 9500 Gilman Drive, MC0412, PFBH402

department: Bioengineering

institute: University of California, San Diego

type: Methylation profiling by high throughput sequencing

summary: In this study, we investigated the interaction between CpG methylation and genetic polymorphisms by taking the advantage of the family structure in 22 nuclear pedigrees. We have identified CpG sites that exhibit heritable methylation patterns, among which the majority are SNPs ditrectly disrupting CpG dinucleotides. We also identified 27.2% of the heritable non-SNP CpGs were associated with cis-regulatory SNPs. Additionally, we have identified hundreds of CpG clusters whose the degree of DNA methylation variation is associated with genetic polymorphism.

overall_design:
Investigate the influence of genetic variances on blood DNA methylation patterns in the human genome of 96 subjects from 22 pedigrees by using different approaches, including mid-parent offspring analysis (MPO), methylation quantitative trait loci (mQTL) analysis and allele-specific DNA methylation (ASM)
Raw data not provided since the files contain genetic information of the human subject that should be protected.

first: Kristel

last: van Eijk

first: Simone

last: de Jong

first: Tina

last: Wang

first: Jae-Hun

last: Sul

first: Marco

middle: P

last: Boks

first: René

last: Kahn

first: Ho-Lim

last: Fung

first: Roel

last: Ophoff

first: Kun

last: Zhang


title: Gene expression of LDS-OECs

city: Hamburg

first: Thomas

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

country: Germany

institute: University Medical Center Hamburg-Eppendorf

summary: The Loeys-Dietz syndrome (LDS) is an inherited connective tissue disorder caused by mutations in the transforming growth factor β (TGF-β) receptors TGFBR1 or TGFBR2. Most patients with LDS develop severe aortic aneurysms resulting in early need of surgical intervention. We investigated circulating outgrowth endothelial cells (OEC) from the peripheral blood of LDS to gain further insight into the pathophysiology of the disorder. We performed gene expression profiling using microarray analysis followed by quantitative PCR for verification of gene expression. OECs isolated from age- and sex-matched healthy donors served as reference control.

overall_design: 3 OEC clones from different LDS patients were compared to their respective age- and sex-matched OEC clone isolated from healthy donors.

first: Jasmin

last: Wellbrock

first: Walter

last: Fiedler

first: Benjamin

last: Otto


title: Profile of Bmpr1a-/- embryonic stem cells in ESC media and N2B27

city: London

first: Tristan

last: Rodriguez

address: Du Cane Road, Hammersmith Hospital Campus

department: National Heart and Lung Institute

institute: NHLI Imperial College London

summary:
A fundamental question in developmental biology is whether there are mechanisms to detect stem cells with mutations that although do not adversely affect their viability, would compromise their ability to contribute to further development. Here we show that cell competition is a novel mechanism regulating the fitness of embryonic stem cells (ESCs). We find that ESCs displaying defective BMP signalling, defective autophagy or are tetraploid are eliminated at the onset of differentiation by wild-type cells. This elimination occurs in an apoptotic dependent manner and is mediated by secreted factors. Furthermore, during this process we find that establishment of differential cMyc levels is critical and that cMyc over-expression is sufficient to induce competitive behaviour in ESCs. Cell competition is therefore a process that allows recognition and elimination of defective cells during the early stages of development and is likely to play important roles in tissue homeostasis and stem cell maintenance.
We used microarrays to compare the gene expression profiles of Bmpr1a-/- and control embryonic stem cells (ESCs) in the ESC state and after differentiation in N2B27

overall_design: Microarray profiles of control and Bmpr1a-/- mouse embryonic stem cells in embryonic stem cell culture media and in N2B27

first: Margarida

last: Sancho


title: Spheroid active compound

city: Uppsala

first: Mårten

last: Fryknäs

address: Akademiska sjh ingång 61

department: Medical sciencies

country: Sweden

institute: Uppsala university

summary: Transcriptional expression data for a bioactive small molecule for mechanism identification.

overall_design: MCF7 cells were treated with either the compound NSC620358 or DMSO (control) for 6h prior to RNA isolation, to identify drug specific gene expression changes.

first: Marten

last: Fryknas


title: Time-dependent changes in gene expression after endotoxinic challenge followed by LR12-scrambled or LR12 treatment.

city: Vandoeuvre-lès-Nancy

first: Marc

last: Derive

address: 9, av de la Forêt de Haye

country: France

institute: Inserm U1116

summary: Gene expression assessment in blood from male Cynomolgus monkey after endotoxin challenge followed by intravenous infusion with peptide control (LR12-scrambled) or LR12. The samples were analyzed at different time-points:  0,  2, 4 and 8 hours

overall_design: 56 samples : 4 time points, 4 vehicle samples/time point, 4  peptide control samples/time point, 6 LR12 samples/time point

first: Sébastien

last: Gibot

first: Marie-Eve

last: Duclos

first: Alexandra

last: Rogue

first: Nick

last: Pearson


title: Expression data from Sox4 knockdown cells in the presence and absence of TGFβ in NMuMG cells

city: Basel

first: Neha

last: Tiwari

address: Mattenstrasse 28

country: Switzerland

institute: University of Basel

summary: Expression profiling after Sox4 knockdown (KD) during epithelial to mesenchymal transition (EMT) in NMuMG reveals a significant number of genes that are transcriptionally deregulated.

overall_design: Gene expression profiling is performed in Sox4-ablated (siSox4) NMuMG cells. Cells transfected with siControl is used as a control. The cells were either treated with transforming growth factor-beta (TGFβ; 2ng/ml) or not.


first: Earl

last: Brown

summary:
Gene transcription effects of mutations in the infuenza virus A/Hong Kong/1/1968(H3N2) nonstructural 1 NS1 gene in infected human A549 (lung epithilium) cells
Influenza A/Hong Kong/156/1997(H5N1) virus NS1 gene mutations F103L and M106I both increase IFN antagonism, virulence and cytoplasmic localization but differ in binding to RIG-I and CPSF30 (manuscript submitted to Virology Journal). Human cells were infected with influenza viruses mutants with specific gain of function mutations in the NS1 gene in order to assess the affects of each mutation on host gene expression. Human (A549) and mouse (M1) cells were infected at a multiplicity of infection of 2 (infectious viruses/cell) and incubated for 8 hr before collection of total RNA and microarray anlaysis using the Affymetrix platforms. Samples were compared in triplicate to mock PBS infected (uninfected) cells to detecte dysregulated genes for A/HK/1/1968(H3N2) wt, and the following NS1 gene mutants:  F103L, M106I, M106V, and F103L + M106I.
Background: The genetic basis for avian to mammalian host switching in influenza A virus is largely unknown.  The human A/HK/156/1997(H5N1) virus that transmitted from poultry possesses NS1 gene mutations F103L + M106I that are virulence determinants in the mouse model of pneumonia; however their individual roles have not been determined.  The emergent A/Shanghai/1/2013(H7N9)-like viruses also possess these mutations which may contribute to their virulence and ability to switch species.
Methods: NS1 mutant viruses were constructed by reverse genetics and site directed mutagenesis on human and mouse-adapted backbones.  Mouse infections assessed virulence, virus yield, tissue infection, and IFN induction. NS1 protein proprieties were assessed for subcellular distribution, IFN antagonism (mouse and human), CPSF30 and RIG-I domain binding, effect on host gene transcription (microarray); and the natural prevalence of 103L and 106I mutants was assessed.
Results: Each of the F103L and M106I mutations contributes additively to virulence to reduce the lethal dose by >800 and >3,200 fold respectively by mediating alveolar tissue infection with >100 fold increased infectious yields. The 106I NS1 mutant lost CPSF binding but the 103L mutant maintained binding that correlated with an increased general decrease in host gene expression in human but not mouse cells.  Each mutation positively modulated the inhibition of IFN induction in mouse cells and activation of the IFN-β promoter in human cells but not in combination in human cells indicating negative epistasis.  Each of the F103L and M106I mutations restored a defect in cytoplasmic localization of H5N1 NS1 in mouse cells.  Human H1N1 and H3N2 NS1 proteins bound to the CARD, helicase and RD RIG-I domains, whereas the H5N1 NS1 with the same consensus 103F and 106M mutations did not bind these domains, which was partially or totally restored by the F103L or M106I mutations respectively.
Conclusions: The F103L and M106I mutations in the H5N1 NS1 protein each increased IFN antagonism and mediated interstitial pneumonia in mice that was associated with increased cytoplasmic localization and altered host factor binding. These mutations may contribute to the ability of previous HPAI H5N1 and recent LPAI H7N9 viruses to switch hosts and cause severe disease in mammals.

