title: PU.1 and Spi-B oppose transformation of pre-B cells through activation of key genes involved in B cell receptor signaling

status: Public on Nov 12 2014

city: London

first: Rodney

middle: P.

last: DeKoter

state: Ontario

address: 1151 Richmond Street

department: Microbiology & Immunology

institute: University of Western Ontario

summary:
Deletion of genes encoding the E26 transformation-specific (ETS) transcription factors, PU.1 and Spi-B, in B cells (CD19-CreDPB mice) leads to acute lymphoblastic leukemia at 100% incidence and with a median survival of 21 weeks.
To identify pathways of leukemic transformation, we compared gene expression in leukemia cells from CD19-CreDPB mice (CD19-CreDPB B220- B-ALL) with B cells from Spi-B knockout (Control DB) or B cells from CD19-CreDPB mice (CD19-CreDPB B220+ B cell)

overall_design: RNA was prepared from sorted cells using RNA-Bee (Tel-Test, Friendswood, TX). RNA integrity and purity was checked using a Bioanalyzer 2100 (Agilent Technologies Inc., Santa Clara, CA). RNA was processed and analyzed using Mouse Exon 1.0 ST arrays (Affymetrix, Santa Clara, CA) at the London Regional Genomics Centre according to the manufacturer’s instructions. Data analysis was performed using Partek Genomics Suite (Partek Inc. St. Louis, MO). Batch effect removal was performed using ComBat software. Differentially expressed genes were identified using one-way ANOVA and a cut-off of 1.5 fold with p < 0.05. Heat maps and “volcano” plots were generated using Hierarchical Clustering Explorer. Partek Pathway software was used to identify biological pathways using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, and p values were calculated using Fisher exact test.

first: D

last: Christie

first: S

last: Turkistany

first: R

middle: P


title: Microarray gene expression profiles of peripheral blood mononuclear cells in patients with advanced stage non-small cell lung cancer treated with first line combination chemotherapy with or without Rikkunshito treatment

status: Public on Oct 02 2014

city: Kaohsiung

first: yungche

last: chen

address: 123, Ta-Pei Rd. Niao-Sung Dist.

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

summary: We have extended our investigation to advanced-stage NSCLC by analyzing gene expression in peripheral blood mononuclear cells (PBMC) from patients with newly-diagnosed NSCLC and histopathology of either AC or SCC. Furthermore, to establish a direct link between gene expression and chemotherapy treatment, PBMC from  patients who have received 4 courses of combination chemotherapy with CDDP and GEM, or combination chemotherapy plus Rikkunshito were obtained, and the effects of Rikkunshito during chemotherapy on global gene expression were evaluated using microarray analyses.

overall_design: We analyzed microarray gene expression profiles of peripheral blood mononuclear cells from 17 patients with newly-diagnosed advanced stage NSCLC, and 20 age, sex, and co-morbidity-matched healthy controls (HC). All the cancer patients received a maximum of six courses of chemotherapy with cisplatin and gemcitabine of a 28-day cycle as first line treatment. Furthermore, to establish a direct link between gene expression and Rikkunshito treatment, PBMC from patients who have received 4 courses of combination chemotherapy with CDDP and GEM puls Rikkunshito (9 pateints) or dry powder placebo (8 patients) were obtained, and the effects of chemotherapy on global gene expression were evaluated using microarray analyses.

first: Yung-Che

last: Chen

first: Ding-Wei


title: Expression data of MLL-AF9-transformed murine leukemia progenitor cells, following treatment with UNC1999, a dual Ezh1 and Ezh2 inhibitor, or knockdown of EED

status: Public on Oct 10 2014

city: Chapel Hill

first: Bowen

last: Xu

state: NC

address: 450 West Drive, CB7295, Lineberger Cancer Center, GREG WANG Lab, RM 31-331

department: Biochemistry and Biophysics

country: USA

institute: UNC-Chapel Hill

summary:
Ezh2 and EZH1 are histone H3 lysine 27 specific methyltransferase. Their hyperactive mutations and overexpression were found in cancer including various hematological malignancies. UNC1999 is a highly selective inhibitor for both enzymes. It suppresses H3K27 tri- and di-methylation globally and inhibits growth of MLL-rearranged acute leukemia cell lines. UNC2400, a di-methylated derivative of UNC1999, is employed an inactive analog compound for assessment of off-target effects. EED knockdown was used to demonstrate gene targets of PRC2.
Here we performed microarray analysis in MLL-AF9 transformed acute leukemia cells following treatment with DMSO, UNC2400 or UNC1999, or after induction of EED shRNA (Renilla shRNA as control). This study allows us to identify UNC1999-responsive gene signatures as well as their overlap with PRC2 targets in MLL-AF9-bearing leukemia cells.

overall_design: We analyzed 5 of DMSO-treated, 5 of UNC2400 (inactive analog of UN1999)-treated, and 6 of UNC1999-treated MLL-AF9 leukemia cell samples to identify UNC1999-responsive gene signatures. We also performed microarray in 3 of shRNA control lines (Renilla or Ren) and 3 of shEED lines to identify downstream targets of PRC2 complex in MLL-AF9 leukemia cells.

first: Doan

last: ON

first: Gang

middle: G

last: Wang


title: Gene expression profiles of mouse ESC cardiomyocyte-specific differentiation

status: Public on Sep 25 2014

city: Aachen

first: Lin

last: Gan

address: Pauwelsstr. 30

department: IZKF

country: Germany

institute: University Hospital Aachen

summary: The differentiation to cardiomyocytes is a prerequisite and an important part of heart development. A good understanding of the complicated cardiomyocyte differentiation process benefits cardiogenesis study. Embryonic stem cells (ESCs), cell lines with infinite ability to proliferate and to be differentiated into all cell types of the adult body, are important research tools for investigation of differentiation and meanwhile good models for developmental research. In the current study, genome-wide gene expression of ESCs is profiled through high throughput platform during cardiomyocyte-specific differentiation and maturation. Gene expression patterns of undifferentiated ESCs and ESC-derived cardiomyocytes provide a global overview of genes involved in cardiomyocyte-specific differentiation, whereas marker gene expression profiles of both ESC-related genes and cardiac-specific genes presented the expression pattern shift during differentiation in a pure ESC-derived cardiomyocyte cell culture system.

overall_design: Transgenic mouse ESC clone  with α-MHC–Pac–IRES–EGFP vector containing the EGFP gene and the PuromycinR (Pac) cassette under control of the cardiac α-myosin heavy chain (α-MHC) promoter was cultured and induced into differentiation. Puromycin was applied after differentiation start to enable cardiomyocyte-specific differentiation. Cells were harvested at 4 time points after differentiation start (day0, day12, day19 and day26). Two biological replicates were taken for every time point.

first: Silke

last: Schwengberg

first: Bernd

last: Denecke


title: Transcriptomic analysis of a NaCl-resistant Saccharomyces cerevisiae mutant obtained by evolutionary engineering

status: Public on Sep 30 2014

city: TOULOUSE

first: CEREN

last: ALKIM

address: Laboratoire d'Ingénierie des Systèmes Biologiques & des Procédés

country: France

institute: INRA

summary: NaCl-resistant Saccharomyces cerevisiae mutant was obtained by evolutionary engineering. EMS mutagenized culture was used as the initial population for the selection procedure. Gradually increasing levels of NaCl stress was applied through 40 successive batch cultivations. The reference strain could not grow even at 0.85 M NaCl whereas this mutant was shown to be resistant up to 1.45 M NaCl concentration. Whole-genome microarray analysis was used to identify the NaCl resistance mechanisms by comparing NaCl-resistant mutant strain and the reference strain in the absence of NaCl stress.

overall_design: The reference Saccharomyces cerevisiae strain and the NaCl-resistant mutant were grown in minimal medium to an Optical Density (OD600) of 1.00 which corresponds to the logarithmic growth phase of the yeast cells. Cultures were harvested and whole RNA isolation was carried out. The experiment was repeated three times.

middle: H

last: Tekarslan

first: T

last: Sezgin

first: C

last: Alkım

first: U

last: Yılmaz

first: H

middle: I

last: Kısakesen

first: Z

last: Cakar


title: Loss and dysfunction of Vdelta2+ gammadelta-low T cells is associated with clinical tolerance to malaria

status: Public on Aug 26 2014

city: San Francisco

first: Charlie

last: Kim

state: CA

address: 1001 Potrero Ave

department: Medicine

institute: University of California, San Francisco

summary: Gammadelta T cells from Ugandan children were tested for their responsiveness to stimulation with malaria parasites.

overall_design: Independent PBMC samples from children were incubated with Plasmodium falciparum-infected red blood cells for 6 h post-treatment, and Vdelta2+ gammadelta T cells were double sorted by FACS directly into an RNA lysis buffer. RNA was isolated, amplified using 2 rounds of linear amplification, and hybridized to Agilent Human 8x60k microarrays as a single color experiment.

first: Charles

middle: C

first: Prasanna

last: Jagannathan

first: Margaret

middle: E

last: Feeney


title: Expression analysis of control and KLF4-overexpressing podocytes

status: Public on Nov 01 2014

city: Shinjuku-ku

first: Hiroyuki

last: Sasamura

state: Tokyo

address: 35 Shinanomachi

department: Internal Medicine

country: Japan

institute: Keio University School of Medicine

summary: To investigate podocyte gene expression and promoter methylation affected by KLF4, we examine about whole genome expression profiles using Agilent microarray and its correlation with promoter methylation profiles using Illumina DNA methylation array (GSE41689) as shown in supplementary data.

overall_design: Genome wide expression profiling of control (vector-transfected n=1) and KLF4-overexpressing (n=1) human podocytes (parental cell line: Saleem et al. JASN 13:630, 2002) and DNA methylation profile of promoter regions were shown.

first: Kaori

last: Hayashi


title: Expression data from mouse kidney epithelial cells

status: Public on Nov 19 2014

city: Glasgow

first: Leon

last: zheng

address: Garscube Estate

country: United Kingdom

institute: Beatson Institute

summary:
Fumarate hydratase (FH) is the enzyme in the Krebs cycle, which transforms fumarate to malate. Loss of fumarate hyrdragase leads to hereditary leiomyomatosis and renal cell cancer (HLRCC). The biallelic inactivation has been highly accumulated in FH-deficient cells and is considered a major pro-oncogenic factor for HLRCC tumorigenesis.
We used microarrays to understand the global readaptation of cell metabolism of gene expression underlying the truncated Krebs cycle by loss of function of fumarate hydratase.

overall_design: The fumarate hydratase wild type and knock out cells were generated for RNA extraction and hybridization on Affymetrix microarrays.

first: Christian

last: Frezza

first: Elaine

last: Mackenzie


title: Human hepatocytes support the hypertrophic but not the hyperplastic response to the murine nongenotoxic hepatocarcinogen sodium phenobarbital in an in vivo study using a chimeric mouse with humanized liver [Chimeric Liver Experiments]

status: Public on Aug 29 2014

city: Osaka

first: Kayo

last: Sumida

address: 1-98, Kasugadenaka 3-chome, Konohana-ku

department: Environmental Health Science Laboratory

institute: Sumitomo Chemical Co., Ltd.

