title: Alterations in Cell Growth and Signaling in  ErbB3 Binding Protein -1 (Ebp1) Deficient Mice

city: Baltimore

first: Anne

last: Hamburger

state: MD

address: 655 W. Baltimore St

department: Cancer Center

institute: University of Maryland Baltimore

summary:
Background: The ErbB3 binding protein-1 (Ebp1) belongs to a family of DNA/RNA binding proteins implicated in cell growth, apoptosis and differentiation. However, the physiological role of Ebp1 in the whole organism is not known. Therefore, we generated Ebp1-deficient mice carrying a gene trap insertion in intron 2 of  the Ebp1 (pa2g4) gene.
Results: Ebp1 -/- mice were on average 30% smaller than wild type and heterozygous sex matched littermates. Growth retardation was apparent from Day 10 until Day 30. IGF-1 production and IGBP-3 and 4 protein levels were reduced in  both embryo fibroblasts and adult knock-out mice. The proliferation of fibroblasts derived from Day 12.5  knock out embryos was also decreased as compared to that of wild type cells. Microarray expression analysis revealed changes in genes important in cell growth including members of the MAPK signal transduction pathway. In addition, the expression or activation of proliferation related genes such as AKT and the androgen receptor, previously demonstrated to be affected by Ebp1 expression in vitro,  were altered in adult tissues.
Conclusions: These results indicate that Ebp1 can affect growth in an animal model, but that the expression of proliferation related genes is cell and context specific. The Ebp1-/- mouse line represents a new in vivo model to investigate Ebp1 function in the whole organism.

overall_design: Isolation of   Mouse Embryo Fibroblasts (MEFS) and proliferation assays. Embryos (12.5 days) were minced and incubated in 0.25% trypsin and 5 U of DNAse I for 37º C for 30 min. Dulbecco’s MEM supplemented with 10% fetal bovine serum and penicillin and streptomycin were added to the cell suspension and cells centrifuged at 1000 rpm for 10 min. The pellet was resuspended in medium and cells were grown in MEM and passaged by trypsinization.

first: Yuexing

last: Zhang


title: Assessment of Thermotolerance in preshocked hsp70(-/-) and (+/+) cells

status: Public on Apr 09 2009

city: Nashville

first: Josh

middle: T

last: Beckham

state: TN

address: 5824 Stevenson Center

department: Biomedical Engineering

country: USA

institute: Vanderbilt University

summary:
From preliminary experiments, HSP70 deficient MEF cells display moderate thermotolerance to a severe heatshock of 45.5 degrees after a mild preshock at 43 degrees, even in the absence of hsp70 protein. We would like to determine which genes in these cells are being activated to account for this thermotolerance.
Keywords: thermal stress, heat shock response, knockout, cell culture, hsp70

overall_design: Two cell lines are analyzed - hsp70 knockout and hsp70 rescue cells. 6 microarrays from the (-/-)knockout cells are analyzed (3 Pretreated vs 3 unheated controls). For the (+/+) rescue cells, 4 microarrays are used (2 pretreated and 2 unheated controls). Cells were plated at 3k/well in a 96 well plate, covered with a gas permeable sealer and heat shocked at 43degrees for 30 minutes at the 20 hr time point. The RNA was harvested at 3hrs after heat treatment.

first: Duco

last: Jansen


title: Expression data from developing thymocytes of N15TCR transgenic Rag2 deficient mice

status: Public on Mar 31 2009

city: Boston

first: Young

middle: IL

last: Choi

state: MA

address: 77 Avenue Louis Pasteur

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary:
T cell development relies on the precise developmental control of various cellular functions for appropriate positive and negative selection. Previously, gene expression profiling of peptide-driven negative selection events in the N15 TCR class I MHC-restricted mouse and D011.10 TCR class II MHC-restricted mouse has offered insights into the coordinate engagement of biological processes affecting thymocyte development. However, there has been little comparable detailed in vivo global genome expression analysis reported for positive selection.
We used microarrays to identify the genes differentially expressed during CD8 single positive T cell development in N15 TCR transgenic Rag2 deficient mice.

overall_design: We have analyzed gene expression in the individual populations as development proceeds from DP, intermediate (Int), to SP subsets. To this end, we sorted the individual populations from six age and sex matched 5-6 week old N15 TCR tg+/+ RAG-2-/- H-2b mice for two independent experiments. For sorting subpopulations, cells were stained with anti-CD4 (L3T4) and anti-CD8 (Ly-2) antibodies (Pharmingen, San Diego, CA USA) and DP, Int and SP thymocytes were sorted on a MoFlo (Cytomation, Fort Collins, CO USA).

middle: I

first: Ellis

middle: L

last: Reinherz


title: Microarray of Mouse Brain Tumors grown from injections of GL26 cell line

city: Los Angeles

first: Gretchen

last: Duvall

state: CA

address: 8700 Beverly BLVD

institute: Cedars Sinai Medical Center

summary:
RNA was extracted from the tumors that grew in the brains of mice that were injected with the GL26 cell line. RNA from GL26 cells was also taken. The chip used for all was an affymetrix mouse genome chip (GPL1261). This is the mouse model compliment to a human experiment in which the human chip was used for GBM tumors.
Keywords: disease state analysis

overall_design: Samples include GL26 tumors taken from C57BL6 untreated wild type, 10 month Old C57BL6 untreated wild type,  C57BL6 Foxline Mutated Nudes, and from C57BL6 wild types that received a dendritic cell vaccine against GL26.


title: Skeletal muscle gene expression after myostatin knockout in mature mice

status: Public on Mar 24 2009

city: Rochester

first: Stephen

last: Welle

state: NY

address: 601 Elmwood Avenue

institute: University of Rochester

summary: RNA from 5 mice with postdevelopmental knockout of myostatin and 5 mice with normal myostatin expression was analyzed with comprehensive oligonucleotide microarrays. Myostatin depletion affected the expression of several hundred genes at nominal P < 0.01, but fewer than a hundred effects were statistically significant according to a more stringent criterion (false discovery rate < 5%). Most of the effects were less than 1.5-fold in magnitude. In contrast to previously-reported effects of constitutive myostatin knockout, postdevelopmental knockout did not downregulate expression of genes encoding slow isoforms of contractile proteins or genes encoding proteins involved in energy metabolism. Several collagen genes were expressed at lower levels in the myostatin-deficient muscles, and this led to reduced tissue collagen levels as reflected by hydroxyproline content. Myostatin knockout tended to down-regulate the expression of sets of genes with promoter motifs for Smad3, Smad4, myogenin, NF-κB, serum response factor, and numerous other transcription factors. Main conclusions: in mature muscle, myostatin is a key transcriptional regulator of collagen genes, but not genes encoding contractile proteins or genes encoding proteins involved in energy metabolism.

overall_design: Comparison of muscle gene expression in 5 mice with postdevelopmental myostatin knockout and 5 control mice


title: E2-RING expansion of the NEDD8 cascade confers specificity to cullin modification

city: Memphis

first: Geoffrey

last: Neale

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

summary:
Ubiquitin and ubiquitin-like proteins (UBLs) are directed to targets by cascades of E1, E2, and E3 enzymes. The largest ubiquitin E3 subclass consists of cullin-RING ligases (CRLs), which contain one each of several cullins (CUL1, -2, -3, -4, or -5) and RING proteins (RBX1 or -2). CRLs are activated by ligation of the UBL NEDD8 to a conserved cullin lysine. How is cullin NEDD8ylation specificity established? Here we report that, like UBE2M (also known as UBC12), the previously uncharacterized E2 UBE2F is a NEDD8-conjugating enzyme in vitro and in vivo. Biochemical and structural analyses indicate how plasticity of hydrophobic E1-E2 interactions and E1 conformational flexibility allow one E1 to charge multiple E2s. The E2s have distinct functions, with UBE2M/RBX1 and UBE2F/RBX2 displaying different target cullin specificities. Together, these studies reveal the molecular basis for and functional importance of hierarchical expansion of the NEDD8 conjugation system in establishing selective CRL activation.

Mol Cell 33:483-495, 2009.

Keywords: Comparison of gene expression profiles

overall_design:
Ube2m and Ube2f are E2 enzymes that direct protein modification by NEDD8. Here we explore the specific functions of Ube2f and Ube2m by comparing gene expression profiles following knockdown of their function in NIH 3T3 cells.

We used microarrays to detail the global programme of gene expression changes following knockdown of Ube2m and Ube2f in NIH 3T3 cells.

NIH 3T3 cells were transduced with retroviral constructs containing shRNA directed against Ube2m or Ube2f. Three replicates of each condition were analyzed.

first: Olivier

last: Ayrault

first: Danny

last: Huang

middle: A

first: Peter

middle: J

last: Murray

first: Martine

middle: F

last: Roussel

first: Brenda

last: Schulman


title: Gene expression data from mouse hematopoietic cells, Ikaros wt and null mutant

status: Public on Apr 03 2009

city: Cambridge

first: Jiangwen

address: 7 Divinity Ave

department: FAS Center for Systems Biology

institute: Harvard University

summary:
Regulation of lineage potential and transcriptional priming by Ikaros. New insight is provided into a bivalent regulation of lineage priming in the HSC and its lympho-myeloid restricted progeny the LMPP by the lymphoid lineage-determining factor Ikaros
Whereas Ikaros is responsible for the activation of a cascade of lymphoid expression programs and for the establishment of lymphoid potential from the HSC to the LMPP it is also responsible for the repression of stem cell and erythroid genetic programs that are incompatible with further lineage restrictions emanating from the LMPP

Keywords: Ikaros null versus wt

overall_design: Ikaros null versus wt

first: Samuel

last: Ng

first: Toshimi

last: Yoshida

first: Katia

last: Georgopoulos


title: Comparative analysis of gene expression in A/J CS vs Air lungs.

status: Public on Mar 23 2009

first: vikas

last: misra

address: 615 N. Wolfe street, E6609

department: Environmental health sciences

institute: Johns Hopkins University School of public health

summary:
We hypothesize that gene expression in the CS-exposed lungs of this strain (A/J) of mice would be able to give clues about the molecular mechanism of emphysema development, thus contributing to this phenotype. More specifically, although imbalance in oxidants/antioxidants and proteinase/antiproteinase pathways drives the pathogenesis of COPD, the molecular mechanisms involved in the development of emphysema are poorly understood. In order to test this hypothesis at the gene expression level, we utilized microarray analysis to examine transcriptional differences between CS-exposed and Air-exposed groups of mice.
Keywords: comparative expression profiling

overall_design: This study utilizes microarray analysis to test these hypotheses. Three sets of lungs were harvested from both groups at each time point (A/J - CS exposed OR Air-exposed: 5 hr, 8 days, 1.5 mos, and 6 mos). RNA was isolated and used for global gene expression profiling (Affymetrix Mouse 430 2.0 array). Statistically significant gene expression was determined as a minimum 6 counts of 9 pairwise comparisons, minimum 1.5-fold change, and p < 0.05.

