title: MicroRNA-offset RNA regulates gene expression and cell proliferation (BeadChip)

city: Boston

first: Gavin

middle: R.

last: Schnitzler

address: 800 Washington St. Box 80

department: Molecular Cardiology Research Institute

institute: Tufts Medical Center

summary: MicroRNA-offset RNAs (moRs) were first identified in simple chordates and subsequently in mouse and human cells by deep sequencing of short RNAs. MoRs are derived from sequences located immediately adjacent to microRNAs (miRs) in the primary miR (pri-miR). Currently moRs are considered to be simply a by-product of miR biosynthesis that lack biological activity. Here we show for the first time that a moR is biologically active. We now demonstrate that endogenous and over-expressed moR-21 significantly alters gene expression and inhibits the proliferation of vascular smooth muscle cells (VSMC). We report that the seed region of moR-21 as well as the seed match region in the target gene 3'UTR are indispensable for moR-21-mediated gene down-regulation. We further demonstrated that moR-21-mediated gene repression is Argonaute 2 (Ago2) dependent. In addition, we find that miR-21 and moR-21 may regulate different genes in a given pathway and can oppose each other in regulating certain genes. Taken together, these findings provide the first evidence that microRNA offset RNA regulates gene expression and is biologically active.

overall_design: Primary mouse aortic smooth muscle cells (AoSMCs) were transfected with scrambled control or moR-21 mimetics at 5nM final concentration. Triplicate samples were prepared for each treatment. Total RNA was isolated at 48hr post-transfection. Labeling and hybridization to MouseRef-8 v2.0 Expression BeadChip (llumina) were performed according to the Yale Center for Genome Analysis protocol (YCGA, http://ycga.yale.edu/). Beadstudio suite of programs were used to calculate the quantile normalized expression values for probe sets. Bioconductor packages Lumi and Limma Linear models and empirical Bayes methods for assessing differential expression in microarray experiments were use to process and annotate the expression values and calculate the fold changes and P-values.

first: J

last: Zhao

first: G

first: L

middle: K

last: Iyer

first: W

last: Baur

first: R

last: Karas


title: Gene expression of E12.5 laser capture microdissected embryonic mouse dermal fibroblast progenitors

status: Public on Jun 16 2016

city: Cleveland

first: Radhika

middle: Paresh

last: Atit

state: Ohio

address: 2074 Adelbert Road, Millis 316

department: Biology

country: USA

institute: Case Western Reserve University

summary: Determined genes that are expressed in E12.5 dermal fibroblasts progenitors.  The purpose was to identify cell type specific genes.

overall_design: Total RNA was isolated from E12.5 Engrailed1Cre/+; Rosa26Reporter/+ mouse dorsal dermal fibrobast cells obtained by laser capture microdissection from 5 embryos and pooled before amplifying with Ambion kit.   Technical replicates of pooled labeled RNA was performed. Samples were hybridized on commercial Illumina MouseRef-8 v2.0 expression bead chip.

middle: P


title: Functional genomics-assisted identification of the Ypel5 gene as a novel negative regulator of the TBK1/IKBKE kinases and interferon-beta

status: Public on May 06 2016

city: Montreal

first: Christian

middle: F

last: Deschepper

state: QC

address: 110 Pine Ave West

department: Institut de recherches cliniques de Montréal (IRCM)

country: Canada

institute: Université de Montréal

summary: Effects of siRNA-mediated knockdown of Ypel5 expression on the transcriptome of mouse RAW264.7 cells

overall_design: Total RNA was obtained from mouse RAW264.7 cells, 24 hours after transfection with either scrambled or Ypel5-specific siRNA


title: Malnutrition during lactation programs the hypothalamic gene networks controlling reproductive function through generations

status: Public on May 04 2016

city: Olsztyn

first: Monika

middle: M

last: Kaczmarek

address: Tuwima 10

country: Poland

institute: Institute of Animal Reproduction and Food Research, Polish Academy of Sciences

summary: The timing of pubertal initiation and progression in mammals is likely influenced by the nutritional and metabolic state, leading us to the hypothesis that transient malnutrition experienced at critical times during development may contribute to alterations in the rate of pubertal progression through generations. Accordingly, using a mouse model of lactation under-nutrition during suckling, we predicted that body composition, reproductive performance parameters and expression of genes responsible for hypothalamic neural circuits controlling among others reproductive function will be changed in F1 and F2 offspring.

overall_design: Microarray analysis of gene expression was performed on hypothalamic tissue dissected from 21-day-old female mice raised from birth to weaning in the control or lactation under-nutrition condition.

first: Leslie

last: Kozak

first: Susan

last: Newman


title: Transcriptionally inactive ATF2 variant drives melanomagenesis [Array]

status: Public on May 02 2016

city: San Diego

first: brian

last: james

address: 10901 North Torrey Pines Road

institute: Sanford Burnham

summary: Characterized by striking metastatic propensity and chemoresistance, melanoma is among the most lethal cutaneous malignancies. The transcription factor ATF2 was shown to elicit oncogenic activities in melanoma, and its inhibition attenuates melanoma development. Here, a mouse model engineered to express a transcriptionally inactive form of Atf2 (Atf2?8,9) was found to be sufficient to induce nevi formation and, when crossed with BrafV600E animals, to promote melanoma development. The cross of Atf2?8,9 with BrafV600E;Pten-/- mice augmented pigmentation, tumorigenicity, and metastasis. Similar to mouse Atf2?8,9, the human ATF2 splice variant 5 enhanced growth and migration capacity of cultured melanoma and immortalized melanocytes. Induced Melan-A, CXCL9, S100A8, CCR7 expression, seen in Atf2?8,9-driven tumors associate with their enhanced pigmentation, immune infiltration and propensity to metastasize. Notably, elevated ATF2SV5 expression in melanoma specimens coincided with poor prognosis. The gain-of-function activity elicited by the truncated ATF2 form offers unexpected insight into mechanisms underlying melanoma development and progression.

overall_design: Compared gene expression profiles of tumor samples from Atf2Δ8,9/Δ8,9;BrafV600E/V600E;Pten–/– and Atf2+/+;BrafV600E/V600E;Pten–/– mice

first: Giuseppina

last: Claps

first: Tongwu

last: Zhang

first: Jian-Liang

last: Li

first: Brian

last: James

first: Ze’ev

middle: A

last: Ronai


title: L929 vs L929IRF8 following 4hr IFNbeta treatment (1000U/ml)

status: Public on Apr 30 2016

city: Clayton

first: Christine

last: White

state: VIC

address: 27 - 31 Wright St

country: Australia

institute: Hudson Institute of Medical Research

summary: Identify genes like Ifit1 which are induced in L929 cells but not L929 cells expressing ectopic IRF8

overall_design: Total RNA obtained from L929 fibroblasts or L929 fibroblasts ectopically expressing IRF8 following treatment with 1000U/ml IFNbeta for 4h. 2 independent replicates.

first: Ganes

middle: C

last: Sen

middle: L


title: Orphan Nuclear Receptor ERRγ is required for pancreatic islet beta-cell maturation

status: Public on Apr 27 2016

city: La Jolla

first: Ruth

middle: T

last: Yu

state: CA

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

summary: We characterized the effect of loss of ERRγ expression in mouse pancreatic islets using adenoviral constructs.

overall_design: Total RNA was extracted from Ad-EGFP or Ad-Cre infected pancreatic islets from ERRγfl/fl mice. Gene expression profiles were compared between the wild-type control (Ad-EGFP) and ERRγKO (Ad-Cre) islets.

first: Eiji

last: Yoshihara

first: Ronald

last: Evans


title: Effect of NIK overexpression on Foxp3+CD4+ and Foxp3-CD4+ T cell subsets [Illumina]

status: Public on Apr 29 2016

city: Portland

last: Murray

state: OR

address: 3181 SW Sam Jackson Park Rd.

department: Molecular microbiology and immunology

institute: OHSU

summary: We previously found that NF-kB inducing kinase (NIK) overexpression in T cells via CD4 promoter driven transgene induction caused lethal autoimmunity in mice. Autoimmunity was associated with increased conventional T cell effector function and decreased regulatory T cell (Foxp3+CD4+) suppression. The goal in this study was to elucidate global transcriptional changes in Foxp3+CD4+ and Foxp3-CD4+ T cells intrinsically caused by chronic NIK overexpression in these cell types.

overall_design: Total RNA from FACS-sorted NIKtg and WT Foxp3RFP+CD4+ and Foxp3RFP-CD4+ harvested from NIKtg/CD4Cre/Foxp3RFP + WT/Thy1.1/Foxp3RFP mixed bone marrow chimeric mice, >8 weeks after bone marrow reconstitution.

first: Fanny

last: Polesso

first: Minhazur

last: Sarker

first: Arian

last: Anderson

first: David

last: Parker

middle: E

first: Chris

last: Harrington

first: Aimee

last: Potter

first: Julja

last: Burchard

first: Mark

last: Fisher


title: B-cell Differentiation is Regulated by Targeted DNA Hypomethylation [array]

status: Public on May 01 2016

city: Atlanta

first: Benjamin

middle: G

last: Barwick

state: GA

address: 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37

department: Hematology and Medical Oncology

institute: Emory University

summary: B cells provide humoral immunity by differentiating into antibody secreting plasma cells.  Differentiation is dependent upon division and transcriptional changes, with commitment to B cell lineages associated with epigenetic changes.  Analysis of early transcriptional and epigenetic events in B cell differentiation revealed that plasmablasts and plasma cells undergo dynamic changes in gene expression and a progressive DNA hypomethylation targeted to at least 10% of genes/loci.  Of the differentially methylated loci, more than 99.7% were demethylated during differentiation and these clustered in cis-regulatory features such as enhancers and transcription factor binding sites.  Changes in gene expression and DNA methylation coincided with each other at specific divisions during differentiation and inhibition of DNA methylation resulted in augmented plasma cell commitment in a division-dependent manner.  These data identify a major epigenetic reprogramming event during early B cell differentiation coupled division and provide an approach to modulating humoral immune responses.

overall_design: Splenic B cells (B220+ CD43-) from naïve C57/BL6J mice, and Day 3 LPS-induced Plasmablasts (B220mid CD138+) and Plasma Cells (B220low CD138+) were analyzed by Illumina Gene Expression Microarray and Reduced Representation Bisulfite Sequencing

first: Jeremy

last: Boss


title: Perturbed rhythmic activation of signaling pathways in mice deficient for Sterol Carrier Protein 2-dependent diurnal lipid transport and metabolism

status: Public on Apr 22 2016

city: St Lucia

first: Frédéric

last: Gachon

state: QLD

address: 306 Carmody Road

department: Institute for Molecular Bioscience

institute: University Of Queensland

summary: Through evolution, most of the living species have acquired a time keeping system to anticipate daily changes caused by the rotation of the Earth. In all of the systems this pacemaker is based on a molecular transcriptional/translational negative feedback loop able to generate rhythmic gene expression with a period close to 24 hours. Recent evidences suggest that post-transcriptional regulations activated mostly by systemic cues play a fundamental role in the process, fine tuning the time keeping system and linking it to animal physiology. Among these signals, we consider the role of lipid transport and metabolism regulated by SCP2. Mice harboring a deletion of the Scp2 locus present a modulated diurnal accumulation of lipids in the liver and a perturbed activation of several signaling pathways including PPAR, SREBP, LRH-1, TORC1 and its upstream regulators. This defect in signaling pathways activation feedbacks upon the clock by lengthening the circadian period of animals through post-translational regulation of core clock regulators, showing that rhythmic lipid transport is a major player in the establishment of rhythmic mRNA and protein expression landscape.

