title: Expression data from mesodermal Tbx1-knockout otic vesicles and periotic mesenchyme at E11.5

city: Bronx

first: Tingwei

last: Guo

address: 1301 Morris Park Avenue, Room 408

department: Genetics

institute: Albert Einstein College of Medicine

summary:
The T-box transcription factor Tbx1 is expressed in the otic vesicle and surrounding periotic mesenchyme during inner ear development. Mesenchymal Tbx1 is essential for inner ear development, with conditional mutants displaying defects in both auditory and vestibular systems. We have previously identified reduced expression of retinoic acid metabolic genes in the periotic mesenchyme of mesoderm conditional Tbx1 mutants, using the T-Cre mouse line, implicating retinoic acid in mesenchymal-epithelial signaling downstream of Tbx1 in the periotic mesenchyme.

In order to identify downstream effectors of mesenchymal-epithelial signaling downstream of mesenchymal Tbx1, we have utilized a gene profiling approach comparing embryonic day 11.5 otic vesicle and surrounding periotic mesenchyme from T-Cre-mediated conditional Tbx1 mutants (Mest-KO) and conditional heterozygous control litter mates (control). This data was used in conjunction with OV-only data (GSE34064) to identify expression changes within the periotic mesenchyme.

overall_design: E11.5 T-Cre-mediated conditional Tbx1 mutants (Mest-KO) and control (T-Cre conditional Tbx1 heterozygotes) embryos were microdissected to isolate the otic vesicle and surrounding periotic mesenchyme. Left and right ears from 3 embryos of the same genotype were pooled for each chip, and 3 biological replicates of each chip were performed.

first: Dennis

last: Monks

first: Evan

middle: M

last: Braunstein

first: Bernice

last: Morrow


title: Coordinated Chromatin Remodeling induced by Demethylation requires SRCAP mediated H2A.Z exchange [expression]

status: Public on Jan 01 2013

city: Detroit

first: Houtan

last: Noushmehr

state: MI

address: 2799 W. Grand Blvd

country: USA

institute: Henry Ford Health System

summary: Genome wide gene expression profiling of RKO cells with combination treatments of non-target siRNA or SRCAP siRNA and PBS or 1uM 5-Aza-CdR treatment. The sample treated with non target siRNA and PBS serves as control sample.

overall_design: Total RNA obtained from isolated RKO cells.

first: Yang

last: Xiaojing

first: Noushmehr

last: Houtan

first: Jones

last: Peter


title: Coordinated Chromatin Remodeling induced by Demethylation requires SRCAP mediated H2A.Z exchange

type:
Expression profiling by array
Methylation profiling by array

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

overall_design: Refer to individual Series


title: Hedgehog signaling in T cell differentiation

city: London

first: Anna

last: Furmanski

address: 30 Guilford Street

country: United Kingdom

institute: ICH UCL

summary:
Despite Hedgehog’s influence on T-cell activation and proliferation, the transcriptional targets of Gli2 in lymphocytes are not known.  We therefore examined the Hedgehog-dependent transcriptional response of resting and early-stage activated T-cells in order to define their transcriptional response to Hedgehog pathway activation.
We have established transgenic models where transcription of target genes by Gli2 is either constitutively activated or repressed in cells of the T-lineage.  Gli2 has an N-terminal repressor domain and a C-terminal activator domain.    Lck-Gli2ΔN2 (Gli2A) mice carry a transgene encoding a truncated form of Gli2 that acts as a permanent transcriptional activator of Hh target genes.  Conversely, Lck-Gli2ΔC2 (Gli2R) mice express a repressor of Gli2-dependent transcription, which by binding to Gli binding sites inhibits physiological Hh-dependent transcription, and hence Hh signal transduction, in the cell.  These transgenes are driven by the Lck promoter and are only expressed in T-lineage cells

overall_design: Purified fresh, resting CD4 cells (unstimulated) and from CD4 cells stimulated with anti-CD3/CD28 for 6h (stimulated) were analysed in order to obtain transcriptional profiles before and during the early stages of T-cell activation.

first: A

first: M

last: Ono

first: T

last: Crompton


title: Keratinocyte Growth Factor and Dexamethasone Plus Elevated cAMP Levels Synergistically Support Pluripotent Stem Cell Differentiation into Alveolar Epithelial Type II Cells.

city: Aachen

first: Martin

last: Zenke

state: NRW

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

country: Germany

institute: Institute for Biomedical Engineering

summary: Alveolar epithelial type II (ATII)-like cells can be generated from murine embryonic stem cells (ESCs), although to date, no robust protocols applying specific differentiation factors are established. We hypothesized that the keratinocyte growth factor (KGF), an important mediator of lung organogenesis and primary ATII cell maturation and proliferation, together with dexamethasone, 8-bromoadenosine-cAMP, and isobutylmethylxanthine (DCI), which induce maturation of primary fetal ATII cells, also support the alveolar differentiation of murine ESCs. Here we demonstrate that the above stimuli synergistically potentiate the alveolar differentiation of ESCs as indicated by increased expression of the surfactant proteins (SP-) C and SP-B. This effect is most profound if KGF is supplied not only in the late stage, but at least also during the intermediate stage of differentiation. Our results indicate that KGF most likely does not enhance the generation of (mes)endodermal or NK2 homeobox 1 (Nkx2.1) expressing progenitor cells but rather, supported by DCI, accelerates further differentiation/maturation of respiratory progeny in the intermediate phase and maturation/proliferation of emerging ATII cells in the late stage of differentiation. Ultrastructural analyses confirmed the presence of ATII-like cells with intracellular composite and lamellar bodies. Finally, induced pluripotent stem cells (iPSCs) were generated from transgenic mice with ATII cell-specific lacZ reporter expression. Again, KGF and DCI synergistically increased SP-C and SP-B expression in iPSC cultures, and lacZ expressing ATII-like cells developed. In conclusion, ATII cell-specific reporter expression enabled the first reliable proof for the generation of murine iPSC-derived ATII cells. In addition, we have shown KGF and DCI to synergistically support the generation of ATII-like cells from ESCs and iPSCs. Combined application of these factors will facilitate more efficient generation of stem cell-derived ATII cells for future basic research and potential therapeutic application.

overall_design:
10 samples in total.

mESCs at d8 of differentiation (Control)
mESCs at d8 of differentiation with KGF treatment
mESCs at d17 of differentiation (Control)
mESCs at d17 of differentiation with KGF treatment
mESCs at d17 of differentiation with DCI treatment
mESCs at d17 of differentiation with KGF and DCI treatment
mESCs at d24 of differentiation (Control)
mESCs at d24 of differentiation with KGF treatment
mESCs at d24 of differentiation with DCI treatment
mESCs at d24 of differentiation with KGF and DCI treatment

first: Sabrina

last: Schmeckebier

first: Christina

last: Mauritz

first: Qiong

last: Lin

first: Ulrich

last: Martin


title: Genome-wide survey of mRNA stability in human B-lymphoblastoid cell lines

city: Evanston

first: Jubao

last: Duan

state: IL

address: 1001 University Place

department: Psychiatry and Behavioral Sciences

institute: Northshore University HealthSystem/University of Chicago

summary: Transcript abundance results from the balance between transcription and mRNA decay, and varies pervasively in humans. We have examined the effect of DNA variation on mRNA half-life differences by conducting a genome-wide survey of mRNA stability in seven human HapMap lymphoblastoid cell lines (LCLs). We determined the mRNA half-life for each gene from the ratio of 4-thio-uridine (4sU)-labeled nascent RNAs to total RNAs. 5,145 (46%) of 11,132 analyzed genes showed inter-individual mRNA half-life differences at a false discovery rate, FDR<0.05. As previously reported, we found transcription to be the main factor influencing transcript abundance. Although mRNA half-life explained only ~6% of transcript abundance on average, it explained ~16% for the subset of genes (~10%) showing inter-individual mRNA half-life differences (P<0.001). We confirmed previously reported correlations of mRNA half-life with transcript length, 3’-UTR length, and number of exon-junctions per kb of transcript. The number of miRNA targets in 3’-UTRs was negatively correlated with half-life (P=2.2×10-16), a new observation that is consistent with the role of miRNA in inducing mRNA degradation. Notably, coding GC and GC3 content showed positive correlations with mRNA half-life in genes with inter-individual mRNA half-life differences, implying a role of mRNA stability in shaping synonymous codon usage bias. Consistently, G or C alleles of coding SNPs were found associated with longer mRNA half-life (P=0.021). As expected, we also found that nonsense SNPs were associated with shorter mRNA half-life (P=0.009). Our results strongly suggest that inter-individual mRNA stability differences are widespread and affected by DNA sequence and composition variation.

overall_design: A total of 7 HapMap LCLs were used to measure mRNA half-life. Total RNAs and the 4sU-labeled-newly synthesized RNAs (nascent RNAs) were isolated from the same cell culture and were assayed simultaneously with human Exon array. For 3 LCLs, we included 3 biological replicates (i.e., independent cell cultures) and for 1 LCL we also included technical duplicates. mRNA half-life was calculated from the ratio of nascent RNAs/total RNAs. We used ANOVA to test inter-individual difference of mRNA half-life between 3 subjects who have biological replicates and technical duplicates. We examined the Spearman rank correlation of mRNA half-life with a number of gene features, including transcript length, intron length, 5'-UTR length and folding energy, 3'-UTR length and folding energy, microRNA target sites, GC and GC3 contents, etc. We also performed linear regression to test the effects of specific type of sequence variants (nonsense SNPs, SNPs within miRNA target sites, and coding synonymous and nonsynonymous SNPs) on mRNA half-life across 3 subjects that have whole genome sequencing data available (1000 genome project June 2011 release).


title: ZNF335 regulates stem cell proliferation and neuronal differentiation via Trithorax complex and REST/NRSF [gene expression]

status: Public on Dec 31 2012

city: Boston

first: Christopher

middle: A

last: Walsh

state: MA

address: 3 Blackfan Circle

institute: Children's Hospital Boston

summary: The progression from stem cell to differentiated neuron is associated with extensive chromatin remodeling that controls gene expression, but the mechanisms that connect chromatin to gene expression are not well defined. Here we show that mutation of ZNF335 causes severe human microcephaly ("small brain"), small somatic size, and neonatal death. Germline Znf335 null mutations are embryonically lethal in mice, whereas RNA-interference studies and postmortem human studies show that Znf335 is essential for neural progenitor self-renewal, neurogenesis, and neuronal differentiation. Znf335 is a component of a vertebrate-specific, trithorax H3K4 methylation complex, while global ChIP-seq and mRNA expression studies show that Znf335 is a previously unsuspected, direct regulator of REST/NRSF, a master regulator of neural gene expression and neural cell fate, as well as other essential neural-specific genes. Our results reveal ZNF335 as an essential link between H3K4 complexes and REST/NRSF, and provide the first direct evidence that this pathway regulates human neurogenesis and neuronal differentiation.

overall_design: ShRNA knockdown cells were FACS sorted and analyzed for changes in gene expression

first: Yawei

middle: J

last: Yang


title: MicroRNA-449a Enhances Radiosensitivity in Lung Adenocarcinoma Cells

status: Public on Dec 30 2012

city: Taipei

first: Mong-Hsun

last: Tsai

address: 4F, No. 81, Chang-Xing St.