first: Tirumalai

last: Rangasamy

first: Vikas

last: Misra

first: Ugonma

last: Chukwuke

first: Lijie

last: Zhen

first: Rubin

last: Tuder

first: Shyam

last: Biswal

first: Clarke

middle: G

last: Tankersley


title: The PPARg2 A/B-domain plays a gene specific role in transactivation and co-factor recruitment

status: Public on Mar 27 2009

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: We have previously shown that adenoviral expression of peroxisome proliferator-activated receptors (PPARs) leads to rapid establishment of transcriptionally active complexes and activation of target gene expression within 5-8 h following transduction. Here we have used the adenoviral delivery system combined with expression array analysis to identify novel putative PPARgamma target genes in murine fibroblasts and to determine the role of the A/B-domain in PPARgamma mediated transactivation of genomic target genes. Of the 257 genes found to be induced by PPARgamma2 expression, only 25 displayed A/B-domain dependency, i.e. significantly reduced induction in the cells expressing the truncated PPARgamma lacking the A/B-domain (PPARgammaCDE). Nine of the 25 A/B-domain dependent genes were involved in lipid storage and in line with this, triglyceride accumulation was considerably decreased in the cells expressing PPARgammaCDE compared to cells expressing full length PPARgamma2. Using chromatin immunoprecipitation (ChIP) we demonstrate that PPARgamma binding to genomic target sites and recruitment of the mediator component TRAP220/MED1/PBP/DRIP205 is not affected by the deletion of the A/B-domain. By contrast, the PPARgamma-mediated CBP and p300 recruitment to A/B-domain dependent target genes is abolished by deletion of the A/B-domain. These results indicate that the A/B-domain of PPARgamma2 is specifically involved in the recruitment or stabilization of CBP and p300 containing co-factor complexes to a subset of target genes.

overall_design: Total RNA samples were obtained from three individual experiments in which NIH-CAR (i.e. a clonal cell line of NIH-3T3 fibroblasts stably expressing the coxsackie-adenovirus receptor (CARΔ1)) cells were transduced with adenovirus containing empty vector (AdEmpty) followed by addition of vehicle (DMSO) or transduced with adenovirus encoding either full length HA-tagged PPARg2 or A/B-domain deleted HA-PPARgCDE and treated with rosiglitazone.

first: Anne

last: Bugge

first: Lars

last: Grøntved

first: Mads

middle: M

last: Aagaard

first: Rehannah

last: Borup


title: Stepwise development of hematopoietic stem cells from embryonic stem cells

status: Public on Mar 18 2009

city: Tokyo

first: Hideo

last: Ema

address: 4-6-1 Shirokanedai, Minato-ku

department: The Institute of Medical Science

country: Japan

institute: The University of Tokyo

summary: The cellular ontogeny of hematopoietic stem cells (HSCs) remains poorly understood because their isolation from and their identification in early developing small embryos are difficult. We attempted to dissect early developmental stages of HSCs using an in vitro mouse embryonic stem cell (ESC) differentiation system combined with inducible HOXB4 expression. Here we report the identification of pre-HSCs and an embryonic type of HSCs (embryonic HSCs) as intermediate cells between ESCs and HSCs. Both pre-HSCs and embryonic HSCs were isolated by their c-Kit+CD41+CD45- phenotype. Pre-HSCs did not engraft in irradiated adult mice. After co-culture with OP9 stromal cells and conditional expression of HOXB4, pre-HSCs gave rise to embryonic HSCs capable of engraftment and long-term reconstitution in irradiated adult mice. Blast colony assays revealed that most hemangioblast activity was detected apart from the pre-HSC population, implying the early divergence of pre-HSCs from hemangioblasts. Gene expression profiling suggests that a particular set of transcripts closely associated with adult HSCs is involved in the transition of pre-HSC to embryonic HSCs.

overall_design: Experimental strategy consisted of EB formation, co-culture with OP9 cells, and functional assays. iHOXB4 ESCs were allowed to differentiate spontaneously into EBs for 6 days without HOXB4 expression. We decided to fractionate EB6 cells mainly because by day 6 of culture the number of multipotent progenitors reaches a plateau and several surface markers become detectable. CD41 is known as a marker for the initiation of definitive hematopoiesis. CD41 appeared in a significant proportion of EB cells on day 6 of culture. Induced HOXB4 expression during EB formation did not affect the generation of colony forming cells and repopulating cells in the OP9 and iHOXB4 system or the appearance of surface markers in EB cells. EB6 cells were analyzed and sorted by flow cytometry. Sorted EB6 cells were co-cultured with OP9 cells for various days under HOXB4-on or -off conditions. The minimal requirement of the co-culture period appeared to be only 4 days, which is much shorter than previously thought. After a second analysis and fractionation by flow cytometry, cells were subjected to in vivo repopulating assays under HOXB4-on or -off conditions.

first: Kenji

last: Matsumoto

first: Takayuki

last: Isagawa

first: Toshinobu

last: Nishimura

first: Takunori

last: Ogaeri

first: Koji

last: Eto

first: Satsuki

last: Miyazaki

first: Hiroyuki

last: Aburatani

first: Hiromitsu

last: Nakauchi


title: Control of CD8+ T cell proliferation by the transcription factor ELF4

city: Houston

first: Toni-Ann

last: Mistretta

state: TX

address: 1 Baylor Plaza, BCM 315

department: Pathology

institute: Baylor College of Medicine

summary: Transcription factors that regulate quiescence, proliferation, and homing of lymphocytes are critical for effective immune system function. In the present study, we demonstrated that the transcription factor ELF4 directly activates the tumor suppressor KLF4 downstream of T cell receptor (TCR) signaling to induce cell cycle arrest in naïve CD8+ T cells. Elf4- and Klf4-deficient mice accumulated CD8+CD44hi T cells during steady-state conditions and generated more memory T cells after immunization. The homeostatic expansion of CD8+CD44hi T cells in Elf4-null mice resulted in a redistribution of cells to non-lymphoid tissue due to reduced expression of the transcription factor KLF2, and the surface proteins CCR7 and CD62L. This work describes the combinatorial role of lymphocyte-intrinsic factors in the control of T cell homeostasis, activation and homing.

overall_design:
CD8 T cells were purified from spleen of wild type and Elf4-/- mice and CD8 T cells were left untreated or activated in vitro by culturing on anti-CD3 coated plates and anti-CD28 in media (RPMI 10% FBS supplemented with 5% T-stim) for 3.5 days.

RNAs isolated from wild type and Elf4 -/- CD8+ T cells were used in Affimetrix oligonucleotide arrays either untreated or after 3.5 days of activation.

first: Takeshi

last: Yamada

first: Daniel

last: Lacorazza


title: Gene and exon expression of Human Umbilical Vein Endothelial Cell under Mimic Hypoxia Stress

status: Public on Apr 01 2009

city: Beijing

first: Xingyi

last: Hang

address: No. 27 Taiping Road

country: China

institute: Beijing Institute of Radiation Medicine

summary: Human umbilical vein endothelial cells (HUVECs) were insulted with cobalt chloride to induce cell apoptosis and alternative splicing in the mimic-hypoxia environment. We use Affymetrix exon array to reveal differential expression from transcript-level and exon-level in genome-wide.

overall_design: 6 samples, 2 conditions: mimic hypoxia and normoxia, 3 replicates per condition

first: Peiyao

last: Li

first: Zhifeng

first: Ying

last: Yu

first: Hualing

first: Wubin

last: Qu

first: Hao

last: Zheng

first: Zhiyong

last: Shen

first: Yan

last: Gao

first: Yonghong

last: Wu

first: Zhixian

last: Sun

first: Minghua

last: Deng

first: Chenggang

last: Zhang


title: Hedgehog signaling is dispensable for adult hematopoietic stem cell function

status: Public on Mar 11 2009

city: New York

first: Iannis

last: Aifantis

address: 550 First Ave

institute: NYU Sch of Medicine

summary:
The Hedgehog (Hh) signaling pathway is a developmentally conserved regulator of stem cell function. Several reports suggested that Hh signaling is an important regulator of hematopoietic stem cell (HSC) maintenance and differentiation. Here we test this hypothesis in vivo using both gain- and loss-of-function Hh genetic models. Surprisingly, our studies demonstrate that conditional Smoothened (Smo) deletion or over-activation has no significant effects on adult HSC self-renewal and function. Moreover, they indicate a lack of synergism between the Notch and Hh pathways in HSC function, as RBPJ- and Smo-deficiency do not affect hematopoiesis. In agreement with this notion, detailed genome-wide transcriptome analysis reveals that silencing of Hh signaling does not significantly alter the HSC-specific gene expression “signature”. Our studies demonstrate that the Hh signaling pathway is dispensable for adult HSC function and suggest that the Hh pathway can be targeted in future clinical trials addressing the effect of Hh inhibition on leukemia-initiating cell maintenance.
Transcriptional consequences of inactivating Smo (hh loss-of-function) in LKS cells.

overall_design: Four samples were analyzed: wild-type (WT) control and Smo-deficient (SMO) Lin-ckit+Sca1+ (LSK) cells, as well as Lin-ckit+Sca1- myeloid progenitor (MP) cells, which served as a control for LSK-enriched/specific genes.  Total bone marrow cells were pooled from four WT and four SMO mice before sorting LSK and MP populations.

first: Jie

first: Stephanie

last: Graves

first: Ute

last: Koch

first: Suqing

last: Liu

first: Vladimir

last: Jankovic

first: Silvia

last: Buonamici

first: Abdeljabar

last: El Andaloussi

first: Stephen

last: Nimer

first: Barbara

last: Kee

first: Russel

last: Taichman

first: Freddy

last: Radtke


title: Expression data of induced pluripotent stem cell

city: Guangzhou

first: Duanqing

last: Pei

state: Guangdong

address: Room 301, International Business Incubator, Guangzhou science park

department: Center for Molecular Medicine

institute: Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences(GIBH.CAS)

summary:
We present a robust serum-free system for the rapid and efficient reprogramming of mouse somatic cells by Oct4, Sox2 and Klf4.  The elimination of fetal bovine serum and oncogene c-Myc allowed reprogramming cells to be detected as early as Day 2 and reached greater than 10% of the population at Day 7 post retroviral transduction. The resulting iPS colonies were isolated with high efficiency to establish pluripotent cell lines. Based on this method, we further developed iPS-SF1 as a dedicated reprogramming medium for chemical screening and mechanistic investigations.
Comparasion of iPS cell lines derived from serum-free culture condition, MEF cells cultured in serum and serum-free condition and ES cell lines was shown.

overall_design: Selected induced pluripotent stem cell lines and its original mouse embroynic fibroblast were comparaed to defined mouse embroynic stem cell lines: R1 and CGR8.

first: Jiekai

last: Chen

first: Wenzhi

last: He

first: Lingwen

last: Zeng


title: Genes plus and minus LIF

status: Public on Mar 17 2009

first: Kymora

last: Scotland

address: 1300 York Ave

department: Pharmacology

institute: Weill Cornell Medical College

summary:
This study was undertaken in order to characterize the functions of Rex-1 and identify potential Rex-1 target genes.Both alleles of the Rex-1 gene were disrupted in J1 mouse embryonic stem cells. Gene expression levels in one of the resulting Rex-1 knockout cell lines was compared to that of J1 wild type cells.
Keywords: cell type comparison

overall_design: Gene expression in Rex-1 knockout mouse embryonic stem cells compared to that of J1 wild type cells. Cells were cultured in the presence and absence of LIF. This series utilized eight samples.There are two biological replicates per cell type cultured under this condition. The J1 samples serve as the control.

