title: Comparison of gene expression patterns between Lgr5 positive cells in adenomas and small intestine

status: Public on Aug 13 2012

summary: The generation of the Lgr5_EGFP_ires_CreERT2 knock-in mouse allows marking of Lgr5 positive cells of different tissues by GFP expression. Here we use these mice to sort GFP positive cells from intestinal adenomas and compare those to GFP positive cells from normal small intestine.

overall_design: In Lgr5_EGFP_ires_CreERT2 knock-in mice, GFP is expressed under the control of the Lgr5 promoter, leading to high GFP levels in Lgr5 positive cells (GFP-high). In normal small intestine, GFP-high cells mark crypt base columnar cells, the stem cells of small intestine. Intestinal adenomas can be generated in these mice when crossed to Apc_fl/fl mice by inducing Apc deletion through the Lgr5 driven Cre. We isolated GFP-high cells both from intestinal adenomas and normal small intestine of Lgr5-ki mice without the Apc_fl/fl allele and compared them to each other on 4X44K Agilent Whole Mouse Genome dual colour Microarrays (G4122F). Three independent sorts were performed and RNA of GFP-high adenoma cells hybridized directly against RNA of GFP-high cells from normal small intestine in three dye swap experiments, resulting in six individual arrays.


title: Gene expression profiling of Lgr5 positive cells within intestinal adenomas

city: Dresden

first: Daniel

middle: E.

last: Stange

address: Fetscherstr. 74

country: Germany

institute: University Clinic Dresden

summary: The generation of the Lgr5_EGFP_ires_CreERT2 knock-in mouse allows marking of Lgr5 positive cells of different tissues. Here we use these mice to sort Lgr5 positive cells and their daughter cells form intestinal adenomas and describe the expression profile of these two cell populations.

overall_design: Intestinal adenomas were generated by inducing Apc deletion through tamoxifen injection in Apc_fl/fl-Lgr5_EGFP_ires_CreERT2 mice. In these mice, GFP is expressed under the control of the Lgr5 promoter, leading to highest GFP levels in Lgr5 positive cells (GFP-high). Dividing GFP-high cells pass on Gfp two their daughter cells, thereby diluting the GFP. Daughter cells can therefore be isolated based on their lower GFP positivity (GFP-low). We sorted these two cell fractions (GFP-high and GFP-low) and compared them to each other on 4X44K Agilent Whole Mouse Genome dual colour Microarrays (G4122F). Three independent sorts were performed and RNA of GFP-high cells hybridized directly against RNA of GFP-low cells in three dye swap experiments, resulting in six individual arrays.

middle: E

first: Marc

last: van de Wetering

first: Hans

last: Clevers


title: COMPARATIVE TRANSCRIPTOMIC AND PROTEOMIC ANALYSIS OF LGR5+ve STEM CELLS AND THEIR DAUGHTERS (AGILENT ARRAYS)

summary: The identification of Lgr5 as an intestinal stem cell marker has made it possible to isolate and study primary intestinal stem cells. Applying quantitative mass spectrometry as well as transcriptomic analysis, we profiled the protein and gene changes between FACS-sorted Lgr5+ve stem cells and their immediate undifferentiated daughter cells. The overall comparison of mRNA and protein levels revealed a high level of correlation, implying that the initial control of intestinal stem cell biology occurs largely at the mRNA level. Taken together, our study presents a valuable resource for the study of intestinal stem cell biology.

overall_design: We used cell fractions of intestines from Lgr5-EGFP-ires-CreERT2 mice, expressing GFP under the control of the Lgr5 promoter. RNA was isolated from two FACS sorted cell populations, one expressing GFP at high levels (GFPhi) and the other expressing GFP at low levels (GFPlow). The gates set to sort cells for the expression profiling were the same as for the cells used for the mass spectrometry analysis. Differentially labelled cRNA from GFPhi and GFPlow cells from two different sorts (each combining three different mice) were hybridized on 4X44K Agilent Whole Mouse Genome dual colour Microarrays (G4122F) in two dye swap experiments, resulting in four individual arrays.


title: Transcriptional profiling of lung cancer cells over-expression miR-34a.

status: Public on Aug 09 2012

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

country: USA

institute: Baylor College of Medicine

summary: The Zeb1 transcriptional repressor plays a key role in metastasis through the down-regulation of genes that are strong inducers of epithelial differentiation and inhibitors of stem-ness. Here we report that Zeb1 controls the expression of numerous oncogenic and tumor suppressive microRNAs (miRs). Zeb1 stimulated pro-migratory cytoskeletal processes by down-regulating miR-34a and activated Rho GTPases through Arhgap1, a Cdc42 GTPase activating protein and novel miR-34a target gene. Poor-prognosis human lung adenocarcinomas were highly enriched in a cytoskeletal gene signature activated by miR-34a down-regulation. These findings suggest that Zeb1 regulates a miR network and drives pro-migratory cytoskeletal processes through miR-34a.

overall_design: Total RNA was extracted from primary tumors from mice injected with 344SQ-vector and -miR-34a cells, and then hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 array. Determination of differentially expressed genes was carried out.

first: Jon

last: Kurie

first: Young-Ho

last: Ahn

first: Don

last: Gibbons


title: Expression profiling of Lgr5 positive adenoma cells.

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

overall_design: Refer to individual Series


title: Knockdown of Hnrnpa0, a del(5q) Gene, Alters Myeloid Cell Fate in Murine Cells

status: Public on Aug 08 2012

city: Chicago

first: David

last: Young

state: IL

department: Department of Medicine

institute: University of Chicago

summary: To understand the effect of loss of Hnrnpa0, an RNA-binding protein shown to regulate transcript stability via binding to the AU-rich elements (AREs) of mRNAs, on myelopoiesis, we used RNAi interference to model Hnrnpa0 loss in an experimental murine cell system, and then used global expression profiling techniques to determine the impact of that knockdown on gene expression, especially ARE-containing genes. The PUER system is a murine myeloid progenitor cell line expressing the tamoxifen (4-OHT) responsive, PU.1-ER fusion gene, allowing controlled myeloid differentiation in cells in which Hnrnpa0 expression has been altered via RNAi technology. By examining perturbations in gene expression both before and during myeloid differentiation, we have shown the Hnrnpa0 loss preferentially alters ARE-containing genes, leading to a shift in myeloid specification away from the monocytic lineage.

overall_design: Gene expression in the PUER cell line expressing the construct of interest, was measured before and 24 hours after 4-OHT induced differentiation. Three independent experiments using unique clones for the control vector and Hnrnpa0 shRNA vector were carried out in parallel.

middle: J

first: Angela

last: Stoddart

first: Zhijian

last: Qian

first: Michelle

middle: M

last: Le Beau


title: Gene expression profiles in the adult liver, fetal liver and bone marrow

city: Kyoto

first: Soo Ki

last: kim

address: Shogoin-Kawaharacho 54, Sakyo-ku

country: Japan

institute: Graduate School of Medicine, Kyoto University

summary: We speculate that the genes that acquired mutations in liver cancer  tissues might be preferentially and actively transcribed in hepatic lineage cells. Therefore, to examine whether the mutated genes in liver cancer tissues in mice were transcribed at relatively higher levels in liver-lineage cells compared with hematopoietic lineage cells, we aim to analyze and compare the gene expression profiles in the adult liver, fetal liver and bone marrow.

overall_design: The gene expression levels of the adult liver, fetal liver and bone marrow are compared.

first: Takahiro

last: Shimizu

first: Soo

middle: K

last: Kim


title: Gene expression analysis of IL-17 induced mice small intestinal smooth muscle strips with or without 6-shogaol.

status: Public on Sep 15 2012

city: Inashiki-gun

first: Mitsue

last: Nishiyama

state: Ibaraki

address: 3586 Yoshiwara, Ami-machi

department: Tsumura Research Laboratories

institute: Tsumura & Co.

summary: The etiology of post-inflammatory gastrointestinal (GI) motility dysfunction, after resolution of acute symptoms of inflammatory bowel diseases (IBD) and intestinal infection, is largely unknown. Here, using an established mouse model of experimental enteritis, we show that enhancement of smooth muscle cell (SMC) contraction by interleukin (IL)-17A may be involved in postinflammatory GI hypermotility. To examine the effect of IL-17 in the small intestinal smooth muscle, we used whole genome microarray expression profiling to find out the genes which respond to IL-17 stimulus. The smooth muscle strips were peeled off from mouse small intestine and incubated 24h with or without IL-17. And we also examined the effect of 6-shogaol, which is one of the ingredients of Japanese traditional medicine for intestinal mortor disorder, Daikenchuto, in IL-17 stimulated small intestinal smooth muscle strip.

overall_design: The smooth muscle strips were peeled off from mice small intestine and incubated in the culture media for 24h with or without IL-17. A part of IL-17 stimulated strips were co-incubated with 6-shogaol. Six independent experiments were performed.

first: Masahiro

last: Yamamoto

first: Hirotada

last: Akiho

first: Kazuko

last: Satoh


title: Role of SIRT1 in diet-induced metabolic diseases

status: Public on Aug 01 2012

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: The purpose of this study is to investigate the role of SIRT1 in high-fat diet-induced liver steatosis and insulin resistance. SIRT1 is a nuclear enzyme that could remove an acetyl-group from target proteins by using NAD as co-substrate. Homologs of this protein in yeast and the roundworm C. elegans are able to delay the aging process in response to nutrients. However, the molecular mechanism by which SIRT1 sense the environment to mediate this response are poorly understood. We have shown that when chronically fed with a 40%-fat diet, SIRT1 heterozygous animals gain significantly more weight compared to wild type littermates. They are also hyperinsulimia, more insulin-resistant, and accumulate more lipids in liver. Interestingly, these animals also show signs of premature aging, such as an early appearance of gray fur, defective motor activity, and decreased fertility. In this microarray study, we analyzed the gene expression profiles in the liver of WT low-fat diet, Het low-fat diet, WT high-fat diet, and Het high-fat diet using Agilent Whole Genome Mouse 4x44 multiplex format oligo arrays following the Agilent-1-color microarray-based gene expression analysis protocol. This microarray analysis concluded that SIRT1 Het mice reponsed to the high-fat diet differently from the WT control mice.

overall_design: Liver total RNAs from SIRT1 WT and Het mice that were fed with either a low-fat diet or a high-fat diet for 34 weeks were used for a microarray gene expression study. Three biological replicates for each group were used.

first: Aparna

last: Purushotham

first: Qing

last: Xu

first: Xiaoling

last: Li


title: Expression analysis of neural stem cells isolated from Olig1-wt and Olig1-ko embryos

status: Public on Jul 28 2012

city: Boston

first: John

last: Alberta

address: 450 Brookline Ave.

institute: Dana-Farber Cancer Institute

summary:
Olig1 is a bHLH transcription factor which is important for Oligodendrocyte development
We used microarray profiling to assess which genes are differentially expressed in absence of Olig1 in neural stem cells.

overall_design: Neural stem cells were isolated from ganglionic eminences of E14.5 wild-type and Olig1-KO brains. The cells were cultured in serum-free neural stem cell media and RNA extracted.

first: Charles

last: Stiles


title: Comparison expression data from wild-type and NFATc1-deficient osteoclasts

status: Public on Aug 18 2012

first: Julia

middle: F.