overall_design: Comparison of liver mRNA expression from Scp2 KO and wild-type mice harvested every 2 hours during 3 consecutive days

first: Céline

last: Jouffe

first: Frederic

first: Sylviane

last: Metairon

first: Cédric

last: Gobet

last: Raymond


title: Effect of NIK overexpression on Foxp3+CD4+ and Foxp3-CD4+ T cell subsets

first: Susan

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

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

platform_organism:
Mus musculus
synthetic construct

overall_design: Refer to individual Series


title: ASC controls T-bet-dependent CTL differentiation and defines transplant outcome independent of the inflammasome

status: Public on Apr 01 2016

city: Brisbane

first: Glen

last: Boyle

state: Queensland

address: 300 Herston Road Herston

department: Department of Cell and Molecular Biology, Cancer Program

institute: QIMR Berghofer Medical Research Insitute

summary: The adaptor protein ASC is known to facilitate caspase-1 activation essential for innate host immunity via the formation of the inflammasome complex - a multi-protein structure responsible for processing IL-1beta and IL-18 to their active moieties.  Here we demonstrate that ASC-deficient CD8+ T cells fail to induce graft-versus-host disease (GVHD) and have impaired capacity for graft rejection and graft-versus-leukemia (GVL) activity. These effects are the result of an inability to differentiate into fully cytolytic, granzyme B-expressing effector cells, with a developmental bias instead towards CD127+KLRG1- memory CD8+ T cells. These alterations in differentiation are inflammasome-independent, since GVHD lethality and CTL differentiation are not altered in recipients of caspase-1-deficient T cells. We demonstrate that ASC binds to T-bet in CD8+ T and in the absence of ASC, the binding of T-bet to the granzyme B promoter is impaired. Thus, the inhibition of ASC represents an attractive therapeutic target to manipulate transplant outcomes.

overall_design: Single colour, Illumina MouseRef-8 v2.0 Beadarrays.

first: Melody

last: Cheong

first: Kate

middle: H

last: Gartlan

first: Jason

middle: S

last: Lee

first: Siok-Keen

last: Tey

first: Rachel

middle: D

last: Kuns

first: Mary

last: Lor

first: Katie

last: Lineburg

first: Bianca

last: Teal

first: Wei

last: Shi

first: Kelly

middle: R

last: Locke

first: Jyothy

last: Raju

last: Bunting

first: Antiopi

last: Varelias

first: Lucie

last: Leveque-El mouttie

first: Steven

middle: W

last: Lane

first: Slavica

last: Vuckovic

first: Ping

last: Zhang

last: Markey

first: Frank

last: Gannon

middle: J

last: Smyth

first: Jenny

last: Ting

first: Kum

last: Khanna

first: Christian

last: Engwerda

first: Kelli

last: MacDonald

first: Motoko

last: Koyama

first: Geoffrey

last: Hill


title: Comparative analysis of mouse oropharyngeal cells expressing HPV16 E6/E7, hRas, and luciferase (mEERL) with mEERL lung metastasis cell lines (MLM)

status: Public on Apr 15 2016

city: Sioux Falls

first: Paola

middle: Drapkin

last: Vermeer

state: SD

address: 2301 East 60th street north

department: Cancer Biology and Immunotherapies Group

institute: Sanford Research

summary: Human papillomavirus (HPV) is currently the most identifiable cause of head and neck squamous cell carcinoma (HNSCC) accounting for approximately 25% of these cases.  HPV+ cancer incidence is on the rise with metastatic disease accounting for nearly all HPV+ HNSCC related deaths.  Thus, developing a relevant in vivo pre-clinical model for these invasive cancers is necessary for testing new disease therapeutics and improving survival. To this end, we characterize a novel metastatic HPV+ murine model of HNSCC. Individual metastatic clonal cell lines were isolated from an animal with late pulmonary metastasis that developed recurrent disease after standard of care cisplatin-radiation therapy. Similar to the parental cells, all metastatic cell lines retain expression of HPV16  E6 and E7 oncogenes and degrade P53.  While the in vitro growth rates of these metastatic clones are slower than the parental tumor line their in vivo growth is greatly enhanced.   Moreover, resistance to standard therapies (cisplatin and radiation) is dramatically increased in 3 of the 4 clones in vivo. Lymphatic and/or lung metastasis occurs 100% of the time in 2 of the clonal lines while it is nearly undetectable in the parental line.  In addition, expression and protein array analyses were completed to investigate the mechanisms driving these phenotypic changes.   This model not only provides an economical and rapid screening system in which to develop and test improved therapeutic regimens but may also provide mechanistic insights into tumor metastasis.

overall_design:
Comparison of four individual MLM metastatic lines to the parental mEERL cells.
These data demonstrate heterogeneity found in metastastatic cells lines compared to the parental tumor cell line

first: John

last: Lee


title: Tracking resilience to infections by mapping disease space

status: Public on Apr 18 2016

city: Stanford

first: David

last: Schneider

state: CALIFORNIA

address: 299 Campus Drive

department: Microbiology and Immunology

institute: Stanford University

summary: Individuals that recover from infections travel a path through disease space that returns to its origin. By following Plasmodium infected mice longitudinally from sickness to recovery, we show that these routes trace simple looping paths that can serve as maps.  These maps can predict outcomes, reveal safe avenues and can help us avoid bad neighborhoods. Hosts that will suffer adverse effects enter regions of disease space that are not traversed by resilient individuals. Here we show that we can map disease outcomes using both longitudinal mouse data and cross-sectional human data.  These maps identify relationships that could be useful in predicting and treating infections; they also show us that we commonly lack samples in regions of disease space that would help to build better predictive models.

overall_design: Total RNA was collected from tail nicks of female mice infected with Plasmodium chabaudi (10^5 iRBCs). Each mouse was monitored daily for 26 days.  MIcroarray analysis was done on all 26 days for 3 surviving mice and for four mice that only survive up to 8-11 days after the infection (non-survivors). Control samples for two uninfectetd mice for days 0,8,10,14, & 24 are included.

first: Brenda

middle: Y

last: Torres

first: Jose

last: Oliveira


title: Effect of deletion of liver Mitofusin 1 (Mfn1) on energy metabolism in high fat diet fed mice

status: Public on Mar 31 2016

city: Lausanne

first: Sameer

last: Kulkarni

address: EPFL Innovation Park

country: Switzerland

institute: Nestle Institute of Health Sciences

summary: Microarray analysis of the livers from Mfn1 WT and Mfn1 LKO mice fed with high fat diet. We hypothesised that deletion of Mfn1 will lead reduced mitochondrial fusion thus leading to an increase in the number of smaller but higher functional mitochondria and increase in mitochondrial proteins.

overall_design: Total RNA obtained from isolated livers from a six hours fasted Mfn1 WT or Mfn1 LKO mice.

first: Frédéric

last: Raymond

first: Sylvianne

last: Métairon


title: Transcriptional responses in various normal mouse tissues after 24 h following 4 MV photon beam irradiation using three partial body irradiation set-ups

city: Gothenburg

first: Britta

last: Langen

address: Gula stråket 2B

department: Department of Radiation Physics

country: Sweden

institute: Sahlgrenska Academy at University of Gothenburg

summary:
Female BALB/c nude mice (n=3/group) were subjected to partial body irradiation under anesthesia using 2 Gy external photon (4 MV, nominal) irradiation.
In group A, the collum (i.e. the thyroid) was irradiated; in group B, thorax+abdomen were irradiated, and in group C, collum+thorax+abdomen were irradiated.
The control group (n=5) was anesthetized but not irradiated. At 24 h after treatment, the kidneys, liver, lungs, spleen, and thyroid were excised, flash-frozen, and stored at -80°C.
Total RNA was extracted from homogenized tissue samples (kidney cortex and kidney medulla were treated separately) and subjected to expression analysis using RNA microarray technology.

overall_design: The study consisted of 3 irradiated groups with 3 animals each and one non-irradiated control group with 5 animals. Six tissues were analyzed per animal, each sample was analyzed individually, i.e. no samples were pooled.

first: Nils

last: Rudqvist

first: Johan

last: Spetz

last: Swanpalmer

first: Khalil

last: Helou

first: Eva

last: Forssell-Aronsson


title: Keratin-dependent TSLP expression suggests a link between skin blistering and atopic disease

status: Public on Mar 26 2016

city: Helsinki

first: Vinod

last: Kumar

address: Vinkinkaari 9

department: Developmental Biology

country: Finland

institute: University of Helsinki

summary: Atopic dermatitis (AD) is a pruritic and inflammatory disorder characterized by elevated levels of thymic stromal lymphopoietin (TSLP). Pruritus is prevalent in epidermolysis bullosa (EB). Currently, epidermal barrier disruption is known to trigger TSLP upregulation, however, mechanisms controlling TSLP expression remain incompletely understood. Tslp levels were highly upregulated in the epidermis and in the serum of keratin-deficient mice. Cultured keratinocytes either lacking keratins or expressing the dominant K14p.Arg131Pro show highly increased TSLP. Re-expression of wild-type K14 normalized TSLP levels. We demonstrate that keratins regulate Tslp expression in parts through MEK1/2 activation. The finding that 8 out of 17 EBS patients show elevated TSLP serum levels supports a major role of keratins in TSLP regulation. Our data identify a novel, keratin-dependent and cell-intrinsic regulation of Tslp. Elevated TSLP levels likely explain the high prevalence of pruritus in EBS and additional forms of EB, suggesting TSLP as novel biomarker for pruritus in EB. MEK1/2, in addition to calcineurin inhibitors, might be suitable drugs to treat itch in EB.

overall_design: Investigation was carried out using Keratin deficient keratinocytes isolated from typeI keratin mice.

first: Thomas

last: Magin


title: Keratins control Nrf2 by regulating mitochondrial activity and barrier composition / Keratin-dependent TSLP expression suggests a link between skin blistering and atopic disease

summary: The epidermal barrier protects the body against mechanical injury, infection and dehydration. The respective contribution of type I and type II keratins which form the major cytoskeleton in epidermal keratinocytes in barrier formation and stress protection is incompletely understood. Here, we reveal a novel mechanism by which keratins control anti-oxidant responses through barrier-dependent and cell-autonomous mechanisms. Mice lacking the entire type I (KtyI) or type II (KtyII) keratin gene clusters suffer from distinct prenatal barrier defects. Comparative transcriptome profiling identifies essential cornified envelope components and reveals strong upregulation of the bZIP transcription factor Nrf2 in situ. Isolated keratinocytes from both strains of mice show elevated mitochondrial oxygen consumption and Nrf2 activity, decreased upon keratin re-expression. We propose a model in which keratins control mitochondria-derived oxidative stress via Nrf2 activation. Our findings reveal major contributions of keratins to chronic inflammation and autoimmune disorders.