department: Institute of Biotechnology

country: Taiwan

institute: National Taiwan University

summary:
Twenty-five miRNAs were identified as having differential expression post-irradiation in CL1-0 or CL1-5 cells. Among these miRNAs, miR-449a, which was down-regulated in CL1-0 cells at 24 h after irradiation, was chosen for further investigation.
Overexpression of miR-449a in CL1-0 cells effectively increased irradiation-induced DNA damage and apoptosis, altered the cell cycle distribution and eventually led to sensitization of CL1-0 to irradiation. MiR-449a might be a novel radiosensitizer for clinical applications.

overall_design: Two lung adenocarcinoma cell lines (CL1-0 and CL1-5) with different metastatic ability and radiosensitivity were used. In order to understand the regulatory mechanisms of differential radiosensitivity in these isogenic tumor cells, both CL1-0 and CL1-5 were treated with 10 Gy radiation, and were harvested respectively at 0, 1, 4, and 24 h after radiation exposure. The changes in expression of miRNA upon irradiation were examined using Illumina Human microRNA BeadChips.

first: Liang-Chuan

last: Lai

first: Yi-Jyun

last: Liu


title: Genome-wide analysis of gene expression in human embryonic stem cells (hESCs) and their differentiated cells

city: Mainz

first: Hyobin

last: Jeong

state: Germany

address: Richard shirrmann Str 12.

institute: IMB

summary: In order to investigate the gene expression changes in human embryonic stem cells (hESCs) during differentiation, we performed a microarray analysis from RNAs isolated from undifferentiated hESCs and their differentiated cells incubated for 1 week or 2 weeks in ESC medium.

overall_design: Human SNUhES3 ESCs (Seoul National University Hospital, Seoul, Korea) were cultured on mitotically-arrested STO feeder cells (ATCC, Manassas, USA) in DMEM/F12 supplemented with 20% knockout serum replacement (KSR). The embryoid bodies were incubated for 1 or 2 weeks in the above ESC medium without bFGF. Cells were then lysed and RNA was isolated.

first: Daehee

last: Hwang

first: Kwang

middle: P

last: Kim

first: Dong

middle: W

first: Jeong

last: Kang

first: Hye

middle: Y

last: Ha

first: Sojeong

last: Yun

first: Jae

middle: K

first: Ji

middle: H

last: Park

first: Kyung

middle: C

last: Cho

first: Gum

first: Jin

last: Jung

middle: S


title: Expression data from E18 mouse embryonic retina in wild-type mouse and Sox11 knockout mouse

status: Public on Dec 28 2012

city: Minato-ku, Tokyo

first: Sumiko

last: Watanabe

address: 4-6-1 Shirokane-dai

department: Institute of Medical Science

country: Japan

institute: University of Tokyo

summary:
The early retinal progenitor-expressed gene Sox11 regulates the timing of the differentiation of retinal cells.

Sry-related HMG box (Sox) proteins play diverse and critical roles in a variety of morphogenetic processes during embryonic development. Sox11 and Sox4 are members of the SoxC subtype, and we found that Sox11 was strongly expressed in early retinal progenitor cells, and that when expression of Sox11 subsided around birth, Sox4 expression began. To analyze the role of Sox11 and Sox4 in retinal development, we perturbed their expression pattern by expressing them ectopically in retinal explant culture. Overexpression of Sox11 or Sox4 in retinal progenitors resulted in similar phenotypes, that is, increased cone cells and decreased Muller glia. Sox11-knockout retinas showed delayed onset and progress of differentiation of early-born retinal cells during the embryonic period. After birth, retinal differentiation took place relatively normally, probably because of the redundant activity of Sox4, which starts to differentiate around birth. Neither overexpression nor loss-of-function analysis gave any evidence that Sox11 and Sox4 directly regulate transcription of genes critical to early-born retinal cells. However, histone H3 acetylation status of the early neurogenic genes was lowered in knockout retinas, suggesting that Sox11 regulates the timing of differentiation in early-born retinas by creating an epigenetic state that helps to establish the competency to differentiate. We also found that the unique expression patterns of Sox11 and Sox4 may be achieved by the Notch signaling pathway and by epigenetic regulation. Taking our findings together, we propose that the precise regulation of Sox11 and Sox4 expression during retinogenesis by multiple mechanisms leads to the fine adjustment of retinal differentiation.

overall_design: To delineate the molecular mechanisms underlying the retinal action of Sox11, we performed microarray analysis of E18 retinas from wild-type and Sox11 knockout mice. Total RNA was obtained from each one retina of Sox11 knockout and wild-type littermate embryos at E18.

first: Hiroyuki

last: Aburatani


title: Temporal response of mouse peritoneal cells to a non-pathogenic E. coli infection

city: Starkville

first: Minny

last: Bhatty

state: Mississippi

address: 240 Wise Center Dr, Mississippi State

institute: Mississippi State University

summary: Analysis of early and late changes in the mouse peritoneal cells in response to E. coli induced sepis. Result provide an insight into the molecular function and pathways expressed at these different time points.

overall_design: The mice were divided in two groups; the first group of mice were not treated with E. coli and was referred to as the naive group. Each mouse of the second group was injected with 2 X108 cells of a non- pathogenic isolate of E. coli suspended in a phosphate buffered saline (PBS) solution. After 1h, 2h and 18h of E. coli administration, peritoneal lavage fluid was obtained from two mice each for E. coli treated group at 1 and 2h and three mice of both groups (control and E. coli treated) at 18h. A common naive group of 2 mice harvested at 2h served as a control for both 1h and 2h.

first: Stephen

middle: B

last: Pruett


title: Nutrigenomics study in Atlantic salmon (Salmo salar) fed novel diets supplemented with marine by-products

city: Moncton

first: Francis

last: LeBlanc

state: NB

address: 343 University Ave.

department: Aquatic Animal Health

country: Canada

institute: Fisheries & Oceans Canada

summary: The processing of seafood for human or animal consumption creates vast amounts of by-product, which is often considered waste. Although some of these by-products are used as fishmeal, bone-meal or fertilizer, as a whole, it remains under utilized. Significant amounts of proteins, lipid fractions, vitamins, and other bioactive molecules are present in these by-products, all with potential beneficial properties that could be used as alternatives to fishmeal or as supplements for aquaculture species. In an attempt to investigate their potential benefit in Atlantic salmon fish nutrition, nine experimental diets were formulated using by-products originating from various seafood processing plants. A control basal diet (no by-product added) was also formulated. Juvenile Atlantic salmons were fed one of the nine experimental diets (30% marine by-product, 70% basal diet) or the basal diet and hepatic gene expression profiling was done on fish fed each diet after 14 and 56 days. Analysis of hepatic gene expression revealed a significant amount of differentially expressed genes for each diet with roles in various pathways and biological processes. By comparing differences in hepatic gene expression levels with the nutritional composition of the various feeds, we were able to identify a number of nutritional elements that affect specific gene families. This information will be very useful for the formulation of novel fish feeds, which may be designed with specific aims, such as rapid growth, increased immunity or better general health

overall_design: This specific study is aimed at evaluating the hepatic transcriptional responses in juvenile Atlantic salmon fed with fish feed formulation supplemented with one of nine marine by-products.

first: Mark

last: Laflamme

first: France

last: Beland

first: Nellie

last: Gagné

first: Sébastien

last: Plante


title: Expression data from brain, liver and spleen of Npc1-/- mice

status: Public on Dec 27 2012

city: Notre Dame

first: Md Suhail

last: Alam

state: IN Indiana

address: 103 Galvin, University of Notre Dame, IN

department: Center for Rare and Neglected Diseases/Biological Sciences

institute: University of Notre Dame

summary:
Niemann-Pick Type C (NPC) disease is a rare, genetic, lysosomal disorder with progressive neurodegeneration. Poor understanding of the pathophysiology and lack of blood-based diagnostic markers are major hurdles in the treatment and management of NPC and several additional neurological, lysosomal disorders. To identify disease severity correlates, we undertook whole genome expression profiling of sentinel organs, brain, liver, and spleen of Balb/c Npc1-/- mice (Npc1nih)relative to Npc1+/- at an asymptomatic stage, as well as early- and late-symptomatic stages.  Unexpectedly, we found prominent up regulation of innate immunity genes with age-dependent change in their expression, in all three organs. We shortlisted a set of 12 secretory genes whose expression steadily increased with age in both brain and liver, as potential plasma correlates for the neurological disease. Ten were innate immune genes with eight ascribed to lysosomes. Several are known to be elevated in diseased organs of murine models of other lysosomal diseases including Gaucher’s disease, Sandhoff disease and MPSIIIB. We validated the top candidate lysozyme, in the plasma of Npc1-/- as well as Balb/c Npc1nmf164 mice (bearing a point mutation closer to human disease mutants) and show its reduction in response to an emerging therapeutic. We further established elevation of innate immunity in Npc1-/- mice through multiple functional assays including inhibition of bacterial infection as well as cellular analysis and immunohistochemistry.
We used microarrays on the diseased organs, brain, liver and spleen of the Npc1-/- mice  to unserstand the molecular changes occur during the progression of NPC diseases. From the data, we have identified 12 potential genes which can be potentially developed as blood-based biomarker. We have also discovered up regulation of innate iimunity genes in all three organs of Npc1-/- mice and functionally validated them in liver and spleen.

overall_design: Brain from 11 female Npc1−/− and 16 control female mice (Npc1+/+ and Npc1+/−) from 6 age groups (20-25, 37-40, 54-55, 59-62, 67-71 and 81-84 days) were surgically harvested. Liver and spleen from 6 Npc1-/- and 6 Npc1+/-  female mice from three age group ( 20-25, 54-55 and 67-71 days) were surgically harvested. Organs were kept in RNA later and stored at -20 °C until used. RNA was isolated and Affymetrix mouse 430 2.0 array hybridizations were performed by ‘UCLA Clinical Microarray Core’, UCLA, Los Angeles, CA, USA. Subsequent raw data were analyzed using DNA-Chip Analyzer (D-Chip) with the .CEL files obtained from AGCC. Data from Npc1-/- mice from all age groups were compared to control mice (Npc1+/- and/or Npc1-/- mice) from all age groups separately for brain, liver and spleen. 'Matrix Table1' corrsponds for brain, 'Matrix Table2' corresponds for liver and 'Matrix Table3' corresponds for spleen. Thresholds for selecting significant genes were set at a relative difference ³1.5-fold, absolute difference ³100 signal intensity units and p<0.05. Genes that met all three criteria simultaneously were considered as significant change.