last: Charles

state: MA

address: 75 Francis Street, Smith Building 6th floor

department: Division of Rheumatology, Immunology and Allergy

institute: Brigham and Women's Hospital

summary: Genetic deletion of Nfatc1 in mice results in profound osteoclast-poor osteopetrosis, a high bone mass state caused by a lack of osteoclast activity.  We hypothesized that the family of NFATc1 regulated transcripts in the osteoclast would be enriched for genes associated with osteoclast function. We used microarrays profile gene expression in wild-type and NFATc1-deficient osteoclasts generated in vitro to identify NFATc1-dependent transcripts in osteoclasts.

overall_design: Bone marrow macrophages from wild-type and mice with an induced deficiency of NFATc1 (NFATc1 fl/fl MxCre+ mice where NFATc1 excision was induced by polyIC treatment) were cultured ex vivo in MCSF and RANKL for 3 days.  2 biological replicates were assayed for each genotype.

first: Antonios

middle: O

last: Aliprantis


title: Membrane Vesicles of a Bacterial Mutualist Mediate Immune Regulation via Dendritic Cells

status: Public on Jul 23 2012

city: Pasadena

first: Yue

last: Shen

state: CA

address: 1200 E California Blvd

department: Biology

institute: California Institute of Technology

summary: Microbial molecules have evolved to promote transient and/or permanent associations with mammals. Although numerous examples of secretion systems employed by pathogens have been described, mechanisms by which commensal bacteria export molecules during symbiosis remain unknown. The human gut mutualist Bacteroides fragilis produces a capsular polysaccharide (PSA) that directs host immune development. We reveal herein that outer membrane vesicles (OMVs) deliver PSA to dendritic cells (DCs), promoting regulatory T cells and inducing anti-inflammatory cytokines during protection from intestinal disease. In addition, we found that TLR2 signaling by DCs is required for OMV sensing. Following internalization into DCs and engagement of TLR2, OMVs initiate a gene expression program that results in IL-10 production by DCs. Although it is known that the outcome of PSA sensing by the immune system is Treg induction, nothing is known about the intracellular signaling pathway(s) activated by PSA within DCs. We analyzed the gene expression profile of DCs treated with OMVs to uncover factors that are expressed in a PSA-dependent, TLR2-dependent manner. Our findings demonstrate DC-induced protection from disease via OMV-delivery of a beneficial microbial molecule, uncovering a novel paradigm for inter-kingdom communication between the microbiota and mammals.

overall_design: RNA samples (1ug total RNA) from BMDCs were labeled with fluorescent dyes using the Quick Amp Labeling Kit (Agilent). Microarray (AgilentWhole Mouse Genome chip) hybridizations (65°C for 16 hours) and washes were performed with Agilent reagents following standard protocols. Microarrays were analyzed using an Agilent DNA Microarray Scanner G2565CA, and data were acquired using Agilent's Feature Extraction Software version 10.1.1.1. Significant genes were selected based on p< 0.01 and fold change >2.0.

first: Sarkis

last: Mazmanian


title: Microarray analysis of FXR-regulated genes in murine small intestine.

status: Public on Jul 19 2012

first: Scott

middle: Andrew

last: Ochsner

address: One Baylor Plaza

department: Molecular and Cellular Biology

summary: Obstruction of bile flow results in bacterial proliferation and mucosal injury in the small intestine that can lead to the translocation of bacteria across the epithelial barrier and systemic infection. These adverse effects of biliary obstruction can be inhibited by administration of bile acids. Here we show that the farnesoid X receptor (FXR), a nuclear receptor for bile acids, induces genes involved in enteroprotection and inhibits bacterial overgrowth and mucosal injury in ileum caused by bile duct ligation. Mice lacking FXR have increased ileal levels of bacteria and a compromised epithelial barrier. These findings reveal a central role for FXR in protecting the distal small intestine from bacterial invasion and suggest that FXR agonists may prevent epithelial deterioration and bacterial translocation in patients with impaired bile flow.  In this report we have examined the role of FXR in the ileum. We demonstrate that it plays a crucial role in preventing bacterial overgrowth and maintaining the integrity of the intestinal epithelium

overall_design: Mice were administered the FXR ligand GW4064 or vehicle for 14h.  The ilium was removed and processed for array analysis.  Each sample group was done in duplicate.

first: Takeshi

last: Inagaki

first: Steven

middle: A

last: Kliewer


title: Transcriptional Alterations in Skeletal Muscle Following Desmin Deletion

status: Public on Jul 11 2012

city: La Jolla

first: Gretchen

last: Meyer

address: 9500 Gilman Dr

department: Bioengineering

institute: University of California San Diego

summary: Desmin is a cytoskeletal protein in muscle involved in integrating cellular space and transmitting forces.  In this study we sought to determine the effects of desmin deletion on skeletal muscle at the transcriptional level across many pathways of muscle physiology.

overall_design: RNA was isolated from the TA muscle of mice of two genotypes (wildtype (WT) and desmin knockout (KO)) and two ages (7-9 weeks (Adult) and 12-14 months (Aged)).  Numbers per group are as follows: WT_Adult (5), WT_Aged (5), KO_Adult (5), KO_Aged (4).

first: Richard

middle: L

last: Lieber


title: Identification of Sox9-Regulated Pathways During Pancreas Development

status: Public on Aug 02 2012

first: Brandon

last: Taylor

address: Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Dr., Room 3101

department: Pediatrics and Cellular & Molecular Medicine

institute: University of California, San Diego


title: Gene-expression profiles of PD-L1-affected CD8+ T cells

status: Public on Jul 10 2012

first: Kaoru

last: Abiko

address: 54 Shogoin Kawaharacho, Sakyo-ku

department: Department of Gynecology and Obstetrics

institute: Kyoto University Graduate School of Medicine

summary: Programmed cell death 1 ligand 1 (PD-L1) is known to suppress immune system and to be an unfavorable prognostic factor in ovarian cancer. The purpose of this study was to elucidate the function of PD-L1 in peritoneal dissemination. Tumor cell lysis by CTLs was attenuated when PD-L1 on tumor cells was overexpressed and promoted when it was silenced. PD-L1 overexpression also inhibited gathering and degranulation of CTLs. Gene expression profile of mouse CTLs caused by PD-L1-overexpressing ovarian cancer was related to human CTLs exhaustion. In mouse ovarian cancer dissemination models, depleting PD-L1 expression on tumor cells resulted in inhibited tumor growth in the peritoneal cavity and prolonged survival. Restoring immune function by inhibiting immune-suppressive factors such as PD-L1 may be a promising therapeutic strategy for peritoneal dissemination.

overall_design: Genome-wide transcriptional changes in OT-1 mouse CD8+ T cells that were co-incubated with OVA peptide-loaded ID8 mouse ovarian cancer cell lines. CTLs from 4 mice were devided into 2 groups, and co-incubated with PD-L1-overexpressed ID8 or PD-L1-depleted ID8.

first: Masaki

last: Mandai


title: Silencing of Irf7 pathways in breast cancer cells promotes bone metastasis through immune escape mechanisms

status: Public on Jul 18 2012

city: Clayton

first: Sam

last: Forster

state: Victoria

address: 27 - 31 Wright Street

department: Monash Institute

country: Australia

institute: Monash University

summary: Breast cancer metastasis to bone is a critical determinant of long-term survival after treatment of primary tumors. We used a mouse model of spontaneous bone metastasis to determine new molecular mechanisms. Differential transcriptome comparisons of primary and metastatic tumor cells revealed that a substantial set of genes suppressed in bone metastases were highly enriched for promoter elements for the type I interferon (IFN) regulatory factor, Irf7, itself suppressed in mouse and human metastases. The critical function of the Irf7 pathway was demonstrated by restoration of exogenous Irf7 or systemic interferon administration, which significantly reduced bone metastases and prolonged metastasis free survival. Using mice deficient in the type I receptor (Ifnar1-/-) or mature B, T and NK cell responses (NOD Scid IL-2rγ-/- mice) we demonstrated that Irf7-driven suppression of metastasis was reliant on IFN signaling to host immune cells. Metastasis suppression correlated with decreased accumulation of myeloid-derived suppressor cells and increased CD4++, CD8 T cells and NK cells in the peripheral blood and was reversed by depletion of CD8+ cells and NK cells. Clinical importance of our findings was demonstrated as increased primary tumor Irf7 expression predicted prolonged bone and lung metastasis-free survival. Thus we report for the first time, a novel innate immune pathway, intrinsic to breast cancer cells, whose suppression in turn restricts systemic immunosurveillance to enable metastasis. This pathway may constitute a novel therapeutic target for restricting breast cancer metastases.

overall_design: Comparison of basal gene expression in breast cancer 4T1.2 cell line stably transfected using the pMSCV retroviral expression vector system with IRF7 or the base vector. Three independent experiments were performed comparing the IRF7 expressing cells to the base vector cells

first: Paul

last: Hertzog

first: Belinda

last: Parker

first: Jodee

last: Gould


title: Identification of Sox9-Regulated Pathways During Early Pancreas Organogenesis

summary: Sox9 target genes were identified by comparing gene expression in Sox9-ablated versus wild-type pancreata using microarray analysis.

overall_design: Sox9 was conditionally ablated in the developing pancreas via recombination of a Sox9-flox allele (Kist et al., 2002) using the Pdx1-Cre transgene (Gu et al., 2002). Total RNA was isolated and pooled from dorsal pancreatic epithelia of e12.5 Sox9fl/fl; Pdx1-Cre (mutant) versus Sox9fl/fl (wild-type) littermates for three biological replicates.

first: HungPing

last: Shih

first: Philip

last: Seymour

first: Maike

last: Sander


title: Expression data from low expressing T58A Mutant Myc Induced Tumors

status: Public on Jul 09 2012

city: East Lansing

first: Daniel

middle: Patrick

last: Hollern

state: MI

address: 2194 Biomedical Physical Sciences

institute: Michigan State University

summary: We used microarrays to futher characterize the effects of T58A mutation in Myc on mammary tumorigenesis.

overall_design: 17 MMTV-Myc T58A mammary tumors were used for RNA extraction and hybridization on Affymetrix microarrays.

middle: P

first: Eran

middle: R

last: Andrechek


title: Gene expression profiles of Hepa1-6 tumors in C57Bl/6 mice

status: Public on Jul 03 2012

city: Kanazawa

first: Yoshio

last: Sakai

state: Ishikawa

address: 13-1 Takara-machi

department: Department of Gastroenterology

institute: Kanazawa University

summary: Chronological change of gene expression profile of Hepa1-6 tumors in C57Bl/6

overall_design: Two-condition experiment


title: Gene expression profiles of whole blood cells of C57Bl/6 mice with Hepa1-6 tumors

summary: Chronological change of gene expression profile of whole blood cells of C57Bl/6 with Hepa1-6 tumors


title: Essential roles for chromatin protein L3mbtl2 in pluripotent stem cells

first: Endre

last: Anderssen

state: Massachusetts

address: 185 Cambridge Street

department: Cancer center

institute: MGH

summary: In order to determine the impact of L3mbtl2 on genome wide mRNA expression microarray analysis was carried out in L3mbtl2 knock out ES cells and wild type ES cells. The same analysis was also carried out in knock out cells infected with L3mbtl2-F vector and a control vector.

overall_design: Experiment to study targets of L3mbtl2 in C57bl6/129 hybrid ES cells. 4 samples: wild type, L3mbtl2 knock out, L3mbtl2 knock out rescue and rescue with empty vector

first: Jinzhong

last: Qin

first: Warren

last: Whyte

first: Effie

last: Apostolou

first: Hsu-Hsin

last: Chen

first: Schahram

last: Akbarian

first: Roderick

middle: T

last: Bronson

first: Konrad

last: Hochedlinger

first: Sridhar

last: Ramaswamy

last: Young

first: Hanno

last: Hock


title: Gene expression analysis of blood cells and tumor

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


title: Expression data from mouse skeletal muscle

status: Public on Jun 30 2012

first: Pere

last: Puigserver

address: 450 Brookline Av. CLSB-11144

summary:
We generated skeletal muscle-specific knockout mice lacking the transcription factor Yin Yang 1 (YY1) and analyzed expression patterns in the skeletal muscle these mice.
We used microarrays to detail the global programme of gene expression regulated by YY1.