overall_design: Total RNA obtained from E18.5 embryo back skin from typeI and II keratin knockout compared with respective wild type.


title: Cardiac fibrosis in the BACHD mouse model of Huntington’s Disease

status: Public on Mar 01 2016

city: Los Angeles

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

summary:
Aims: While Huntington’s disease is classified as a neurological disorder, HD patients exhibit a high incidence of cardiovascular events leading to heart failure and death. In this study, we sought to better understand the cardiovascular phenotype of HD using the BACHD mouse model.
Methods and Results: The age-related decline in cardiovascular function was assessed by echocardiograms, electrocardiograms, histological and microarray analysis. We found that structural and functional differences between WT and BACHD hearts start at 3mo of age and continue throughout life. The aged BACHD mice develop cardiac fibrosis. The BACHD mice exhibited adaptive physiological changes to chronic isoproterenol challenge; however, the treatment exacerbated fibrotic lesions in the heart. Gene expression analysis indicates a strong tilt toward apoptosis in the young mutant tissue as well as changes in genes involved in cellular metabolism and proliferation. With age, the number of genes with altered expression increased with the largest changes occurring in the cardiovascular disease and cellular metabolism clusters.
Conclusions: The BACHD model of HD exhibit a number of changes in cardiovascular function that start early in the disease progress and may provide an explanation for the higher CV risk in HD. These changes are consistent with dysfunction in ANS regulation although the hearts did respond adaptively to β-adrenergic challenge. Gene expression pattern changes are subtle but suggests biomarkers focusing on apoptosis, metabolism, immune function are worth further exploration.

overall_design: Microarray-based gene expression analysis in tissue from transgenic mice and controls at different ages

first: Analyne

last: Schroeder

first: Huei-Bin

last: Wang

first: Maria

last: Jordan

first: Fuying

last: Gao

first: Michael

last: Fishbein

first: Kenneth

middle: P

last: Roos

first: Christopher

last: Colwell


title: Adaptaquin is an inhibitor of oxygen-sensing prolyl-hydroxylase domain enzymes that abrogates ATF4-dependent death and  improves outcomes from brain hemorrhage

summary: Disability or death secondary to intracerebral hemorrhage (ICH) is attributed to blood lysis, liberation of iron and generation of oxidative stress. Iron chelators bind free iron and prevent neuronal death induced by oxidative stress and disability due to ICH, but the mechanisms remain unclear. Here we show that the hypoxia-inducible factor prolylhydroxylase (HIF PHD) family of iron-dependent oxygen sensors is an effector of iron chelation in abrogating ICH-induced death. Molecular reduction of the three HIF PHD isoforms in mouse striatum improves functional recovery following ICH. A low molecular weight, hydroxyquinoline inhibitor of the HIF PHDs, which we call adaptaquin, reduces neuronal death and behavioral deficits following ICH in distinct rodent models. Unexpectedly, adaptaquin protects from oxidative death by suppressing ATF4- dependent prodeath gene expression rather than by activating a HIF-dependent prosurvival pathway.

overall_design: Adaptaquin treated neurons

first: Saravanan

last: Karuppagounder

first: Ishraq

last: Alim

first: Soah

last: Khim

first: Megan

last: Bourassa

first: Sama

middle: F

last: Sleiman

first: Roseleen

last: John

first: Cyrille

last: Thinnes

first: Tzu-Lan

last: Yeh

first: Marina

last: Demetriades

first: Sandra

last: Neitemeier

first: Dana

last: Cruz

first: Irina

last: Gazaryan

first: David

last: Killilea

first: Lewis

last: Morgenstern

first: GuoHua

last: Xi

first: Richard

last: Keep

first: Timothy

last: Schallert

first: Ryan

middle: V

last: Tappero

first: Jian

last: Zhong

first: Sunghee

last: Cho

first: Frederick

last: Maxfield

first: Theodore

last: Holman

first: Carsten

last: Culmsee

first: Guo-Hua

last: Fong

first: John

last: Cave

last: Schofield

last: Colbourne

first: Rajiv

last: Ratan


title: A Myc-driven self-reinforcing regulatory network maintains mouse embryonic stem cell identity (BeadChip)

city: Milan

first: Alessio

last: Zippo

address: Via Francesco Sforza, 35

country: Italy

institute: National Institute of Molecular Genetics

summary: We address the molecular mechanisms through which Myc supports mESC identity, by performing gene expression profile analyses of Myc- and LIF-maintained ESCs, together with Epiblast Stem Cell (EpiSC), as a control for a primed state of stemness. We then investigated whether the Myc-driven self-reinforcing circuit, installed in Myc-dependent ESCs, could support the maintenance of ES cell identity in absence of the originating stimulus, namely the MycER activation achieved by OHT stimulation. To this end, we derived ESCs from Myc-dependent cells, following MycER inactivation upon withdrawal of OHT and profile their gene expression.

overall_design: Total RNA extracted from LIF-, Myc- and -Myc-ESCs at the indicated passages were processed to profile gene expression by microarray analysis.  Gene-expression profiling was also perfomed on EpiSC as control for primed stem cell state.

first: Luca

last: Fagnocchi

first: Hiroshi

last: Hatsuda


title: Activation of myenteric glia during acute inflammation in vitro

status: Public on Mar 11 2016

city: Würzburg

first: Corinna

last: Rosenbaum

address: Röntgenring 11

department: Department of Tissue Engineering and Regenerative Medicine

country: Germany

institute: University Hospital Wuerzburg

summary: Enteric glial cells (EGCs) are the main constituent of the enteric nervous system and share similarities with astrocytes from the central nervous system including their reactivity to an inflammator microenvironment. In this study we isolated GFAP-positive myenteric glia from FVB/hGFAP-eGFP transgenic postnatal day 7 mice.  Following cell sorting for the eGFP reporter, GFAP-positive EGCs were cultured for 3 weeks to generate neurosphere-like bodies. This cell culture was stimulated with LPS for 48 h and cells were employed for gene expression profiling. LPS-stimulated cell cultures were compared to untreated control cell cultures. Enriched GFAP+ EGC cultures secreted increased levels of prominent inflammatory cytokines upon LPS stimulation.  Further, in vitro cultures were compared to GFAP-eGFP-positive cells directly analyzed after cell sorting of small intestinal LMMP digests (in vivo) to assess alterations in transcriptomic profiles due to the in vitro culture.

overall_design: In vivo data and in vitro data were collected in three independent replicates. For each replicate one litter of FVB/hGFAP-eGFP transgenic mice at postnatal day 7 was employed. GFAP-eFP-positive small intestines were digested enzymatically and from the single cell suspensions eGFP-positive GFAP-expressing cells were sorted by fluorescence-activated cell sorting. For the in vivo data the cells were directly sorted into lysis buffer and further processed . For the in vitro data GFAP-eGFP cells were seeded onto coated plastic dishes for adherent growth and cultured in DMEM/F12-medium supplemented with antibiotics, N2, B27, bFGF and EGF. In the first passage cells were divided into two uncoated six well dishes to promote spheroid growth. One well was supplemented with LPS (100 µg/ml, from E. coli O26:B6, Sigma Aldrich, potency 3 EU/ng) for 48 h, the corresponding second well was left untreated and used as respective control. After 48 h, cells were processed for total RNA isolation.

first: Marco

last: Metzger

first: Knut

last: Krohn


title: Gene expression profiling of PBMC from petstore mice, C57Bl/6 laboratory mice, and C57Bl/6 laboratory mice cohoused with petstore

status: Public on Mar 09 2016

city: Boston

first: Kevin

last: Bi

state: MA

address: 450 Brookline Ave.

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

summary: Transcriptional analysis of immunological characteristics of petstore mice, C57Bl/6 laboratory mice, and C57Bl/6 laboratory mice cohoused with petstore. We hypothesized that cohousing would confer a basal transcriptional signature of immune activation to laboratory mice from petstore mice. Comparison of these data with existing human adult vs. neonatal PBMC expression profiling data (GSE27272) revealed close concordance of laboratory mice with human neonates, and of cohoused or petstore mice with human adults. Results highlight the impact of environment on the basal immune state and suggest that restoring physiological microbial exposure in laboratory mice could provide a relevant tool for modeling immunological events in free-living organisms, including humans.

overall_design: Total RNA was isolated from PBMC of C57Bl/6 laboratory mice, petstore mice and C57Bl/6 laboratory mice cohoused with petstore mice (at least after 60 days post-cohousing)and transcriptional comparison among 3 groups were performed.

first: Lalit

middle: K

last: Beura

first: Emily

middle: A

last: Thompson


title: In silico analyses  of survival-associated microRNA signatures in pediatric osteosarcoma

status: Public on Mar 22 2016

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: Osteosarcoma is the most common bone tumor in children, adolescents, and young adults.  In contrast to other childhood malignancies, no biomarkers have been consistently identified as predictors of outcome.  This study was conducted to assess the microRNAs (miRs) expression signatures in pre-treatment osteosarcoma specimens and correlate with outcome to identify biomarkers for disease relapse

overall_design: The cohort consisted of 25 patients of 70% Mexican-American ethnicity. High-throughput RT-qPCR approach was used to generate quantitative expression of 754 miRs in the human genome.

first: Patricia

middle: C

last: Sanchez-Diaz

first: Tzu-Hung

last: Hsiao

first: Yi

last: Zou

first: Aaron

last: Sugalski

first: Josefine

last: Heim-Hall

first: Anne-Marie

last: Langevin

first: Jaclyn

last: Hung


title: RhoA Determines Lineage Fate of MSCs by Modulating CTGF-VEGF Complex in Extracellular Matrix

city: Charlottesville

first: Charles

last: Farber

state: VA

department: Center for Public Health Genomics

institute: University of Virginia

summary: Mesenchymal stem cells (MSCs) participate in the repair/remodeling of many tissues, where MSCs commit to different lineages dependent on the cues in the local microenvironment. Here we show that TGFβ-activated RhoA/ROCK functions as a molecular switch regarding the fate of MSCs in arterial repair/remodeling after injury. MSCs differentiate into myofibroblasts when RhoA/ROCK is turned on, endothelial cells when turned off. The former is pathophysiologic resulting in intimal hyperplasia, whereas the latter is physiological leading to endothelial repair.  Further analysis revealed that MSC RhoA activation promotes formation of an extracellular matrix (ECM) complex consisting of connective tissue growth factor (CTGF) and vascular endothelial growth factor (VEGF). Inactivation of RhoA/ROCK in MSCs induces matrix metalloproteinase-3-mediated CTGF cleavage, resulting in VEGF release and MSC endothelial differentiation. Our findings uncover a novel mechanism by which cell-ECM interactions determine stem cell lineage specificity and offer additional molecular targets to manipulate MSC-involved tissue repair/regeneration.

