title: Low dose Leptin (25 ng/hr and 12.5 ng/hr) in ob/ob mice

status: Public on Nov 25 2009

city: New York

first: Kristina

last: Hedbacker

state: NY

address: 1230 York Avenue

institute: Rockefeller University

summary: Ob/ob mice were given 0, 12.5 or 25 ng/hr leptin through an osmotic pump. After 12 days, livers RNA was prepared and illumina microarrays were done. We tested whether leptin can ameliorate diabetes independent of weight loss by defining the lowest dose at which leptin treatment of ob/ob mice reduces plasma [glucose] and [insulin].  We found that a leptin dose of 12.5 ng/hour significantly lowers blood glucose and that 25 ng/hour of leptin normalizes plasma glucose and insulin without significantly reducing body weight, thus establishing that leptin exerts its most potent effects on glucose metabolism. To find possible mediators of this effect, we profiled liver mRNA using microarrays and identified IGF Binding Protein 2 as being regulated by leptin with a similarly high potency. Over-expression of IGFBP2 by an adenovirus reversed diabetes in insulin resistant ob/ob, Ay/a and diet-induced obese mice (DIO), as well as insulin deficient streptozotocin-treated mice.  Hyperinsulinemic clamp studies showed a three-fold improvement in hepatic insulin sensitivity following IGFBP2 treatment in ob/ob mice. These results show that IGFBP2 can regulate glucose metabolism, a finding with potential implications for the pathogenesis and treatment of diabetes.

overall_design: n=3 for zero and 25 ng/hr. n=2 for 12.5 ng/hr

first: Jeffrey

middle: M

last: Friedman


title: Gene expression in respiratory epithelial cells treated to induce resistance with synthetic TLR ligands

status: Public on Oct 30 2009

city: Houston

first: Scott

middle: E

last: Evans

state: TX

address: 1400 Holcombe Blvd

department: Pulmonary Medicine - Unit 1462

country: USA

institute: University of Texas-M.D. Anderson Cancer Center

summary:
Among both healthy and immunocompromised patient populations, pneumonia is a leading cause of death worldwide.  Yet, despite structural vulnerability resulting in recurrent exposure to pathogens, the lungs’ mucosal immunity successfully suppresses most infections. We recently reported that these innate defenses can be substantially augmented by inhalational exposure to a crude bacterial lysate, protecting broadly against respiratory pathogens, including lethal pneumonia caused by bacteria, fungi or viruses.    The phenomenon of inducible resistance is associated with rapid pathogen killing in the lungs and persists in the absence of the typical leukocytes of innate immunity.  Rather, the respiratory epithelium appears to be the predominant effector.  Toll-like receptors (TLRs) are highly conserved pattern recognition receptors crucial to host defense through the sensing of pathogen associated molecular patterns.  Given the importance of TLRs to mucosal immunity, the presence of numerous pathogen associated molecular patterns in the bacterial lysate, and the induction of many TLR-dependent genes following lysate treatment, we hypothesized that induced resistance follows simultaneous stimulation of multiple TLRs.  To test this, we challenged mice deficient in TLR/IL1R adaptor proteins and found that resistance could not be induced in mice lacking MyD88.  Having identified this phenomenon to be MyD88-dependent, we sought to determine whether the protective phenomenon could be recapitulated by treatment with synthetic TLR agonists.  Mice were treated with aerosolized TLR ligands, alone and in combination, prior to infection with virulent pathogens.  While limited protection against pneumonia was afforded by the individual TLR ligands, we discovered that the synergistic combination of diacylated lipopetide TLR2/6 agonist Pam2CSK4 and CpG oligodeoxynucleotide TLR9 agonist ODN2395 induced profound resistance against all tested pathogens.  This combination also induced greater than additive pathogen killing in the lungs of challenged mice, and we found that the combination could effectively induce pathogen killing by respiratory epithelial cells in vitro.  In order to better understand the mechanisms underlying the inducible pathogen killing by this unique combination of TLR agonists, we performed microarray analysis of murine MLE-15 respiratory epithelial cells following 4 h treatment with PBS (sham treatment), Pam2CSK4 alone, ODN2395 alone, or the combination of both agonists, using Illumina Sentrix MouseRef-8 v2 BeadChips.  This allows for assessment of differential gene expression, not only between treated and untreated, but between single and combination treated.  The intent of the experiment is to gain insight into the transcriptionally-regulated means by which TLR2/6 and TLR9 signaling pathways synergistically interact.