summary: High doses of sodium phenobarbital (NaPB), a constitutive androstane receptor (CAR) activator, have been shown to produce hepatocellular tumors in rodents by a mitogenic mode of action (MOA) involving CAR activation. The effect of 1 week dietary treatment with NaPB on liver weight and histopathology, hepatic CYP2B enzyme activity and CYP2B/3A mRNA expression, replicative DNA synthesis and  selected genes related to cell proliferation and functional transcriptomic and metabolomic analyses was studied in male CD-1 mice, Wistar Hannover (WH) rats and chimeric mice with human hepatocytes. The treatment of chimeric mice with 1000-1500 ppm NaPB resulted in plasma levels around 3-5 fold higher than those observed in human subjects given therapeutic doses of NaPB. NaPB produced dose-dependent increases in hepatic CYP2B activity and CYP2B/3A mRNA levels in all animal models. Integrated functional metabolomic and transcriptomic analyses demonstrated the responses to NaPB in human liver were clearly different from those in rodents. While NaPB produced a dose-dependent increase in hepatocyte replicative DNA synthesis in CD-1 mice and WH rats, no increase in replicative DNA synthesis was observed in human hepatocyte-originated areas of chimeric mice. In addition, treatment with NaPB had no effect on Ki-67, PCNA, GADD45β, and MDM2 mRNA expression in chimeric mice, whereas significant increases were observed in CD-1 mice and/or WH rats. Thus, while NaPB could activate CAR in rodent and human hepatocytes, NaPB did not increase replicative DNA synthesis in human hepatocytes of chimeric mice, whereas it was mitogenic to rat and mouse hepatocytes. As human hepatocytes are refractory to the mitogenic effects of NaPB, the MOA for NaPB-induced rodent liver tumor formation is thus not relevant for humans.

sample_organism:
Homo sapiens
Mus musculus

overall_design: Male chimeric mice (4-5 animals/dose) also fed diets containing 0 (control) or 1000 ppm NaPB for 7 days. Liver samples were used for gene expression analysis.

first: Tomoya

last: Yamada

first: Yu

last: Okuda

first: Masahiko

last: Kushida

first: Hayato

last: Takeuchi

first: Hirohisa

last: Nagahori

first: Takako

last: Fukuda

first: Brian

last: Lake

first: Samuel

middle: M

last: Cohen

first: Satoshi

last: Kawamura


title: AR function is altered by polyglutamine expansion and by SUMO

status: Public on Aug 23 2014

city: Ann Arbor

first: Andrew

last: Lieberman

state: MI

address: 3510 MSRB I 1150 W Medical Center Dr

department: Pathology

institute: University of Michigan

summary:
Expansion of a polyglutamine (polyQ) tract in the gene for the androgen receptor (AR) results in partial loss of transactivation function and causes spinobulbar muscular atrophy (SBMA). Modification of AR by small ubiquitin-like modifier (SUMO) reduces AR function in a promoter context-dependent manner.
We used microarrays to confirm and demonstrate loss of AR function from polyQ expansion and to test the degree to which AR function is altered by preventing polyQ AR SUMOylation.

overall_design: PC12 cells expressing AR10Q, AR112Q, or nonSUMOylatable AR112Q (KRKR) in the presence or absence of synthetic androgen R1881 were assessed for alterations in AR function by comparing gene expression changes with each AR variant in response to ligand.

first: Jason

last: Chua


title: Integrated Control of Hepatic Lipogenesis vs. Glucose Production Requires FoxO Transcription Factors

status: Public on Aug 20 2014

city: New York

first: Rebecca

last: Haeusler

state: NY

address: 1150 Saint Nicholas Ave Room 303A

department: Pathology and Cell Biology

institute: Columbia University

summary:
Insulin integrates hepatic glucose and lipid metabolism, directing nutrients to storage as glycogen and triglyceride. In type 2 diabetes, levels of the former are low and the latter are exaggerated, posing a pathophysiologic and therapeutic conundrum. A branching model1 of insulin signaling, with FoxO1 presiding over glucose production2-5 and Srebp–1c regulating lipogenesis,6-8 provides a potential explanation. Here we illustrate an alternative mechanism that integrates glucose production and lipogenesis under the unifying control of FoxO. Liver–specific ablation of three FoxOs (L–FoxO1,3,4) prevents the induction of glucose–6–phosphatase and the repression of glucokinase during fasting, thus increasing lipogenesis at the expense of glucose production. We document a similar pattern in the early phases of diet-induced insulin resistance, and propose that FoxOs are required to enable the liver to direct nutritionally derived carbons to glucose vs. lipid metabolism. Our data underscore the heterogeneity of hepatic insulin resistance during progression from the metabolic syndrome to overt diabetes, and the conceptual challenge of designing therapies that curtail glucose production without promoting hepatic lipid accumulation.
We used microarrays to detail the change of gene expression in liver after knocking out FoxO1,3 and 4.

overall_design: Liver tissue samples were collected from hepatocyte- specific triple FoxO(1,3, and 4) KO and their littermates control (WT) mice after fasting (22 h) or refeeding (4 h). Gene expression was analyzed by microarray. Mice were on a mixed background of C57BL/6J and 129.

first: Domenico

last: Accili

middle: A


title: Human hepatocytes support the hypertrophic but not the hyperplastic response to the murine nongenotoxic hepatocarcinogen sodium phenobarbital in an in vivo study using a chimeric mouse with humanized liver

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

sample_organism:
Homo sapiens
Mus musculus
Rattus rattus

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Male CD-1 mice and WH rats (4 animals/dose) were fed diets containing 0 (control) or 2500 ppm NaPB for 7 days. Male chimeric mice (4-5 animals/dose) also fed diets containing 0 (control) or 1000 ppm NaPB for 7 days. Liver samples were used for gene expression analysis.


title: Metabolic Inflexibility Impairs Insulin Secretion And Results In MODY-like Diabetes In Triple FoxO-deficient Mice

city: NEW YORK

address: 1150 St. Nicholas Ave

summary:
Pancreatic b-cell failure in type 2 diabetes is associated with functional abnormalities of insulin secretion and deficits of b-cell mass. It’s unclear how one begets the other. We have shown that loss of b-cell mass can be ascribed to impaired FoxO1 function in different models of diabetes. Here we show that ablation of the three FoxO genes (1, 3a, and 4) in mature b-cells results in early-onset, maturity onset diabetes of the young (MODY)-like diabetes, with signature abnormalities of the MODY networks of Hnf4a, Hnf1a, and Pdx1. Transcriptome and functional analyses reveal that FoxO-deficient b-cells are metabolically inflexible, i.e., they preferentially utilize lipids rather than carbohydrates as source of acetyl-CoA for mitochondrial oxidative phosphorylation. This results in impaired ATP generation, and reduced Ca2+-dependent insulin secretion. When viewed in the context of prior data illustrating a role of FoxO1 in b-cell dedifferentiation, the present findings define a seamless FoxO-dependent mechanism linking the twin abnormalities of b-cell function in diabetes.
We used microarrays to detail the change of gene expression in pancreatic beta cells after knocking out FoxO1,3 and 4.

overall_design: Primary islets were isolated from pancretic beta cell- specific triple FoxO(1,3, and 4) KO and their littermates control (WT) mice. Gene expression was analyzed by microarray.

first: Ja

middle: Y

last: Kim-Muller


title: LncRNA/mRNA expression profiling for 20 human samples

status: Public on Aug 19 2014

city: Shanghai

first: Ye

last: Hu

address: 145 Middle Shandong Rd

country: China

institute: Division of Gastroenterology and Hepatology, Shanghai Jiao-Tong University School of Medicine Renji Hospital

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

summary: Transcriptional profiling of comparing human gatric cancerous tissue with noncancerous tissue. Goal was to determine the different  gene expression between gastric cancer and noncancerous tissue.(reference manuscript titled"Long non-coding RNA GAPLINC regulates CD44-dependent cell invasiveness and associates with poor prognosis of gastric cancer" submitted to Cancer Research)

overall_design: Tissue based experiment: 10 gastric cancerous tissue,10 gastric noncancerous tissue

first: Jie

last: Xu

first: Jing-Yuan

last: Fang


title: Gene Expression in Effector T cells, wildtype of Thpok-deficient

status: Public on Aug 15 2014

city: Frederick

first: David

last: Salomon

state: MD

address: 1050 Boyles Drive, Bldg. 560 Room 1246

department: NCI

institute: NIH

summary:
The transcription factor Thpok is essential for CD4 T cell development in the thymus and remains expressed in post-thymic CD4 T cells. We post-thymically inactivated Thpok and compared microarray gene expression in Thpok-deficient CD4 T cells to that in their wildtype CD4 or CD8 counterparts
We show that Thpok constrains the transcriptional circuitry to maintain CD4+-lineage integrity in naïve cells and to couple effector differentiation to environmental cues after antigenic stimulation. Redundantly with the related factor LRF, Thpok is continuously needed to prevent the trans-differentiation of mature CD4+ into -CD8+ T cells.

overall_design: We activated naïve CD4 T cells (either wild-type or Thpok-deficient) and CD8 T cells (wild-type) in vitro under Th1 conditions. Differentiated effectors were sorted 4 days after activation into CD4+CD8- and CD4-CD8+ (wild-type) and CD4+CD8- and CD4+CD8+ (Thpok-deficient) subsets. Total RNA was extracted from sorted subsets and processed for microarray analyses (Affymetrix Mouse Exon 1.0 ST array) at the NCI microarray facility, following the manufacturer’s recommendation. Data is from 3 replicates (except wild-type CD4-CD8+ cells, for which two samples only were processed), generated from two distinct cell preparations.

first: Lie

last: Wang

first: Remy

last: Bosselut


title: Blockade of oncogenic IkappaB kinase activity in ABC DLBCL by small molecule BET protein inhibitors

status: Public on Aug 01 2014

city: Bethesda

first: Louis

middle: M.

last: Staudt

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

summary: In the activated B cell-like (ABC) subtype of diffuse large B cell lymphoma (DLBCL), NF-kappaB activity is essential for viability of the malignant cells and is sustained by constitutive activity of IkappaB kinase (IKK) in the cytoplasm. Here, we report an unexpected role for the bromodomain and extraterminal domain (BET) proteins BRD2 and BRD4 in maintaining oncogenic IKK activity in ABC DLBCL. IKK activity was reduced by small molecules targeting BET proteins as well as by genetic knockdown of BRD2 and BRD4 expression, thereby inhibiting downstream NF-kappaB-driven transcriptional programs and killing ABC DLBCL cells. Using a high-throughput platform to screen for drug-drug synergy, we observed that the BET inhibitor JQ1 combined favorably with multiple drugs targeting B cell receptor signaling, one pathway that activates IKK in ABC DLBCL. The BTK kinase inhibitor ibrutinib, which is in clinical development for the treatment of ABC DLBCL, synergized strongly with BET inhibitors in killing ABC DLBCL cells in vitro and in a xenograft mouse model. These findings provide a mechanistic basis for the clinical development of BET protein inhibitors in ABC DLBCL, particularly in combination with other modulators of oncogenic IKK signaling.

overall_design: For JQ1 time course gene expression profiling, HBL1 and LP1 cells were treated with either DMSO or 100nM JQ1 for 1h, 3h, 8h, and 24h. For shRNA gene expression profiling, HBL1 cells were infected with either a Ctrl shRNA or with shRNA targeting BRD2 or BRD4. Following puromycin selection, shRNA expression was induced for 1 day and 2 days.


