title: Haploinsufficiency of Hedgehog interacting protein causes increased emphysema induced by cigarette smoke through network rewiring

status: Public on Jan 21 2015

city: Boston

first: Jarrett

last: Morrow

state: MA

address: 181 Longwood Ave.

department: Channing Division of Network Medicine

institute: Brigham and Women's Hospital

summary: BACKGROUND: The HHIP gene, encoding Hedgehog interacting protein, has been implicated in chronic obstructive pulmonary disease (COPD) by genome-wide association studies (GWAS), and our subsequent studies identified a functional upstream genetic variant that decreased HHIP transcription. However, little is known about how HHIP contributes to COPD pathogenesis.   METHODS: Here, we exposed Hhip haploinsufficient mice (Hhip+/-) to cigarette smoke (CS) for 6 months to model the biological consequences caused by CS in human COPD risk-allele carriers at the HHIP locus. Gene expression profiling in murine lungs was performed followed by an integrative network inference analysis, PANDA (Passing Attributes between Networks for Data Assimilation) analysis.  RESULTS: We detected more severe airspace enlargement in Hhip+/- mice vs. wild-type littermates (Hhip+/+) exposed to CS. Gene expression profiling in murine lungs suggested enhanced lymphocyte activation pathways in CS-exposed Hhip+/- vs. Hhip+/+ mice, which was supported by increased numbers of lymphoid aggregates and enhanced activation of CD8+ T cells after CS-exposure in the lungs of Hhip+/- mice compared to Hhip+/+ mice. Mechanistically, results from PANDA network analysis suggested a rewired and dampened Klf4 signaling network in Hhip+/- mice after CS exposure.   CONCLUSIONS: In summary, HHIP haploinsufficiency exaggerated CS-induced airspace enlargement, which models CS-induced emphysema in human smokers carrying COPD risk alleles at the HHIP locus. Network modeling suggested rewired lymphocyte activation signaling circuits in the HHIP haploinsufficiency state.

overall_design: Total RNA was obtained from the lung tissue of C57BL/6J mice exposed to cigarette smoke (CS) or filtered air (air) for 6 months. Six mice from each of four groups with different genotypes (Hhip+/+ or Hhip+/-) and treatments (air or CS) were randomly chosen for gene expression profiling

first: Taotao

last: Lao

first: Kimberly

last: Glass

first: Weiliang

last: Qiu

first: Francesca

last: Polverino

first: Kushagra

last: Gupta

last: Mancini

first: Linh

last: Vuong

first: Mark

last: Perrella

first: Craig

last: Hersh

first: Caroline

last: Owen

last: Quackenbush

first: Guo-Cheng

last: Yuan

first: Edwin

last: Silverman

first: Xiaobo

last: Zhou


title: Genome wide gene expression analysis BQ.Ncf1.m1J mutated and BQ wild type mice

status: Public on Nov 01 2014

city: Turku

first: Tiina

middle: Kelkka

last: Ilona

address: Tykistökatu 6A

department: Medicity

country: Finland

institute: University of Turku

summary: Whole blood and spleen tissue was collected from naïve untreated mice. We compared the gene expression profiles of naïve autoimmunity prone BQ.Ncf1.m1J mutated mice and wild type BQ mice. The samples from specific pathogen-free animal facility were collected in two sample sets (marked I and II respectively) and the germ-free facility samples (marked GF / germ free) formed the third analyzed batch. The data revealed a pronounced type I interferon signature in the Ncf1.m1J mutated mice housed in both conditions.

overall_design: RNA was isolated and globin removal was performed for all samples. The cells were not stimulated or selected ex vivo.

last: Kelkka

first: Deborah

last: Kienhöfer

first: Markus

last: Hoffmann

first: Marjo

last: Linja

first: Kajsa

last: Wing

first: Outi

last: Sareila

first: Malin

last: Hultqvist

first: Essi

last: Laajala

first: Zhi

last: Chen

first: Paulo

last: Rodriques-Santos

first: Júlia

last: Vasconcelos

first: Esmeralda

last: Neves

first: Margarida

last: Guedes

first: Laura

last: Marques

first: Gerhard

last: Krönke

first: Merja

last: Helminen

first: Leena

last: Kainulainen

first: Peter

last: Olofsson

first: Harri

last: Lähdesmäki

first: Sirpa

last: Jalkanen

first: Riitta

last: Lahesmaa

last: Souto-Carneiro

first: Rikard

last: Holmdahl


title: Genome-wide changes in gene expression during the development and after recovery from heart failure in a mouse model of transient cardiomyopathy.

status: Public on Nov 03 2014

city: Baltimore

first: Andreas

middle: Sebastian

last: Barth

state: MD

address: 720 Rutland Ave.

department: Medicine, Division of Cardiology

country: USA

institute: Johns Hopkins University

summary: Altered myocardial gene expression from heart failure (HF) has mostly been identified by single-point analysis of end-stage disease.  This may miss earlier changes in gene expression that are transient and/or directionally opposite to those observed later. By sampling left ventricular myocardial tissue at different time points in a mouse model of cardiomyopathy, we examined differentially expressed transcripts between non-failing controls, early-HF (2 and 3 days after cardiac insult), peak-HF (10 days) and after recovery from HF (28 days). As a results, we found that gene expression followed varying patterns:  Downregulation of metabolic pathways occurred early and was sustained into late stage-HF. In contrast, most signaling pathways undergo a complex biphasic pattern: Calcium signaling, p53, apoptosis and MAP-kinase pathways displayed a bi-directional response, declining early but rising late, while NF-κB-related transcription displayed the opposite pattern. The HF-induced transcriptomic changes were reversed after recovery at 28 days. We conclude that the myocardial transcriptome in evolving HF displays distinct and dynamic transcript clusters. Therapies targeting different phases of HF should consider these dynamic features when identifying high-value targets.

overall_design: Mice expressing mutated estrogen receptor-coupled Cre under transcriptional control of cardiac-specific myosin heavy chain (MerCreMer, MCM, 005650;Jackson Laboratories, Bar Harbor, ME) were back-crossed for >10 generations with C57Bl6/J.  Transient cardiomyopathy develops in these mice following 5 day exposure to tamoxifen free base (T5648, Sigma), with peak dysfunction at day 10 and full recovery after 4 weeks.  Full transcriptome analyses were generated from flash-frozen left ventricular myocardium at different time points (control = baseline, day 2, day 3, day 10, and day 28).

middle: S

first: Janelle

last: Rowell

first: David

middle: A

last: Kass


title: Uncoupling Malt1 threshold function from paracaspase activity results in destructive autoimmune inflammation

status: Public on Oct 27 2014

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

summary:
The paracaspase Malt1 is a central regulator of antigen receptor signaling that is frequently mutated in human lymphoma. As a scaffold, it assembles protein complexes for NF-kB activation, and its proteolytic domain cleaves negative NF-kB regulators for signal enforcement. Still, the physiological functions of Malt1-protease are unknown. We demonstrate that targeted Malt1-paracaspase inactivation induces a lethal inflammatory syndrome with lymphocyte-dependent neurodegeneration in vivo.
Paracaspase activity is essential for regulatory T-cell and innate-like B-cell development, but it is largely dispensable for overcoming Malt1-dependent thresholds for lymphocyte activation. In addition to NF-kB inhibitors, Malt1 cleaves an entire set of mRNA stability regulators, including Roquin-1, Roquin-2 and Regnase-1, and paracaspase inactivation results in excessive IFNγ production by effector lymphocytes that drives pathology.
Together, our results reveal distinct threshold and modulatory functions of
Malt1 that differentially control lymphocyte differentiation and activation pathways and demonstrate that selective paracaspase blockage skews systemic immunity towards destructive autoinflammation.

overall_design: Total RNA obtained from T cells with (1h and 4 h) and without stimulation, 3 biological replicates, 3 genotypes (Malt+/-, Malt-/-, MaltPM/-)

first: Beckers

last: Johannes

first: Horsch

last: Marion


title: The probiotic mixture VSL#3 has differential effects on intestinal immune parameters in healthy female BALB/c and C57BL/

status: Public on Oct 23 2014

city: Leiden

first: Rob

last: Mariman

address: Zernikedreef 9

country: Netherlands

institute: TNO

summary:
Probiotic bacteria may render mice resistant to the development of various inflammatory and infectious diseases. This study aimed to identify underlying mechanisms by which probiotic bacteria may influence intestinal immune homeostasis in non-inflammatory conditions.
To this end, we studied the effect of short term (3 days) and long term (28 days) oral administration of VSL#3, a mixture of 8 probiotic bacteria, to healthy BALB/c and C57BL/6 mice, with dominant humoral or cellular immunity, respectively.
Long-term treatment with VSL#3 resulted in an increase of B cells and a decrease of CD4+ T cells in the Peyer’s patches (PP) and mesenteric lymph nodes (MLN) of both mouse strains, compared to untreated mice. However, genome wide gene expression profiling using micro-arrays revealed that prolonged administration of VSL#3 to BALB/c and C57BL/6 mice was associated with host-specific modulation of gene expression in colon and small intestine. Whereas VSL#3 treatment resulted in down-regulation of Il13 and Epx, and up-regulation of Il12rb1, Ccr5, Cxcr3 and Cxcl10 in BALB/c mice, such effects were not observed in C57BL/6 mice. In BALB/c mice, a 2-fold increase in CD103+ CD11c+ dendritic cells was found both in PP and in MLN, 18 hours after the first treatment with VSL#3. Prolonged treatment with VSL#3 was associated with increased numbers of Th17 cells and Foxp3+ regulatory T cells in the MLN of these mice. In conclusion, these experiments in healthy mice show that probiotic bacteria may alter the immunological phenotype of the host; the nature of these effects is dependent on mouse strain.
In conclusion, these experiments in healthy mice show that probiotic bacteria may alter the immunological phenotype of the host; the nature of these effects is dependent on mouse strain.

overall_design: 40 samples (4 experimental groups, 5 biological replicates), performed in two inbred mice strains


title: Mutant p53 in fallopian tube epithelium and high-grade serous cancer formation

status: Public on Oct 25 2014

city: Chicago

first: Joanna

last: Burdette

state: IL

address: 900 S. Ashland Ave

institute: University of Illinois at Chicago

summary:
Ovarian cancer is the fifth leading cause of cancer death among US women.  Evidence supports the hypothesis that high-grade serous ovarian cancers (HGSC) may originate in the distal end of the fallopian tube.  Although a heterogeneous disease, 96% of HGSC contain mutations in p53.  In addition, the “p53 signature”, or overexpression of p53 protein (usually associated with mutation), is a potential precursor lesion of fallopian tube derived HGSC suggesting an essential role for p53 mutation in early serous tumorigenesis. To further clarify p53-mutation dependent effects on cells, murine oviductal epithelial cells (MOE) were stably transfected with a construct encoding for the R273H DNA binding domain mutation in p53, the most common mutation in HGSC. Mutation in p53 was not sufficient to transform MOE cells, but did significantly increase cell migration.  A similar p53 mutation in murine ovarian surface epithelium (MOSE), another potential progenitor cell for serous cancer, was not sufficient to transform the cells nor change migration suggesting tissue specific effects of p53 mutation.  Microarray data confirmed expression changes in pro-migratory genes in p53R273H MOE compared to parental cells, which could be reversed by suppressing Slug expression.  Combining p53R273H with KRASG12V activation caused transformation of MOE into high-grade sarcomatoid carcinoma when xenografted into nude mice.  Elucidating the specific role of p53R273H in the fallopian tube will improve understanding of changes at the earliest stage of transformation and could help develop chemopreventative strategies to prevent the accumulation of additional mutations and reverse progression of the “p53 signature” thereby, improving survival rates.
We used a microarray to determine global changes in gene expression as a result of the p53 mutation specifically in mouse oviductal epithelium.