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Triplicate biological replicates of mock PBS treated (uninfected) cells to detecte dysregulated genes for A/HK/1/1968(H3N2) wt, and the following NS1 gene mutants:  F103L, M106I, M106V, and F103L + M106I.
Cells were infected at a multiplicty of infection of 2 and cells were incubated for 8 hr at 37 C for 8 hrs before RNA extraction and analysis of 3 biological replicates relative to mock PBS infected cells.

first: Martin

last: Pelchat

first: Samar

last: Dankar


title: Expression data from Patients with Bipolar (BP) Disorder and Matched Control Subjects

city: New York

first: Catherine

last: Clelland

address: 630 West 168th Street, P&S 12-461A

institute: Columbia University Medical Center

summary:
There are currently no biological tests that differentiate patients with bipolar disorder (BPD) from healthy controls. While there is evidence that peripheral gene expression differences between patients and controls can be utilized as biomarkers for psychiatric illness, it is unclear whether current use or residual effects of antipsychotic and mood stabilizer medication drives much of the differential transcription. We therefore tested whether expression changes in first-episode, never-medicated bipolar patients, can contribute to a biological classifier that is less influenced by medication and could potentially form a practicable biomarker assay for BPD.
We employed microarray technology to measure global leukocyte gene expression in first-episode (n=3) and currently medicated BPD patients (n=26), and matched healthy controls (n=25). Following an initial feature selection of the microarray data, we developed a cross-validated 10-gene model that was able to correctly predict the diagnostic group of the training sample (26 medicated patients and 12 controls), with 89% sensitivity and 75% specificity (p<0.001). The 10-gene predictor was further explored via testing on an independent test cohort consisting of three pairs of monozygotic twins discordant for BPD, plus the original enrichment sample cohort (the three never-medicated BPD patients and 13 matched control subjects), and a sample of experimental replicates (n=34). 83% of the independent test sample was correctly predicted, with a sensitivity of 67% and specificity of 100% (although this result did not reach statistical significance). Additionally, 88% of sample diagnostic classes were classified correctly for both the enrichment (p=0.015) and the replicate samples (p<0.001).

overall_design: Peripheral blood leukocytes (PBLs) from whole blood were collected from 26 patients with bipolar disorder who had previously received medication, three patients with bipolar disorder who were experiencing their first hospitalization and had not previously received medication, and 25 matched control subjects, for RNA extraction and hybridization on Affymetrix microarrays. Immediately after blood collection,  blood samples were split into two (when a sufficient volume had been collected); an  "1" and replicate "2" sample (thus two separate RNA extractions, cDNA and cRNA syntheses and array hybridizations were performed).

first: James


title: Gene expression analysis of Early immature  and Late mature T-ALL cell lines

status: Public on Jun 18 2013

first: Alberto

last: Ambesi-Impiombato

address: 1130 St. Nicholas Avenue

department: ICG

institute: Columbia University

summary: Early immature T-cell acute lymphoblastic leukemias (T-ALLs) account for about 5-10% of pediatric T-ALLs and are associated with poor prognosis. However, the genetic defects that drive the biology of these tumors remain largely unknown. Analysis of microarray gene expression signatures in adult T-ALL demonstrated a high prevalence of early immature leukemias and revealed a close relationship between these tumors and myeloid leukemias. Consistently, adult immature T- ALLs showed characteristic mutations in myeloid specific oncogenes and tumor suppressors including IDH1, IDH2, DNMT3A, FLT3 and NRAS. Moreover, we identified ETV6 mutations as a novel genetic lesion uniquely present in immature adult T-ALL. All together, our results demonstrate that early immature adult T- ALL represents a heterogeneous category of leukemias characterized by the presence of overlapping myeloid and T-ALL characteristics and highlight the role of ETV6 mutations in these tumors.

overall_design: Samples for microarray analysis were prepared and hybridized in Affymetrix Human U133 Plus 2.0 arrays according to the manufacturer’s instructions and as previously described. RNA was extracted from duplicate cultures of T-ALL cell lines treated for 24 h with vehicle. Interarray intensity differences were normalized with GCRMA.

first: Pieter

last: Van Vlierberghe

first: Arianne

last: Perez-Garcia

first: Erika

last: Haydu

first: Isaura

last: Rigo

first: Michael

last: Hadler

first: Valeria

last: Tosello

first: Giusy

last: Della Gatta

first: Elisabeth

last: Paietta

first: Janis

last: Racevskis

first: Peter

middle: H

last: Wiernik

first: Jacob

last: Rowe

first: Montserrat

last: Rue

first: Adolfo

last: Ferrando


title: Expression data in H1299 after retinoblastoma binding protein-2 (RBP2) knockdown

city: Hsin-Chu

first: Feng-Mao

last: Lin

state: Taiwan

address: 75 Bo-Ai Street

country: Taiwan

institute: National Chiao Tung University

summary: To identify genes whose expression was affected by RBP2, we performed gene expression microarray analysis in control and RBP2 depletion human lung cancer cell line. Two individual shRNA (RBP2 KD1 and RBP2 KD2) were used to limit potential off-target effects.

overall_design: One scramble short haripin RNA (shRNA) and two individual shRNAs to the human RBP2 gene  (RBP2 KD1 and RBP2 KD2) were used. Two replicates per group were used. H1299 cells were infected with lentivirus which carriy shRNAs for 3 days. RNA was isloated by Trizol reagent and analyzed by bioanalyzer. Microarray experiments was performed by the Affymetrix Gene Expression Service Laboratory at Academia Sinica.

first: Juan

last: Li-Jung


title: Expression data from Avian Pathogenic Escherichia coli

city: Campinas

first: Jacqueline

last: Boldrin de Paiva

state: Brasil

address: Av. Candido Rondon, 400

department: Genetics, Evolution and Bioagents

country: Brazil

institute: UNICAMP

summary: Avian Pathogenic Escherichia coli (APEC) are a group of extra-intestinal E. coli that infect poultry, and are able to cause a variety of diseases, systemic or localized, collectively designated as colibacillosis. Colibacillosis is the most common bacterial illness in poultry production, resulting in significant economic losses world-wide. Despite of its importance, pathogenicity mechanisms of APEC strains remain not completelly elucidated and available vaccines are not fully effectives. In order to better understand which genes could be related to pathogenicity in different APEC isolated, a microarray analyses of two APEC strains representing: Swollen Head Syndrome and Omphalitis was carried out.

