title: Global gene expression analysis of fresh-frozen, furan-exposed mouse liver using one-colour Agilent microarrays

first: Anna

last: Jackson

summary: Furan is a mouse and rat hepatocarcinogen. We sought to determine if furan-induced gene expression changes could be detected in paired fresh-frozen and formalin-fixed paraffin embedded (FFPE) samples using one-colour microarrays.  All samples in this study (fresh-frozen, 18 hours in formalin, 3 weeks in formalin) were also examined using two-colour microarrays and RNA-seq (ribo-depletion and polyA-enrichment protocols) in order to determine the effect of the technology on gene expression profiles.

overall_design: In this study we examined the transcriptional response in liver tissue of female B6C3F1 mice exposed to furan for 3 weeks to 8 mg/kg bw furan (or vehicle control) and sacrificed four hours after the final exposure.  Each dose group had 4 biological replicates. There were a total of 8 samples included in the final analysis of the one-colour microarrays. We used a randomized block design and SurePrint G3 Mouse GE 8x60K microarrays (Agilent).

first: A

last: Webster

first: Andrew

last: Williams

first: Leslie

last: Recio

first: Carole

middle: L

last: Yauk


title: Disruption of histone methylation in developing sperm impairs offspring health transgenerationally [sperm]

status: Public on Oct 08 2015

city: Ste-anne-de-Bellevue

first: Sarah

last: Kimmins

state: Quebec

address: 21,111 Rue Lakesshore

country: Canada

institute: McGill University

summary:
A father’s lifetime experiences can be transmitted to his offspring to affect
health and development. The mechanisms underlying paternal epigenetic
transmission are unclear. Unlike somatic cells, there are few nucleosomes
in sperm and their function in epigenetic inheritance is unknown. We
generated transgenic mice in which overexpression of the histone H3 lysine
4 (H3K4) demethylase LSD1/KDM1A during spermatogenesis reduced
H3K4 dimethylation in sperm. KDM1A overexpression in one generation
severely impaired development and survivability of offspring. These
defects persisted transgenerationally in the absence of KDM1A germ line
expression and were associated with altered RNA profiles in sperm and
offspring. We show that epigenetic inheritance of aberrant development
can be initiated by histone demethylase activity in developing sperm,
without changes to DNA methylation at CpG-rich regions.

overall_design: Identification of the RNA population in sperm of wildtype mice, KDM1A transgenic mice and their non-transgenic littermates using gene expression array.

first: Keith

last: Siklenka

first: Serap

last: Erkek

first: Antoine

middle: H

last: Peters


title: Disruption of histone methylation in developing sperm impairs offspring health transgenerationally

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

overall_design: Refer to individual Series


title: Disruption of histone methylation in developing sperm impairs offspring health transgenerationally [embryo]

overall_design: Identification of the RNA population in 2-cell embryos sired by wildtype mice, KDM1A transgenic mice and their non-transgenic littermates to C57BL/6 control females using gene expression array.


title: BCAT1 expression associates with ovarian cancer progression

status: Public on Oct 01 2015

city: Quebec

first: Dimcho

last: Bachvarov

address: 9, rue McMahon

institute: CHU-Q, Centre de recherche-HDQ

summary: Previously, we have identified cytosolic form of the branched chain amino-acid transaminase 1 (BCAT1) as notably hypomethylated in low-malignant potential (LMP) and high-grade (HG) serous epithelial ovarian tumors, compared to normal ovarian tissues. Here we show that BCAT1 is strongly overexpressed in both LMP and HG serous EOC tumors, thus suggesting that epigenetic mechanisms might be implicated in BCAT1 overexpression in serous epithelial ovarian cancer (EOC). Knockdown of the BCAT1 expression in EOC cells led to sharp decrease of cell proliferation and induced S-phase cell cycle arrest. Additionally, BCAT1 suppression significantly inhibited EOC cell migration and invasion. Gene expression profiling and consecutive network and pathway analyses confirmed these findings, as numerous genes and pathways known previously to be implicated in ovarian tumorigenesis, including EOC tumor invasion and metastasis, were found to be downregulated upon BCAT1 suppression, while some tumor suppressor genes were induced.   Taken together, our data are indicative for a strong oncogenic potential of the BCAT1 gene in advanced EOC and identify this transaminase as a novel EOC biomarker and putative EOC therapeutic target.

overall_design: To better understand the molecular mechanisms of BCAT1 gene action in ovarian cancer cells, we employed the Agilent Whole Human Genome microarrays, containing ~ 44,000 genes to identify global gene expression changes upon BCAT1 suppression in SKOV3 cells. We compared the gene expression of the previously selected clone shRNA-mediated BCAT1-knockdown SKOV3 clones B1 & B2 (sh-clB1 & sh-clB2) against the corresponding control (ctrl) clone. The microarray experiments were performed in duplicates, as four hybridizations were carried out for the BCAT1-suppressing cell clones against the corresponding control, using a fluorescent dye reversal (dye-swap) technique.


title: The epigenetic processes of meiosis in male mice are broadly affected by the widely used herbicide atrazine [Affymetrix]

city: rennes

first: Chunxiang

last: HAO

address: 263, ave du Général Leclerc

country: France

institute: Université de Rennes 1

summary: Environmental factors such as pesticides are widely used in the agriculture of many countries and their negative impact on human health and fertility are largely unknown. There is a rapidly growing body of evidence that human reproductive health is negatively affected by the various environmental factors, including life style and exposure to the chemical compounds such as certain drugs and pesticides. Sexually reproducing organisms produce haploid gametes via a process called meiosis. Meiosis is dependent on androgen action within the testis. Pesticides and herbicides interfere with natural hormones system and are considered to be endocrine disruptors. We hypothesize that atrazine (ATZ), a herbicide used globally, adversely affects meiosis. To test this idea we used the mouse as a model organism. Mice were treated three weeks with atrazine in drinking water at concentration of 100 mg/l. To assess the molecular mechanisms of effects of ATZ on spermatogenesis we performed comparative analysis of genes expression by using Affymetrix microarray by using three biological testis samples from ATZ treated and control mice. Using a fold-change cutoff value of 1.5 and p value <0.05 (statistical Limma test (linear models test for microarray data)), we identified 51 genes that were differentially expressed in ATZ treated mice.

overall_design: To assess molecular mechanism of effects of ATZ on spermatogenesis we performed comparative analysis of genes expression by using Affymetrix microarray

last: Hao

first: Fatima

last: Smagulova

first: Aurore

last: Gely-Pernot


title: Gene expression signatures for human iPSC and ESC lines

status: Public on Oct 28 2015

city: Tsukuba

first: Yuzuru

last: Ito

state: Ibaraki

address: Central 6, Higashi 1-1-1

department: Biotechnology Research Institute for Drug Discovery

country: Japan

institute: National Institute of Advanced Industrial Science and Technology (AIST)

summary: In comprehensive glycome analysis with a high-density lectin microarray, we have previously shown that the recombinant N-terminal domain of the lectin BC2L-C from Burkholderia cenocepacia (rBC2LCN) binds exclusively to undifferentiated human induced pluripotent stem (iPS) cells and embryonic stem (ES) cells but not to differentiated somatic cells. Here we demonstrate that podocalyxin, a heavily glycosylated type1 transmembrane protein, is the predominant glycoprotein ligand of rBC2LCN on human iPS cells and ES cells. When analyzed by DNA microarray, podocalyxin was found to be highly expressed in both iPS cells and ES cells. Western and lectin blotting revealed that rBC2LCN binds predominantly to podocalyxin with a high molecular weight of more than 240 kDa in undifferentiated iPS cells of six different origins and four ES cell lines, but no binding was observed in either differentiated mouse feeder cells or somatic cells. The specific binding of rBC2LCN to podocalyxin prepared from a large set of iPS cells (138 types) and ES cells (15 types) was also confirmed using a high-throughput antibody-overlay lectin microarray. Alkaline digestion greatly reduced the binding of rBC2LCN to podocalyxin, indicating that the major glycan ligands of rBC2LCN are presented on O-glycans. Furthermore, rBC2LCN was found to exhibit significant affinity to a branched Oglycan comprising an H type3 structure as the most probable rBC2LCN glycan ligand (Kd, 4.0 x 10-5 M) prepared from human 201B7 iPS cells, suggesting that H type3 is a novel potential pluripotency marker. We conclude that podocalyxin is the predominant glycoprotein ligand of rBC2LCN on human iPS cells and ES cells.

overall_design: Gene expressions in human embryonic stem cells (ESCs) and human induced pluripotent stem cells (iPSCs). Human iPS cells (MRC5-iPS, AM-iPS, UtE-iPS, PAE-iPS) were induced from four different somatic cells by infection of the retroviral vectors pMXs encoding OCT3/4, SOX2, KLF4 and c-MYC, simultaneously. Human iPS cells (TIG/MKOS#19, #56, #106) were generated through reprogramming by Sendai virus infection-mediated expression of OCT4, SOX2, KLF4, and c-MYC.

first: Yasuko

last: Onuma


title: Epithelial inactivation of Yy1 abrogates lung branching morphogenesis

status: Public on Oct 20 2015

city: Lausanne

first: Eric

middle: R

last: Paquet

state: Vaud

address: Station 15  CH - 1015

department: Life sciences

country: Switzerland

institute: EPFL

summary: Yin Yang 1 (YY1) is a multifunctional zinc-finger-containing transcription factor that  plays crucial roles in numerous biological processes by selectively activating or repressing transcription, depending upon promoter contextual differences and specific protein interactions. In mice, Yy1 null mutants die early in gestation while Yy1 hypomorphs die at birth from lung defects. We studied how the epithelial-specific inactivation of Yy1 impacts on lung development. The Yy1 mutation in lung epithelium resulted in neonatal death due to respiratory failure. It impaired tracheal cartilage formation, altered cell differentiation, abrogated lung branching, and caused airway dilation similar to those seen in human congenital cystic lung diseases. The cystic lung phenotype in Yy1 mutants can be explained by the reduced expression of Shh in lung endoderm, a transcriptional target of YY1, and the subsequent derepression of mesenchymal Fgf10 expression. Accordingly, SHH supplementation partially rescued the lung phenotype in vitro. Analysis of human lung tissues revealed decreased YY1 expression in children with pleuropulmonary blastoma (PPB), a rare pediatric lung tumor arising during fetal development and associated with DICER1 mutations. No evidence for a potential genetic interplay between murine Dicer and Yy1 genes during lung morphogenesis was observed. However, the cystic lung phenotype resulting from the epithelial inactivation of Dicer function mimics the Yy1 lung malformations with similar changes in Shh and Fgf10 expression. Together, our data demonstrate the critical requirement for YY1 in lung morphogenesis and identify Yy1 mutant mice as a potential model for studying the genetic basis of PPB.

overall_design: Total RNA was isolated from lungs of E14.5 Shh+/Cre embryos (control), from E14.5 Shh+/Cre;Yy1flox/flox embryos (experimental), and from E14.5 Shh+/Cre;Dicerflox/flox embryos (experimental). Four specimens were analyzed per genotype.

first: Lucie

last: Jeannotte

first: Jean

last: Charron

first: Olivier

last: Boucherat


title: Activin/Nodal signaling supports retinal progenitor specification in a narrow time window during pluripotent stem cell differentiation to anterior neuroectoderm

city: Genova

first: Luca

last: Pandolfini

state: Genova

address: Via Enrico Melen 83, Building B

department: Center for Human Technologies

country: Italy

institute: Istituto Italiano di Tecnologia - I

summary: In this study, we used chemically-defined media to induce the in vitro differentiation of mouse embryonic stem cells (ESCs) towards eye field fates. Inhibition of Wnt/ß-Catenin signalling was sufficient to drive ESCs to telencephalic, but not retinal fates. Instead, retinal progenitors could be generated from competent differentiating mouse and human ESCs by the activation of Activin/Nodal signaling within a narrow temporal window corresponding to the emergence of primitive anterior neural progenitors. Our results reveal insights into the mechanisms of eye field specification and open new avenues towards the generation of retinal progenitors for translational medicine.