first: Suhail

first: Jenny

last: Shin

first: Pamela

last: Tamez

first: Kasturi

last: Haldar


title: Dynamic changes in the functions of Klf5 in maturing mouse corneas revealed by the changes in its target genes at postnatal days 11 and 56

status: Public on Dec 25 2012

city: Pittsburgh

first: Shivalingappa

middle: Kottur

last: Swamynathan

state: PA

address: 203 Lothrop Street Room 1025

department: Ophthalmology

institute: University of Pittsburgh

summary: Purpose: Klf5 plays a critical role in the mouse ocular surface (Kenchegowda et al., 2011. Dev Biol. 356:5-18). Here, we compare wild-type (WT) and Klf5-conditional null (Klf5CN) corneal gene expression at postnatal day-11 (PN11) and PN56 to identify the Klf5-target genes.  Methods: Gene expression was compared using Affymetrix microarrays with QPCR validation. Transient transfection assays examined the effect of Klf5 on selected target gene promoter activities. Whole-mount corneal immunofluorescent staining examined neovascularization and CD45+ macrophage influx.  Results: Expression of 714 and 753 genes was increased, and 299 and 210 genes decreased in PN11 and PN56 Klf5CN corneas, respectively, with 366 concordant increases, 72 concordant decreases and 3 discordant changes. Canonical pathway analysis identified 35 and 34 significantly (p<0.001) enriched pathways at PN11 and PN56, respectively, with 24 common pathways. PN56 Klf5CN corneas shared 327 increases and 91 decreases with the previously described Klf4CN corneas (Swamynathan et al., 2008. IOVS 49:3360-70). Angiogenesis and immune response-related genes were affected consistent with lymphangiogenesis and macrophage influx in Klf5CN corneas, respectively. Expression of 1574 genes was increased and 1915 decreased, in the WT PN56 compared with PN11 corneas. Expression of many collagens, matrix metalloproteinases and other extracellular matrix associated genes decreased in WT corneas between PN11 and PN56, while that of solute carrier family members increased.   Conclusions: Differences in PN11 and PN56 corneal Klf5-target genes reveal dynamic changes in Klf5 functions during corneal maturation. Klf4- and Klf5-target genes do not overlap, consistent with their non-redundant roles in the mouse cornea.

overall_design: Wild type and Klf5-conditional null mouse corneal gene expression at postnatal day-11 and -56 was compared by Affymetrix mouse whole genome 430 2 arrays. Four age-matched PN56 WT and Klf5CN mice, and 3 age-matched PN11 WT and Klf5CN mice each were used for comparison of corneal gene expression by microarrays. Two dissected corneas from each mouse were pooled for isolation of total RNA using the RNeasy Mini kit (Qiagen, Germantown, MD). The quality and integrity of the isolated total RNA was confirmed using an Agilent Bioanalyzer. Total RNAs were amplified and labeled using a 3' IVT Express Kit (Affymetrix Inc., Santa Clara, CA), and hybridized to Affymetrix MG 430 2 chips following the protocol suggested by the manufacturer.

first: Doreswamy

last: Kenchegowda

last: Harvey

first: Sudha

first: Kira

last: Lathrop


title: A Novel Tumor suppressor network in squamous malignancies

status: Public on Dec 21 2012

city: Madrid

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

country: Spain

institute: CIEMAT

summary: The specific ablation of Rb1 gene in stratified epithelia (RbF/F;K14cre) promotes proliferation and altered differentiation but is insufficient to produce spontaneous tumors. The pRb relative, p107, compensates some of the functions of pRb in these tissues, however RbF/F;K14cre;p107-/- mice die postnatally. Acute pRb loss in stratified epithelia, using an inducible mouse model (RbF/F;K14creERTM), shows that p107 exerts specific tumor suppressor functions in its absence. After simultaneous absence of pRb and p107, p53 transcriptional function is impaired and Pten expression is reduced. All mutant mice develop spontaneous squamous tumors carcinomas rapidly. Gene expression analysis of mouse tumors, besides supporting the impaired p53 function and the susceptibility to Akt/mTOR inhibitors, also revealed significant overlap with human squamous carcinomas. Thus, RbF/F;K14creERTM;p107-/- may constitute a new mouse model for these malignancies. Collectively, these data demonstrate the existence of a previously unreported functional connection between pRb, Pten and p53 tumor suppressors, through p107, of a particular relevance in squamous tumor development.

overall_design: Gene expression was compared between normal mouse skin and carcinomas arising in the skin of RbF/F;K14creERTM;p107-/- mouse. All mice were treated with tamoxifen.

first: Clotilde

last: Costa

first: Mirentxu

last: Santos

first: Camen

last: Segrelles

first: Marta

last: Duenas

first: Maria

middle: F

last: Lara

first: Aguirre

last: Xabier

first: Jesus

last: Paramio


title: Comparing expression profiles of NIH3T3 cells with and without LPAR1 mutation

status: Public on Dec 22 2012

city: Gaithersburg

first: Peter

last: Johansson

state: Maryland

address: 8717 Grovemont Circle

department: Pediatric Oncology Branch

institute: National Cancer Institute

summary: To explore the signaling pathways of mutant LPAR1, we performed gene expression profiling for NIH3T3 cells expressing wild-type and mutant LPAR1 receptors using Affymetrix mouse 430 2.0 arrays

overall_design: 6 RNA samples from the same cell line. 3 samples contained LPAR1 mutant and 3 samples were wild-type. Cells were harvested at 0, 60, and 120 minutes.

first: Jun

last: Wei

first: Young

last: Song

first: Javed

last: Khan


title: Differential gene expression of Kit+Sca1+Lin- (KSL) cells from arthritic versus control mice

city: Saint Louis

first: Kwadwo

last: Oduro Jnr

address: 4940 Parkview Place, Room 1024

department: Pathology and Immunology

institute: Washington University School of Medicine

summary:
The involvement of mature hematopoietic cells in disease pathogenesis is well recognized. However it is not clear how if and how primitive progenitors might contribute to inflammatory disease processes.
This microarray experiment  is used together with data from functional assays to determine how  primitive progenitors are altered in a mouse model of autoimmune arthritis and  how this in turn might contribute to the disease process.

overall_design:
KSL cells  were FACS sorted from 7 to 9  6-7 week old arthritic (KRNxG7) mice as well as from two strains of non-arthritic age-matched control mice: KRN and B6xG7 mice. Cells were sorted using identical conditions and identical sorting gates. To verify the primitive status of the KSL cells, Lin+ cells were also MACS sorted from these same mice.
All the mice used in this study were C57BL/6 background strain. G7 mice are congenic with C57BL/6 but with MHC II I-Ab replaced with MHC II I-Ag7.

last: Oduro Jr.

first: Jason

last: Mills

first: Kyunghee

last: Choi


title: The Disruption of Celf6, a Gene Identified by Translational Profiling of Serotonergic Neurons, Results in Autism-Related Behaviors

city: St Louis

first: Joseph

middle: D

last: Dougherty

state: Missouri

address: 4566 Scott Ave, box 8232

department: Genetics and Psychiatry

institute: Washington University

summary:
The immense molecular diversity of neurons challenges our ability to deconvolve the relationship between the genetic and the cellular underpinnings of neuropsychiatric disorders.
We suspected that comprehensive approaches to parsing this complexity may inform human genetics studies.
The serotonergic system has long been suspected in disorders that involve repetitive behaviors and resistance to change, including autism.  We generated a bacTRAP mouse line to permit the in vivo profiling of all ongoing translation in serotonergic neurons.
From this, we identified 174 serotonergic-cell enriched and specific genes, including all known markers of these cells.  Analysis of common variants in these genes in human families with autism implicated two genes, C1QTNF2 and the RNA-binding protein CELF6.
This work provides a reproducible and accurate method to assess the translational profiles of serotonergic neurons under a variety of conditions in vivo, and suggests cell-specific information may provide some insight into the genetic etiology of complex psychiatric disorders

overall_design:
For each cell population, three independent TRAP replicates were collected, and total RNA from both the immunoprecipitate and unbound fractions were seperately amplified and hybridized.
For each tissue, several representative unnbound fractions are provided to serve as controls.  Biological replicates are GCRMA normalized within groups.
Following averaging of replicates, we recommend further global normalization between groups, using affymetrix biotinylated controls, to correct for any broad biases in scanning and hybridization.
Finally for many analyses, we also recommend filtering to remove those probesets with low IP/UB fold change values from each cell type(see PMID:20962086).
Researchers can contact us for spreadsheets where these additional steps have been completed.

first: Lisa

last: Sonnenblick

first: Giovanni

last: Coppola

first: Juliet

last: Zhang

first: Susan

middle: E

last: Maloney

first: David

last: Wozniak

first: Brett

last: Abrahams

first: Daniel

last: Geschwind

first: Nathaniel

last: Heintz


title: Resveratrol treatment of 3T3-L1 cells

city: Toronto

first: Sara

last: Arab

state: ONT

address: 610 University Avenue

department: Cardiology

institute: Toronto General Hospital

summary:
Murine 3T3-L1 progenitor adipocytes cell cultures, treated and untreated (Control) with resveratrol before the induction of differentiation and the effects on adipogenesis and insulin signaling was investigated.
Keywords: Treatment response

overall_design: 3 Replicates of treated and untreated (Control) cell cultures

last: Liu

first: Haytham

last: Ibrahim


title: Hedgehog and metabolism

city: Durham

first: Cynthia

last: Moylan

state: NC

address: 595 LaSalle Street, GSRB1, DUMC 3256

department: Gastroenterology

institute: Duke University Medical Center

summary:
Deregulated accumulation of myofibroblasts (MF) is central to liver fibrosis pathogenesis, but the mechanisms controlling myofibroblast fate remain poorly understood. Here we investigated whether Hedgehog (Hh) signaling regulates MF fate by modulating MF metabolism.
We performed microarrays to screen hepatic stellate cells (HSC) for transition-associated changes in metabolism.  To capture early and late events in their MF transition process, we compared gene expression in freshly isolated primary HSC with gene expression in the same cells after 7 days in culture.

overall_design: We analyzed total RNA from 3 replicates of HSC in the early transition or quiescent state (n=3) as well as in the late phase of transition (MF) (n=3).

first: Chen

last: Yuping

first: Diehl

last: Anna Mae


title: The genes affected by Triptolide in activated  mouse primary T cells

status: Public on Dec 29 2012

city: Nanjing

first: Zichun

last: Hua

state: Jiangsu

address: Hankou Road

country: China

institute: Nanjing University

summary:
Triptolide possesses immunosuppressive activity and its efficacy is commonly believed to be related to the suppression of T cells. However, the underlying mechanism is still not well documented and most of the previous study adopted tumor cell lines of immune system as model cells in mechanism research, these cells’ signal transduction pathway can not reflect the real situation of immune system. In this study, we investigated the immunosuppressive mechanism of triptolide on T cell activation and proliferation using mouse primary T lymphocytes. These effects were analyzed along with activation of the TCR and AP-1 pathway.
We used microarrays to detail the global programme of gene expression underlying stimulation and triptolide treatment.

overall_design: Mouse primary T cells stimulated with anti-CD3/CD28 antibodies treated with triptolide or not treated with triptolide were selected for RNA extraction and hybridization on Affymetrix microarrays.

first: Luan

last: Shu

first: Bo

last: Tang


title: Extraction of high quality total RNA from liquid nitrogen stocks

city: Yokohama

first: Alistair

middle: R

last: Forrest

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: RIKEN OMICS science centre

institute: RIKEN

summary: Microarray expression arrays on THP-1 acute myeloid leukemia cell line samples, contrasting expression profiles of freshly harvested cell pellets, cells replated into fresh media for 24 hours and cells directly pelleted from liquid nitrogen stocks.

overall_design: Nine samples were analysed, composed of 3 biological replicates for each state (fresh, replated, frozen)


title: Expression data from mesodermal Tbx1-knockout otic vesicles at E11.5

city: Bronx

first: Tingwei

last: Guo

state: NY

address: 1301 Morris Park Avenue, Room 408

institute: Albert Einstein College of Medicine

summary:
The T-box transcription factor Tbx1 is expressed in the otic vesicle and surrounding periotic mesenchyme during inner ear development. Mesenchymal Tbx1 is essential for inner ear development, with conditional mutants displaying defects in both auditory and vestibular systems. We have previously identified reduced expression of retinoic acid metabolic genes in the periotic mesenchyme of mesoderm conditional Tbx1 mutants, using the T-Cre mouse line, implicating retinoic acid in mesenchymal-epithelial signaling downstream of Tbx1 in the periotic mesenchyme.