sample_organism:
Escherichia coli SCI-07
Escherichia coli O08

overall_design: We used the microarray methodology to evaluate the expression profile of two different APEC strains

first: Fernanda

last: de Pace

first: Thais

last: Rojas

middle: B

last: de Paiva.

first: Vanessa

last: Sperandio

first: Wanderley

last: Dias da Silveira


title: Effects of Citalopram Exposure on Osteogenesis in Mouse Calvarial Pre-Osteoblasts

status: Public on Jun 19 2013

city: Augusta

first: James

last: Cray Jr.

state: GA

institute: Georgia Regents University

summary: Recently, serotonin and serotonin reuptake inhibitor (SSRI) drugs have been shown to have an effect on the development and maintenance of bone. However, little is known about its role in craniofacial development. We used microarray as one tool to determine the gene expression profile of intramembranous (calvarial) derived murine pre-osteoblasts after citalopram (SSRI) exposure.

overall_design: We isolated whole RNA from MC3T3-E1 cells treated with proliferation media or proliferation media with SSRI at a dose of 10^-4 mol./liter for 3 or 7 days in culture. We then used an Affymetrix array and compared expression profiles between control and experimental treatments.

middle: J


title: Expression data of Jurkat cells stably expressing HBZ with or without stimulation

city: kyoto

first: Azusa

last: Tanaka

address: sakyo-ku

institute: Kyoto university

summary:
Human T-cell leukemia virus type 1 (HTLV-1) encodes HTLV-1 bZIP factor (HBZ), which is thought to be crucial for neoplastic and inflammatory diseases caused by HTLV-1. So, we analyzed the transcriptional profile of HBZ expressing cells and how HBZ affect the expression of apoptosis-related genes.
We used microarrays to detail the effect of HTLV-1 bZIP factor (HBZ), which is encoded in the minus strand of HTLV-1 genome on gene expression. Especially how HBZ affect the expression of apoptosis-related genes.

overall_design: Jurkat cells stably expressing HBZ were stimulated with or without PMA and ionomycin for 9hours. Then  RNA extraction and hybridization on Affymetrix microarrays were performed.

first: Ken

last: Takai

last: Tanaka-Nakanishi


title: Gene expression in IRfl/fl Cre- and IRfl/fl Cre+ mice

city: Silverthorne

first: Margaret

last: Neville

state: CO

address: 712 Eveningstar Rd

department: OB/GYN

institute: UCDenver

summary:
The floxed insulin receptor was specifically targetted for deletion in the mammary gland  using a mouse strain bearing Cre recombinase under the BLG promoter.
Data analysis: Genespring was used for data analysis
All entities (28853) were filtered on variance between samples, eliminating from further analysis of genes whose coefficient of variation was greater than 50%.
The remaining 2239 genes were filtered on expression levels between 20 and 20,000 intensity units
An unpaired T-test was used to find genes that differed significantly (P<0.05) between experimentals and controls
The remaining 2014 genes were filtered for a 1.1 absolute fold change between experimentals and controls.
Of the remaining   expression of 890 genes was down in the Cre+ mice and expression was up for 457 genes in the Cre+ mice.

overall_design:
Mouse strains containing a floxed insulin receptor (IRfl/fl) were crossed with a mouse expressing Cre recombinase from a BLG promoter
RNA was applied to  Affymetrix MoGene_1_0-st-v1 chips
Three replicates from each strain were used  for analysis.

first: Patricia

last: Webb

first: Palanippian

last: Ramanathan


title: Gene expression profiles MCF-10A cells overexpressing MBD2

status: Public on Jun 17 2013

city: Montreal

first: Moshe

last: Szyf

state: Quebec

address: McIntyre Medical Building, 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology

institute: McGill University

summary: Methylated DNA binding protein 2 (MBD2) has been shown to bind specific methylated promoters and suppress transcription. Here we systematically investigate MBD2 suppression by overexpressing MBD2 in MCF-10A cells and generating gene expression profiles of overexpressing cells and normal MCF-10A cells.

overall_design: MCF-10A cells were infected with MBD2 lentivirus in order to increase MBD2 expression. Total RNA was extracted from both infected and non-infected cells and hybridized to Affymetrix gene expression microarrays. Three technical replicates were hybridized for infected and non-infected cells.

first: Sebastian

last: Alvarado

first: Johanne

last: Wyglinski

first: Matthew

last: Suderman

first: Stephen

last: Andrews


title: Expression data from embryonic mouse cervical spinal cords

status: Public on Jun 15 2013

city: Bronx

first: Zaven

last: Kaprielian

address: Kennedy Center RM 616, 1410 Pelham Parkway South

institute: Albert Einstein College of Medicine

summary: Mammalian motor circuits control voluntary movements by transmitting signals from the central nervous system (CNS) to muscle targets.  To form these circuits, motor neurons (MNs) must extend their axons out of the CNS.  Although motor axon exit from the CNS is an indispensable phase of motor axon pathfinding, the underlying molecular mechanisms remain obscure.  Here, we present the first identification of a genetic pathway that regulates motor axon exit from the vertebrate spinal cord, utilizing spinal accessory motor neurons (SACMN) as a model system.  SACMN are a homogeneous population of spinal MNs whose axons leave the CNS through a discrete lateral exit point (LEP) and can be visualized by the expression of the cell surface protein, BEN.  We show that the homeodomain transcription factor, Nkx2.9, is selectively required for SACMN axon exit and identify the Robo2 guidance receptor as a likely downstream effector of Nkx2.9; loss of Nkx2.9 leads to a reduction in Robo2 mRNA and protein within SACMN and SACMN axons fail to exit the spinal cord in Robo2-deficient mice.  Consistent with short-range interactions between Robo2 and Slit ligands regulating SACMN axon exit, Robo2-expressing SACMN axons normally navigate through LEP-associated Slits as they emerge from the spinal cord, and fail to exit in Slit-deficient mice.  Our studies support the view that Nkx2.9 controls SACMN axon exit from the mammalian spinal cord by regulating Robo-Slit signaling.

overall_design: We utilized microarray technology to identify novel downstream effectors of the homeodomain transcription factor, Nkx2.9, that regulate spinal accessory motor neuron development.

first: Arlene

last: Bravo-Ambrosio


title: CD4+ TIL in human breast cancer

city: Brussels

first: Chunyan

last: GU

address: Bld de Waterloo 127

department: Medecine (Jules Bordet Institute)

country: Belgium

institute: Free University of Brussels

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

overall_design: Refer to individual Series

first: Karen

last: Willard-Gallo

last: Gu-Trantien


title: IL-17 and TNF synergistically induce growth-associated cytokines in melanocytes while suppressing melanogenesis

first: Claire

last: Wang

address: 1230 York Ave

country: USA

institute: Rockefeller University

summary: In this study, we sought to determine how IL-17 and TNF influence normal human melanocytes,  either alone, or with both cytokines together. We reveal a dichotomous effect of IL-17 and TNF, which not only elicit essential mitogenic cytokines but also suppress melanogenesis by down-regulating genes of melanogenesis pathway

overall_design: Comparison of one batch of primary human melanocyte line cultured in serum free media, treated with TNF and/or IL-17, for either 24 or 48 hours.