overall_design: Wild type or knockout mice at 6 months were sacrificed and the soleus was isolated for RNA extraction.

first: Sharon

last: Blättler


title: Expression data from spleen and lymph node conventional CD11c+ Dendritic cells

city: Milan

first: Francesca

last: Granucci

address: Piazza della Scienza 2

country: Italy

institute: University of Milano-Bicocca

summary: Spleen and lymph node dendritic cells have a differential capacity do induce and retain iTreg cells. Therefore we performed a comparative analysis of the dendritic cells derived from these two compartments to identify the responsible genes

overall_design: CD11c+ conventional dendritic cells were facs sorted from spleens and lymph nodes of BALB/c animals for RNA extraction and hybridization on Affymetreix microarray

first: Ivan

last: Zanoni


title: Gene expression profiles of whole blood cells and the fraction enriched with tumor-infiltrating inflammatory cells of Balb/c athymic mice with Hepa1-6 tumors

summary: Chronological change of gene expression profile of whole blood cells and features of the fraction enriched with tumor-infiltrating inflammatory cells of Balb/c athymic mice with Hepa1-6 tumors


title: Astrocyte elevated gene-1 (AEG-1) promotes hepatocarcinogenesis: novel insights from a mouse model

status: Public on Jul 25 2012

city: Richmond

first: Devanand

last: Sarkar

state: VA

address: 1220 E Broad St, Room 7044

department: Department of Human and Molecular Genetics

institute: Virginia Commonwealth University

summary: Astrocyte elevated gene-1 (AEG-1) as a positive inducer of hepatocellular carcinoma (HCC). Transgenic mice with hepatocyte-specific expression of AEG-1 were challenged with N-nitrosodiethylamine (DEN) and developed multinodular HCC with steatotic features. Thus, we have identified the follwoing AEG-1 functions: induction of steatosis, inhibition of senescence and activation of coagulation pathway to augment an aggressive hepatocarcinogenic phenotype.

overall_design: Transgenic Mice liver tumors compared against WT mice liver tumors.

first: Catherine

middle: I

last: Dumur

first: Jyoti

last: Srivastava


title: Parallel selection mapping using artificially selected mice reveals body weight control loci (gene expression)

city: Tübingen

first: Yingguang Frank

last: Chan

address: Max-Planck-Ring 9

institute: Friedrich Miescher Laboratory

summary:
Understanding how polygenic traits evolve and respond to selection is a major unsolved problem, because challenges exist for identifying genes underlying a complex trait and understanding how multi-locus selection operates in the genome. Here we used artificial selection experiments to study polygenic response to selection. Inbred strains from seven independent long-term selection experiments in mice for extreme bodyweight (“High” lines weigh 77-42g vs. 40-16g in “Controls” lines), were genotyped at 527,572 SNPs to identify genetic variants controlling bodyweight. We identified 67 high-resolution parallel selected regions (PSRs) where multiple High lines share variants rarely found among the Controls. By comparing allele frequencies in one selection experiment against its unselected control, we found classical selective sweep signatures centered on the PSRs. Multiple lines of evidence support two G protein-coupled receptors GPR133 and Prlhr, as positional candidate genes controlling bodyweight. Artificial selection may mimic natural selection in the wild: compared to control loci, we detected reduced heterozygosity in PSRs in wild populations of unusually large mice on islands. Many PSRs overlap loci associated with human height variation, possibly through evolutionary conservation of functional pathways. Our data suggest that parallel selection on complex traits may evoke parallel responses at many genes involved in diverse but relevant pathways.
These samples were used to test the enrichment of certain gene functional categories.

overall_design: Mouse tissue samples (muscle and liver) were collected from 44 and 45 days old males from each of the nine out of thirteen lines (5 High lines: BEHi, DUHi, EDHi, MUHi, ROHi and 4 Control lines: BELi, EDLi, MULi and ROLi; n=23 total) at the University of Edinburgh. Frozen tissue samples were stored at -80ºC until use. Tissues were dissociated using TissueLyser II with steel beads (both Qiagen) following manufacturers’ instructions. mRNA was extracted and purified using TRIzol Reagent and the PureLink RNA Mini Kit (Life Technologies GmbH, Darmstadt, Germany). cDNA was synthesized using Maxima First Strand cDNA synthesis kit (Thermo Fisher Scientific, St. Leon-Rot, Germany).  Muscle and liver cDNA samples were hybridized on a Mouse GE 4x44k Microarray (Agilent Technologies, Inc., Waldbronn, Germany) according to manufacturer’s recommendations. Three technical replicate each was done on pooled cDNA samples from each mouse line.

first: F

middle: Y

middle: C

last: Jones

first: E

last: McConnell

first: J

last: Bryk

first: L

last: Bunger

first: D

last: Tautz


title: Peyer’s Patch M cells derive from Lgr5+ stem cells require SpiB and are induced by RankL in cultured ‘organoids’

status: Public on Jun 19 2012

city: London

first: Vivian

last: Li

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

summary: Peyer’s Patches consist of domains of specialized intestinal epithelium overlying Gut-Associated Lymphoid Tissue (GALT). Luminal antigens reach the GALT by translocation through epithelial gatekeeper cells, so-called M cells. We have recently demonstrated that all epithelial cells required for the digestive functions of the intestine are generated from Lgr5-expressing stem cells. Here, we show that M cells also derive from these crypt-based Lgr5 stem cells. The Ets family transcription factor Spi-B, known to control effector functions of bone marrow-derived immune cells, is specifically expressed in M cells. In Spi-B-/- mice, M cells are entirely absent, which occurs in a cell-autonomous fashion. It has been shown that Tnfsf11 (RankL) can induce M cell development in vivo. In intestinal organoid (‘mini-gut’) culture, we show that stimulation with RankL induces SpiB expression within 24hrs and subsequently of other M cell markers. We conclude that RankL-induced expression of Spi-B is essential for Lgr5 stem cell-derived epithelial precursors to develop into M cells.

overall_design: Small intestinal organoids were derived from wildtype (WT) mice. Recombinant mouse RankL (BioLegend) was added to the organoid culture medium in concentrations of 50-200ng/ml and fresh medium was added at day 2 and day 5. At the indicated time points, organoids were harvested for RNA isolation and microarray analysis to look for gene expression changes in reponse to RanKL.

middle: S

first: Wim

last: de Lau

first: Hans

last: Clevers


title: Elucidation of the expression profile of independent clones of mutant mtBALB and wild type control mtB6 murine cybrid cells

status: Public on Jun 26 2012

city: Tucson

first: Jaroslav

last: Janda

state: AZ

address: 1515 N Campbell Ave

department: Dept. of Medicine

institute: University of Arizona

summary: We generated murine fibroblast cybrid cell lines that have identical nuclear genomes and differ only in their mtDNA. We observed increased cellular proliferation and resistance to apoptosis in the mtBALB compared to the mtB6 cybrid cells, phenotypes seen in malignant cells. Based on these observations we investigated whether these phenotypic differences could be caused by a unique spectrum of nuclear gene expression alterations induced by the mtDNA changes. Microarray analysis (Agilent, 44K mouse whole genome chip) was conducted in order to elucidate the expression profile of three independent clones of mtBALB and mtB6 cybrid cells.

overall_design: Two-condition experiment, mtB6 vs. mtBALB cells. Biological replicates: 4 control replicates, 4 mutant replicates.

first: Jana

last: Jandova

first: James

middle: E

last: Sligh


title: Histone/Protein Deacetylase-6, -9, and Sirtuin-1 Control Foxp3+ Treg Through Shared and Isotype-Specific Mechanisms

status: Public on Jun 21 2012

city: Philadelphia

first: Wayne

middle: W

last: Hancock

state: PA

address: 916B ARC, 3615 Civic Ctr Blvd

institute: CHOP/UPenn

summary: Targeting histone/protein deacetylase (HDAC)-6, -9, or Sirtuin-1 (Sirt1) augments the suppressive functions of Foxp3+ T regulatory (Treg) cells, but it is unclear if this involves different mechanisms, such that combined inhibition would be beneficial. We compared the suppressive functions of Tregs from wild-type C57BL/6 mice or mice with global (HDAC6-/-, HDAC9-/-, dual HDAC6/9-/-) or conditional deletion (CD4-Cre or Foxp3-Cre and floxed Sirt1; GSE26425) alone, or after treatment with isoform-selective HDAC inhibitors (HDACi). We found the heat shock response was crucial in mediating the effects of HDAC6, but not Sirt1 inhibition. Furthermore, while HDAC6, HDAC9 and Sirt1 all deacetylate Foxp3, each has diverse effects on Foxp3 transcription, and loss of HDAC9 is associated with stabilization of Stat5 acetylation and its transcriptional activity. Targeting different HDAC can increase Treg function by multiple and additive mechanisms, indicating the therapeutic potential for combinations of HDACi in the management of autoimmunity and alloresponses post-transplant.

overall_design: RNA from three independent samples of magnetically separated CD4+CD25+ Treg of HDAC9-/- mice, compared to wild type (C57BL/6) control.

first: Ulf

middle: H

last: Beier

first: Liquing

last: Wang

first: Rongxiang

last: Han

first: Tatiana

last: Akimova

first: Yujie

last: Liu


title: Parallel selection mapping using artificially selected mice reveals body weight control loci

first: Yingguang Frank

last: Chan

type:
Expression profiling by array
Genome variation profiling by SNP array

overall_design: Refer to individual Series


title: Expression data from region-specific postnatal astrocytes

status: Public on Jun 01 2012

city: Majadahonda

first: Helena

last: Mira

state: Madrid

address: Ctra. Majadahonda-Pozuelo, km 2.2

department: Área de Biología Celular y Desarrollo

country: Spain

institute: Instituto de Salud carlos III

summary:
Astroglial cells in the adult brain constitute a heterogeneous population endowed with region-specific properties. Recently, they have acquired greater relevance as active components of the adult neural stem cell (aNSC) niches. Astrocytes located in the vicinity of aNSC reservoirs are thought to regulate aNSC behaviour. We have compared the function of glial cells isolated from the postnatal and adult subventricular zone and hippocampus (two stem cell niches, where aNSCs self-renew and give rise to immature neurons), from the olfactory bulb (a neurogenic region where the immature neurons cease to proliferate and terminally differentiate) and from a non-stem and non-neurogenic area such as the ventral mesencephalon. Co-culture experiments demonstrate that subventricular zone glial cells secrete soluble signals that promote NSC self-renewing divisions.
We used microarrays to detail the global gene expression of astroglial cells isolated from four different brain regions (olfactory bulb, ventral mesencephalon, hippocampus and subventricular zone) and identified up-regulated genes coding for secreted proteins in astrocytes from the subventricular zone.

overall_design: Primary astrocytes were cultured from four CD-1 mouse brain regions and cells were employed for RNA extraction and hybridization on Affymetrix microarrays. Primary tissue for the astrocyte cultures was dissected from four postnatal day 3 littermate pups. The tissue from the three pups was pooled in order to reduce individual differences of expression profiles.