In order to identify downstream effectors of mesenchymal-epithelial signaling downstream of mesenchymal Tbx1, we have utilized a gene profiling approach comparing embryonic day 11.5 otic vesicle tissue from T-Cre-mediated conditional Tbx1 mutants (Mest-KO) and conditional heterozygous control litter mates (control).

overall_design: E11.5 T-Cre-mediated conditional Tbx1 mutants (Mest-KO) and control (T-Cre conditional Tbx1 heterozygotes) embryos were microdissected to isolate the otic vesicle. Left and right ears from 3 embryos of the same genotype were pooled for each chip.

first: Dennis

last: Monks

first: Evan

last: Braunstein

first: Bernice

last: Morrow


title: Effect of Lira treatment on heart in obese mice

summary:
C57BL/6 Male mice were treated with high fat diet at the age of 8 weeks and continue the diet for 16 weeks(4 mo) and then injected them with placebo/drug for 1  week before scarifice. Their were sacrifised at the age of 6 months.

Drug: Lira is used to reduce morbidity and mortality due to obesity and its effect on heart.

overall_design: 10 C57BL/6 Male mice under high fat diet for 16 weeks treated with eithe Placebo/drug were chosen for the microarray analysis.  Heart from each mouse was disected and the left ventricle was used for TRNA extraction.

first: Hossein

last: Noyanashraf

first: Mansoor

last: Husain


title: Leukemogenesis by CDX2 involves KLF4 repression and deregulated PPARgamma signaling.

city: Berlin

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

institute: Charité

summary: Aberrant expression of the homeodomain transcription factor CDX2 occurs in most cases of acute myeloid leukemia (AML) and promotes leukemogenesis, making CDX2, in principle, an attractive therapeutic target. Conversely, CDX2 acts as a tumor suppressor in colonic epithelium. The effectors mediating the leukemogenic activity of CDX2 and the mechanism underlying its context-dependent properties are poorly characterized, and strategies for interfering with CDX2 function in AML remain elusive. We report data implicating repression of the transcription factor KLF4 as important for the oncogenic activity of CDX2, and demonstrate that CDX2 differentially regulates KLF4 in AML versus colon cancer cells through a mechanism that involves tissue-specific patterns of promoter binding and epigenetic modifications. Furthermore, we identified deregulation of the PPARγ signaling pathway as a feature of AML expressing CDX2, and observed that PPARγ agonists derepress KLF4 and are preferentially toxic to CDX2-positive leukemic cells. These data delineate transcriptional programs associated with CDX2 expression in hematopoietic cells; provide insight into the antagonistic duality of CDX2 function in AML versus colon cancer; and suggest reactivation of KLF4 expression, through modulation of PPARγ signaling, as a new therapeutic modality in a large proportion of AML patients.

overall_design:
Experiment 1 (Samples 1-6): The transcriptional changes induced by Cdx2 were assessed ex vivo in primary murine hematopoietic stem and progenitor cells. Bone marrow cells were harvested from 3x15 C57BL/6 mice, and differentiated cells were removed by incubation with rat antibodies against lineage antigens (CD3, CD4, CD8, Gr-1, B220, CD19, IL-7R, Ter119) followed by depletion with magnetic beads (Dynabeads, Invitrogen). Lineage-depleted cells were stained with APC-conjugated anti-c-Kit and PE-Cy5-conjugated goat anti-rat antibodies, and c-Kit+ Lin– cells were sorted using a BD FACSAria cell sorter (BD Biosciences). Cells were plated in RetroNectin-coated tissue culture dishes (Takara Bio) and transduced twice with pMSCV-Cdx2-IRES-GFP or pMSCV-IRES-GFP retroviral constructs. After 48 hours, GFP-positive cells were sorted using a BD FACSAria cell sorter.

Experiment 2 (Samples 7-10): The transcriptional changes induced by Cdx2 were assessed in vivo in Cdx2-initiated murine leukemias and compared with those of leukemias initiated by 5 different MLL fusion oncogenes (previously published data, available at GSE13690). Bone marrow cells isolated from C57BL/6 mice were transduced with pMSCV-Cdx2-IRES-GFP, and 8x10e5 GFP-positive cells were injected into lethally irradiated syngeneic recipient mice after 48 hours, followed by injection of 1x10e6 spleen cells from primary leukemic animals into sublethally irradiated secondary recipients. Spleen cells from secondary leukemic animals were harvested.

first: Claudia

last: Scholl

first: Stefan

last: Fröhling


title: High Fat Diet Triggers SIRT1 Cleavage in Adipose Tissue Providing a Link between Dietary Stress   and Metabolic Dysfunction.

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

summary: Adipose tissue plays an important role in storing excess nutrients and preventing ectopic lipid accumulation in other organs. Obesity leads to excess lipid storage in adipocytes, resulting in the generation of stress signals and the derangement of metabolic functions. SIRT1 is an important regulatory sensor of nutrient availability in many metabolic tissues. Here we report that SIRT1 functions in adipose tissue to protect from the development of inflammation and obesity under normal feeding conditions, and the progression to metabolic dysfunction under dietary stress. Genetic ablation of SIRT1 from adipose tissue leads to gene expression changes that highly overlap with changes induced by high fat diet in wild type mice, suggesting that dietary stress signals inhibit the activity of SIRT1. Indeed, we show that high fat diet induces the cleavage of SIRT1 in adipose tissue by the inflammation-activated caspase-1, providing a link between dietary stress and predisposition to metabolic dysfunction.

overall_design: Four replicates from four different biological conditions: 1) SIRT1 wild-type fed low fat diet, 2) SIRT1 wild-type fed high fat diet, 3) SIRT1 knock-out fed low fat diet, 4) SIRT1 knock-out fed high fat diet

first: Angeliki

last: Chalkiadaki

first: Leonard

last: Guarente


title: Expression data of mouse gastric tumors (TNF KO-Gan and BALB/c-Gan mice )

city: kanazawa

first: masanobu

last: oshima

address: Kakuma-machi

institute: kanazawa university

summary:
Gan mice express Wnt1, Ptgs2, and Ptges, which develop inflammation-associated gastric tumors (Oshima et al, Gastroenterology 131: 1086, 2006).  We examined the role of TNF-alpha in tumorigenesis by construction of TNF-/- Gan mice.  We also examined genetic background difference in tumor phenotype by changing Gan mouse background from C57BL/6(B6) to BALB/c.
Microarray analyses were performed to examine changes of expression profiles in tumors by TNF gene disruption or by changing genetic background.

overall_design: Total RNA was prepared from B6 Gan mice (n=3: Gan1-Gan3), B6-Gan TNF-/- mice (n=3: Gan(TNF KO)1-Gan(TNF KO)3), BALB-Gan mice (n=3: Gan(BALB/c)1-Gan(BALB/c)3), and wid-type normal glandular stomach (n=3: WT1-WT3).  We used Affymetrix microarrays for hybridization, and examined expression profiles.

first: Yoichi

last: Yamada

first: Hiroko

last: Oshima

first: Masanobu


title: MicroRNA-138: A Pro-survival OncomiR for Glioma Stem Cells is Associated with Tumor Recurrence [mRNA]

status: Public on Dec 20 2012

city: Singapore

first: Prabha

last: Sampath

state: Singapore

address: 8A Biomedical Grove

department: Institute of Medical Biology

country: Singapore

institute: Institute of Medical Biology

summary:
We report the identification of microRNA-138 (miR-138), as a molecular signature of GSCs and demonstrate a vital role for miR-138 to promote growth and survival of bona fide tumor-initiating cells with self-renewal potential.

Keywords: Expression profiling by array

overall_design: Total RNA from GSCs 5 days after transduction with lentivirus expressing anti-miR-138 or scrambled sequence was subjected to microarray analysis

first: Derryn

middle: X

last: Chan

first: Srikanth

last: Nama


title: Expression data comparing human DKK1 and control vector transfected murine osteochondrosarcoma cells (MOS-J)

city: Temple

first: Joni

last: Ylostalo

state: TX

address: 5701 Airport Rd., Module C

department: Institute for Regenerative Medicine

institute: Texas A&M

summary: Canonical Wnt signaling controls proliferation and differentiation of osteogenic progenitor cells, and tumor-derived secretion of the Wnt antagonist Dickkopf-1 (Dkk1) is correlated with osteolyses and metastasis in many bone malignancies. However, the role of Dkk1 in the oncogenesis of primary osteosarcoma (OS) remains unexplored. Here, we over-expressed Dkk1 in the OS cell line MOS-J. Contrary to expectations, Dkk1 had autocrine effects on MOSJ cells in that it increased proliferation and resistance to metabolic stress in vitro. In vivo, Dkk1 expressing MOS-J cells formed larger and more destructive tumors than controls.   These effects were attributed in part to up-regulation of the stress response enzyme and cancer stem cell marker aldehyde-dehydrogenase-1 (ALDH1) through Jun-N-terminal kinase signaling. This is the first report linking Dkk1 to tumor stress resistance, further supporting the targeting of Dkk1 not only to prevent and treat osteolytic bone lesions but also to reduce numbers of stress-resistant tumor cells.

overall_design: Two samples were analyzed, one human DKK1 transfected MOS-J cell sample and one control vector transfected MOS-J cell sample.

first: Carl

middle: A

last: Gregory

first: Ulf

last: Krause


title: A Pro-survival OncomiR for Glioma Stem Cells is Associated with Tumor Recurrence

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: The estrogen receptor α is required and sufficient to maintain physiological glucose uptake in the mouse heart

city: Wuerzburg

first: Susanne

middle: Elma

last: Kneitz

address: Biozentrum, Am Hubland

department: Physiologigcal Chemistry

institute: University of Wuerzburg

summary: Rationale: Estrogens attenuate cardiac hypertrophy and increase cardiac contractility via their cognate receptors ERα and ERβ. Since female sex hormones enhance global glucose utilization and because myocardial function and mass are tightly linked to cardiac glucose metabolism we tested the hypothesis that expression and activation of the estrogen receptor α (ERα) might be required and sufficient to maintain physiological cardiac glucose uptake in the murine heart. Methods and Results: Cardiac glucose uptake quantified in vivo by 18F-fluorodeoxyglucose positron emission tomography (FDG-PET) was strongly impaired in ovarectomized compared to gonadal intact female C57BL/6JO mice. The selective ERα agonist 16α-LE2 and the non-selective ERα and ERβ agonist 17β-estradiol completely restored cardiac glucose uptake in ovarectomized mice. Cardiac FDG uptake was strongly decreased in female ERα knockout mice (ERKO) compared to wild type littermates. Biochemical assays, affymetrix cDNA array analysis, western blotting and immuno-staining of cardiac glucose transporters revealed a positive correlation of ERα dependent cardiac FDG uptake with preserved cardiac glucose transporter-1 expression and micro-vascular localization. Conclusions: Systemic activation of the ERα estrogen receptor is sufficient and its expression is required to maintain physiological glucose uptake in the murine heart, which is likely to contribute to known cardio-protective estrogen effects.