title: GDF15 overexpression dreived from tumor-associated macrophages and cancer cells in the microenvironment of human esophageal squamous cell carcinoma promotes tumor growth and poor prognosis

city: Kobe

first: Naoki

last: Urakawa

address: 7-5-1, Kusunoki-cho, Chuo-ku

institute: Kobe University Graduate School of Medicine

summary: Tumor-associated macrophages (TAMs) are known to be involved in progression, angiogenesis and motility of various cancers. We have previously reported the association between increased number of infiltrating TAMs with tumor progression and poor prognosis in esophageal squamous cell carcinomas (ESCCs). To study roles of TAMs in ESCC, we first exposed peripheral blood monocytes (PBMo) derived macrophages from healthy volunteers to conditioned media of TE series human ESCC cell line (TECM) and confirmed the induction of expression of M2 macrophage marker, CD204, and protumorigenic factors, interleukin (IL)-10, VEGFA and MMPs. Next, we compared gene expression profile between PBMo-derived macrophages and PBMo-derived macrophages stimulated with TECM by cDNA microarray. Based on the result, we focused on growth differentiation factor 15 (GDF15) among highly expressed genes including IL-6, IL-8 and CXCL1. Immunohistochemical study on 70 cases of surgically resected ESCCs revealed that GDF15 was detected not only in macrophages but also in cancer cells. High expression of GDF15 in ESCCs was significantly correlated with more malignant phenotypes including lymph and blood vessel invasion, lymph node metastasis as well as clinical stages. Patients with high expression of GDF15 showed poor disease-free survival (p = 0.011) and overall survival (p = 0.041). Furthermore, we found that recombinant human GDF15 promote cell proliferation and phosphorylation of both Akt and Erk1/2 in ESCC cell lines in vitro. These results indicate that GDF15 is secreted by both TAMs and cancer cells in tumor microenvironment and is associated with aberrant growth and poor prognosis of human ESCC.

overall_design: We exposed PBMo-derived macrophages from healthy volunteers to TECM and observed their acquisition of TAM-like characters in this study. We further investigated specific cancer-associated gene expression profile in TECM induced TAM-like macrophages by cDNA microarray analysis.

first: Hiroshi

last: Yokozaki


title: Gene expression changes with treatment of hsa-miR-215

status: Public on Jun 30 2014

city: Singapore

first: Wanwen

last: Lan

address: 9 Hospital Drive SON Blk C #02-03

country: Singapore

institute: Singapore Eye Research Institute

summary: Comparison of gene expression in pterygium fibroblast cells after 24 h treatment with hsa-miR-215 mimic or non-specific oligonucleotide control

overall_design: 100nM miR-215 mimic (Thermo Scientific) or non-specific control oligonucleotides are added to cultured fibroblast cells for 24 hours

last: Tong


title: Influences of fibulin-5 and cleaved fibulin-5 on gene expression patterns of fibroblasts

status: Public on Jul 20 2014

city: Hamburg

first: Bastian

last: Spruth

state: Hamburg

address: Unnastr. 48

department: Front End Innovation

institute: Beiersdorf AG

summary:
To investigate the relevance and the impact of the cleaved FBLN5 variant on fibroblast’s physiology, we have employed whole genome microarrays. Human neonatal dermal fibroblasts from three different donors were seeded in duplicates on plates pre-coated with FBLN5, cleaved FBLN5 or heat denatured BSA as a control. After cultivation for 24 h, RNA was isolated and microarrays were performed. Statistical analysis of microarrays resulted in 367 genes significantly differentially expressed in cells cultured on a FBLN5 matrix and 525 genes differentially expressed in cells cultured on a cleaved FBLN5 matrix compared to control (adjusted p-value <0.05).
To further validate these gene expression changes identified by microarray analysis 10 randomly choosen genes were reanalyzed by qRT-PCR (quantitative real time polymerase chain reaction). In nine cases the fold changes measured by qRT-PCR were comparable with those measured by microarray analysis, revealing reproducibility and validity of analysis.

overall_design: Fibulin-5 and cleaved FBLN5 contributed to changes in expression pattern of human neonatal dermal fibroblasts after cultivation for 24 h. Three different donors were used in technical duplicates.

first: Anja

last: Knott


title: Host genetic diversity enables experimental Ebola hemorrhagic fever pathogenesis

status: Public on May 01 2014

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

summary: Zaire ebolavirus (ZEBOV) is among the deadliest known human pathogens, causing severe hemorrhagic fever with high case fatality rates ranging from 70-90%.  The lack of effective vaccines or treatment available for ZEBOV renders this pathogen as a significant global biodefense threat, as evidenced by the current, highly lethal outbreak of a novel ZEBOV variant in western Africa.  Existing mouse models of lethal ZEBOV infection do not reproduce hallmark symptoms of Ebola hemorrhagic fever (EHF) including prolonged blood coagulation, acute hepatitis, disseminated intravascular coagulation (DIC), and death from hemorrhagic shock, thus restricting pathogenesis studies to non-human primates (NHP).  This has prevented rapid evaluation of countermeasures in outbreak scenarios, and impeded a comprehensive understanding of how host responses to infection contribute to severe EHF disease.  Here we demonstrate that mice from the Collaborative Cross (CC), a panel of reproducible, recombinant inbred animals that span the genetic breadth of three murine subspecies, are susceptible to a spectrum of disease phenotypes following ZEBOV infection.   In contrast to C57Bl6/J mice, which develop lethal disease without symptoms of EHF, CC recombinant inbred intercrossed (CC-RIX) lines develop either complete resistance to lethal disease or severe EHF characterized by prolonged coagulation times and 100% mortality.  Disease resistance and survival is not dependent on viral tropism, as both resistant and EHF-susceptible lines show similar inflammation and cytopathic effect in target organs.  Transcriptomics reveal potential mechanisms for both induction of severe hemorrhage in EHF mediated by IL-6 and vascular activation, and resistance to lethal infection by induction of lymphocyte differentiation and cellular adhesion.  These data demonstrate that host responses specific to unique genetic backgrounds determine susceptibility to hemorrhagic syndrome independent of virus replication.  The CC represents a novel mouse model for studying EHF pathogenesis, and we anticipate that it will be applied immediately to developing and evaluating therapeutic countermeasures.

overall_design: Microarrays were performed on liver and spleen samples from mice collected at days 1, 3, and 5 post-infection with mouse adapted Zaire ebolavirus or from time-matched mock-infected animals.

first: Angela

middle: L

last: Rasmussen

first: Atsushi

last: Okumura

first: Martin

middle: T

last: Ferris

first: Richard

last: Green

first: Friederike

last: Feldmann

first: Sara

last: Kelly

first: Dana

last: Scott

last: Safronetz

first: Elaine

last: Haddock

first: Rachel

last: LaCasse

first: Matthew

middle: J

last: Thomas

first: Pavel

last: Sova

first: Victoria

middle: S

last: Carter

first: Darla

last: Miller

first: Ginger

last: Shaw

first: Marcus

last: Korth

first: Mark

last: Heise

first: Ralph

last: Baric

first: Fernando

last: Pardo-Manuel de Villena

first: Heinz


title: Development of FGF2-dependent pluripotent stem cells showing naïve state characteristics from murine preimplantation inner cell mass

city: Minato

first: Manabu

last: Ozawa

address: 4-6-1, Shirokanedai

department: Institute of Medical Science

institute: The University of Tokyo

summary:
A unique embryonic stem cells showing naïve state was established from primplantation mouse blastocyst but maintaind their self renew under FGF2 stimulus condition
We used microarray to compare gene expression patterns of our pluripotent stem cell line (named FGF-ESC) with ESCs or EpiSCs in addition to inner cell mass from E3.5 preimplantation blastocyst as in vivo control.

overall_design: Total RNA was extracted from FGF-ESC, ESC, EpiSC and  inner cell mass from E3.5 preimplantation blastocyst, and served for microarray analysis using Affymetrix Mouse Gene 2.1 Array

first: Eri

last: Kawakami

first: Reiko

last: Sakamoto

first: Takayuki

last: Shibasaki

first: Akiteru

last: Goto

first: Nobuaki

last: Yoshida


title: Correlation of gene expression with bladder capacity in interstitial cystitis/bladder pain syndrome

status: Public on May 13 2014

city: Winston Salem

first: Stephen

last: Walker

address: Medical Center Blvd

institute: Wake Forest University Health Sciences

summary: Interstitial cystitis (IC) and bladder pain syndrome are terms used to describe a heterogenous chronic pelvic and bladder pain disorder of unknown etiology. The goal of this pilot study was to determine if gene expression profiling of bladder biopsy tissue from patients experiencing symptoms could be used to separate the patients based on some clinical parameter.

overall_design: Gene expression profiles in bladder biopsy tissue from patients with: (1) low bladder capacity (defined here as <400 ml upon hydordistension), (2) normal capacity (≥400 ml), and (3) controls were compared. Gene expression profiles from low bladder capacity tissues differed significantly from normal capacity and control tissue, suggesting gene expression profiling may be a useful tool for better understanding IC disease pathophysiology.

first: Marc

last: Colaco

first: David

last: Koslov

first: Tristan

last: Keys

first: Robert

last: Evans

first: Gopal

last: Badlani

first: Karl

last: Erik-Andersson


title: Distinct functional programming of human fetal and adult monocytes [set 2]

status: Public on May 02 2014

first: Joseph

last: McCune

state: California

institute: UCSF

summary: Microarray profiling of unstimulated and IFNg-stimulated human fetal and adult bone marrow classical monocytes

overall_design: Classical monocytes were stimulated or no with IFNg for 4 hours, sort purified, RNA isolated, and amplified. 4 of each sample was collected and used

first: Elisabeth

last: Krow-Lucal

first: Charles

last: Kim

first: Trevor

middle: D

last: Burt


title: Aberrant expression of long noncoding RNA in vivo in the cystic fibrosis bronchial epithelium.

status: Public on Mar 10 2014

city: Dublin

first: Paul

middle: Joseph

last: McKiernan

address: Beaumont Hospital - ERC

country: Ireland

institute: RCSI

summary: Long non-coding RNAs (lncRNAs) have emerged recently as key regulatory molecules with diverse roles at almost every level of the regulation of gene expression. The roles of these RNAs in the pathogenesis of cystic fibrosis (CF); a lethal multisystem, autosomal recessive disorder have yet to be explored.  Our aim was to examine the expression profile of lncRNA, in the airway epithelium of people with CF.  We examined the expression of 30,586 lncRNAs by microarray (Human LncRNA Array v3.0, Arraystar, Inc), in vivo in bronchial cells isolated from endobronchial brushings obtained from CF and non-CF individuals.  In total, we identified 1,063 lncRNAs with differential expression between CF and non-CF individuals (fold change≥3, p≤0.001).  The microarray also contained probes for ~26,109 protein coding transcripts, of which 720 were differentially expressed between CF and non-CF brush samples (fold change≥3, p≤0.001).  Confirmation of a selection of differentially expressed coding mRNA and lncRNA transcripts such as TLR8 and XIST was achieved using qRT-PCR. Gene ontology bioinformatics analysis, highlighted that many processes over-represented in the CF bronchial epithelium are related to inflammation.  These data show a significantly altered lncRNA and mRNA expression profile in CF bronchial cells in vivo.  Dysregulation of some of these lncRNAs may play important roles in the chronic infection and inflammation that exists in the lungs of people with CF.

overall_design: RNA was extracted from bronchial epithelial cells obtained from bronchial brushings at bronchoscopy. Three individual biological replicates from each group (Non-CF and CF) were profiled by microarray.