middle: Q

first: Mayte

last: Suárez-Fariñas

last: Krueger


title: mRNA expression of  Qa2+ and Qa2- CD4+ thymocytes isolated from WT and miR-142-/- mice

status: Public on Jun 14 2013

city: Rehovot

first: Alexander

last: Mildner

address: 234 Herzl street

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary:
Developing CD4+ T-cells in the thymus mature from CD69+Qa2- cells to CD69-Qa2+ T-cells. This maturation is accombanied by increased expression of CD62L and S1PR1 in Qa2+ cells, which allows mature T-cells to emigrate from the thymus to the periphery. However, miR-142-/- mice are characterized by an altered thymocytes homeostasis, characterized by reduced CD62L protein levels on their cell surface.
To characterize the underlying molecular mechanisms, which lead to reduced CD62L expression in miR-142-/- CD4+ thymocytes, we investigated the mRNA levels in immature Qa2- as well as mature Qa2+ thymocytes isolated ex vivo from WT and miR-142 deficient Bl6 mice.

overall_design: Thymi were isolated from a pool of 4-5 mice per genotype and cells were isolated by FACS sorting. After sorting, total mRNA was isolated and expression levels were investigated with an Affymetrix microarrage Gene 1.0ST chip.

first: Steffen

last: Jung


title: Effect of human breast tumor supernatant on normal CD4+ T cells (Confirmation Set SN)

summary:
CD4+ helper T (Th) cells are critical regulators of immune responses but their role in breast cancer is currently unknown. This work aims to characterize Th cells infiltrating invasive primary human breast tumors, analyze the influence by the tumor microenvironment and identify Th cell specific prognostic gene signatures.  CD4+ T cells isolated from the tumor (TIL), axillary lymph node (LN) and blood (PB) of 10 patients were analyzed on Affymetrix U133 Plus 2.0 arrays. A confirmation set of 60 patients were studied by flow cytometry, qRT-PCR or immunohistochemistry and analyzed according to the extent of the tumor immune infiltrate. Gene expression profiles of freshly isolated TIL were also compared with TIL that had been rested overnight or with CD4+ T cells [non-stimulated (NS) or stimulated (S)] from healthy donor PB treated with tumor supernatant (SN).
Comparing gene expression profiles of donor blood derived memory CD4+ T cells [non-stimulated (NS) or stimulated (S)] with and without tumor supernatant (SN) treatment

overall_design: Memory CD4+ T cells isolated from a healthy donor blood (NS or S) were treated (and as control: untreated samples in biological triplicate) with SN obtained from fresh breast tumor homogenates of 4 patients and analyzed on Affymetrix U133 Plus 2.0 arrays


title: Gene changes of CD4+ T cells infiltrating human breast cancer in the absence of tumor environment (Confirmation Set 24h)

summary:
CD4+ helper T (Th) cells are critical regulators of immune responses but their role in breast cancer is currently unknown. This work aims to characterize Th cells infiltrating invasive primary human breast tumors, analyze the influence by the tumor microenvironment and identify Th cell specific prognostic gene signatures.  CD4+ T cells isolated from the tumor (TIL), axillary lymph node (LN) and blood (PB) of 10 patients were analyzed on Affymetrix U133 Plus 2.0 arrays. A confirmation set of 60 patients were studied by flow cytometry, qRT-PCR or immunohistochemistry and analyzed according to the extent of the tumor immune infiltrate. Gene expression profiles of freshly isolated TIL were also compared with TIL that had been rested overnight or with CD4+ T cells [non-stimulated (NS) or stimulated (S)] from healthy donor PB treated with tumor supernatant (SN).
Analysis of CD4+ TIL with or without 24h ex-vivo rest, including donor blood memory CD4+ T cells treated in the same conditions as control

overall_design: CD4+ T cells isolated from primary tumors of 2 patients and memory CD4+ T cells from a healthy donor blood were immediately analyzed or incubated for 24h without stimulation before being analyzed on Affymetrix U133 Plus 2.0 arrays


title: Gene expression profiling of CD4+ T cells infiltrating human breast cancer (Discovery Set)

summary:
CD4+ helper T (Th) cells are critical regulators of immune responses but their role in breast cancer is currently unknown. This work aims to characterize Th cells infiltrating invasive primary human breast tumors, analyze the influence by the tumor microenvironment and identify Th cell specific prognostic gene signatures.  CD4+ T cells isolated from the tumor (TIL), axillary lymph node (LN) and blood (PB) of 10 patients were analyzed on Affymetrix U133 Plus 2.0 arrays. A confirmation set of 60 patients were studied by flow cytometry, qRT-PCR or immunohistochemistry and analyzed according to the extent of the tumor immune infiltrate. Gene expression profiles of freshly isolated TIL were also compared with TIL that had been rested overnight or with CD4+ T cells [non-stimulated (NS) or stimulated (S)] from healthy donor PB treated with tumor supernatant (SN).
Analysis of CD4+ TIL by comparing their expression profiles to those of their conterparts from patient axillary lymph nodes and peripheral blood and healthy donor blood

overall_design: CD4+ T cells were isolated from primary tumors, axillary lymph nodes and peripheral blood of 10 patients with invasive breast carcinomas and blood of 4 healthy donors and analyzed on Affymetrix U133 Plus 2.0 arrays


title: Identification of transcripts bound by an RNA binding protein (RBP) in early erythroid progenitor using RNA-binding protein immunoprecipitation-microarray (RIP-Chip) experiment

city: Cambridge

first: Lingbo

last: Zhang

address: Nine Cambridge Center

institute: Whitehead Institute for Biomedical Research and MIT Department of Biology

summary: Early erythroid progenitors were isolated from mouse E14.5 fetal liver. After cell lysing, control IgG or RBP specific antibody were incubated with cell lysis. Immunoprecipitation followed by microarray experiments were carried out to identify transcripts that are immunoprecipitated by either control IgG or RBP specific antibody.

overall_design: Examination of transcripts that are immunoprecipitated by either control IgG or RBP specific antibody in primary mouse early erythroid progenitor


title: Expression data of E16 GFAP-tTA: TetO-VEGF-A164 bitransgenic embryos compared to wild type

city: Cincinnati

first: Steven

last: Potter

state: OH

address: 3333 Burnet Ave.

department: Developmental Biology

institute: Cincinnati Children's Hospital

summary:
Overexpression of VEGF (vascular endothelial growth factor) in the germinal matrix of the brain causes GMH-IVH-like anomalies (Germinal matrix hemorrhage [GMH]; intraventricular hemorrhage [IVH]).
This dataset provides the list of differentially expressed genes in the brain cortices of embryos with transgene directed overexpression of VEGF.

overall_design: Eight samples were analyzed, including four control and four with induced over expression of VEGF. A simple unpaired T-test was used for analysis, with GeneSpring software,

first: Chia-Yi

last: Kuan

first: Steve


title: Role of glucocorticoids and an RNA binding protein (RBP) in early erythroid progenitors


title: Antitumoral activity of acadesine and rituximab in MCL

status: Public on Jun 13 2013

city: BARCELONA

first: DOLORS

last: COLOMER

address: VILLARROEL 170

country: Spain

institute: IDIBAPS-HOSPITAL CLINIC

summary:
Acadesine is a nucleoside analogue with known antileukemic effects in different neoplasms. We investigated the activity of acadesine ne exerts a cytotoxic effect in MCL and synergizes with rituximab supporting clinical examination of this strategy for MCL patients
We used microarrays to detail the gene expression changes in acadesine-, rituximab- and combination-treated tumors.