first: Moreno-Estelles

last: Mireia

first: Mira

last: Helena


title: Gene expression analysis of developing limbs

status: Public on Jun 18 2012

city: Chapel Hill

first: Anna

last: Spagnoli

address: 103 Mason Farm Road

department: Pediatrics

institute: University of North Carolina at Chapel Hill

summary: To evaluate geneexpression profile in developing joints vs adjacent growth plate in control and TGF-beta type II receptor conditional knock-out in limb mesenchyjme

overall_design: We obtained E14.5 autopods from two normal controls and two Tgfbr2Prx1KO littermate embryos. Samples were frozen in OTC and cryosectioned and subjected to laser-capture microdissection for RNA sampling for interzone, growth plate chondrocytes and interdigital tissue. RNas were subjected to microarray analysis

first: Lara

last: Longobardi

first: Lynda

last: O'Rear


title: Gene expression profiles of blood and the enriched fraction of tumor-infiltrating inflammatory cells of C57Bl/6 mice with Hepa1-6 tumors

first: Yoshio

last: Sakai

summary: Examination of gene expression profile of blood and tumor-infiltrating inflammatory cells


title: Bone marrow-induced Mef2c deficiency delays B cell development and alters the expression of key B cell regulatory proteins

city: Salt Lake City

first: John

last: Weis

state: UT

address: 15 North Medical Drive

department: Pathology

institute: Univ of Utah

summary: The Mef2 family transcriptional regulator Mef2c is highly expressed in maturing bone marrow and peripheral mature B cells. To evaluate the role of this transcription factor in B cell development, we generated a B cell specific conditional deletion of Mef2c using the Mb-1-Cre transgene that is expressed during the early stages of immunoglobulin rearrangement.  Young mice possessing this defect demonstrated a significant impairment in B cell numbers in bone marrow and spleen. This phenotype was evident in all B cell subsets; however, as the animals mature, the deficit in the peripheral mature B cell compartments was overcome.  The absence of Mef2c in mature B cells led to unique CD23+ and CD23- subsets that were evident in Mef2c KO primary samples as well as cultured, differentiated B cells but not in WT cell populations. Genome wide expression analysis of immature and mature B cells lacking Mef2c indicated altered expression for a number of key regulatory proteins for B cell function including Ciita, CD23, Cr1/Cr2, and Tnfsf4.  Chromatin immunoprecipitation analysis confirmed Mef2c binding to the promoters of these genes indicating a direct link between the presence (or absence) of Mef2c and altered transcriptional control in mature B cells.

overall_design: Four samples are submitted.


title: Analysis of brain cortices of SAMP8 and SAMR1 mice after an exercise intervention

status: Public on Jun 05 2012

city: Barcelona

first: Perla

last: Kaliman

address: Corsega 176 bajos

institute: IDIBAPS

summary: Microarrays has been used to analyze the effect of voluntary wheel running in the SAMP8 mice using the SAMR1 mouse strain as control.

overall_design: Cortex gene expresion of SAMP8 which have been resting or exercising and SAMR1 sedentary.

first: Maria

middle: J

last: Alvarez-Lopez

first: Marco

last: Castro-Freire


title: Gene array analysis of embryonic vs adult hypothalamic NPY expressing cell lines

city: Toronto

first: carl

last: virtanen

state: Ontario

address: 101 College St

department: Princess Margaret Genomics Centre

country: Canada

institute: University Health Network

summary:
Microarrays were used to examine gene expression changes between two hypothalamic cell lines derived from adult and embryonic tissues. Both cell lines endogenously express the protein Npy (neuropeptide y) which is involved in feeding and reproductive processes.
Results identify novel gene candidates that are implicated in the development of hypothalamic sub-poplulations.

overall_design: Immortalized hypothalamic cell lines were created by overexpression of SV40 T-antigen from tissue sources derived from both embryonic and adult mice.  Triplicate plates of each cell line were grown to 70% confluence and RNA was harvested for microarray analysis.

first: Carl

last: Virtanen

first: Sandeep

last: Dhillon

first: Sarah

last: Gingerich

first: Denise

last: Belsham


title: Expression of ventromedial hypothalamus (VMH) from electroconvulsive seizure (ECS) treated C57Bl/6 mice

status: Public on May 30 2012

city: Tokyo

first: Eri

last: Segi-Nishida

state: Tokyo

address: Niijuku 6-3-1

institute: Tokyo University of Science

summary: The ventromedial nucleus of the hypothalamus (VMH) is thought to a satiety center and a potential target for anti-obesity therapy. Electroconvulsive seizure (ECS) therapy is highly effective in psychiatric diseases including depression, but also implicated beneficial effects on other neurological diseases. Although it has been reported that the neurons in the VMH are strongly activated by ECS stimulation, the effect of ECS in this hypothalamic subnucleus remains unknown. To address this issue, we investigated molecular changes in the VMH in response to ECS by utilizing a method of laser-capture microdissection coupled with microarray analysis, and examined behavioral effects of ECS via VMH activation. ECS significantly induced gene expression not only immediate-early genes such as Fos, Fosb and Jun, but also Bdnf, Adcyap1, and Hrh1 in the VMH after a single or repeated stimulus.

overall_design: Mice received one or 7 times shock of ECS and their brains were collected at 2 h (VMH_1stECS2h, VMH_7thECS2h) or 6 h after shock (VMH_1stECS6h, VMH_7thECS6h). The brains of sham-treated animals were collected at 2 h after treatment(VMH_sham). The VMH was microdissected from dehydrated brain sections, and its total RNA was extracted. RNA samples from two or three animals were pooled to minimize the impact of biological variance. After nucleotide amplification by the ovation amplification, the gene expression profiles were obtained by the Affymetrix microarray analysis. The microarray analysis was performed twice using different sets of animals.

first: Mari

last: Sakaida


title: Microbiota-dependent gene expression in small intestinal epithelial cells (IECs)

status: Public on May 17 2012

city: Hannover

first: Mathias

middle: W.

last: Hornef

address: Carl Neuberg Str. 1

department: Inst. of Medical Microbiology

institute: Hannover Medical School

summary: Intestinal epithelial cells were isolated from total small intestine of each four 28-day old conventionally raised (conv) and germ-free (GF) bred C57BL/6 mice (protocol according to: Lotz et al., J. Exp Med. 2006). Total RNA was isolated by TriZol and ist purity was examined using a Bioanalyszer. We used microarrays to comparatively detail the global gene expression in primary total isolated intestinal epithelial cells.

overall_design: Four biological replicates from isolated intestinal epithelial cells obtained from each 4 germ-free bred and conventionally raised mice. Colour change.

first: Frederik

last: Bäckhed


title: Comparison of gene expression profiles among Nrf1 liver-specific conditional knockout, Nrf2 knockout and Keap1 knockdown mice.

status: Public on May 18 2012

city: Sendai

first: Masayuki

last: Yamamoto

address: 2-1 Seiryo-machi, Aoba-ku

department: Medical Biochemistry

institute: Tohoku University Graduate School of Medicine

summary: To identify Nrf1-dependent and Nrf2-dependent genes in the liver, we examined the gene expression profiles of Nrf1 Alb-CKO, Nrf2 knockout and Keap1 knockdown mouse livers by microarray analyses.

overall_design: Total RNAs from Nrf1dN/-::Alb-Cre, Nrf1dN/+, Nrf2-/-, Nrf2+/+, Keap1KD/- and Keap1KD/+ mouse livers were used for the microarray analyses.

first: Yosuke

last: Hirotsu

first: Nami

last: Hataya

first: Fumiki

last: Katsuoka


title: Changes in gene expression in implantation sites by absence of Cbs

status: Public on May 31 2012

city: Zaragoza

first: Jesus

last: Osada

address: Miguel Servet, 177

institute: Universidad de Zaragoza

summary:
The change in gene expression on the 8th day of gestation was investigated using DNA microarrays.

Uterine gene expression of implantation sites  was analysed in female mice.

overall_design: Female mice, C57BL/6jXOla129 genetic background were used for experiments. Mice, housed in sterile filter-top cages (3-4 per cage), were acclimatized in a room maintained at 20ºC with a 12-h light-dark fr four months.  Two groups were established: a) The control group and b) homozygous Cbs deficient mice and sacrificed at the eight day post-coitum.

first: Mario

last: Nuño

first: María

last: Navarro

first: Carmen

last: Arnal

first: Lourdes

last: Osaba

first: Jesús


title: Transcriptomics and Proteomics Analyses of the PACAP38 influenced Ischemic Brain in Permanent Middle Cerebral Artery Occlusion Model Mice

status: Public on May 01 2012

city: Tsukuba

first: RANDEEP

last: RAKWAL

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

institute: University of Tsukuba

summary:
The neuropeptide pituitary adenylate cyclase-activating polypeptide (PACAP) is considered to be a potential therapeutic agent for prevention of cerebral ischemia. Ischemia is a most common cause of death after heart attack and cancer causing major negative social and economic consequences.
- This study was designed to investigate the effect of PACAP38 injection intracerebroventrically in a mouse model of permanent middle cerebral artery occlusion (PMCAO) along with corresponding sham control that used 0.9% saline injection. Ischemic and non-ischemic brain tissues were sampled at 6 and 24 hours post-treatment.
- Following behavioral analyses to confirm whether the ischemia has occurred, we investigated the genome-wide changes in gene and protein expresison using DNA microarray chip (4x44K, Agilent) and one-/two-dimensional gel electrophoresis (1-/2-DGE) coupled with matrix assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS), respectively.
- Our results revealed numerous changes in the transcriptome of ischemic (ipsilateral) hemisphere treated with PACAP38 over the saline-injected SHAM control hemisphere. In parallel, 2-DGE analysis revealed a highly expressed protein spot in the ischemic region that was identified as dihydropyrimidinase-related protein 2 (DPYL2). The DPYL2, also known as Crmp2, is a marker for the activated neuronal defense mechanisms, and interestingly, PACAP strongly suppresed this induction.
- This study provides the first inventory of  PACAP influenced gene and protein targets in ischemic hemisphere, and provides new targets for thereaupetic interventions.

overall_design:
The PMCAO model mice were generated as described previously. Briefly, the mice were anesthetized with 4% sevoflurane (induction) and 2% sevoflurane (maintenance) in a 30% O2 and 70% N2O gas mixture via a face mask. An incision was then made in the cervical skin followed by opening of the salivary gland, and the right common carotid artery was visualized. A midline cervical incision was made to expose the external carotid artery. The intraluminal filament technique was used, to generate the PMCAO model.
- The PACAP38 (1 µl containing 1 pmol) or 1 µl of saline (0.9% NaCl) was injected intracerebroventrically, immediately after PMCAO. PACAP38 (Peptide Institute Inc., Osaka, Japan; supplier temperature was -20ºC and was stored at -80ºC) was dissolved in, and diluted ×10 times with 0.9% NaCl just before use.
- In the sham control animals, following exposure of the external carotid artery, the wound was sutured. The PACAP38 or saline was injected intracerebroventrically in the same concentrations as above. After injections, the animals were returned to their cages.
- A total of eight groups were prepared: four groups of three, seven, four and five mice in the PMCAO plus PACAP38 and PMCAO plus saline cohorts at 6 and 24 h after operation, respectively, and five mice each in the control (sham) plus PACAP and saline groups at 6 and 24 h after operation, respectively.
- We used three mice each in PMCAO groups that exhibited neurological grades G1 and G2 and three mice each at random in sham groups for the subsequent downstream analysis. Six or 24 hours post-injection of PACAP38 or saline, the mice were removed from their cages, decapitated, and their brains carefully removed on ice. The left (contralateral) and right (ipsilateral; ischemic) hemispheres were dissected and placed in 2 mL Eppendorf tubes, which were then quickly immersed in liquid nitrogen before being stored in -80ºC prior to further analysis.
- For analysis of gene components, the tissues were ground to a very fine powder with liquid nitrogen, used for total RNA extraction, quantity and quality check, followed by cDNA synthesis, and RT-PCR. A mouse 4 x 44K whole genome oligo DNA microarray chip (G4122F, Agilent Technologies, Palo Alto, CA, USA) was used for global gene expression analysis using the ipsilateral (ischemic) hemisphere. Briefly, total RNA (900 ng; 300 ng each replicate pooled together) was labeled with either Cy3 or Cy5 dye using an Agilent Low RNA Input Fluorescent Linear Amplification Kit (Agilent). Fluorescently labeled targets of control (sham) as well as treated (PMCAO) samples with PACAP38 or without PACAP38 (saline) were hybridized to the same microarray slide with 60-mer probes.
- Here, we compared the PMCAO plus PACAP38 injected mice to PMCAO plus saline, i.e. the ipsilateral brain region of the PMCAO mice was compared with the same right hemisphere of the control mice. Similarly, Sham control plus PACAP38 injected mice to Sham control plus saline were analyzed to identify only the PACAP38 influenced genes. A flip labeling (dye-swap or reverse labeling with Cy3 and Cy5 dyes) procedure was followed to nullify the dye bias associated with unequal incorporation of the two Cy dyes into cDNA.