overall_design:
Mouse bone marrow MSCs were purchased from Texas A&M Health Science Center College of Medicine Institute for Regenerative Medicine.
All MSCs were cultured in αMEM supplied with 10% FCS. The transfection of DNA plasmids were performed with Lipofectamine® LTX with Plus Reagent (Life Technologies). Myc-L63RhoA or empty vector (control) was transfected into mouse bone marrow MSCs. Three days later, the cells were harvested and total RNA was isolated using RNeasy Mini kit (Qiagen).  A total of four independent experiments were performed. RNA samples were assessed for quality and integrity using Synergy HT (Biotek, Winooski, VT).
Microarray expression profiles were generated using the Illumina MouseRef-8 v2.0 Expression BeadChip (Illumina, San Diego, CA). Biotin-labeled cRNA was synthesized by the total prep RNA amplification kit from Ambion (Austin, TX). cRNA was quantified and normalized to 75 ng/µl, and then 1µg was hybridized to Beadchips. The hybridized chip was scanned using the Illumina iScan system and background corrected signal intensities were extracted using the GenomeStudio software (Illumina). The lumi R package was used to transform the data using a Variance Stabilizing Transformation (VST) and normalized using quantile normalization. Differential expression analysis was performed using the R/Mannova package.  P-values were calculated by performing 1000 permutations, then corrected for multiple comparisons by false-discovery rate (FDR) transformation, using a 20% FDR cutoff.

first: Mei

last: Wan


title: Genetic suppression reveals DNA repair-independent antagonism between BRCA1 and COBRA1 in mammary gland development

status: Public on Mar 18 2016

first: Rong

last: Li

state: TX

address: 7703 Floyd Curl Drive

department: Molecular Medicine

institute: University of Texas Health Science Center at San Antonio

summary: Gene expression profiles of sorted mammary epithelial cells from animals at 4, 6, and 8 weeks of age. Each individual sample was RNA obtained from an individual mouse. Our mice are mammary epithelium specific knocknout mouse models for gene Cobra1 and/or Brca1. For Cobra1, the first four exons were floxed. For Brca1, the largest exon, exon 11, was floxed. The mammary epithelium specific deletions were driven by cre recombinase under MMTV promoter (MMTV-cre). Animal genotype abbreviations used: wild-type (WT), meaning one of the following three: Cobra1f/f (Cff), Brca1f/f (Bff), and Brca1f/f;Cobra1f/f (Dff). Brca1 knockout (BKO), meaning MMTV-cre;Brca1f/f. Cobra1 knockout (CKO), meaning MMTV-cre;Cobra1f/f. Brca1 and Cobra1 double knockout (DKO), meaning MMTV-cre;Brca1f/f;Cobra1f/f

overall_design: Total RNA isolated from CD24+ sorted primary mammary epithelial cells from three time points in different genotypes.

first: Xiaowen

last: Zhang

first: Sreejith

last: Nair

first: Huai-Chin

last: Chiang

first: Yao

last: Wang

first: M

last: Jamiul Jahid

first: Craig

last: April

first: Neeraj

last: Salathia

first: Fahad

last: Alenazi

first: Jianhua

last: Ruan

first: Jian-Bing

last: Fan

first: Victor

middle: X

last: Jin

first: Yanfen

last: Hu


title: Genome-wide analysis of total skin gene expression from presenilin (1&2)-null (PSmut), RBPjk-null (RBPjmut), Presenilin (1&2)-RBPjk-null (PSRmut) and wild-type (WT) littermates

status: Public on Feb 29 2016

city: Cincinnati

first: Raphael

last: Kopan

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital

summary: Analysis of differential gene expression of total skin from different Notch signaling pathway mutants (specifically PSmut, RBPjmut, and PSRmut). Preselin1&2 are the core components of g-secretase enzyme which essential for the Notch receptor activation. RBPjk is the DNA-binding partner of the Notch Intracellular Domain. The hypothesis tested in the present study was RBPjmut skin would resemble the wild-type skin at the transcriptional level, since RBPjmut mice exhibit milder phenotype than PSmut or PSRmut mice.

overall_design: Total RNA obtained from 4x RBPjmut, 4x PSmut, 4x PSRmut total skin at P0 and compared to wild-type total skin from littermates. All mice were raised in mixed genetic background.

first: Mustafa

last: Turkoz


title: cDNA microarray analysis of splenic B220+CD138+ plasma cells from K/BxNsf and K/BxN mice

city: Seoul

first: Eunkyeong

last: Jang

address: 17, Haengdang 1-dong, Seongdong-gu,

country: South Korea

institute: Hanyang University

summary: Long-lived plasma cells (LLPCs) develop under the help of follicular helper T (Tfh) cells and reside mainly in the bone marrow. However, these cells are unusually abundant in the spleen of several autoimmune models including K/BxNsf mice, yet their pathogenic impact remains unknown. To investigate a previously unappreciated role of splenic LLPCs, we sorted splenic plasma cells (PCs) from K/BxNsf and K/BxN mice, corresponding to LLPCs and conventional short-lived PCs, respectively, and compared their transcriptomes.

overall_design: The B220+CD138+ fraction from K/BxNsf and their control K/BxN mice were sorted by FACSariaIII.

first: Jeehee

last: Youn

first: Wangsik

last: Cho


title: Differential gene expression following MafG overexpression

status: Public on Feb 04 2016

first: Thomas

last: Vallim

address: 650 Charles E. Young Drive South, A2-237 CHS

summary: Specific bile acids are potent signaling molecules that modulate metabolic pathways affecting lipid, glucose and bile acid homeostasis, and the microbiota. Bile acids are synthesized from cholesterol in the liver, and the key enzymes involved in bile acid synthesis (Cyp7a1, Cyp8b1) are regulated transcriptionally by the nuclear receptor FXR. We have identified an FXR-regulated pathway upstream of a transcriptional repressor that controls multiple bile acid metabolism genes. We identify MafG as an FXR target gene and show that hepatic MAFG overexpression represses genes of the bile acid synthetic pathway and modifies the biliary bile acid composition. In contrast, loss-of-function studies using MafG(+/-) mice causes de-repression of the same genes with concordant changes in biliary bile acid levels. Finally, we identify functional MafG response elements in bile acid metabolism genes using ChIP-seq analysis. Our studies identify a molecular mechanism for the complex feedback regulation of bile acid synthesis controlled by FXR

overall_design:
Wild-type C57BL/6 mice were treated with either Ad-Control (Ad-CMV) or Ad-MafG for 5 days. Livers were then harvested following a 4-6h fast, RNA was isolated and analyzed by Illumina Microarray.
6 samples were analyzed, 3 per condition. Each sample represents one mouse.

last: de Aguiar Vallim

first: Peter

last: Edwards


title: REST knock-out ESCs: a role for REST in embryonic stem cells' cardiac lineage specification

status: Public on Feb 01 2016

city: Lyon

first: Irene

last: Aksoy

address: 18 avenue du Doyen Lepine

country: France

institute: Stem Cell and Brain Research Institute

summary:
During development, lineage specification is controlled by several signaling pathways involving various transcription factors (TFs). Here, we studied the RE1-silencing transcription factor (REST) and identified an important role of this TF in cardiac differentiation.  Using mouse embryonic stem cells (ESC) to model development, we analyzed the effect of REST knock-out on the ability to these cells to differentiate into the cardiac lineage. Detailed analysis of specific lineage markers expression showed selective down-regulation of endoderm markers in REST-null cells, thus contributing to a loss of cardiogenic signals.
We propose here a new role for REST in cell fate specification besides its well-known repressive role of neuronal differentiation.

overall_design: REST knock-out (REST-/-) and control cells (REST+/+) were induced to differentiate by embryoid-body (EB) formation that mimicks the early gatsrulation steps of  development. After 3, 6 and 9 days EBs were collected and their transcriptome was compared to control cells (d0).

first: Lawrence

last: Stanton


title: Estrogens Antagonize RUNX2-Mediated Osteoblast-Driven Osteoclastogenesis

first: Nyam-Osor

last: Chimge

address: 2250 Alcazar street

department: IGM

institute: USC

summary: Primary osteoblast NEMCO cells have been transduced with lentivirus conditionally (doxycycline) expressing RUNX2 and treated with E2 to demonstrate effects of estrogen signaling on RUNX2 response

overall_design: NEMCO cells kept at charcoal stripped serum have been treated with dox and/or E2 for 48h


title: Fatty acid oxidation is impaired in an orthologous mouse model of Autosomal Dominant Polycystic Kidney Disease

status: Public on Jan 26 2016

city: Bethesda

first: Luis Fernando

last: Menezes

state: MD

address: Room 8D12A, Building 10, 10 Center Dr

department: NIDDK

institute: National Institutes of Health

summary:
Background
The major gene mutated in autosomal dominant polycystic kidney disease was first identified over 20 years ago, yet its function remains poorly understood. We have used a systems-based approach to examine the effects of acquired loss of Pkd1 in adult mouse kidney as it transitions from normal to cystic state.

Methods
We performed transcriptional profiling of a large set of male and female kidneys, along with metabolomics and lipidomics analyses of a subset of male kidneys. We also assessed the effects of a modest diet change on cyst progression in young cystic mice. Fatty acid oxidation and glycolytic rates were measured in five control and mutant pairs of epithelial cells.

Results
We find that females have a significantly 46 less severe kidney phenotype and correlate this protection with differences in lipid metabolism. We show that sex is a major determinant of the transcriptional profile of mouse kidneys and that some of this difference is due to genes involved in lipid metabolism. Pkd1 mutant mice have transcriptional profiles consistent with changes in lipid metabolism and distinct metabolite and complex lipid profiles in kidneys. We also show that cells lacking Pkd1 have an intrinsic fatty acid oxidation defect and that manipulation of lipid content of mouse chow modifies cystic disease.

Interpretation
Our results suggest PKD could be a disease of altered cellular metabolism.

overall_design: Fifth-generation C57/BL6 Pkd1cko mice were crossed to the reporter mice C57/BL6 congenic B6.129S4-Gt(ROSA)26Sortm1Sor/J (stock 003474, Jackson Laboratories) and to C57/BL6 tamoxifen-Cre (B6.Cg-Tg(Cre/Esr1)5Amc/J mice (stock 004682), Jackson Laboratories). Adult mice were induced at P40 by one intraperitoneal injection of 0.2mg/g tamoxifen (Sigma, T5648) in corn oil (Sigma-Aldrich, C8267) and animals harvested between P102 and P210 were used for gene expression assays. All animals used for gene assays were Pkd1 cko/cko and either cre negative ('N', used as controls) or cre positive ('P', conditionally deleted mutants).

first: Gregory

last: Germino


title: Activating injury-responsive genes with hypoxia enhances axon regeneration through neuronal HIF-1α

status: Public on Jan 21 2016

city: Saint Louis

first: Valeria

last: Cavalli

state: Missouri

address: 660 S. Euclid Ave.

department: Anatomy and Neurobiology

institute: Washington University in St. Louis

summary: Injured peripheral neurons successfully activate a pro-regenerative transcriptional program to enable axon regeneration and functional recovery. How transcriptional regulators coordinate the expression of such programs remains unclear. Here we show that hypoxia-inducible factor 1α (HIF-1α) controls multiple injury-induced genes in sensory neurons and contribute to the pre-conditioning lesion effect. Knockdown of HIF-1α in vitro or conditional knockout in vivo impairs sensory axon regeneration. The HIF-1α target gene Vascular Endothelial Growth Factor A (VEGFA) is expressed in injured neurons and contributes to stimulate axon regeneration. Induction of HIF-1α using hypoxia enhances axon regeneration in vitro and in vivo in sensory neurons. Hypoxia also stimulates motor neuron regeneration and accelerates neuromuscular junction reinnervation. This study demonstrates that HIF-1α represents a critical transcriptional regulator in regenerating neurons and suggests hypoxia as a tool to stimulate axon regeneration.