first: Siming

first: Renia

last: Sylvester

first: Lorraine

last: Gudas


status: Public on Mar 06 2009

city: Stanford

first: Rami

last: Rauch

address: 300 Pasteaur Dr

institute: Stanford U

type: Methylation profiling by high throughput sequencing

summary:
Publication title:  Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver
To investigate the role of DNA methylation during human development, we developed Methyl-seq, a method that assays DNA methylation at more than 90,000 regions throughout the genome.  Performing Methyl-seq on human embryonic stem cells (hESCs), their derivatives and human tissues allowed us to identify several trends during hESC and in vivo liver differentiation.  First, differentiation results in DNA methylation changes at a minimal number of assayed regions, both in vitro and in vivo (2-11%).  Second, in vitro hESC differentiation is characterized by both de novo methylation and demethylation, whereas in vivo fetal liver development is characterized predominantly by demethylation.  Third, hESC differentiation is uniquely characterized by methylation changes specifically at H3K27me3-occupied regions, bivalent domains and low-density CpG promoters (LCPs) suggesting that these regions are more likely to be involved in transcriptional regulation during hESC differentiation.  Although both H3K27me3-occupied domains and LCPs are also regions of high variability in DNA methylation state during human liver development, these regions become highly unmethylated, which is a distinct trend from that observed in hESCs.  Taken together, our results indicate that hESC differentiation has a unique DNA methylation signature that may not be indicative of in vivo differentiation.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

This SuperSeries is composed of the SubSeries listed below.

relation:
SuperSeries of: GSE29070
SuperSeries of: GSE29071

overall_design: lumina gene expression beadchips of human ES cell lines, ES-derived cells, and normal liver (15 samples). High-throughput sequencing of ES cell lines, ES-derived cells, and fetal and normal livers (17 samples). Raw sequence data available as SRA008154: http://www.ncbi.nlm.nih.gov/sites/entrez?db=sra&cmd=search&term=SRA008154

first: Alayne

last: Brunner

first: David

middle: S

last: Johnson

first: Si

middle: W

last: Kim

first: Anton

last: Valouev

first: Timothy

middle: E

last: Reddy

first: Norma

last: Neff

first: Elizabeth

last: Anton

first: Catherine

last: Medina

first: Loan

last: Nguyen

first: Eric

last: Chiao

first: Chuba

middle: B

last: Oyolu

first: Gary

middle: P

last: Schroth

first: Devin

last: Absher

first: Julie

middle: C

last: Baker

first: Richard

last: Myers


title: Expression data from WT and Aire deficient mTECs

status: Public on Mar 15 2009

city: Melbourne

first: Francois-Xavier

last: Hubert

state: Victoria

address: 1G Royal Parade

department: Immunology

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

summary:
Aire is an important transcription regulator that mediates a role in central tolerance via promoting the promiscuous expression of tissue-specific antigens in the thymus. Although several mouse models of Aire-deficiency have been described, none has analysed the phenotype induced by a mutation that emulates the common 13bp deletion in human APECED by disrupting the first PHD domain in exon 8. Aire-deficient mice with a corresponding mutation showed some disturbance of the medullary epithelial compartment, but at the phenotypic level their T cell compartment appeared relatively normal in the thymus and periphery. An increase in the number of activated T cells was evident, and autoantibodies against several organs were detected. At the histological level, lymphocytic infiltration of several organs indicated the development of autoimmunity, though symptoms were mild and quality of life for Aire-deficient mice appeared equivalent to wild-type littermates, with the exception of male infertility. Vbeta and CDR3 length analysis suggested that each Aire-deficient mouse developed it own polyclonal autoimmune repertoire. Finally, given the prevalence of candidiasis in APECED patients, we examined the control of infection with Candida albicans in Aire-deficient mice. No increase in disease susceptibility was found for either oral or systematic infection. These observations support the view that additional genetic and/or environmental factors contribute substantially to the overt nature of autoimmunity associated with Aire mutations, even for mutations identical to those found in humans with APECED.

Keywords: Gene expression comparison between genotypes

overall_design: In this experiment there are 5 samples altogether which consist of two biological replicates of Aire knock-out mTECs and 3 biological replicates of wild type mTECs.

first: Sarah

last: Kinkel

first: Belinda

last: Phipson

first: Hamish

last: Scott


title: Time course of bone marrow-derived macrophages simulated with LPS

city: Seattle

first: Bruz

last: Marzolf

state: WA

institute: Institute for Systems Biology

summary: The innate immune system is a two-edged sword; it is absolutely required for host defense against infection, but if left uncontrolled can trigger a plethora of inflammatory diseases.  Here we used systems biology approaches to predict and validate a gene regulatory network involving a dynamic interplay between the transcription factors NF-κB, C/EBPδ, and ATF3 that controls inflammatory responses.  We mathematically modeled transcriptional regulation of Il6 and Cebpd genes and experimentally validated the prediction that the combination of an initiator (NF-κB), an amplifier (C/EBPδ) and an attenuator (ATF3) forms a regulatory circuit that discriminates between transient and persistent Toll-like receptor 4-induced signals. Our results suggest a mechanism that enables the innate immune system to detect the duration of infection and to respond appropriately.

overall_design: Bone marrow-derived macrophages stimulated with LPS for 0, 20, 40, 60, 80, 120, 240 and 360 minutes.

first: Vladimir

last: Litvak

first: Stephen

last: Ramsey

first: Alistair

last: Rust

first: Alan

last: Diercks

first: Daniel

last: Zak

first: Kathleen

last: Kennedy

first: Aaron

last: Lampano

first: Matti

last: Nykter

first: Ilya

last: Shmulevich

last: Aderem


title: Comparison of mouse NK cell subsets defined by CD27 and CD11b expression

city: Marseille

first: Thierry

last: Walzer

address: Case 906, Campus de Luminy

country: France

institute: Centre d'Immunologie de Marseille-Luminy, INSERM U631

summary: Previous reports have defined three subsets of mouse NK cells on the basis of the expression of CD27 and CD11b. The developmental relationship between these subsets was unclear. To address this issue, we evaluated the overall proximity between mouse NK cell subsets defined by CD27 and CD11b expression using pangenomic gene expression profiling. The results suggest that CD27+CD11b-, CD27+CD11b+ and CD27-CD11b+ correspond to three different intermediates stages of NK cell development.

overall_design: Spleen cells from RAG-/- mice have been isolated and stained with anti-NK1.1, anti CD27 and anti CD11b antibodies. NK1.1+ cells were sorted into CD27+ CD11b-, CD27+ CD11b+ and CD27- CD11b+ subsets by flow cytometry. There are two independent replicates for each sample. Total RNA was extracted with the RNeasy microkit (Qiagen) and gene expression profiles were performed according to manufacturer instructions (Affymetrix mouse 430 2.0).

first: Eric

last: Vivier


title: ERK1/2 in Ovarian Granulosa Cells are Essential for Female Fertility

status: Public on Mar 20 2009

first: JoAnne

last: Richards

address: One Baylor Plaza

department: Molecular and Cellular Biology

summary: A surge of luteinizing hormone (LH) from the pituitary gland triggers ovulation, oocyte maturation, and luteinization for successful reproduction in mammals. Since the signaling molecules RAS and ERK1/2 are activated by a LH surge in granulosa cells of preovulatory follicles, we disrupted Erk1/2 in mouse granulosa cells and provide in vivo evidence that these kinases are necessary for LH-induced oocyte resumption of meiosis, ovulation, and luteinization. In addition, biochemical analyses and selected disruption of the Cebpb gene in granulosa cells demonstrate that C/EBP  is a critical downstream mediator of ERK1/2 activation. These mouse models provide in vivo systems in which to define the context specific and molecular mechanisms by which granulosa cells respond to LH and these mechanisms are relevant to the regulation of human fertility and infertility.

overall_design: Immature wild type or ERK1/2 conditonal knock-out mice were injected with 5IU equine chorionic gonadotropin (eCG)-48h followed by 5 IU hCG injection. The ovarian granulosa cells were collected at hCG 0h, 2.5h, or 4h and the gene expression pforiles were compared by microarray method.

first: Heng-Yu

last: Fan

first: Zhilin

last: Liu

first: Masayuki

last: Shimada

first: Esta

last: Sterneck

first: Peter

last: Johnson

last: Hedrick


title: Expression data from murine gastric epithelium

status: Public on Mar 05 2009

city: Zurich

first: Anne

last: Müller

address: Winterthurerstr. 190

department: IMCR

country: Switzerland

institute: University of Zurich

summary:
Chronic infection with the bacterial pathogen Helicobacter pylori is a risk factor for the development of gastric cancer, yet remains asymptomatic in a majority of individuals. We report here that the C57Bl6 mouse model of experimental infection with the closely related H. felis recapitulates this wide range in host susceptibility. A majority of infected mice develop premalignant lesions such as gastric atrophy, compensatory epithelial hyperplasia and intestinal metaplasia, whereas a minority is completely protected from preneoplasia. Protection is associated with the failure to mount an IFN-gamma response to the infection and an associated high Helicobacter burden. We demonstrate that IFN-gamma is essential for clearance of Helicobacter, but also mediates the formation of preneoplastic lesions. We further provide evidence that IFN-gamma triggers a specific transcriptional program in murine gastric epithelial cells in vitro and in vivo, and induces their preferential transformation to the hyperplastic phenotype. In summary, our data suggest a dual role for IFN-gamma in Helicobacter pathogenesis that could provide an explanation for the differential susceptibility to H. pylori-induced gastric pathology in the human population.

Keywords: response to in vitro stimulus / comparison of histopathological states

overall_design: We chose mice for gene expression profiling that following Helicobacter infection had (a) symptoms of gastritis, but no epithelial changes, (b) atrophic gastritis accompanied by corpus gland hyperplasia or (c) atrophic gastritis accompanied by intestinal metaplasia. An uninfected control group was also included in the analysis, as were two groups of mice that lacked mature T- and B-cells due to a deletion mutation in the rag1 gene (Rag-1-/-) and that were either experimentally infected or served as Rag-1-/- uninfected controls. To see the effects of IFNg on murine gastric epithelial cells we analysed an immortalized murine primary gastric epithelial cell line treated with three different concentrations of IFNg in comparison to an untreated control.

first: Iris

last: Hitzler


title: Fog2 regulation of gene expression in the adult heart

first: Sek Won

last: Kong

address: 300 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

summary:
MHCaCre induced knockout of Fog2flox.
Aberrant transcriptional regulation contributes to the pathogenesis of both congenital and adult forms of heart disease. While the transcriptional regulator FOG2 is known to be essential for heart morphogenesis and coronary development, its tissue specific function has not been previously investigated. Additionally, little is known about the role of FOG2 in the adult heart. Here we use spatiotemporally regulated inactivation of Fog2 to delineate its function both in embryo and adult heart. Early cardiomyocyte-restricted loss of Fog2 recapitulated the cardiac and coronary defects of the Fog2 germline knockouts. Later cardiomyocyte-restricted loss of Fog2 (Fog2MC) did not result in defects in cardiac structure or coronary vessel formation. However, Fog2MC adult mice had severely depressed ventricular function and died at 8-14 weeks. Fog2MC adult hearts displayed a paucity of coronary vessels. This was associated with myocardial hypoxia, increased cardiomyocyte apoptosis, and cardiac fibrosis. Induced inactivation of Fog2 in adult heart resulted in similar phenotype, as did ablation of FOG2 interaction with the transcription factor GATA4. Loss of FOG2 or FOG2-GATA4 interaction altered expression of a panel of angiogenesis-related genes. Collectively, our data indicated that FOG2 regulates adult heart function and coronary angiogenesis.

overall_design: Fog2flox/delta; MHCaCre (3) compared to Fog2flox/delta; no Cre (3). One heart per sample.

first: Bin

last: Zhou

first: William

last: Pu

first: SekWon


title: Caveolin-1 Knockout Hearts

status: Public on Mar 04 2009

city: Philadelphia

first: Michael

last: Lisanti

state: PA

address: 233 S. 10th St BLSB 939

department: Cancer Biology

institute: Thomas Jefferson University

summary:
Hearts Lacking Caveolin-1 Develop Hypertrophy with Normal Cardiac Substrate Metabolism
Keywords: gene knockout

overall_design: 3 wild types, 3 knockouts

first: A

last: Augustus


title: Efficient Array-based Identification of Novel Cardiac Genes through Differentiation of Mouse ESCs

city: Baltimore

first: John

middle: D.

last: Gearhart

address: 733 North Broadway

department: School of Medicine

institute: Jons Hopkins University

summary:
Cardiac disease accounts for the largest proportion of adult mortality and morbidity in the industrialized world. However, progress toward improved clinical treatments is hampered by an incomplete understanding of the genetic programs controlling early cardiogenesis. To better understand this process, we set out to identify genes whose expression is enriched within early cardiac fated populations, obtaining the transcriptional signatures of mouse embryonic stem cells (mESCs) differentiating along a cardiac path.