first: Motohide

last: Hori

first: Tomoya

last: Nakamachi

first: Randeep

last: Rakwal

first: Junko

last: Shibato

first: Toshihiro

last: Aiuchi

first: Keiji

last: Tamaki

first: Seiji

last: Shioda


title: Hematopoietic stem cells lacking Ott1 display aspects associated with aging and are unable to maintain quiescence during proliferative stress

status: Public on Apr 24 2012

city: Cambridge

first: Jonathan

middle: Lee

last: Jesneck

address: 77 Massachusetts Ave., 35-208

department: Lab for Manufacturing and Productivity

institute: MIT

summary:
The infant leukemia-associated gene, Ott1 (Rbm15), has broad regulatory effects on embryonic development and hematopoiesis. Embryonic deletion of Ott1 results in defects to the placenta, spleen and heart. Conditional deletion within the adult hematopoietic compartment demonstrates a requirement in pre-B development and inhibitory roles in myeloid progenitor and megakaryocyte populations. Ott1-deleted bone marrow has an expansion of the Lin- Sca-1+ c-Kit+ (LSK) population which includes the hematopoietic stem cell (HSC) population. Functional HSC testing through competitive repopulation of irradiated recipients demonstrated however, a severe defect in Ott1-deficient HSCs, despite adequate numbers of immunophenotypically identified long term HSCs. Although mice deleted in situ for Ott1 are able to maintain hematopoiesis in steady state over a normal lifetime, but when subjected to proliferative stress, the HSC population loses the self-renewing, G0 fraction and undergoes bone marrow failure.
Therefore, Ott1 is required for maintaining HSC quiescence during proliferative stress. To investigate the downstream effects of Ott1 loss, LSK cells were sorted from Ott1-deleted mice and controls then global gene expression profiles were generated through hybridization of total RNA onto microarrays. Gene set enrichment analysis showed significant enrichment with genes altered in aged HSCs. Ott1-deficient HSCs were found to have other aging-associated features such as increased DNA damage, NF kappa B activation and p38Mapk activation, suggesting Ott1 controls pathways also involved in the aging process.

overall_design: Six week old Ott1 flox/null Tg-Mx1cre mice and littermate controls possessing a wild type Ott1 allele were injected with 250 mcg intraperitoneal pIpC every other day for 3 doses. Six weeks post-pIpC, bone marrow was harvested, labeled with lineage markers (B220, CD19, CD4, CD8, CD3, IL7R, Terr119 and Gr-1) and depleted using magnetic beads. The remaining cells were labeled for c-Kit and Sca-1 and the Lin- Sca-1+ c-Kit+ (LSK) population was sorted using a FACSAria cell sorter (BD Biosciences). Approximately 10,000 LSK cells per mouse were isolated from 3 Ott1 flox/null Tg-Mx1cre mice and 3 controls. RNA was extracted using the RNeasy Micro kit (Qiagen, Valencia, CA) and treated with RNAse-free DNAse (Qiagen, Valencia, CA). 50 ng of purified total RNA was linearly amplified using the Ovation RNA amplification system V2 (Nugen, San Carlos, CA) and biotinylated with the FL-Ovation Biotin Module V2 (Nugen, San Carlos, CA) per the supplied protocol. cDNA was then hybridized to Affymetrix Mouse expression array 430A2.0 chips by the Dana Farber Microarray Core Facility (Boston, MA). The raw gene expression values were preprocessed with robust multi-array analysis (RMA) algorithm using BioConductor software.

first: Glen

middle: D

last: Raffel


title: Changes in gene expression in implantation and inter-implantation sites by absence of Cbs

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


title: Expression analysis of resting and stimulated naïve and MP CD8 T cells

status: Public on May 11 2012

first: Joanna

last: DiSpirito

address: 3610 Hamilton Walk, University of Pennsylvania

department: Microbiology

institute: University of Pennsylvania

summary: Memory T cells respond to stimulation with more rapid expression of effector cell functions than their naïve counterparts, yet the gene expression signature underlying this enhanced recall response is not known. Therefore, we performed comprehensive, whole-genome expression profiling of murine memory CD8 T cells before and shortly after ex vivo stimulation. We compared this differential expression profile to its counterpart from stimulated naive cells. Given that memory cells arise from naive cells, the quiescent state of both cell populations prior to stimulation, and the early time point analyzed (four hours post-stimulation), it was possible that the stimulation-induced changes in gene expression were identical between the two populations. While there was a high degree of overlap, we found that the majority of up-regulated genes were more highly induced following stimulation of memory cells. This more robust increase in transcript levels was observed for a functionally diverse set of genes, including cytokines, chemokines, amino acid metabolic enzymes and transporters, transcription factors and regulators of RNA processing. We also identified the unique, stimulation-induced signatures of naive and memory CD8 T cells and found that the former was enriched for factors involved in regulating chromatin modifications. Specifically, we found that Hdac 5,7 and 8 transcript levels were rapidly down-regulated following stimulation of naive cells, which correlated with an increase in their total level of acetylated histone H3 (AcH3). This was in contrast to stimulated memory cells, which had higher levels of total AcH3 ex vivo that did not change following short-term stimulation. Furthermore, the unique stimulation-induced expression profile of memory cells was enriched for factors involved in regulating transport of molecules between the nucleus and cytoplasm, including multiple members of the nuclear pore complex. Together, these results support a model whereby the chromatin modifications that occur during the differentiation of naïve cells into memory cells are preserved in resting memory populations, facilitating their more robust re-activation of a functionally diverse set of genes that contribute to rapid recall of effector functions.

overall_design: Naïve (CD44lo) and memory phenotype (CD44hi) CD8 T cells from 7-wk old female B6 mice were FACS-purified and cultured in vitro for four hours in the presence or absence of PMA and ionomycin. Total RNA was purified from un-stimulated (resting) naïve, resting memory, stimulated naive, and stimulated memory cells and hybridized to individual single-color arrays. This purification and stimulation protocol was performed four independent times.

first: DiSpirito

last: Joanna

first: Shen

last: Hao


title: H. pylori infection blocks DNA damage induced apoptosis by T4SS-dependent upregulation of miR-155

status: Public on Apr 03 2012

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

summary: The innate immune response against Helicobacter pylori is mainly controlled by pattern recognition receptors that lead to the up-regulation of pro-inflammatory cytokines. A new player in this field is the miR-155 being regulated by TLR ligands in monocytic derived cells influencing certain intracellular pathways by down-regulating targets involved in signaling and development. By using primary bone marrow derived macrophages (BMMs) from mice deficient in the key TLR signals the regulation of miR-155 was explored. Further on the biological impact of a lack of miR-155 in BMMs was analyzed by micro-array studies and apoptosis assays. We observed that miR-155 is up-regulated in response to H. pylori via TLR2 and TLR4 in a NF-κB dependent manner, but also identified a TLR2/TLR4 independent mechanism that was strongly connected to a functional TypeIV secretion system. Down-stream the high expression of miR-155 down-regulated many mRNA targets during H. pylori infection. Thereby we could validate Tspan14, Lpin1, and Pmaip1 as new targets of miR-155 and identified their binding site. These and other already published targets showed a substantial pro-apoptotic potential. We observed that H. pylori infected wild type BMMs were much more resistant to DNA damage induced apoptosis by cisplatin when compared to their respective miR-155-/- BMMs. Our data strongly suggests that there is an additional innate immune mechanism of BMMs leading to the upregulation of the anti-apoptotic miR-155 that causes resistance to DNA damage in BMMs.

overall_design: Microarray experiments were performed as dual-color hybridizations. To compensate for dye-specific effects, an independent dye-reversal color-swap was applied. Bone marrow derived macrophages were 'in vitro' infected with H.pylori P12 and the expression changes were measured.

first: Manuel

last: Koch

first: Thonas

middle: F

last: Meyer


title: Altered gene expression in the small intestine of IE-Cpr-null mice

status: Public on Apr 11 2012

city: Ann Arbor

first: Jaime

last: D'Agostino

address: 2025 S huron Parkway apt 102

institute: University of Michigan

summary: The NADPH-cytochrome P450 reductase (CPR) is essential for the functioning of microsomal cytochrome P450 (P450) monoxygenases. The biological functions of the CPR-dependent enzymes in the intestine are not known, despite the vast knowledge available on the biochemical properties of the various oxygenases. A mouse model with intestinal epithelium (IE)-specific Cpr-knockout (IE-Cpr-null) was recently generated in this laboratory (Zhang et al., Drug Metab. Dispos., 37, 651-657, 2009). The IE-Cpr-null mice did not display any obvious abnormalities in growth, development, or reproduction, and their intestines appeared to have a normal structure. Despite the absence of observable phenotypes, we hypothesized that loss of the enterocyte CPR expression will impact homeostasis of endogenous compounds, and expression of genes, that have critical biological function in the small intestine. In the present study, we have performed genomic analyses for enterocytes from IE-Cpr-null mice and their wild-type littermates, using Affymetrix Mouse Expression Set 430A 2.0 GeneChip Arrays. Our aim was to identify small intestinal gene-expression changes, which may shed light on potential biological roles of CPR and CPR-dependent enzymes in the small intestine. Our analysis revealed significant expression increases in P450s, transporters, cholesterol biosynthesis, and (unexpectedly) antigen presentation/processing. Further genomic and biochemical analyses revealed potential mechanisms linking CPR-dependent enzymes and the expression of major histocompatibility complex class II genes in the small intestine.

overall_design: Adult (2.5-3.0 month-old) male IE-Cpr-null and WT litermates were used for all experiments. RNA was collected from eight mice of each genotype and RNA from two mice of the same genotype was pooled prior to hybridization to the microarray to create a total of four samples for each genotype.

first: J

first: X

last: Ding

first: P

last: Zhang

first: K

last: Jia

first: C

last: Fang

first: Y

last: Zhu

first: D

last: Spink

first: Q


title: Changes in gene expression in inter-implantation sites by absence of Cbs

first: Jesus

last: Osada

summary: The change in gene expression on the 8th day of gestation was investigated using DNA microarrays. Uterine gene expression of interimplanted sites was analyzed in female mice.