overall_design: Global RNA expression in tumors treated with  acadesine, rituximab and the combination in a xenograft model of MCL (Jeko-1). Tumors were collected 18 days after the initiation of the treatments.

first: Arnau

last: Montraveta

first: Dolors

last: Colomer


title: IMPACT: Unraveling intracellular signal transduction and pathway crosstalk by exploring pathway landscape

status: Public on Sep 07 2013

city: Arlington

first: Jinghua

last: Gu

address: 900 N.Glebe Rd

institute: Virginia Tech

type:
Expression profiling by array
Third-party reanalysis

summary:
Understanding complicated modularization and crosstalk of intracellular signal transduction pathways holds the key to battle against drug resistance in human cancer research. We propose an integrative approach, namely Inferring Modularization of PAthway CrossTalk (IMPACT), to identify aberrant pathway modules and their between-module crosstalk by exploring pathway landscape that is reconstructed from a sampling strategy. The pathway identification method (i.e., IMPACT) was applied to breast cancer data to uncover aberrant pathway modules, which were further investigated with cell line studies to understand drug resistance in breast cancer.

The patient datasets we mentioned are published and are available in the GEO database as GSE6532 and GSE17705.

The re-processed GSE6532 and GSE17705 patient datasets are linked below as supplementary files. The GSE6532_matrix.txt and GSE17705_matrix.txt are processed by Affy Gene console with plier as normailization. But importantly, we also used 'Combat' method (http://www.bu.edu/jlab/wp-assets/ComBat/Abstract.html) to remove potential institutional batch effect.

overall_design: Four MCF7 derived cell models were included in the study: MCF7-STR, MCF7RR-STR, LCC1 and LCC2 cell lines. MCF7-STR and MCF7RR-STR were grown in phenol red-free IMEM supplemented with 5% charcoal-stripped calf serum and 1nM estradiol for 72 h prior to RNA extraction. LCC1 and LCC2 cells were grown in phenol red-free IMEM supplemented with 5% charcoal-stripped calf serum. The cell line data were used to validate computational results derived from patient datasets.

first: Jianhua

last: Xuan

first: Ayesha

middle: N

last: Shajahan-Haq

first: Diane

last: Demas

first: Yue

first: Robert

last: Clarke


title: EpCAM overexpression prolongs proliferative capacity of primary human breast epithelial cells and supports hyperplastic growth.

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

summary:
Introduction: The Epithelial Cell Adhesion Molecule (EpCAM) has been shown to be strongly expressed in human breast cancer and cancer stem cells and its overexpression has been supposed to support tumor progression and metastasis. However, effects of EpCAM overexpression on normal breast epithelial cells have never been studied before. Therefore, we analyzed effects of transient adenoviral overexpression of EpCAM on proliferation, migration and differentiation of primary human mammary epithelial cells (HMECs).
METHODS:
HMECs were transfected by an adenoviral system for transient overexpression of EpCAM. Thereafter, changes in cell proliferation and migration were studied using a real time measurement system. Target gene expression was evaluated by transcriptome analysis in proliferating and polarized HMEC cultures. A Chicken Chorioallantoic Membrane (CAM) xenograft model was used to study effects on in vivo growth of HMECs.
RESULTS:
EpCAM overexpression in HMECs did not significantly alter gene expression profile of proliferating or growth arrested cells. Proliferating HMECs displayed predominantly glycosylated EpCAM isoforms and were inhibited in cell proliferation and migration by upregulation of p27KIP1 and p53. HMECs with overexpression of EpCAM showed a down regulation of E-cadherin. Moreover, cells were more resistant to TGF-beta1 induced growth arrest and maintained longer capacities to proliferate in vitro. EpCAM overexpressing HMECs xenografts in chicken embryos showed hyperplastic growth, lack of lumen formation and increased infiltrates of the chicken leukocytes.
CONCLUSIONS:
EpCAM revealed oncogenic features in normal human breast cells by, inducing resistance to TGF-beta1-mediated growth arrest and supporting a cell phenotype with longer proliferative capacities in vitro. EpCAM overexpression resulted in hyperplastic growth in vivo. Thus, we suggest that EpCAM acts as a prosurvival factor counteracting terminal differentiation processes in normal mammary glands.

Differential expression was assessed with the moderated t-test (Bioconductor's limma package) with pairing of the samples by the donor. Raw p-values were adjusted for multiple hypothesis testing using the method from Benjamini and Hochberg for a strong control of the false discovery rate.

overall_design: EPCAM and GFP over-expression in proliferating mammary epithelial cells from two donors (6 and 8). Expression levels between EPCAM and control samples were compared to determine whether, and to which extent EPCAM over-expression alters the gene expression profile of the cells.

first: Agnieszka

last: Martowicz

first: Julien

last: Lelong

first: Gilbert

last: Spizzo

first: Guenther

last: Gastl

first: Gerold

last: Untergasser


title: Gene expression data from pilocytic astrocytoma tumour samples and normal cerebellum controls

status: Public on Jun 12 2013

city: Heidelberg

first: Marcel

last: Kool

address: Im Neuenheimer Feld 580

department: Pediatric Neuro Oncology

institute: German Cancer Research Center

summary: Pilocytic astrocytomas (PA) are the most common brain tumor in pediatric patients and can cause significant morbidity, including chronic neurological deficiencies. They are characterized by activating alterations in the mitogen-activated protein kinase (MAPK) pathway, but little else is known about their development. To further define their molecular development, we analysed the global DNA methylation profiles of 61 PAs and 6 normal cerebellum samples and integrated this data with transcriptome profiling. These data revealed two subgroups of PA that separate according to tumor location (infratentorial versus supratentorial), and identified key neural developmental genes that are differentially methylated between the two groups. Significant expression differences were identified for the majority of differentially methylated genes, and these were unexpectedly associated with a strong positive correlation between methylation and expression. We also identified a large number of differentially methylated/expressed genes between cerebellar PAs and normal cerebellum, which included additional developmental genes.

overall_design: Total RNA from 49 PA tumour samples and 9 normal cerebellum samples (from commercial sources) were hybridised to the Affymetrix HG U133 Plus 2.0 microarrays.

first: Sally

last: Lambert

first: Hendrik

last: Witt

first: Volker

last: Hovestadt

first: Manuela

last: Zucknick

first: Danita

last: Pearson

first: Andrey

last: Korshunov

first: Marina

last: Ryzhova

first: Koichi

last: Ichimura

first: Nada

last: Jabado

first: Adam

last: Fontebasso

first: Peter

last: Lichter

first: Stefan

last: Pfister

first: V

last: Collins

first: David

middle: T

last: Jones


title: Expression profile from PCE-Epi and derived cell lines

city: ANN ARBOR

first: Hernan

last: Roca

state: MI

address: 1011 N. University Ave.