first: Kevin

last: Molloy

first: Sally

last: Cryan

first: Noel

last: McElvaney

first: Catherine

last: Greene


title: A whole genome map of alternative splicing events in precancerous lung dysplasia and adenocarcinomas of c-Raf mice

status: Public on Jun 23 2014

city: Hannover

first: Kishor

middle: Bapu

last: Londhe

state: Niedersachsen

address: Carl-Neuberg-Str. 1

department: Institut für Pharmako- und Toxikogenomikforschung

institute: Medizinische Hochschule Hannover

summary:
Alternative splicing analysis of laser micro-dissected lung dysplasia RNA samples
Lung dysplasia is a precancerous condition with high risk of malignant transformation. Little is known about alternative spliced (AS) genes in dysplasia. We therefore investigated laser micro-dissected microscopic foci of non-contaminant dysplasia and/or lung adenocarcinoma of c-Raf transgenic mice and searched genome wide for AS genes using exon arrays. Notably, bioinformatics defined 34 and 36 AS genes in the comparison dysplasia versus transgenic unaltered and non-transgenic lung tissue while the comparison adenocarcinoma versus transgenic unaltered and non-transgenic lung tissue revealed 54 and 56 genes, respectively. So far only 6 of these were reported for lung cancer.  Importantly, dysplasia related AS genes were also regulated in lung cancer to suggest a role in disease onset.  Next to exon skipping/inclusion alternative splicing at the 3’ and 5’ was common and included genes of the splicing regulatory pathway. Disease dependent changes of variant transcripts were confirmed by RT-PCR while Western blotting identified alternative splicing to modulate protein levels of AS genes. For the AS genes Add3, Cast, Osbpl6, Nedd4l, Numb, Picalm and Slk transcript and protein level agreed well, whereas for Arhgef11, Clstn1, Dlg1, Dock9, Mbnl2, Mfge8, Npnt, Pdlim5, Ppp2r5c, Tjp1 notable differences in the abundance of variant transcripts were observed by RT-PCR and gel electrophoresis. Moreover, expression of individual variants differed between dysplasia and carcinoma to suggest their disease dependent regulation. Western blotting of IQGAP1, MYO6, PTPRM, RABGAP1L and RAD50 confirmed significant regulation of isoforms in lung cancer as compared to non-transgenic, transgenic unaltered and dysplastic lung tissue. For 46 AS genes expression of the non-variant protein was reported in human lung cancer (www.proteinatlas.org) and for 13 of these, cancer related AS events are known.  Overall, new insight into lung dysplasia was obtained with 43 new cancer related AS genes to aid diagnosis and molecular intervention strategies.

overall_design: We analyzed and compared dysplastic (n=4) and adenocarcinoma (n=4) lesions and with transgenic but unaltered (n=4) and non-transgenic (n=5) lung tissue obtained from SPC/c-Raf transgenic mice with aid of laser micro dissection pressure catapulted (LMPC) technique. Dysplasia is a pre-neoplastic condition and developed at 5 month of age in the proposed mouse model. LMPC provides precise microscopic lesion collection without contamination. The RNA samples were analyzed using the Affymetrix Mouse Exon 1.0 ST platform. Alternative splicing was analyzed using Biotique XRAY tool. No technical replicates were performed.

middle: B

first: Jeurgen

last: Borlak


title: Expression data from rat hepatocyte during liver regeneration after partial hepatectomy

status: Public on Feb 28 2014

city: Xinxiang

first: Cunshuan

last: Xu

address: No. 46, Construction East Road

institute: Henan Normal University

summary:
The recovery of liver mass is mainly mediated by proliferation and enlargement of hepatocytes after partial hepatectomy. Studying the gene expression profiles of hepatocytes after partial hepatectomy will be helpful in exploring the mechanism of liver regeneration.
We used microarrays to further highlight the regulatory role of hepatocyte in liver regeneration at gene transcription level.

overall_design: Rat liver regeneration after partial hepatectomy (PH) is a good model to study the regulation of cell proliferation. We isolated hepatocytes from regenerating liver at 9 time points (2, 6, 12,24, 30, 36, 72, 120, and 168h) after PH and measured gene expression profiles of hepatocytes from 2h to 168h with rat Genome 230 2.0 gene chip. Each sample corresponding to one time point was hybridized onto one array. The experiment was repeated 3 times for each time point. In total, 10 time points were measured and 0h was used control group. After careful quality control analyses of each chip, Affymetrix GCOS 2.0 software was used to analyze the data. The relevance of gene expression profiles and biological processes was analyzed by bioinformatics and systems biology.

first: Xinsheng

last: Zhang

first: Gaiping

last: Wang

first: Yun

last: Zhou


title: Regulation of host weight gain and lipid metabolism by bacterial bile acid modification in the gut

status: Public on May 09 2014

city: Cork

first: John

middle: Andrew

last: Mac Sharry

state: Cork

address: College Road

department: APC, Biosciences Instiute

institute: UCC

summary: Alterations in the gastrointestinal microbiota have been implicated in obesity in mice and humans, but the conserved microbial functions that influence host energy metabolism and adiposity have not been determined. Here we show that bacterial bile salt hydrolase (BSH) controls a microbe-host dialogue which functionally regulates host lipid metabolism and weight gain. Expression of cloned BSH enzymes in the GI tract of gnotobiotic or conventional mice significantly altered plasma bile acid signatures and regulated transcription of key genes involved in lipid metabolism (PPARgamma angptl4), cholesterol metabolism (abcg5/8), gastrointestinal homeostasis (regIIIgamma) and circadian rhythm (dbp, per1/2) in the liver or small intestine. High-level expression of BSH in conventionally raised mice resulted in significant reduction of host weight-gain, plasma cholesterol and liver triglycerides. We demonstrate that bacterial BSH activity significantly impacts systemic metabolic processes and adiposity in the host, and represents a key mechanistic target for the control of obesity and hypercholesterolaemia.

overall_design:
Germ free Swiss Webster mice were monocolonised with EC containing the bacterial gene, Bile salt hydroalse. The treatment groups and relevant controls were;
1. Germ Free(GF) n=4 ,
2. GF and EC n=4,
3. GF and EC +BSH1 n=4,
4. GF and EC+ BSH2 n=4,
5. GF re-conventionalised (CONV-D) n= 5.
The Ileum and Liver were removed and the RNA extracted (RNAeasy plus universal  kit (Qiagen), quantified and Microarrays were carried out using mouse Exon ST1.0 arrays (Affymetrix) by Almac Group, Craigavon, Northern Ireland. Analysis and pathway mapping was carried out by ALMAC and  using Subio Platform software (Subio Inc) and Genesis Software.

first: Susan

last: Joyce

last: MacSharry

first: Pat

middle: G

last: Casey

first: Cormac

last: Gahan


title: Huntington disease protein accelerates tumour development and metastasis

status: Public on Apr 14 2014

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

summary: Huntington disease is a severe neurological disorder caused by an abnormal polyglutamine expansion in the N-terminal of the huntingtin protein. Here we show that breast tumours appear earlier when mutant huntingtin is expressed in an activated polyomavirus middle T antigen (PyVT) mouse breast cancer model as compared to the control mice expressing wild-type huntingtin. Tumours bearing mutant huntingtin have a modified gene expression pattern revealing increases in the IGF-1/Akt signalling, epithelial-mesenchymal transition and metastatic properties. Indeed, polyQ-huntingtin expressing tumours show hyper-activation of Akt pathway. Also, when mutant huntingtin is expressed, cancer cells in culture change morphology and the levels of cell adhesion and mesenchymal markers are affected in primary tumour or corresponding derived cells. As a consequence, PyVT induced lung metastasis is higher in Huntington disease mice than in the control mice. Finally, analysis of cases of Huntington disease patients developing breast cancer may suggest an increased aggressiveness of breast cancer when compared to the control population.

overall_design: 8 Total samples were analyzed: 4 x MMTV-PyVT/HdhQ7/Q7 breast tumours; 4 x MMTV-PyVT/HdhQ111/Q111 breast tumours;

first: Cristovão

last: Sousa

middle: R

last: McGuire

first: Morgane

last: Thion

first: David

last: Gentien

first: Sophie

last: du Montcel

first: Anne

last: Vincent-Salomon

first: Alexandra

last: Dürr

first: Sandrine

last: Humbert


title: Gene Level Expression Profiling: Activity dependent genes in the olfactory epithelium

status: Public on Apr 21 2014

city: Lexington

first: Timothy

middle: Scott

last: McClintock

state: KY

address: 138 Leader Avenue

department: Physiology

institute: University of Kentucky College of Medicine

summary:
Gene level analysis of RNA samples from mice olfactory epithelium
Gene expression profiling in the olfactory epithelium was performed to obtain a better understanding of the processes mediating activity dependent gene regulation

overall_design: We analyzed total RNA from olfactory epithelium tissue from 3 mice at 5 days following unilateral naris occlusion (NO) using the Affymetrix Mouse Exon 1.0 ST Array, comparing unilateral and ipsilateral epithelia.

first: Adrian

last: Fischl

first: Paula

last: Heron

first: Arnold

last: Stromberg


title: Sulforaphane protects from T cell mediated autoimmune disease by inhibition of interleukin 23 and 12 in dendritic cells

status: Public on Feb 13 2014

city: Tuebingen

first: Michael

middle: H.

last: Walter

address: Calwer Str. 7

department: Department of Medical Genetics

institute: University of Tuebingen

summary: Sulforaphane (SFN), an isothiocyanate, is part of an important group of naturally occurring small molecules with antiinflammatory properties. Even though the published reports are vague, most are best conceivable with an inhibition of T cell functions. We therefore analyzed the effect of SFN on T cell-mediated autoimmune disease. Feeding mice with SFN protected from severe experimental autoimmune encephalomyelitis (EAE). Disease amelioration was associated with reduced interleukin (IL)-17 and IFN-gamma expression in draining lymph nodes. In vitro, SFN treatment of T cells did not directly alter T cell cytokine secretion. In contrast, SFN treatment of dendritic cells (DC) inhibited TLR4-induced IL-12 and IL-23 production and the cytokine profile of T cells stimulated by SFN-treated DC. SFN suppressed TLR4-induced nuclear factor kappa B (NFκB) activity, without affecting the degradation of its inhibitor (IκB). Instead, SFN treatment of DC resulted in strong expression of the stress response protein heme oxygenase-1 (HO-1), which interacts with NFκB p65 and inhibits its activity. Consistent with these findings, HO-1 bound to p65 and subsequently inhibited the p65 promoter activity within the IL23a and IL12b promoter region. Importantly, SFN suppressed Il23a and Il12b expression in vivo and silenced Th17/Th1 responses within the CNS . Our data show that SFN improves Th17/Th1-mediated autoimmune disease by inducing HO-1 and inhibiting p65-regulated IL-23 and IL-12 expression.

overall_design: Treatment-control experiment with two replicates per condition

first: Julia

last: Geisel

first: Jürgen

last: Brück

first: Ivana

last: Glocova

first: Katja

last: Dengler

first: Tobias

last: Sinnberg

first: Oliver

last: Rothfuss

first: Klaus

last: Schulze-Osthoff

first: Martin

last: Röcken

first: Kamran

last: Ghoreschi


title: Profiling data on the developing olfactory/GnRH system reveal cellular and molecular pathways potentially relevant for the Kallmann syndrome.

status: Public on Jan 31 2014

city: Torino

first: Paolo

last: Provero

address: Via Nizza 52

department: Molecular Biotechnology and Health Sciences

country: Italy

institute: University of Turin

summary:
The olfactory sensory system is formed by the coordinated morphogenesis and differentiation of the peripheral olfactory epithelium (OE) and the anterior forebrain. At early stages, immature olfactory receptor neurons (ORN) elongate their axons to penetrate the brain basement membrane, contact and form synapses with projection neurons of the olfactory bulb primordium. Axonal elongation is accompanied by migration of the GnRH+ neurons, followed by their ingression in the septo-hypothalamic area of the forebrain. This process is specifically impaired in the Kallmann’s syndrome (KS), a disorder characterized by anosmia and central hypogonadism.
A set of transcription factors are master regulators of olfactory connectivity and GnRH neuron migration.  We explored the transcriptional network underlying this  process, by profiling the OE and adjacent mesenchyme at distinct embryonic ages. We also profiled the OE from embryos null for Dlx5, a homeogene essential for olfactory development, that causes a KS-like phenotype when deleted. We also applied analysis of conserved co-expression to integrate the obtained data with information on KS disease genes. The prevalent categories of genes differentially expressed during development are neuronal differentiation, extracellular remodelling and cell adhesion. From the analysis of Dlx5 mutant tissues we identify about 120 genes with a prevalence of intermediate filaments, cell signalling, epithelial and neuronal differentiation. Filtering for true OE expression and for the presence of Dlx5 binding sites, yielded twenty genes, of the following categories: 1) transmembrane adhesion/receptor molecules, 2) axon-glia interaction molecules, 3) synaptic proteins, 4) scaffold/adapter for signalling molecules. To functionally analyze these genes in vivo, we used three zebrafish fluorescent reporter zebrafish strains, in which we monitored early phases of olfactory/GnRH development upon gene downmodulation. The depletion of three (of five) Dlx5 targets affected axonal extension and targeting, while two (of two) altered GnRH neuron position and neurite organization.