Keywords: Differential expression, epithelium, in vitro

overall_design: MLE-15 cells were treated with 20 ul volumes of PBS (sham treatment), ODN2395 (0.4 ug), Pam2CSK4 (0.2 ug) or ODN2395+Pam2CSK4.  4 unique samples per group. Treated for 2 hours. Hybridized to Illumina Sentrix MouseRef-8 v2 Beadhips.


title: Global gene expression analysis of (1) chemically reprogrammed iPS cells, and (2) chemical-treated cells

status: Public on Nov 04 2009

city: Cambridge

first: Esther

middle: Yesde

last: Son

state: MA

address: 7 Divinity Avenue

department: Stem Cells and Regenerative Biology

institute: Harvard University

summary:
Analysis of iPS cells generated with a small molecule, RepSox (RS), as well as a time-course of gene expression changes in cells treated with RS.

The former was done to verify the similarity of the iPS cells with mES cells; the latter was aimed at elucidating the mechanism of drug action in the context of reprogramming.

overall_design: Total RNA obtained from iPS cells compared with mES and fibroblasts; total RNA obtained from untreated cells compared with RepSox-treated cells at various timepoints.

middle: Y

first: Justin

middle: K

last: Ichida

first: Kevin

last: Eggan


title: Genetic inactivation of serine racemase produces behavioral phenotypes related to schizophrenia in mice

status: Public on Sep 05 2009

city: Toronto

first: Paul

middle: C

last: Boutros

state: Ontario

address: 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

summary:
Abnormal N-methyl-D-aspartate receptor (NMDAR) function has been implicated in the pathophysiology of schizophrenia.  D-serine is an important NMDAR modulator, and to elucidate the role of the D-serine synthesis enzyme serine racemase (Srr) in schizophrenia, we identified and characterized mice with an ENU-induced mutation that results in a complete loss of Srr activity and drastically reduced D-serine levels.  Mutant mice displayed behaviors relevant to schizophrenia, including impairments in prepulse inhibition, sociability and spatial discrimination.  Behavioral deficits were rescued by D-serine and the atypical antipsychotic clozapine, and were conversely, amplified by NMDAR inhibition.  Expression profiling revealed that the Srr mutation influenced several genes that have been linked to schizophrenia and cognitive ability.  Furthermore, analysis of Srr genetic variants in humans identified a robust association with schizophrenia.  This study demonstrates that aberrant serine racemase function and diminished D-serine may contribute to schizophrenia pathogenesis, and that D-serine may be a beneficial form of treatment

Keywords: genetic-mutant vs. wildtype comparison

overall_design: Four wild-type and four SRR mice were analyzed for each of three brain regions (cerebellum, hippocampus, and frontal cortex).

first: Viviane

last: Labrie

first: Ryutaro

last: Fukumura

first: Anjali

last: Rastogi

first: Laura

middle: J

last: Fick

first: Wang

last: Wei

first: Mawahib

middle: O

last: Semeralul

first: Frankie

middle: H

last: Lee

first: Glen

middle: B

last: Baker

first: Denise

middle: D

last: Belsham

first: Steven

middle: W

last: Barger

first: Yoichi

last: Gondo

first: Albert

last: Wong

first: John

last: Roder


title: Normal lung transcriptome distinguishes mouse lines with different susceptibility to inflammation and to tumorigenesis

status: Public on Jun 09 2009

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

summary: AIRmax and AIRmin mouse lines show a differential lung inflammatory response and differential lung tumor susceptibility after urethane treatment, thus constituting a good genetic model to investigate differences in gene expression profiles related to inflammatory response and lung tumor susceptibility. The transcript profile of ~24,000 known genes was analyzed in normal lung tissue of untreated and urethane-treated AIRmax and AIRmin mice.  In lungs of untreated mice, inflammation associated genes involved in pathways such as “leukocyte transendothelial migration”, “cell adhesion” and “tight junctions” were differentially expressed in AIRmax versus AIRmin mice. Moreover, gene expression levels differed significantly in urethane-treated mice even at 21 days after treatment. In AIRmin mice, modulation of expression of genes involved in pathways associated with inflammatory response paralleled the previously observed persistent infiltration of inflammatory cells in the lung of these mice. In conclusion, a specific gene expression profile in normal lung tissue is associated with mouse line susceptibility or resistance to lung tumorigenesis and with different inflammatory response, and urethane treatment causes a long-lasting alteration of the lung gene expression profile that correlates with persistent inflammatory response of AIRmin mice.