overall_design: To study the genes regulated by HIF-1α in DRG neurons, we examined changes in gene expression in cultured DRG by microarray analysis, comparing DRG control condition to DRG overexpressing HIF-1α or to DRG in which HIF-1α was knocked down, in uninjured conditions as well as 3 and 12 h after in vitro axotomy. To express HIF-1α in cultured DRG neurons, human HIF-1α cDNA (Addgene, 18949) was sub-cloned into FUGW lentiviral vector for constitutively overexpression. HA-HIF1alpha-pcDNA3 was a gift from Dr. William Kaelin (Addgene plasmid #18949 (Kondo et al., 2002). To knock down HIF-1α MISSION shRNAs from Sigma were used and lentiviruses were generated as previously described (Cho and Cavalli, 2012). MISSION shRNAs from Sigma were used: HIF-1α, TRCN0000232222, TRCN0000232223. Total RNA was extracted 0, 3 and 12 h after axotomy and purified using PureLink RNA mini kit (Life Technologies) according to the manufacturer’s protocol. The RNA quality was verified using an Agilent Bioanalyzer 2100 (Agilent Technologies; Palo Alto, CA, USA) using the Eukaryotic Total RNA Nano Assay. Samples were then run using the Mouse Ref-8 v2.0 Expression BeadChip (Illumina, Inc.; San Diego, CA, USA) by the Genome Technology Access Center at Washington University.

first: Yongcheol

first: Jung

last: Shin

first: Eric

middle: E

last: Ewan

first: Young

last: Oh

first: Wolfgang

last: Pita-Thomas


title: Profound chemopreventative effects of a hydrogen sulfide-releasing NSAID in the APCMin/+ mouse model of intestinal tumorigenesis

status: Public on Jan 20 2016

city: London

first: Mark

middle: John

last: Paul-Clark

state: London

address: Dovehouse Street

department: National Heart and Lung Institute

country: United Kingdom

institute: Imperial College London

summary: Nonsteroidal anti-inflammatory drugs have been shown to reduce the incidence of gastrointestinal cancers, but the propensity of these drugs to cause ulcers and bleeding limits their use.  H2S has been shown to be a powerful cytoprotective and anti-inflammatory substance in the digestive system.  This study explored the possibility that a H2S-releasing nonsteroidal anti-inflammatory drug (ATB-346) would be effective in a murine model of hereditary intestinal cancer (APCMin+ mouse) and investigated potential mechanisms of action via transcriptomics analysis.  Daily treatment with ATB-346 was significantly more effective at preventing intestinal polyp formation than naproxen.  Significant beneficial effects were seen with a treatment period of only 3-7 days, and reversal of existing polyps was observed in the colon.  ATB-346, but not naproxen, significantly decreased expression of intestinal cancer-associated signaling molecules (cMyc, β-catenin).  Transcriptomic analysis identified 20 genes that were up-regulated in APCMin+ mice, 18 of which were reduced to wild-type levels by one week of treatment with ATB-346. ATB-346 is a novel, gastrointestinal-sparing anti-inflammatory drug that potently and rapidly prevents and reverses the development of pre-cancerous lesions in a mouse model of hereditary intestinal tumorigenesis.  These effects may be related to the combined effects of suppression of cyclooxygenase and release of H2S, and correction of most of the APCMin+-associated alterations in the transcriptome.  ATB-346 may represent a promising agent for chemoprevention of tumorigenesis in the GI tract and elsewhere.

overall_design: Total RNA obtained from colon of APCMin/+ mice treated for 7 days with vehicle, ATB-346 or naproxen. Tissue collected 7 weeks after the final dose of drug


title: Genetic deletion of osteopontin in TRAMP mice enhances the growth of aggressive prostate cancer with feature of human neuroendocrine tumors

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

institute: IRCCS Ospedale San Raffaele

summary: Osteopontin (OPN) is a secreted glycoprotein, belonging to the non-structural extracellular matrix (ECM), and its over expression in human prostate cancer cells has been associated with disease progression, androgen independence and metastases. Nevertheless the pathophysiology of OPN in prostate tumorigenesis has never been studied. We crossed TRansgenic Adenocarcinoma of the Mouse Prostate (TRAMP) mice with OPN deficient (OPN-/-) mice and followed tumor onset and progression in these double mutants. Ultrasound examination detected the early onset of a spherical homogeneous tumor in about 60% of OPN-/- TRAMP mice that seldom occurs in parental TRAMP mice. Histology and immunohistochemistry characterized these tumors for being Tag positive but negative for AR, highly proliferative and endowed of neuroendocrine (NE) features. Gene expression profiling showed up-regulation of genes involved in tumor progression, cell cycle and neuronal differentiation in OPN-deficient versus -sufficient TRAMP tumors. Down-regulated genes included key genes of TGF pathway, and a role for TGF in NE differentiation of prostate cancer was also confirmed at the protein level. Furthermore, NE genes and particularly those characterizing early prostatic lesions of OPN-deficient mice were found to correlate with those of human NE tumours. These data underscore a novel role of OPN at early stages of prostate cancer growth, protecting against the development of aggressive NE tumors.

overall_design: Total RNA obtained from prostate tumors from 18 and 30 weeks old TRAMP mice, compared to RNA extracted from prostate tumors and prostate tissue from Osteopontin-deleted TRAMP mice

first: Mauri

last: Giorgio

first: Colombo

middle: M

last: Paolo


title: Influence of LKB1 on contraction-induced gene expression in skeletal muscle

city: Provo

first: David

middle: M.

last: Thomson

state: Utah

department: PDBIO

institute: Brigham Young University

summary: Assessment of gene expression after muscle contraction with the hypothesis that the lack of LKB1 will alter gene expression, especially inflammation-related genes.

overall_design: RNA was obtained from the gastrocnemius/plantaris/soleus complex from wild-type and skeletal muscle specific LKB1 knockout mice at rest or immediately after 15 minutes of in situ muscle contraction via sciatic nerve stimulation. 7 samples per group.

middle: T

last: Ebbert


title: Inactivation of interferon signaling promotes the establishment of an immunosuppressive microenvironment in colorectal cancers

status: Public on Jan 15 2016

city: Philadelphia

first: daniel

last: beiting

state: PA

address: 380 S. University Ave

department: Pathobiology

institute: University of Pennsylvania

summary: Tumors arise and grow despite anti-cancer immune responses. These responses can be stimulated by immunotherapies such as immune checkpoint inhibitors (e.g. anti-PD1 antibodies) and chimeric antigen receptors (CAR). Efficacy of these agents in solid tumors including colorectal cancers (CRC) is limited by immunosuppressive tumor microenvironment (TME) that prevents killing of malignant cells by cytotoxic T lymphocytes (CTL). Understanding the nature of TME-generated immunosuppression is of paramount importance. Here we report that TME elicited immunosuppression via eliminating activated CTL; this elimination required TME stress-induced downregulation of the IFNAR1 chain of type I interferon (IFN) receptor and attenuation of its signaling. Downregulation of IFNAR1 was observed in human colorectal cancers (CRC) and in mouse CRC models where it was required for efficient tumor development and progression. Stabilization of IFNAR1 on CTL improved their survival and increased anti- tumor activities of CAR T cells and PD1 inhibitors thereby providing a rationale for targeting IFNAR1 degradation for immunotherapies optimization.

overall_design: Two genotypes of mice were examined either 9 or 21 days post injection of MC38 colon cancer cells or MC38mRFP cells, respectively.  2-3 replicate mice were analyzed on separate arrays for each condition.  6 conditions in total were analyzed.

first: Daniel

last: Beiting

first: Serge

last: Fuchs

first: Kanstantsin

last: Katlinski


title: Mitochondrial functional aberrations in a mouse model of non-ischemic heart failure

status: Public on Jan 19 2016

city: Houston

first: Anisha

last: Gupte

address: 6565 Fannin St F8-073

department: Bioenergetics Center

institute: Houston Methodist Hospital

summary: We characterized the metabolic and cardiac mitochondrial function in a mouse model of non-ischemic HF. Inhibition of nitric oxide synthesis and hypertension, which often present together, are two important risk factors in human non-ischemic HF. Compared with L-NAME L-NG-Nitroarginine methyl ester (L-NAME), an inhibitor of nitric oxide synthesis or Angiotensin II (AngII), a hypertensive agent treatment alone, L-NAME+AngII induced the most severe HF phenotype characterized by edema, hypertrophy, fibrosis, increased blood pressure and reduced ejection fractions. L-NAME+AngII treated mice had robust deterioration of cardiac mitochondrial function we observed. Microarray analyses revealed majority of the gene changes attributed to the combination of L-NAME+AngII. Pathway analyses indicated significant changes in metabolic pathways such as mitochondrial oxidative phosphorylation, fatty acid metabolism and tricarboxylic acid pathways etc.in L-NAME+AngII hearts. We conclude that combination of L-NAME+AngII exacerbates cardiac contractile and mitochondrial functional de-regulation compared with L-NAME and AngII alone, resulting in non-ischemic HF. This model of heart failure may be highly valuable in studying mechanisms and treatments for non-ischemic heart failure.

overall_design: Twelve week-old C57BL6 male mice were randomly assigned to 4 groups: 1. Control, 2. L-NAME treatment, 3. AngII treatment, 4. L-NAME+AngII treatment.L-NAME (0.3 mg/ml with 1% NaCl) was administered in drinking water. AngII (0.7 mg/kg/day) was administered via subcutaneous micro-osmotic pumps. L-NAME and AngII were administered to mice for 5 weeks and 4 weeks in combination to induce HF or alone to study the effects of the individual agents.

first: Aijun

last: Zhang

first: Shumin

last: Li

first: Dale

last: Hamiltion


title: Gene expression in liver tissues derived from wild-type and Siglec-E-deficient mice at 55 weeks of age

city: La Jolla

first: Ajit

last: Varki

state: California

address: 9500 Gilman Drive

institute: UC San Diego

summary: We show that mice lacking Siglec-E, the main member of the CD33rSiglec family, exhibit reduced survival. Removal of Siglec-E causes the development of exaggerated signs of aging at the molecular, structural, and cognitive level. We found that accelerated aging was related both to an unbalanced ROS metabolism, and to a secondary impairment in detoxification of reactive molecules, ultimately leading to increased damage to cellular DNA, proteins and lipids. Taken together, our data suggest that CD33rSiglecs co-evolved in mammals to achieve a better management of oxidative stress during inflammation, which in turn reduces molecular damage and extends lifespan.