overall_design: Murine oviductal cells (MOE) were obtained from Dr. Barbara Vanderhyden at the University of Ottawa.  Stable cell lines were generated using antibiotic resistant plasmids containing p53 R273H (Addgene, plasmid: 16439, donated by Dr. Vogelstein, Johns Hopkins University school of Medicine, Baltimore, MD) or pCMV-Neo (Origene PCMV6XL4, Rockville, MD).  Total RNA was extracted from cell pellets collected from consecutive passages.

first: Suzanne

middle: M

last: Quartuccio

first: Subbulakshmi

last: Karthikeyan

first: Sharon

middle: L

last: Eddie

first: Daniel

middle: D

last: Lantvit

first: Eoghainín

last: Ó hAinmhire

first: Dimple

last: Modi

middle: E


title: Intrinsic regenerative potential of murine cochlear supporting cells

status: Public on Oct 22 2014

city: Stanford

first: Byron

middle: H

last: Hartman

state: CA

address: 300 Pasteur Drive Edwards R219

department: Otolaryngology - Head and Neck Surgery

institute: Stanford University School of Medicine

summary: P3 Math1-nGFP mouse cochlear sensory epithelia, consisting of greater and lesser epithelial ridges (GER & LER) including the organ of Corti with nGFP-positive hair cells, were dissected, dissociated into single cells, and labeled with propidium iodide and  three CD marker antibodies. The cell suspension was subjected to FACS purification. 83.6 ±2.8% of the total input of cells were viable, determined by exclusion of propidium iodide. Only viable cells were collected into 5 distinct populations: GFP+ cells (Samples HC_A-D), GFP−/CD271High (Samples Mac_A-C), as well as GFP−/CD271Low/CD326+/CD146Low (Samples SC_A-B), GFP−/CD271Low/CD326+/CD146Hig (Samples GER_A-B), and GFP−/CD271Low/CD326− (Sample BM_B).  Please see Sinkkonen et al 2011 PMID: 22355545

overall_design: Total RNA was isolated from 5 different FACS sorted cell poulations from P3 Math1-nGFP cochlea.

first: Stefan

last: Heller


title: The effect of HDAC inhibitor, 4b, on skeletal muscle gene expression

city: Los Angeles

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

summary: To assess the effects of histone deacetylase (HDAC) inhibitor, HDACi 4b, treatment on muscle function on a molecular level, we performed microarray analysis on skeletal muscle (gastrocnemius) samples from wt and N17182Q mice treated with the HDAC inhibitor 4b for 3 months (50 mg/kg; s.c. injection 3x weekly; n=4 per group).  The transcriptome pattern in N17182Q mice compared to wt controls consisted of deficits in the expression of genes related to mitochondrial function and oxidative metabolism.  In addition, we noted that numerous genes associated with basal contractile function were altered in HD N17182Q mice.  These include genes related to the muscle contractile complex, Tnnt3 and Myh8, as well as several additional myosin genes: myosin heavy chain genes, Myh10 and Myh4, and myosin light chain genes, Myl1, Mylc2 and Mylk.  These findings implicate deficits in the underlying contractile function in skeletal muscle from HD mice.  Further, we found robust effects of 4b treatment on the expression of genes in skeletal muscle, with 556 genes showing significantly altered expression, at p<0.005, in 4b-treated N17182Q muscle compared to vehicle-treated control mice.

overall_design: n=4 vehicle-treated WT mice, n=5 HDACi 4b-treated WT mice, n=4 vehicle-treated N17182Q transgenic mice,  and n=3 HDACi 4b-treated N17182Q transgenic mice.

first: Haiqun

last: Jia

first: Elizabeth

last: Thomas


title: Leukemia dynamics and heterogeneity traced by barcoding in a pre-clinical Cbx7 mouse model

status: Public on Oct 01 2014

city: Groningen

first: Leonid

last: Bystrykh

state: Groningen

address: A. Deusinglaan 1

department: European Research Institute for the Biology of Ageing - ERIBA

institute: University Medical Center Groningen

summary: Gene expression analysis of different leukemia types after overexpression of Cbx7 in mice hematopoietic stem and progenitor cells followed by transplantation. Mice developed three different types of leukemia, 1) erythroid, 2) T-cell, 3) undifferentiated, as shown in K.Klauke et al. Nat Cell Biol 2013

overall_design: Total RNA obtained from spleen cells (unsorted) was extracted

first: Karin

last: Klauke

first: Mathilde

last: Broekhuis

first: Ellen

last: Weersing

first: Bertien

last: Dethmers-Ausema

first: Martha

last: Ritsema

first: Marta

last: Vilà González

first: Erik

last: Zwart

first: Gerald

last: de Haan


title: Brown adipose tissue from WT and SIRT1tg mice

status: Public on Oct 15 2014

city: Lausanne

first: Marie

last: Boutant

address: EPFL Innovation Park, Bâtiment G

country: Switzerland

institute: Nestle Institute of Health Sciences

summary: SIRT1 is a NAD+-dependent protein deacetylase. SIRT1 plays key roles in metabolic regulation and adaptation. In this study, we examined the difference of gene expression in brown adipose tissue from WT and SIRT1tg mice.

overall_design: SIRT1 transgenic model (heterozygous transgenic model) has already been described (Pfluger et al., 2008). Here we used homozygote transgenic mice which had been backcrossed to C57Bl/6N background. 3 months old WT and SIRT1tg mice were fed with a low fat diet. After sacrifice, total mRNA obtained from brown adipose were used for microarray.

first: Carles

last: Cantó

first: Frederic

last: Raymond

first: Sylviane

last: Metairon


title: Mice lacking DUF1220 protein domains are hyperactive  and show reduced fecundity

status: Public on Sep 22 2014

first: Martin

last: Irmler

summary: Sequences encoding DUF1220 protein domains show the most extreme human lineage-specific copy number increase of any coding region in the genome and have been linked to human brain evolution. In addition, DUF1220 copy number (dosage) has been implicated in influencing brain size within the human species, both in normal populations and in individuals associated with brain size pathologies (1q21-associated microcephaly and macrocephaly).  More recently, increasing dosage of a subtype of DUF1220 has been linked with increasing severity of the primary symptoms of autism. Despite these intriguing associations, a function for these domains has not been described. As a first step in addressing this question we have developed the first transgenic model of DUF1220 function by removing the single DUF1220 domain (the ancestral form) encoded in the mouse genome. While resulting DUF1220-minus (KO) mice show no obvious anatomical peculiarities, they exhibit a significantly reduced fecundity (χ2= 19.1, df = 2, p = 7.0 x 10-5). Further extensive phenotypic analyses suggest that DUF1220 KO mice are hyperactive (p < 0.05) relative to wild type litter mates. The linking of DUF1220 loss to a hyperactive phenotype is consistent with separate findings in which DUF1220 over expression results in a down-regulation of mitochondrial function, suggesting a possible role in the prolongation of developmental processes (neoteny) that is most pronounced in the human lineage.

overall_design: Total RNA obtained from brain of 3 male homozygous Duf1220 ko and 4 male wildtype mice

first: Johannes

last: Beckers

first: Marion

last: Horsch


title: B lymphoma from TRAF3-deficient mice

status: Public on Sep 11 2014

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

summary: Spleen samples with B lymphoma from TRAF3 knockout mice compared with littermate controls

overall_design: 3 lymphoma samples, 4 control samples

middle: P

first: Ping

last: Xie


title: microRNA (miRNA) expression profiling of A549 with H5N1 Influenza A Virus (hm/06)infection

status: Public on Sep 25 2014

city: Wuhan

first: Zhao

middle: Lian

last: Zhong

address: Shizishan Street

country: China

institute: Huazhong Agriculture University

summary: To study miRNA expression profiles during highly pathogenic avian influenza  virus infection, we conducted global miRNA expression profiling in human lung epithelial cells (A549) with or without H5N1 IAV infection. .

platform_organism:
Homo sapiens
Human alphaherpesvirus 1
Human betaherpesvirus 5
Lymphocryptovirus
Human immunodeficiency virus 1
Betapolyomavirus macacae

overall_design: Total RNA was prepared from uninfected and hm/06-infected A549 cells.The involved labelling, hybridization, scanning, normalization, and data analysis steps were performed with Exiqon miRNA arrays

first: Zhou

last: Hongbo

first: Zhu

last: Jiping

last: Lianzhong


title: SIRT1 deficiency in microglia contributes to cognitive decline in aging and neurodegeneration via epigenetic regulation of IL-1beta

first: Giovanni

last: Coppola

summary: Aging is the predominant risk factor for neurodegenerative diseases. One key phenotype as brain ages is the aberrant innate immune response characterized by proinflammation. However, the molecular mechanisms underlying aging-associated proinflammation are poorly defined. Whether chronic inflammation plays a causal role in cognitive decline in aging and neurodegeneration has not been established. Here we established a mechanistic link between chronic inflammation and aging microglia, and demonstrated a causal role of aging microglia in neurodegenerative cognitive deficits. Expression of microglial SIRT1 reduces with the aging of microglia. Genetic reduction of microglial SIRT1 elevates IL-1β selectively, and exacerbates cognitive deficits in aging and in transgenic mouse models of frontotemporal dementia (FTD). Interestingly, the selective activation of IL-1β transcription by SIRT1 deficiency is likely mediated through hypomethylating the proximal promoter of IL-1β. Consistent with our findings in mice, selective hypomethylation of IL-1β at two CpG sites are found in normal aging humans and demented patients with tauopathy. Our findings reveal a novel epigenetic mechanism in aging microglia that contributes to cognitive deficits in neurodegenerative diseases.

overall_design: Study of changes related to alterations of SIRT1 levels in microglia of young and aged animals and in models of neurodegenerative dementia

first: Seo-Hyun

last: Cho

first: Jason

last: Chen

first: Michael

last: Ward

first: Fuying

last: Gao

first: Grietje

last: Krabbe

first: Peter

last: Sohn

first: Iris

last: Lo

first: Sakura

last: Minami

first: Nino

last: Devidze

first: Yungui

last: Zhou

first: Li

last: Gan


title: Genome-wide expression profiling analysis of the Ali35 mutant mouseline carrying a mutation in the Shc2 gene

status: Public on Sep 01 2014

first: Martin

last: Irmler

summary: Analysis of changes on gene expression levels in brain and bone for the linkage to phenotypical alterations found in behavior, neurology, nociception, bone remodelling and development.

overall_design: Total RNA isolated from bone and brain of Ali35 mutant mice compared to wildtype controls

first: Marion

last: Horsch

first: Gerhard

last: Przemeck

first: Johannes

last: Beckers

first: Yasunari

last: Matsuzaka


title: Translation initiation at a non-AUG start codon for mouse and human NELF-B

status: Public on Oct 11 2014

city: San Antonio

first: Haihui

last: Pan

state: Texas

address: 8403 Floyd Curl Dr.

department: Molecular Medicine

institute: University of Texas Health Science Center at San Antonio

summary: Negative elongation factor (NELF), a four-subunit protein complex in metazoan, plays an important role in regulating promoter-proximal pausing of RNA polymerase II (RNAPII).  Genetic studies demonstrate that the B subunit of mouse NELF (NELF-B) is critical for embryonic development and homeostasis in adult tissue.  We report here that both human and mouse NELF-B proteins are translated from a non-AUG codon upstream of the annotated AUG.  This non-AUG codon sequence is conserved in mammalian NELF-B but not NELF-B orthologs of lower metazoan.  The full-length and a truncated NELF-B that starts at the first AUG codon interact with the other three NELF subunits with comparable efficiency.  Furthermore, these two forms of NELF-B have a similar impact on the transcriptomics and proliferation of mouse embryonic fibroblasts.  These results strongly suggest that additional amino acid sequence upstream of the annotated AUG is dispensable for the essential function of NELF in supporting cell growth in vitro.  While the majority of mouse adult tissues surveyed exclusively express the full-length NELF-B protein, mouse kidney only contains a truncated NELF-B protein with the same apparent size as the AUG-initiated version.  This result raises the distinct possibility that translational initiation of mouse NELF-B is regulated in a tissue-dependent manner.