overall_design: Female mice, C57BL/6jXOla129 genetic background were used for experiments. Mice, housed in sterile filter-top cages (3-4 per cage), were acclimatized in a room maintained at 24ºC with a 12-h light-dark fr four months. Two groups were established: a) The control group and b) homozygous Cbs deficient mice and sacrificed at the eight day post-coitum.

first: Mario

last: Nuño

first: María

middle: A

last: Navarro

first: Carmen

last: Arnal

first: Lourdes

last: Osaba

first: Jesús


title: Expression data from RU486 treated FVB wild-type and MMTV- PAX8PPARg mouse mammary tumors

status: Public on Apr 30 2012

city: Washington

first: Robert

last: Glazer

state: DC

address: 3970 Reservoir Rd, NW

department: Oncology

institute: Georgetown University

summary: To determine if RU-486 would be effective as a chemopreventive agent, microarrays were used to analyse global gene expression changes in wild-type vs. MMTV-PAX8PPARg mice to determine their differential response to RU486

overall_design: RNA was isolated (RNeasy Mini Kit, Qiagen) from progestin/DMBA induced mammary tumors from wi transgenic and wild-type mice treated with placebo or 2.5mg RU486 60-day release pellets

first: Hongyan

last: Yuan


title: Gene expression profiles of LPS-stimulated RAW264.7 macrophages overexpressing Tbc1d23 novel innate immune gene

status: Public on Apr 04 2012

city: Denver

first: Scott

last: Alper

state: CO

address: 1400 Jackson St

department: Center for Genes, Environment and Health

institute: National Jewish Health

summary: We previously identified Tbc1d23 as a candidate novel regulator of innate immunity using comparative genomics RNAi screens in C. elegans and mouse macrophages. Using mice with an engineered knockout mutation in Tbc1d23 and macrophages engineered to overexpress Tbc1d23, we now show that Tbc1d23 is a general but not universal inhibitor of the innate immune response, inhibiting multiple Toll-like receptor (TLR) and Dectin signaling pathways but not NOD signaling pathways. Tbc1d23 likely acts downstream of the TLR signaling adaptors MyD88 and Trif and upstream of the transcription factor XBP1. Importantly, like XBP1, Tbc1d23 affects the maintenance but not initiation of inflammatory cytokine production induced by lipopolysaccharide (LPS). The identification of a novel temporal regulator of innate immunity signaling validates the comparative genomics approach for innate immunity gene discovery.

overall_design: Total of 24 samples; Tbc1d23-overexpressing line and control line; 0, 1, 3, and 5 hour LPS treatment; 3 biological replicates per group

first: Lesly

last: De Arras

first: Ivana

middle: V

last: Yang

first: Brad

last: Lackford

first: David

last: Riches

first: Rytis

last: Prekeris

first: Jonathan

last: Freedman

last: Schwartz


title: Exposure of pregnant mice to carbon black by intratracheal instillation: toxicogenomics effects in dams and offspring (offspring samples)

status: Public on Apr 02 2012

city: Ottawa

first: Andrew

last: Williams

state: ON

address: 50 Columbine

institute: Health Canada

summary: Exposure to nanomaterials (NM) during sensitive stages of development may predispose organisms to diseases later in life. However, direct translocation of NM from mother to fetus through the placenta is limited. The present study tests the hypothesis that pulmonary exposure to NM and NM-induced stress, such as inflammation during gestation, can lead to secondary effects in the growing fetus. Time mated C57BL/6BomTac mice were exposed by intratracheal instillation to vehicle (Milli Q water) or one of three concentrations (2.75, 13.5 or 67 µg/animal) of carbon black Printex 90 (CB) dispersions on gestational days 7, 10, 15 and 18 to a total final dose of 11, 54 or 268 µg/animal. Male and female newborns were sacrificed on day 2 after birth (PND2, 4 days after the last maternal exposure) and dams were sacrificed after weaning of offspring (26-27 days post-exposure).  Histopathology, DNA microarrays, pathway-specific RT-PCR arrays, focussed RT-PCR, and tissue protein analysis were employed to characterize pulmonary response in dams exposed to CB during gestation.  Gene expression profiles in newborn livers were interpreted in light of toxic effects of CB to dams indicated by gene expression profiles of dam lungs. Although retention of CB particles was observed in dams from both medium and high dose groups, neutrophil-marked inflammation was significant only in the high dose group dams. Inflammation in dams was accompanied by altered expression of several cytokines and chemokines both at the transcriptional and tissue protein levels. Analysis of newborn livers by DNA microarrays revealed that female offspring were much more sensitive to maternal stress than males. Cellular signalling, inflammation, immune response, cell cycle and lipid metabolism were among the biological pathways affected in female offspring. Males however, responded with subtle changes in genes involved in metabolism.  At present, the implications of altered biological pathways in offspring in response to in utero exposure to particles are not well understood. Further investigation will be required to determine if there are long term consequences to offspring in terms of health and responses to environmental stresses.

first: Petra

last: Jackson

first: Karin

last: Hougaard

first: Ulla

last: Vogel

first: Dongmei

last: Wu

first: Lorraine

last: Casavant

first: Mike

last: Wade

first: Carole

middle: L

last: Yauk

first: Håkan

last: Wallin

first: Sabina

last: Halappanavar


title: Gene expression signatures for fractions of E7.5 whole embryos based on Endoglin and Flk-1 markers

status: Public on Apr 23 2012

city: Minneapolis

first: Rita

last: Perlingeiro

state: MN

address: 312 Church ST SE; NHH 4-124

department: Medicine

institute: University of Minnesota

summary: Much remains unknown about the signals that induce early mesoderm to initiate hematopoietic differentiation. Here we show that endoglin (Eng), a receptor for the TGFβ superfamily, identifies all cells with hematopoietic fate in the early embryo. These arise in an Eng+Flk1+ mesodermal precursor population at E7.5, a cell fraction also endowed with endothelial potential. In Eng knockout embryos, hematopoietic colony activity and numbers of CD71+Ter119+ erythroid progenitors were severely reduced.  This coincided with severely reduced expression of embryonic globin and key BMP target genes including the hematopoietic regulators Scl, Gata1, Gata2 and Msx-1. To interrogate molecular pathways active in the earliest hematopoietic progenitors, we applied transcriptional profiling to sorted cells from E7.5 embryos.  Eng+Flk-1+ progenitors co-expressed TGFβ and BMP receptors and target genes.  Furthermore, Eng+Flk-1+ cells presented high levels of phospho-SMAD1/5, indicating active TGFβ and/or BMP signaling.  Remarkably, under hematopoietic serum-free culture conditions, hematopoietic outgrowth of endoglin-expressing cells was dependent on TGFβ superfamily ligands: BMP4, BMP2, or TGF-β1. These data demonstrate that the E+F+ fraction at E7.5 represents mesodermal cells competent to respond to TGFb1, BMP4, or BMP2, shaping their hematopoietic development, and that endoglin is a critical regulator in this process by modulating TGF/BMP signaling.

overall_design: E7.5 pooled embryos (25 litters; 300 embryos approximately) were dissected and 3,000 cells were sorted in triplicate for Eng-Flk1-, Eng-Flk1+, Eng+Flk1+, and Eng+Flk1- fractions. Microarray results were analyzed with GeneSpring GX software.

first: Luciene

last: Borges

first: Michelina

last: Iacovino


title: Exposure of pregnant mice to carbon black by intratracheal instillation: toxicogenomics effects in dams and offspring

summary:
Exposure to nanomaterials (NM) during sensitive stages of development may predispose organisms to diseases later in life. However, direct translocation of NM from mother to fetus through the placenta is limited. The present study tests the hypothesis that pulmonary exposure to NM and NM-induced stress, such as inflammation during gestation, can lead to secondary effects in the growing fetus. Time mated C57BL/6BomTac mice were exposed by intratracheal instillation to vehicle (Milli Q water) or one of three concentrations (2.75, 13.5 or 67 µg/animal) of carbon black Printex 90 (CB) dispersions on gestational days 7, 10, 15 and 18 to a total final dose of 11, 54 or 268 µg/animal. Male and female newborns were sacrificed on day 2 after birth (PND2, 4 days after the last maternal exposure) and dams were sacrificed after weaning of offspring (26-27 days post-exposure).  Histopathology, DNA microarrays, pathway-specific RT-PCR arrays, focussed RT-PCR, and tissue protein analysis were employed to characterize pulmonary response in dams exposed to CB during gestation.  Gene expression profiles in newborn livers were interpreted in light of toxic effects of CB to dams indicated by gene expression profiles of dam lungs. Although retention of CB particles was observed in dams from both medium and high dose groups, neutrophil-marked inflammation was significant only in the high dose group dams. Inflammation in dams was accompanied by altered expression of several cytokines and chemokines both at the transcriptional and tissue protein levels. Analysis of newborn livers by DNA microarrays revealed that female offspring were much more sensitive to maternal stress than males. Cellular signalling, inflammation, immune response, cell cycle and lipid metabolism were among the biological pathways affected in female offspring. Males however, responded with subtle changes in genes involved in metabolism.  At present, the implications of altered biological pathways in offspring in response to in utero exposure to particles are not well understood. Further investigation will be required to determine if there are long term consequences to offspring in terms of health and responses to environmental stresses.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Exposure of pregnant mice to carbon black by intratracheal instillation: toxicogenomics effects in dams and offspring (dams samples)

overall_design: Time mated C57BL/6BomTac mice were exposed by intratracheal instillation to vehicle (Milli Q water) or one of three concentrations (2.75, 13.5 or 67 µg/animal) of carbon black Printex 90 (CB) dispersions on gestational days 7, 10, 15 and 18 to a total final dose of 11, 54 or 268 µg/animal. Male and female newborns were sacrificed on day 2 after birth (PND2, 4 days after the last maternal exposure) and dams were sacrificed after weaning of offspring (26-27 days post-exposure).  Histopathology, DNA microarrays, pathway-specific RT-PCR arrays, focussed RT-PCR, and tissue protein analysis were employed to characterize pulmonary response in dams exposed to CB during gestation.  Gene expression profiles in newborn livers were interpreted in light of toxic effects of CB to dams indicated by gene expression profiles of dam lungs.


title: DNA Damage Response and Inflammatory Signaling Limit the MLL-ENL-induced Leukemogenesis in vivo

status: Public on Apr 22 2012

city: Prague

first: Viktor

last: Stranecky

address: Ke Karlovu 2

department: 1st Faculty of Medicine

country: Czech Republic

institute: Charles University

summary: Activation of the MLL-ENL-ERtm oncogene initiates aberrant proliferation of myeloid progenitors. Here, we show induction of a fail-safe mechanism mediated by the DNA damage response (DDR) machinery that results in activation of the ATR/ATM-Chk1/Chk2-p53/p21 checkpoint and cellular senescence at early stages of cellular transformation caused by a regulatable MLL-ENL-ERtm in mice. Furthermore, we identified the transcription program underlying this intrinsic anti-cancer barrier, and DDR-induced inflammatory regulators that fine-tune the signaling towards senescence, thereby modulating the fate of MLL-ENL-immortalized cells in a tissue-environment-dependent manner. Our results indicate that DDR is a rate-limiting event for acquisition of stem cell-like properties in MLL-ENL-ERtm-mediated transformation, as experimental inhibition of the barrier accelerated the transition to immature cell states and acute leukemia development.