overall_design: Gene expression was evaluated in sorted RAX::GFP-positive and -negative ES cells at 10 days of in vitro differentiation upon treatment with Wnt inhibitor and Activin A or Sonic Hedgehog Agonist; global profiles were compared to E12.5 mouse embryo cortex, hypothalamus/diencephalon and eye.

first: Michele

last: Bertacchi

first: Giuseppe

last: Lupo

first: Simona

last: Casarosa

first: Mara

last: D'Onofrio

first: Roger

middle: A

last: Pedersen

first: William

last: Harris

first: Federico

last: Cremisi


title: Global gene expression analysis of formalin-fixed paraffin-embedded (FFPE), furan-exposed mouse liver using two-colour Agilent microarrays

status: Public on Oct 14 2015

city: Ottawa

first: Anna

middle: Francina

last: Jackson

state: Ontario

address: 50 Colombine Drive, Tunney's Pasture

department: Environmental Health Center

institute: Health Canada

summary: Furan is a mouse and rat hepatocarcinogen. We sought to determine if furan-induced gene expression changes could be detected in paired fresh-frozen (GSE48644) and formalin-fixed paraffin embedded (FFPE; this study) samples using two-colour microarrays.  To determine the effect of time-in-formalin on gene expression signatures we performed microarray analysis of livers that were fixed in formalin for 18 hours or 3 weeks. All samples (fresh-frozen, 18 hours in formalin, 3 weeks in formalin) were also examined using one-colour microarrays and RNA-seq (ribo-depletion and polyA-enrichment protocols) in order to determine the effect of the technology on gene expression profiles.

overall_design: In this experiment we examined the transcriptional response of liver tissue of female B6C3F1 mice exposed to furan for 3 weeks to 8 mg/kg bw furan (or vehicle control) and sacrificed four hours after the final exposure.  Each dose group had 4 biological replicates. Samples were formalin-fixed (for 18hrs or 3wks) and paraffin embedded. There were a total of 8 samples included in the final analysis of the two-colour microarrays. We used a reference design (using pooled sample cDNA as a reference), randomized block design and SurePrint G3 Mouse GE 8x60K microarrays (Agilent).

first: A

middle: F

last: Webster

first: Andrew

last: Williams

first: Leslie

last: Recio

first: Carole

last: Yauk


title: Sub-chronic transcriptional response in adult male MutaTMMouse following oral exposure to 7 individual PAHs in the lung, liver, and forestomach tissues

first: Sarah

last: Labib

address: 204b-50 Colombine


title: Sub-chronic transcriptional response in adult male MutaTMMouse following oral exposure to benzo(k)fluoranthene in lung, liver, and forestomach tissues [BkF]

summary: Polycyclic aromatic hydrocarbons (PAHs) are a class of hundreds of structurally similar chemicals ubiquitously present in our environment. They are created during the incomplete combustion of organic materials, such as oil, wood, tobacco, and charbroiled meat. As such, human exposure to mixtures of PAHs can occur through consumption of PAH-containing foods and water, inhalation of polluted air, or dermal contact. Several PAHs have been classified as carcinogenic to humans or probably carcinogenic to humans by the International Agency for Research on Cancer. Benzo(k)fluoranthen is one such compound. In the present study, we sought to determine the dose-dependent changes in gene expression upon oral exposure to benz(a)anthracene in the lung, liver, and forestomach tissues. Adult male MutaTMMouse were exposed to three doses of benzo(k)fluoranthene or vehicle control (olive oil) for 28 days and sacrificed three days after the final exposure.

overall_design: This experiment examined the pulmonary, hepatic, and forestomach transcriptional response of male mice exposed to benzo(k)fluoranthene  for 28 days at three different doses, including D1 (25 mg/kg-bw/day), D2 (50 mg/kg-bw/day), and D3 (100 mg/kg-bw/day) and vehicle control (D0).  Each dose group was examined 72 hours following the final exposure.  Each dose group had 2-4 biological replicates. There were a total 15, 13, and 14 samples (arrays) from the lung, liver, and forestomach, respectively, included in the final analysis using a two-colour reference design.

first: Sabina

last: Halappanavar

first: Charles

last: Guo


title: Murine fibroblast-like synoviocytes: Control vs Ad-Epas1 infected

status: Public on Oct 02 2015

city: Gwangju

first: Jang-Soo

last: Chun

department: School of Life Science

country: South Korea

institute: Gwangju institute of science and technology

summary: Transcriptional profiling of mouse fibroblast-like synoviocytes (FLS) comparing FLS infected with empty adenovirus and Epas1 adenovirus. RNA was extracted from each FLS. We used microarrays to determine the effect of Epas1 overexpression on FLS and identifying the noble regulatory molecules during rheumatoid arthritic pathogenesis

overall_design: Two-condition experiment, Mock vs. Ad-Epas1 FLS. Biological replicates: 3 mock adenoviral infected replicates, 3 Ad-Epas1 infected replicates.

first: Je-Hwang

last: Ryu


title: Gene expression signature of in vitro activated CD8 T cells in response to antigen and B7-1 alone or along with IL-21

status: Public on Sep 30 2015

city: Minneapolis

first: Lynn

last: Heltemes Harris

state: MN

address: 2101 6th St. SE

country: USA

institute: University of Minnesota

summary:
Differentiation of naive CD8 T cells into cytotoxic effector cells requires three distinct signals- antigen (signal 1), costimulation -B7-1 (signal 2) and cytokine, either interleukin-12, interferon-a/b, or IL-21 (signal 3). Interaction of naive CD8 T cells with antigen and B7-1 programs cell division and proliferation whereas the presence of cytokines- IL-12, IFNa/b or IL-21 promote survival, differentiation and memory establishment. In the absence of signal 3, the cells interacting with antigen/B7-1 undergo tolerance induction. Previous work had analyzed the regulation of mRNA expression changes induced by IL-12 and IFN-a and cells stimulated with antigen, B7-1 and cytokine by comparing mRNA expression levels in naïve CD8 T cells, cells stimulated with 2 signals (antigen and B7-1) (Agarwal, P.A., A. Raghavan, S.L. Nandiwada, J.M. Curtsinger, P.R. Bohjanen, D.L. Mueller and M.F. Mescher.  Gene regulation and chromatin remodeling by IL-12 and Type I interferon in programming for CD8 T cell effector function and memory.  J. Immunol. 183:1695-1704 (2009).  PMCID: PMC2893405). That microarray data was deposited in the NCI GEO database and can be found at http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc_GSE15930.
The objective of the current study was to carry out the same analysis to determine IL-21-dependent changes in mRNA expression in CD8 T cells responding to antigen and B7-1-dependent costimulation in the absence or presence of IL-21.

overall_design: The programming for development of function and memory in presence of signal 3 occurs over three days of initial stimulation, and antigen, B7-1 and either IL-12, IFNa/b or IL-21 must be present for most of this period to achieve maximal responses. We analyzed gene expression at 48 and 72 hours in cells stimulated in vitro with antigen and B7-1 alone or along with IL-21.

first: Pujya

last: Agarwal

first: Matthew

last: Mescher


title: Sub-chronic transcriptional response in adult male MutaTMMouse following oral exposure to indeno(123,cd)pyrene in lung, liver, and forestomach tissues [IP]

summary: Polycyclic aromatic hydrocarbons (PAHs) are a class of hundreds of structurally similar chemicals ubiquitously present in our environment. They are created during the incomplete combustion of organic materials, such as oil, wood, tobacco, and charbroiled meat. As such, human exposure to mixtures of PAHs can occur through consumption of PAH-containing foods and water, inhalation of polluted air, or dermal contact. Several PAHs have been classified as carcinogenic to humans or probably carcinogenic to humans by the International Agency for Research on Cancer. Indeno(123,cd)pyrenee is one such compound. In the present study, we sought to determine the dose-dependent changes in gene expression upon oral exposure to benz(a)anthracene in the lung, liver, and forestomach tissues. Adult male MutaTMMouse were exposed to three doses of indeno(123,cd)pyrene or vehicle control (olive oil) for 28 days and sacrificed three days after the final exposure.

overall_design: This experiment examined the pulmonary, hepatic, and forestomach transcriptional response of male mice exposed to indeno(123,cd)pyrene for 28 days at three different doses, including D1 (12.5 mg/kg-bw/day), D2 (25 mg/kg-bw/day), and D3 (50 mg/kg-bw/day) and vehicle control (D0).  Each dose group was examined 72 hours following the final exposure.  Each dose group had 4-5 biological replicates. There were a total 20, 19, and 20 samples (arrays) from the lung, liver, and forestomach, respectively, included in the final analysis using a two-colour reference design.


title: Sub-chronic transcriptional response in adult male MutaTMMouse following oral exposure to dibenz(ah)anthracene in lung and forestomach tissues [DBahA]

summary: Polycyclic aromatic hydrocarbons (PAHs) are a class of hundreds of structurally similar chemicals ubiquitously present in our environment. They are created during the incomplete combustion of organic materials, such as oil, wood, tobacco, and charbroiled meat. As such, human exposure to mixtures of PAHs can occur through consumption of PAH-containing foods and water, inhalation of polluted air, or dermal contact. Several PAHs have been classified as carcinogenic to humans or probably carcinogenic to humans by the International Agency for Research on Cancer. Dibenz(ah)anthracene is one such compound. In the present study, we sought to determine the dose-dependent changes in gene expression upon oral exposure to benz(a)anthracene in the lung and forestomach tissues. Adult male MutaTMMouse were exposed to three doses of dibenz(ah)anthracene or vehicle control (olive oil) for 28 days and sacrificed three days after the final exposure.

overall_design:
This experiment examined the pulmonary and forestomach transcriptional response of male mice exposed to dibenz(ah)anthracene  for 28 days at three different doses, including D1 (6.25 mg/kg-bw/day), D2 (12.5 mg/kg-bw/day), and D3 (25 mg/kg-bw/day) and vehicle control (D0).  Each dose group was examined 72 hours following the final exposure.  Each dose group had 4-5 biological replicates. There were a total 19 and 19 samples (arrays) from the lung and forestomach, respectively, included in the final analysis using a two-colour reference design.
Please note that only lung and forestomach tissues were analyzed in this series of experiments. The liver from this project was previously submitted [GSE35509].


title: New functional signatures for understanding melanoma biology from tumor cell lineage-specific analysis

city: VILLEJUIF

first: Bastien

last: Job

address: 39 rue Camille Desmoulins

institute: Institut Gustave Roussy


title: Sub-chronic transcriptional response in adult male MutaTMMouse following oral exposure to benz(a)anthracene in lung, liver, and forestomach tissues

summary: Polycyclic aromatic hydrocarbons (PAHs) are a class of hundreds of structurally similar chemicals ubiquitously present in our environment. They are created during the incomplete combustion of organic materials, such as oil, wood, tobacco, and charbroiled meat. As such, human exposure to mixtures of PAHs can occur through consumption of PAH-containing foods and water, inhalation of polluted air, or dermal contact. Several PAHs have been classified as carcinogenic to humans or probably carcinogenic to humans by the International Agency for Research on Cancer. Benz(a)anthracene is one such compound. In the present study, we sought to determine the dose-dependent changes in gene expression upon oral exposure to benz(a)anthracene in the lung, liver, and forestomach tissues. Adult male MutaTMMouse were exposed to three doses of benz(a)anthracene or vehicle control (olive oil) for 28 days and sacrificed three days after the final exposure.