overall_design: Six AIRmax (3 males and 3 females) and six AIRmin (3 males and 3 females) mice were treated with two intraperitoneal injections of 1 mg/g body weight urethane or saline solution (total of 24 AIR mice: 12 AIRmax and 12 AIRmin mice, 6 urethane- and 6 saline-treated respectively) with a 48-h interval and sacrificed 21 days later

first: L

first: F

last: Colombo


title: Malaria primes the innate immune response due to IFNg induced enhancement of Toll-like receptor expression and function.

status: Public on Mar 14 2009

city: Malmö

first: Harry

last: Björkbacka

address: CRC 91:12, UMAS entrance 72

department: Dept. of Clinical Sciences, Malmö

country: Sweden

institute: Lund University

summary: Patients with febrile malaria were recruited in order to determine Peripheral Blood Mononuclear Cell (PBMC) gene expression during malaria.  Blood was harvested from patients during the acute phase of the illness, and then patients were given a curative regimen of antimalarials.  Three to four weeks after treatment, patients returned to the malaria clinic and blood was collected again, in order that each patient could serve as his or her own control.  PBMC were isolated at the time of blood collection and forzen in RNA extraction buffer.  At the end of the study, each patient was arrayed for ~47,000 transcripts, comparing gene expression at the end of therapy to that at the beginning.  The goal was to determine which genes were altered as a result of disease at least 2 fold in a statistically significant manner and to assess if the genes involved could be related to  Toll-like receptor signaling pathways.  Approximately 60 genes involved in inflammation were confirmed by qPCR.

overall_design: Gene expression profiles of blood cells from 14 individuals with malaria are compared to gene expression in blood cells from the same 14 individuals medicated and recovered from malaria symptoms (28 arrays in total).

first: Rosane

last: De Oiiviera

first: Bernardo

middle: S

last: Franklin

first: Ricardo

last: Gazzinelli

first: Douglas

middle: T

last: Golenbock

first: Luis

last: Da Silva

first: Fanny

last: Lauw

first: Peggy

last: Parroche


title: Cardiac left ventricles of 12 week-old male C57BL/6J and C57BL/6J-chrY<A/J/NaJ> mice

status: Public on May 01 2009

city: Montreal

first: Christian

middle: F

last: Deschepper

state: QC

address: 110 ave des Pins Ouest

institute: IRCM

summary: We have reported previously that when chromosome Y (chrY) from the mouse strain C57BL/6J (abbreviated as B) was substituted for that of A/J mice (ChrY<A>), cardiomyocytes from the resulting 'chromosome substitution' C57BL/6J-chrY<A> strain (abbreviated as B.Y) were smaller than that of their C57BL/6J counterparts.  In reverse, when chrY<A> from A/J mice was substituted for that of chrY<B>, cardiomyocytes from the resulting A/J-chrY<C57> strain were larger than in their A/J counterparts.  We further used these strains (B and the consomic B.Y) to test whether the origin of chrY could also be linked to differences in the profile of gene expression in their cardiac left ventricles in adult mice where either sham surgery (intact animals)  or  castration has been performed at 3-4 weeks of age..

overall_design: Samples from 4 different mice were used in each group.  For hybridization, probes generated from samples were randomized on 2 different Illumina MouseRef v2.0 BeadChips.

first: Bastien

last: Llamas

middle: A

last: Verdugo

first: Gary

last: Churchill


title: E11.5 Mouse Endodermal Organ Gene Expression

status: Public on Dec 30 2008

first: Richard

last: Sherwood

address: 7 Divinity Ave

department: Department of Molecular and Cellular Biology

summary:
To study gene expression during endodermal organogenesis, we sought to identify genes expressed in restricted domains during organogenesis. For gene expression analysis, six morphologically distinct endodermal domains were dissected at E11.5: the esophageal region; the lung and distal tracheal region; the stomach region; the hepatic region; the dorsal and ventral pancreatic region; and the intestinal region.  Through flow cytometric separation using EpCAM expression to distinguish endoderm from surrounding mesenchyme, pure populations of endoderm progenitors from the esophageal, lung, stomach, pancreatic, and intestinal regions were isolated. Expression of Liv2 was used to isolate a pure population of hepatic endoderm progenitors.