overall_design: triplicates for ATG-Nelf-B, triplicates for FL-Nelf-B

first: Rong

last: Li

first: Jian-Bing

last: Fan

first: Yanfen

last: Hu


title: Gene expression analysis of DBC1 KO B cells

status: Public on Sep 04 2014

first: Sin Yi

last: Kong

address: 300 E Chicago

department: pathology

institute: Northwestern University

summary: DBC1 KO B cells were either unstimulated, activated with anti-IgM, anti-CD40 of LPS for 4 hours. Genes differentially expressed in DBC1 KO B cells were compared to WT B cells.

overall_design: RNA was collected from unstimulated for stimulated B cells, and gene expression between WT and DBC1 KO B cells were compared

first: Sin

middle: Y


title: Jag1K295*/+ as a mouse model for Alagille syndrome

summary: A new mouse mutant was identified at the Munich ENU mutagenesis project due to hyperactivity, head tossing, and circling behaviour. Neurological and gross morphological phenotyping of these mutant mice revealed impairment of the vestibular system. Using whole genome exome sequencing and a custom-made variant calling pipeline, we identified the causative mutation as an A->T substitution on the chromosome 2 at the position 128 in the exon 6 of jagged 1 (Jag1) gene. This introduces a premature termination codon at the position 883 of the cDNA. In humans, mutations in the JAG1 gene are associated with Alagille syndrome (ALGS1 ), a multisystem developmental disorder mainly affecting small bile ducts in the liver, but also heart, skeleton, and eyes, and occasionally also kidney or inner ears. Further examination of the Jag1K295*/+ mutant mouse line disclosed multiorgan deficiencies, such as cardiac liver congestion, bile duct hypoplasia, mild nephropathy, subvalvular hypertrophy of the right ventricle, and mild growth retardation. No skeletal abnormalities could be detected. In summary, we report a novel mouse model for Alagille syndrome, Jag1K295*/+, which resembles most of the features of the mild form of Alagille syndrome observed in patients.

overall_design: Total RNA obtained from liver of 4 male heterozygous Jag1K295*/+ and 4 male wildtype mice


title: Analysis of microRNA expression profile in malignant glioma tissues

status: Public on Sep 26 2014

city: Warsaw

first: Magdalena

last: Łój

address: Nowoursynowska 166

department: Department of Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences

summary: Malignant gliomas represent the most devastating group of brain tumors in adults, among which glioblastoma multiforme (GBM) exhibits the highest malignancy rate. Despite combined modality treatment, GBM recurs and is invariably fatal. A further insight into molecular background of gliomagenesis is required to improve patient outcome. The first aim of this study was to gain broad information on miRNA expression pattern in malignant gliomas, mainly GBM. We investigated the global miRNA profile of malignant glioma tissues by means of miRNA microarrays, deep sequencing and meta-analysis. We selected miRNAs the most frequently deregulated in glioblastoma tissues as well as peritumoral brain areas in comparison to normal human brain. We found candidate miRNAs contributing to progression from gliomas grade III to gliomas grade IV. The meta-analysis of miRNA profiling studies in GBM tissues summarizes the past and recent advances in an investigation of miRNA signature in GBM versus noncancerous human brain and provides a comprehensive overview. We proposed a set of 35 miRNAs which expression is the most frequently deregulated in GBM patients and 30 miRNA candidates recognized as novel GBM biomarkers.

overall_design: miRNA expression profile in the adult malignant gliomas, glioma peritumoral tissues and normal human brain.

first: Monika

last: Piwecka

first: Katarzyna

last: Rolle

last: Hulanicka

first: Mirosława

middle: Z

last: Naskręt-Barciszewska

first: Jan

last: Barciszewski


title: Gene (mRNA) expression profiling in frontal cortex of ethanol-treated mice

status: Public on Aug 24 2014

first: Yury

middle: O.

last: Nunez

state: TX

address: 7703 Floyd Curl Drive MC6220

department: Pharmacy

institute: University of Texas at Austin

summary: Analysis of early stages of alcohol dependence at the gene expression level. The hypothesis tested in the present study was that ethanol-treatment impact gene expression in a mouse model of high ethanol consumption. Results provide important information of genes and pathways being affected by ethanol actions in the mouse frontal cortex.

overall_design: Total RNA obtained from frontal cortex from mice treated with 20% ethanol solution for 20 days. Control group is composed of untreated animals. Frontal cortex (FCtx) tissue was dissected to produce a 2-mm coronal section from the most rostral portion of the mouse brain devoid of olfactory bulbs (coordinates Bregma +1.56 to +3.56). The dorsal part of this coronal section, cut immediately above the forceps minor of the corpus callosum as the anatomical landmark, was used for RNA extraction. This section of the cortex is mostly composed of frontal associated cortex (FrA), cingulate cortex area 1 (Cg1), prelimbic cortex (PrL), and primary (M1) and secondary (M2) motor cortices, as depicted in the mouse brain atlas (Franklin and Paxinos 2007). Samples from both alcohol-treated and control groups were always included in each batch of extracted RNA. Total RNA was extracted using the mirVana® miRNA Isolation kit (Ambion, Austin, TX) according to the manufacturer’s instructions. Yield and quality of the total RNA preparation was determined using the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA). For mRNA expression profiling, biotin-labeled cRNA was prepared using Illumina TotalPrep RNA Amplification kit (Ambion, Austin, TX) and then hybridized to Illumina MouseRef-8 v2.0 Expression BeadChips (Illumina, San Diego, CA). The quality of the Illumina bead summary data was assessed using the Bioconductor packages Lumi and arrayQualityMetrics. Data preprocessing included variance stabilization and quantile normalization using the Lumi package. Statistical analysis comparing ethanol-treated and control groups was performed using the Bioconductor package limma, which implements an empirical Bayes approach in R (Smyth 2005). False discovery rate (FDR) was assessed using the Benjamini-Hochberg method.

middle: O

first: Jay

last: Truit

first: Giorgio

last: Gorini

first: Olga

middle: N

last: Ponomareva

first: Yuri

last: Blednov

first: R

last: Harris

last: Mayfield


title: ENU derived mouse line AEA001: A model for osteoporosis carrying a mutation in Ednra

first: Martin

last: Irmler

summary: Transcriptome analysis of white adipose tissue and bone (femur of the hind limbs) of the AEA001 mutant mouse. ENU generated mouse lines for osteoporosis. The mutation in the Ednra gene causes big ears and a flat short head. Due to a decreased body mass and a trend towards decreased glucose level white adipose tissue was analysed.

overall_design: Total RNA obtained from 4 male mutant mice was compared to 4 controls.

first: Johannes

last: Beckers

first: Sibylle

last: Wagner

first: Marion

last: Horsch


title: Commensal bacteria protect against food allergen sensitization

status: Public on Aug 15 2014

first: Cathryn

last: Nagler

address: 924 E 57th St

institute: University of Chicago

summary:
Analysis of colonic epithelial cell gene expression in germ-free, Bacteroides uniformis-colonized, and Clostridia-colonized gnotobiotic mice.
Bacteria were isolated from our SPF mouse facility and were used to selectively colonize germ-free mice.

overall_design: Germ free mice were left germ free or were colonized with Bacteroides uniformis or a consortium of Clostridia. Total RNA was extraced from colonic epithelial cells.

first: Andrew

middle: T

last: Stefka

middle: R

first: Taylor

last: Feehley


title: Identification of eQTLs for Hepatic Xbp1s and Socs3 Gene Expression in Mice fed a High-Fat, High Caloric Diet

status: Public on Aug 02 2014

first: Richard

last: Green

address: 675 N Saint Clair

summary: Non-alcoholic fatty liver disease (NAFLD) is a highly prevalent form of hepatic disease and feeding mice a High-Fat, High-Caloric (HFHC) diet is a standard model of NAFLD. In order to better understand the genetic basis of NAFLD, we conducted an expression quantitative trait locus (eQTL) analysis of mice fed a HFHC diet. 265 (A/J × C57BL/6J) F2 male mice were fed a HFHC diet for 8 weeks. QTL analysis was utilized to identify genomic regions that regulate hepatic gene expression of Xbp1s and Socs3. We identified two overlapping loci for Xbp1 and Socs3 on Chr 1 (164.0-185.4 Mb and 174.4-190.5 Mb, respectively) and Chr 11 (41.1-73.1 Mb and 44.0-68.6 Mb, respectively), and an additional locus for Socs3 on Chr 12 (109.9-117.4 Mb). C57BL/6J-Chr 11A/J/ NaJ mice fed a HFHC diet manifested the A/J phenotype of increased Xbp1s and Socs3 gene expression (p<0.05), while C57BL/6J-Chr 1A/J/ NaJ mice retained the C57BL/6 phenotype. In addition, we replicated the eQTLs on Chr 1 and 12 (LOD scores ? 3.5) using mice from the BXD murine reference panel challenged with CCl4 to induce chronic liver injury and fibrosis. We have identified overlapping eQTLs for Xbp1 and Socs3 on Chr 1 and 11, and consomic mice confirmed that replacing the C57BL/6 with the A/J Chr 11 resulted in an A/J phenotype for Xbp1 and Socs3 gene expression. Identification of the genes for these eQTLs will lead to a better understanding of the genetic factors responsible for NAFLD and potentially other hepatic diseases.

overall_design: Liver samples from eight-week-old AJ and C57BL6J males fed a High Fat High Calorie diet.


title: Characterising Host Gene Expression during the Recovery from Hepatic Schistosomiasis Japonica

status: Public on Aug 31 2014

city: Brisbane

first: Geoffrey

last: Gobert

address: 300 Herston Rd

country: Australia

institute: QIMR

summary: In schistosomiasis japonica, the egg-induced granulomatous response and the development of extensive hepatic fibrosis is the main pathology. Information regarding the specific mechanisms associated with granuloma regression and the subsequent recovery events in the host liver are still limited. In this study, a murine model of schistosomiasis japonica was used to characterise the multicellular pathways occurring during liver regeneration. Schistosoma japonicum-infected C57BL/6 mice were administered with the drug praziquantel (PZQ), on a daily basis for five consecutive days to eliminate all adult parasites. The pathological changes of PZQ-treated groups after 3, 6 and 7 weeks post PZQ treatment were examined, along with the assessment of cellular infiltration to the liver. PZQ treatment significantly reduced the degree of splenomegaly, granuloma density and the collagen deposition of liver fibrosis. The infiltration of inflammatory cells, including neutrophils, eosinophils and macrophages to the liver were as well significantly decreased. Transcriptomic analysis revealed the significant up-regulation of fatty acid metabolism genes and the identification of peroxisome proliferator-activated receptor alpha (PPAR-α) as the upstream regulator during the process of liver recovery. Aryl hydrocarbon receptor (AhR) signalling pathway that is involved primarily in the regulation of hepatic enzymes responsible for xenobiotic metabolism was as well differentially up-regulated. These findings indicate that schistosome egg-induced fibrogenesis process is reversible, and provide a better understanding of the regression mechanisms associated with hepatic schistosomiasis. These results hold important implications for the future alleviation of this and other fibrotic diseases of clinical significance.

overall_design: C57BL/6 murine model infected with S. japonicum were treated orally with Praziquantel (PZQ) after 7 weeks post infection to examine the hepatic regression process following drug treatment. These PZQ-treated, non PZQ-treated and uninfected mice were then euthanised at 10, 13, and 14 weeks p.i. Livers were collected from each mice, and subjected to total RNA isolation and gene expression analysis. Microarray analysis of this study was performed using samples derived from 3 individual mice per group/time-point.