overall_design: total samples analysed are 20

first: Paula-Anahi

last: Arias-Loza

first: Michael

last: Kreissl

first: Franz

last: Kaiser

first: Ina

last: Israel

first: Kai

last: Hu

last: Frantz

first: Barbara

last: Bayer

first: Karl-Heinz

last: Fritzemeier

first: Kenneth

last: Korach

first: Theo

last: Pelzer


title: The downstream gene expression of AnxA4 in AGS cells

city: Taipei

first: Hsueh-Fen

last: Juan

address: No. 1, Sec. 4, Roosevelt Road

department: institute of molecular and cellular biology

institute: National Taiwan university

summary:
AnxA4 expression is increased in H. pylori associated tumors. Moreover, in renal-cell cancer, AnxA4 increases tumor cell dissemination and promotes cell migration, and in colorectal cancer, it is identified as a potential diagnostic marker. How AnxA4 might be involved in tumorgenesis has remained unclear.
Here, we compared the gene expression profiles between the cells transfected with pcDNA3.1 (+)/AnxA4 and control (empty vector) to study the downstream genes of AnxA4 using Exon array technique.

overall_design: Four samples are analyzed.

first: Li-Ling

last: Lin

first: Hsuan-Cheng

last: Huang

first: Chiung-Nien

last: Chen


title: Consequences of exchanging carbohydrates for proteins in the cholesterol metabolism of mice fed a high-fat diet

status: Public on Dec 19 2012

city: Lausanne

first: Frederic

last: Raymond

address: Campus EPFL - Quartier de l'Innovation

department: Functional Genomics

country: Switzerland

institute: Nestle Institute of Health Sciences

summary: Dietary proteins have profound effects on lipid metabolism but the mechanism remains to be elucidated. In the present study, we examined the temporal impact of dietary proteins in isoenergetic high fat diets on lipid metabolism of C57BL/6J mice.

overall_design: Mice were first fed a low protein (P) to carbohydrate (C) ratio high-fat diet (L-P/C-HF) for 10 weeks and then a half of mice were changed to a high protein to carbohydrate ratio high-fat diet (H-P/C-HF) for additional 4 weeks whereas the remaining mice continued eating the L-P/C-HF diet.

first: Long

last: Wang

first: Chieh

middle: J

last: Chou

first: Robert

last: Mansourian

first: Sylviane

last: Metairon


title: Retinoic acid (RA) induction time-course to profile gene expression during mES cell differentiation

city: Kansas City

first: Julia

last: Zeitlinger

state: MO

institute: Stowers Institute for Medical Research

summary: Murine ES cell gene expression before RA induction are used to compare gene expression for time-points of 8, 12, 16, 24, 36, 48, 60 and 72 hours post-induction.

overall_design: KH2 ES Cell RA Differentiation Time-course

first: Bony

last: De Kumar

first: Jeff

last: Johnston

first: Robb

last: Krumlauf


title: Transcriptional responses to Sonic Hedgehog pathway stimulation in in vitro derived neural progenitors

status: Public on Dec 15 2012

city: Los Angeles

first: Kevin

last: Peterson

state: CA

address: 1425 San Pablo St.

department: Department of Stem Cell Biology and Regenerative Medicine

institute: Eli and Edythe Broad-CIRM Center for Regenerative Medicine, University of Southern California Keck School of Medicine

summary: The objective of this study was to identify genes regulated by Sonic Hedgehog pathway stimulation in neural progenitors.

overall_design: Paired (parallel culture) triplicates of neuralized embryoid body cultures with and without Shh pathway stimulation (Ag1.3-treatment)

first: Yuichi

last: Nishi

first: Andrew

middle: P

last: McMahon


title: Early response of gene expression in the distal intestine of Atlantic salmon (Salmo salar L.) during the development of soybean meal induced enteritis

status: Public on Dec 17 2012

city: Victoria

first: Ben

last: Koop

state: BC

address: PO Box 3020 STN CSC

department: Biology

institute: The University of Victoria

summary: In the present study a 44k oligonucleotide salmonid microarray, qPCR and histology were used to investigate transcriptomic responses in the distal intestine during the first week of oral exposure to soybean meal in order to gain insight into early molecular response mechanisms. Intestinal tissue samples were taken on day one, two, three, five and seven after introduction of a soybean-containing diet and compared to a control group fed fishmeal.

overall_design: Day 1, day 2, day 3, day 5 and day 7 (n=10 per condition) post-soybean meal feeding Atlantic salmon hybridized to common reference and compared against control (day 0 of SBM feeding). Tissue = distal intestine.

first: Christian

last: Sahlmann

last: Sutherland

first: Trond

middle: M

last: Kortner

first: A

last: Krogdahl

first: Anne

last: Bakke


title: Characteristics of Cross-Hybridization and Cross-Alignment in Pseudo-Xenograft samples by RNA-Seq and Microarrays [Illumina HumanWG-6 v3.0]

status: Public on Dec 14 2012

city: Miami

first: Camilo

last: Valdes

state: FL

address: Locator C-213.  1120 NW 14 Street

department: Center for Computational Science

institute: University of Miami

summary: In order to study molecular changes in the stroma from tissue samples it is recommended to separate tumor tissue from stromal tissue. This is particularly relevant to mouse tumor xenograft models where tumor, particularly metastatic tumors, can be small and difficult to separate from the host tissue. In our research we compared qualitatively the ability of high-throughput mRNA sequencing, RNA-Seq, and microarrays to detect tumor (human) and stromal (mouse) expression from mixed tumor-stromal samples in terms of the genes and pathways that are involved in cross-alignment (RNA-Seq) and cross-hybridization (microarrays).

sample_organism:
Homo sapiens
Mus musculus

overall_design: Human samples consisted of total RNA obtained from MDA-MB-231 human breast carcinoma cell line and isolated from three independent cultures of sub-confluent MDA-MB-231 cell lines in exponential phase of growth.  Mouse samples were obtained from NOD scid gamma mice, and normal lung tissue was harvested from three independent age-matched mice.

first: Jennifer

last: Clarke


title: Expression data from mice peritoneal cells

status: Public on Dec 13 2012

city: Mississippi State

first: Teresia

last: Buza

state: Mississippi

address: 240 Wise Center Drive

department: Basic Sciences

institute: Mississippi State University

summary:
Sodium methyldithiocarbamate (SMD) is one of the most abundantly used conventional pesticides in the U.S.  At dosages relevant to occupational exposure, it causes major effects on the immune system in mice, including a decreased resistance to sepsis.  This lab has identified some of the mechanisms of action of this compound and some of the immunological parameters affected, but the global effects have not previously been assessed.
We used microarrays to analyze the effect of SMD on lipopolysaccharide-induced mediators important in innate immunity and inflammation and reveal a broad effect on expression of transcription factors involved in Toll-like Receptors 4 (TLR4) signaling.

overall_design: Female (C57Bl/6 x C3H F1) mice at 12-16 weeks old were housed in filter top shoebox cages with 5 mice per cage in a temperature (70-78°F) and humidity (40-60%) controlled environment. Then the mice were anesthetized with halothane and 50 µl of SMD solution was placed on the nares. SMD was administered by inhalation at (1) 100 mg/kg, (2) 200 mg/kg or (3) 300 mg/kg. 30 minutes after administering SMD the mice were challenged with ultra pure LPS from Salmonella minnesota at 60 µg/mouse (in PBS) intravenously in a tail vein.

first: Stephen

last: Pruett


title: Expression data from knock-down ES stable cell line

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

summary:
In order to identify the effects of the knock-down of the gene of interest on the mouse ES transcriptome, we performed Affymetrix Gene-Chip hybridization experiments for the knock-down cell line.
Transcriptome analysis of the knock-down transgenic mouse ES cell line.
The knock-down cell line (shE13) was generated by stably expressing a specific short-hairpin RNA against E13 sequence thus knocking-down E13 expression in parental mouse ES cell line E14Tg2a.4 (E14, Hooper M et al., 1987).
The specific mouse gene knocked down in the ES cell line is E130012A19Rik.

overall_design: For the analysis on knock-down cell line, total RNA extracted from three different shE13 clones was compared to total RNA extracted from two shCTL clones


status: Public on Dec 16 2012

city: Columbus

first: Xianghong

last: Zou

state: OH

address: 1645 Neil Ave

department: Pathology

institute: Ohoi State University

summary: Impact of  CDK4-deficiency on Eµ-myc driven B-lymphoma By crossing mating CDK4 Knockout mice with Eµ-myc mice,We found CDK4-deficiency enhances the Eµ-myc induced  B-lymphoma.We further to discover the molecular mechanism

overall_design: B-lymphoma cells form the cdk4+/+ Eµ-myc and cdk4-/-Eµ-myc mice and then culturing for RNA extraction and hybridization on Affymetrix microarrays.

first: Yongsheng

last: Wu

first: YuanZhi

last: Lu

first: Xiaoling

last: Feng


title: E130012A19Rik: Biomarker of Pluripotent Stem Cells


title: Evolution of human-specific microRNA miR-941 [cerebellum gene expression]

city: shanghai

first: Song

last: Guo

address: 320 Yue Yang Road

institute: PICB

summary: miRNA-mediated gene expression silencing has previously been shown to be important for a variety of physiological and pathological processes. Here, we have explored the role of one bona fide human-specific miRNA (miR-941) in evolution of the human-specific expression and function. Using combination of high-throughput sequencing (GSE26545), miRNA transfection and large-scale PCR of various human populations, we have shown that emergence and rapid expansion of miR-941 might take place on the human evolutionary linage between six and one million years ago. Functionally, miR-941 could be associated with hedgehog and insulin signaling pathways, and thus might potentially play a role in evolution of human longevity. Human-specific effects of miR-941 regulation are detectable in human brain and affect genes involved in neurotransmitter signaling. Furthermore, emergence of miR-941 on the human evolutionary linage was accompanied by the accelerated loss of its binding sites. Taken together, these results strongly implicate the contribution of miR-941 in evolution of the human-specific phenotype.

sample_organism:
Macaca mulatta
Pan troglodytes
Homo sapiens

overall_design: Cerebellum mRNA samples from 5 human, 5 chimpanzee and 1 rhesus macaque for Affymetrix Human Exon 1.0 ST Arrays were prepared following the standard GeneChip Whole Transcript (WT) Sense Target Labelling Assay.