department: Periodontics and Oral Medicine

institute: University of Michigan

summary: To study the mechanisms of the epithelial-mesenchymal transition (EMT) in prostate cancer metastasis, we first generated an epithelial model cell line derived from prostate cancer epithelial PC3 cells. We isolated a subpopulation of cells that showed a stable epithelial phenotype in culture and designated them PC3-Epi. We next developed mesenchymal cell lines from PC3-Epi cells, through interactions with macrophages. These mesenchymal cell lines were designated PC3-EMT1, PC3-EMT12 and PC3-EMT14. We transfected two of these mesenchymal lines (PC3-EMT1 and PC3-EMT14) with lentiviral ZEB1-shRNA vector (sh4) or the scrambled control (Scr). Consistent with ZEB1's role in EMT and maintenance of the mesenchymal state, silencing of ZEB1 induced the mesenchymal-epithelial transition (MET) in PC3-EMT1 and PC3-EMT14.

overall_design: Cells were plated and allowed to recover for 2 days prior to RNA extraction. PC3-Epi served as a reference sample.

first: Kenneth

last: Pienta


title: DNA methylation data from pilocytic astrocytoma tumor samples and normal cerebellum controls

city: London

address: Blizard Institute, 4 Newark Street

department: Centre for Cutaneous Research

institute: Queen Mary, University of London

summary: Pilocytic astrocytomas (PA) are the most common brain tumor in pediatric patients and can cause significant morbidity, including chronic neurological deficiencies. They are characterized by activating alterations in the mitogen-activated protein kinase (MAPK) pathway, but little else is known about their development. To map the global DNA methylation profiles of these tumors, we analysed 61 PAs and 6 normal cerebellum samples using Illumina's Infinium HumanMethylation450 BeadChips.  These data revealed two subgroups of PA that separate according to tumor location (infratentorial versus supratentorial), and identified key neural developmental genes that are differentially methylated between the two groups. Integration with transcriptome microarray data highlighted significant expression differences, which were unexpectedly associated with a strong positive correlation between methylation and expression. Differentially methylated probes were often identified within the gene body and/or regions up- or downstream of the gene, rather than at the transcription start site. We also identified a large number of differentially methylated genes between cerebellar PAs and normal cerebellum, which included additional developmental genes.

overall_design: Bisulphite converted DNA from 61 PA tumours (fresh frozen) and 6 normal cerebellum (from commerical sources) were hybridised to the Illumina Infinium HumanMethylation450 BeadChips.

first: Marcel

last: Kool


title: RNA Expression Data from IL-15-/- and IL-15+/+ TAX-LUC Mouse Tumors

status: Public on Jun 11 2013

city: St Louis

first: Rekha

last: Meyer

address: 4320 Forest Park Av

institute: Washington University School of Medicine

summary:
IL-15 is recognized as a promising candidate for tumor immunotherapy and has been described as both a promoter of cancer and a promoter of anti-cancer immunity. IL-15 was discovered in cells transformed by HTLV-1, the etiologic agent of adult T cell leukemia / lymphoma (ATL) and the human retrovirus that carries the Tax oncogene. We have developed the TAX-LUC mouse model of ATL in which Tax expression drives both malignant transformation and luciferase expression, enabling non-invasive imaging of tumorigenesis in real time. To identify the role of IL-15 in spontaneous development of lymphoma in vivo, an IL-15-/- TAX-LUC strain was developed and examined. The absence of IL-15 resulted in aggressive tumor growth and accelerated mortality and demonstrated that IL-15 was not required for Tax-mediated lymphoma but was essential for anti-tumor immunity.  Further analysis revealed  a unique transcriptional profile in tumor cells that arise in the absence of IL-15 that included a significant increase in the expression of IL-1α and IL-1α-regulated cytokines. Moreover, anti-IL-1α antibodies and an IL-1 receptor antagonist (Anakinra) were used to interrogate the potential of IL-1α  targeted therapies in this model.  Taken together, these findings identify IL-15 and IL-1α as therapeutic targets in lymphoma.
We used microarrays to compare the gene expression profile of tumors in IL-15-/- TAX-LUC mice to IL-15+/+ TAX-LUC mice

overall_design: RNA was obtained from CD16/32HI and CD16/32LO cells harvested from n=2 IL-15+/+ (control)and n=2 IL-15-/- Tax tumors and was compared to look for alterations in gene expression in malignant and tumor infiltrating cells resulting from loss of IL-15 in vivo

first: Daniel

last: Rauch

first: Lee

last: Ratner


title: Gene expression profiling of NK cells isolated from the pancreas of BDC TCR expressing NOD mice before or after Treg ablation by DTR.  Also, NK cells cultured in vitro with activating cytokines IL12 and IL-18 with or without regulatory TGFb.

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: Following Treg ablation in the BDC/NOD.Foxp3-DTR strain, NK cells produce IFNg and accumulate to higher percentage and number.  We explored the signature pathways responsible for this phenomenon using microarray prolifing and comparison to other activation signatures.

overall_design: All microarray populations were obtained from highly purified (double sorted) NK cell populations from the pancreas or the spleen following Treg ablation. Triplicates were generated for all ex vivo data. Raw data were preprocessed with the RMA algorithm in GenePattern and averaged expression values were used for analysis.

first: Jonathan

last: Sitrin

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Gene repression with H3K27me3 modification in human small cell lung cancer

city: Meguro-ku

first: Atsushi

last: Kaneda

state: Tokyo

address: 4-6-1 Komaba

department: RCAST

institute: The University of Tokyo

summary: Small cell lung cancer (SCLC) is a subtype of lung cancer with poor prognosis due to early dissemination and rapid growth. We here analyze gene expression profile of 23 clinical SCLC samples. EZH2 was found to be highly expressed in SCLC samples compared to 42 normal tissues including the normal lung, and other PRC2 members, SUZ12 and EED, were also highly expressed in SCLC. To obtain target genes of PRC2 in SCLC, H3K27me3 mark was mapped in three SCLC cell lines, Lu130, H209 and DMS53, and compared to normal small airway epithelial cells (SAEC). Whereas H3K27me3(+) genes in SAEC were significantly overlapped with PRC-target genes in ES cells (P=1.7x10-31), genes with H3K27me3 in SCLC cell lines but not in SAEC were not significantly overlapped with PRC-target genes in ES cells (P=0.64). These genes with H3K27me3 specifically in SCLC cell lines but not in SAEC showed decreased expression, not only in SCLC cell lines but also in clinical SCLCs, and showed enrichment of GO-terms such as plasma membrane (P=8.1x10-21) and cell adhesion (P=1.7x10-8). Introduction of JUB, a gene showing specific H3K27me3 modification and the strongest repression in the three SCLC cell lines, resulted in repression of cellular growth in DMS53. In clinical SCLC cases, lower JUB level correlated to shorter survival (P=0.002), or a set of PRC target genes (JUB, EPHB4) and marker genes of classic type SCLC (GRP, ASCL1) correlated to shorter survival (P=0.0001) and classified SCLC into two groups with distinct prognosis. Growth of SCLC cell lines was repressed when treated with 3-Deazaneplanocin A, an inhibitor against PRC2. It is suggested that high expression of PRC2 in SCLC contributed to repression of genes including non-PRC-target genes in ES cells, and that the gene repression may play a role in genesis of SCLC.

overall_design: Gene expression in 23 clinical SCLC samples, 42 normal tissue samples, 3 small cell lung cancer (SCLC) cell lines, and normal small airway epithelial cell (SAEC) was analyzed by Affymetrix arrays.