overall_design: Total RNA obtained from liver tissues from two wild-type and three Siglec-E-deficient mice

first: Oliver

last: Pearce


title: Microarray studies on genes stimulated by RANKL in bone marrow macrophages in a cyclooxygenase-2-dependent manner

status: Public on Jan 07 2016

city: Farmington

first: Carol

last: Pilbeam

state: CT

address: 263 Farmington Avenue

department: Medicine and New England Musculoskeletal Institute

institute: UConn Health

summary: Overall goal was to look for the differentially expressed genes between receptor activator of nuclear factor kappa-B ligand (RANKL)-stimulated wild type (WT) bone marrow macrophages (BMMs) and the BMMs in which the expression or the enzyme activity of cyclooxygenase-2 (Cox2), the major enzyme for prostaglandin E2 (PGE2) synthesis, is absent. For this purpose, two separate microarrays (experiment 1 and 2) were done. In both the experiments, Serum Amyloid A3 (Saa3) was one of the most highly differentially expressed gene.

overall_design: For experiment 1, BMMs were isolated from the bone marrow of Cox2 knockout (KO) and WT mice. Out of the three sample groups, two were treated with 30 ng/ml each of macrophage-colony stimulating factor (M-CSF) and RANKL, while the third group was treated with M-CSF only, for 1 day. Two of the sample groups had n=3 biological replicates (i.e. samples), while the third one had n=4 biological replicates. The differential gene expression comparisons among the sample groups were done as (A) WT+MCSF+RANKL_d1 versus Cox2KO+MCSF+RANKL_d1 and (B) WT+MCSF+RANKL_d1 versus WT+MCSF_d1.   For experiment 2 also, BMMs were obtained from Cox2 KO and WT mice. All the four sample groups were treated with M-CSF and RANKL for 3 days. All the four sample groups had n=4 biological replicates. One of the WT sample group was also treated with an inhibitor of Cox2 activity,NS398 (0.1 µm) and one of the KO sample group was also treated with the product of Cox2 enzyme, PGE2 (1 µm). The differential gene expression comparisons among the sample groups were done as (A) WT+MCSF+RANKL_d3 versus Cox2KO+MCSF+RANKL_d3; (B) WT+MCSF+RANKL_d3 versus WT+MCSF+RANKL+NS398_d3 and  (C) Cox2KO+MCSF+RANKL+PGE2_d3 versus Cox2KO+MCSF+RANKL_d3.

first: Shilpa

last: Choudhary

first: Anupinder

last: Kaur

first: Janet

last: Hager


title: Gene expression in the hypothalamus that responds to STZ-induced type 1 diabetes and can be reversed by central leptin action

status: Public on Feb 02 2016

first: Qingchun

last: Tong

address: 1825 Pressler Street

institute: The Account Payable, University of Texas at Houston

summary:
Central leptin action is sufficient to restore euglycemia in type 1 diabetes via an insulin-independent manner. To examine the mechanism in the hypothalamus at the transcription level,
numerous genes that showed expression changes to STZ-induced type 1 diabetes and were reversed by central leptin action were identified.

overall_design: Hypothalamus tissues from control mice, mice with STZ-induced type 1 diabetes, and mice with STZ-induced type 1 diabetes corrected by central leptin infusion were used.

first: Yuanzhong

last: Xu

first: Martin

last: Myers

first: Jeffrey

last: Chang

first: Yong


title: Cutting Edge: IL-4, IL-21, and IFN-g Interact to Govern TBET and CD11c Expression in TLR-Activated B Cells

status: Public on Jan 23 2016

first: daniel

last: beiting

summary: T-Box Expressed in T cells (TBET) and CD11c expression in B cells is linked with IgG2c isotype switching, virus-specific immune responses, and humoral autoimmunity. However, the activation requisites and regulatory cues governing TBET and CD11c expression remain poorly defined. In this article, we reveal a relationship among TLR engagement, IL-4, IL-21, and IFN-g that regulates TBET expression in B cells. We find that IL-21 or IFN-g directly promote TBET+ expression in the context of TLR engagement. Further, IL-4 antagonizes TBET induction. Finally, IL-21, but not IFN-g, promotes CD11c expression independent of TBET. Using influenza virus and Heligmosomoides polygyrus infections, we show that these interactions function in vivo to determine whether TBET+ and CD11c+ B cells are formed. These findings suggest that TBET+ B cells seen in health and disease share the common initiating features of TLR-driven activation within this circumscribed cytokine milieu.

overall_design: Splenic B cells from replicate mice, for two different genotypes (WT and Tbx21-/-), were stimulated with either interferon-gamma (IFNG) or interleukin-21 (IL21).

first: Daniel

last: Beiting

first: Michael

last: Cancro

last: Naradikian


title: Type I Interferons Control Proliferation and Function of Intestinal Epithelium

status: Public on Jan 05 2016

summary: Wnt pathway-driven proliferation and renewal of the intestinal epithelium must be tightly controlled to prevent development of cancer and barrier dysfunction. Although type 1 interferons (IFN) produced in the gut under influence of microbiota are known for their anti-proliferative effects, the role of these cytokines in regulating intestinal epithelial renewal is largely unknown. Here we report a novel role for IFN in the context of intestinal knockout of casein kinase 1α (CK1α), which controls ubiquitination and degradation of both β-catenin and the IFNAR1 chain of the IFN receptor. Ablation of CK1α leads to activation of both β-catenin and IFN pathway and prevents unlimited proliferation of intestinal epithelial cells despite constitutive β-catenin activity. IFN signaling contributes to activation of the p53 pathway and appearance of apoptotic and senescence markers in the CK1α-deficient gut. Concurrent genetic ablation of CK1α and IFNAR1 leads to intestinal hyperplasia, robust attenuation of apoptosis, and rapid and lethal loss of the barrier function. These data indicate that IFN plays an important role in controlling proliferation and function of intestinal epithelium in the context of β-catenin activation.

overall_design: Two conditions were examined, with 2 replicates for each condition, yielding 4 samples in total.

first: Serge

last: Fuchs

first: Yuliya

last: Katlinskaya


title: MicroRNA and gene expression profiling of primary human hepatocytes after berberine chloride treatment

status: Public on Dec 31 2015

city: Taipei

first: Ting-fang

last: Lo

address: 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan

department: Institute of Biological Chemistry

country: Taiwan

institute: Academia Sinica

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

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

overall_design: Refer to individual Series


title: DNMT1 KNOCKOUT IN MURINE LIVER (expression)

status: Public on Apr 01 2016

city: Copenhagen

first: Jesper

middle: B

last: Andersen

address: Ole Maaloes Vej 5

department: Biotech Research and Innovation Centre

country: Denmark

institute: Copenhagen University

summary: Gene expression analysis of liver after DNMT1 knock down. DNMT1 KO versus control livers at week 4, 8 and 20.

overall_design: 24 Samples analyzed

first: Snorri

middle: S

last: Thorgeirsson


title: Suppression of type I interferon signaling overcomes the oncogene-induced senescence and mediates melanoma development and progression

status: Public on Jan 14 2016

summary: Activation of oncogenes often leads to induction of the DNA damage responses and onset of the cell senescence. Given that DNA damage can also trigger production of type I interferons (IFN) that contribute to senescence development, we sought to determine the role of IFN in the oncogene-induced senescence. Our data in mouse model demonstrate that inactivation of IFN signaling is sufficient for inducing melanomas in melanocytes harboring mutant Braf. Restoration of IFN signaling in IFN-deficient melanoma cells induces cell senescence and suppresses melanoma progression. In addition, data in human patients that received high dose IFN therapy and in mouse transplanted tumor models strongly suggest the importance of the non-cell-autonomous IFN signaling. Suppression of IFN signaling mediated by the downregulation of IFN receptor IFNAR1 invariably occurs during development of mouse melanoma. Mice harboring the IFNAR1 mutant, which is relatively resistant to downregulation, delay melanoma development, suppress the metastatic disease, and better respond to treatment with BRAF or PD1 inhibitors. These results suggest that IFN signaling is an important tumor suppressive pathway that inhibits melanoma development and progression. Accordingly, the inhibition of IFN pathway via IFNAR1 downregulation plays a key role in melanoma pathogenesis. Conversely, these data also argue for targeting IFNAR1 downregulation to prevent the metastatic disease and improve the efficacy of molecularly targeted and immune-targeted therapies.

overall_design: Two genotypes of mice were examined at 2 to 3 times after tamoxifen adminstration, with 2 replicates for each condition, yielding 8 samples in total.

first: Kanstantsin

last: Katlinski


title: RAG-mediated DNA double strand breaks activate a cell-type-specific checkpoint to inhibit pre-B cell receptor signals

status: Public on Jan 13 2016

city: St. Louis

middle: J

last: Bednarski

department: Pediatrics

institute: Washington University School of Medicine

summary: Pre-B cell receptor (pre-BCR) signals initiate immunoglobulin light (Igl) chain gene assembly leading to RAG-mediated DNA double-strand breaks (DSBs).  These signals also promote cell cycle entry, which could cause aberrant DSB repair and genome instability in pre-B cells.  Here we show that RAG DSBs inhibit pre-BCR signals through the ATM- and NF-κB2-dependent induction of SPIC, a hematopoietic-specific transcriptional repressor.  SPIC inhibits expression of the SYK tyrosine kinase and BLNK adaptor to prevent the pre-BCR from inducing additional Igl chain gene rearrangements and driving pre-B cells with RAG DSBs into cycle.  We propose that pre-B cells toggle between pre-BCR signals and this RAG DSB-dependent checkpoint to maintain genome stability while iteratively assembling Igl chain genes.

overall_design: Three independent IL-7 cultures for each genotype (Rag1-/-:μIgH:Bcl2, Art-/-:μIgH:Bcl2 and Art-/-:Nfkb2-/-:μIgH:Bcl2) were withdrawn from IL-7 for 2 days.  RNA was isolated using RNeasy (Qiagen).  Gene expression profiling was performed using Illumina MouseRef-8 expression microarrays.

first: Barry

last: Sleckman


title: Genome-wide analysis of bone marrow-derived dendritic cells, unstimulated or stimulated with Bifidobacterium in vitro.

status: Public on Nov 12 2015

city: Chicago

first: Thomas

middle: F.

last: Gajewski

state: ILLINOIS

address: 929 E 57th St GCIS W423H

institute: University of Chicago

summary: Comparison of gene expression in bone marrow-derived dendritic cells (DCs) unstimulated or stimulated with Bifidobacterium in vitro.

overall_design: BMDC stimulation with Bifidobacterium in vitro: Cells isolated from the tibiae and femurs of WT C57BL/6 mice were cultured in DMEM medium containing 10% FBS and 1% penicillin/streptomycin, in the presence of rmGM-CSF (20 ng/ml; BioLegend) for 8 days at 37°C with 5% CO2.  BMDCs were then stimulated for 4 hours with medium alone or with rehydrated Bifidobacterium-containing medium at a ratio of 1:10 BMDCs to bacterial cells.  Total RNA was isolated using RNeasy® Micro kit (Qiagen) and submitted to the Functional Genomics Facility at the University of Chicago for gene expression profiling.  RNA integrity and concentration were assessed using an AgilentBioanalyzer 2100, and all RNA samples used for microarray analysis had an RNA Integrity Number = 10.0.

first: Sivan

last: Ayelet

first: Gajewski

last: Thomas


title: Ssb1 and Ssb2 have essential and overlapping functions in adult stem cell homeostasis - megakaryocyte-erythroid progenitor data.