first: Haiyang

last: Hu

first: Philipp

last: Khaitovich


title: Microarray gene expression profiling of aortic genes of APOE-deficient mice receiving atherosclerosis treatment with the antioxidant vitamin E

status: Public on Dec 11 2012

city: Zurich

first: Ursula

last: Quitterer

address: Winterthurerstrasse 190

department: Molecular Pharmacology

institute: ETH Zurich

summary: Hypercholesterolemic APOE-deficient mice are a widely used experimental model of atherosclerosis and increased generation of reactive oxygen species (ROS) is a prominent feature of atherosclerosis development. To study the impact of ROS on atherogenesis, we treated APOE-deficient mice for 7 months with the antioxidant vitamin E (2000 IU/kg diet) and performed whole genome microarray gene expression profiling of aortic genes. Microarray gene expression profiling was performed of whole aortas isolated from vitamin E-treated APOE-deficient relative to untreated APOE-deficient mice with overt atherosclerosis, and nontransgenic B6 control mice. Microarray gene expression profiling revealed that vitamin E treatment prevented atherosclerosis-related gene expression changes of the aortic intima and media.

overall_design: Microarray gene expression profiling was performed of whole aortas isolated from APOE-deficient mice with atherosclerosis relative to vitamin E-treated APOE-deficient mice, and nontransgenic B6 control mice. Three study groups were analyzed, i.e. 8 months-old untreated APOE-deficient mice with overt atherosclerosis, age-matched APOE-deficient mice treated for 7 months with the antioxidant vitamin E  (2000 IU/kd diet), and nontransgenic B6 control (C57BL/6J) mice. Two biological replicates were made of each group, and total RNA of three aortas was pooled for one gene chip. The study complements microarray study GSE19286.

first: Joshua

last: Abd Alla


title: Expression data from inducible ES stable cell line

summary:
In order to identify the effects of the induction of the gene of interest on the mouse ES transcriptome, we performed Affymetrix Gene-Chip hybridization experiments for the inducible not-tagged cell line.
Transcriptome analysis of the inducible transgenic mouse ES cell line.
The E13 inducible cell lines derived from parental EB3 cell line. The cell line EB3 was obtained from the laboratory of Dr Hitoshi Niwa as previously described in (Masui S et al., 2005).
Tthe specific mouse gene is E130012A19Rik.

overall_design: For the analysis on the inducible not-tagged cell line, total RNA was extracted from three biological replicates grown in medium deprived of Tetracycline for 48 hours; RNA extracted from un-induced clones was used as control.


title: Differential gene expression in APOE3 and APOE4 gene targeted replacement mice

city: Rostock

first: Gregor

last: Warsow

address: Ernst-Heydemann-Str. 8

department: Medical Department

institute: University of Rostock

summary: The aim of the study was to investigate hepatic gene expression profiles differentially regulated by the APOE genotype in gene targeted replacement mice. The APOE4 genotype is associated with increased mortality in the elderly and is an independent risk factor for age-dependent chronic diseases. However, little is known about the underlying mechanisms and molecular targets involved in the APOE4-risk association. As APOE is centrally involved in lipid and cholesterol metabolism and in large part is produced in the liver, we analyzed hepatic RNA profiles of APOE4- and APOE3-expressing mice.

overall_design: 2 groups of 5 animals with 1 liver extract per animal. Mice were homozygous for a human APOE3 or APOE4 gene targeted replacement of the endogenous mouse Apoe gene (B6.129P2-Apoetm2(APOE*3)Mae N8 or B6.129P2-Apoetm3(APOE*4)Mae N8, Taconic Transgenic Models™, http://www.taconic.com/wmspage.cfm?parm1=2542), purchased at the age of 6-8 weeks, strain C57BL/6, 3 months old at the performance of the microarray, 6 weeks on a high-fat diet containing 41% energy from milk fat and 2 g/kg cholesterol.

last: Graeser

first: F

last: Doering

first: R

last: Haesler

first: S

last: Schreiber

first: P

last: Huebbe

first: G

last: Rimbach


title: Expression profiles of C2C12 myotubes in response to PGC-1α (peroxisome proliferator-activated receptor gamma, coactivator 1 alpha) overexpression and/or iron chelation

status: Public on Dec 10 2012

city: Madison

first: David

middle: J.

last: Pagliarini

state: WI

address: 433 Babcock Dr.

department: Biochemistry

institute: University of Wisconsin-Madison

summary: Mitochondria are centers of metabolism and signaling whose content and function must adapt to changing cellular environments. The biological signals that initiate mitochondrial restructuring and the cellular processes that drive this adaptive response are largely obscure. To better define these systems, we performed matched quantitative genomic and proteomic analyses of mouse muscle cells as they performed mitochondrial biogenesis. We find that proteins involved in cellular iron homeostasis are highly coordinated with this process, and that depletion of cellular iron results in a rapid, dose-dependent decrease of select mitochondrial protein levels and oxidative capacity. We further show that this process is universal across a broad range of cell types and fully reversed when iron is reintroduced. Collectively, our work reveals that cellular iron is a key regulator of mitochondrial biogenesis, and provides quantitative datasets that can be leveraged to explore post-transcriptional and post-translational processes that are essential for mitochondrial adaptation.

overall_design: C2C12 mouse myoblasts were differentiated into myotubes for 3 days, at which point they were infected with adenovirus expressing either green fluorescent protein (GFP) or GFP-tagged PGC-1α (GFP-PGC-1α) ± treatment with the iron chelator deferoxamine (DFO) (for 4 treatments total). The cells were grown for three more days, then RNA was extracted and applied to Affymetrix Mouse 430 2.0 arrays. Gene expression was measured in biological duplicate (4 treatments × 2 replicates = 8 arrays).

first: Jarred

middle: W

last: Rensvold

first: Shao

last: Ong

first: Athavi

last: Jeevananthan

first: Steven

last: Carr

first: Vamsi

middle: K

last: Mootha


title: Global gene expression profiling of hepatocellular carcinomas in B6C3F1 mice induced by Ginkgo biloba extract by gavage for two years

status: Public on Dec 07 2012

city: RTP

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: Ginkgo biloba leaf extract (GBE) has been used for centuries in traditional Chinese medicine and today is used as an herbal supplement for various indications such as improving neural function, anti-oxidant and anti-cancer effects. As part of the herbal supplement industry, these compounds are largely unregulated, and may be consumed in large concentrations over extended periods of time. This is of particular concern, because the long-term effects in terms of toxicity and carcinogenicity data is lacking for many herbal products, including GBE. The 2-year B6C3F1 mouse carcinogenicity bioassay indicated a marked dose-related increase in hepatocellular carcinoma (HCC) development associated with exposure to GBE. We have shown that the mechanism of this increase in tumorigenesis is related to a marked increase in the incidence of β-catenin mutation, and report a novel mechanism of constitutive β-catenin activation through post-translational modification leading to constitutive Wnt signaling and unregulated growth signaling and oncogenesis. Furthermore, using global gene expression profiling, we show that GBE-induced HCC exhibit overrepresentation of gene categories associated with human cancer and HCC signaling including upregulation of relevant oncogenes and suppression of critical tumor suppressor genes, as well as chronic oxidative stress, a known inducer of calpain-mediated degradation and promoter of hepatocarcinogenesis in humans. These data provide a molecular mechanism to GBE-induced HCC in B6C3F1 mice that is relevant to human cancer, and provides relevant molecular data that will provide the groundwork for further risk assessment of unregulated compounds, including herbal supplements.

overall_design: Six hepatocellular carcinomas induced by GBE, six spontaneous hepatocellular carcinomas, and six normal liver samples, three technical replicates each.

first: Mark

last: Hoenerhoff

first: Arun

last: Pandiri

first: Stephanie

last: LaHousse

first: Hue-Hua

last: Hong

first: Thai-Vu

last: Ton

first: Shyamal

last: Peddada

first: Robert

middle: C

last: Sills


title: Knockout of GPx4 gene in mouse keratinocyte

status: Public on Dec 06 2012

city: Bethesda

first: Bradley

last: Carlson

state: MD

address: 9000 Rockville Pike

institute: National Cancer Institute

summary:
Comparative analysis of gene expression in cultured primary keratinocytes isolated from newborn control (K14-cre; GPx4fl/+) and knockout (K14-cre; GPx4fl/fl) mice.
Selenoproteins are essential for skin function, as targeted abolition of selenoproteins in epidermal tissue results in newborn mice manifesting gross abnormalities of skin and hair, accompanied by retarded growth and premature death. To investigate whether lack of a single selenoprotein could induce similar phenotypic effect in mice, we generated keratinocyte-specific knockout mice lacking glutathione peroxidase 4 (GPx4), an essential selenoprotein in skin, to examine phenotypic changes resulting from the lack of GPx4 in skin. Ablation of GPx4 results in focal alopecia and disturbed hair follicle morphogenesis, with GPx4 being essential during early stages of hair follicle morphogenesis as well as for keratinocyte adhesion and proliferation in culture.

overall_design: We have generated mice with selective removal of the GPx4 gene in keratinocytes under the control of Keratin-14-cre (K14-cre) promoter. Comparative microarray analysis was performed on RNA samples taken from pooled primary keratinocytes from knockout and control mice from the same litter. Array replicates were performed using RNA samples from three different litters.

first: Aniruddha

last: Sengupta

first: Ulrike

last: Lichti

first: Andrew

middle: O

last: Ryscavage

first: Marcus

last: Conrad

first: Stuart

middle: H

last: Yuspa

first: Dolph

middle: L

last: Hatfield


title: Cross-species transcriptional networks in Diabetic Glomerulopathy in mouse and man

city: Ann Arbor

first: Viji

last: Nair

address: 1152 West Medical Centre Dr.

institute: University of Michigan

summary:
Murine models have been valuable instruments in defining the pathogenesis of diabetic nephropathy (DN), but they only partially recapitulate disease manifestations of human DN, limiting their utility . In order to define the molecular similarities and differences between human and murine DN, we performed a cross-species comparison of glomerular transcriptional networks.  Glomerular gene expression was profiled in  patients with early type 2 DN and in three mouse models (streptozotocin DBA/2 mice, db/db C57BLKS, and eNOS-deficient C57BLKS db/db mice).  Species-specific transcriptional networks were generated and compared with a novel network-matching algorithm. Three shared, human-mouse cross-species glomerular transcriptional networks containing 143 (Human-STZ), 97 (Human- db/db), and 162 (Human-  eNOS-/- db/db) gene nodes were generated.  Shared nodes across all networks reflected established pathogenic mechanisms of diabetic complications, such as elements of JAK-STAT and VEGFR signaling pathways .  In addition, novel pathways not formally associated with DN and  cross-species gene nodes and pathways unique to each of the human-mouse networks were discovered. The human-mouse shared glomerular transcriptional networks will assist DN researchers in the selection of mouse models most relevant to the human disease process of interest. Moreover, they will allow identification of new pathways shared between mice and humans.
We used microarrays to analyze the  transcriptome of three different diabetic mouse models

overall_design: Glomerular RNA was extracted  using the RNeasy Mini Kit and processed for hybridization on Affymetrix GeneChip Mouse Genome 430 2.0  microarrays.