overall_design: We created a mouse model wherein the protein function of the MLL-ENL oncogene depends on tamoxifen due to fusion with the mutated estrogen-binding domain of the estrogen receptor (ERtm). After 7 months of tamoxifen administration, the MLL-ENL-ERtm mice developed a myeloproliferative disease, which progressed into the terminal stage after a long period (mean survival: 592 ± 112 days) of continuous tamoxifen provision. We have profiled gene expression at three time-points of tamoxifen treatment corresponding to three distinct cellular states of the MLL-ENL-ERtm-induced myeloproliferation in the bone marrow: 1. 7 months - high proliferation state with low DDR signaling (4 biological replicates), 2. 7-8 months - the transition period of lower proliferation and high DDR activity (4 biogical replicates) and 3. 8 months - the senescence (3 biological replicates). Time-matched tamoxifen-treated wild-type bone marrow analysed in 4 biological replicates. We have profiled gene expression in three disease stages in the spleen: 1. 7 months - early stage - induced proliferation and DDR (3 biological replicates), 2. 9-10 months - progression - partial senescence and DDR is maintained (3 biological replicates) and 3. 16-23 months - terminal stage - proliferation, low or absent DDR and no senescence (3 biological replicates). Time-matched tamoxifen-treated and age-matched wild-type spleens analysed in 5 biological replicates.

first: Sylvia

last: Takacova

first: Jiri

last: Zavadil


title: Sequential Reprogramming Leads to a Specific Hepatic Expression Pattern during Mouse Bone Marrow Derived Hepatocyte Formation In Vivo

status: Public on Apr 01 2012

city: Madrid

first: Ramon

last: Garcia-Escudero

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

institute: CIEMAT

summary: The fusion of bone marrow (BM) hematopoietic cells with hepatocytes to generate BM derived hepatocytes (BMDH) is a natural process, which is enhanced in damaged tissues. However, the reprogramming needed to generate BMDH and the identity of the resultant cells are essentially unknown. In a mouse model of chronic liver damage, here we identify a modification in the chromatin structure of the hematopoietic nucleus during BMDH formation, accompanied by the sequential loss of the key hematopoietic transcription factor PU.1/Sfpi1 (SFFV proviral integration 1) and gain of the key hepatic transcriptional regulator HNF-1A homeobox A (HNF-1A/Hnf1a). Through genome-wide expression analysis of laser captured BMDH, a differential gene expression pattern was detected and the chromatin changes observed were confirmed at the chromatin regulator gene level. Similarly, Tranforming Growth Factor-β1 (TGF-β1) and neurotransmitter (e.g. Prostaglandin E Receptor 4 [Ptger4]) pathway genes were over-expressed. In summary, in vivo BMDH generation is a sequential process in which the hematopoietic cell nucleus changes its identity and acquires hepatic features. These BMDHs have their own cell identity characterized by an expression pattern different from hematopoietic cells or hepatocytes. The role of these BMDHs in the liver requires further investigation.

overall_design: C57BL/6JxDBA/2 F1 female mice were subjected to lethal irradiation and intravenously injected with bone marrow cells harvested from C57BL/6J-βactinEGFPxDBA/2 F1 male mice. The livers of female mice were injured with CCl4.  Liver individual cells were laser captured from frozen sections. Bone marrow derived hepatocytes (BMDH), hematopoietic cells, and hepatocytes, were analyzed individually.

first: Oscar

last: Quintana-Bustamante

first: Esther

last: Grueso

first: Ramón

first: Elvira

last: Arza

first: Alberto

last: Alvarez-Barrientos

first: María

last: Garcia-Bravo

first: Nestor

last: Meza

first: Jose

last: Segovia


title: Gene Expression in the Lrrc10 knockout heart

status: Public on Mar 15 2012

city: Madison

first: Matt

last: Brody

state: WI

address: 1300 University Ave.

institute: UW-Madison

summary: LRRC10 is a heart-specific gene required for proper cardiac function.  The effects of Lrrc10 deletion on gene expression in the adult mouse heart was investigated.

overall_design: Lrrc10 knockout mice or wildtype controls, housed in 12 hour light:12 dark, ad lib feeding and drinking conditions were sacrificed at two months of age for cardiac gene expression analysis.  A two color, reference design experiment in which heart RNA from 2 Lrrc10 knockout mice was pooled and labeled with Cy5 and hybridized according to Agilent protocols against a reference pool of RNA madeup from respective tissue taken from 2 month wildtype mice  which was labeled with Cy3.

first: Youngsook

last: Lee


title: Characterization of Directly Regulated Thyroid Hormone Mediated Gene Expression Following Short-Term Perturbations in Thyroid Hormone Levels in Juvenile Mice

status: Public on Mar 30 2012

first: Morie

last: Malowany

address: 50 Colombine Driveway, Tunney's Pasture

department: Environmental Health Science and Research Bureau

summary:
We investigated the effects of thyroid hormone disruptions on gene expression in juvenile mice liver to develop a stronger understanding of the mechanisms by which thyroid disrupting chemicals impair development.  Gene expression was examined by hybridization of hepatic RNA to Agilent mouse microarrays for hyper-, hypo-, hypo-replacement (hypo+) and euthyroid animals.

Keywords: Toxicogenomics, biomarkers of thyroid disruptors

overall_design: Hypothyroidism was induced from post natal day (PND) 13 to 15 by adding model thyroid toxicants methimazole and sodium perchlorate to drinking water of pregnant females.  Hyperthyroidism was induced by intraperitoneal injections (i.p.) of THs at PND 15, 4 hours before decapitation and tissue collection.  For the hypothyroid/replacement group; dams were provided with drinking water for 3 days (PND 13 to 15), containing a mixture of methimazole/sodium perchlorate.  Pups then received intraperitoneal injections of thyoid hormones on PND 15, 4 hours before decapitation and tissue collection.

first: Martin

last: Paquette

first: Hongyan

last: Dong

first: Mike

last: Wade

first: Carole

last: Yauk


title: Analysis of SAMP8 and SAMR1 mice after an exercise intervention

status: Public on Mar 20 2012

city: Barcelona

first: Perla

last: Kaliman

address: Corsega 176 bajos

institute: IDIBAPS

summary: Microarrays have been used to analyze the effect of voluntary wheel running in the SAMP8 mice using the SAMR1 mouse strain as control.

overall_design: Hippocampal gene expresion of SAMP8 which have been resting or exercising and SAMR1 sedentary.

first: Maria

last: Alvarez-Lopez

first: Marco

last: Castro-Freire


title: Expression data of Dnmt1 haploinsufficient leukemia stem cells and bulk leukemia

status: Public on Mar 14 2012

city: Boston

first: Jennifer

last: Trowbridge

state: MA

address: 44 Binney St., Mayer 652

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

summary:
Leukemia stem cells (LSCs) are an attractive target in treatment of many types of blood cancers. There remains an incomplete understanding of the epigenetic mechanisms driving LSC formation and maintenance, and how this compares to the epigenetic regulation of normal hematopoietic stem cells (HSCs).
To investigate novel mechanisms underlying the dependence of MLL-AF9 leukemia stem cells on Dnmt1, we used genome-wide expression profiling to examine changes in gene expression in Dnmt1 haploin sufficient L-GMPs as well as more differentiated leukemia cells (the bulk population of leukemia cells) compared to their control counterparts.

overall_design: Bone marrow LSK (Lin- Sca-1+ c-Kit+) cells were isolated from Dnmtfl/+ Mx-Cre+ or control Dnmtfl/fl mice. These cells were transduced with MLL-AF9-IRES-GFP retrovirus for 2 days, then GFP+ cells were sorted and transplanted into C57BL/6 syngeneic sublethally irradiated (600 rad) recipients. After 2 weeks, Dnmt1 haploinsufficiency was achieved in the leukemia cells by seven injections of poly(I)poly(C). Upon development of terminal stage acute myeloid leukemia, populations of L-GMPs or bulk GFP+ leukemia cells were FACS sorted from leukemic spleens, RNA was extracted, amplified and hybridized to Affymetrix 430A 2.0 microarrays to compare changes in gene expression. There are 2 biological replicates of Dnmtfl/+ Mx-Cre+ and control L-GMPs and bulk leukemia cells.

first: Stuart

last: Orkin


title: Transcriptome Alteration in the Diabetic Heart by Rosiglitazone: Implications for Cardiovascular Mortality

status: Public on Mar 29 2012

city: Stanford

first: Kitchener

middle: D.

last: Wilson

state: CA

address: S140 Grant Bldg

institute: Stanford University

summary: The type 2 diabetes medication, rosiglitazone, has come under scrutiny for possibly increasing the risk of cardiac disease and death. To investigate the effects of rosiglitazone on the diabetic heart, we performed cardiac transcriptional profiling  of a murine model of type 2 diabetes, the C57BL/KLS-leprdb/leprdb (db/db) mouse. We compared cardiac gene expression profiles from three groups: untreated db/db mice (db-c), db/db mice after rosiglitazone treatment (db-t), and non-diabetic db/+ mice.

overall_design: Mice were divided into three groups: Non-diabetic controls (db/+), untreated diabetic controls (db-c), and rosiglitazone-treated diabetic mice (db-t). Whole-heart RNA from five mice from each of the three groups after four months with or without treatment was used for microarray analysis.Universal Reference RNAs for mouse (Stratagene, La Jolla, CA) were purchased as microarray reference controls.

first: Roger

last: Wagner

first: Zongjin

last: Li

first: Gergana

last: Nestorova

first: David

last: Hirschberg

first: Joseph

last: Wu


title: DNA Microarray Analysis Approach for Unraveling the Ischemic Mouse Brain Transcriptome

first: RANDEEP

last: RAKWAL

state: Ibaraki

summary: Brain ischemia, also termed cerebral ischemia, is a condition in which there is insufficient blood flow to the brain to meet metabolic demand, and results in brain tissue death (cerebral infarction) due to poor oxygen supply (cerebral hypoxia). Our group is interested in the protective effects of neuropeptides for alleviating brain ischemia, and mechanisms therein. However, before proceeding to the neuroprotection aspect of our research, we initiated a study with a primary aim to investigate the molecular responses at the level of gene expression in ischemic brain tissue. To do so, we used permanent middle cerebral artery occlusion (PMCAO) model mice in combination with high-throughput DNA microarray analysis on an Agilent microarray platform. Briefly, saline injected mice brain in sham (control, n=3) and PMCAO (treatment, n=3) mice were dissected into left (contralateral) and right hemispheres (ipsilateral) at two time points, 6 and 24 h after injection. The ipsilateral hemisphere shows ischemia, within 24 h, and is marked by cell death as visualized by TTC staining. Tissues were ground into fine powder with liquid nitrogen and total RNA was extracted, followed by quality check using gel electrophoresis and cDNA synthesis in conjunction with RT-PCR using certain marker genes. The obtained good quality total RNA from ipsilateral hemisphere was used for DNA microarray analysis on a mouse (Mus musculus) whole genome 4x44K DNA chip by using the dye-swap approach. Results revealed a large number of changed gene expressions at both 6 (1237 up- and 620 down-regulated) and 24 h (2759 up- and 2102 down-regulated). 792 and 167 genes were found to be commonly up- and down-regulated 6 and 24 h post-ischemia, respectively. Functional categorization using the gene ontology (GO, MGD/AMIGO) of these gene expressions revealed major categories of cellular processes, biological regulation, regulation of biological processes, metabolic processes, and response to stimulus. In addition, RT-PCR using specific primers of randomly selected genes was used to validate the changed gene expressions. This study provides the first inventory of ischemia-related transcriptome in mouse brain.