first: Candy

last: Chuah

first: Malcolm

middle: K

last: Jones

first: Melissa

last: Burke

first: Helen

last: Owen

first: Donald

last: McManus

first: Grant

last: Ramm


title: Critical requirement of ERK/MAPK signaling in respiratory tract development

status: Public on Sep 02 2014

first: Eric

last: Paquet

state: Vaud

address: Station 15  CH - 1015

department: Life sciences

institute: EPFL

summary: The mammalian genome contains two ERK/MAP kinase kinase genes, Mek1 and  Mek2, which encode dual-specificity kinases responsible for ERK/MAP kinase  activation. To define the function of ERK/MAPK signaling pathway in lung  development, we performed tissue-specific deletions of Mek1 function in a Mek2 null  background. Inactivation of both Mek genes in mesenchyme resulted in several  phenotypes including giant omphalocele, skeletal defects, pulmonary hypoplasia,  abnormal trachea patterning, and death at birth. Microarray analysis with RNA extracted from lungs of E15.5 Dermo1+/Cre, Mek1+/flox;Mek2-/-;Dermo1+/Cre and Mek1flox/flox;Mek2-/-;Dermo1+/Cre embryos was performed to evaluate the molecular impact of the loss of all Mek alleles in mesenchyme on lung development. .

overall_design: Total RNA was isolated from lungs of E15.5 Dermo1+/Cre embryos (control), from E15.5 Mek1+/flox;Mek2-  /-;Dermo1+/Cre embryos (experimental) and from E15.5 Mek1flox/flox;Mek2-/-;Dermo1+/Cre embryos (experimental). Four specimens were analyzed per genotype.

first: Lucie

last: Jeannotte

first: Jean

last: Charron

first: Olivier

last: Boucherat


title: PGC-1α mediates mitochondrial biogenesis and oxidative phosphorylation in cancer cells to promote metastasis

status: Public on Sep 23 2014

city: Houston

first: Valerie

last: LeBleu

address: 1881 East Road

institute: MDACC

summary: The study aimed to analyse the transcriptome of mouse cancer cells while in primary tumor, in circulation and after homing to metastatic site. The model used here is the 4T1 cancer cell orthotopic model.

overall_design: GFP-labeled 4T1 breast cancer cells were orthotopically implanted in the mammary pads of mice. In this mouse model for breast cancer, primary breast tumors emerge following injection of cancer cells in the breast pad of female mice and subsequently develop lung metastases with 100% penetrance. Circulating cancer cells (CCC) and cancer cells from the primary tumors (PCC) and metastatic lungs (MCC) were FACS purified and their transcriptome assayed by gene expression microarray. RNA was extracted from PCC, MCC, and CCC using RNeasy Plus Mini Kit (Qiagen) and submitted to the Molecular Genetics Core Facility at Children’s Hospital (Boston, MA). Microarray analysis was performed using Mouse Ref8 Gene Expression BeadChip (Illumina platform).

first: Raghu

last: Kalluri


title: Microarray analysis of gene expression profiles in Map2k1+/-Map2k2+/- and Map2k1flox/-Map2k2+/-Tg+/Sox2Cre placentas

status: Public on Aug 01 2014

summary: The mammalian genome contains two ERK/MAP kinase kinase genes, Map2k1 and Map2k2, encoding dual-specificity kinases responsible for ERK/MAP kinase activation. Loss of Map2k1 function in mouse causes embryonic lethality due to placental defects, while Map2k2 mutant mice survive with a normal lifespan. The Map2k1 mutation interferes with the growth of the labyrinthine region of the placenta and its vascularization. Map2k1+/-Map2k2+/- embryos also die during gestation of underdevelopment of the labyrinth. In Map2k1+/-Map2k2+/- mutants, the vascularization of the labyrinth is reduced and defects in SynT-II formation lead to the accumulation of multinucleated trophoblasts giant cells (MTG).  Deletion of both Map2k1 alleles in allantoïs-derived tissues in Map2k1+/ Map2k2+/- placenta (Map2k1flox/-Map2k2+/-Tg+/Sox2Cre) increases the penetrance and the expressivity of the MTG placental phenotype.  Microarray analysis with RNA extracted from placentas of E12.5 wt,  Map2k1+/-Map2k2+/- and Map2k1flox/-Map2k2+/-Tg+/Sox2Cre embryos was performed to evaluate the molecular impact of the loss of  Map2k alleles on placenta development.

overall_design: Total RNA was isolated from placentas of E12.5 Map2k1+/+Map2k2+/+(control), from E12.5 Map2k1+/-Map2k2+/- embryos (experimental) and from E12.5 and Map2k1flox/-Map2k2+/-Tg+/Sox2Cre embryos (experimental). Four specimens were analyzed per genotype.

first: Valérie

last: Nadeau


title: Epigenetic activation of neuronal gene expression by JMJD3 is required for postnatal and adult brain neurogenesis

status: Public on Jul 30 2014

city: SAN FRANCISCO

first: John

last: Liu

state: California

address: 35 Medical Center Way

institute: UCSF

summary: The epigenetic mechanisms that enable lifelong neurogenesis from neural stem cells (NSCs) in the adult mammalian brain are poorly understood.  Here we show that JMJD3, a histone H3-lysine 27 (H3K27) demethylase, acts as a critical activator of neurogenesis.

overall_design: 3 biological replicates of JMJD3 null (P9 UBC-Cre/ERT2;Jmjd3F/F) and 3 biological replicates of littermate controls were used to analyze the effect of JMJD3 deletion on gene expression.

first: Dae

last: Park

first: Daniel

middle: A

last: Lim

first: Siyuan

middle: J


title: REDD1 (regulated in development and DNA damage response 1) dissociates therapeutic and adverse effects of topical steroids in skin

city: Tempe

first: Ben

last: Readhead

state: AZ

address: 797 E. Tyler Street

institute: ASU-Banner Neurodegenerative Disease Research Center

summary: Even though cutaneous atrophy is the major adverse effect of topical glucocorticoids, its molecular mechanisms are poorly understood. We found that glucocorticoids strongly increased the expression of REDD1 (regulated in development and DNA damage response 1), a stress-inducible inhibitor of mTOR, in mouse and human epidermis. We found that REDD1 knockout animals are partially resistant to glucocorticoid-induced epidermal and subcutaneous adipose atrophy which correlated with the protection of CD34+ follicular epithelial stem cells as well as p63+ keratinocyte progenitors in REDD1 knockout epidermis during chronic steroid treatment. At the same time, REDD1 knockout did not affect anti- inflammatory effect of glucocorticoids, as evaluated by ear edema test. Expression profiling revealed that ~ 50% of the glucocorticoid receptor (GR) target genes were not activated in epidermis of REDD1 knockouts, however, the negative effect of glucocorticoids on gene expression was similar to that in w.t. animals. Overall, our findings reveal a novel pathway in GR activation by its target gene/protein REDD1; and indicate an important role of REDD1 in glucocorticoid-induced skin atrophy, and maintenance of the epidermis and subcutaneous adipose. In addition, our findings form the foundation for the development of safer topical glucocorticoid treatment regimens by combining this therapy with REDD1 inhibitors.

overall_design: Seven wk old B6D2 females in the telogen stage of the hair cycle were shaved, and treated 3 days later. Glucocorticoid FA was applied topically (2 ug/animal) in 200 ul acetone to the back skin once or up to four applications every third day as described previously (Chebotaev et al., 2007b). Control animals were treated with acetone only. Skin was harvested 24 h after last FA application or 4-8 h after single FA application as indicated in Figure legends. To evaluate the anti-inflammatory effect of glucocorticoid FA in REDD1 KO and w.t. B6x129 mice, we used ear edema test (Schoepe et al., 2010; Schäcke et al., 2004; Park et al., 2006). Seven wk old female animals were pretreated with FA or vehicle applied to the back of the ear lobe one h before application of nonspecific contact irritant croton oil . Mice were sacrificed and ears were harvested nine hours after CO application, the time point at which we observed maximum ear edema in F1 C57Bl x 129 animals (data not shown). Four mm ear punch biopsies were immediately weighted to assess ear edema. Animals were injected i.p. with bromodeoxyuridine 1 hr before skin was harvested. Total RNA from murine epidermis and whole human skin was isolated with RiboPure kit (Ambion). Total RNA from murine s.c. adipose was isolated with RNeasy Lipid Tissue Kit (Qiagen). The RNA samples were treated with TURBOTM DNase (Ambion). Purity of RNA samples isolated from epidermis and s.c. fat was confirmed by the expression of adipose and keratinocyte cell markers.

first: Irina

last: Budunova


title: The effects of muscular dystrophy, exercise and sActRIIB-Fc on molecular signature of skeletal muscle in mice

status: Public on Oct 13 2014

city: Jyväskylä

first: Juha

last: Hulmi

address: Rautpohjankatu 8a Viv

department: Biology of Physical Activity

institute: University of Jyväskylä

summary:
To study the combined effect of myostatin/activin inhibition and exercise on muscle mass and pathophysiology, young mdx mice, a model for Duchenne Muscular Dystrophy, were injected with soluble activin receptor-Fc (sActRIIB-Fc) or placebo (PBS) 1x/week for a 7-week period, in combination with or without voluntary running. C57Bl/10ScSnJ mice injected with PBS acted as wildtype controls. Microarray expression analysis from skeletal muscle was performed using m. gastrocnemies as the sample.
We found thatexercise or a combination of exercise and sActRIIB-Fc treatment is more effective in correcting gene expression profiles of dystrophic muscles than the sActRIIB-Fc treatment alone. We also identified several pathways and proteins that were affected by exercise and sActRIIB-Fc together or independently.

overall_design:
Total RNA obtained from gastrocnemius muscle of mdx mice divided into four groups:
1) control (injected with PBS, n=5), 2) runners (voluntary wheel running for 7 weeks, injected with PBS, n=5), 3) sActRIIB-Fc -treated (n=5), and 4) runners with sActRIIB-Fc-treatment (n=5).
sActRIIB-Fc or PBS was injected intraperitoneally once a week with a 5-mg/kg dose of sActRIIB-Fc. In addition, wildtype mice served as healthy controls (n=4).

first: Heikki

last: Kainulainen

first: Konstantinos

middle: G

last: Papaioannou

first: Mika

last: Silvennoinen

first: Janne

last: Saarela

first: Bernardo

middle: M

last: Oliveira

first: Miro

last: Nyqvist

first: Arja

last: Pasternack

first: Peter

last: ’t Hoen

first: Urho

last: Kujala

first: Olli

last: Ritvos

first: Reija

last: Autio


title: Gene expression in small intestinal and colonic goblet cells from C57Bl/6 mice

city: ROCHESTER

first: Kathryn

last: Knoop

state: MN

address: 2511 Boulder Ridge Dr NW

department: Internal Medicine, Gastroenterology Division

institute: Mayo Clinic

summary: Microarray analysis of goblet cells isolated from the small intestine or colon was completed to compare the cells between the two parts of the intestine.

overall_design: Total epithelium was isolated from the intestine by incubation in HBSS+0.05% EDTA at 37 C for 15 minutes. Goblet cells were isolated by FACS sorting CD45-CD24-CK18+UEA-I+ cells.

first: Rodney

middle: D

last: Newberry


title: Analysis of classical and migratory DC from the skin draining LNs of Flt3L treated mice and comparison to LPS treated DC from skin draining LN and peritoneal macrophages

city: Boston

first: Niroshana

last: Anandasabapathy

address: 221 Longwood Ave. EBRC 513

department: Department of Dermatology

institute: Brigham and Women’s Hospital

summary: Analysis of the differential transcriptome of DC derived from tissue vs. LN origin. The overall hypothesis is these data would reveal how migratory DC may be differently programmed from classical DC and might also suggest difference within migratory DC subsets relating to function.