first: Jeffrey

middle: B

last: Hodgin

first: Hongyu

last: Zhang

first: Ann

last: Randolph

first: Raymond

last: Harris

middle: G

last: Nelson

first: E

last: Weil

first: Jignesh

last: Patel

first: Frank

last: Brosius

first: Matthias

last: Kretzler


title: the influence of a modification of the gut microbiota composition on the hepatic steatosis induced by n-3 polyunsaturated fatty acid (PUFA) depletion

status: Public on Dec 12 2012

city: Brussels

first: Jean-Baptiste

last: Demoulin

address: av Hippocrate 75, B1.74.05

department: de Duve Institute

country: Belgium

institute: Université catholique de Louvain

summary: in the present study, we evaluated whether microbiota modulation is able to restore hepatic steatosis induced by n-3 PUFA depletion in mice. For this purpose, mice were fed during three months with a n-3 PUFA-depleted diet (presenting a high n-6/n-3 PUFA ratio), and then supplemented with fructooligosaccharides (FOS, 0.25g/day/mice), a prebiotic, during the last ten days of the experiment (DEF/FOS). In the same time, some n-3 PUFA-depleted mice were returned on a control diet during the last 10 days of treatment (DEF/CT) to compare the effect of FOS supplementation to a restored intake in n-3 PUFA. Microarray analyses were performed to identify the molecular targets modified by FOS supplementation in the liver of n-3 PUFA depleted mice. These mice were compared to control mice (fed a control diet during the 112 days of experiment) and to n-3 PUFA-depleted mice (fed a n-3 PUFA-depleted diet during the 112 days of experiment) for which the results have been previously published (Pachikian B.D. et al. PLoS One. 2011;6(8):e23365, accession number GSE26986)

overall_design: Male C57Bl/6J mice (9 weeks old; Charles River, Brussels, Belgium) were housed in groups of 4 mice per cage at 22°C in a 12 h light/dark cycle and given free access to diet and water.   After an acclimatisation period of 1 week, mice were fed a control (CT) (D08041805, Research Diets, New Brunswick, USA) or an n-3 PUFA-depleted diet (DEF) (D08041806, Research Diets, New Brunswick, USA) for 112 days ad libitum. The CT diet contained the following (percent w/w): casein 20, total carbohydrate 72.4 (including corn starch 44.2, sucrose 10, maltodextrin 13.2, cellulose 5), soybean oil 5, mineral mix 3.5 and vitamin mix 1. The depletion was induced by replacing the soybean oil with sunflower oil, which exhibited a higher n-6/n-3 PUFA ratio. The n-6/n-3 PUFA ratio was 6.9 and 127.2 for the CT diet and the DEF diet, respectively. Ten days before the end of the experiment, DEF mice were divided into three groups: DEF, DEF/FOS and DEF/CT mice. The DEF mice were still fed with the n-3 PUFA depleted diet (DEF). The DEF/FOS mice were still fed the DEF diet and were supplemented for 10 days with fructooligosaccharides (DEF/FOS). FOS (Beneo P95 gift from Orafti; Tienen, Belgium) was added to tap water in a concentration adequate to reach an intake of 0.25g of FOS per day. For DEF/CT mice, the DEF diet was replaced by the CT diet during the last 10 days of treatment. At the end of the study period, mice fed the CT (n=4), DEF (n=7), DEF/CT (n=8) or DEF/FOS diet (n=8) were anaesthetised (ketamine/xylazine i.p., 100 and 10 mg/kg of body weight, respectively). The liver tissue was immediately clamped in liquid N2 and kept at -80°C until analysis.   All mice experiments were approved by the local animal ethics committee and the housing conditions were as specified by the Belgian Law of April 6, 2010 on the protection of laboratory animals (agreement n° LA 1230314).

first: Barbara

middle: D

last: Pachikian

first: Ahmed

last: Essaghir

first: Nathalie

last: Delzenne


title: Gene expression profiling of in vitro derived induced and natural FOXP3+ regulatory T cells and ex-iTreg cells in the mouse

city: Milwaukee

first: Martin

last: Hessner

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

summary: Induced Treg (iTreg) cells are essential for tolerance and can be used therapeutically, yet their stability in vivo and mechanisms of suppression are unresolved. Here, we used a treatment model of colitis to examine the role of autologous IL-10 in iTreg cell function.  Mice treated with IL-10+/+ iTreg cells in combination with IL-10–/– natural Treg (nTreg) cells survived and gained weight, even though iTreg cells were numerically disadvantaged and comprised just ~20% of all Treg cells in treated mice.   Notably, ~85% of the transferred iTreg cells lost Foxp3 expression (ex-iTreg) but retained a portion of the iTreg transcriptome which failed to limit their pathogenic potential. The TCR repertoires of iTreg and ex-iTreg cells exhibited almost no overlap, which indicates that the two populations are clonally unrelated and maintained by different selective pressures.  These data demonstrate a potent and critical role for iTreg cell produced IL-10 that can supplant the IL-10 produced by nTreg cells and compensate for the inherent instability of the iTreg population.

overall_design: BALB/c Rag1-/- mice were treated with 500,00 WT nTreg cells plus 500,000 WT in-vitro-derived iTreg cells.  After 125 days cells were sorted by flow cytometry from spleens and mesenteric lymph nodes from 14 treated mice.  EGFP+ Thy1.1+ iTreg cells, EGFP+ Thy1.1– nTreg cells, and EGFP–Thy1.1+ ex-iTreg cells were pooled  and used to generate total RNA for each iTreg, nTreg, and ex-iTreg array set, which was labeled and hybridized to Affymetrix 430 2.0 GeneChips in accordance to the manufacturer’s protocol. Two sets of arrays were performed, and the results were averaged. Both iTreg and nTreg array sets were compared to a) naïve CD4+EGFP– Tconv cells from Foxp3EGFP.  The subset of probe sets whose expression increased or decreased by twofold or more relative to Tconv cells as a common standard was identified and used for further analysis.

first: Erica

last: Schmitt

first: Dipica

last: Haribhai

first: Jason

last: Williams

first: Praful

last: Aggarwal

first: Shuang

last: Jia

first: Ke

last: Yan

first: Rachel

last: Lorier

first: Amy

last: Turner

first: Ziegelbauer

last: Jennifer

first: Pippa

last: Simpson

first: Nita

last: Salzman

first: Ulrich

last: Broeckel

first: Calvin

last: Wiliams


title: Gene expression profiling unravels cancer-related hepatic molecular signatures in steatohepatitis but not in steatosis

city: Heidelberg

first: Julia

last: Starmann

address: Im Neuenheimer Feld 460

department: Molecular Genetics

institute: German Cancer Research Center (DKFZ) and National Center for Tumor Diseases Heidelberg (NCT)

summary: Pathogenesis and factors for determining progression of alcoholic and non-alcoholic steatosis to steatohepatitis with risk of further progression to liver cirrhosis and cancer are poorly understood. In the present study, we aimed to identify potential molecular signatures for discrimination of steatohepatitis from steatosis. Global gene expression analysis was applied to unravel differentially expressed genes between steatohepatitis compared to steatosis and control samples. For functional annotation as well as the identification of disease-relevant biological processes of the differentially expressed genes the gene ontology (GO) database was used. Genes down-regulated in steatohepatitis were mainly involved in metabolic processes. Genes up-regulated in steatohepatitis samples were associated with cancer progression and proliferation. Further statistical and pathway analysis lead to the selection of 46 candidate genes which were validated in two sample cohorts by quantitative real-time PCR. In surgical liver resection samples 39 genes and in percutaneous liver biopsies 30 genes were significantly up-regulated in steatohepatitis.  Conclusion: The development of steatohepatitis is characterized by distinct molecular changes.

overall_design: 44 human liver tissue surgical samples (normal n=13; steatosis n=19; steatohepatitis n=12, 8/2 cirrhotic/non-cirrhotic) obtained from patients undergoing liver surgery for HCC, other malignancy/metastatic disease, benign tumors of the liver and organ dedicated to transplantation. Virtually normal control samples in this cohort were taken from patients undergoing surgical resection of liver metastasis, but the surrounding liver tissue used for the molecular analyses was normal, non-tumorous liver tissue without detectable pathological changes. The samples were provided by the Biobank at the Medical University of Graz.

first: Holger

last: Sültmann

first: Maria

last: Fälth

first: Michael

last: Trauner

first: Kurt

last: Zatloukal


title: Neutrophil-derived IL-1β is sufficient for abscess formation in immunity against Staphylococcus aureus in mice

status: Public on Dec 05 2012

first: Lloyd

last: Miller

address: 52-121 Center for Health Sciences, 10833 Le Conte Avenue

department: Medicine, Orthopaedic Surgery

institute: UCLA

summary: Neutrophil abscess formation is critical in innate immunity against many pathogens. Here, the mechanism of neutrophil abscess formation was investigated using a mouse model of Staphylococcus aureus cutaneous infection. Gene expression analysis of S. aureus-infected skin revealed that induction of neutrophil recruitment genes was largely dependent upon IL-1beta/IL-1R activation. Unexpectedly, using IL 1beta reporter mice, neutrophils were identified as the primary source of IL-1beta at the site of infection. Furthermore, IL-1beta-producing neutrophils were necessary and sufficient for abscess formation and bacterial clearance. S. aureus-induced IL 1beta production by neutrophils required TLR2, NOD2, FPRs and the ASC/NLRP3 inflammasome. Taken together, IL-1beta and neutrophil abscess formation during an infection are functionally, spatially and temporally linked as a consequence of direct IL-1beta production by neutrophils.

overall_design: Lesional skin biopsies obtained from C57BL/6J WT mice or IL-1R-deficient mice at 4 hours post-infection with Staphylococcus aureus.  Uninfected skin biopsies were also collected from WT and IL-1R-deficient mice.

first: John

middle: S

last: Cho


title: Microarray gene expression profiling of transgenic mice with myocardium-specific expression of RKIP or a GRK-specific peptide inhibitor

first: Ursula

last: Quitterer

summary: The Raf kinase inhibitor protein (RKIP) is a dual inhibitor of the Raf kinase and the G-protein-coupled receptor kinase 2 (GRK2). GRK2 is an indispensable kinase, which exerts a major role in the pathogenesis of heart failure, and inhibition of GRK2 is cardioprotective in experimental models of heart failure. To investigate the cardiac function of RKIP as GRK2 inhibitor, we generated transgenic mice with myocardium-specific expression of RKIP under control of the alpha-MHC promoter. For comparison, mice with myocardium-specific expression of a GRK-specific peptide inhibitor (GRK-Inh) were also generated. Two different transgenic mouse models were established. Transgenic RKIP mice and transgenic GRK-Inh mice were born at Mendelian frequencey and grew to adulthood normally.

overall_design: Microarray gene expression profiling was performed with heart tissue isolated from three study groups: (i) RKIP-transgenic mice, (ii) GRK-Inh-transgenic mice, and (iii) B6 control mice.