overall_design:
In one experiment we compare the olfactrory sensory epithelium from wild-type embryos, at three times of development, i.e. E11.5, E12.5 and E14.5.
In a second experiment we compare the olfactory sensory epithelium from wild-type embryo with that from Dlx5 knock-out embryos, at the age E12.5

first: Giulia

last: Garaffo

first: Ivan

last: Molineris

first: Patrizia

last: Pinciroli

first: Clelia

last: Peano

first: Cristina

last: Battaglia

first: Giorgio

last: Merlo

first: Massimo

last: Santoro

first: Yoav

last: Gothilf

first: Talya

last: Etzion


title: Analysis of cord blood CD4T cells

status: Public on Jun 04 2014

first: Richard

last: Lo-Man

address: 25-28 Rue du Docteur Roux

institute: Institut Pasteur

summary: Purified CD4 T cells isolated from the cord blood were divided in subsets according to IL2R, IL7R and chemokine receptors (CCR6, CXCR3 and CCR4) and compared by whole genome microarray analysis.

overall_design: CD4 T cell memory subsets and Naive T cell collected from 3 donors (#480, #487, #488)


title: Transcriptome study of THP-1 human monocytes following exposure for 4 h or 24 h to 50 uM S-Nitrosoglutathione, 50 and 200 ug/ml S-Nitrosoglutathione-loaded polymeric and empty Eudragit RL nanoparticles

status: Public on Dec 19 2013

city: nancy

first: Olivier

last: Joubert

address: 2 allée guinier

department: Dpt 4

institute: Université de lorraine

summary: To further study the transcriptome of THP-1 human monocytes after exposure to S-Nitrosoglutathione (GSNO), we investigate whole genome microarray expression to identify genes regulated by exposure or not to GSNO. To further study the transcriptome of THP-1 human monocytes after exposure for 4 h to 50 ug / mL of S-Nitrosoglutathione-loaded polymeric Eudragit RL nanoparticles (GSNO-loaded ENP), we investigate whole genome microarray expression to identify genes regulated by exposure or not to 50 ug / mL of GSNO-loaded ENP. To further study the transcriptome of THP-1 human monocytes after exposure for 4 h to 200 ug / mL of empty polymeric Eudragit RL nanoparticles (empty ENP), we investigate whole genome microarray expression to identify genes regulated by exposure or not to 200 ug / mL of empty ENP. To further study the transcriptome of THP-1 human monocytes after exposure for 24 h to 50 ug / mL of S-Nitrosoglutathione-loaded polymeric Eudragit RL nanoparticles (GSNO-loaded ENP), we investigate whole genome microarray expression to identify genes regulated by exposure or not to 50 ug / mL of GSNO-loaded ENP. To further study the transcriptome of THP-1 human monocytes after exposure for 24 h to 50 ug / mL of empty polymeric Eudragit RL nanoparticles (empty ENP), we investigate whole genome microarray expression to identify genes regulated by exposure or not to 50 ug / mL of empty ENP.  To further study the transcriptome of THP-1 human monocytes after exposure for 4 h to 50 ug / mL of empty polymeric Eudragit RL nanoparticles (empty ENP), we investigate whole genome microarray expression to identify genes regulated by exposure or not to 50 ug / mL of empty ENP.  To further study the transcriptome of THP-1 human monocytes after exposure for 4 h to 200 ug / mL of S-Nitrosoglutathione-loaded polymeric Eudragit RL nanoparticles (GSNO-loaded ENP), we investigate whole genome microarray expression to identify genes regulated by exposure or not to 200 ug / mL of GSNO-loaded ENP.

overall_design: Changes in gene expression in THP-1 cells incubated without (control) or with 50 uM GSNO for 4 h, were measured. Five biological replicates were performed as controls: F_01; F_07; F_13; S_01; S_02. Four biological replicates were performed in GSNO exposed cells: S_13; S_14; S_15; S_16. Changes in gene expression in THP-1 cells incubated without (control) or with 50 ug / mL of GSNO-loaded ENPs (300 nm) for 4 h were measured. Five biological replicates were performed as controls: F_01; F_07; F_13; S_01; S_02. Three biological replicates were performed in 50 ug / mL of GSNO-loaded ENP exposed cells: S_06; S_07; S_08.  Changes in gene expression in THP-1 cells incubated without (control) or with 200 ug / mL of empty ENPs (300 nm) for 4 h were measured. Five biological replicates were performed as controls: F_01; F_07; F_13; S_01; S_02. Three biological replicates were performed in 200 ug / mL of empty ENP exposed cells: S_17; S_19; S_20. Changes in gene expression in THP-1 cells incubated without (control) or with 50 ug / mL of GSNO-loaded ENPs (300 nm) for 24 h were measured. Five biological replicates were performed as controls: F_04; F_10; F_16; S_03; S_04. Four biological replicates were performed in 50 ug / mL of GSNO-loaded ENP exposed cells: S_09; S_10; S_11; S_12. Changes in gene expression in THP-1 cells incubated without (control) or with 50 ug / mL of empty ENPs (300 nm) for 24 h were measured. Five biological replicates were performed as controls: F_04; F_10; F_16; S_03; S_04. Three biological replicates were performed in 50 ug / mL of empty ENP exposed cells: F_05; F_11; F_17. Changes in gene expression in THP-1 cells incubated without (control) or with 50 ug / mL of empty ENPs (300 nm) for 4 h were measured. Five biological replicates were performed as controls: F_01; F_07; F_13; S_01; S_02. Three biological replicates were performed in 50 ug / mL of empty ENP exposed cells: F_02; F_08; F_14. Changes in gene expression in THP-1 cells incubated without (control) or with 200 ug / mL of GSNO-loaded ENPs (300 nm) for 4 h were measured. Five biological replicates were performed as controls: F_01; F_07; F_13; S_01; S_02. Four biological replicates were performed in 200 ug / mL of GSNO-loaded ENP exposed cells: S_21; S_22; S_23; S_24.

first: Carole

last: Ronzani

first: Ramia

last: Safar

first: Roudayna

last: Diab

first: Bertrand

middle: H

last: Rihn


title: Detection of oncoantigens suitable for lung cancer vaccination

status: Public on Dec 30 2013

first: Raffaele

middle: A

last: Calogero

state: To

department: Molecular Biotechnology Center

institute: University of Torino

summary: The lung cancer tumor K-rasLA1/ p53 R172HDeltag mouse model was used to identify genes associated to the tumor mass increase in lungs. Those genes were then ranked on the basis of their oncogenic potential using a metadataset encompassing 695 human lung adenocarcinomas and ranking them on the basis of their expression in normal tissues. The genes characterized by the higher oncogenic potential combined to a low expression in normal tissues were selected as putative targets for preclinical studies on lung cancer vaccination.

overall_design: Two prototypic situations (WT, and MUT) were examined using Exon arrays over a three-points time course (10, 20, and 30 weeks old animals), for each time point two/three male and female animals were used. A total of 30 mouse Exon 1.0 arrays were hybridized.

first: Federica

last: Riccardo

first: Elena

last: Quaglino

first: Maddalena

last: Arigoni

first: Manuela

last: Iezzi

first: Dario

last: Longo

first: Elisabetta

last: Ercole

first: Silvio

last: Bicciato

first: Simona

last: Nuzzo

first: Stefania

last: Crispi

first: Guido

last: Forni

last: Cavallo


title: Apoptosis-regulated low avidity cancer-specific CD8+ T cells can be rescued to eliminate HER-2/neu expressing tumors by costimulatory agonists in tolerized mice

status: Public on Jan 14 2014

city: Baltimore

first: Elizabeth

middle: M

last: Jaffee

address: 1850 Orleans street

department: Oncology

institute: Johns Hopkins School of Medicine

summary: A major barrier of vaccines as cancer treatment is their failure to activate and maintain a complete cancer-specific CD8+ effector T cell repertoire. Low avidity T cells are more likely to escape clonal deletion in the thymus when compared to higher avidity T cells, and therefore comprise the major population of effector T cells available for activation in cancer patients.  However, low avidity T cells fail to traffic into the tumor microenvironment and function in eradicating tumor under optimal vaccination conditions as opposed to higher avidity T cells that escape clonal deletion and do function in tumor killing.   We utilized high and low avidity TCR transgenic CD8+ T cells specific for the immunodominant epitope of HER-2/neu (RNEU420-429) to identify signaling pathways responsible for the inferior activity of low avidity T cells.  Adoptive transfer of these cells into tumor-bearing vaccinated mice identified members of apoptosis pathways as being upregulated in low avidity T cells.  The increased expression of pro-apoptotic proteins by low avidity T cells promoted their own cell death and also that of other tumor-specific CD8+ T cells within their local environment. Importantly, this pro-apoptotic effect was overcome using a strong costimulatory signal that prevents activation-induced cell death and enables low avidity T cells to traffic into the tumor and assist in tumor clearance.  These findings identify new therapeutic opportunities for activating the most potent anticancer T cell responses.

overall_design: High and low avidity T cells were isolated from TCR transgenic mice and adoptively transferred into Cy-treated, vaccinated, neu-N mice.  Three days after adoptive transfer T cells were isolated from the tumor draining nodes and RNA was extracted for gene expression analysis.

first: Chelsea

last: Black

first: Todd

last: Armstrong


title: Blood expression profiles of fragile X premutation carriers identify genes involved in neurodegenerative and infertility phenotypes [SHSY5Y]

status: Public on Feb 20 2014

city: Barcelona

first: Elisabet

last: Mateu Huertas

state: Barcelona

address: Dr. Aiguader, 88

department: Bioinformatics and Genomics

country: Spain

institute: Center for Genomic Regulation

summary: Fragile X premutation carriers (fXPC) of the CGG expansion in the 5’-UTR of the fragile X mental retardation 1 (FMR1) gene are at high risk of Fragile X Tremor/Ataxia Syndrome (FXTAS), and females might undergo Premature Ovarian Failure (POF1). We have evaluated the peripheral blood gene expression profiles of fXPC and detected a strong deregulation of genes enriched in FXTAS-relevant biological pathways, including inflammation, and neuronal homeostasis and survival. More than 30% of differentially expressed correspond to long non-coding RNAs (lncRNAs). Several deregulated genes (CASP3, DFFA, APP, AKT1, COX6C, COX7B, SOD1, RNF10, HDAC5, ATXN7, ATXN3 and EAP1) were validated in brain samples of a mouse model of FXTAS and in neuronal cells expressing the expanded FMR1 5’-UTR. One of the validated genes is the early at menopause 1 (EAP1) gene. We confirmed the EAP1 deregulation both in male and female fXPC. Down-regulation was stronger in female fXPC with POF1 compared with female fXPC without POF1. Increased levels of FMR1 mRNA were detected in all brain areas of the CGG-KI mouse model. EAP1 was significantly downregulated in the brainstem and cerebellum of the KI mouse, suggesting that EAP1 levels in certain brain areas could contribute to POF in this model. All together, these results suggest that gene expression profiling in blood of fXPC reflects changes in the brain transcriptome that may underlie neuropathological aspects in FXTAS and of POF.