first: Teruyuki

last: Sato

first: Shingo

last: Tsuji

first: Takayuki

last: Isagawa

first: Shogo

last: Yamamoto

first: Takanori

last: Fujita

first: Yukiko

last: Tanaka

first: Yuichi

last: Ishikawa

first: Hiroyuki

last: Aburatani


title: Nontransformed, GM-CSF-dependent macrophage lines are a unique model to study tissue macrophage functions

status: Public on Jun 08 2013

city: Freiburg im Breisgau

first: Thomas

last: Manke

address: Stuebeweg 51

department: Bioinformatics and Deep-Sequencing Unit

institute: Max-Planck-Institute for Immunobiology and Epigenetics

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

overall_design: Refer to individual Series


title: Effect of human breast tumor supernatant on normal CD4+ T cells (Preliminary Experiment)

first: Chunyan

last: GU

summary:
CD4+ helper T (Th) cells are critical regulators of immune responses but their role in breast cancer is currently unknown. This work aims to characterize Th cells infiltrating invasive primary human breast tumors, analyze the influence by the tumor microenvironment and identify Th cell specific prognostic gene signatures.  CD4+ T cells isolated from the tumor (TIL), axillary lymph node (LN) and blood (PB) of 10 patients were analyzed on Affymetrix U133 Plus 2.0 arrays. A confirmation set of 60 patients were studied by flow cytometry, qRT-PCR or immunohistochemistry and analyzed according to the extent of the tumor immune infiltrate. Gene expression profiles of freshly isolated TIL were also compared with TIL that had been rested overnight or with CD4+ T cells [non-stimulated (NS) or stimulated (S)] from healthy donor PB treated with tumor supernatant (SN).
Comparing gene expression profiles of donor blood derived total CD4+ T cells [non-stimulated (NS)] with and without tumor supernatant (SN) treatment

overall_design: Total CD4+ T cells from a healthy donor blood (NS) were treated (and as control: untreated samples in biological triplicate) with SN from fresh breast tumor homogenates of 3 patients and analyzed on Affymetrix U133 Plus 2.0 arrays

first: Karen

last: Willard-Gallo


title: COHCAP MIRA / 450k Comparison [450k]

city: Duarte

first: Charles

middle: David

last: Warden

state: CA

address: 1500 East Duarte Rd

department: Department of Molecular and Cellular Biology

institute: City of Hope

summary: Compare a single sample run with two different technologies: Illumina 450k methylation array and MIRA on NimbleGen

overall_design:
This data is being published as a technical test of utility for a novel integrative genomic algorithm (COHCAP)
Keywords: HES-2

first: Joshua

last: Tompkins

first: Art

last: Riggs

first: Xiaojin

last: Li

last: Wang


title: Global gene expression profiling using newly synthesized RNA [mock and LPS]

summary:
Innate stimulation with TLR ligands leads to the activation of various genes  in macrophages and various populations of these cells may exhibit different responses. Here wanted to delineate and characterize these transcriptional responses in newly established, self-renewing, in vitro grown non-transformed lines (MPI cells) and bone marrow derived macrophages
We used microarrays to detail the global programme of gene expression

overall_design: Newly synthesized RNA from independently established MPI lines and bone marrow derived macrophages was extracted and hybridized to Affymetrix microarrays

first: Gyorgy

last: Fejer

first: Marina

last: Freudenberg

first: Lars

last: Dolken


title: COHCAP: City of Hope CpG Island Analysis Pipeline

summary:
COHCAP (City of Hope CpG Island Analysis Pipeline) is an algorithm to analyze single-nucleotide resolution DNA methylation data. It provides QC metrics, differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, and visualization of methylation values.  COHCAP is currently the only DNA methylation package that can handle integration with gene expression data, and the results of this study show that COHCAP can identify regions of differential methylation with ~50% concordance with gene expression.  COHCAP is scalable for analysis of both cell line data and heterogeneous patient data, and it can identify known cancer biomarkers as well as intriguing new roles of epigenetic regulation in cancer (such as methylation of estrogen receptor in breast cancer patients). This study also uses cell line data to show that COHCAP is capable of analyzing Illumina methylation array and targeted bisulfite sequencing data, with either 1-group or 2-group study designs.  The accuracy of COHCAP is accessed using qPCR, EpiTect, and comparison of COHCAP regions of differential methylation with MIRA peaks.  This software is freely available at https://sourceforge.net/projects/cohcap/.

The following third-party datasets were utilized in the paper:
BS-Seq data: GSE26826
Additional Microarray Data: GSE29290

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series.


title: Expression data of breast tumors in MMTV-PyMT+ female mice treated with DPM or vehicle

status: Public on Jun 06 2013

city: Memphis

first: Meiyun

last: Fan

address: 19 S. Manassas Street

institute: University of Tennessee

summary:
Dipyridamole (DPM) is widely used to prevent strokes and vascular thrombosis. Combination therapy of DPM and antimetabolites has shown synergistic anticancer activity. This study investigated the chemopreventive effects of DPM in the mouse mammary tumor virus promoter driven polyoma middle T oncoprotein (MMTV-PyMT) metastatic breast cancer model. We also investigated the effects of DPM on gene and miRNA expression. Chemopreventive activity was assessed by comparing the time to onset of palpable lesions, primary tumor growth kinetics and the number of lung metastases in transgenic mice treated with DPM or vehicle. Gene expression and microRNA (miRNA) expression profiles of mammary tumor tissues were then analyzed using the Affymetrix GeneChip® or miRNA 2.0 arrays. Real-time quantitative PCR (qPCR) was used to confirm changes in gene expression. Treatment with DPM beginning at the age of four weeks delayed the  onset of palpable lesions, delayed tumor progression and suppressed lung metastasis. Microarray gene expression analysis identified 253 genes differentially expressed between DPM-treated and control mammary tumors. miRNA expression analysis revealed that 53 miRNAs were altered by DPM treatment. The results indicate that DPM has chemoprevention activity against breast cancer tumorigenesis and metastasis in mice.
The array analyses provide insights into potential mechanisms of DPM’s chemopreventive effects, involving upregulation of several genes and miRNAs known to suppress cancer growth and/or metastasis and downregulation of genes known to promote cancer. Some of these genes have not been previously studied in breast cancer and may serve as novel molecular targets for breast cancer chemoprevention.

overall_design: MMTV-PyMT+ female mice were randomly divided into a DPM treatment group (n=10 mice, total of 100 glands) and a vehicle (control) group (n=7 mice, total of 70 glands). When mice were four weeks old, when hyperplasia lesions begin to develop in the FVB strain (21), DPM (10 mg/kg) or vehicle was injected IP into the peritoneum of each mouse on a 5 days on/2 days off dosing schedule for a total of 11 weeks (week one=injection one), until mice were 15 weeks of age. Each of the 10 mammary tumors per mouse was monitored until the study end point. A total six breast tumor RNA samples were used for microarray analysis, with three form mice treated with DPM and three from mice treated with vehicle.