We compared the RNA profiles of cardiac precursors cells (CPCs) with time-matched non-CPCs and undifferentiated mESCs, using a transgenic mESC line harboring an Nkx2-5 cardiac-specific regulatory sequence driving green fluorescent protein (GFP) to facilitate selection of CPCs. Approximately 24% (43/176) of the transcripts enriched in the CPC population have known roles in cardiac function or development. Importantly, we evaluated the biological relevance of a subset 31/133 (23%) of the remaining candidate genes by in situ hybridization and report that all were expressed in key cardiac structures during cardiogenesis (embryonic day, E7.5 - 9.5), many of which were previously uncharacterized. These data demonstrate the power of mESC differentiation to model specific developmental processes and provide a valuable resource that may be mined to further elucidate the genetic programs underlying cardiogenesis.
Keywords: time course, differentiated cardiac cell fate

overall_design:
Transgenic mouse embryonic stem cell line (Nkx2-5-GFP, PMID:9834187) contains an Nkx2-5 cardiac-specific transcription factor driving expression of green fluorescent protein (GFP).  Cells were differentiated through embryoid body formation (hanging droplet technique) as described in PMID:8155574. Following primary mouse embryonic fibroblasts (PMEF) feeder subtraction, mESCs were dissociated and resuspended in differentiation medium. Cells at this time point were designated as day 0. Following incubation for two days, the EBs were transferred, in suspension, to poly-HEMA coated tissue culture dishes to prevent cell attachment and grown in medium containing ascorbic acid PMID:12668514) which was replenished every 3 days thereafter.

Cells were harvested on days 0, 4 and 6 in three biological replicates
each (1a, 2a and 3a), washed in PBS for 30 minutes at 37ºC then resuspended in 0.25% trypsin for 7 minutes.

Cells from day 6 were then sorted using the BD Biosciences FACSAria™ Cell sorting system into GFP+ and GFP- fractions into RLT buffer (RNeasy, Qiagen). This sorting separates cells into two groups reflecting their differentiation into those fated to a non-cardiac lineage (GFP negative) and to a cardiac lineage (GFP positive).

first: Ronald

last: Miller

first: Nicolas

last: Christoforou

first: Jonathan

last: Pevsner

first: Andrew

last: McCallion

middle: D


title: microRNA-1 negatively regulates expression of the hypertrophy-associated genes calmodulin and Mef2a

city: Boston

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

summary: Calcium signaling is a central regulator of cardiomyocyte growth and function. Calmodulin is a critical mediator of calcium signals. Because the amount of calmodulin within cardiomyocytes is limiting, precise regulation of calmodulin expression may be an important for regulation of calcium signaling. In this study, we show for the first time that calmodulin levels are regulated post-transcriptionally in heart failure. The cardiomyocyte-restricted microRNA miR-1 inhibited translation of calmodulin-encoding mRNAs via highly conserved target sites within their 3’-untranslated regions. In keeping with its effect on calmodulin expression, miR-1 downregulated calcium-calmodulin signaling through the calcineurin to NFAT. miR-1 also negatively regulated expression of Mef2a and Gata4, key transcription factors that mediate calcium-dependent changes in gene expression. Consistent with downregulation of these hypertrophy-associated genes, miR-1 attenuated cardiomyocyte hypertrophy in cultured neonatal rat cardiomyocytes and in the intact adult heart. Our data indicate that miR-1 regulates cardiomyocyte growth responses by negatively regulating the calcium-signaling components calmodulin, Mef2a, and Gata4.

overall_design: We show that miR-1 is downregulated in a murine heart failure model. miRNAs expression changes were measured in calcineurin transgenic model of heart failure and control mice using a Luminex platform. Reduced miR-1 expression was associated with broad alteration in expression of predicted target genes. To test this, we measured miRs including miR-1 and genome wide transcriptome changes in vivo and in vitro system. Calcineurin transgenic heart was compared to nontransgenic heart (NTg vs. CNTg). We also investigated the gene expression changes during the course of cardiomyocytes differentiation using DMSO treated P19CL6 cell lines. Two time points (day 6 and day 10) were compared to identified the gene expression changes of predicted miR-1 targets (Day 6 vs. Day 10).

first: Sadakatsu

last: Ikeda

first: Aibin

last: He

first: Sek-Won

first: Jun

last: Lu

first: Rafael

last: Bejar

first: Natalya

last: Bodyak

first: Kyu-Ho

last: Lee

first: Qing

last: Ma

last: Kang

first: Todd

middle: R

last: Golub

middle: T


title: Gene expression profiling of natural and induced regulatory T cells

status: Public on Mar 01 2009

city: los angeles

first: Brian

last: O'Connor

address: 2018 Griffith Park Blvd

institute: UCLA

summary:
The gene expression profile of peripheral Foxp3+ natural regulatory T cells isolated from Foxp3/EGFP bicistronic mice was compared to that of in vitro-induced regulatory T cells and to CD4+ conventional (Foxp3-) T cells. The role of the regulatory T cell transcription factor Foxp3 in shaping the transcriptosomes of natural and induced regulatory T cells was analyzed using mice expressing a mutant FOXP3-EGFP fusion protein (Foxp3deltaEGFP).
We used gene expression microarrays to examine the transcriptional programs of natural and induced regulatory T cells and the function of Foxp3 in organizing the transcriptosomes of the respective cell type

Keywords: Cell population analysis

overall_design: Conventional T cells and natural and induced regulatory T cells were derived from Foxp3/EGFP bicistronic mice and analyzed for their gene expression profile. Conventional T cells, regulatory T cell precursors (CD4+Foxp3deltaEGFP+) and induced regulatory T cell precursors (CD4+Foxp3deltaEGFP+) cells were deriv ed from Foxp3deltaEGFP mice

first: Marc

last: Carlson

first: Talal

last: Chatila


title: Gene expression profiling of Galgt2 overexpression in mdx skeletal muscle

city: Columbus

first: Paul

last: Martin

state: OH

address: 700 Children's Drive

institute: Columbus Children's Research Institute

summary:
Transgenic overexpression of Galgt2 in the skeletal muscles of mdx mice inhibits the development of disease pathology associated with muscular dystrophy.  This is the case both in transgenic mice, where Galgt2 overexpression occurs from embryonic timepoints onward and in mdx mice where Galgt2 is overexpressed in the early postnatal period using Adeno-associated virus (AAV).  Here, we use gene expression profiling to compare transcriptional changes resulting from embryonic and postnatal Galgt2 overexpression in mdx skeletal muscle.  A surprising number of changes were in genes known to ameliorate muscular dystrophy when overexpressed (agrin, integrin alpha 7, ADAM12, Bcl2) or to cause muscular dystrophy when mutated (collagen VI (alpha1,alpha2), plectin 1, dystroglycan, selenoprotein N1, integrin alpha7, biglycan, dysferlin).    Several genes involved in calcium homeostasis were also changed.  In Galgt2 transgenic mice, where embryonic overexpression of Galgt2 in skeletal muscles alters neuromuscular development and muscle growth, the number of gene expression changes was vastly greater, however, 14% of genes altered in postnatal AAV-Galgt2 infected mdx muscles were also changed with embryonic overexpression.  These experiments suggest that postnatal overexpression of Galgt2 inhibits muscular dystrophy in mdx mice via induction of a group of genes that, in aggregate, can govern membrane stability, membrane repair, calcium homeostasis, and apoptosis.
Keywords: disease state analysis, gene therapy, comparative gene expression, muscular dystrophy, glycosylation, collagens, integrins, dysferlin, dystroglycan

overall_design: Microarrays were done in three groups at a time. 1) Transgenic Overexpression of Galgt2 - comprised to Wild Type (WT), Galgt2 Transgenic (CT), Dystrophin-Deficient (mdx), and Galgt2 Transgenic and Dystrophin-Deficient (CTmdx) each in duplicate 2) AAV-Mediated Galgt2 Gene Delivery in to the mdx gastrocnemius muscle in the postnatal period - comprised of AAVGalgt2 and PBS each in duplicate, and 3) Myoblasts and myotubes - comptised of one sample each of C1C12 myoblasts and myotubes, C2C12 myoblasts and myotubes stably transfected with Galgt2

first: Kumaran

last: Chandrasekharan


title: Caveolin-3 Knockout Hearts

first: Michael

last: Lisanti

summary:
Energy Substrate Uptake and Metabolism are Preserved in Hypertrophic Caveolin-3 Knockout Hearts
Keywords: gene knockout

first: A

last: Augustus


title: Srf conditional knockout in the mouse liver

city: Charleston

first: Stephen

last: Duncan

state: SC

address: 173 Ashley Avenue, BSB 6th Floor, Room 657A

department: Regenerative Medicine and Cell Biology

institute: Medical University South Carolina

summary: Serum response factor (SRF) is a transcription factor that binds to the serum response element (SRE) of genes that are expressed in response to mitogens. SRF plays essential roles in muscle and nervous system development; however, little is known about the role of SRF during liver growth and function. To examine the function of SRF in the liver, we generated mice in which the Srf gene was specifically disrupted in hepatocytes. The survival of mice lacking hepatic SRF activity was lower than that of control mice; moreover, surviving mutant mice were smaller and had lower blood glucose and triglyceride levels compared with control mice. Srf-deficient livers were also smaller than control livers, hepatocyte morphology was abnormal, and liver-cell proliferation and viability was compromised. Gene array and quantitative RT-PCR analysis of SRF depleted livers revealed a reduction in mRNAs encoding components of the growth hormone/IGF1 pathway, cyclins, several metabolic regulators, and cytochrome p450 enzymes. Conclusion: SRF is essential for hepatocyte proliferation and survival, liver function, and control of postnatal body growth by regulating hepatocyte gene expression.