overall_design: In the study presented here, we have 6 biological replicats for the Mock conditions, 6 biological replicates for the expression of the wild type FMR1 5'UTR,  6 biological replicates for the expression of the mutant FMR1 5'UTR and 6 biological replicates for the overexpression of the muatnt FMR1 5'UTR.

last: Mateu-Huertas

first: Laia

last: Rodriguez-Revenga

first: Maria

middle: I

last: Alvarez-Mora

first: Irene

last: Madrigal

first: Rob

last: Willemsen

first: Montserrat

last: Milá

first: Eulàlia

last: Martí

first: Xavier

last: Estivill


title: Expression data from Gprc5a wild type or knockout mouse tracheal epithelial cells (MTECs)

status: Public on Oct 29 2013

city: Shanghai

first: Jiong

last: Deng

state: Shanghai

address: 280 South Chongqing Road, 2-801

department: Department of Pathophysiology

institute: Shanghai Jiao Tong University School of Medicine

summary:
Gprc5a is a lung tumor suppressor gene. Gprc5a-knockout (ko) mice can develop spontaneous lung cancer and Gprc5a-ko mouse model is relevant to human lung cancer. Thus, exploration of the mechanisms underlying lung tumorigenesis in Gprc5a-ko mice would be very helpful for revealing those in human lung cancer.
We used microarrays to detail the global gene expression profile that underlies oncogenesis by Gprc5a-knockout gene deletion in mouse tracheal epithelial cells.

overall_design: Wild type and gene-knockout mouse tracheal epithelial cells that were divided into two groups were used for RNA extraction.


title: Expression data from OT-I CD8 T cells activated with DC in the presence or absence of CpG-Induced Inflammation

status: Public on Dec 10 2013

city: Iowa City

first: John

last: Harty

state: Iowa

address: 3-501 Bowen Science Building, 51 Newton Road

institute: University of Iowa

summary: Inflammatory cytokines promote the accumulation of activated CD8 T cells.  Here, we transfer 600 OT-I CD8 T cells iv into naïve C57BL/6 hosts.  One day later, 500,000 LPS-matured and OVA257 peptide-coated DC were injected iv into OT-I CD8 T cell seeded hosts with (DC+CpG) or without (DC).  Other seeded mice were infected with 2x10^4 virulent Listeria monocytogenes (vLM-OVA) iv.  OT-I CD8 T cells were harvested from the spleen, flow sort purified, then RNA was extracted using RNeasy (Qiagen) kit.  Naive OT-I CD8 T cells (Naive) were purified from the spleens of OT-I transgenic mice. Each group had three independent biological replicates.Transcriptomes were compared using DAVID analysis (with genes scoring FDR<0.01) and GSEA analysis.

overall_design: 3 biological replicates per group.  Groups included Naïve OT-I CD8 T cells, DC+CpG OT-I CD8 T cells, DC OT-I CD8 T cells, and vLM-OVA OT-I CD8 T cells.  Most comparisons used Naïve OT-I CD8 T cells as a baseline comparison

first: G

last: Starbeck-Miller

first: T

last: Bair

last: Hauser

first: J


title: F11R is a novel monocyte prognostic biomarker for malignant glioma [Affymetrix]

status: Public on Nov 13 2013

city: St Louis

first: Winnie

middle: W

last: Pong

state: MO

address: 660 S. Euclid Avenue

department: Department of Neurology

institute: Washington University School of Medicine

summary:
Objective:
Brain tumors (gliomas) contain large populations of infiltrating macrophages and recruited microglia, which in experimental murine glioma models promote tumor formation and progression. Among the barriers to understanding the contributions of these stromal elements to high-grade glioma (glioblastoma; GBM) biology is the relative paucity of tools to characterize infiltrating macrophages and resident microglia. In this study, we leveraged multiple RNA analysis platforms to identify new monocyte markers relevant to GBM patient outcome.

Methods:
High-confidence lists of mouse resident microglia- and bone marrow-derived macrophage-specific transcripts were generated using converging RNA-seq and microarray technologies and validated using qRT-PCR and flow cytometry. Expression of select cell surface markers was analyzed in brain-infiltrating macrophages and resident microglia in an induced GBM mouse model, while allogeneic bone marrow transplantation was performed to trace the origins of infiltrating and resident macrophages. Glioma tissue microarrays were examined by immunohistochemistry, and the Gene Expression Omnibus (GEO) database was queried to determine the prognostic value of identified microglia biomarkers in human GBM.

Results:
We generated a unique catalog of differentially-expressed bone marrow-derived monocyte and resident microglia transcripts, and demonstrated that brain-infiltrating macrophages acquire F11R expression in GBM and following bone-marrow transplantation.  Moreover, mononuclear cell F11R expression positively correlates with human high-grade glioma and additionally serves as a biomarker for GBM patient survival, regardless of GBM molecular subtype.

Significance:
These studies establish F11R as a novel monocyte prognostic marker for GBM critical for defining a subpopulation of stromal cells for future potential therapeutic intervention.

overall_design:
Total RNA was isolated from three independently-generated sets of flow sorted bone marrow monocytes (CD11b+ CD45high CD115+ Ly6G- cells) and brainstem microglia (CD11b+ CD45low CD115low Ly6G- cells) for Illumina RNA-Seq, and two additional pools were subsequently generated and submitted for Affymetrix Mouse Exon 1.0ST microarray. Two of the RNA-Seq samples were additionally analyzed by the microarray, for a total of 6 samples (3 monocyte, 3 microglia) in each platform. Data outputs were analyzed by two analysis methods each (RNA-Seq data: ALEXA-Seq and Cufflinks; microarray data: Partek and Aroma). All four lists were merged into a new high-confidence gene list of transcripts that were significantly differentially expressed (DE) in three out of the four analyses.
In this dataset, we include exon expression data obtained from flow sorted mouse bone marrow monocytes and brainstem microglia.

first: Jason

last: Walker

last: Wylie

first: Vincent

last: Magrini

first: Jingqin

last: Luo

first: Ryan

last: Emnett

first: Jaebok

last: Choi

first: Matthew

middle: L

last: Cooper

first: Malachi

last: Griffith

first: Obi

first: Joshua

last: Rubin

first: Gregory

middle: N

last: Fuller

first: David

last: Piwnica-Worms

first: Xi

last: Feng

first: Dolores

last: Hambardzumyan

middle: F

last: DiPersio

first: Elaine

last: Mardis

last: Gutmann


title: lncRNAs expression signatures of colon cancer

status: Public on Nov 16 2013

city: shanghai

first: shi

last: debing

state: shanghai

address: 270 Dongan Road

institute: Fudan University Shanghai Cancer Center

summary: LncRNAs have been recently implicated as having oncogenic and tumor suppressor roles.To further investigate the function of lncRNA in colon cancer, we have employed lncRNA microarray to identify lncRNA with the potential to involve the metastasis of colon cancer.   Human peripheral blood from healthy donors was irradiated ex vivo, and a 74-gene consensus signature was identified that distinguished between four radiation doses (0.5, 2, 5 and 8 Gy) and control samples.  The same set of genes separated samples by exposure level at both six and 24 hours after treatment, with overlap evident only at the highest two doses (5 and 8 Gy).  Expression of five genes (CDKN1A, FDXR, SESN1, BBC3 and PHPT1) from this signature was quantified in the same RNA samples by real-time PCR, confirming low variability between donors as well as the predicted radiation response pattern.

overall_design: The experimental samples  are divided into three groups(normal、primary tumor and metastatic tumor) to compare lncRNA expression profiling of those

first: S

last: Debing


title: Induction of trophoblast stem cells from embryonic stem cells by forced repression of Oct3/4.

status: Public on Oct 17 2013

city: Wako

first: Itoshi

last: NIKAIDO

state: Saitama

address: 2-1 Hirosawa

department: Center for Biosystems Dynamics Research

institute: RIKEN

summary: To characterize the transdifferentiation of embryonic stem (ES) cells into trophoblast stem (TS) cells triggered by forced repression of Oct3/4, we performed whole-genome expression analysis after tetracycline (Tet)-induced knockout of Oct3/4.

overall_design: A Tet-inducible Oct3/4 knockout ES cell line ZHBTc4 was treated with Tet for 4 days in the presence of FGF4 and mouse embryonic fibroblasts (MEFs). A total of 21 samples from Day 0 to Day 4 were analyzed in three biological replicates.

first: Kenjiro

last: Adachi

last: Nikaido

first: Hiroki

last: Ueda

first: Hitoshi

last: Niwa


title: ABT-737 treatment induces regulation and activation of pathways implicated in cell survival, proliferation and stem cells in treated AML mice  survival, proliferation and stem cells in treated AML mice

status: Public on Nov 06 2013

first: Pierre

last: de la Grange

summary: Myelodysplastic syndrome (MDS) transforms into an acute myelogenous leukemia (AML) with associated increased bone marrow blast infiltration. Using a transgenic mouse model, MRP8[NRASD12/hBCL-2], in which the NRAS:BCL-2 complex at the mitochondria induces MDS progressing to AML with dysplastic features, we studied the therapeutic potential of a BCL-2 homology domain 3 (BH3) mimetic inhibitor, ABT-737. Treatment significantly extended lifespan, increased survival of lethally irradiated secondary recipients transplanted with treated cells compared with cells from untreated mice,  with a reduction of bone marrow (BM) blasts, LSK and progenitor populations by increased apoptosis of infiltrating blasts of diseased mice assessed in vivo by Tc-99m-labeled Annexin V single photon emission computed tomography (SPECT) and ex vivo by Annexin V/7AAD flow cytometry, TUNEL, caspase 3 cleavage and re-localization of the NRAS:BCL-2 complex from mitochondria to plasma membrane. Phosphoprotein analysis showed restoration of wild-type AKT, ERK1/2 and MEK patterns in spleen cells after treatment, which show reduced mitochondrial membrane potential. Exon specific gene expression profiling corroborates the reduction of leukemic cells, with an increase in expression of genes coding for stem cell development and maintenance, myeloid differentiation and apoptosis. Myelodysplastic features persist underscoring targeting of BCL-2-mediated effects on MDS-AML transformation and survival of leukemic cells.

overall_design: NRASD12/BCL-2 double transgenic mice were analysed by enriching for primitive Sca1+ cells from splenocytes from untreated and ABT-737 treated mice. RNA was extracted analysed for gene expression profiles using exon specific arrays.

first: Stephanie

last: Beurlet

first: Patricia

last: Krief

first: Rose

last: Padua


title: Conditional knockout of Sox2 in embryonic and trophoblast stem cells.

summary: To compare the transcriptional networks governed by Sox2 in embryonic stem (ES) cells and trophoblast stem (TS) cells, we performed whole-genome expression analysis after tetracycline (Tet)-induced knockout of Sox2 in each cell type.

overall_design: A Tet-inducible Sox2 knockout ES cell line 2TS22C or its derivative TSC line 22CEROH2-TSC1 were treated with Tet for 4 days. A total of 12 samples from ES or TS cells cultured with or without Tet were analyzed in three biological replicates.


title: From mouse to humans: detecting preventing vaccination targets associated to breast cancer stem cells. Exon-level analysis

status: Public on Nov 30 2013

first: Raffaele

last: Calogero

summary: TuBo cell line (E) was compared to passage 1 (P1), 2 (P2) and 3 (P3) mammospheres to detect specific transcription isoforms associated to cancer stem cell.