overall_design: RNA obtained from migratory DC subsets and classical CD8a DC isolated by flow cytometry sorting from skin draining LNs of Flt3L treated mice or LPS treated mice

first: Ines

last: Matos


title: Functional phenotypes alteration on dendritic cells between tolerance and immnunity

status: Public on Jul 26 2014

city: Seongnam

first: Dae-seog

last: Lim

country: South Korea

institute: CHA medical science University

summary: Dendritic cells (DC) are key regulators of immunological responses, immunity and tolerance. Due to their differentiation capacities, they have emerged as a promising tool for therapeutic applications. However, there are poorly understood functional DC-specific markers and cellular mechanisms for in-vitro research and clinical usage.   This study’s aim is to evaluate the gene expression profiling of  up-regulated or down-regulated by DC maturation and explore their function.   The dendritic cells were prepared using GM-CSF and IL-4 (imDC) and subsequently maturated by adding type II collagen as antigen with LPS (mDC) or TNF-alpha(tDC). Also, surface markers, cytokine profiles, and induction of Treg cell were examined in same DC. Then, transcriptional profile was analyzed by using cDNA microarray and gene clustering programs. The selected genes, marker candidates were validated by using quantitative real-time PCR.   By supervised selection, we identified 75 signitures , which 63 genes were consistently upregulated in mDC and 12 genes  were expressed only in tDC . In addition, we introduced 10 genes overexpressed or equally expressed in both tDC and mDC.  These selected genes were clustered into various functional categories according to GO ontology analysis. Hspa1 and Scin as tDC-specific genes, Orm1, Pdlim4, and Enpp2 as mDC-specific genes were found correlation between microarray data and mRNA expression by qRT-PCR.   This work may contribute to identifying specific modulating markers for mDC and tDC, which could in the future serve as therapeutic targets in the treatment of cancer and autoimmune diseases.

overall_design: Total RNA obtained from isolate Bone-marrow derived Dendritic cell subset, immature DC, semi-mature or tolerogenic DC, and fully mature DC were generated in-vitro, used microarray Chip : Illumina MouseRef-8 v2 Expression BeadChip

first: Dae-Seog

first: Eun

last: Lee

first: Jun-Ho


title: Role of the hypoxia-inducible histone H3K9 methylation regulating enzymes Jmjd1a and G9a in stem cell self-renewal and tumorigenesis

city: Singapore

first: Kian Leong

last: LEE

state: Singapore

address: #07-21, 8 College Road

department: Duke-NUS Medical School

country: Singapore

institute: National University of Singapore (NUS)

summary: Hypoxia is one of the major driving forces mediating tumor angiogenesis, aggressiveness, as well as resistance to chemo- and radiotherapy. It has also been suggested to play important roles in stem cell maintenance for both normal and cancer tissues. However, the mechanisms by which hypoxia-driven epigenetic changes modulate tumorigenesis remain poorly understood. As the histone H3 lysine 9 (H3K9) demethylase Jmjd1a and methyltransferase G9a are upregulated downstream targets of hypoxia, we focused on these two catalytically opposing epigenetic modifiers to address this question. Through the use of homozygous Jmjd1a and G9a knockout mouse embryonic stem (ES) cells, we found that Jmjd1a was not required for stem cell self-renewal and that anti-angiogenesis related genes were epigenetically dysregulated in both Jmjd1a- and G9a deficient ES cells under hypoxic conditions, accompanied by corresponding changes in H3K9 dimethylation and H3K4 trimethylation levels in the proximal promoter regions of these target genes. Most importantly, these genetic alterations led to opposing tumor phenotypes: loss of Jmjd1a results in increased tumor growth, whereas loss of G9a produces smaller tumors. These findings provide new insights on the importance of hypoxia signalling in regulating the epigenetic status and expression of angiogenesis genes that promote tumor progression.

overall_design: 63 microarray samples consisting of 7 mouse ES cell lines of which 2 are wild type (control), 2 Jmjd1a knockout, 2 G9a knockout and 1 G9a knockout that was reconstituted for G9a (G9a control). Each cell line and condition was seeded at 3 different densities (2X10^5, 4X10^5 and 6X10^5) in 6 cm dishes to control for the effects of cell confluency on gene expression. 18 hours after plating, the cells were subjected to normoxia (21% O2) for 24 hours (control), normoxia 20 hours followed by hypoxia (1% O2) for 4 hours (acute hypoxia) and 24 hours hypoxia (chronic treatment). Total RNA was harvested from all samples for microarrays after the 24 hour treatments.

first: Jun

last: Ueda

first: Jolene

middle: C

last: Ho

first: Kian

middle: L

first: Kitajima

last: Shojiro

first: Henry

last: Yang

first: Wen

last: Sun

first: Noriko

last: Fukuhara

first: Norazean

last: Zaiden

first: Shing

last: Chan

first: Makoto

last: Tachibana

first: Yoichi

last: Shinkai

first: Hiroyuki

last: Kato

first: Lorenz

last: Poellinger


title: The Sex-Specific Changes in Gene Expression and Behavior Induced by Chronic Toxoplasma Infection in Mice

status: Public on Jul 28 2014

city: Baltimore

first: JC

last: xiao

address: 600 N. Wolfe Street, Blalock 1109

institute: Johns Hopkins University

summary: The goal of this study was to identify the neural systems that underlie the behavorial changes in intermediate hosts of Toxoplasma gondii.  Using a mouse whole genome microarray, we analyzed gene expression in the frontal cortex during the latent stages of infection.  We found marked sex-dependent effects on gene transcription in mice.  In female mice, Toxoplasma infection altered the expression of genes involved in the development of the forebrain, neurogenesis, sensory and motor coordination.  In male mice, infection led mainly to modulation of genes associated with olfaction. Our results indicate that the gender of the host plays a major role in determining variable brain changes following Toxoplasma infection.

overall_design: Male and female BALB/c mice (infected female: n=5; infected male: n=5; female control: n=5; male control: n=4) were used in this study.  They were sacrificed approximately 6 month post infection and the frontal cortices harvested. RNA transcript levels were quantified by microarray analyses using Illumina Mouse Ref-8 v2.0 Expression BeadChips.

first: Jianchun

last: Xiao

first: Geetha

last: Kannan

first: Lorraine

last: Jones-Brando

first: Christie

last: Brannock

first: Irina

last: Krasnova

first: Jean

last: Lud Cadet

first: Mikhail

last: Pletnikov

first: Robert

middle: H

last: Yolken


title: Gene expression from aged and young sciatic nerve after nerve injury

first: Michio

last: Painter

address: 3 Blackfan Circle

department: Neurobiology

institute: Children's Hospital Boston

summary: Sciatic nerve ligation was performed on cohorts of 2-month and 24-month old animals. Resulting gene-expression data were generated from sciatic nerve 1 and 4 days after injury compared to naïve animals. Results show differences in sciatic nerve responses with normal aging.

overall_design: Total RNA taken from sciatic nerves from 2-month and 24-month old animals at either day 0, 1 and 4 after sciatic nerve crush injury.

first: Clifford

last: Woolf


title: Gene expression from aged and young dorsal root ganglia after nerve injury

summary: Sciatic nerve crush was performed on cohorts of 2-month and 24-month old animals. Resulting gene-expression data were generated from dorsal root ganglia 5 days after injury compared to naïve animals. Results show differences in intrinsic growth responses with normal aging.

overall_design: Total RNA taken from L4 and L5 dorsal root ganglia 5 days after injury 2-month and 24-month old animals at either day 0 or day 5 after sciatic nerve crush injury.


title: Regulatory consequences of TARBP2 knock-down in Dicer-null MEFs

status: Public on Jul 24 2014

city: San Francisco

first: Hani

last: Goodarzi

department: Biochemistry and Biophysics

summary: siRNA-mediated knock-down followed by transcriptomic profiling revealed that silencing of TARBP2 resulted in a significant up-regulation of sRSE-carrying transcripts.

overall_design: Two independent siRNAs were used to knock down TARBP2 in metastatic Dicer-null cells. The cells were then subjected to transcripome profiling in comparison to mock-transfected cells.

first: H

first: S

last: Zhang

first: C

last: Buss

first: L

last: Fish

last: Tavazoie

middle: F


title: Divergent influence of microRNA-21 deletion on murine colitis phenotypes [mRNA]

status: Public on Jul 23 2014

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

summary: Background:  MicroRNAs (miRNAs) acting as negative regulators of gene expression are differentially expressed in intestinal tissues of patients with inflammatory bowel disease (IBD). Assessing the functional role of miRNAs in murine models of colitis facilitates elucidating the role of specific miRNAs in human IBD.  The aim of this study was to determine the miRNA signature of murine models of colitis and to assess the influence of miR-21 on intestinal inflammation.   Methods: miRNAs expression was accessed by microarray for acute and chronic murine model of colitis induced by DSS or TNBS. miR-21-deficient mouse and littermates controls were assessed in the standard DSS, TNBS and CD4+ T cell transfer models of colitis. RNAs of mouse colon and CD4+CD45RBHigh cells were analyzed by miRNA and mRNA microarray, and quantitative RT-PCR. Th1 polarization was accessed by flow-cytometry and ELISA. Results:  Alterations of in miRNAs expression were identified for acute and chronic DSS colitis and TNBS colitis, receptively.  The Expression of miRs-21, -142-3p and -223 was were distinct between DSS and TNBS models while overlap of numerous miRNAs was seen. Importantly, miRs-19b, -192 and -215, that are decreased in IBD, were significantly decreased in all 4 models of colitis. miR-21, which is increased in IBD, was increased in TNBS colitis but not the DSS colitis models.  Further assessment of the miR-21-deficient 1-/- mice revealed that the deletion of miR-21 results in the exacerbation of both the TNBS and T cell-transfer models of colitis.  Conclusions:  miRNAs are differentially expressed in both human IBD and murine colitis, with overlap of several IBD-associated miRNAs.  The demonstration that miR-21 deletion exacerbated CD4+ T cell-mediated models of colitis provides further evidence that miRNAs play significant roles in the pathogenesis of IBD.

overall_design: Gene expression profiles were established for normal miR-21-/- mice and wild type c57BL/6 mice (WT). Total of 6 samples with replicates were included in this study.

first: Feng

last: Wu

first: Fengshi

last: Dong

first: Nicholai

last: Arendovich

first: Jing

last: Zhan

first: John

last: Kwon


title: Overexpression of disease-associated CYFIP1 alters cellular and synaptic morphology through mTOR dysregulation of mTOR signaling

status: Public on Jan 01 2015

city: Los Angeles

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

institute: UCLA

summary: Rare genomic gains at 15q11-q13 are observed in 1-2% of individuals with an Autism Spectrum Disorder (ASD). Because many genes are included here and breakpoints vary between cases, the potential contribution of specific genes is unclear. Cytoplasmic FMR1 interacting protein 1 (CYFIP1) is interesting in this regard given the association of smaller overlapping deletions with each of schizophrenia and intellectual disability. Towards an understanding of how increased CYFIP1 dosage might predispose to neurodevelopmental disease we investigated the consequence of overexpression in multiple systems. We show that CYFIP1 mRNA is increased in lymphoblastoid cells and human brain as a function of 15q dosage. Towards mechanisms, we determined that overexpression of CYFIP1 results in cellular abnormalities in SY5Y cells and mouse neuronal progenitors. Identical abnormalities, as well as anomalies in synaptic morphology, were seen after comparing two BAC transgenic strains to controls. Gene expression profiling at embryonic day 15 identified genes differentially expressed between transgenic and control mice and highlighted dysregulation of mTOR signaling. Finally, treatment of mouse neuronal progenitors with an mTOR inhibitor (Rapamycin) rescued morphologic abnormalities resulting from CYFIP1 overexpression. Together, these data are consistent with the notion that normalization of mTOR signaling, emerging as an important point of convergence in the ASDs, may be of clinical utility in genetically selected populations with a variety of neurodevelopmental disorders.