overall_design: This experiment examined the pulmonary, hepatic, and forestomach transcriptional response of male mice exposed to benz(a)anthracene for 28 days at three different doses, including D1 (20 mg/kg-bw/day), D2 (40 mg/kg-bw/day), and D3 (80 mg/kg-bw/day) and vehicle control (D0).  Each dose group was examined 72 hours following the final exposure.  Each dose group had 4-5 biological replicates. There were a total 20, 19, and 19 samples (arrays) from the lung, liver, and forestomach, respectively, included in the final analysis using a two-colour reference design.


title: Effects of hepatocyte-restricted Fra-1 overexpression on hepatic gene expression in High-fat diet (HFD) fed mice

city: Boston

first: Sebastian

middle: Christoph

last: Hasenfuss

address: 44 Binney Street

institute: Dana-Farber Cancer Institute

summary: Hepatic mRNA expression was compared between control and Fra-1hep mice, which were fed High fat diet (45%kcal fat)

overall_design: Liver RNA pooled from 5 HFD fed control mice (control pool) was Cy3-labeled and liver RNA from 4 individual Fra-1hep mice was Cy5-labeled. On each microarray, Cy3‐labeled control pool and one Cy5-labeled mutant sample were hybridized at 65°C for 17 hours.

middle: C


title: Sub-chronic transcriptional response in adult male MutaTMMouse following oral exposure to chrysene in lung, liver, and forestomach tissues [Chr]

summary: Polycyclic aromatic hydrocarbons (PAHs) are a class of hundreds of structurally similar chemicals ubiquitously present in our environment. They are created during the incomplete combustion of organic materials, such as oil, wood, tobacco, and charbroiled meat. As such, human exposure to mixtures of PAHs can occur through consumption of PAH-containing foods and water, inhalation of polluted air, or dermal contact. Several PAHs have been classified as carcinogenic to humans or probably carcinogenic to humans by the International Agency for Research on Cancer. Chrysene is one such compound. In the present study, we sought to determine the dose-dependent changes in gene expression upon oral exposure to benz(a)anthracene in the lung, liver, and forestomach tissues. Adult male MutaTMMouse were exposed to three doses of chrysene or vehicle control (olive oil) for 28 days and sacrificed three days after the final exposure.

overall_design: This experiment examined the pulmonary, hepatic, and forestomach transcriptional response of male mice exposed to chrysene for 28 days at three different doses, including D1 (17.5 mg/kg-bw/day), D2 (50 mg/kg-bw/day), and D3 (150 mg/kg-bw/day) and vehicle control (D0).  Each dose group was examined 72 hours following the final exposure.  Each dose group had 4-5 biological replicates. There were a total 18, 19, and 19 samples (arrays) from the lung, liver, and forestomach, respectively, included in the final analysis using a two-colour reference design.


title: The Immunobiology of Aging [I]

status: Public on Sep 16 2015

city: palo alto

first: weiqi

last: wang

state: ca

address: 1291 welch road

institute: stanford

summary: The overriding objective of this application is to seek funding for the development of a crossectional profile of immune phenotype of over 600 normal subjects between the ages of 50 and 90. As a consequence, we will infer changes in immune phenotype of normal subjects as they age. These immune phenotypic data, as well as standard laboratory tests and evaluations of questionnaires, will be used to generate a large and comprehensive database of demographic and biological information. The proposal utilizes the strengths of the Stanford Human Immune Monitoring Core (HIMC) and the unique expertise in basic immunology, immune monitoring, the development of patient registries, biostatistics and bioinformatics at Stanford.

overall_design: The dataset will comprise a crossectional analysis of the local San Francisco Peninsula general population between the ages of 50 and 90 (representing equal gender and representative ethnic population, and equal distribution by decade of life). The registry will contain demographic data, race/ethnicity, prescribed medications, over the counter medications, vitamins, alternative therapies, physical function questionnaire, alternative contact person, and HIPPA release. Fasting blood will be obtained for immune phenotyping. The immune profile will contain the results of both conventional and novel immune profiling assays to develop the normative immune profile of aging (using PBMC subset analysis, cytokines, and activation induced signaling of PBMCs for phosphoepitope and gene expression analyses). Data from these analyses will be useful in identifying biomarkers of the normal immune profile associated with aging as well as correlation with phenotypic aspects of aging such as sarcopenia and disability The immune profile (as well as normal blood chemistries and demographic data) of these subjects will be made available to serve as the basis for future longitudinal study of change in the immune profile over time in association with the development of co-morbidities associated with aging. in the PBMC gene expression, 120 samples were analyzed (no replicates), containing patients and controls.

first: Garry

last: Fathman


title: Sub-chronic transcriptional response in adult male MutaTMMouse following oral exposure to benzo(ghi)perylene in lung, liver, and forestomach tissues [BghiP]

summary: Polycyclic aromatic hydrocarbons (PAHs) are a class of hundreds of structurally similar chemicals ubiquitously present in our environment. They are created during the incomplete combustion of organic materials, such as oil, wood, tobacco, and charbroiled meat. As such, human exposure to mixtures of PAHs can occur through consumption of PAH-containing foods and water, inhalation of polluted air, or dermal contact. Several PAHs have been classified as carcinogenic to humans or probably carcinogenic to humans by the International Agency for Research on Cancer. benzo(ghi)perylene is one such compound. In the present study, we sought to determine the dose-dependent changes in gene expression upon oral exposure to benz(a)anthracene in the lung, liver, and forestomach tissues. Adult male MutaTMMouse were exposed to three doses of benzo(ghi)perylene or vehicle control (olive oil) for 28 days and sacrificed three days after the final exposure.

overall_design: This experiment examined the pulmonary, hepatic, and forestomach transcriptional response of male mice exposed to benzo(ghi)perylene for 28 days at three different doses, including D1 (6.25 mg/kg-bw/day), D2 (12.5 mg/kg-bw/day), and D3 (25 mg/kg-bw/day) and vehicle control (D0).  Each dose group was examined 72 hours following the final exposure.  Each dose group had 4-5 biological replicates. There were a total 20, 20, and 20 samples (arrays) from the lung, liver, and forestomach, respectively, included in the final analysis using a two-colour reference design.


title: Catalytically inactive Ring1B maintains near wildtype levels of gene expression in mESCs

status: Public on Sep 20 2015

city: Edinburgh

first: Rob

middle: S

last: Illingworth

state: Midlothian

address: Centre for Regenerative Medicine

department: Centre for regenerative Medicine

country: United Kingdom

institute: The University of Edinburgh

summary: This experiment was designed to determine the extent of gene misregulation in mESCs containing catalytically dead Ring1B in comparison to mESCs lacking Ring1B.

overall_design: Polyadenylated mRNA was prepared from wildtype mESCs (WT), mESCs deficient for Ring1B (KO) and mESCs cells containing catalytically dead Ring1B (I53A). Each sample is represented by 3 biological replicate hybridisations.

first: Michael

last: Moffat

first: Robert

first: Abigail

last: Wilson

first: David

last: Read

first: Pradeepa

middle: M

last: Marulasiddappa

first: Ian

last: Adams

first: Wendy

last: Bickmore


title: Gene expression profile of TIARP-deficient macrophages or neutrophils, compared with WT macrophages or neutrophils

status: Public on Sep 23 2015

first: Asuka

last: Inoue

state: IBARAKI

address: 1-1-1 Tennodai

institute: University of Tsukuba

summary:
[Background] TNFa-induced adipose-related protein (TIARP) is a six-transmembrane protein that is expressed on macrophages, neutrophils and synoviocytes. We have recently reported that TIARP deficient mice (TIARP-/-) spontaneously developed arthritis, and had the high susceptibility to collagen-induced arthritis (CIA) with enhanced interleukin (IL)-6 production. However, the effect of TIARP to neutrophils and fibroblast-like syonoviocytes (FLS) has not been clearly elucidated.
[Methods] We analyzed the roles of TIARP in K/BxN serum transfer model using TIARP-/- mice. We characterized the differences of neutrophils between WT and TIARP-/- mice by DNA microarray. Transmigration assays of TIARP-/- neutrophils were performed in vitro and in vivo. FLS were cultured with TNFα and the production of CXCL2 (a specific ligand of CXCR1 and CXCR2) and IL-6 were measured by ELISA. Moreover, TIARP-/- mice transferred with K/BxN serum were treated with anti-IL-6R antibodies.
[Results] Arthritis in TIARP-/- mice transferred with K/BxN serum was significantly exacerbated. We identified overexpression of CXCR1 and CXCR2 in TIARP-/- neutrophils by DNA microarray. Neutrophils from TIARP-/- mice showed strong migration activity. The enhancement of chomotactic activity of TIARP-/- neutrophil was greatly facilitated by CXCL2 in vitro and in vivo. In addition, TIARP-/-FLS has enhanced the production of CXCL2 and IL-6 and the cell proliferation in the presence of TNFa, and the blockade of IL-6R significantly attenuated arthritis in vivo.
[Conclusion] Our findings indicate that TIARP might down-regulate the production of CXCL2 and IL-6 in FLS, and the expression of chemokine receptors (CXCR1 and CXCR2) in neutrophils, resulting in the protective ability of neutrophils migration into arthritic joints.

overall_design: Mice were treated with thiogycollate medium intraperitoneally. After 3 days, peritoneal macrophages were isolated from three WT or TIARP-deficient mice, and these cells were stimulated by TNFα for 24 hours. Ly6G+ Neutrophils were isolated from splenocytes by MACS.

first: Isao

last: Matsumoto

first: Takayuki

last: Sumida


title: Expression data comparing KRas(G12D/+);CreT, R26(H1047R/+);KRas(G12D/+);CreT, and MMTV-Neu mouse mammary tumors

city: Toronto

first: Sean

middle: Eoin

last: Egan

address: 686 Bay Street, Room 15-9704

department: Program in Developmental and Stem Cell Biology

institute: The Hosital for Sick Children

summary:
Breast Cancer (BC) has been associated with alterations in signaling through a number of growth factor and hormone regulated pathways.  Mouse models for metastatic BC have been developed using oncoproteins that activate PI3K, Stat3 and Ras signaling.  To determine the role of each pathway, we analyzed mouse mammary tumor formation when they were activated singly or pairwise.
We used microarrays to detect differentially expressed genes in the KRas(G12D/+);CreT and R26(H1047R/+);KRas(G12D/+);CreT tumors

overall_design: Total RNA was extracted from tumors developed by Qiagen RNAeasy kit and hybridized on Affymetrix microarrays.