first: Joshua

last: Abd Alla


title: Specific transcriptional response of four blockers of estrogen receptors on estradiol-modulated genes in the mouse mammary gland

city: Quebec

first: Ezequiel

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

institute: CRCHUL

summary: The efficacy and exceptionally good tolerance of estrogen blockade in the treatment of breast cancer is well recognized but novel agents are required, especially to take advantage of the multiple consecutive responses obtained in breast cancer progressing following previous hormone therapy, thus delaying the use of cytotoxic chemotherapy with its usually serious side effects. Acolbifene (ACOL) is a novel and unique antiestrogen completely free of estrogen-like activity in both the mammary gland and uterus while preventing bone loss. From the preclinical and clinical data so-far available, this new antiestrogen represents a unique opportunity for a highly potent and specific blockade of estrogen action in the mammary gland and uterus while exerting estrogen-like beneficial effects in other tissues (selective estrogen receptor modulator or SERM activity). In order to better understand the specificity of action of acolbifene, we have used Affymetrix GeneChips containing 45,000 probe sets to analyze 34,000 genes to determine the specificity of this compound compared to the pure antiestrogen fulvestrant, as well as the mixed antagonists/agonists tamoxifen and raloxifene to block the effect of estradiol (E2) and to induce effects of their own on gene expression in the mouse mammary gland. The genes modulated by E2 were those identified in two separate experiments and validated by quantitative real-time PCR (Q_RT-PCR). Three hours after the single subcutaneous injection of E2 (0.05 ug), the simultaneous administration of acolbifene, fulvestrant, tamoxifen and raloxifene blocked by 98%, 62%, 43% and 92% the number of E2-upregulated genes, respectively. On the other hand, 70%, 10%, 25% and 55% of the genes down-regulated by E2 were blocked by the same compounds. Acolbifene was also the compound which, when used alone, modulated the smallest number of genes also influenced by E2, namely 4%, thus possibly explaining the potent tumoricidal action of this compound in human breast cancer xenografts where 61% of tumors disappeared, thus bringing a new paradigm in the hormonal therapy of breast cancer.

overall_design: Female C57BL6 mice were ovariectomized (OVX). One week after OVX, mice were treated with EM-652.HCl (acolbifene), tamoxifen citrate, raloxifene or ICI 182780 (fulvestrant). Compounds were administered to OVX mice or to OVX mice simultaneously treated with 17b-estradiol (E2). Control groups received an injection of the vehicle alone. All animals were sacrificed after 3h of treatment.Mammary glands from all mice of the same group were collected and pooled. Total mRNA was isolated and converted to biotinylated cRNA.A microarray analysis was performed using Murine U74Av2 Affymetrix microarrays.

first: Van

last: Luu-The

first: Céline

last: Martel

first: Pascal

last: Belleau

first: Fernand

last: Labrie


title: Gene expression analysis of male and female embryonic day 14 genital tubercle (GUDMAP Series ID: 45).

status: Public on Dec 04 2012

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

institute: IGMM MRC Human Genetics Unit

summary: The long term objective is to create an encyclopedia of the expression levels of all genes in multiple components of the developing urogenital system. The central thesis is straightforward. The combination of microdissected and laser capture microdissection (LCM) plus Microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing urogenital system. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene. The ensuing rapid read-out provides an expression atlas that is more sensitive, more economical and more complete than would be possible by in situ hybridizations alone. The data submitted here represents the gene expression profiles of the embryonic day 14 genital tubercle of the male and the female.

overall_design: The genital tubercle region from E14 (TS22) FVB/N males and females were microdissected and total RNA isolated for gene expression analysis using the Affymetrix MOE430 microarray chip.

first: James

last: Lessard


title: Expression analysis of G9C8 clone and NOD.G9C8 tg CTLs

city: Chicago

first: Alexander

last: Chervonsky

state: IL

address: 924 E 57th Street

institute: University of Chicago

summary:
Diabetogenic CD8+ G9C8 clone cells and the T cells from a transgenic mouse bearing the same TCR as the clone, displayed differences in their ability to induce disease in vivo.Microarray analysis was done to identify the molecular basis for  such differences between the two sets of CD8 T cells.
Microarray analysis was done to identify the molecular basis for such differences between the two sets of CD8 T cells

overall_design: 3 vials of frozen G9C8 clone cells and spleen cells from 2 NOD.G9C8 transgenic mice were similarly peptide stimulated for 3 days and rested in IL2 for 2 days in order to obtain uniformly activated cells for analysis.

first: Lia

last: Avanesyan

first: Vineeth

last: Varanasi


title: Apelin/APJ targeted microRNAs in pulmonary artery endothelial cells

city: New Haven

first: hyung

last: chun

state: CT

address: 300 George St Room 770H

department: Internal Medicine

institute: Yale University

summary: Evaluation of microRNAs that are downstream of apelin/APJ signaling in the pulmonary artery endothelial cells.

overall_design: Triplicates per group, subjected to: 1) control siRNA, 2) apelin siRNA, 3) APJ siRNA, 4) apelin + APJ siRNA

first: Hyung

last: Chun


title: PGC-1 alpha isoforms and muscle hypertrophy

city: Boston

first: Bruce

last: Spiegelman

state: MA

address: DFCI, Dept of Cancer Biology, 450 Brookline Ave. CLSB, 11115

institute: Dana Farber Cancer Institute

summary: An alternative promoter of the PGC-1alpha gene gives rise to three new PGC-1alpha isoforms refered to as PGC-1a2 (A2), PGC-1a3 (A3) and PGC-1a4 (A4). The proximal PGC-1 alpha promotor transcribes the canonical PGC-1 alpha which is refered to as PGC-1a1 (A1).G1/G2/G3 samples refer to the Green fluorescent protein (GFP) control samples used in this experiment. Forced expression of the PGC-1a4 isoform results in muslce hypertrophy associated with increased IGF-1 signaling and repression of myostatin signaling.

overall_design: Mouse primary myoblasts isolated from C57BL/6 mice were differentiated in vitro. Fully differentiated myotubes were transduced with adenoviral vectors expressing GFP (as control) or each of the PGC-1alpha isoforms originating from the proximal or alternative promotor.

first: Jorge

last: Ruas

last: White

first: Rajesh

middle: R

last: Rao

first: Sandra

last: Kleiner

first: Kevin

middle: T

last: Brannan

first: Brooke

last: Harrison

first: Nicholas

last: Greene

first: Jun

last: Wu

first: Jennifer

last: Estall

first: Brian

last: Irving

first: Ian

last: Lanza

first: Kyle

last: Rasbach

first: Mitsuharu

last: Okutsu

first: Sreekumaran

last: Nair

first: Zhen

last: Yan

first: Leslie

last: Leinwand


title: Expression analysis of eu-miR-155 transgenic mice B-cells.

status: Public on Dec 03 2012

first: Sukhinder

last: Sandhu

address: 460 W 12th Ave

institute: The Ohio State University

summary: miR-155 transgenic mice develop pre-B cell leukemia/lymphoma. Though some targets of miR-155 are known, understanding of the mechanism by which miR-155 overexpression drives malignant transformation is not known. MicroRNAs regulate multiple genes.

overall_design: 3 transgenic and 4 wild type mice B-cells were analyzed

first: Carlo

last: Croce

first: Stefano

last: Volinia


title: Transcription factor AP-2 gamma is a core regulator of tight junction biogenesis and cavity formation during mouse early embryogenesis

status: Public on Dec 01 2012

city: East Lansing

first: Jason

last: Knott

address: 1230 H Anthony Hall

department: Animal Science

institute: Michigan State University

summary: We characterzised global changes in gene expresseion between 8 cell embryos and blastocysts to identify potential genes required for blastocyst formation.

overall_design: Expression data from mouse 8-cell embryos and blastocysts.  Eight-cell embryos and blastocysts were obatained from B6D2F1 female X B6D2F1 male. We  analyzed a total of four samples at both stages.

first: Inchul

last: Choi


title: Expression data from inducible ES stable cell lines

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

institute: Tigem

summary:
In order to identify the effects of the induction of the gene of interest on the mouse ES transcriptome, we performed Affymetrix Gene-Chip hybridization experiments for the different inducible cell lines
Transcriptome analysis of the inducible transgenic mouse ES cell lines

overall_design: For the analysis on the different inducible cell lines, total RNA was extracted from three biological replicates grown in medium deprived of Tetracycline for 17 and 24 hours; RNA extracted from un-induced clones was used as control. Total RNA extracted from parental cell line EBRTcH3 (EB3) was used as additional control.


title: Direct cell conversion from human dermal fibroblast to adipocyte

city: Yokohama

first: Ryota

last: Hasegawa

state: Kanagawa

address: 1-7-22 Suehiro-cho Tsurumi-ku

department: Omics science center

institute: RIKEN Yokohama

summary: To investigate the effect of ZNF395 on adipogenesis, we tested whether ZNF395 enhance cell conversion from human dermal Fibroblast (FIB) to Adipocyte (ADP). PPARG2 was reported as a master regulator and can induce adipogenesis in non-adipogenic fibroblasts. We transduced PPARG2 with or without ZNF395 in FIB with lentivirus. Interestingly, co-transduction of PPARG2 and ZNF395 showed higher occurrence of adipocyte-like cells as compared with PPARG2 alone. Moreover, genes related with lipid metabolic process and lipid transport was significantly up-regulated in combination of PPARG2 and ZNF395. These results suggest that ZNF395 co-ordinate the transcriptional regulatory pathway with PPARG2, necessary for the induction of adipogenesis.

overall_design: Total RNA was obteined from human dermal fibroblast transduced with mock lentivirus vector (FIB_ctrl), PPARG2 (FIB_PPARG2) and co-transduced with PPARG2 and ZNF395 (FIB_PPARG2+ZNF395).

first: H

last: Ryota

first: A

last: Ogawa

last: Yoshihide

last: Suzuki

first: Jay

last: Shin


title: Transcriptional regulation of myoblasts in HMGA2 KO mice

city: Cambrdige

first: Yunyu

last: Zhang

address: 22 Windsor Ave

institute: Novartis Institute for Biomedical Research

summary: We sought to identify critical factors regulating muscle stem cell activation and commitment, and determined through loss-of-function analyses that HMGA2 (high mobility group AT-hook 2) is a key regulator of myogenesis both in vitro and in vivo.

overall_design: mRNAs were isolated from Hmga2 -/- and Hmga2 +/+ mice myoblasts, and a microarray experiment was performed.

first: Zhizhong

last: Li

first: David

last: Glass


title: Differentially expressed zinc finger proteins during human adipogenesis

summary: To investigate the collective role of zinc finger proteins in adipogenesis, we induced adipogenesis using human mesenchymal stem cells (MSC) and compared the gene expression profiles using human Illumina beads arrays. We performed three independent experiments of time-series analysis (0h, 1h, 12h, 24h, 2d, 4d, 6d, 9d, 12d, 15d after induction of adipogenesis) in order to comprehensively capture the dynamic profiles of transcriptome during differentiation. Statistical filtering based on Analysis of Variance (ANOVA; p-value < 0.001, FDR 5%) and Gene Ontology classification using the Human Gene Nomenclature Database (HGNC) identified 618 out of 678 zinc finger proteins (ZFPs) that were significantly expressed during adipogenesis. Moreover, 34 out of 618 genes were differentially expressed more than 2-fold up or down regulated. The K-means clustering analysis further revealed four dynamic expression patterns: one gene in early-response, seven genes in transient, twenty genes in progressively-induced and four genes in the down-regulated, demonstrating the dynamic involvement of ZFPs in the process of adipocyte differentiation and maturation.

overall_design: Total RNA obteind from 10  different time points (0h, 1h, 12h, 24h, 2d, 4d, 6d, 9d, 12d, 15d) during adipogenesis from human Mesenchymal stem cell (MSC) to Adipocyte (ADP). Adipogensis was induced by the different cocktail of  chemical compunds  containing human-insulin, dexamethasone, indomethacin and IBMX.