status: Public on Jan 01 2016

city: Brisbane

first: Glen

last: Boyle

address: 300 Herston Road Herston

department: Department of Cell and Molecular Biology, Cancer Program

institute: QIMR Berghofer Medical Research Insitute

summary: The single-stranded DNA binding proteins SSB1 and SSB2 are crucial regulators of the DNA damage response, however the overlapping functions of these related proteins is incompletely understood. We generated mice where both Ssb1 and Ssb2 were constitutively or conditionally deleted. Constitutive Ssb1/Ssb2 double knockout (DKO) caused early embryonic lethality, while conditional Ssb1/Ssb2 double knockout (cDKO) in adult mice resulted in acute lethality due to bone marrow failure and intestinal atrophy featured by stem and progenitor cell depletion. cDKO cells exhibited increased replication stress, R-loop accumulation, genome wide double strand breaks and cytosolic single-stranded DNA. Transcriptional profiling of cDKO cells revealed activation of p53 DNA damage and interferon responses. Hematopoietic stem and progenitor cells in cDKO mice showed enforced cell cycling, with subsequent apoptotic cell death. Collectively, these results demonstrate that Ssb1 and Ssb2 have compensatory functions in maintaining genomic stability and are collectively necessary for adult stem cell homeostasis.

overall_design: Single colour, Illumina MouseRef-8 v2.0 Beadarrays.

first: Wei

last: Shi

first: Therese

last: Vu

first: Didier

last: Boucher

first: Anna

last: Biernacka

first: Jules

last: Nde

first: Raj

last: Pandita

first: Fares

last: Al-Ejeh

first: Jessie

last: Jeffery

first: Janelle

last: Hancock

first: Amanda

last: Bain

first: Marta

last: Grzelak

first: Magdalena

last: Skrzypczak

first: Anbhishek

last: Mitra

first: Norbert

last: Dojer

first: Nicole

last: Cloonan

first: Olivier

last: Becherel

first: John

last: Finnie

middle: R

last: Skaar

first: Carl

last: Walkley

first: Tej

first: Maga

last: Rowicka

first: Krzysztof

last: Ginalski

first: Steven

middle: W

last: Lane

first: KumKum

last: Khanna


title: Ssb1 and Ssb2 have essential and overlapping functions in adult stem cell homeostasis

first: Glen

last: Boyle


title: Gene expression profiling reveals a novel regulatory role for Sox21 in mouse trophoblast stem cell differentiation.

status: Public on Nov 10 2015

first: Mana

last: Parast

address: 9500 Gilman drive #0695

department: Pathology

institute: University of California San Diego

summary: In this study we introduced Sox21 as a new regulator of trophoblast stem cell (TSC) differentiation. The transcriptome of different cell types were analyzed and compared to identify a TSC gene signature.

overall_design: In order to identify novel TSC specific genes, we performed genome-wide expression profiling of TSCs, embryonic stem cells, epiblast stem cells, and mouse embryo fibroblasts derived from mice of the same genetic background (129S1/SvImJ).

first: Matteo

last: Moretto-Zita

first: Francesca

last: Soncin

first: David

last: Natale

first: Donald

last: Pizzo


title: Genome-wide analysis in ESET+/+ and ESET-/- thymocytes

city: Ichikawa-shi

first: SHOICHI

last: TAKIKITA

state: Chiba

address: 1-7-1 Kounodai

department: Department of Immunology and Pathology

country: Japan

institute: The Research Center for Hepatitis and Immunology, Research Institute, National Center for Global Health and Medicine

summary: Analysis of ESET deficient thymocytes at gene expression level. Each thymocyte developmental stage (preselected DP, postselected DP and CD4SP) was analysed.

overall_design: Total RNA obtained from isolated subpopulations of thymocytes from ESET+/+ and ESET-/- mice were analysed.

first: Shoichi

last: Takikita

first: Takaho

last: Endo

first: Takeshi

last: Otsubo

first: Yuki

middle: I

last: Kawamura

first: Taeko

last: Dohi

first: Kenshiro

last: Oshima

first: Masahira

last: Hattori

first: Tetsuro

last: Toyoda

first: Ryunosuke

last: Muro

first: Toshiyuki

last: Takai

last: Weis

first: Yoichi

last: Shinkai

first: Harumi

last: Suzuki


title: Ssb1 and Ssb2 have essential and overlapping functions in adult stem cell homeostasis - granulocyte-macrophage progenitor data.

first: Glen

last: Boyle

first: Wei

last: Shi

first: Therese

last: Vu

first: Didier

last: Boucher

first: Anna

last: Biernacka

first: Jules

last: Nde

first: Raj

last: Pandita

first: Fares

last: Al-Ejeh

first: Jessie

last: Jeffery

first: Janelle

last: Hancock

first: Amanda

last: Bain

first: Marta

last: Grzelak

first: Magdalena

last: Skrzypczak

first: Anbhishek

last: Mitra

first: Norbert

last: Dojer

first: Nicole

last: Cloonan

first: Olivier

last: Becherel

first: John

last: Finnie

first: Jeffrey

last: Skaar

first: Carl

last: Walkley

first: Tej

first: Maga

last: Rowicka

first: Krzysztof

last: Ginalski

first: Steven

last: Lane

first: KumKum

last: Khanna


title: Overlapping and distinct roles of LIN28 paralogs in reprogramming and stem cell metabolism

city: Boston

first: JIN

last: ZHANG

state: Massachusetts

address: 1 Blackfan Circle

department: Hematology/Oncology

institute: Harvard Medical School/Boston Children's Hospital

summary: The RNA binding protein paralogs LIN28A and LIN28B play critical roles in embryonic development, tumorigenesis, and pluripotency. Somatic cells can be reprogrammed to induced pluripotent stem (iPS) cells by overexpression of OCT4 and SOX2 together with NANOG and LIN28A (OSNA), but the exact roles LIN28A/B play are still poorly understood. Here we show that LIN28B likewise promotes reprogramming, and that reactivation of both endogenous LIN28A and B loci are required for maximal reprogramming efficiency. The LIN28B locus has open chromatin and is activated early during reprogramming, whereas LIN28A is activated at later stages by OCT4, marking the transition to bona fide iPS cells. By proteomic and metabolomic analysis, we demonstrate that LIN28A chiefly regulates let-7 and protein translation, whereas LIN28B promotes embryonic metabolism by repressing oxidative phosphorylation and enhancing glycolysis. Thus, LIN28A and LIN28B play independent and cooperative roles in reprogramming and pluripotent stem cell metabolism.

overall_design: 8 samples in total were analyzed. 2 replicates for each phenotypes. Controls are the wild type (flox) without lin28a/b loss of function.

first: Jin

last: Zhang

first: George

middle: Q

last: Daley


title: The choroid plexus transcriptome reveals changes in type I and II interferon responses in a mouse model of Alzheimer's disease

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

summary: Alzheimer’s disease (AD) is a neurodegenerative disease characterized by a marked decline in cognition and memory formation. Increasing evidence highlights the essential role of neuroinflammatory and immune-related molecules, namely the ones that are produced at the brain barriers, on brain immune surveillance, cellular dysfunction and amyloid beta (Aβ) pathology in AD. Therefore, understanding the response at the brain barriers may unravel novel pathways that are relevant for the pathophysiology of AD. Herein, we focused on the study of the choroid plexus (CP), which constitutes the blood-cerebrospinal fluid barrier, in aging and in AD. Specifically, we used the PDGFB-APPSwInd (J20) transgenic mouse model of AD, which presents early memory decline and progressive Aβ accumulation, and littermate age-matched wild-type (WT) mice, to characterize the CP transcriptome at 3, 5-6 and 11-12 months of age. The most striking observation was that the CP of J20 mice displayed an overall overexpression of type I interferon (IFN) response genes at all ages. Moreover, J20 mice presented a high expression of type II IFN genes in the CP at 3 months, which became lower than WT at 5-6 and 11-12 months. Importantly, along with a marked memory impairment and increased glial activation, J20 mice also presented a similar overexpression of type I IFN genes in the dorsal hippocampus at 3 months. Altogether, these findings provide new insights on a possible interplay between type I and type II IFN responses in AD and point to IFNs as mediators of cognitive decline in aging and in AD.

overall_design: The CP transcriptome of at least 3 mice of each age (3, 5-6 and 11-12 months) and of each genotype (WT or J20) was analyzed and compared.

first: Sandro

middle: D

last: Mesquita

first: Ana

last: Ferreira

first: Fuying

last: Gao

first: Daniel

middle: H

last: Geschwind

first: João

last: Sousa

first: Margarida

last: Correia-Neves

first: Nuno

first: Joana

last: Palha

first: Fernanda

last: Marques


title: MicroRNA expression profiling of primary human hepatocytes after berberine chloride treatment

first: Ting-fang

last: Lo

summary: Berberine, an isoquinoline alkaloid isolated from many medicinal herbs such as Coptis chinensis, has a wide range of pharmacological effects. Since xenobiotic drug-induced micoRNAs have recently emerged as key regulators in guiding their pharmacological effects and toxicity, we were interested in whether or not micoRNA expression was differentially altered by berberine treatment in liver. Here, we used miRNA microarray to analyze microRNA expression profiles of primary human hepatocytes after berberine chloride treatment or 0.08% DMSO as control.

overall_design: Comparing miRNA profiles of 40 M berberine-treated primary human hepatocytes to those of control cells sampled after 2 hours treatment. A 50 mM stock solution of Berberine chloride was prepared in DMSO. Cells were treated with 40 M berberine chloride or 0.08% DMSO as control.

first: Ting-Fang

first: Shui-Tein

last: Chen


title: mRNA analysis of gene expression in adipose tissue to compare high fat fed sgp130Fc transgenic vs IL6 knock-out vs wild-type mice

city: Clayton

first: Wei

last: Shi

state: Victoria

address: Wellington Rd

institute: Monash University

summary: We want to analyse on a broad level the difference of gene expression in the adipose tissue between high fat fed sgp130Fc Transgenic which have no IL6 transsignalling and the IL6 knockout which have no IL6 signalling at all. Because the sgp130Tg mice show a marked adipogenic phenotype we want to compare it with the IL6 KO.

overall_design: Total RNA extracted from flash frozen adipose tissue from obese, 5hr-fasted mice.

first: Michael

last: Kraakman

first: Helene

middle: L

last: Kammoun

first: Mark

middle: A

last: Febbraio


title: Tc17 cells are a pro-inflammatory, plastic lineage of pathogenic CD8+ T-cells that induce GVHD without anti-leukemic effects

status: Public on Sep 13 2015

first: Glen

last: Boyle

state: Queensland

summary: IL-17-producing cells are important mediators of graft-versus-host disease (GVHD) after allogeneic stem cell transplantation (SCT). Here we demonstrate that a distinct CD8+ Tc17 population develops rapidly after SCT but fails to maintain lineage fidelity such that they are unrecognizable in the absence of a fate reporter. Tc17 differentiation is dependent on alloantigen presentation by host-DC together with IL-6. Tc17 cells express high levels of multiple prototypic lineage-defining transcription factors (e.g. RORgt, T-bet) and cytokines (e.g. IL-17A, IL-22, IFNg, GM-CSF, IL-13). Targeted depletion of Tc17 early after transplant protects from lethal acute GVHD, however Tc17 cells are non-cytolytic and fail to mediate graft–versus–leukemia (GVL) effects. Thus, the Tc17 differentiation program during GVHD culminates in a highly plastic, hyper-inflammatory, poorly-cytolytic effector population which we term inflammatory Tc17 (iTc17). Since iTc17 mediate GVHD without contributing to GVL, therapeutic inhibition of iTc17 development in a clinical setting represents an attractive approach for separating GVHD and GVL.