first: Katherine

last: Wright

first: Jessica

first: Jeff

last: Liu

first: Eldad

last: Zacksenhaus

middle: E


title: Loss of Tifab, a del(5q) MDS gene, alters hematopoiesis through derepression of Toll-like receptor/TRAF6 signaling

status: Public on Sep 12 2015

city: Cincinnati

first: Daniel

middle: T

last: Starczynowski

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary: TRAF-interacting protein with forkhead-associated domain B (TIFAB) is a haploinsufficient gene in del(5q) Myelodysplastic syndrome (MDS). Hematopoietic-specific deletion of Tifab results in progressive bone marrow (BM) and blood defects, including skewed hematopoietic stem/progenitor cells (HSPC) proportions, altered myeloid differentiation, and progressive cytopenia. A subset of mice transplanted with Tifab knockout (KO) hematopoietic cells develop a bone marrow failure (BMF)-like disease with neutrophil dysplasia and cytopenia. In competitive transplants, Tifab KO HSPC are out-competed by wild-type (WT) cells, suggesting a cell-intrinsic HSPC defect. Gene expression analysis of Tifab KO HSPC identified dysregulation of immune-related signatures, and hypersensitivity to Toll-like receptor 4 (TLR4) stimulation. TIFAB also forms a complex with TRAF6, a mediator of immune signaling, and reduces TRAF6 protein stability by a lysosome-dependent mechanism. In contrast, TIFAB loss increases TRAF6 protein and the dynamic range of TLR4 signaling in HSPC, contributing to ineffective hematopoiesis. Moreover, combined deletion of TIFAB and miR-146a, two genes associated with del(5q) MDS/AML, results in a cooperative increase in TRAF6 expression and hematopoietic dysfunction in vivo. Re-expression of TIFAB in human del(5q) leukemic cells results in attenuated TLR4 signaling and reduced cell viability. These findings underscore the importance of efficient regulation of innate immune/TRAF6 signaling within HSPC by TIFAB, and its cooperation with miR-146a as it relates to the pathogenesis of hematopoietic malignancies, such as del(5q) MDS/AML.

overall_design: We performed an expression analysis on sorted lineage-Sca1+cKit+ (LSK) isolated from bone marrow (BM) of 3 month old mice transplanted with Tifab+/+ (WT) or Tifab-/- (KO) BM cells (n = 3 mice/group). We selected this time point to capture the gene expression profile of Tifab-/- LSK after engraftment but prior to overt hematopoietic failure. Total RNA was extracted, purified, reverse transcribed, labeled, and hybridized onto the GeneChip MoGene 2.0 ST Array (Affymetrix). Comparison comprises mRNA expression profile of Tifab+/+ LSK vs. Tifab-/- LSK.

first: Melinda

last: Varney

first: Madeline

last: Niederkorn

first: Hiroyasu

last: Konno

last: Matsumura

first: Jin

last: Gohda

first: Nobuaki

last: Yoshida

first: Taishin

last: Akiyama

first: Susanne

last: Christie

first: Jing

last: Fang

last: Miller

first: Andres

last: Jerez

first: Aly

last: Karsan

first: Jaroslaw

middle: P

last: Maciejewski

first: Ruhikanta

last: Meetei

first: Jun-ichiro


title: Sub-chronic transcriptional response in adult male MutaTMMouse following oral exposure to benzo(b)fluoranthene in lung, liver, and forestomach tissues [BbF]

first: Sarah

last: Labib

summary: Polycyclic aromatic hydrocarbons (PAHs) are a class of hundreds of structurally similar chemicals ubiquitously present in our environment. They are created during the incomplete combustion of organic materials, such as oil, wood, tobacco, and charbroiled meat. As such, human exposure to mixtures of PAHs can occur through consumption of PAH-containing foods and water, inhalation of polluted air, or dermal contact. Several PAHs have been classified as carcinogenic to humans or probably carcinogenic to humans by the International Agency for Research on Cancer. Benzo(b)fluoranthene is one such compound. In the present study, we sought to determine the dose-dependent changes in gene expression upon oral exposure to benz(a)anthracene in the lung, liver, and forestomach tissues. Adult male MutaTMMouse were exposed to three doses of Benzo(b)fluoranthene or vehicle control (olive oil) for 28 days and sacrificed three days after the final exposure.

overall_design: This experiment examined the pulmonary, hepatic, and forestomach transcriptional response of male mice exposed to benz(a)anthracene for 28 days at three different doses, including D1 (25 mg/kg-bw/day), D2 (50 mg/kg-bw/day), and D3 (100 mg/kg-bw/day) and vehicle control (D0).  Each dose group was examined 72 hours following the final exposure.  Each dose group had 4-5 biological replicates. There were a total 19, 20, and 20 samples (arrays) from the lung, liver, and forestomach, respectively, included in the final analysis using a two-colour reference design.

first: Andrew

last: Williams

first: Sabina

last: Halappanavar


title: Both gain and loss of function of miR-126 promote t(8;21) leukemia progression with different consequences and through different mechanisms

status: Public on Sep 07 2015

city: Monrovia

first: Jianjun

last: Chen

state: CA

department: Systems Biology

institute: Beckman Research Institute of City of Hope

summary: To investigate the pathological effect of miR-126 on the progression of acute myeloid leukemia (AML) induced by AML1-ETO9a (AE9a), we conducted a series of mouse bone marrow transplantation (BMT) assays with the following groups: AE9a (primary donor cells were wild-type mouse bone marrow progenitor (i.e., lineage negative; Lin-) cells retrovirally transduced with MSCV-PIG-AE9a), AE9a+miR-126 (primary donor cells were wild-type mouse bone marrow progenitor (i.e., Lin-) cells retrovirally transduced with MSCV-PIG-AE9a-miR-126), and miR-126KO+AE9a (primary donor cells were miR-126 knockout mouse bone marrow progenitor (i.e., Lin-) cells retrovirally transduced with MSCV-PIG-AE9a), along with a control group (primary donor cells were wild-type mouse bone marrow progenitor (i.e.,  Lin-) cells retrovirally transduced with MSCV-PIG empty vector). The control group was only used in the primary and secondary BMT assays, whereas the three leukemic groups including AE9a, AE9a+miR-126 and miR-126KO+AE9a were used in four passages (i.e., primary, secondary, tertiary and quaternary) of BMT assays. Then, gene expression profiling was conducted with bone marrow samples collected from different groups to decipher the molecular mechanisms underlying miR-126 effects on leukemia initiation and progression and maintenance and self-renewal of leukemia stem/initiating cells.

overall_design: A total of 39 mouse bone marrow samples including 36 mouse AML samples with AE9a, AE9a+miR-126, and miR-126KO+AE9a collected from the 1st, 2nd, 3rd and 4th passages of BMT recipient mice (3 mice for each group in each passage), along with 3 normal controls from the 1st passage of BMT, were analyzed by use of Affymetrix GeneChip Mouse Gene 2.0 ST Array (Affymetirx, Santa Clara, CA). For each sample, the CD45.1+ cells (i.e., transplanted donor cells) were sorted with flow cytometry from whole BM cells collected from BMT recipient mice at the end stage. Then total RNA was isolated by use of miRNeasy extraction kit (Qiagen, Valencia, CA).

first: Zejuan

last: Li

first: Ping

first: Yuanyuan

first: Zhixiang

last: Zuo

first: Abdel

last: Elkahloun

first: Paul

last: Liu


title: Placental gene expression in intestinal nematode-infected and protein-deficient mice

status: Public on Sep 09 2015

city: Montreal

first: Lisa

last: Starr

address: 1001 Boul. Decarie

department: Child Health and Human Development

institute: McGill University Health Centre

summary: Protein deficiency and intestinal parasite infection during pregnancy impair fetal growth through passage of signals from the maternal environment which signal impairment of fetal growth. The placenta is an important regulator of the transfer of these signals through differential expression of key placental genes. We used microarrays to examine placental gene expression responses to maternal protein deficiency (6% vs. 24% protein) and Heligmosomoides bakeri infection.

overall_design: 2x2 factorial.

first: Kristine

middle: G

last: Koski

first: Marilyn

last: Scott


title: Cardiac adiposity is regulated by Klf4 and c-Myc

status: Public on Sep 01 2015

city: Kyoto

first: Satoshi

last: Gojo

address: 465 Kajii-cho, Kamigyo-ku

institute: Kyoto Prefectural University of Medicine

summary: In this study, we examined if KLF4 and c-MYC (KM)-transduced murine cardiac mesenchymal progenitors (CMPs) played a role in the differentiation into adipocytes in the absence of adipogenic stimulation cocktails. These progenitors exhibited increased expression of adipogenic-related genes, such as C/EBPα, PPARγ, and Fabp4, activation of the PPAR signaling pathway, and formation of cytoplasmic lipid droplets within 10 days. Moreover, these KM genes sharply increased following a reperfusion insult, resulting in increased ectopic fat formation. Thus, understanding CMP adipogenesis will clarify the pathophysiology of ischemic reperfusion injury and myocardial infarction and may pave the way for better treatment strategies.

overall_design: Adult mouse cardiac mesenchymal progenitor cells were treated with OSKM for 0, 4, 6, or 8 days.

first: Daisuke

last: Kami


title: Murine Primary Thymocytes: RadioAdaptive Response (RAR) vs Control

city: Madrid

first: Javier

last: Santos

address: Nicolás Cabrera, 1,

country: Spain

institute: Department of Cellular Biology and Immunology. Severo Ochoa Molecular Biology Center. Autonomous University (CBMSO-UAM)

summary: Transcriptional profiling of mouse primary thymocytes from males and females comparing radioadapted cells with either control untreated cells, high dose irradiated cells or low dose irradiatiated cells with ES cells tr. Goal was to determine the effects of sex differences associated to RAR on global thymocyte gene expression.

overall_design: Three experimental conditions; Two-condition experiment for each condition, RAR vs Control, RAR vs High dose irradiation, RAR vs Low dose irradiation

first: J

first: P

last: Fernandez-Navarro

last: López-Nieva

last: Fernández-Piqueras


title: New functional signatures for understanding melanoma biology from tumor cell lineage-specific analysis [two channel experiments]

first: Bastien

last: Job

summary: The identification of molecular signatures specific to distinct tumor types is urgently required for the design of therapies overcoming treatment resistance. It remains unclear whether such signatures are shared among tumors and corresponding cell lines, a key issue given the use of cell lines for drug development. We developed SCA (similarity core analysis) an unsupervised computational framework for extracting the core molecular features common to tumors and corresponding cell lines. We  applied this algorithm to mRNA and miRNA expression data from various sources, comparing melanoma cell lines with melanoma metastases as an example. The signature obtained was associated with phenotypic characteristics  in vitro and the core genes  CAPN3 and  TRIM63 were identified as new actors in melanoma cell migration and invasion. About 90% of the genes in the melanoma signature are potentially regulated by an intrinsic network of transcription factors known to regulate neural development (TFAP2A, DLX2, ALX1, MITF, PAX3, SOX10, LEF1 and GAS7) and three miRNAs (211-5p, 221-3p, 10a-5p). The SCA signature effectively discriminated between two subpopulations of melanoma patients with significant difference in overall survival. Furthermore, it classified MEKi and BRAFi resistant and sensitive melanoma cell lines. The SCA algorithm is potentially applicable to any tumor cell type.

overall_design: 23 melanoma cell lines are analyzed in two color. Only the test (Cy5) channel of these data sets were used for analysis.

first: Forian

last: Rambow

first: Valérie

last: Petit

first: Franck

last: Gesbert

first: Véronique

last: Delmas

first: Hannah

last: Seberg

first: Guillaume

last: Meurice

first: Eric

last: Van Otterloo

first: Philippe

last: Dessen

first: Caroline

last: Robert

first: Daniel

last: Gautheret

first: Robert

last: Cornell

first: Alain

last: Sarasin

first: Lionel

last: Larue


title: Effects of hepatocyte-restricted Fra-1 overexpression on hepatic gene expression

first: Sebastian

last: Hasenfuss

summary: Hepatic mRNA expression was compared between control and Fra-1hep mice, which were fed chow diet

overall_design: Liver RNA pooled from 5 chow-diet fed control mice (control pool) was Cy3-labeled and liver RNA from 6 individual Fra-1hep mice was Cy5-labeled. On each microarray, Cy3‐labeled control pool and one Cy5-labeled mutant sample were hybridized at 65°C for 17 hours.


title: Regulation of steatohepatitis and PPARg signaling by distinct AP-1 dimers.