overall_design:
Total RNA was harvested from the following sources and used for Affymetrix array analysis following manufacturer defined protocols:

control liver (Srf loxP/+ AlfpCre): 3 male mice (3 weeks old)

mutant liver (Srf loxP/loxP AlfpCre): 3 male mice (3 weeks old), tissue used lacked Srf

first: Kai

last: Sun

first: Michele

last: Battle

first: Ravindra

last: Misra


title: Gene array for identifying molecules involved in IL-10 regulation during Th17 polarization

status: Public on Mar 03 2009

first: Jiangnan

last: Xu

address: 1425 Madison Ave

department: Gene and Cell Medicine

institute: Mount Sinai School of Medicine

summary: IL-10 production by Th17 cells is critical for limiting autoimmunity and inflammatory responses. Gene array analysis on Stat6 and T-bet double deficient Th17 cells identified the Th2 transcription factor c-Maf to be synergistically up-regulated by IL-6 plus TGFbeta, and associated with Th17 IL-10 production. Both c-Maf and IL-10 induction during Th17 polarization depended on Stat3, but not Stat6 or Stat1, and mechanistically differed from IL-10 regulation by Th2 or IL-27 signals. TGFbeta was also synergistic with IL-27 to induce c-Maf, and induced Stat1 independent IL-10 expression in contrast to IL-27 alone. Retroviral transduction of c-Maf was able to induce IL-10 expression in Stat6 deficient CD4 and CD8 T cells, and c-Maf directly transactivated IL-10 gene expression through binding to a MARE motif in the IL-10 promoter. Together, these data reveal a novel role for c-Maf in regulating T effector development, and suggest that TGFbeta may antagonize Th17 immunity by IL-10 production through c-Maf induction.

overall_design: Our recent studies showed that IL-6 combined with TGFbeta differed from IL-6 combined with IL-23 for IL-10 production and pathogenic activities in CD4 T cells deficient in Stat6 and T-bet, despite similar IL-17 production. We performed gene array analysis on Stat6 and T-bet double deficient cells. We rationalized that by comparing gene expression in cells treated with IL-6 plus TGFbeta versus TGFbeta alone, we would be able to identify genes specific for standard Th17 polarization, and responsible for both IL-17 and IL-10 expression. By next comparing gene expression in cells treated with IL-6 plus TGFbeta versus IL-6 plus IL-23, we could eliminate molecules involved solely in IL-17 regulation, and obtain genes specifically responsible for IL-10 regulation.

first: Yaozhong

last: Ding


title: Non muscle myosin light chain kinase isoform is an attractive molecular target in acute inflammatory lung injury

status: Public on Mar 02 2009

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

summary:
Acute lung injury (ALI), a major cause of acute respiratory failure with high morbidity and mortality, isare characterized by significant pulmonary inflammation and both alveolar and vascular barriers dysfunction.  In Pprior studies have highlighted the role of nonmuscle myosin light chain kinase (nmMLCK) as an essential element of inflammatory response with MYLK polymorphisms associated withwhich alters ALI susceptibility. In the present study we sought to further define nmMLCK in acute inflammatory syndromes and examined We examined nmMLCK as a molecular target involved in increase of lung epithelial and endothelial barrier permeability. We utilized in two muirine models of inflammatory lung injury: intratracheal administration of endotoxin/lipopolysaccharide (LPS, 2.5 mg/kg) and VILI (ventilator-induced lung injury, tidal volume 40ml/kg).  Two complementary strategies were used to reduce nmMLCK activity or expression. We found that membrane permeant oligopeptide, PIK, inhibited MLC kinase activity in vitro in aand displayed dose-dependent mannerinhibition of MLC kinase activity.. Intravenous delivery of PIK significantly attenuated LPS-induced lung inflammation reflected by decreasing accumulation of bronchoalveolar lavage (BAL) albumin (~ 50% reduction) as well as reduction in BAL cells, tissue MPO activity and tissue albumin in lung homogenates. A second regulatory approach explored targeting murine nmMLCK by administration of siRNA (5mg/kg) 3 days prior to LPS challenge. siRNA decreased of nmMLCK expression in lungs (~ 70% reduction) and resulted in significant attenuation LPS-induced lung inflammation (~ 40% reduction) as reflected by decreased BAL protein level and BAL cells. For targeting pulmonary vessels nmMLCK we used ACE antibody-conjugated liposomes with nmMLCK siRNA in murine ventilator-induced lung injury (VILI) model. Protein silencing of nmMLCK was evident by immunohistochemical analysis with a decrease in relative intensity of fluorescence in lung vessels compared with control animals. Furthermore, the inhibition of nmMLCK expression by siRNA in vessels significantly attenuated VILI lung injury as reflected by decreased BAL protein level (40% reduction). Finally, MLCK knockout mice were significantly protected (reduced BAL protein and albumin) when exposed to a model of severe VILI (4h, 40ml/kg tidal volume). Conclusion: the MLCK gene KO and chemical biology results indicate that the targeting of nmMLCK in vivo attenuate the severity of LPS-induced or VILI acute lung injury.
We used microarrays to detail the global programme of gene expression induced by VILI in Wild type and nmMLCK-/- mouse.

overall_design: four group (n=3) of animals were treated by SB (Spontaneouse breathing) or VILI (4 hours, 30 ml/kg tidal volume) in Wild type or nmMLCK-/- animals;

first: Tamara

last: Mirzapoiazova

first: Jaideep

last: Moitra

first: Saad

last: Sammani

first: Lilianna

last: Moreno-Vinasco

first: Yves

last: Lussier

first: Joe

last: Garcia


title: Foxo1 target genes in mouse T cells

status: Public on Feb 28 2009

first: Ming

last: Li

address: 408 East 69th Street

institute: Memorial Sloan-Kettering Cancer Center

summary: CD4+ and CD8+ T cells isolated from wild-type and Foxo1-deficient mice were analyzed by global gene expression profiling with Affymetrix array MOE 430 2.0. Results indicate Foxo1 regulates the expression of genes encoding positive regulators of T cell activation, differentiation, homeostasis, cell adhesion, cell migration, and cellular stress responses.

overall_design: CD4+ and CD8+ T cells were isolated for RNA extraction and hybridization on Affymetrix microarrays.

first: M

middle: O

first: W

last: Ouyang


title: Gene expression profiling in acute murine autoimmune hepatitis

city: Hanover

first: Jennifer

middle: L

last: Sargent

state: NH

address: Dartmouth College; HB7400

department: Genetics

institute: Dartmouth Medical School

summary:
The etiology of autoimmune hepatitis is poorly understood but likely involves Th1 cells producing IFN-γ. BALB/c background TGF-β1-/- mice rapidly develop fulminant Th1-mediated autoimmune hepatitis. Our aims are to profile liver gene expression in TGF-β1-/- mice, to identify gene expression pathways dependent on IFN-γ as possible targets for rational therapy, and to test potential targets directly in vivo in mice.
Keywords: Comparative analysis of gene expression in livers of WT, TGFB1 & IFN knockout mice

overall_design: DNA microarray analyses were applied to liver RNA from TGF-β1-/- mice, TGF-β1-/- /IFN-γ-/- mice, and TGF-β1+/+ littermate controls. 3 mice from each group were analyzed in this study.

first: Michael

last: Milks

first: James

last: Cripps

first: Heping

last: Lin

first: Wang

last: Jin

first: Robinson

last: Richard

last: Whitfield

first: Robert

last: Strieter

last: Gorham


title: Role of Transglutaminase 2 in Liver Injury via Crosslinking and Silencing of Transcription Factor, Sp1

status: Public on Feb 24 2009

city: Wako

first: Hideki

last: Tatsukawa

state: Saitama

address: Hirosawa 2-1

institute: RIKEN

summary:
Gene expression of Ethanol-treated hepatocytes from WT and transglutaminase 2 knockout mice
Keywords: transglutmianse 2

overall_design:
Non or 100mM Ethanol-treated WT hepatocytes, Non or 100mM Ethanol-treated TG2KO hepatocytes.
8 of Samples were analysed (its replicates are included)


title: Colonic transcriptional changes evoked by E. rectale-B. thetaiotaomicron co-colonization

city: St Louis

first: Federico

last: Rey

state: MO

address: 4444 Forest Park Blvd

institute: Washington University

summary: The adult human gut microbial community is typically dominated by two bacterial phyla (divisions), the Firmicutes and the Bacteroidetes. Little is known about the factors that govern the interactions between their members. Here we examine the niches of representatives of both phyla in vivo.  Finished genome sequences were generated from E. rectale and E. eligens, which belong to Clostridium Cluster XIVa, one of the most common gut Firmicute clades. Comparison of these and 25 other gut Firmicutes and Bacteroidetes indicated that the former possess smaller genomes and a disproportionately smaller number of glycan-degrading enzymes. Germ-free mice were then colonized with E. rectale and/or a prominent human gut Bacteroidetes, Bacteroides thetaiotaomicron, followed by whole genome transcriptional profiling of both organisms in their distal gut (cecal) habitat as well as host responses, high resolution proteomic analysis of cecal contents, and biochemical assays of carbohydrate metabolism. B. thetaiotaomicron adapts to E. rectale by upregulating expression of a variety of polysaccharide utilization loci (PULs) encoding numerous glycoside hydrolase gene families, and by signaling the host to produce mucosal glycans that it, but not E. rectale, can access. E. rectale adapts to B. thetaiotaomicron by decreasing production of its glycan-degrading enzymes, increasing expression of selected amino acid and sugar transporters, and facilitating glycolysis by reducing levels of NADH, in part via generation of butyrate from acetate, which in turn is utilized by the gut epithelium. This simplified model of the human gut microbiota illustrates niche specialization and functional redundancy within members of major gut bacterial phyla, and the importance of host glycans as a nutrient foundation that ensures ecosystem stability.

overall_design: four biological replicates per group. NMRI mice, males (12-14 weeks old).

middle: A

last: Mahowald

first: Henning

last: Seedorf

first: Peter

last: Turnbaugh

first: Jeffrey

middle: I

last: Gorodn


title: Expression Profile of Skeletal Muscle from Young and Aged C57B1/6 Mice

status: Public on Feb 26 2009

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

summary:
Our laboratory wanted to define the transcription profile of aged skeletal muscle. For this reason, we performed a triplicate microarray study on young (3 weeks) and aged (24 months) gatrocnemius muscle from wild-type C57B16 Mice

Keywords: other

overall_design: this experiment include 2 samples and 6 replicates


title: IL-2 dependent genes of T regulatory and T effector cells

status: Public on Feb 22 2009

city: Miami

first: Thomas

last: Malek

state: FL

address: 1600 NW 10th Avenue

department: Microbiology/Immunology

institute: University of Miami

summary: Interleukin-2 receptor (IL-2R) signaling is essential for T regulatory (Treg) cell development and homeostasis. Here we show that expression of IL-2Rbeta chains that lack tyrosine residues important for the association of the adaptor Shc and the transcription factor STAT5 in IL-2Rbeta-deficient mice resulted in production of a normal proportion of natural Treg cells that suppressed severe autoimmunity related with deficiency in IL-2 or IL-2R. These mutant IL-2Rbeta chains supported suboptimal and transient STAT5 activation that upregulate the transcription factor Foxp3 to normal amounts in natural, but not induced, Treg cells. Using cells T cell obtained from normal C57BL/6 mice and mice harboring Treg cells with impaired IL-2R signaling, gene expression profiling revealed many targets in peripheral natural Treg cells that were IL-2-dependent and a substantial overlap between the Treg cell IL-2-dependent gene program and the Treg cell transcriptional signature. Collectively, these findings demonstrate that a critical, and perhaps minor, subset of IL-2-dependent targets in Treg cells is indexed to a low IL-2R signaling threshold and that a substantial proportion of the Treg cell gene program is regulated by IL-2. CD4 T effector cells also showed many IL-2R-dependent gene and these also overlapped in a distintive manner with the IL-2-dependent genes of Treg cells and the Treg gene signature.