overall_design: Mice harboring a Cyfip1 spanning BAC clone (RP24-333C15) were generated in the UCLA transgenic core (http://tmc.ctrl.ucla.edu/tg-core/) by injection into C57BL/6J pronuclei. Transgenic mice were identified by PCR screening of tail derived DNA.

first: Asami

last: Oguro-Ando

first: Clark

last: Rosensweig

first: Edward

last: Herman

first: Yuhei

last: Nishimura

first: Donna

last: Werling

first: Brent

last: Bill

first: Jamee

last: Berg

first: Fuying

last: Gao

first: Brett

last: Abrahams

first: Daniel

last: Geschwind


title: Gene expression profiles of NIH3T3 cells stably transfected with the plasmids encoding the wild type PreS/S gene or the nonsense mutant gene (sW182*) of HBV.

city: Miaoli County

first: Shih Sheng

last: Jiang

address: No. 35 Keyan Road, Zhunan County

department: National Institute of Cancer Research

country: Taiwan

institute: National Health Research Institutes

summary: Background and Aims: Whether hepatitis B virus (HBV) could play a direct role in hepatocarcinogenesis remains uncertain. The 3' end nonsense mutations of HBV PreS/S gene have been found to encode transcriptional transactivation activity, suggesting these mutations may contribute to HBV-associated oncogenesis.  Recently, we have identified a potent oncogenic HBV surface (S) gene nonsense mutant sW182*.  Results: Gene expression microarray study revealed that sW182* mutant was significantly enriched by gene sets associated with cell cycle regulation, DNA repair, or genome instability.  The transforming growth factor-induced (TGFBI) gene was downregulated in the sW182* mutant clones, and irresponsive to TGF- treatment. The level of Cyclin D1, a negatively regulated TGFBI target, was highly elevated in sW182* mutant cells.  Exogenous expression of TGFBI alleviated the oncogenic activity of sW182* in mouse xenograft study. In human HBV-related HCC cancerous tissue, expression of TGFBI was downregulated in 25 of the 55 (45%) patients.  Conclusions: Dysregulation of transforming growth factor-induced (TGFBI) gene is involved in the oncogenic activity of the sW182* mutant of hepatitis B virus S gene. This has never been described before.

overall_design: NIH3T3 cells were stably transfected with plasmids encoding the wild type PreS/S gene or the nonsense mutant (sW182*) of HBV PreS/S gene. Totoal RNAs were extracted from those stable clones for gene expression microarray analysis using Illumina MouseRef-8 V2 BeadChip.

first: S

middle: S

last: Huang


title: Divergent influence of microRNA-21 deletion on murine colitis phenotypes

first: Yong

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

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

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Refer to individual Series


title: Microarray analysis of differential gene expression of whole testis extracts from transgenic Musashi-2 and transgenic Musashi-1 over-expression mice

status: Public on Jul 12 2014

city: Callaghan

first: Jessie

last: Sutherland

address: University Drive

institute: University of Newcastle

summary: Analysis of testis-specific over-expression of Musashi-1 and Musashi-2 at gene expression level. The hypothesis tested in the present study was that testis-specific over-expression of Musashi-1/Musashi-2 would result in differential gene expression profiles from the Wildtype control. Results provide important information of the genes affected by Musashi-2 overexpression during spermatogenesis.

overall_design: Total RNA obtained from whole adult testis of transgenic testis-specfic Musashi-1 and Musashi-2 overexpression mice compared to Wildtype (control) littermates. 4 replicates, 16 samples, 2 comparisons: Wt (Musashi-1) vs. TgMsi1 & Wt (Musashi-2) vs. TgMsi2

first: Eileen

last: McLaughlin


title: Genome-wide transcriptome analysis of neuron-enriched DRG cultures exposed to Wnt3a

status: Public on Jul 07 2014

city: Mainz

first: Emil

last: Karaulanov

address: Ackermannweg 4

institute: Institute of Molecular Biology

summary: To test the potential of canonical Wnt signalling to modulate nociception via transcriptional regulation in dorsal root ganglion (DRG) neurons, we performed a genome-wide transcriptome analysis of neuron-enriched DRG cultures treated with Wnt3a or vehicle for 6 hours.

overall_design: Total RNA obtained from neuron-enriched mouse DRG culture subjected to Wnt3a treatment for 6 hours was compared to a matched control (vehicle-treated) DRG culture.

first: Manuella

last: Simonetti

first: Christof

last: Niehrs

first: Rohini

last: Kuner


title: CIRCADIAN RHYTHM REPROGRAMMING DURING LUNG INFLAMMATION/ Microarray Experiment #2

status: Public on Jul 16 2014

city: New Haven

first: Jen-hwa

last: Chu

state: CT

department: Pulmonary, Critical Care and Sleep Medicine

institute: Yale University School of Medicine

summary: In this study we utilized a genome-wide approach to analyze circadian patterns of gene expression in mouse lung lungs, both in the basal state and in the setting of systemic inflammation caused by endotoxemia.  We chose the lung because it represents a primary portal for systemic infection and organ failure in critically ill patients, and because the lung exhibits strong physiological circadian rhythms in health and in diseases such as asthma.  The gene expression the data presented here was correlated to histological observations and metabolite measurements derived from the same biological samples, in order to obtain a broad picture of how inflammation impacts circadian rhythms in mouse lung.

overall_design: To examine circadian regulation in mouse lung we performed 2 independent time-series experiments (Microarray Experiments #1 and #2), in which groups of mice were euthanized at 4 hour intervals for 48 hours.  The purpose of Microarray Experiment #2 was to compare circadian gene expression in healthy lungs (samples labeled with the prefix “NT”) to lungs derived from endotoxemic animals (samples labeled with the prefix “LT”).  For Microarray Experiment #2, 94 mice were placed under constant light conditions (LL 12:12, food ad libitum) at CT12 the prior day (7:00 PM local time). At CT10 (5:00 PM) on the day of the experiment a sub-group of 40 mice received a single intraperitoneal injection of 12 mg/kg E. coli O127:B8 endotoxin (LPS, Sigma L3129, Lot 029K4055), and sample collection began directly after.  3-4 mice per group were sacrificed at consecutive 4 hour intervals for 2-3 days.  The left lung and the right upper lobe were frozen immediately in liquid nitrogen for microarray analysis.  For mRNA isolation lung tissue was immersed in RNAlater (Qiagen) and total RNA was then extracted using the RNeasy Mini Kit (Qiagen).  RNA quality (RIN>=7) was confirmed using an Agilent 2100 Bioanalyzer.  RNA from all biological samples was labeled at once using the Ambion TotalPrep-96 RNA Amplification Kit.  The samples were then blinded, randomized to chip position and hybridized to the Illumina MouseRef-8 v2.0 Expression BeadChips.  For Microarray Experiment #2 at the Channing Division of Network Medicine (Brigham and Women’s Hospital).  Two biological samples (NT00L1 and LT00L1) were represented by 2 technical replicates on the microarray.  The remaining biological samples were represented by a single technical replicate.

first: J

last: Haspel

last: Chettimada

first: R

last: Shaik

first: B

last: Raby

first: M

last: Cernadas

first: V

last: Carey

last: Process

first: G

last: Hunninghake

first: E

last: Ifedigbo

last: Lederer

last: Englert

first: A

last: Pelton

last: Coronata

first: L

last: Fredenburgh

last: Choi


title: CIRCADIAN RHYTHM REPROGRAMMING DURING LUNG INFLAMMATION


title: Axin2/Runx2 mouse calvaria expression

status: Public on Jul 04 2014

city: Rochester

first: Jie

last: Sun

address: 200 First Street SW

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

platform_organism:
Mus musculus
synthetic construct


title: CIRCADIAN RHYTHM REPROGRAMMING DURING LUNG INFLAMMATION/ Microarray Experiment #1

last: Chu

overall_design: To examine circadian regulation in mouse lung we performed 2 independent time-series experiments (Microarray Experiments #1 and #2), in which groups of mice were euthanized at 4 hour intervals for 48 hours.  The purpose of Microarray Experiment #1 was to control for environmental influences (light and nutrition) on the detection of circadian rhythms in gene expression.  In Microarray Experiment #1, 72 mice were segregated equally into 2 equal groups the day prior to the experiment at the beginning of the dark phase (Circadian Time 12 (CT12) or 7:00 PM local time).  In one group (samples labeled with the suffix “MR”) the mice were kept under standard lighting and nutritional conditions (LD 12:12).  In the second group (samples labeled with the suffix “DD”), mice were kept in constant darkness and food pellets were removed from their cages at the start of sample acquisition (DD 12:12+STV).  Sample acquisition commenced at CT4 (or 11:00 AM local time).  For each group 3 animals were sacrificed per time point (12 time points total).  For mRNA isolation lung tissue was immersed in RNAlater (Qiagen) and total RNA was then extracted using the RNeasy Mini Kit (Qiagen).  RNA quality (RIN>=7) was confirmed using an Agilent 2100 Bioanalyzer.  RNA from all biological samples was labeled at once using the Ambion TotalPrep-96 RNA Amplification Kit.  The samples were then blinded, randomized to chip position and hybridized to the Illumina MouseRef-8 v2.0 Expression BeadChips.  For Microarray Experiment #1 RNA labeling and microarray hybridization were conducted at the Partners Center for Personalized Genetic Medicine.  All biological samples were represented by a single technical replicate on the microarray.

first: S


title: Srf is essential for mesodermal cell migration during elongation of the embryonic body axis

status: Public on Jul 01 2014

city: Berlin

first: Phillip

last: Grote

address: Ihnestr. 73

department: Developmental Genetics

institute: Max Planck Institute for Molecular Genetics

summary: Timecourse analysis of SRF dependent genes in the nascent mesoderm of mouse embryos. Srf was conditionally deleted by a T::cre driver and the three embryonic stages analyzed represent embryos before onset of the phenotype (E8.5) and progressive appearance of the phenotype (E8.75 and E9.0).

overall_design: Total RNA obtained from dissected caudal ends of SRF(flex/flex); T:cre and control littermate embryos at three different stages.

first: Benedikt

last: Schwartz

first: Lars

last: Wittler

first: Martin

last: Werber

first: Sandra

last: Waehrisch

first: Alfred

last: Nordheim

first: Bernhard

last: Herrmann


title: Gene expression profiles of neonatal cardiomyocytes and immortalized heart muscle cells exposed to inflammatory stimuli

city: Jena

first: S.

last: Lambeck

address: Erlanger Allee 101

institute: JUH

summary:
We used a transcriptomic approach to systematically compare the response to inflammatory stimuli for two murine cardiomyocyte models.
Our results indicate that murine neonatal cardiomyocytes (NNC) are able to exhibit a pronounced response upon inflammatory stimuli, while HL-1 cells were predominantly recruiting transcripts corresponding to Jak-Stat-signalling.

overall_design: RNA from murine HL-1 cardiomyocytes and isolated neonatal cardiomyocytes (NNC) stimulated by infectious (PCI) serum or LPS or a cytokine mix (CM) were extracted (n=4 each group) and subjected to microarray analysis for comparison of transcriptomic responses.

first: Sandro

last: Lindig

first: Sebastian

last: Stehr


title: Murine study of combined LPS and modified immunoglobulins associated gene expression changes in vivo

summary:
We systematically assessed the transcriptomic changes of lipopolysaccharides (LPS) of mice upon stimulation with immunoglobulins (IVIg), modified immunoglobulins (modIVIg) or vehicle controls in kidney, blood and liver in vivo.
Data indicate different in vivo responses to LPS in conjunction with IVIg, modIVIg or vehicle.