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

overall_design: Refer to individual Series


title: Rescue of CD8+ T cell vaccine memory in mice following sublethal g radiation exposure

city: BETHESDA

first: abdel

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

summary: In two disparate models, we show that rapid revaccination following sublethal gamma radiation exposure rescues memory CD8+ T cell Responses.

overall_design: To investigate the mechanism of rescue we performed RNA microarray analyses to identify whether there was a genetic “signature” of rescue.  mRNA was obtained from whole spleens 6 hrs after revaccination with LM-DActA at D1 and D4 PI for RNA microarray analysis

first: Hugh

last: McFarland

first: Abdel

first: Amy

last: Rosenberg


title: Transcriptional regulation in the ovary of estrogen-deficient mouse

status: Public on Sep 29 2015

city: Nankoku

first: Katsumi

last: Toda

state: Kochi

address: Oko-cho, Kohasu

department: Biochemistry

institute: Kochi University, School of Medicine

summary: Microarray analysis coupled with quantitative RT-PCR analysis identified seven genes (Fgd5, Gulo, Phex, Serpina5, Sfrp4, Kif26b and Tdgf1) of which the mRNA expression levels in ArKO ovaries were significantly different from those in the WT ovaries in the basal state, and were not normalized by E2 supplementation

overall_design: 4 samples, wild-type ovary without treatment,  wild-type ovary 4 hours after 5 IU of eCG, estrogen-deficient ovary without treatment and estrogen-deficient ovary 4 hours after s.c injection of estrgen at 18 mg/kg.


title: Molecular characterization of diabetic heart of akita (array)

city: omaha

first: Paras

middle: Kumar

last: Mishra

state: Nebraska

address: DRC1 Room 5047

department: Cellular and Integrative Physiology

institute: University of Nebraska medical center

summary: To understand the molecular profile of diabetic heart in animal model of type 1 diabeties Akita, we performed RNA sequencing of heart tissue (male) at the 12 week to understand systemic changes.

overall_design: There were two groups. Wlid type and Akita (Ins2+/-). Both have same genetic background and akita has mutation in Insulin 2 gene.

first: Varun

last: Kesherwani

middle: K


title: Transcriptional profiling of 2 SCCOHT PDX models and the SCCOHT cell lines BIN67 and SCCOHT1

status: Public on Aug 28 2015

city: Phoenix

first: Pilar

last: Ramos

state: Arizona

address: 445 N. 5th Street

institute: Translational Genomics Research Institute (TGen)

summary: Transcriptional profiling of 2 SCCOHT patient-derived xenograft (PDX) models and 2 SCCOHT cell lines compared to normal ovary to investigate underlying biology of SCCOHT.

overall_design: RNA from 2 SCCOHT PDXs and 2 SCCOHT cell lines were individually hybridized with a pool of 2 commercial normal ovary RNA on Agilent whole human genome 4x44K microarrays.

first: Jeffrey

last: Trent


title: Multi-platform assessment of transcriptional profiling technologies utilizing a precise probe mapping methodology (Agilent_4x44K)

status: Public on Sep 28 2015

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

summary: We present a more extensive and yet precise assessment to elucidate differences and similarities in performance at numerous aspects including signal range, sensitivity to fold-change, and fidelity with TaqMan qRT-PCR. There were three levels of data examined: entire data sets, data derived from gene name annotation oriented subset of 15442 RefSeq genes, and data derived from transcript pattern defined subset of 7034 RefSeq genes.  Our results showed a fair degree of overall correlation between all 6 platforms evaluated; but, to varying degrees, two RNA-seq protocols outperformed three of the microarray platforms in most categories.  Notably, a fourth microarray platform, Agilent, was comparable, or marginally superior, to the RNA-seq protocols within these same assessments.  Furthermore, 3 platforms (Agilent and two RNA-seq methods) demonstrated over 80% concordance with the gold standard TaqMan assay in terms of fold-change accuracy.  Our study suggests that the use of transcript patterns can enhance a number of the observed cross-platform correlations, indicating a potential usefulness for similar evaluations.

overall_design: The study assessed differences and similarities in performance at numerous aspects including signal range, sensitivity to fold-change, and fidelity with TaqMan qRT-PCR. There were three levels of data examined: entire data sets, data derived from gene name annotation oriented subset of 15442 RefSeq genes, and data derived from transcript pattern defined subset of 7034 RefSeq genes.

first: Richard

middle: D

last: Head


title: TCF1 is required for the differentiation of T follicular helper (TFH) cells during viral infections

status: Public on Sep 18 2015

summary: TFH and Th1 cells generated after viral or intracellular bacterial infections are critical for the control of infections and the development of immunological memories. However, the mechanisms that govern the choice of activated CD4 T cells to the two alternative fates remain unclear. Here, we found that reciprocal expression of TCF1 and Blimp1 between viral-specific TFH and Th1 cells started early after infection. TCF1 was intrinsically required for the differentiation of TFH cells. In the absence of TCF1, TFH cells failed to maintain their transcriptional and metabolic signatures, distinct from those in Th1 cells. Mechanistically, TCF1 functioned through forming negative feedback loops with IL-2 and Blimp1 signaling. Thus, we have demonstrated an essential role of TCF1 in TFH-cell differentiation.

overall_design: Tcf7 deficient and WT SMARTA CD4 T cells were isolated from mice 8 days after Lymphocytic Choriomeningitis Virus (LCMV) infection. TFH and Th1 cells were separated by FACS.

first: Tuoqi

last: Wu


title: Protective Effects of Estrogen in a Genetically Defined Mouse Model of Lung Adenocarcinoma

status: Public on Sep 25 2015

city: Indianapolis

first: Jeanette

middle: Nance

last: McClintick

state: IN

address: 635 Barnhill Dr.

department: Biochemistry & Molecular Biology

institute: Indiana University School of Medicine

summary: The role of reproductive hormones in lung cancer is controversial;  obervations from epidemiological studies support the possibilities that estrogen either promotes or protects against the disease.  In an earlier study we reported that estradiol (E2) stimulated tumorigenesis in a genetically defined mouse model based on the conditional expression of oncogenic Kras and concomitant deletion of p53.  The present study was meant to further examine the effects of estrogens in this model.  Instead we found that tumorigenesis was inhibited by the presence of the ovaries and that E2 proved protective against tumorigenesis in ovariectomized animals.  Specifically, E2 and the Esr1-specific agonist PPT reduced the number and size of tumors that developed;  furthermore, the protective effects of these two steroids were dose-dependent.  However, the Esr2 agonist DPN produced no effect.  Since Esr2 predominates in the lung, these results suggest that the E2 effect is indirect, perhaps being mediated by an endocrine factor from another organ.  Furthermore, the fact that the E2 effect in this second iteration of the mouse model was diametrically opposed to our earlier results suggests that genetic background plays a critical role in determining the effect of estrogen.

overall_design: Control vs. treatment with estradiol for WT and conditional knockout of TP53

last: Bigsby

middle: N

last: Creekmore

first: Andrea

last: Caperell-Grant


title: Spatial reorganization of telomeres in long-lived quiescent cells

status: Public on Aug 27 2015

city: Paris

first: Angela

last: Taddei

address: 26 rue d'Ulm

institute: Institut Curie

type: Genome variation profiling by genome tiling array

summary: Two conditions experiment, ChIP-chip anti-Sir3 comparing Sir3 occupancy in exponentially growing S.cerevisiae cells to Sir3 occupancy in the dense fraction of 7 days YPD culture of S.cerevisiae

overall_design: Two conditions experiment with biological duplicates. Both conditions were processed on the same array, duplicates have been carried separately


title: Expression data from Bone marrow and Fetal liver Lineage-c-Kit+Sca-1+ (LSK) cells

city: Chiba

first: Motohiko

last: Oshima

state: State...

address: 1-8-1 Inohana

institute: Chiba University

summary: Loss of polycomb-group gene Ezh2 causes activation of fetal gene signature in adult mouse bone marrow (BM) hematopoietic stem and progenitor cells (HSPCs). Ezh2 directly represses fetal-specific let-7 target genes, including Lin28, thereby cooperates with let-7 microRNAs in silencing fetal gene signature in BM HSPCs.

overall_design: We purified Lineage-Sca-1+c-Kit+ (LSK) HSPCs from E14.5 FL and adult BM and subjected them to microarray analysis.

first: Atsushi

last: Iwama


title: Gene expression induced by LPS, two amyloidogenic peptides, Tau 623-628 and Amylin 28-33, in peritoneal macrophages and B1a cells

status: Public on Sep 15 2015

city: Stanford

first: Jonathan

last: Rothbard

state: California

address: 2230 CCSR

department: Medicine

institute: Stanford University School of Medicine

summary: Amyloidogenic peptides are therapeutic in EAE, reducing systemic levels of IL6, TNF, and INFg. The fibrils are bound and endocytosed in peritoneal MFs and B1a cells. Differential gene expression was used to further understand the process.

overall_design: Groups of three female C57BL/6 mice were injected with 10ug of Tau 623-628, Amylin 28-33, LPS, or PBS. 30-40 minutes post injection, the peritoneal cavity was lavaged, CD11b high (MFs) and CD5+CD19+ (B1a lymphocytes) were purified by flow cytometry directly into Trizol. RNA was extracted from the aqueous phase using the Qiagen RNeasy microkits. RNA quality was assessed using the Agilent 2100 bioanalyzer and the RNA 6000 nano reagents kit. One color microarray, Agilent-028005 SurePrint G3 Mouse GE 8x60K Microarray,  was performed at the human immune monitoring center. All samples were processed and run at the same time.

middle: B


title: Expression data from mouse liver

status: Public on Aug 25 2015

city: Munich

first: Thomas

last: Michler

address: Trogerstr. 30

country: Germany

institute: Virology of Technische Universitaet Muenchen

summary: HBV-transgenic mice were treated i.v. with 1x10e11 particles AAV serotype 8 vectors expressing different RNAi-triggers targeting the HBV transcripts. To determine possible toxicities caused by the different vectors (including off-target activity against endogenous genes) we performed a whole transcriptome analysis of RNA of livers harvested 15 days after injection.

overall_design: 4 replicates per treatment group were analyzed. As controls, one group of mice was treated with 0.9% saline (mock) and another group of animals was treated with an empty AAV8 vector (1x10e11 particles i.v.).

first: Silvia

last: Weidner

first: Bettina

last: Knapp


title: Expression data from the aortas of ApoE knockout, ApoE/Caspase-1 double knockout, and wild-type mice

status: Public on Aug 21 2015

city: Philadelphia

first: Xiao-Feng

last: Yang

state: PA

address: 3500 N. Broad St

department: Cardiovascular Research Center

institute: Temple University School of Medicine

summary: Caspase-1 activation senses metabolic danger-associated molecular patterns and mediates the initiation of inflammation. Here, we reported that caspase-1 contributes to hyperlipidemia-induced modulation of vascular cell gene expression during early atherosclerosis in vivo. Our results demonstrate the therapeutic potential of caspase-1 inhibition in the treatment of cardiovascular diseases.

overall_design: All mice were in a C57B/L6 strain background. Male wild-type mice, Apolipoprotein E (ApoE) gene knockout mice, and ApoE/Caspase-1 double gene deficient mice were fed with high fat diet for 3 weeks starting from 8 weeks to induce early dyslipidemia.  At 11-week of age, aortas from these mice were used for microarray analysis. 5 biological replicates in each group.