overall_design: For each strain, we analyzed two cell populations, freshly isolated Treg cells and T effector cells. These latter cells were obtained after spleen cells activated with anti-CD3 for 48 hr and then isolating the CD4+ CD25+ activated effector T cells. The IL-2R defective T cells were obtained from C57BL/6-2Rbeta-WT/thymus transgenic mice after breeding to IL-2Rbeta-deficient mice. Each sample consisted of 3 distinct biological replicates.  After GC-RMA normalization, intensity values were average for the replicates within the groups. We compared the differentially expressed genes within each group  and these differential expressed genes were then compared between each other and Treg gene signature.

first: Aixin

last: Yu

first: Linjian

last: Zhu

first: Norman

middle: H

last: Altman


title: Effects of DZNep and 5-Aza-CdR on gene expression in MCF7 cells

city: Los Angeles

first: Tina

last: Miranda

address: 1441 Eastlake Ave

institute: USC

summary: DNA methylation, histone modifications, and nucleosomal occupancy collaborate to cause silencing of tumor related genes in cancer.  The development of drugs that target these processes is therefore important for cancer therapy.   Inhibitors of DNA methylation and histone deacetylation have already been approved by the FDA for the treatment of hematologic malignancies.  However, drugs that target the other mechanisms still need to be developed.  Recently, 3-deazaneplanocin A (DZNep) was reported to selectively inhibit the trimethylation of lysine 27 on histone H3 (H3K27me3) and lysine 20 on histone H4 (H4K20me3) as well as re-activate silenced genes in cancer cells.  This finding opens the door to pharmacological inhibition of histone methylation and we therefore wanted to further study the mechanism of action of 3-deazaneplanocin A in cancer cells.  Western blot analysis showed that two other drugs, sinefungin and adenosine-dialdehyde (Adox), have similar effects on the trimethylation H3K27 as 3-deazaneplanocin A and that DZNep is not selective, but globally inhibits histone methylation.  Intriguingly, chromatin immunoprecipitation of various histone modifications and microarray analysis show DZNep acts via a different pathway to 5-aza-2´-deoxycytidine (5-azaCdR), a DNA methyltransferase inhibitor and gives us an interesting insight into how chromatin structure effects gene expression.  We also determine the kinetics of gene activation in order to understand if the induced changes were somatically heritable.  We have found that upon removal of DZNep, gene expression is reduced to its original state suggesting that there is a homeostatic mechanism which returns the histone modifications to their “ground state” after DZNep treatment.  Not only do these studies show the strong need for further development of histone methylation inhibitors but also allow us to better understand how chromatin structure affects gene expression.

overall_design: There are two different drug treatments (DZNep and 5-Aza-CdR).  Each drug treatment was harvested on two separated days (D1 and D7).  There was also and untreated control sample.  Each treatment has 4 technical repeats.

first: Terry

middle: K

last: Kelly

last: Jones

first: Connie

last: Cortez


title: ENCODE H1_ES cell phenotyping study

status: Public on Feb 17 2009

city: Rensselaer

first: Sridar

middle: V

last: Chittur

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

summary:
These samples are part of the ENCODE consortium’s proposed time-limited Pilot Study for confirmation of the utility of RNA abundance measurements as a standard reference phenotyping tool.

Keywords: cell type comparison

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and  http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: Each batch of H1-ES cells cultured by Cellular Dynamics International for use by the ENCODE labs was processed on Affymetrix Exon 1.0 ST arrays to obtain phenotyping data.


title: Comparison of gene expression between the thyroid of mice lacking Slc26a4 and heterzygous controls.

status: Public on Feb 19 2009

city: Manhattan

first: Philine

last: Wangemann

state: KS

address: 1600 Dension Avenue

department: Anatomy and Physiology

institute: Kansas State University

summary:
Determination of differential expression of genes in the thyroid of pendrin (Slc26a4) heterozygous and knockout mice at a time point corresponding to maximal thyroid gland activity, postnatal day 15 (P15).
Keywords: Differential expression under disease state

overall_design: A total of Six samples of thyroid RNA obtained from P15 mice were analyzed. Triplicates from pendrin (Slc26a4) heterozygous and knockout mice were run and analyzed.

first: Ruchira

last: Singh

first: Peying

last: Fong


title: Gene expression in stria vascularis of mice lacking Slc26a4 and heterzygous controls before the onset of hearing.

summary:
Determination of differential expression of genes in the stria vascularis of  pendrin (Slc26a4) heterozygous and knockout  mice before the onset of hearing at postnatal day 10 (P10).
Keywords: differential expression under disease state

overall_design: A total of Six samples  of stria vascularis RNA obtained from P10 mice were analyzed.  Triplicates from  pendrin (Slc26a4) heterozygous and knockout mice were run and analyzed.


title: Differentially regulated genes in control and c-myc N-myc deficient progenitors

status: Public on Feb 20 2009

city: Epalinges

first: Elisa

last: Laurenti

address: Chemin Des Boveresses 155

department: ISREC

institute: EPFL

summary: Analysis of HSCs from control and c-myc N-myc deficient long-term hematopoietic stem cells. HSCs lacking both c-myc and N-myc display increased apoptosis rates. Data provide insight into the molecular changes occuring upon complete loss of Myc activity, clarifying the resulting apoptotic mechanism and the role of Myc family proteins in HSCs and commited progenitors.

overall_design: Commited progenitors (Lin-Sca1+CD150+CD48+) cells were sorted from the BM of MxCre c-myc flox2 N-myc flox2 (experimental) and c-myc flox2 N-myc flox2 (control) mice 3 days after the last pI-pC injection. Each condition was analysed in triplicates, with each replicate consisting of a pool of 3 dKO mice or 2 control mice.

first: Barbara

middle: v

last: Finney

first: Anne

last: Wilson

first: Isabel

last: Ferrero

first: William

last: Blanco-Bose

first: Armin

last: Ehninger

first: Paul

middle: S

last: Knoepfler

first: Pei-Feng

last: Cheng

first: Robson

last: MacDonald

first: Robert

middle: N

last: Eisenman

first: Irwin

last: Bernstein

first: Andreas

last: Trumpp


title: Copy number variation and gene expression in the mouse

city: Lausanne

first: Charlotte

middle: N.

last: Henrichsen

address: Quartier Sorge

department: Center for Integrative Genomics

institute: University of Lausanne

summary:
Copy number variation (CNV) of DNA segments has recently been identified as a major source of genetic diversity, but a more comprehensive understanding of the extent and phenotypic effect of this type of variation is only beginning to emerge. In this study we generated genome-wide expression data from 6 mouse tissues to investigate how CNVs influence gene expression.
Keywords: genetic background, gene expression profiling

overall_design: C57BL/6J, DBA2/J, AKR/J, A/J and C3HeB/FeJ were purchased from The Jackson Laboratory and 129S2 from Charles River, France. Six tissues were dissected from three males of 11-14 weeks of age, for each strain.

first: Evelyne

last: Chaignat

first: Sylvain

last: Pradervand

first: Alexandre

last: Reymond


title: Differentially regulated genes in control and c-myc N-myc deficient LT-HSCs and progenitors

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

overall_design: Refer to individual Series


title: BALB/c mice genetically susceptible to proteoglycan-induced arthritis and spondylitis

status: Public on Feb 15 2009

city: Chicago

first: Tibor

last: Glant

state: IL

address: 1735 West Harrison

department: Orthopedic Surgery

institute: Rush University Medical Center

summary:
BALB/c mice are susceptible to proteoglycan (PG) aggrecan-induced arthritis (PGIA), a murine model of rheumatoid arthritis (Glant,T.T. and Mikecz,K., Proteoglycan aggrecan-induced arthritis.  A murine autoimmune model of rheumatoid arthritis. Methods Mol.Med. 2004. 102: 313-338.). However, there are marked differences among BALB/c colonies (maintained by different vendors at different locations) in PGIA onset and severity, which could be the result of subtle variations in their genetic background.
In the present microarray study, we have identified differences among BALB/c colonies, and an altered immunization-related gene expression pattern in PGIA model.

Keywords: Genetic modification

overall_design: In this study we compared the gene expression profile of 12 spleens from PG-immunized (RNA was isolated 12 days after immunization) and naive mice from BALB/cJ and BALB/cByJ colonies (3-3 from each group), then made comparisons between colonies and based on immunization.

first: Balint

last: Farkas

first: Ferenc

last: Boldizsar

first: Oktavia

last: Tarjanyi

first: Anna

last: Laszlo


title: Differentially regulated genes in control and c-myc N-myc deficient LT-HSCs

first: Elisa

last: Laurenti

summary: Analysis of HSCs from control and c-myc N-myc deficient long-term hematopoietic stem cells. HSCs lacking both c-myc and N-myc display increased apoptosis rates. Data provide insight into the molecular changes occuring upon complete loss of Myc activity, clarifying the resulting apoptotic mechanism and the role of Myc family proteins in HSCs.

overall_design: LT-HSC (Lin-Sca1+CD150+CD48-) cells were sorted from the BM of MxCre c-myc flox2 N-myc flox2 (experimental) and c-myc flox2 N-myc flox2 (control) mice 3 days  after the last pI-pC injection. Each condition was analysed in triplicates, with each replicate consisting of a pool of 3 dKO mice or 2 control mice.

first: Barbara

last: Finney

first: Anne

last: Wilson

first: Isabel

last: Ferrero

first: William

middle: E

last: Blanco-Bose


title: Mammary tumors from K14-cre; ApcCKO/+ mice vs control mammary glands

status: Public on Feb 10 2009

city: Cambridge

first: Dmitriy

last: Sonkin

state: MA

address: 250 Massachusetts Avenue

institute: Novartis Institutes for BioMedical Research

summary: Many components of Wnt/β-catenin signaling pathway also play critical roles in mammary tumor development.  To study the role of Apc in mammary tumorigensis, we introduced conditional Apc mutations specifically into two different mammary epithelial populations using K14-Cre (progenitor) and WAP-cre (lactaing luminal) transgenic mice.  Only the K14-cre mediated Apc heterozygosity developed mammary adenocarcinomas demonstrating histological and molecular heterogeneity, suggesting the progenitor cell origin of these tumors.  These tumors harbored truncation mutation in a very defined region in the remaining wild-type allele of Apc that would retain some down-regulating activity of β-catenin signaling.  Our results suggest that not only the epithelial origin but also a certain Apc mutations are selected to achieve a specific level of β-catenin signaling optimal for mammary tumor development.

overall_design: We have compared 3 mammary tumors from K14-cre; ApcCKO/+ mice  with 3 control mammary glands.

first: Mari

last: Kuraguchi

first: Nana

middle: Y

last: Ohene-Baah

first: Roderick

last: Bronson

first: Raju

last: Kucherlapati


status: Public on Feb 06 2009

city: Manchester

first: Tim

middle: C

last: Somervaille

state: Lancashire

address: Wilmslow Road

country: United Kingdom

institute: Cancer Research UK Manchester Institute

summary:
Hierarchical maintenance of MLL myeloid leukemia stem cells employs a transcriptional program shared with embryonic rather than adult stem cells