Keywords: cell type comparison

overall_design: Three biological replicates each containing dissected organ domains from 10-12 pooled embryos flow cytometrically sorted to isolate endoderm were amplified using Ambion Illumina TotalPrep RNA Amplification kit and arrayed on Illumina MouseRef8 v2 chips


title: Reticulocyte 3 timepoints

status: Public on Oct 12 2009

city: Boston

first: meng

last: tian

address: 320 Longwood Ave Enders1110

department: Pathology

institute: Children's Hospital Boston

summary:
Mouse models have proven invaluable for understanding erythropoiesis. Here, we describe an autosomal recessive inherited anemia in the mouse mutant hem6. Hematologic and transplantation analyses revealed a mild, congenital, hypochromic, microcytic anemia intrinsic to the hematopoietic system that is associated with a decreased red blood cell zinc protoporphyrin to heme ratio, indicative of porphyrin insufficiency. Iron uptake experiments showed that hem6 reticulocytes are defective in heme production, but not cellular iron uptake defects. Male hem6 mice are infertile due to defects in sperm structure and motility. Through positional cloning and BAC complementation, we identified the gene responsible for the hem6 anemia. We hypothesized that the relative deficiency in erythroid-specific mRNAs in hem6 reticulocytes might be due to decreased mRNA stability. Indeed, serial microarray analysis of reticulocytes aged in vitro showed that numerous, abundantly expressed erythroid-specific transcripts decayed at faster rates in hem6 reticulocytes compared to control reticulocytes. Furthermore, these mRNAs also have progressively shorter poly (A) tails, suggesting a mechanism for the increased rate of decay.

Keywords: serial time points

overall_design: Reticulocyte rich blood were collected and cultured ex vivo for 24 hours, samples were collected at 0, 12,24 hours for microarray analysis. There are 3 wild type (wt) biological replicates and 5 mutant (mut) biological replicates in each time point.

first: Meng

last: Tian


title: Generation of Induced Pluripotent Stem Cells using Recombinant Proteins

status: Public on May 20 2009

city: La Jolla

first: Hongyan

last: Zhou

state: CA

address: 10550 North Torrey Pines Road

institute: the scripps research institute

summary: Groundbreaking work demonstrated that ectopic expression of four transcription factors, Oct4, Klf4, Sox2, and c-Myc, could reprogram murine somatic cells to induced pluripotent stem cells (iPSCs) (Takahashi and Yamanaka, 2006), and human iPSCs were subsequently generated using similar genetic manipulation (Takahashi et al., 2007,Yu et al., 2007). To address the safety issues arose from harboring integrated exogenous sequences in the target cell genome, a number of modified genetic methods have been developed and produced iPSCs with potentially reduced risks (for discussion, see Yamanaka, 2009, and references therein). However, all of the methods developed to date still involve the use of genetic materials and thus the potential for unexpected genetic modifications by the exogenous sequences in the target cells. Here we report generation of protein-induced pluripotent stem cells (piPSCs) from murine embryonic fibroblasts using recombinant cell-penetrating reprogramming proteins. We demonstrated that such piPSCs can long-term self-renew and are pluripotent in vitro and in vivo.

overall_design: Global gene-expression analyses of the piPS cells

first: H

first: S

last: Wu

first: J

last: Joo

last: Zhu

first: D

last: Han

first: T

last: Lin

last: Trauger

first: G

last: Bien

last: Yao

first: Y

last: Siuzdak

middle: R

last: Schöler

last: Duan

last: Ding


title: Mild vs advanced liver fibrosis

status: Public on May 24 2008

city: ROUEN

first: Jean

middle: Philippe

last: SALIER

address: Bvd Gambetta

department: Inserm Unit 519

country: France

institute: Faculty of Medicine and Pharmacy

summary:
The aim of this study is to compare mild and advanced liver fibrosis gene expression profiling and to identify novel markers of fibrosis progression. By transcriptome analysis with a cDNA array virtually covering every transcript in liver, we compared transcript levels in mild (F1 Metavir score) and advanced (F4 Metavir score) fibrosis. A stringent selection identified a list of 16 transcripts which completely separated the 2 groups of patients (8 F1 and 8 F4). We report that dysregulations at the transcriptional level do exist between mild fibrosis (F1) and advanced fibrosis (F4).

Keywords: fibrosis stage-dependent analysis

overall_design: Fibrosis samples were analyzed for 16 patients : 8 mild fibrosis (F1-1 to F1-8) and 8 advanced fibrosis (F4-1 to F4-8). All data in the current study were obtained from 3 separate hybridizations per RNA sample.

first: F

last: Caillot

first: M

last: Hiron

first: O

last: Goria

last: Gueudin

first: A

last: François

last: Scotte

last: Daveau

middle: P

last: Salier