first: Ying

last: Yin

first: Ya-feng

last: Li

first: Xinyuan


title: The role of ER stress transducer ATF6 in the long bone growth

status: Public on Aug 15 2015

city: Tokushima

first: Seiichi

last: Oyadomari

state: Tokushima

address: 3-18-15 Kuramoto

department: Division of Molecular Biology

institute: Institute for Genome Research

summary: To identify the non-canocical role of ATF6α and ATF6β in the long bone growth plate, we have employed whole genome microarray expression profiling as a discovery platform.

overall_design: Total RNA from growth plate in the tibia of 4-weeks aged mice was extracted using laser microdissector.

first: Ryosuke

last: Sato

last: Ogura

first: Masato

last: Miyake

first: Kazue

last: Tsugawa

first: Kazutoshi

last: Mori


title: Gene expression analysis at three different stages of myelination in dorsal root ganglion (DRG) explant cultures isolated from E13.5 C57BL/6J mouse embryos.

status: Public on Aug 16 2015

city: Oulu

first: Salla

middle: Maria

last: Kangas

address: PL 5000 (Aapistie 7A)

department: Institute of Biomedicine

country: Finland

institute: University of Oulu

summary: Myelin sheath formation in the peripheral nervous system is a complex event resulting from spatially and temporally regulated reciprocal interactions between the neuron and myelin-forming Schwann cells. Although many of the components of the sheath have been identified and well-characterized, our knowledge of the dynamic cellular and molecular processes and of the protein functional networks that participate in its formation is still weak. This paper describes a robust approach, combining transcriptomics, proteomics and immunocytochemistry analyses of myelinating dorsal root ganglion cultures derived from C57BL/6J mice, which can be exploited to identify protein networks, and their constituent modules, involved in peripheral nerve myelin formation. The approach allows distinguishing clear, reproducible and predictable differences between the structural properties of the cultures and their genome-wide and proteomic expression profiles at different stages of the myelination process. The expression profiles of selected neuronal and Schwann cell genes and proteins in the cultures reflect those observed in vivo, and the structural and ultrastructural properties and myelination schedule of the cultures closely resemble those observed in peripheral nerves in situ. The approach provides a unique and powerful tool to study comprehensive transcriptome and proteomic changes taking place simultaneously in Schwann cells and neurons during PNS myelination.

overall_design: We performed both biological and technical replicates. Biological replicates represent different DRG batches (M1-M3), collected at different times from different pools of embryos. Technical replicates are samples from same DRG batch (R1 and R2). This allows comparison of both the inter-batch and intra-batch variations and provides a fair estimation of the reproducibility and robustness of the methodology. DRG explant cultures representing biological replicates that were collected 0 days (N = 3), 10 days (N = 3) and 22 days (N = 3) after switching to myelination medium, and two technical replicates (n = 2) for each sample (i.e. a total of 6 replicates for each time point, altogether 18 samples), were processed for gene expression analysis.

first: Anthony

last: Heape

first: Eeva-Mari

last: Jouhilahti

first: Juha

last: Peltonen

first: Sirkku


title: ISR target genes revealed by comprehensive microarray network study using Perk -/-, Atf4 -/-, eIF2a S51A mutant, Fv2E-PERK

summary: To identify the target genes of integrated stress reponse (ISR), we have employed whole genome microarray expression in MEF cells.

overall_design: ISR gene setimation under ER stress condition using Perk -/-, Atf4 -/-, eIF2a S51A mutant, Fv2E-PERK MEF cells

first: A

first: M

first: K

last: Takahara

last: Kurahashi

first: R

first: H

last: Inoue

first: S


title: Expression data in CD4 T cells from lungs of PBS or house dust mite treated mice

status: Public on Aug 13 2015

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

summary:
CD4 T cells are essential mediators of the asthmatic process. We used the clinically relevant allergen house dust mites to induce signs of allergy in mice and performed gene expression arrays specifically on CD4 T cells infiltrating the lung
Reference: IL-21-producing CD4+ T cells promote type 2 immunity to house dust mites

overall_design: Primary CD4+ T cells were isolated from mice sensitised and challenged to either house dust mites or PBS. Purification of CD4 T cells was performed by flow cytometry. RNA was isolated, converted to cDNA and then hybridised on Affymetrix GeneChip Mouse Gene 2.0 ST Arrays

first: Jonathan

last: Coquet

first: Martijn

last: Schuijs

first: Mark

last: Smyth

first: Kim

last: Deswarte

first: Rudi

last: Bayaert

first: Harald

last: Braun

first: Louis

last: Boon

first: Gunilla

last: Hedestam

first: Steve

last: Nutt

first: Hamida

last: Hammad

first: Bart

last: Lambrecht


title: Loss of ATM accelerates pancreatic cancer formation and epithelial–mesenchymal transition

status: Public on Aug 07 2015

city: Aachen

first: Martin

last: Zenke

state: NRW

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

institute: Institute for Biomedical Engineering

summary: Pancreatic ductal adenocarcinoma (PDAC) is associated with accumulation of particular oncogenic mutations and recent genetic sequencing studies have identified ataxia telangiectasia-mutated (ATM) mutations in PDAC cohorts. Here we report that conditional deletion of ATM in a mouse model of PDAC induces a greater number of proliferative precursor lesions coupled with a pronounced fibrotic reaction. ATM-targeted mice display altered TGFβ-superfamily signalling and enhanced epithelial-to-mesenchymal transition (EMT) coupled with shortened survival. Notably, our mouse model recapitulates many features of more aggressive human PDAC subtypes. Particularly, we report that low expression of ATM predicts EMT, a gene signature specific for Bmp4 signalling and poor prognosis in human PDAC. Our data suggest an intimate link between ATM expression and pancreatic cancer progression in mice and men.

overall_design: KC (Atm+/+) and AKC (Atm-/-) mouse pancreata at 5 weeks old (n= 3 KC; n= 3 AKC) or 10 weeks old (n=3 KC; n=4 AKC) were subjected to microarray analysis.

first: Ronan

last: Russell

first: Lukas

last: Perkhofer

first: Stefan

last: Liebau

first: Qiong

last: Lin

first: André

last: Lechel

first: Fenja

last: Feld

first: Elisabeth

last: Hessmann

first: Jochen

last: Gaedcke

first: Melanie

last: Guethle

first: Daniel

last: Hartmann

first: Guido

last: von Figura

first: Stephanie

last: Weissinger

first: Karl

middle: L

last: Rudolph

first: Peter

last: Möller

last: Lennerz

first: Thomas

last: Seufferlein

last: Wagner

first: Alexander

last: Kleger


title: Transcriptomic Analysis of Stage 1 Versus Advanced Adult Granulosa Cell Tumors

status: Public on Aug 14 2015

city: Clayton

first: Maria

last: Alexiadis

state: Victoria

address: 27-31 Wright St

department: Centre for Endocrinology & Metabolism

country: Australia

institute: Hudson Institute Of Medical Research

summary: To identify the changes in gene expression that reflect the transition from Stage 1 to advanced GCT.

overall_design: Established transcriptome profiles for 6x Stage 1 and 6x advanced adult GCT (as defined by FOXL2 C134W mutation status).

middle: J

last: Fuller


title: Alteration in global transcriptome after Notch inhibition with gamma-secretase inhibitor MRK003 in Glioblastoma Cells

city: Baltimore

first: Luigi

last: Marchionni

state: MD

address: 1550 Orleans St., CRB2, Room 1M52

department: Oncology

institute: Johns Hopkins University

summary: We used DNA microarrays to compare RNA transcript expression from various glioma neurospheres after treatment with gamma-secretase inhibitor MRK003.

overall_design: Four glioma cell lines grown as neurospheres (GBM1, GBM2, GBM10 and GBM14) were treated two concentrations of with gamma-secretase inhibitor MRK003 (High and low dose, 0.4µM and 2.0µM respectively) and compared to vehicle (DMSO) control. Whole human genome gene expression was performed at the Johns Hopkins Oncology Microarray Core using 44k microarray technology (Agilent Technologies, CA, USA) according to manufacturer’s description including labeling, hybridization and detection. Gene annotation and expression analyses were performed using software packages available from the R/Bioconductor platform for statistical computing. In this series we provide raw expression data along with MIAME (Minimal Information about a Microarray Experiment).

first: Charles

last: Eberhart

first: Karisa

middle: C

last: Schreck

first: Ulf

last: Kahlert


title: Arc/Arg3.1 functionally defines migrating 1 dendritic cells and regulates actin dynamics

status: Public on Aug 12 2015

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: We compared the expression profiles of bone marrow-derived dendritic cells (BMDC) derived from Arc/Arg3.1 knockout and wildtype animals.

overall_design: We generated bone marrow-derived dendritic cells (BMDC) from Arc/Arg3.1 knockout and wildtype animals. BMDC were either stimulated with LPS or left untreated and analysed by microarray.

first: Manuel

last: Friese

first: Frederike

last: Ufer

first: Jan

last: Engler


title: Toxicogenomic Screen of Replacements for bis(2-ethylhexyl) phthalate (DEHP) Using the Immortalized TM4 Sertoli Cell Line

status: Public on Aug 06 2015

city: Montreal

middle: Constantine

last: Nardelli

state: Quebec

address: 3655 Prom. Sir-William-Osler

department: Pharmacology and Therapeutics

institute: McGill University

summary: Phthalate plasticizers are being phased out of consumer products because of their endocrine disrupting properties. This has resulted in a need to find safe alternatives that can plasticize polyvinyl chloride (PVC) while being inexpensive and biodegradable. We aim to study the toxicogenomic profile of mono-(2-ethylhexyl) phthalate (MEHP, the active metabolite of bis(2-ethylhexyl) phthalate, DEHP), the commercial plasticizer 1,2-cyclohexane dicarboxylic acid diisononyl ester (DINCH), and three plasticizers in development (1,4 butanediol dibenzoate (BDB), dioctyl succinate (DOS), and dioctyl maleate (DOM)) using the immortalized TM4 Sertoli cell line.

overall_design: Each sample contains four biological replicates except for DOS that contains three. The control is 1.0% DMSO as this was the vehicle used to solubilize the test compounds.

first: Bernard

last: Robaire


title: Genetic deletion or pharmacologic blockade of the amino acid transporter Slc6a14 in mice suppresses breast cancer induced by Polyoma middle T oncogene

status: Public on Aug 05 2015

city: Augusta

first: Pachiappan

last: Arjunan

state: Georgia

address: 1120 15th ST, Laney walker Blvd,

department: Anatomy, Unit on Retinal Vascular Neurobiology, BMB

institute: NUS, NIH, GRU

summary:
Tumor cells have an increased need for amino acids. Mammalian cells cannot synthesize essential amino acids; they must obtain these amino acids via specific transporters. Glutamine, though a non-essential amino acid, is critical for tumor cells (glutamine addiction). Entry of amino acids into tumor cells is enhanced by upregulation of specific transporters. If the transporters that are specifically induced in tumor cells are identified, blockade of the induced transporters would constitute a logical strategy for cancer treatment.
The transporter SLC6A14 is unique and transports all essential amino acids as well as glutamine and is expressed only at low levels in normal tissues, but induced in colon cancer and in ER+ breast cancer. We have now established the potential of this transporter as a drug target for breast cancer treatment using genetic and pharmacologic approaches. We then examined the progression of breast cancer in Polyoma middle T antigen (Py-MT) Tg mouse on Slc6a14+/+ and Slc6a14-/- background using microarray analysis.