overall_design: TuBo cell line (E) was compared to passage 1 (P1), 2 (P2) and 3 (P3) mammospheres. Exon-level transcription profiling was done using Affimetrix GeneChip® Exon 1.0 ST. Exon-level analysis is more complex than gene-level analysis. The number of probesets to be investigated is at least 10 times larger in number than gene-level probesets. Thus results, upon statistical analysis, are massively contaminated by type I statistical errors, i.e. false positive [Della Beffa et al. 2008]. Furthermore, exon-level probesets are based only on four probes, which makes exon-level signal summarization more noisy than gene-level, where signal summarization is based on the overall probes encompassed by all exons of a gene. To moderate these issues we have expanded the number of experimental replications: six for TuBo and passage 1 mammosphere, four for passage 3 mammosphere and three for passage 2 mammosphere. Furthermore, after data summarization with RMA and normalization with sketch quantile method, alternative splicing detection between epithelial and mammospheres passages, was assessed using MiDAS, a two way anova developed by Affymetrix for the detection of alternative splicing events. We considered suitable for further investigations the splicing events in common between the sets of exons detected as spliced in each of the following comparisons: E vs P1, E vs P2 and E vs P3.

first: Stefania

last: Lanzardo

first: Laura

last: Conti

first: Guido

last: Forni

first: Daniela

last: Cantarella

first: Federica

last: Cavallo


title: Short telomeres compromise β-cell signaling and survival

status: Public on Oct 01 2013

first: Nini

last: Guo

address: 725 North Wolfe St. PCTB605

institute: Johns Hopkins University

summary: The factors that underlie the increasing incidence of diabetes with age are poorly understood.  We examined whether telomere length, known to decrease with age, plays a role in the age-dependent increased incidence of diabetes.  We show that in mice with short telomeres, insulin secretion is impaired and leads to glucose intolerance despite the presence of an intact β-cell mass.  Islets from mice with short telomeres displayed evidence of β-cell dysfunction, and in response to glucose, had defective mitochondrial membrane depolarization as well as Ca2+ handling which limited insulin release.  Short telomeres induced the hallmarks of senescence including premature accumulation of p16INK4a, and altered gene expression of key pathways essential for signaling and insulin secretion.  Short telomeres also had an additive damaging effect to endoplasmic reticulum stress which occurs in the late stages of type 2 diabetes.  This manifested as more severe hyperglycemia in insulin mutant Akita mice which had a more profound loss of β-cell mass and increased β-cell apoptosis.  Our data identify impaired signaling in the setting of senescence as a novel mechanism of telomere-mediated disease, and implicate telomere length as a determinant of risk and pathogenesis in diabetes.

overall_design: The experiment is designed to analyze gene expression profiles of islets from mice with short telomeres compared to those of wildtype mice.

first: Mary

last: Armanios


title: BET bromodomain inhibition suppresses TH17-mediated pathology

status: Public on Sep 20 2013

city: Cambridge

first: Barbara

last: Bryant

state: MA

address: 215 First Street

institute: Constellation Pharmaceuticals

summary: IL-17-producing T helper (TH17) cells have been selected through evolution for their ability to control fungal and bacterial infections. It is also firmly established that their aberrant generation and activation results in autoimmune conditions. Using a characterized potent and selective small molecule inhibitor, we show that the bromodomain and extra-terminal domain (BET) family of chromatin adaptors plays fundamental and selective roles in human and murine TH17 differentiation from naïve CD4+ T cells, as well as in the activation of previously differentiated TH17 cells. We provide evidence that BET controls TH17 differentiation in a bromodomain-dependent manner through a mechanism that includes the direct regulation of multiple effector TH17-associated cytokines, including IL17, IL21 and GMCSF. We also demonstrate that BET family members Brd2 and Brd4 associate with the Il17 locus in TH17 cells, and that this association requires bromodomains. We recapitulate the critical role of BET bromodomains in TH17 differentiation in vivo and show that therapeutic dosing of the BET inhibitor is efficacious in mouse models of autoimmunity.  Our results identify the BET family of proteins as a fundamental link between chromatin signaling and TH17 biology, and support the notion of BET inhibition as a point of therapeutic intervention in autoimmune conditions.

overall_design: 4 samples were analyzed: two conditions in duplicate.  Naive T cells were placed in conditions leading to TH17 differentiation, with and without BET inhibitor.  RNA was collected at 48 hours.

first: Deanna

last: Mele

first: Andres

last: Salmeron

first: Srimoyee

last: Ghosh

first: Hon-Ren

last: Huang

first: Jose

last: Lora


title: Expression profiling data of Mta1 from E9.0 mouse embryonic fibroblasts

status: Public on Aug 30 2013

city: washington

first: krishna

last: ghanta

state: DC

address: 2300 eye st NW

institute: GWU

summary:
Mta1 gene expression reveals new targets and functions. Mta1 functions in p53 dependent and independent manner. Genes regulated by Mta1 in the presence and absence of p53 were indetified
This expression data contains 5 different samples (MEFs) 1.wild type 2. Mta1 knockout 3. Mta1 re-expression in the knock out MEFs 4. P53 knockout and 5. Mta1 over expression in P53 knock out MEFs. Various sample comparisons were done and genes with p-value< 0.05 and fold change ≥ 2.0 were considered statistically significant

overall_design: 5 samples (triplicates of each, total 15) were analyzed. We generated pairwise comparisons between the WT vs Mta1-KO; Mta1-KO vs Mta1-KO/Mta1; P53-KO vs P53-KO/Mta1.

first: Krishna

middle: S

last: Ghanta

first: Rakesh

last: Kumar


title: Microarray analysis of CD14+ CD163low cells in human intestinal lamina propria

status: Public on Aug 24 2013

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Mouse intestinal innate immune cells have been identified as inducing Th17 cell differentiation. However, few studies have investigated innate immune cells that are involved in CD (Crohn's disiease) pathogenesis in humans. The present study aimed to identify a human intestinal lamina propria cell subset that induces Th17 cells, and to clarify its role in CD pathogenesis. Intestinal mucosa samples were obtained from patients who underwent resection of colorectal cancer or CD. Lamina propria cells (LPCs) were obtained by enzymatic digestion, and were analyzed for expression of HLA-DR, lineage markers (Lin), CD14, and CD163 using flow cytometry. Among HLA-DRhigh Lin- cells, we identified a CD14+ CD163low cell subset that was selectively present in intestinal LPCs. We identified CD14+ CD163low cells as having a potent capacity to induce Th17 cell differentiation in human intestinal lamina propria. The Th17-inducing activity of these cells was enhanced in CD patients.

overall_design: The Cy3-labeled cDNAs were hybridized on Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray (G4845A) in one color experiments, resulting in four individual microarrays.

first: Takayuki

last: Ogino


title: Gene Set Enrichment Analysis reveals lineage relationships between mouse and human gliomas and identifies stem cells and PNET as distinct entities

status: Public on Jul 29 2013

city: London

first: Nick

last: Henriquez

address: 29 Gordon Square

department: Enterprise

institute: UCL

summary: Murine and human genome-wide microarray expression profiles (including GSE19404) were compared using Partek and Gene Set Enrichment Analysis (GSEA) in order to identify similarities. A murine PNET-like tumour by morphology was found to resemble human ATRT, whereas experimental glioma resembled a particular human glioblastoma subclass.

overall_design:
Tumour material was resected or neurosphere cultures pelleted. Part of the material was processed for histological analysis, another was snap-frozen for isolation of RNA. RNA was then labelled and hybridised to Affymetrix MoEx-v1 arrays and analysed using Partek.
This array dataset comprises Affymetrix MoEx-v2 microarrays hybridised with RNA from brain-derived tumour material (CA), subventricular zone (SVZ)-derived growth transformed neurospheres (CATR) and control neurospheres (CS, GFP).

first: Nico

middle: V

first: Sebastian

last: Brandner


title: Transcriptome study of human mammary epithelial cells following exposure to polymeric Eudragit RS nanoparticles part 2

status: Public on Aug 01 2013

city: Nancy

first: Bertrand

last: Rihn

address: 5 rue A Lebrun

department: Faculté de Pharmacie

institute: Université de Lorraine

summary: To further study the transcriptome of human mammary epithelial cells (HMEC 184) after exposure to polymeric Eudragit RS nanoparticles (ENP), we investigate whole genome microarray expression to identify genes regulated by exposure or not to ENP.

overall_design: Changes in gene expression in HMEC 184 cells (90 % confluence) incubated with 25 µg/mL ENPs (70 nm) for 24 h, and without incubation (control) were measured. Three biological replicates were performed as controls (US_09; US_10; US_11) and ENP exposed ones (US_12; US_13; US_14).

first: Carole

last: Ronzani

first: Olivier

last: Joubert

first: Rajaa

last: Hussien

first: George

last: Brooks


title: Identification of a Unique TGF-β Dependent Molecular and Functional Signature in Microglia

status: Public on Jul 08 2013

city: Boston

first: Oleg

last: Butovsky

address: 77 Avenue Louis Pasteur, Office 614

department: Center of Neurologic Diseases

institute: Brigham and Women's Hospital, Harvard Medical School

summary: Microglia are myeloid cells of the central nervous system (CNS) that participate both in normal CNS function and disease. We investigated the molecular signature of microglia and identified 239 genes and 8 microRNAs that were uniquely or highly expressed in microglia vs. myeloid and other immune cells. Out of 239 genes, 106 were enriched in microglia as compared to astrocytes, oligodendrocytes and neurons. This microglia signature was not observed in microglial lines or in monocytes recruited to the CNS and was also observed in human microglia. Based on this signature, we found a crucial role for TGF-β in microglial biology that included: 1) the requirement of TGF-β for the in vitro development of microglia that express the microglial molecular signature characteristic of adult microglia; and 2) the absence of microglia in CNS TGF-β1 deficient mice. Our results identify a unique microglial signature that is dependent on TGF-β signaling which provides insights into microglial biology and the possibility of targeting microglia for the treatment of CNS disease.

overall_design:
miRNA/gene expression profiles of microglia during development and adult mice.
MG400 custom-design Nanosting chips, miRNA chips and Afymetrix arrays were used to identify unique molecular microglia signature in microglia as compared to immune and neural cells.
Total RNA was isolated from FACS sorted adult FCRLS+ microglia, neuroglial cells and immune cells. Total RNA was extracted using mirVanaTM miRNA isolation kit (Ambion) according to the manufacturer's protocol. nCounter Nansotring custom-made MG400 chip and nCounter Mouse miRNA Assay Kit were used for gene and miRNA expression profile.


title: Transcriptome study of human mammary epithelial cells following exposure to polymeric Eudragit RS nanoparticles

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

overall_design: Refer to individual Series


title: Conditional knockdown of DNA methyltransferase-1 (Dnmt1) reveals a key role of retinal pigment epithelium integrity in photoreceptor outer segment morphogenesis

status: Public on Jan 31 2013

city: Bethesda

first: Matthew

middle: J

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

summary: To explore the epigenetic contribution to retinal development, we generated conditional knockout alleles of DNA methytransferase-1 (Dnmt1) mediated by Rx-Cre in mice.  The results demonstrate a unique function of DNMT1-mediated DNA methylation in controlling RPE apicobasal polarity and neural retina differentiation.

overall_design: Retinal samples were harvested from both Dnmt1 mutant and wt animals at embryonic day 16.5 and postnatal days 0.5, 6.5, and 10.5 for microarray analysis.  Each experiment was performed with biological quadruplicates.  One microgram of total RNA was used for cDNA systhesis in target molecule production.

first: Igor

middle: O

last: Nasonkin

first: Shannath

last: Merbs

first: Kevin

last: Lazo

first: Verity

last: Oliver

first: Krushangi

last: Patel

first: Raymond

last: Enke

first: Jacob

last: Nellissery

first: Milan

last: Jamrich

first: Yun

middle: Z

last: Le

first: Kapil

last: Bharti

first: Robert

last: Faris

first: Rivka

last: Rachel

first: Donald

last: Zack

first: Enrique

last: Rodriguez-Boulan

first: Anand

last: Swaroop


title: Transcriptome study of human mammary epithelial cells following exposure to polymeric Eudragit RS nanoparticles part 1

first: Bertrand

last: Rihn

overall_design: Changes in gene expression in HMEC 184 cells (50 % confluence) incubated with 25 µg/mL ENPs (70 nm) for 24 h, and without incubation (control) were measured. Three biological replicates were performed as controls (US_01; US_02; US_04) and ENP exposed ones (US_6; US_07; US_08).