overall_design: RNA from murine liver and kidney tissues (LPS+vehicle, LPS+IVIg, LPS+modIVIg; four samples each group) as well as circulating leukocytes from WBC (three samples each group) was extracted and subject to microarray analysis for comparison of transcriptomic responses. Normalization and quality control was performed for each organ separately.

first: Michael

last: Bauer

first: Tchavdar

last: Vassilev


title: A systems biology approach to understand the pathophysiological mechanisms of cardiac pathological hypertrophy associated with rosiglitazone

status: Public on Jun 30 2014

city: Zeist

last: Verschuren

address: Utrechtseweg 48

department: Microbiology and Systems Biology

institute: TNO

summary: Cardiac pathological hypertrophy is associated with a significantly increased risk of coronary heart disease and has been observed in diabetic patients treated with rosiglitazone, whereas most published studies do not suggest a similar increase in risk of cardiovascular events in pioglitazone-treated diabetic subjects. This study sought to understand the pathophysiological mechanisms underlying the disparate cardiovascular effects of rosiglitazone and pioglitazone and yield knowledge as to the causative nature of rosiglitazone-associated cardiac hypertrophy.

overall_design: Total RNA obtained from mouse Apex from LDLr-/- mice treated with High Fat diet (HF) diet as control (n=6) or HF+Pio (n=5) or HF+Rosi (n=5).

first: Peter

middle: Y

last: Wielinga

first: Thomas

last: Kelder

first: Marijana

last: Radonjic

first: Kanita

last: Salic

first: Robert

last: Kleemann

first: Ben

last: van Ommen

first: Teake

last: Kooistra


title: Insights into microbial modulation of host peripheral lipid and glucose metabolism using mouse gut organoids

first: Guus

last: Roeselers

department: Microbiology & Systems Biology

summary: The gastrointestinal microbiota is involved in the development of various diseases, such as obesity and diabetes, by affecting nutrient acquisition, energy balance, and metabolic signaling of the host. However, the underlying mechanisms of these host-microbiota interactions remain unclear. The aim of this study was to characterize effects of the microbiota on the host epithelium using a novel gastrointestinal model based on mouse organoids. We have explored the transcriptional response of organoids upon exposure to short chain fatty acids (SCFA) and products generated by two conspicuous members of the gastrointestinal microbiota; Akkermansia muciniphila and Faecalibacterium prausnitzii. We observed that A. muciniphila metabolites affect a large variety of transcription factors and genes involved in cellular lipid metabolism and growth, supporting previous in vivo findings. F. prausnitzii products exerted only a weak effect on the host transcription profile. While, A. muciniphila, and its main metabolite propionate, both stimulate fasting-induced adipose factor/angiopoietin-like protein 4 (Fiaf/Angptl4) and Ppar? expression, important regulators of lipolysis and satiety. This work illustrates that specific members of the microbiota and their metabolites differentially modulate epithelial transcription in mouse organoid lines.

overall_design:
Organoid culture:
In short, murine (WT C57BL/6) small intestinal crypts were isolated and embedded in 250 µl Matrigel (BD Biosciences) and submerged in 500 ul basal culture medium supplemented with penicillin/streptomycin, HEPES, Glutamax, N2, B27, N-acetylcysteine, and the murine growth factors EGF, noggin, and R-spondin-1 (ENR), as previously described (Sato et al., 2009. Nature 459:262–5). Organoids were passaged every 7 days with a 1:4 splitting ratio.

Exposure to bacterial cultures and SCFA:
A. muciniphila (ATTC BAA-835) was grown anaerobically at 37C in a basal liquid medium which contained (per liter of deionized water) the following: 0.4g KH2PO4, 0.669g, Na2HPO4 + 2H2O, 0.3g NH4CL, 0.3gNaCl, 0.1g MgCl2 + 6H2O, 10g casitone, 1mM L-threonine, 1 ml trace mineral solution, 5mM L-fucose, and 5mM D-glucose.
F. prausnitzii strain A2-165 (DSM 17677) was grown anaerobically at 37ºC a liquid medium which contained (per liter of deionized water) the following: 10 g casitone, 2.5 g yeast extract, 4 g NaHCO3, 1 ml resazurine (0.1%w/v), 0.45g K2HPO4, 0.45g KH2PO4, 0.9g (NH4)2SO4, 0.9g NaCL, 0.09g MgSO4, 0.09g CaCL2, 2.5 mM acetate, 9 mM propionate, 1 mM n-valerate, 1 mM isovalerate, 1 mM isobutyrate, 0.28g KOH, 2.5 ml ethanol (95%), 10 mg haemin,, 10 ug biotin, 10 ug cobalamin, 30 ug para-aminobenzoic acid, 50 ug folic acid, 150 ug pyridoxamine, 1 g L-cysteine, and 25 mM glucose (Duncan et al., 2002. Int. J. Syst. Evol. Microbiol. 52:2141–6). The concentration of the following organic acids and sugars were determined in the culture medium before and after growth using a high performance liquid chromatography (HPLC) equipped with a Shodex Sugar SH-G and Shodex SH1821 column as has been described previously (Stams et al., 1993.  Appl. Environ. Microbiol. 59:1114–9): glucose, mannose, galactose, L-fucose, glucose-N-acetylglucosamine, lactate, formate acetate, propionate, 1,2-propendiol and butyrate. Overnight-grown cultures were pelleted by centrifugation at 20 000 ×g for 10 min and supernatant was collected. At t=7 days after splitting organoids were exposed to 250 μl A. muciniphila supernatant, 250 μl unconditioned A. muciniphila culture medium, 85 μl F. prausnitzii supernatant, or 85 μl F. prausnitzii culture medium for 3 hours at 37ºC, prior to RNA extraction. 250 μl A. muciniphila supernatant and culture medium Short chain fatty acids (SCFA) sodium butyrate, sodium propionate, and sodium acetate (Sigma-Aldrich, Zwijndrecht, the Netherlands) were administered at a final concentration of 5 mM. At t=7 days after splitting mature organoids were exposed to individual SCFAs for 3 hours at 37ºC, prior to RNA extraction. Data is presented from n = 4 independent biological replicates from one line of organoids.

total RNA was isolated from mouse intestinal organoids exposed for 3h to SCFA and strain-specific culture medium:
Am- (organoids exposed to A. muciniphila culturing medium), Am+ (A. muciniphila-conditioned medium), Fp- (F. prausnitzii-culturing medium), Fp+ (F. prausnitzii-conditioned medium), Ace (acetate), But (butyrate), Pro (propionate) and Con (standard organoid culturing medium).

first: Sabina

last: Lukovac


title: Mouse brain tissue after methanol and normal saline treatment

status: Public on Jun 10 2014

city: Moscow

first: Anastasia

last: Shindyapina

state: Moscow

address: Mosfilmovskaya 76

department: Biengineering

country: Russia

institute: MSU Lomonosov

summary: We recently showed that methanol emitted by wounded plants might function as a signaling molecule for plant-to-plant  and plant-to-animal communications. In mammals, methanol is considered a poison because the enzyme alcohol  dehydrogenase (ADH) converts methanol into toxic formaldehyde. However, the detection of methanol in the blood and  exhaled air of healthy volunteers suggests that methanol may be a chemical with specific functions rather than a metabolic  waste product. Using a genome-wide analysis of the mouse brain, we demonstrated that an increase in blood methanol  concentration led to a change in the accumulation of mRNAs from genes primarily involved in detoxification processes and  regulation of the alcohol/aldehyde dehydrogenases gene cluster. Removal of the intestine significantly decreased the rate of methanol addition to the plasma and suggested  that the gut flora may be involved in the endogenous production of methanol.  Liver mRNA quantification showed changes in the accumulation of  mRNAs from genes involved in cell signalling and detoxification processes. We hypothesized that endogenous methanol  acts as a regulator of homeostasis by controlling the mRNA synthesis

overall_design: 4 mouse were treated with methanol for 2 h and 4 with normal saline for 2 h, than we collected brain tissue samples and extracted total RNA by Trizol according to manufacturer's protocol

middle: V

first: Igor

last: Petrunia


title: Total Gene expression analysis of Dppa4-trandformed 3T3s

status: Public on Jun 21 2014

city: Sacramento

first: Po-Yuan

last: Tung

address: 2425 Stockton Blvd

institute: UC Davis

summary: Total gene expression analysis was performed on 3T3s transfomed by SV40, cMyc, or mDppa4 in relative to vector transduced control 3T3s. Intent was to analyze the role of mDppa4 in oncogenic transformation.

overall_design: Oncogenic foci transduced with different oncogenes (SV40, c-Myc, or mDppa4) were picked and culture for RNA isolation. Vector transduced 3T3s were included as control. Total RNA was isolated for gene analysis.

first: Paul

last: Knoepfler


title: Lin28 sustains early renal progenitors and induces Wilms tumor

status: Public on Jun 01 2014

city: Ramat Gan

first: Achia

last: Urbach

address: Bar Ilan

department: Faculty of Life Sciences

country: Israel

institute: Bar Ilan University

summary: Wilms Tumor, the most common pediatric kidney cancer, evolves from the failure of terminal differentiation of the embryonic kidney. Here we show that over-expression of the heterochronic regulator Lin28 during kidney development in mice markedly expands nephrogenic progenitors by blocking   their final wave of differentiation, ultimately resulting in pathology highly reminiscent of Wilms tumor.

overall_design: Gene expression analysis was performed on a total of 8 kidneys samples, including 4 tumors samples from Lin28 transgenic mice and 4 control kidneys

first: George

last: Daley


title: Dynamic study of In vitro murine follicle maturation in 3% alginate gels

city: Chicago

first: and

last: PhD

state: Illinois

address: 5841 South Maryland Avenue, MC 5032 Room AB540

department: Department of Surgery

institute: University of Chicago

summary:
Multilayer murine follicles were grown in 3% alginate and follicles were isolated for transcriptomics analysis at day 0, 2, 4,5,6,and 8 after encapsulation.
This data complements to the GSE42795, where follicles were grown in vitro in 0.5% alginate gels

overall_design: A total of 8 samples were analyzed, each of them repeted in triplicate

first: Beatriz

last: Penalver Bernabe

first: Eugene

last: Galdones

first: Lonnie

last: Shea

first: Teresa

last: Woodruff


title: Expression data from mouse testis following chronic exposure to acrylamide via the drinking water

first: Belinda

last: Nixon

state: NSW

summary: Acrylamide is a reproductive toxicant that has been detected in foods such as potato chips and breads. The consequences of chronic exposure to acrylamide in the human diet are unknown; however we previously reported that exposure to acrylamide at levels equivalent to human exposure produced high levels of genetic damage in early male germ cells of mice [Nixon et al. ToxSci 129(1), 135–145 (2012)]. In the present study, we examined changes in testicular gene expression in these mice to examine the potential mechanisms involved in acrylamide induced DNA damage in male germ cells and to provide a better understanding of the reproductive toxic effects of acrylamide in the male.

overall_design: Adult male mice were subjected to chronic acrylamide exposure via the drinking water at concentrations of 0, 0.001, 0.01, 0.1, 1 and 10 µg/ml for 1, 6 and 12 months. The testes were collected at each time point for RNA extraction and hybridization on an Illumina Sentrix Mouse ref-8 v2 Beadchip.