overall_design: We have used three Affy-chips for each tumor sample (Group 1: WT/PyMT; Group 2: Slc6a14-KO/PyMT). Three biological replicates were used for each group.

first: Babu

last: Ellappan

first: Yangzom

last: Bhutia

first: Vadivel

last: Ganapathy

first: Muthusamy

last: Thangaraju

first: Puttur

last: Prasad


title: Expression data from intact and ventilation-preconditioned murine lungs

city: Oviedo

first: Guillermo

middle: M

last: Albaiceta

address: Avenida de Roma s/n

institute: Instituto de Investigación Sanitaria del Principado de Asturias

summary: To study the effects of previous exposure to mechanical ventilation may modify the development of Ventilator-induced lung injury, preconditioning was induced by low-pressure ventilation for 90 minutes. After 1 week, intact (sham) and preconditioned mice were sacrificed, the lungs extracted and gene expression measured in order to identify differences responsible for the observed tolerance to ventilator-induced lung injury observed in preconditioned animals.

overall_design: 6 samples were analyzed, from 3 intact (sham) and 3 preconditioned CD1 mice.

first: Jorge

last: Blazquez-Prieto

first: Inés

last: López-Alonso


title: Intra-subject correlation of brain and blood gene patterns in a mouse model of depression

city: Maebashi

first: Shigeo

last: Miyata

address: 3-39-22 Showa-machi

institute: Gunma University Graduate School of Medicine

summary: Gene expression profiling of blood cells in patients with major depressive disorder (MDD) has been used to identify potential biomarkers and to address the pathophysiology of MDD. However, whether alteration in gene expression in blood cells are reflected in the brain of the same individual is unclear. Here, we used an animal model of depression to investigate intra-subject correlation of gene expression patterns between the whole blood (WB) and the medial prefrontal cortex (mPFC). Ovariectomized mice exposed to the chronic mild stress were used as an animal model of depression.

overall_design: Female mice were subjected to chronic ultra-mild stress, a bilateral ovariectomy, or both. Sham-operated mice without stress were used as the control. Medial prefrontal cortex and whole blood were obtained from the same individual (n = 6 in each group), and analyzed using an Agilent SurePrint G3 Mouse GE 8×60K Microarray (Design ID: 028005)

first: Masashi

last: Kurachi

first: Noriko

last: Sakurai

first: Yasuki

last: Ishizaki

first: Masato

last: Fukuda

first: Masahiko

last: Mikuni


title: miR-130a activates apoptotic signaling through activation of caspase-8 in taxane-resistant prostate cancer cells [total RNA]

status: Public on Jul 31 2015

city: Toyohashi

first: Toshio

last: Kojima

address: 1-1 Hibarigaoka Tenpaku-cho

department: Health Care Center

institute: Toyohashi University of Technology

summary:
Background: The acquisition of drug resistance is one of the most malignant phenotypes of cancer. MicroRNAs (miRNAs) have been implicated in various types of cancers, but its role in taxane-resistance of prostate cancer remains poorly understood.
Methods: In order to identify miRNAs related to taxane-resistance, miRNA profiling was performed using prostate cancer PC3 cells and paclitaxel-resistant PC3 cell lines established from PC3 cells. Microarray analysis of mRNA expression was also conducted to search for potential target genes of miRNA. The effects of ectopic expression of miRNA on cell growth, tubulin polymerization, drug sensitivity and apoptotic signaling pathway were investigated in a paclitaxel-resistant PC3 cell line.
Results: The expression of miR-130a was down-regulated in all paclitaxel-resistant cell lines compared with parental PC3 cells. Based on mRNA microarray analysis, we identified SLAIN1 and CAV2 as potential target genes for miR-130a. Transfection with a miR-130a precursor into a paclitaxel-resistant cell line suppressed cell growth and increased the sensitivity to paclitaxel. Lastly, ectopic expression of miR-130a did not affect the polymerized tubulin level, but activated apoptotic signaling through activation of caspase-8.
Conclusion: These results suggested that miR-130a may be involved in the paclitaxel-resistance and could be a therapeutic target for taxane-resistant prostate cancer.

overall_design: Human hormone-refractory prostate cancer PC3 cells were cultured in RPMI1640 medium supplemented with 10 % of fetal bovine serum, 100 units/ml of penicillin and 100 ug/ml of streptomycin. Paclitaxel-resistant PC3PR20, PC3PR70 and PC3PR200 cells, which respectively could proliferate in the presence of 20, 70 and 200 nM of paclitaxel (Sigma-Aldrich, St. Louis, MO, USA), were previously established from PC3 cells by a stepwise increase of paclitaxel in the culture medium (Kojima et al, 2010, Prostate 70: 1501-12).

first: Yasunori

last: Fujita

first: Kyojiro

last: Kawakami

first: Kosuke

last: Mizutani

first: Taku

last: Kato

first: Takashi

last: Deguchi

first: Masafumi

last: Ito


title: Antagonistic interaction between androgen signaling and vitamin D signaling in prostate cancer [Expression profiling]

status: Public on Aug 01 2015

city: Chicago

first: Yuwen

last: Liu

state: IL

address: 900 East 57th Street. KCDB building. Room 10250

department: Human Genetics

institute: University of Chicago

summary: Vitamin D induces anti-proliferative and differentiating effects in prostate cancer. Thus calcitriol, the hormonally active form of Vitamin D, and its analogs have been extensively studied in prostate cancer cells. Yet despite its importance, relatively little is known about the genome-scale mechanisms by which Vitamin D, through its cognate nuclear vitamin D receptor (VDR), exerts its regulatory functions at the genomic level. In this study, we defined VDR transcriptional networks in the LNCaP prostate cancer cell line by mapping the genomic binding sites of VDR and by identifying differentially expressed genes upon calcitriol treatment. We found that VDR and androgen receptor (AR) antagonistically regulate a subset of cell cycle-related genes that are over-expressed in prostate cancer tumors. The expression balance of these genes is partially regulated through the competition dynamics between AR and VDR binding to shared cis-regulatory elements. On such shared elements, we found that FOXA1 mediates this competition by serving as a pioneering factor for both AR and VDR binding. We also found significant enrichment of AR-, VDR-, and AR/VDR overlapping binding sites in prostate cancer-associated single-nucleotide polymorphism (SNP) intervals identified from genome-wide association studies (GWAS), providing genetic evidence to link AR, VDR and their crosstalk to prostate cancer susceptibilities. In particular, we found that in a cis-regulatory element of the RFX6 gene implicated in prostate cancer progression, an allelic variant increases prostate cancer risk by switching the antagonism between AR and VDR into a synergistic interaction.

overall_design: Gene expression profiling in LNCaP cells after 24hr treatment with different nuclear recpetor ligrands, with time-matching control, in triplicates Expression is assayed with Agilent G4112F.

first: Kevin

last: White


title: Saturated fatty acids induced genes and ISR target genes in pancreatic beta cells

first: Seiichi

last: Oyadomari

summary: To identify the genes induced by lipotoxicity and integrated stress response in pancreatic beta cells, we have employed whole genome microarray expression in panvreatic beta cell line MIN6m9 cells.

overall_design: First microarray analysis : Wild type MIN6m9 cells were treated with Palmitate, Oleate or negative control condition. Second microarray analysis : Wild type and Fv2E-PERK transgened MIN6m9 cells were treated with mock or artificial dimerizer AP20187(AP) in various time course.

first: Kiyoe

last: Kurahashi

first: Tomoko

last: Mori

first: Atsushi

last: Ogura

first: Akitoshi

last: Nomura

first: Chinobu

last: Miyamoto

first: Miho

last: Miyake

last: Matsumoto


title: ISR target genes in WAT and BAT of mAP::Fv2E-PERK

summary: To identify the target genes of integrated stress reponse (ISR) in WAT and BAT, we have employed whole genome microarray expression in WAT and BAT specific Fv2E-PERK transgenic mice.

overall_design: The mAP::Fv2E-PERK transgenic mice were injected by AP20187 or mock.

first: A

first: M

first: K

last: Takahara

first: R

last: Sato

first: H

last: Inoue

first: S


title: A Global Transcriptome Analysis of BMSC from different confluences, But Gene Expression Profiling Suggested Comprised Pro-angiogenesis Effects - part 2

city: Bethesda

first: Jiaqiang

last: Ren

address: 9000 Rockville Pike

institute: National Institutes of Health

summary: Ex vivo expansion of Bone Marrow Stromal Cells (BMSC) is required to obtain clinical dose for cellular therapy, and different labs use different confluence in their practice, however, the impacts of 100% confluence on the biological properties of BMSC remain controversial. In this study, we detected the changes occurred to BMSCs when they reached 100% confluence, including viability, population doubling time (PDT), apoptosis, colony formation, immunosuppression, proteins in the culture supernatant, and surface markers; we also performed gene expression profiling and microRNA profiling on 50%, 80% and 100% confluent BMSCs. Our results showed that 100% confluent BMSCs had similar level of immunosuppression to 80% confluent BMSCs; they increased the expression of CD10, CD54, CD106, CD200, TLR4, but decreased CD49f and PODXL; we detected of 39 proteins in the culture supernatant, which displayed different patterns and an increase on the PEDF/VEGF ratio was observed with higher confluence. We identified 26 differentially expressed microRNAs, which were reported to be involved in the proliferation and differentiation of BMSC; and 2708 genes that were involved in extracellular matrix, cell adhesion, immune response and inflammatory response; particularly, angiogenesis inhibitor PEDF, and Wnt Singling inhibitors DKK1, DKK2, and DKK3 were up-regulated by 100% confluent BMSCs. These data suggest that 100% confluent BMSC may retain immunosuppressive activities but have comprised pro-angiogenesis effects.

overall_design: Gene expression profiling on BMSCs of 3 confluences (50%, 80% and 100%) from 5 healthy donors: 09FC37 (n=3), 09FC43 (n=3), 09FC44 (n=3), 09FC45 (n=3), 09FC49 (n=3) as biological repeats.


title: miR-130a activates apoptotic signaling through activation of caspase-8 in taxane-resistant prostate cancer cells.

first: Toshio

last: Kojima

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

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

overall_design: Refer to individual Series


title: Transcriptional Profiling of Hypoxic Neural Stem Cells to Identify Novel Regulators of Neural Stem Cell Biology

status: Public on Jul 30 2015

city: Barcelona

first: Nuria

last: de la Iglesia

address: Rossello 153

institute: IDIBAPS

summary: Neural stem cells reside in a hypoxic microenvironment within the brain. However, the crucial transcription factors that regulate neural stem cell biology under physiologic hypoxia are poorly understood. Here, we have performed microarray analysis of hypoxic versus normoxic neural stem cells with the aim of identifying pathways and transcription factors that are activated under oxygen concentrations mimicking normal brain tissue microenvironment.

overall_design: To identify the molecular mechanisms mediating the effect of low oxygen levels on NSC biology, we profiled the global effect of sustained, physiologic hypoxia on NSC gene expression using an unbiased approach by genome-wide microarray analysis. NSC were isolated from E13.5 mouse embryos (OF-1 strain) as previously described (Johe et al., 1996). After isolation, cells were immediately cultured at 37°C, 5% CO2 and either 5% or atmospheric (≈21%) oxygen and maintained in these conditions for 2-3 passages (minimum of 10 days). Then, total RNA was extracted, labeled and hybridized in a SurePrint G3 Mouse GE 8x60k array (Agilent Technologies). Four independent experiments were performed using different mouse donors for each experiment.