overall_design: For appropriate control to the PMCAO model, mice were anesthetized with 4% isoflurane (induction) and 2% isoflurane (maintenance) in a 30% O2 and 70% N2O gas mixture via a face mask. An incision was then made in the cervical skin followed by opening of salivary gland, and visualization of the right common carotid artery. The external carotid artery was exposed through a midline cervical incision, and subsequently, the wound was closed by sutures. For the PMCAO model, we used the intraluminal filament technique, where a 7-0 monofilament nylon suture with its tip slightly rounded by heating was inserted into the common carotid artery followed by placement into the middle cerebral artery. In both the control and PMCAO model, saline (0.9% NaCl) was injected into the intracerebroventricle, and the animals were returned to their cages. A total of eight groups were prepared with three mice each in the control (4 groups) and PMCAO model (4 groups).  After 6 and 24 h post-injection of saline, mice were removed from the cages and decapitated using scissors, and the whole brains were carefully dissected on ice. The left (contralateral) and right (ipsilateral) hemispheres were separated and placed in 2 mL Eppendorf tubes followed by quickly immersing the tubes in liquid nitrogen (Lq. N2), and then stored in -80ºC prior to further analysis. A mouse 4 x 44K whole genome oligo DNA microarray chip (G4122F, Agilent Technologies, Palo Alto, CA, USA) was used for global gene expression analysis using the contralateral hemispheres. The effects of ischemia were checked over the SHAM control mice at 6 and 24 h post-saline injection.

first: Motohide

last: Hori

first: Tomoya

last: Nakamachi

first: Randeep

last: Rakwal

first: Junko

last: Shibato

first: Keiji

last: Tamaki

first: Seiji

last: Shioda


title: A supporting environment for hematopoietic stem/progenitor cells is maintained by canonical Wnt signaling

city: Oklahoma City

first: Bart

last: Frank

state: OK

institute: OMRF

summary: Considerable information has accumulated about components of bone marrow that regulate survival, self-renewal and differentiation of hematopoietic cells.  We have now studied Wnt signaling in that context, assessing influences on human and murine hematopoiesis.  Microarray, PCR and staining experiments revealed that OP9 acquired osteoblastic characteristics while down-regulating some features associated with mesenchymal stem cells.  This included down-regulation of Angiopoietin 1, c-Kit ligand and VCAM-1 expression.  In contrast, production of decorin, tenascins and fibromodulin markedly increased.  At least one of these extracellular matrix components, decorin is a regulator of hematopoiesis.  That is, addition of the protein to OP9 co-cultures causes changes similar to Wnt3a.

overall_design: Two control samples (LZR1 & LZR2) were analyzed from OP9 mouse stromal cells transfected with vector only, and two experimental samples  (W3A1 & W3A2) were analyzed from OP9 cells transfected with vector containing the Wnt3A gene.

first: Michiko

last: Ichii

first: Paul

last: Kincade

first: Renato

last: Iozzo

first: Karla

last: Garrett


title: Maternal inhalation of surface-coated nano-sized titanium dioxide (UV-Titan): Effects in prenatally exposed offspring on hepatic DNA damage and gene expression

status: Public on Mar 19 2012

first: Andrew

last: Williams

summary: In the present study we investigate the effect of maternal pulmonary exposure to titanium dioxide (UV-Titan designed for use in the paint and lacquer industry) on prenatally exposed offspring. Time-mated mice (C57BL/6BomTac) were exposed by inhalation for 1 h/day to 42 mg UV-titan/m3 aerosolized powder or filtered air during gestation days (GD) 8-18. We evaluated levels of DNA strand breaks using the comet assay in bronchioalveolar lavage (BAL) cells and liver cells of the time-mated mice, and in liver cells of the offspring. In parallel, we analyzed changes in gene expression in the liver tissue of offspring using DNA microarrays. We demonstrate that UV-Titan did not induce DNA strand breaks in the time-mated mice or their offspring. Transcriptional profiling of newborn liver tissue revealed changes in the expression of genes related to the retinoic acid (RA) signalling pathway in the females, while gene expression in male offspring was relatively unaffected by exposure.

overall_design:
Time-mated, nulliparous mice (C57BL/6BomTac, Taconic Europe, Ejby, Denmark) were exposed to filtered clean air or approximately 42 mg/m3 UV-Titan on GD 8–18 for 1 hr/day by a whole-body exposure.Delivery was expected on GD 20, and designated postnatal day (PND) 0. On PND 2, one offspring (“newborn”) per litter was killed by decapitation, to yield litters with at least 5 offspring per exposure group. The newborn offspring were collected two days after birth. On PND 23-24 (“at weaning”) one male and one female per litter were killed. Organs were dissected, weighed, placed in NUNC cryotubes, snap frozen in liquid N2 and stored at -80°C until analysis. Exposed dams were killed on PND 24-25 (26-27 days after last exposure). DNA strad break detection was carried out in bronchoalveolar lavage fluid in dams by COMET assay. Total RNA was extracted from offspring livers and gene expression profiling was carried out on whole liver tissues from offspring.
9 UV-Titan treated and 7 controls mice consisting of 8 males and 8 females
mRNA, hepatic, developmental, Toxicogenomics, nano-titanium dioxide

first: Petra

last: Jackson

first: Sabina

last: Halappanavar

first: Karin

last: Hougaard

first: Carole

last: Yauk

first: Jacob

last: Lamson

first: Ole

last: Andersen

first: Håkan

last: Wallin

first: Ulla

last: Vogel


title: KLF1, KLF2 and c-myc control a regulatory network essential for embryonic erythropoiesis

status: Public on Mar 12 2012

city: Richmond

first: Christopher

last: Pang

address: 401 College Street

institute: Virginia Commonwealth University

summary: The Krüppel-like factors, KLF1 and KLF2, positively regulate embryonic β-globin expression, and have additional overlapping roles in embryonic (primitive) erythropoiesis. KLF1-/-KLF2-/- double knockout mice are anemic at embryonic day 10.5 (E10.5) and die by E11.5, in contrast to single knockouts. To investigate the combined roles of KLF1 and KLF2 in primitive erythropoiesis, expression profiling of E9.5 erythroid cells was performed. A limited number of genes had a significantly decreasing trend of expression in wild-type, KLF1-/- and KLF1-/-KLF2-/-. Among these, c-myc emerged as a central node in the most significant gene network. c-myc expression is synergistically regulated by KLF1 and KLF2, and both factors bind the c-myc promoters. To characterize the role of c-myc in primitive erythropoiesis, ablation was performed specifically in mouse embryonic proerythroblast cells. After E9.5, these embryos exhibit an arrest in the normal expansion of circulating red cells and develop anemia analogous to KLF1-/-KLF2-/-. In the absence of c-myc, circulating erythroid cells do not show the normal increase in α- and β-like globin expression, but interestingly, have accelerated erythroid maturation, between E9.5 and E11.5. This study reveals a novel regulatory network by which KLF1 and KLF2 regulate c-myc, to control the primitive erythropoietic program.

overall_design: Timed-pregnant KLF1+/-, KLF1+/- KLF2+/- females were anesthetized and sacrificed. E9.5 yolk sacs were dissected from the embryo, cryoprotected in 20% sucrose in PBS and frozen in OCT media. A small portion of the embryo tail was used for PCR genotyping. Eight micron frozen yolk sac sections were obtained and laser capture microdissection (LCM) was used to isolate primitive erythroid precursors. For each biological replicate, 2 to 4 yolk sacs from 2 different litters were used. Total RNA was isolated from 8 different wild-type, 3 KLF1-/-, 3 KLF1-/- KLF2-/- erythroid samples and hybridized to Affymetrix 430 A 2.0 microarrays.

first: Wafaa

last: Lemsaddek

first: Yousef

middle: N

last: Alhashem

first: Cornelius

last: Bondzi

first: Latasha

last: Redmond

first: Nicolas

last: Ahson

first: Catherine

last: Dumur

first: Kellie

last: Archer

first: Jack

last: Haar

first: Joyce

last: Lloyd

first: Marie

last: Trudel


title: control vs. Th3 beta thalassemia kidney

status: Public on Mar 07 2012

city: Nashville

first: Hanako

last: Kobayashi

institute: Vanderbilt University

summary: a comparison of a control and a mutant condition (Th3) of the Hemoglobin Beta major and minor chain, used as Beta Thalassemia mouse model.

overall_design: 4 controls and 4 mutants

first: Volker

last: Haase


title: Gene expression in liver of wild-type and Dicer1-KO mice treated with genotoxic carcinogen N-ethyl-N-nitrosourea

status: Public on Mar 06 2012

city: shanghai

first: Luan

last: Yang

address: 555 Zu Chong Zhi Road , Zhang Jiang Hi-Tech Park, Pudong, Shanghai

country: China

institute: Shanghai Institute of Medicine of Chinese Academy of Medical Sciences

summary: To explore the possible changes of gene expression induced by a carcinogen, we treated wild-type and Dicer1-KO mice with one dose of 120 mg/kg N-ethyl-N-nitrosourea (ENU), a model genotoxic carcinogen, and vehicle control. The gene expression profiles were assessed in the mouse livers in wild-type and Dicer1-KO mice design. Total RNA were isolated from the livers at days 15 after the treatment and their expression was determined using Gene Array.

overall_design: Gene expression in treated wild-type and Dicer1-KO mice was measured at 15 days after exposure to one dose of 120 mg/kg N-ethyl-N-nitrosourea (ENU).  Each treatment duplex ,Drug-ko-a,Drug-ko-b,Drug-wt-a,Drug-wt-b,Control-ko-a,Control-ko-b,Control-wt-a,Control-wt-b.

first: Xinming

last: Qi

first: Liang

last: Xu


title: Translatome of NIH3T3 cells: control vs. stress treatment

status: Public on Mar 02 2012

first: Ivan

last: Ventoso

address: Nicolas cabrera 1. Universidad Autonoma de Madrid

department: Virology and Microbiology

institute: Centro de Biología Molecular Severo Ochoa

summary: Translation efficiencies of mouse mRNAs in control and in cells treated with thapsigargin 10microM for 3h.

overall_design: Two-conditions experiments. Biological replicates: 1 from three pooled control experiments, 1 from three pooled stress experiments

first: Iván

first: Javier

last: Santoyo

first: Joaquín

last: Dopazo

first: David

last: Montaner


title: PPARg agonists induce a white-to-brown fat conversion through stabilization of PRDM16 protein

city: San Francisco

first: Kosaku

last: Shinoda

address: 35 Medical Center Way

department: UCSF Diabetes Center and Department of Cell and Tissue Biology

institute: University of California, San Francisco

summary: Brown adipose tissue dissipates energy through heat and functions as a defense against cold and obesity. PPARγ ligands have been shown to induce the browning of white adipocytes; however, the underlying mechanisms remain unclear. Here we show that PPARγ ligands require full agonism to induce a brown fat gene program preferentially in subcutaneous white adipose. These effects require expression of PRDM16, a factor that controls the development of classical brown fat. Depletion of PRDM16 blunts the effects of the PPARγ agonist rosiglitazone on the induced brown fat gene program. Conversely, PRDM16 and rosiglitazone synergistically activate the brown fat gene program in vivo. This synergy is tightly associated with an increased accumulation of PRDM16 protein, due in large measure to an increase in the half-life of the protein in agonist treated cells. Identifying compounds that stabilize PRDM16 protein may represent a novel therapeutic pathway for the treatment of obesity and diabetes.

overall_design: Microarray analysis of the differentiated inguinal adipocytes expressing sh-scr or sh-PRDM16 in the presence or absence of rosiglitazone (1uM). These samples were profiled using Affymetrix mouse 430A_2 arrays, representing 2 biological replicates for each samples (8 samples in total).

first: Haruya

last: Ohno

first: Bruce

middle: M

last: Spiegelman

first: Shingo

last: Kajimura