first: Shaun

last: Roman


title: Axin2/Runx2 mouse calvaria gene expression

first: Jie

last: Sun

institute: Mayo Clinic

summary: Runx2 and Axin2 regulate skeletal development. We recently determined that Axin2 and Runx2 molecularly interact in differentiating osteoblasts to regulate intramembranous bone formation, but the relationship between these factors in endochondral bone formation was unresolved. To address this, we examined the effects of Axin2 deficiency on the cleidocranial dysplasia (CCD) phenotype of Runx2+/- mice, focusing on skeletal defects attributed to improper endochondral bone formation. Axin2 deficiency unexpectedly exacerbated calvarial components of the CCD phenotype in the Runx2+/- mice; the endocranial layer of the frontal suture, which develops by endochondral bone formation, failed to mineralize in the Axin2-/-:Runx2+/-mice, resulting in a cartilaginous, fibrotic and larger fontanel than observed in Runx2+/- mice. Transcripts associated with cartilage development (e.g., Acan, miR140) were expressed at higher levels, whereas blood vessel morphogenesis transcripts (e.g., Slit2) were suppressed in Axin2-/-:Runx2+/-calvaria. Cartilage maturation was impaired, as primary chondrocytes from double mutant mice demonstrated delayed differentiation and produced less calcified matrix in vitro. The genetic dominance of Runx2 was also reflected during endochondral fracture repair, as both Runx2+/- and double mutant Axin2-/-:Runx2+/- mice had enlarged fracture calluses at early stages of healing. However, by the end stages of fracture healing, double mutant animals diverged from the Runx2+/- mice, showing smaller calluses and increased torsional strength indicative of more rapid end stage bone formation as seen in the Axin2-/- mice. Taken together, our data demonstrate a dominant role for Runx2 in chondrocyte maturation, but implicate Axin2 as an important modulator of the terminal stages of endochondral bone formation.

overall_design: 4 mice per genotype X 4 genotypes: wildtype (WT), Runx2+/- (R-Het), Axin2-/- (A-KO), Axin2-/-:Runx2+/- (A-KO:R-Het).   Total = 16 samples

first: Jennifer

last: Westendorf

first: Meghan

middle: E

last: McGee-Lawrence


title: Decrease of Parkin and CD36 expression and body weight correlate with an increase of non-esterified fatty acids in a mouse model for TDP-43 pathology

status: Public on May 21 2014

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum München GmbH

summary: TDP-43-coding mutations are found among ALS patients. In oder to express human mutant TDP-43 protein in the mouse under the control of the endogenous Tardp promoter, we have generate a mouse line wit 300% elevated TDP-43 level.

overall_design: Total RNA obtained from 4-6 male mutant mice was compared to 4-6 wild type controls.

first: Johannes

last: Beckers

first: Thomas

last: Floss

first: Marion

last: Horsch


title: Genome-wide analysis of gene expression changes in mouse keratinocytes induced by treatment with DAPT

status: Public on May 25 2014

first: Justin

last: Ichida

address: 1425 San Pablo St. Bcc 307

institute: University of Southern California

summary: Analysis of gene expression changes that occur in keratinocytes during reprogramming when they are treated with DAPT, a small molecule gamma-secretase inhibitor. The hypothesis tested in the present study was that Notch inhibition by DAPT treatment would promote reprogramming by inhibiting p21 activity while leaving p53 expression intact. Results provide important information of the gene expression changes in response to DAPT treatment, such as changes in the expression of p21, p21-responsive genes, p53, p53-responsive genes involved in apoptosis, and Notch-responsive genes.

overall_design: Total RNA obtained from mouse keratinocytes transduced with reprogramming transcription factors and treated or not treated with DAPT for 4 days or 7 days.


title: Transcription profiling by array of adipose samples from LDLR-/- mice to study response to anti-diabetic drug and dietary lifestyle interventions

status: Public on May 14 2014

last: Kelder

department: Microbiology & Systems Bioloby

summary: Lean male mice were fed a high fat diet (HFD, lard 24% w/w) for 16 weeks. At 9 weeks, when all hallmarks of prediabetes were established, groups of mice were treated with drug (rosiglitazone, pioglitazone, T0901317, or salicylate) for another 7 weeks together with the high fat diet. An additional group was switched back to a chow diet (dietary lifestyle intervention) after the first 9 weeks of high fat diet. All groups were compared to a control group receiving HFD alone and to a reference group fed chow (baseline reference) for the entire experimental period (16 weeks).

overall_design: One group remained on maintenance chow throughout the entire study period (16 weeks) and served as healthy, age-matched control (n=9, samples hybridized: 7 for gonadal, 7 for subcutaneous, 8 for visceral). After the nine week run-in period, the HFD fed mice were matched into thirteen groups based on body weight. The first group was sacrificed immediately after matching (n=9, samples hybridized: 8 for gonadal, 8 for gonadal, 6 for visceral). The second group was continued on HFD until the end of the experiment at t=16 weeks (n=15, samples hybridized: 8 for gonadal, 7 for subcutaneous, 6 for visceral). The fourth group was switched to regular chow (dietary lifestyle intervention, n=9, samples hybridized: 8 for gonadal, 8 for subcutaneous, 7 for visceral). The other groups continued on HFD supplemented with drugs typically used in clinical practice. More specifically, following drugs were mixed into HFD: rosiglitazone (0.010% w/w, n=9, samples hybridized: 8 for all adipose depots), pioglitazone (0.010% w/w, n=9, samples hybridized: 8 for gonadal, 8 for subcutaneous, 6 for visceral), T0901317 (0.010% w/w, n=9, samples hybridized: 7 for all adipose depots) and salicylate (0.40% w/w, n=9, samples hybridized: 8 for all adipose depots).

first: Marijana

last: Radonjic

first: Peter

last: Wielinga

first: Varshna

last: Goelela

first: Lars

last: Verschuren

first: Wim

last: van Duyvenvoorde

first: Johanna

last: Stroeve

first: Nicole

last: Cnubben

first: Teake

last: Kooistra

first: Ben

last: van Ommen

first: Robert

last: Kleemann


title: Generation and standardized, systemic phenotypic analysis of Kctd1 mutant mice

status: Public on May 02 2014

summary: Increased levels of blood plasma urea were used as phenotypic parameter for establishing novel mouse models for kidney diseases on the genetic background of C3H inbred mice in the phenotype-driven Munich ENU mouse mutagenesis project. The phenotypically mutant line HST014 was established and further analyzed. The causative mutation was detected in the gene Kctd1 which leads to the amino acid exchange Kctd1I27N thereby affecting the functional BTB domain of the protein. This line is the first mouse model harbouring a Kctd1 mutation. Kctd1I27N homozygous mutant mice die perinatally. Standardized, systemic phenotypic analysis of heterozygous mutants was carried out in the German Mouse Clinic. Systematic morphological investigation of the external physical appearance found no mutation-specific differences. Main phenotypic changes were kidney dysfunction, minor cardiovascular and neurological alterations as well as low plasma corticosterone levels. Genome-wide RNA expression analysis at the age of 4 months revealed few regulated genes in brain and heart, and over 100 significantly regulated genes in kidneys of heterozygous mutants.

overall_design: Total RNA obtained from 4 mutant and 5 wild type control mice


title: IFIT2 mediates IFN signaling

summary: IFit2 is highly induced in response to type I and type II interferons, dsRNA, LPS, viral and bacterial infections and it is als found in several chronic diseases.A possible role for the protein in cell proliferation, virion assembly/transport and microtubule dynamices was described. This study focus on IFIT2 proinflammatory cytokine response which might be involved in the development of septic shock. In the IFIT2 knockout mice gene expression levels before and after OVA challenge were analysed.

overall_design: Total RNA obtained from 3-4 male mutant mice (challenged/un-challenged) was compared to 4 wild type controls (challenged/unchallenged).


title: Expression data from adult lungs isolated from TMEM100-deficient mice

status: Public on May 03 2014

city: Incheon

first: Young Jae

last: Lee

address: 155, Gaetbeol-ro, Yeonsu-gu

department: Lee Gil Ya cancer and Diabetes Institute

institute: Gachon University

summary: Tmem100 was identified as a downstream gene of BMP9-ALK1 signaling. The signaling has been implicated in hereditary hemorrhagic telangiectasia. This study was designed to identify affected genes in TMEM100-deficiect mice. Tmem100 was inactivated in adult Tmem1002loxP/2loxP;ROSA26+/CreER mice by tamoxifen tereatment. Microarray data was obtained from the lungs isolated from tamoxifen treated control and mutant mice.

overall_design: Three control mice (Tmem1002loxP/2loxP) and three mutant mice (Tmem1002loxP/2loxP;ROSA26+/CreER) were treated with tamoxifen (two consecutive intraperitoneal injections, 0.1 mg/g of body weight) to activate CreER recombinase. Total RNAs were isolated from lungs 7 days after tamoxifen injection.

first: Young

first: S

last: Oh

first: Eun-Hye

last: Moon


title: Arid1a deletion in collaboration with Pten deletion leads to ovarian tumorigenesis in mouse

status: Public on Apr 05 2014

city: Baltimore

first: Ie-Ming

last: Shih

state: Maryland

address: 1550 Orleans St. CRB-II, Room 305

department: Pathology

institute: Johns Hopkins University School of Medicine

summary: Mice developed ovarian tumors after Arid1a and Pten double knockout. Gene expression profiles of 5 such ovarian tumors were compared with those of 4 normal ovaries. The differentially expressed genes were then used to investigate the similarity between the mouse ovarian tumors and major subtypes of human ovarian cancers.

overall_design: Total RNA obtained from the mouse ovarian tumors developing after Arid1a and Pten knockout compared to normal mouse ovaries.

first: Bin

last: Guan

first: Yohan

last: Rahmanto

first: Ren-Chin

last: Wu

first: Yihong

last: Wang

first: Zhong

first: Tian-Li


title: ENU mutagenesis derived Ednray129F-/- mice as a new model for human velocardiofacial syndrome/DiGeorg syndrome (VCFS/DGS)

first: Martin

last: Irmler

summary: Human velocardiofacial syndrom/DiGeorg (VCFS/DGS) syndrom is a complex developmental disease with various expression of a large number of phenotypes. Craniofacial, cardiac, behavioural and endocrinological phenotypes are cardinal symptoms liked to the 22Q11.2 deletion occuring in 1/4.000 births. Several genes located within the 1.5 to 3 Mb deletion resemble a number of phenotypes demonstrated in mouse models for these genes including the endothelin receptor A (Ednra) gene. This is the first report on gene dosage effects observed in a dominant mouse model carrying an EdnraY129F point-mutation. EdnraY129F/+ mice are viable despite a strong cardiac phenotype alike to Fallot's tetralogy concomitant with cardiofacial, otolaryngeal phenotypes and deafness.

overall_design: Total RNA obtained from 4 male heterzygote and 4 male wildtype mice

first: Johannes

last: Beckers

first: Marion

last: Horsch


title: microRNA expression profiles in far-infrared treated human endothelial precursor cells

status: Public on Apr 03 2014

city: Taipei City

first: Tse-Shun

last: Huang

address: No.155, Sec.2, Linong Street

department: Institute of Microbiology and Immunology

institute: National Yang-Ming University

summary: High glucose impairs the angiogenic activities of late endothelial precursor cells (EPC). We found that far infrared (FIR) treatment restored partially the activity of late EPC. However, the mechanisms are unclear. We applied microRNA expression microarrays to assess the microRNA expression profiles of high glucose-treated late EPC with or without FIR treatment.

overall_design: Late EPCs isolated from peripheral blood were cultured in high glucose condition for 48 hours, and then treated with or without FIR radiation for 30 minutes. Total RNA were extracted and evaluated with the Agilent Human miRNA Oligo Microarray R14 V2 chips.

first: Jaw-Wen

last: Chen

first: Jerry

last: Lo

first: Yu-Neng

last: Chueh

first: Yi-Chieh

last: Cheng

first: Hua-Yong

first: Po-Hsun

first: Chih-Ching

last: Lin

first: Hung-Jui

first: Shing-Jyh

last: Chang

first: Hsei-Wei