title: Unstable Foxp3+ regulatory T cells and altered antigen-presenting cells are associated with lipopolysaccharide-induced fetal loss in pregnant IL10 deficient mice

city: Adelaide

first: John

last: Schjenken

state: South Australia

address: The Robinson Research Institute and School of Paediatrics and Reproductive Health. Level 6. Medical School North. Frome Road

institute: The University of Adelaide

summary: Maternal IL10 deficiency elevates susceptibility to fetal loss induced by the model Toll-like receptor agonist lipopolysaccharide, but the mechanisms are not well elucidated. Here we show that Il10 null mutant (Il10-/-) mice exhibit altered local T cell responses in pregnancy, exhibiting pronounced hyperplasia in para-aortic lymph nodes draining the uterus with >6-fold increased CD4+ and CD8+ T cells compared with wild-type controls. Amongst these CD4+ cells, Foxp3+ Treg cells were substantially enriched, with 11-fold higher numbers at day 9.5 post coitum (pc). Lymph node hypertrophy in Il10-/- mice was associated with more activated phenotypes in dendritic cells and macrophages, with elevated expression of MHCII, scavenger receptor and CD80. Affymetrix microarray revealed an altered transcriptional profile in Treg cells from pregnant Il10-/- mice, with elevated expression of Ctse (cathepsin E), Il1r1, Il12rb2 and Ifng. In vitro, Il10-/- Treg cells showed reduced steady state Foxp3 expression, and polyclonal stimulation caused greater loss of Foxp3 and reduced capacity to suppress IL17 in CD4+Foxp3- T cells. We conclude that despite a substantially expanded Treg cell pool, diminished stability of Treg cells, increased numbers of effector T cells, and altered phenotypes in dendritic cells and macrophages in pregnancy all potentially confer vulnerability to inflammation-induced fetal loss in Il10-/- mice. These findings suggest a pivotal role for IL10 in facilitating robust immune protection of the fetus from inflammatory challenge and suggest IL10 deficiency could contribute to human gestational disorders where altered T cell responses are implicated.

overall_design: RNA was extracted from CD4+CD25+ lymphocytes isolated from para-aortic LNs of day 9.5 pc pregnant Il10+/+ or Il10-/- mice using miRNeasy Mini Kits (Qiagen Inc., Valencia, CA, USA) according to the manufacturer’s instructions. The concentration and purity of each RNA sample was determined using the Nanodrop Spectrophotometer (ND-1000, Nanodrop Technologies Inc., Wilmington, DE). RNA quality was determined using the RNA 6000 Pico Total RNA Kit (Agilent Technologies, Santa Clara CA) prior to use in microarray experiments. RNA with a RIN>7 was used in this study. For microarray analysis, RNA was pooled (from 2-4 mice per pool) resulting in four biological replicates of CD4+CD25+ cells from both Il10-/- and Il10+/+ mice. Microarray analysis was performed using Affymetrix Mouse Gene 2.0 ST Arrays at the Adelaide Microarray Centre. Total RNA was amplified using the Ovation PicoSL WTA System V2 (Nugen Inc., San Carlos, CA, USA) and MinElute Reaction Cleanup Kit (Qiagen Inc., Valencia, CA, USA), according to the manufacturer’s instructions, to provide 5 μg of cRNA for each microarray. The microarray data was normalized and analyzed using Partek Genomics Suite (Partek Inc, MO). Raw data from the Affymetrix platform (.cel files) were imported and normalized using RMA background correction, Partek’s own GC content correction, and mean probe summarization.

first: Sarah

middle: A

last: Robertson

first: Jelmer

middle: R

last: Prins

first: Bihong

last: Zhang

first: Leigh

last: Guerin

first: Simon

last: Barry


title: Lateral ventricle SVZ: 3xTg vs WT

first: Karl

middle: JL

last: Fernandes

address: 900 Rue St-Denis, R09-474

department: Neurosciences

institute: Université de Montréal

summary:
Transcriptional profiling of the microdissected SVZ from 7-month-old mice
Adult neurogenesis is suppressed in the SVZ of 3xTg mice, a model of Alzheimer's disease. To better understand the underlying mechanisms of this suppression, the goals of this experiment were to compare the transcriptional profiles of the SVZ neural stem cell niche in 3xTg-AD mice versus strain controls. We used early middle-aged mice (7-months-old) rather than old mice, in order to identify genetic changes that are not caused secondarily to other degenerative changes occurring in these mice.

overall_design: Two-condition experiment, 3xTg vs WT SVZ. Biological replicates: 4 for each.

first: Laura

last: Hamilton


title: Genes involved in plucking induced hair regeneration

status: Public on Aug 17 2015

city: Taiwan, R.O.C.

first: chihchiang

last: chen

address: No.201, Sec. 2, Shipai Rd., Beitou District, Taipei City, Taiwan 11217, R.O.C

department: Dermatology Department

country: Taiwan

institute: Taipei Veterans General Hospital

summary: Intra-follicular signals are thought to be important in plucking induced hair regenration. We hypothesize that extra-follicular macro-environment (including adipose and dermal tissue) also participates in this process. By using microarray, we want to identify the activating signals emit from extra-follicular macro-environment.

overall_design: First, we used traditional wax stripping to synchronize growth cycles in all dorsal pelage hair follicles. After synchronize, we wax the dorsal pelage hair follicles of mice again then collect the samples from  extra-follicular macro-environment (including adipose and dermal tissue) at different time points after waxing, including 12 hour, 1 day, 2 day, 4 day, 6 day, 10 day and 50 day. Finally we extrat the RNA from each samples and sent these RNA samples for microarray.

first: Chih-Chiang

last: Chen


title: Out-of-Sequence Signal 3 Paralyzes Primary CD4+ T Cell Dependent Immunity

status: Public on Jul 21 2015

city: Sacramento

first: William

last: Murphy

state: CA

address: 2921 Stockton Blvd Ste 1600

department: Dermatology

institute: UC Davis

summary: Primary T cell activation involves the integration of three distinct signals delivered in sequence: 1) antigen recognition, 2) costimulation, and 3) cytokine-mediated differentiation and expansion. Strong immunostimulatory events such as immunotherapy or infection induce profound cytokine release causing bystander T cell activation, thereby increasing the potential for autoreactivity and need for control. We show that during strong stimulation, a profound suppression of primary CD4+ T cell-mediated immune responses ensued and was observed across preclinical models and patients undergoing high-dose interleukin-2 (IL-2) therapy. This suppression targeted naïve CD4+ but not CD8+ T cells and was mediated through transient suppressor of cytokine signaling-3 (SOCS3) inhibition of the STAT5b transcription factor signaling pathway. These events resulted in complete paralysis of primary CD4+ T cell activation affecting memory generation, induction of autoimmunity, as well as impaired viral clearance. These data highlight the critical regulation of naïve CD4+ T cells during inflammatory conditions.

overall_design: The molecular mechanisms of primary T cell activation and regulation in response to strong immunostimulation were investigated in mice treated with immunotherapy. For this, BALB/c mice (3 mice per group) were either treated with immunotherapy (anti-CD40 and IL-2) or with a  control (rat IgG and PBS). Subsequently, peripheral blood mononuclear cells were FACS-sorted based on markers specific for CD4+ or CD8+ T cells and for naive (CD62L+/CD44low) or memory (CD44high) cell marker expression. There are a total of 8 samples, which represent pooled cells from the corresponding T cell subset from all mice in each treatment group. Total cellular RNA was isolated and then microarray gene expression profiling performed with Affymetrix GeneChip Mouse Gene 2.0 Sense Target (ST) Arrays.

first: Gail

last: Sckisel


title: Integration of gene mutations in risk prognostication for patients receiving first-line immunochemotherapy for follicular lymphoma

status: Public on Jul 16 2015

city: Toronto

first: Robert

last: Kridel

state: ON

address: 101 College Street, Rm 12-311

institute: Princess Margaret Cancer Centre

summary: Background: Follicular lymphoma (FL) is a clinically and genetically heterogeneous disease. The prognostic value of somatic mutations has not been systematically evaluated and no genetic factors have been identified that distinguish patients at highest risk of treatment failure.  Methods: We performed deep sequencing of 74 genes in 151 patients treated with R-CHOP from a phase III trial. Mutations and clinical factors were incorporated into a risk model using multivariable L1-penalized Cox regression. We validated the risk model in an independent cohort of 107 patients treated with R-CVP.  Results: The final clinicogenetic index, the “m7-FLIPI”, contained the FL International Prognostic Index (FLIPI), ECOG performance status, and mutation status of 7 genes (EZH2, ARID1A, MEF2B, EP300, FOXO1, CREBBP and CARD11). In the training cohort, the m7-FLIPI defined a high-risk group (28% of patients) with 5-year failure-free survival (FFS) of 38% vs 77% for the low-risk group (Hazard ratio (HR) 4.1, confidence Interval (CI)=[2.5;6.9], p<0.0001). In the validation cohort, the m7-FLIPI defined a high-risk group (22% of patients) with 5-year FFS of 25% versus 68% (HR 3.6, CI=[2.0;6.4], p<0.0001) in the low-risk group. In both cohorts, the m7-FLIPI outperformed the FLIPI alone. Strikingly, all 66 patients with EZH2 mutations in both cohorts were categorized as low-risk m7-FLIPI, and EZH2 mutations defined a distinct transcriptional profile.  Conclusions: The combination of clinical factors and mutations in 7 genes can identify the subset of patients with FL at highest risk of treatment failure. The m7-FLIPI can be widely utilized for risk prognostication and patient stratification.

overall_design: All RNA samples were derived from formalin-fixed paraffin-embedded tissue blocks and processed using the Illumina Whole-Genome DASL assay. The study includes 138 gene expression samples from the BC Cancer Agency cohort, 106 of which are from patients that were used in the final validation cohort of the clinicogenetic risk model.

first: Oliver

last: Weigert


title: Critical role for the DNA receptor AIM2 in stem-cell proliferation and cancer

status: Public on Jul 15 2015

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: Colorectal cancer is a leading cause of cancer-related deaths. Mutations in the innate immune receptor AIM2 are frequently identified in patients with colorectal cancer, but how AIM2 modulates colonic tumorigenesis is unknown. Here, we found that Aim2-deficient mice were hypersusceptible to colonic tumor development. Production of inflammasome-associated cytokines and other inflammatory mediators were largely intact in Aim2-deficient mice, however, intestinal stem cells were prone to uncontrolled proliferation. Aberrant Wnt signaling expanded a population of tumor-initiating stem cells in the absence of AIM2. Susceptibility of Aim2-deficient mice to colorectal tumorigenesis was enhanced by a dysbiotic gut microbiota, which was reduced by reciprocal exchange of gut microbiota with wild-type healthy mice. These findings uncover a synergy between a specific host genetic factor and gut microbiota in determining the susceptibility to colorectal cancer. Therapeutic modulation of AIM2 expression and microbiota has the potential to prevent colorectal cancer.

overall_design: We used microarrays to compare the transcriptome Aim2 deficent mice to wild type mice  in  colon tumor and  colitis samples.  Here were 12 mice in total, 3 for each genotype and tissue combination.

first: Si

last: Man

first: Qifan

last: Zhu

first: Liqin

first: Zhiping

last: Liu

first: Rajendra

last: Karki

first: Ankit

last: Malik

first: Deepika

last: Sharma

first: Liyuan

last: Li

first: R

last: Subbarao Malireddi

first: Prajwal

last: Gurung

first: Geoffrey

last: Neale

first: Scott

last: Olsen

last: Carter

first: Daniel

last: McGoldrick

first: Gang

last: Wu

first: Peter

last: Vogel

first: Richard

last: Gilbertson

first: Thirumala-Devi

last: Kanneganti