The genetic programs that promote retention of self-renewing leukemia stem cells (LSCs) at the apex of cellular hierarchies in acute myeloid leukemia (AML) are not known.  In a mouse model of human AML, LSCs exhibit variable frequencies that correlate with the initiating MLL oncogene and are maintained in a self-renewing state by a transcriptional sub-program more akin to that of embryonic stem cells (ESCs) than adult stem cells.  The transcription/chromatin regulatory factors Myb, Hmgb3 and Cbx5 are critical components of the program and suffice for Hoxa/Meis-independent immortalization of myeloid progenitors when co-expressed, establishing the cooperative and essential role of an ESC-like LSC maintenance program ancillary to the leukemia initiating MLL/Hox/Meis program.  Enriched expression of LSC maintenance and ESC-like program genes in normal myeloid progenitors and poor prognosis human malignancies links the frequency of aberrantly self-renewing progenitor-like cancer stem cells to prognosis in human cancer.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series.


title: Loss of PATCHED (wechs-affy-mouse-512645)

status: Public on Feb 09 2009

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

summary:
We are examining the genes that control initiation and progression of murine medulloblastomas that result from loss of patched. Approximately 25% of human medulloblastomas have mutations in patched or in other elements of the sonic hedgehog pathway. However, the cells from which these tumors originate (neural progenitors or stem cells), the cells that are responsible for tumor propagation (cancer stem cells), and the genes that are required for tumor progression are poorly understood. To address these questions, we have developed conditional patched knockout mice in which the gene is deleted in neural stem cells or progenitors. In addition, we have isolated a population of tumor-propagating cells from these tumors. By studying these models we will gain insight into the mechanisms of tumorigenesis and identify new targets for therapy.
To identify the molecular mechanisms that underlie tumor initiation and propagation, we will compare gene expression in tumors resulting from loss of patched in neural stem cells vs. progentors, and in cancer stem cells vs. non-cancer stem cells.
We hypothesize that medulloblastomas initiated in neural stem cells (using GFAP-Cre) are more aggressive than those initiated in neural progenitors (using Math1-Cre), and will express more genes associated with self-renewal. In addition, we hypothesize that cancer stem cells (CD15+ cells) from a given tumor will express higher levels of self-renewal genes than non-stem cells (CD15- cells) from the same tumor.
Cells from 5 GFAP-Cre tumors, 5 Math1-Cre tumors, and 5 conventional patched-knockout tumors will be isolated using enzymatic digestion and Percoll gradient centrifugation. These procedures have been found to result in 85-95% pure tumor cell populations. In addition, 5 tumors will be FACS-sorted to isolate CD15+ and CD15- populations. RNA will be prepared from each of these samples using an RNeasy kit from Qiagen. Samples of 2 micrograms will be resuspended in 10 microliters of RNase-free water, and sent to the Consortium for labeling, hybridization and analysis. Cells from the three types of tumors, and CD15+ and CD15- cells,  will be compared to one another.

first: Robert

middle: J

last: Wechsler-Reya


title: Transcriptional and post-transcriptional impact of toxic RNA in myotonic dystrophy

status: Public on Feb 05 2009

city: Rochester

first: Stephen

last: Welle

state: NY

address: 601 Elmwood Avenue

institute: University of Rochester

summary:
Myotonic dystrophy type 1 (DM1) is an RNA dominant disease in which mutant transcripts containing an expanded CUG repeat (CUGexp) cause muscle dysfunction by interfering with biogenesis of other mRNAs. The toxic effects of mutant RNA are mediated partly through sequestration of splicing regulator Muscleblind-like 1 (Mbnl1), a protein that binds to CUGexp RNA. A gene that is prominently affected encodes chloride channel 1 (Clcn1), resulting in hyperexcitability of muscle (myotonia). To identify DM1-affected genes and study mechanisms for dysregulation, we performed global mRNA profiling in transgenic mice that express CUGexp RNA, as compared to Mbnl1 knockout and Clcn1 null mice. We found that the majority of changes induced by CUGexp RNA in skeletal muscle can be explained by reduced activity of Mbnl1, including many changes that are secondary to myotonia. The pathway most affected comprises genes involved in calcium signaling and homeostasis. Some effects of CUGexp RNA on gene expression are caused by abnormal alternative splicing or downregulation of Mbnl1-interacting mRNAs. However, several of the most highly dysregulated genes showed altered transcription, as indicated by parallel changes of the corresponding premRNAs. These results support the idea that trans-dominant effects of CUGexp RNA on gene expression in this transgenic model may occur at the level of transcription, RNA processing, and mRNA decay, and are mediated mainly but not entirely through sequestration of Mbnl1.

Keywords: comparison of normal and transgenic mice

overall_design: All experiments involved generating expression profiles of quadriceps muscles taken from mice. Experiments 1 and 2: samples were hybridized to Moe430A and Moe430B arrays. Experiment 3: samples were hybridized to Mouse Genome 430 2.0 array. Experiment 1 compared expression profiles of wild-type mice (FVB strain) with two lines, designated 20b and 41, of CUGexp transgenic mice with FVB background. Experiment 2 compared expression profiles of Clcn1-null (myotonic) mice with the wild-type background strain (BALB). Experiment 3 compared expression profiles of Mbnl1-null mice with the wild-type background strain (FVB).

first: Charles

last: Thornton


title: Expression data from CD8+ T cells undergoing deletional tolerance

city: New Haven

first: Ian

last: Parish

state: CT

address: The Anlyan Center, 300 Cedar St.

department: Immunobiology

institute: Yale School of Medicine

summary:
Peripheral tolerance induction is critical for the maintenance of self-tolerance and can be mediated by immunoregulatory T cells or by direct induction of T cell anergy or deletion. While the molecular processes underlying anergy have been extensively studied, little is known about the molecular basis for peripheral T cell deletion. Here, we determined the gene expression signature of peripheral CD8+ T cells undergoing deletional tolerance, relative to those undergoing immunogenic priming or lymphopenia-induced proliferation. From these data, we report the first detailed molecular signature of cells undergoing deletion.
Consistent with defective cytolysis, these cells exhibited deficiencies in granzyme up-regulation. Furthermore, they showed antigen-driven Bcl-2 down-regulation and early up-regulation of the pro-apoptotic protein Bim, consistent with the requirement of this BH3-only protein for peripheral T cell deletion. Bim up-regulation was paralleled by defective IL-7Ra chain re-expression, suggesting that Bim-dependent death may be triggered by loss of IL-7/IL-7R signaling. Finally, we observed parallels in molecular signatures between deletion and anergy suggesting that these tolerance pathways may not be as molecularly distinct as previously surmised.

overall_design: Naïve (CD44lo) OT-I T cells were CFSE labelled and transferred in a model of deletional tolerance (RIP-OVAhi mice), a model of immunity (mice primed with OVA coated splenocytes and LPS) or a model of lymphopenia induced proliferation (Rag-/- mice).  60 hrs (RIP-OVAhi and OVA coated splenocytes) or 5 days (Rag-/-) after transfer, OT-I cells that had undergone two or more divisions as determined by CFSE dilution were sorted, RNA extracted and samples were prepared for hybridisation to Affymetrix microarrays.  As a control for naive cells, CFSE labelled OT-I cells were injected into antigen-free B6 mice and the undivided naive cells were sorted after 60 hrs and also used for microarray analysis.  Two replicates were prepared for the naive cells, cells from RIP-OVAhi mice and cells from OVA coated splenocyte primed mice, while one replicate was prepared for the cells from Rag-/- mice.

middle: R

last: Heath


title: Gene expression profiling of normal mouse myeloid cell populations

summary: Normal myeloid lineage cell populations (C57BL/6 mice, aged 4-10 weeks, male or female) with three distinct immunophenotypes were prospectively isolated and characterized. In preparation for FACS sorting, bone marrow cells were separated into c-kit+ and c-kit- fractions using an AutoMACS device. C-kit+ cells were further fractionated based on Gr1 and Mac1 expression, and absence of lineage antigen expression (B220, TER119, CD3, CD4, CD8 and IL7Rα), by cell sorting. C-kit+ Gr1+ Mac1lo/- and c-kit+ Gr1+ Mac1+ displayed cytologic features of undifferentiated hematopoietic cells or myeloblasts, whereas c-kit- Gr1+ Mac1+ cells were mature neutrophils.

overall_design: See summary.

first: Christina

last: Matheney

first: Gary

last: Spencer

first: Masayuki

last: Iwasaki

first: John

last: Rinn

first: Daniela

middle: M

last: Witten

first: Howard

last: Chang

first: Shiela

last: Shurtleff

first: James

last: Downing

first: Michael

last: Cleary


title: Gene expression profiling of murine MLL leukemias (whole BM)

summary: The genetic programs that promote retention of self-renewing leukemia stem cells (LSCs) at the apex of cellular hierarchies in acute myeloid leukemia (AML) are not known.  In a mouse model of human AML, LSCs exhibit variable frequencies that correlate with the initiating MLL oncogene and are maintained in a self-renewing state by a transcriptional sub-program more akin to that of embryonic stem cells (ESCs) than adult stem cells.  The transcription/chromatin regulatory factors Myb, Hmgb3 and Cbx5 are critical components of the program and suffice for Hoxa/Meis-independent immortalization of myeloid progenitors when co-expressed, establishing the cooperative and essential role of an ESC-like LSC maintenance program ancillary to the leukemia initiating MLL/Hox/Meis program.  Enriched expression of LSC maintenance and ESC-like program genes in normal myeloid progenitors and poor prognosis human malignancies links the frequency of aberrantly self-renewing progenitor-like cancer stem cells to prognosis in human cancer.

overall_design: Samples are from five separate cohorts of mice where leukemia was initiated using distinct MLL fusion oncogenes: MLL-AF1p (n=9), MLL-AF10 (n=8), MLL-GAS7 (n=5), MLL-AF9 (n=5) and MLL-ENL (n=7). Four normal BM samples were also used as controls.


title: Toll-like Receptor 3-induced Suppression via Binding of Suppressors of Cytokine Signaling 3 to Tyrosine Kinase 2

status: Public on Feb 23 2009

city: Tianjin

first: Rongcun

last: Yang

address: Nankai District, 94 Weijin Lu

department: Department of Immunology

institute: Nankai University School of Medicine

summary:
The Suppressor of cytokine signaling (SOCS) family of negative regulatory proteins are upregulated in response to several cytokines and pathogen-associated molecular patterns (PAMPs), and suppress cellular signaling responses by binding receptor phosphotyrosine residues. Exposure of bone marrow-derived dendritic cells (BMDCs) to 1D8 cells, a murine model of ovarian carcinoma, suppresses their ability to express CD40 and stimulate antigen specific responses in response to PAMPs, and in particular to poly I: C with the upregulated SOCS3 transcript and protein levels. The ectopic expression of SOCS3 in both the macrophage cell line RAW264.7 and BMDCs decreased signaling in response to both poly I:C and IFNα. Further, knockdown of SOCS3 transcripts significantly enhanced the responses of RAW264.7 and BMDCs to both poly I: C and IFNα. Immunoprecipitation and pull-down studies demonstrate that SOCS3 binds to the IFNα receptor TYK2. Since poly I: C triggers autocrine IFNα signaling, binding of SOCS3 to TYK2 may thereby suppress the activation of BMDCs by polyI:C and IFNα. Thus, elevated levels of SOCS3 in tumor-associated DCs may potentially resist the signals induced by TLR3 ligands and type I interferon to decrease DC activation via binding with IFNα receptor TyK2.
Keywords: Response to intracellular signaling from tumor cells by coculture or treated medium

overall_design:
Microarray analysis was used to compare the expression levels of Control mouse bone marrow-derived dendritic cells (BMDC), with cells that had been cocultured (1:5, tumor:BMDC) with mouse ovarian surface epithelial cell line (1D8) cells, with irradiated (50Gy) 1D8 cells, or with the supernatent from 1D8 cells (25%, v/v).