first: Carole

last: Ronzani

first: Olivier

last: Joubert

first: Rajaa

last: Hussien

first: George

last: Brooks


title: Let-7 represses Nr6a1 and a mid-gestation developmental program in adult fibroblasts [Exon array]

status: Public on Apr 10 2013

first: A

last: Bhutkar

address: 77 Massachusetts Avenue

institute: MIT

summary: MicroRNAs (miRNAs) are critical to proliferation, differentiation, and development. Here, we characterize gene expression in murine Dicer-null adult mesenchymal stem cell lines, a fibroblast cell type.  Loss of Dicer leads to de-repression of let-7 targets at levels that exceed 10-100 fold with increases in transcription.  Direct and indirect targets of this miRNA belong to a mid-gestation embryonic program that encompasses known oncofetal genes as well as oncogenes not previously associated with an embryonic state.  Surprisingly, this mid-gestation program represents a distinct period that occurs between the pluripotent state of the inner cell mass at embryonic day 3.5 and the induction of let-7, upon differentiation, at embryonic day 10.5.  Within this mid-gestation program, we characterize the let-7 target Nr6a1, an embryonic transcriptional repressor that regulates gene expression in adult fibroblasts following miRNA loss.  In total, let-7 is required for the continual suppression of embryonic gene expression in adult cells, a mechanism that may underlie its tumor suppressive function.

overall_design: 2 monoclonal mesenchymal cell lines (clones 6 and 12) with Dicer and 4 derivative clones (6.8, 6.9, 12.2 and 12.4) lacking Dicer, all passaged under normal, untreated culture conditions.

first: Allan

last: Gurtan

first: Arvind

last: Ravi

first: Peter

middle: B

last: Rahl

first: Andrew

middle: D

last: Bosson

first: Courtney

middle: K

last: JnBaptiste

first: Arjun

first: Charles

last: Whittaker

first: Richard

last: Young

first: Phillip

last: Sharp


title: Sicd2 mouse hippocampus exon array analysis

status: Public on Jun 07 2013

city: Los Angeles

first: Paula

middle: Elyse

last: Schauwecker

address: 1333 San Pablo Street, BMT 403

department: Cell and Neurobiology

institute: University of Southern California

summary: We used Affymetrix Mouse Exon 1.0 ST arrays to identify potential changes in alternative splicing between a subcongenic interval of the QTL Sicd2 on Chr 15 and their FVB-like littermates.  Results implicate novel candidate genes conferring susceptibility to seizure-induced cell death.

overall_design: Total RNA was extracted from the hippocampus of 8 Sicd2-ISCL4 subcongenic mice and 8 FVB-like littermates.

first: P

middle: E


title: Nkx2.1 represses a latent gastric differentiation program in lung adenocarcinoma

middle: Arthur

institute: Koch Institute

summary: During cancer evolution, cellular differentiation programs become dysregulated. The transcription factor Nkx2-1 is a master regulator of pulmonary differentiation that is downregulated in poorly differentiated lung adenocarcinoma.  Here we use conditional murine genetics to study the fate of lung epithelial cells upon loss of their master cell fate regulator.  Nkx2-1 deletion in normal and neoplastic lung causes not only loss of pulmonary identity but also gastric transdifferentiation.  Nkx2-1 maintains pulmonary identity by sequestering the Foxa1 transcription factor at lung-specific loci and inhibiting Foxa1 binding to gastrointestinal targets.  Murine Nkx2-1-negative lung tumors mimic the mucinous subtype of human lung adenocarcinoma, which also exhibits gastric transdifferentiation.  Nkx2-1-negative lung adenocarcinomas are dependent on the gastrointestinal gene Hnf4a for efficient initiation.  Thus, loss of Nkx2-1 results in transdifferentiation rather than stable dedifferentiation in vivo, suggesting that inactivation of both active and latent differentiation programs may be required for tumors to reach a primitive, dedifferentiated state.

overall_design: The study was designed to compare the expression profiles of Nkx2-1-positive lung adenocarcinomas with tumors in which Nkx2-1 was deleted at the time of initiation or 6-7 months after initiation.

first: Eric

last: Snyder

first: Margaret

last: Magendantz

first: Diana

middle: G

last: Wang

first: Denise

last: Crowley

first: Sebastian

last: Hoersch

middle: A

first: Shioko

last: Kimura

first: Tyler

last: Jacks


title: Expression data from P0 forebrain of wild-type and Elavl3/Elavl4 double knockout mice.

status: Public on Jan 05 2013

city: Helsinki

first: Gulayse

last: Ince Dunn

state: Finland

address: Haartmaninkatu 8

department: Stem Cells and Metabolism Program

country: Finland

institute: University of Helsinki

summary:
Neuronal Elavl-like (nElavl) RNA binding proteins have three paralogs (Elavl2, Elavl3 and Elavl4) in the mouse genome. This family of RNABPs have been implicated in a variety of post-transcriptional RNA processing mechanisms, including regulation of mRNA stability, alternative splicing, and translational regulation.
In this study, using mouse exon arrays, we identify significant differences (p<0.01) in 119 transcripts between wild-type and Elavl3/Elavl4 double knockout forebrain tissue at postnatal day 0.

overall_design: A total of 10 samples were analyzed.  These samples consisted of 5 littermate pairs of wild-type and Elavl3/Elavl4 double knockout mice.

middle: I

last: Dunn

first: Robert

last: Darnell


title: Loss of MeCP2 function is associated with distinct gene expression changes in the striatum

status: Public on Jul 13 2013

city: Old Westbury

first: Ying-Tao

last: Zhao

state: NY

address: Riland building, Room 024 Northern Boulevard, P.O. Box 8000

department: Biomedical Sciences

institute: New York Institute of Technology

summary:
Rett syndrome (RTT) is a neurodevelopmental disorder characterized by developmental regression around 6-18 months after birth, followed by a lifetime of intellectual disability, stereotyped behaviors, and motor deficits. RTT is caused by mutations in MeCP2, a methyl-CpG binding protein that was traditionally believed to repress gene expression. Gene expression studies of individual brain regions, however, have revealed that MeCP2 loss-of-function leads to the subtle activation and repression of its gene targets. However, these results may be confounded by the extensive neuronal cell heterogeneity inherent in these brain structures.
To minimalize this issue of heterogeneity, we assessed whether Mecp2-null mice exhibited alterations in gene expression patterns in the striatum, a brain nucleus with relatively homogenous neuronal types and is highly relevant to the motor deficits observed in RTT. Despite the homogeneity of the tissue, the fold-change of the 127 differentially expressed genes we identified remained low with a mean change consistent with other studies. However, many of those genes differentially expressed in the striatum have not been previously identified in gene expression analyses of other brain regions. This suggests therefore that the differential expression of genes following loss of MeCP2 occurs in a tissue, or cell-type specific manner and thus MeCP2 function should be understood in a cellular context.

overall_design: In initiating this study, we reasoned that reducing the number of cell types in a microarray experiment may reveal transcriptional changes that are masked in a whole tissue analysis. We therefore focused on tissues more homogeneous in regards to the  diversity of neuronal cell types they contain in order to discern gene expression changes in the absence of MeCP2. We chose to isolate the striatum, a tissue composed predominantly of GABAergic medium spiny neurons (MSNs). The striatum was resected from five symptomatic Mecp2-null (KO) male mice bearing the Bird allele and five wild-type (WT) littermates in a C57BL/6 background. We also isolated liver from the same individuals to serve as a non-neuronal control. RNA was isolated from these tissues, converted to cDNA, and hybridized to a single-channel Affymetrix GeneChip Mouse Exon 1.0 ST array for a total of 20 individual arrays.

first: Brian

last: Johnson

first: Zhaolan

last: Zhou


title: Early limb bud transcriptome analysis between anterior and posterior domain

status: Public on Jan 06 2013

city: Nashville

first: jiang

last: liu

state: TN

address: 465 21st ave south, MRB3 RM4114

department: cell and dvelopmental biology

institute: vanderbilt university

summary: Shh signal mediated by Gli family of transcription factors regulates digit growth and patterning in early limb development. Shh expression in the posterior margin of the limb bud defines the zone of polarizing activity. However, much less is know about downstream targets that mediate Shh signal functions. In this dataset, we include the expression data obtained from dissected anterior and posterior halves of mouse limb bud respectively. These data are used to obtain 889 transcripts that were upregulated 1.3 fold or more in the posterior limb bud, and 1189 transcripts that were enriched in the anterior limb bud at 1.3 fold or more.

overall_design: Two samples were analyzed. We generate pairwise comparisons between anterior and posterior limb tissues. Genes with a fold-change ≥1.3 were selected.

first: Jiang

last: Liu

first: Chin

last: Chiang


title: Molecular characterisation of transport mechanisms at the developing mouse blood-CSF interface: a transcriptome approach

status: Public on Jan 01 2013

city: Parkville

first: Shane

last: Liddelow

state: Victoria

address: Level 8 Medical Building, Grattan Street

department: Pharmacology

country: Australia

institute: The University of Melbourne

summary: Transcriptome analysis of lateral ventricular choroid plexus epithelial cells of embryonic day 15 (E15) and adult mice.

overall_design: We analyzed total RNA extracted from plexus epithelial cells from 6 pooled samples (3 E15, 3 adult) using the Affymetrix Mouse Exon 1.0 ST platform.

first: Sally

last: Temple

first: Kjeld

last: Møllgård

first: Renate

last: Gehwold

first: Andrea

last: Wagner

first: Hannelore

last: Bauer

first: Hans

first: Timothy

last: Phoenix

first: Katarzyna

middle: M

last: Dziegielewska

first: Norman

middle: R

last: Saunders


title: Acute and long-term effects of mutant p53 in vivo [B cells]

status: Public on Dec 31 2012

city: Singapore

first: Kanaga

last: Sabapathy

state: Singapore

address: 11 Hospital Drive

institute: National Cancer Centre Singapore

summary: The specific roles of mutant p53’s dominant-negative (DN) or gain-of-function (GOF) properties in regulating acute response and long-term tumorigenesis is unclear.   Using “knock-in” mouse strains expressing varying R246S mutant levels, we show that DN effect on transactivation is universally observed after acute p53 activation whereas the effect on cellular outcome is cell-type specific.  Reducing mutant p53 levels abrogated the DN effect.   Mutant p53’s DN effect protected against radiation-induced death, but did not accentuate tumorigenesis.  Furthermore, the R246S mutant did not promote tumorigenesis compared to p53-/- mice in various models, even in the absence of MDM2, unlike the R172H mutant.  Together, these data demonstrate that mutant p53’s DN property only affects acute responses, whereas GOF is not universal, being mutation-type specific.

overall_design: Transcriptomes of 4 samples of normal B cells and 12 Myc-induced B lymphoma cells harvested from mice of different p53 genotypes were profiled.  Data was analysed by mixed model ANOVA using Partek.

first: Ming

last: Lee

first: Wei

middle: W

last: Teoh


title: Acute and long-term effects of mutant p53 in vivo [MEF]

overall_design: Transcriptomes of mouse embryonic fibroblasts harvested from embyros of different p53 genotypes were profiled.  A total of 6 primary clones of MEFs were used and these cells were transformed with E1A/Ras.  Data was analysed by mixed model ANOVA using Partek.