first: Chunmei

first: Luciana

last: Schwab

first: ChuTiffany

last: Seagroves

first: John

last: Buolamwini


title: KYSE180 cells transfected with HOTAIR compared to control cells

status: Public on Jun 05 2013

city: Beijing

first: Weidong

last: Han

address: #28 Fuxing Road, HaiDian District

department: School of Life Sciences

institute: Chinese PLA General Hospital

type:
Expression profiling by array
Methylation profiling by array

first: X

first: W


title: Gene silencing of BSK65-MONO1 (RNF185) and of its natural antisense RNA (RNF185-AS) using siRNAs

status: Public on Jun 07 2013

city: Berlin

first: Bruno

last: Stuhlmueller

state: Berlin

address: Charitéplatz 1

department: Rheumatology and Clinical Immunology

institute: Charité Universitiy Hospital

summary: Microarray profiles of native HeLa cells and RNF185/BSK65 gene silenced HeLa cells using siRNAs LMG2 and LMG4 were monitored using Affymetrix U133 Plus 2.0 microarrays.

overall_design: Two independent microarray assays of each analysis were used for the comparison of native vs. siRNA treated HeLa cells with LMG2 and LMG4.

last: Stuhlmüller


title: In utero exposure to arsenic via drinking water impairs lung development and mucociliary clearance genes.

status: Public on Jun 04 2013

city: Subiaco

first: Anthony

last: Bosco

state: WA

address: 100 Roberts Road

country: Australia

institute: Telethon Kids Institute

summary:
In utero exposure to arsenic via drinking water increases the risk of lower respiratory tract infections during infancy and mortality from bronchiectasis in adulthood.
Pregnant mice were exposed to arsenic, and gene expression patterns were profiled in peripheral lung tissue obtained from the offspring at 2 weeks of age.

overall_design: Pregnant Mice (BALB/c, C57BL/6, C3H/HeARC) mice were exposed to arsenic (or control) via drinking water from day 8 of gestation until the birth of their offspring. After giving birth, mothers were given control drinking water. At 2 weeks post-natal age, total RNA was extracted from peripheral lung tissue of the offspring and analysed on Affymetrix microarrays.

first: Kathryn

middle: A

last: Ramsey

first: Katherine

last: McKenna

first: Kim

middle: W

last: Carter

first: Peter

last: Sly

first: Alexander

last: Larcombe

first: Graeme

last: Zosky


title: Genome-wide DNA methylation profiling of KYSE180 cells transfected with HOTAIR vector using Illumina HumanMethylation 450 arrays

summary: To analysis of the effect of HOTAIR on global DNA methylation in KYSE180 esophageal cancer cell line, genome-scale DNA methylation was analyzed in a pair of esophageal cancer cell lines, KYSE180 cells stably transfected with HOTAIR and control KYSE180 cells. The results from genome-wide DNA methylation analysis indicate that hypermethylation occurs more frequently than hypomethylation after stably ectopic expressing HOTAIR in KYSE180 cells.

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 manufacture'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. For pairwise differential methylation analysis, the difference of two biological replicates of the ESCC cell lines KYSE180 and KYSE180_HOTAIR was calculated.

first: Xiaolei

last: Li


title: Accelerated progression of chronic lymphocytic leukemia in Eμ-TCL1 mice expressing catalytically inactive RAG1

city: Omaha

first: Patrick

last: Swanson

state: NE

address: 2500 California Plaza

institute: Creighton University

summary: B cell chronic lymphocytic leukemia (CLL) is often preceded by a benign monoclonal or oligoclonal CD5+ B cell lymphocytosis.  We have generated transgenic mice expressing a catalytically inactive, dominant-negative recombination activating gene 1 (dnRAG1 mice) in the periphery.  These animals develop an early-onset indolent CD5+ B cell lymphocytosis, caused in part by a defect in secondary V(D)J rearrangements initiated to alter autoreactive B cell receptor specificity.  Hypothesizing that the CD5+ B cells accumulating in dnRAG1 mice represent a CLL precursor, we crossed dnRAG1 mice with CLL-prone Eµ-TCL1 mice to determine whether dnRAG1 expression in Eµ-TCL1 mice accelerates the onset of CLL-like disease.  We find that CD5+ B cell expansion and CLL progression occurs more rapidly and uniformly in double-transgenic mice (DTG mice) compared to Eµ-TCL1 mice, but with similar phenotypic and leukemogenic features. To gain insight into genes or pathways responsible for CD5+ B cell accumulation in the transgenic mice, we performed comparative gene expression profiling studies using normal and CD5+ B cells isolated from wild-type and transgenic mice at either 12 weeks of age (pre-leukemia) or at CLL onset in DTG mice (using age-matched wild-type and single-transgenic mice as controls). These analyses confirm the upregulation of tolerogenic genes in CD5+ B cells and reveal a possible role for prolactin signaling in the regulation of receptor editing.  This study suggests that a failure to remodel B cell antigen receptor genes in response to autoreactivity may promote the benign accumulation of CD5+ B cells, which may then be subjected to secondary genetic lesions that promote CLL progression.

overall_design: dnRAG1 mice were bred to Eµ-TCL1 mice to obtain cohorts of wild-type (WT), single-transgenic (dnRAG1 and Eµ-TCL1), and DTG mice.  Splenic CD19+B220hiCD5- B cells from WT mice or CD19+CD5+ B cells from transgenic mice were purified using fluorescence activated cell sorting (FACS).  Biotin end-labeled cDNA prepared from the sorted cells was hybridized to Mouse Gene 1.0 ST Arrays.  These experiments were performed two independent times: once with a cohort of 12-week-old mice, and once with older mice (>34 weeks old) consisting of two ill DTG mice and their age-matched counterparts. At least two biological replicates were used where possible.

first: Vincent

last: Nganga


title: Role and function of Ptpn6 in BCR-ABL1 driven pre-B cells

status: Public on Jun 03 2013

city: Los Angeles

first: Markus

last: Müschen

address: 4650 Sunset Blvd

department: Childrens Hospital Los Angeles

institute: University of Southern California

summary: In order to investigate the function of Ptpn6 in ALL, we isolated bone marrow cells from Ptpn6 +/fl mice and transformed them with BCR-ABL1. In a second transduction the BCR-ABL1 driven pre-B cells were transformed either with CRE-ERT2 or ERT2 (PMIP) and after 2 days of treatment with 4OH-Tamoxifen (0.5 micromolar) subjected to gene expression analysis.

overall_design: Two days after treatment with 4OH-Tamoxifen (0.5 micromolar) total RNA of Puromycin resistant cells was extracted and subjected to gene expression analysis.

first: seyedmehdi

last: shojaee


title: Role and function of Inpp5d in BCR-ABL1 driven pre-B cells

summary: In order to investigate the function of Inpp5d in ALL, we isolated bone marrow cells from Inpp5d fl/fl mice and transformed them with BCR-ABL1. In a second transduction the BCR-ABL1 driven pre-B cells were transformed either with CRE-ERT2 or ERT2 (PMIP) and after 2 days of treatment with 4OH-Tamoxifen (0.5 micromolar) subjected to gene expression analysis.


title: Gene expression data of BCR-ABL1 transformed B cell precursors from Dusp6 wild-type and Dusp6 knockout mice

summary: To elucidate the mechanism of Dusp6-mediated pre-B cell survival signaling, we investigated the gene expression pattern in BCR-ABL1-transformed Dusp6+/+ and Dusp6-/- B cell precursors.

overall_design: BCR-ABL1 transformed B cell precursors of Dusp6 wildtype and Dusp6 knockout mice were subjected to RNA isolation