One biologic sample was analyzed for each condition, four samples in all.

first: Bin

last: Zeng

first: Haijie

last: Li

first: Yu

last: Liu

first: Zhuohan

last: Zhang

first: Yuan

first: Roncun


title: Tumor and Self-Recognition Induce Distinct Transcriptional Profiles in Antigen-Specific CD4 T Cells

status: Public on Jan 31 2009

city: Baltimore

first: Charles

middle: G

last: Drake

state: MD

address: 1650 Orleans St CRB I #410

department: Department of Oncology

institute: Johns Hopkins Sidney Kimmel Comprehensive Cancer Center

summary:
Tumors express a wide variety of both mutated and non-mutated antigens. Whether these tumor antigens are broadly recognized as “self” or “foreign” by the immune system is currently unclear. Using an autochthonous prostate cancer model in which hemagglutinin (HA) is specifically expressed in the tumor (ProHA x TRAMP mice), as well as an analogous model wherein HA is expressed in normal tissues as a model self-antigen (C3HAHigh), we examined the transcriptional profile of CD4 T cells undergoing antigen-specific division.  Consistent with our previous data, transfer of antigen-specific CD4 T cells into C3HAHigh resulted in a functionally inactivated CD4 T cell profile.  Conversely, adoptive transfer of an identical CD4 T cell population into ProHA x TRAMP resulted in the induction of a regulatory phenotype (Treg) both at the transcriptional and functional level. Interestingly, this Treg skewing was a property of even early-stage tumors, suggesting Treg induction as an important tolerance mechanism during tumor development.
The goal of this microarray is to detail the transcriptional profile differences between CD4 T cells that recognize their cognate antigen in the context of tumor (ProHA x TRAMP model) or self-antigen recognition (C3HA) or viral-antigen recognition (VaccHA) models or unprimed naïve state (Nontransgenic). The comparison contains both upregulated and downregulated transcripts.

Keywords: Transcriptional Profile comparison, context dependent antigen recognition and T Cell differentiation

overall_design: TCR transgenic CD4 T cells specific for hemagglutinin (HA) were adoptively transferred into tumor-antigen recognition model (ProHA x TRAMP), Self-antigen recognition model (C3HA), viral-antigen recognition model (VaccHA), and naïve control  (Nontrangenic). Divided (CFSE diluted) CD4 T cells were sorted by FACS, RNA was extracted, and biological replicated were hybridized to an Affymetrix Mouse 430 Plus 2 expression array, followed by interrogation with an Affymetrix GeneChip Scanner 3000. RMA normalization was employed to identify differentially expressed transcripts.

first: Derese

last: Getnet


title: Splenic CD8+ and CD8- DCs

status: Public on Feb 01 2009

city: New York

first: Hiroaki

last: Hemmi

address: 1230 York Avenue

department: Laboratory of Cellular Physiology and Immunology

institute: The Rockefeller University

summary: Analysis of gene expressions in mouse splenic dendritic cells (DCs). DCs were purified into two subsets, CD8-positive and -negative ones. DCs were expanded in vivo by injecting Flt3L-producing tumors into the backs of C57BL/6 mice.

overall_design: To expand DCs in vivo, Flt3L-producing B16 melanoma cells were injected to the backs of mice. Then, 10-12 days later, splenic DCs were enriched by MACS and purified  into CD3-B220-CD8a+CD11c+ and CD3-B220-CD8a-CD11c+ cells by FACS cell sorter.

first: Ralph

last: Steinman


title: The in vitro expanded CD8+ T cells and its controls

city: Augusta

first: Jin-Xiong

last: She

state: GA

address: 1120 15th Street, MCG, CA 4126

department: Center for Biotechnology and Genomic medicine

institute: Medical College of Georgia

summary:
CD8+ NKT cells are naturally occurring but rare T cells that express both T cell and natural killer (NK) cell markers.  These cells may play key roles in establishing tolerance to self antigens; however, the mechanism of action and the molecular profiles of these cells are poorly characterized due to their extremely low frequencies.  We developed a highly efficient in vitro conversion/expansion protocol for such cells and extensively characterized their functional and molecular phenotypes using a variety of genomic and immunological techniques.
We used microarrays to elucidate the molecular mechanisms underlying the suppression function of the converted CD8+ NKT cells.
Keywords: Cell type comparison

overall_design: To identify candidate genes that might be related to the suppressive activity, the CD8+ NKT cells with potent suppressive activity were compared to three different control cells: 1) CD4+ T cells (with very weak suppression) cultured under the same condition as a control for culture condition, 2) naïve CD8 T cells as the baseline expression level, and 3) CD8+ T cells activated using conventional activation protocols.  The last two cell populations do not possess suppressive activity.  This data set allows us to examine a number of different questions


title: Expression profiling of MLL-AF10 myeloid leukemia cellular subsets

first: Tim

last: Somervaille

summary: Leukemia cells from mice with MLL-AF10 AML were fractionated into separate sub-populations on the basis of c-kit expression, which correlates with MLL LSC frequency (Somervaille and Cleary, 2006).  The sorted AML sub-populations exhibited substantial differences in their frequencies of AML CFCs/LSCs (mean 14-fold) and morphologic features, consistent with a leukemia cell hierarchy with maturation through to terminally differentiated neutrophils.

overall_design: Leukemic splenocytes from four mice with MLL-AF10 AML were sub-fractionated in to c-kit high and c-kit negative sub-populations by FACS.

first: Christina

last: Matheney

first: Gary

last: Spencer

first: Masayuki

last: Iwasaki

first: John

middle: L

first: Daniela


title: Gene expression changes in Jhdm2a knock-out skeletal muscle as compared to wild-type.

city: Barcelona

first: Eric

middle: M.

last: Kallin

state: Barcelona

address: C/ Dr. Aiguader, 88

department: Differentiation and Cancer

country: Spain

institute: Center for Genomic Regulation

summary: Gene expression changes in mouse skeletal muscle were assessed in wild-type and Jhdm2a null skeletal muscle in an effort to define the role of Jhdm2a in energy expenditure and metabolism.

overall_design: RNA prepared from the skeletal muscle of 3 wild-type mice was combined, amplified, labeled, and hybridized to an Affymetrix 430 2 microarray.  RNA was similarly prepared from the skeletal muscle of 3 Jhdm2a null mice and hybridized to an Affymetrix 430 2 microarray.

first: Keisuke

last: Tateishi

first: Yuki

last: Okada

first: Yi


title: mpkCCD_Cell_Clones

status: Public on Jan 26 2009

city: Taipei

first: Ming-Jiun

last: Yu

address: Rm 816, No. 1 Ren-Ai Road Section 1

department: Institute of Biochemistry and Molecular Biology

country: Taiwan

institute: National Taiwan University College of Medicine

summary: This series of microarray data contain transcript intensity of mpkCCD cells.

overall_design: The mpkCCDc14 cells were cloned into colonies with varying aquaporin 2 (AQP2) expression levels in the presence of vasopressin analogy dDAVP.  Transcript profiling was done for the original cells and cell clones 2, 3, 9, 10, and 11.  By studying transcripts that correlate with AQP2 mRNA levels among cell clones, the objective was to identify transcripts responsible for cell-specific expression of AQP2.


title: Oct4-Induced Pluripotency in Adult Neural Stem Cells

city: Aachen

first: Martin

last: Zenke

state: NRW

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

country: Germany

institute: Institute for Biomedical Engineering

summary: The four transcription factors Oct4, Sox2, Klf4, and c-Myc can induce pluripotency in mouse and human fibroblasts. We previously described direct reprogramming of adult mouse neural stem cells (NSCs) by Oct4 and either Klf4 or c-Myc. NSCs endogenously express Sox2, c-Myc, and Klf4 as well as several intermediate reprogramming markers. Here we report that exogenous expression of the germline-specific transcription factor Oct4 is sufficient to generate pluripotent stem cells from adult mouse NSCs. These one-factor induced pluripotent stem (1F iPS) cells are similar to embryonic stem cells in vitro and in vivo. Not only can these cells be efficiently differentiated into NSCs, cardiomyocytes and germ cells in vitro, but they are also capable of teratoma formation and germline transmission in vivo. Our results demonstrate that Oct4 is required and sufficient to directly reprogram NSCs to pluripotency.

overall_design:
10 hybridizations in total.
NSC-derived iPS cells by one-factor (Oct4) in triplicate:
- NSC_1F_iPS_1
- NSC_1F_iPS_2
- NSC_1F_iPS_3
One-factor (Oct4) iPS cell-derived NSC in triplicate:
- 1F_iPS_NSC_1
- 1F_iPS_NSC_2
- 1F_iPS_NSC_3
Neural stem cell (NSC) derived from brain of OG2/Rosa26 mice:
- NSC_1
- NSC_2
- NSC_3
- NSC_4

first: Jeong-Beom

last: Kim

first: Vittorio

last: Sebastiano

first: Marcos

last: Arauzo-Bravo

first: Philipp

last: Sasse

first: Guangming

last: Wu

first: Luca

last: Gentile

first: Kinarm

last: Ko

first: David

last: Ruau

first: Mathias

last: Ehrich

first: Dirk

last: van den Boom

first: Claudia

last: Ortmeier

first: Bernd

last: Fleischmann

first: Holm

last: Zaehres

first: Hans

last: Schöler


title: Effects of BDNF in Rodent Models of Aging and Alzheimer's Disease

status: Public on Jan 30 2009

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

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

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Refer to individual Series


title: Effect of IL-12 on CTL gene expression

city: St. Louis

first: Andrey

last: Shaw

address: 660 S. Euclid Ave.

department: Pathology and Immunology

institute: Washington University in St. Louis

summary: The goal was to determine how IL-12 affects gene expression by murine CTL.

overall_design: Following RBC lysis, splenocytes from OT-1 TCR transgenic mice (5 million/ml) were cultured in six well-plates (5-6ml/well) in IMDM supplemented with 10% FCS and 55μM 2-ME with 1μM SIINFEKL.  After 4 days, the cells were harvested by purification with Ficoll-Paque PLUS and placed in fresh medium containing 0 or 20ng/ml rmIL-12.  Twenty-four hours later the cells were harvested and used in experiments.  The live cells harvested were >98% CD8+Vα2+ (OT-1).

first: Mary

middle: A

last: Markiewicz


title: Gene expression from bronchial epithelial cell samples of current and never smokers.

status: Public on Jan 29 2009

city: Gaithersburg

first: Sriram

last: Sridhar

address: 1 MedImmune Way

department: Translational Medicine

institute: MedImmune

summary:
mRNA expression was assayed from bronchial epithelial cells collected via bronchoscopy from healthy current and never smoker volunteers in order to determine relationships between microRNA and mRNA expression in bronchial epithelial cell samples across current and never smokers and within the same individual.

Keywords: Global mRNA expression profiling

overall_design: Bronchial epithelial cells were collected from current and never smokers via bronchoscopy. High molecular weight RNA ( > 200 nucleotides) was isolated and hybridized to Affymetrix Human Exon 1.0 ST microarrays to obtain mRNA expression from the airway epithelial cells of current and never smokers, which could be correlated to microRNA expression from the same samples.

first: Avrum

last: Spira