first: Kate

last: Gartlan

last: Markey

first: Antipoi

last: Varelias

last: Bunting

first: Motoko

last: Koyama

first: Rachel

last: Kuns

first: Neil

middle: C

last: Raffelt

first: Stuart

last: Olver

first: Katie

middle: E

last: Lineburg

first: Melody

last: Cheong

first: Bianca

last: Teal

first: Mary

last: Lor

first: Iain

last: Comerford

first: Michele

last: Teng

last: Smyth

first: James

last: McCluskey

first: Jamie

last: Rossjohn

first: Brigitta

last: Stockinger

first: Steven

last: Lane

first: Andrew

last: Clouston

first: Shaun

last: McColl

first: Kelli

middle: P

last: MacDonald

first: Geoffrey

last: Hill


title: BET bromodomain inhibitors synergize with ATR inhibitors to induce DNA damage, apoptosis, senescence-associated secretory pathway and ER stress in Myc- induced lymphoma cells

status: Public on Dec 18 2015

city: Gothenburg

first: Joydeep

last: Bhadury

address: Medicinaregatan 1G, plan 6

department: Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Cancer Center

institute: Universirty of Gothenburg

summary:
The aim of the project was to determine the expression profiles of murine Myc-driven lymphpma cells (Lambda-820) treated with vehicle (DMSO, 1:1000), a BET inhibitor (RVX2135), an ATR inhibitor (VE-821) or a combination of RVX2135 and VE-821.
All experimnets were performed in presence of 10uM Q-VD-OPH to block apoptosis. Cells were harvested 24 h after treatment start.

overall_design: 4 samples (DMSO, RVX2135, VE-821 or RVX2135/VE-821) in duplicates

first: Somsundar

middle: V

last: Muralidharan

first: Jonas

last: Nilsson


title: Systematic Comparison of Mouse and Human Oral Squamous Cell Carcinoma by Using Functional Transcriptomic Analysis

status: Public on Dec 17 2015

city: Kwei-Shan Tao-Yuan

first: An

last: Hsu

address: 259 Wen-Hwa 1st Road

institute: Chang Gung University

summary: This study aims to compare the global expression signature of protein coding genes between oral cancers from carcinogen-induced mice and human patients. Combinatorial treatment of 4NQO and arecoline for 8 weeks consistently induced the formation of mouse oral cancer with morphology and pathology resembling human oral squamous cell carcinoma. In this dataset, 5 mouse normal tongue and 7 tumor samples were used and Illumina Mouse Ref-8 cDNA microarray was conducted.

overall_design: To identify protein coding genes differentially expressed in mice oral cancers, 7 tumor tissues from carcinogen-treated mice and 5 normal tongue tissues from control mice were used in a microarray-based analysis for protein-coding gene expression patterns.

first: Shu-Jen

last: Chen

first: Yi

last: Huang

first: Yi-Shiuan

last: Liu

first: Chieh-Tien

last: Shih

first: Hua-Chien

first: Bertrand

last: Tan


title: Circulating microRNAs as non-invasive biomarkers for early detection of non-small-cell lung cancer

city: Lyon

first: Magdalena

last: Wozniak

address: 150 cours Albert Thomas

department: Genetic Epidemiology

institute: International Agency for Research on Cancer

summary:
Plasma samples from 100 early stage (I to IIIA) non–small-cell lung cancer (NSCLC) patients and 100 non-cancer controls were screened for 754 circulating microRNAs via qRT-PCR, using TaqMan MicroRNA Arrays.
Our objective was to identify a panel of circulating microRNAs in plasma that will contribute to early detection of lung cancer.

overall_design: Case-control design

first: Paul

last: Brennan


title: Foxd3 binding at enhancers controls developmental timing of gene expression by regulation of histone acetylation [expression array]

status: Public on Dec 08 2015

city: San Francisco

first: Raga

last: Krishnakumar

address: 912E RMB, 35 Medical Center Way

institute: UCSF

summary: Transcription factor/enhancer interactions determine cell specific gene expression.  Here, we followed enhancers during differentiations of embryonic stem (ESCs) to epiblast like cells (EpiLCs).  There were highly dynamic changes in histone lysine 27 acetylation at enhancer sites throughout the genome. These sites were enriched for a Foxd3 binding motif, a forkhead transcription factor essential in early embryonic development. Surprisingly, Foxd3 occupied largely mutually exclusive sites in the ESCs versus EpiLCs. Foxd3 bound to nucleosome occupied regions, simultaneously evicting the histones while inhibiting full gene expression through the recruitment of histone deacetylases. Knockout of Foxd3 resulted in hyperacetylation and transcriptional upregulation of neighboring genes, many of which were further upregulated at later stages of differentiation. These data show that Foxd3 primes enhancer sites during pregastrulation by removing nucleosomes, yet suppresses neighboring histone hyperacetylation. Such a mechanism may be common to many transcription factors that prepare enhancers for later gene activation during development.

overall_design: Total RNA obtained Foxd3 knockout embryonic stem cells (ESCs) and epiblast-like cells (EpiLCs) (treated with 1uM tamoxifen for 36h to induce knockout) compared to wild-type controls

first: Robert

last: Blelloch


title: Spatiotemporal characterization of the cellular and molecular contributors to liver fibrosis in a murine hepatotoxic-injury model

status: Public on Dec 01 2015

first: Glen

middle: M

last: Boyle

summary: The interplay between the inflammatory infiltrate and tissue resident cell populations (e.g. epithelial cells, fibroblasts and macrophages) invokes fibrogenesis. However, the temporal and mechanistic contributions of these cell populations to fibrosis remain poorly defined. To address this issue, liver inflammation, ductular reaction (DR) and fibrosis were induced in C57BL/6 mice by thioacetamide (TAA) administration for up to 12 weeks. TAA treatment induced two phases of liver fibrosis.  A rapid peri-central inflammatory infiltrate enriched in F4/80+ monocytes co-localized with SMA+ myofibroblasts resulted in early collagen deposition, marking the start of an initial fibrotic phase (1-6 weeks).  An expansion of bone marrow derived macrophages proceeded a second phase, characterized by accelerated progression of fibrosis (> 6 weeks) followed the migration of the DR from the portal tracts to the centrilobular site of injury, in association an increase in DR/macrophage interactions. Although CCL2 mRNA was rapidly induced in response to TAA, CCL2 deficiency only partially abrogated fibrosis. In contrast, CSF-1R blockade diminished CCR2neg (Ly6Clo) monocytes, attenuated the DR and significantly reduced fibrosis, illustrating the critical role of CSF-1 dependent monocyte/macrophage differentiation and linking the two phases of injury. We demonstrate that in response to liver injury, CSF-1 drives early monocyte mediated myofibroblast activation and collagen deposition, subsequent macrophage differentiation and their association with the advancing DR, the formation of fibrotic septa and the progression of liver fibrosis to cirrhosis.

first: Michelle

last: Melino

first: Victoria

last: Gadd

first: Kylie

last: Alexander

first: Lynette

last: Beattie

first: Katie

last: Lineburg

last: Martinez

first: Bianca

last: Teal

first: Laetitia

last: LeTexier

first: Katharine

last: Irvine

first: Gregory

last: Miller

first: Andrew

last: Clouston

first: Elizabeth

last: Powell


title: ATMIN function in p53-deficient GBM

status: Public on Dec 23 2015

city: London

first: Axel

last: Behrens

address: 44 Lincoln's Inn Fields

institute: Francis Crick institute

summary: We report the expression anaysis of neural stem cells lacking p53, ATMIN, or both.  p53-deficent cells form GBM, which is significanly delayed in the absence of ATMIN.

overall_design: Expression analysis in primary neural stem cells with 4 genotypes.

first: Sophia

last: Blake


title: Expression analysis of KHR and KR oral tumors with intact or deficient Notch1

status: Public on Sep 09 2015

first: Michael

last: Spiotto

state: IL

department: Radiation Oncology

institute: The University of Chicago

summary: KHR and KR tumors grow faster when deficient for Notch1. The hypothesis was to test for differences in gene expression between KHR and KHR oral tumors with intact or deficient Notch1 haplotypes.

overall_design: Total RNA was isolated for KHR (n=5), KHR-N+/- (n=4), KHR-N-/- (n=5), KR-N+/- (n=5), KR-N-/- (n=4) oral tumors. Expression profiling was performed using the Illumina MouseRef-8 v2 (GPL6885) array. Studies were conducted using tumors from C57BL/6 mice.

first: Rong

last: Zhong

first: Riyue

last: Bao

first: Pieter

last: Faber

first: Mark

last: Lingen


title: Interaction between bone marrow mesenchymal stromal cell and neuroblastoma cells leads to a VEGFA-mediated increase in osteoblastogenesis

status: Public on Nov 19 2015

first: Vasu

last: Punj

address: Biggy Street

institute: USC

summary: To identify signature genes associated with increased osteoblastic phenotype in response to co-culture of  mesenchymal  and neuroblastoma cells

overall_design: Total RNA was obtained from co-cultured mesenchymal and neuroblastoma cells. In parallel RNA from Doxycycline treated cells was used as control. Gene expression profiling was performed using Illumina MouseRef-8 v2.0 BeadChipTM

first: Josephine

last: HaDuong

first: John

last: Smith

first: Laurence

last: Blavier

first: Sanjeev

middle: K

last: Baniwal

first: Baruch

last: Frenkel

first: Jemily

last: Malvier

first: Richard

last: Sposto

first: Yves

last: DeClerck


title: Genome-wide analysis of tumor-infiltrating dendritic cells comparing C57BL/6 mice obtained from Jackson laboratories or Taconic farms, untreated or treated with Bifidobacterium.

first: Thomas

last: Gajewski

summary: Comparison of gene expression in dendritic cells (DCs) isolated from tumors of C57BL/6 obtained from Taconic farms vs DCs isolated from tumor of C57BL/6 mice obtained from Jackson Labortaory vs DCs isolated from tumors of C57BL/6 obtained from Taconic farms and orally gavaged with Bifidobacterium prior to tumor implantation

overall_design: Upon arrival in our facility, TAC mice were gavaged with Bifidobacterium once a week for two weeks. Bifidobacterium-fed mice, newly arrived JAX mice, and newly arrived TAC mice were inoculated subcutaneously in both flanks with 5x106 DRAQ5-labeled B16.SIY tumor cells.  40hrs following tumor implantation, whole tumors including infiltrating immune cells were digested in collagenase (Worthington) and filtered into single cell suspensions. Samples from 5 mice in each group were pooled and subsequently stained with Fixable Viability-ef506 (Ebioscience), CD45-AF488 (Bioloegend, 30-F11), CD3-ef450 (Ebioscience, 145-2C11), CD19-PB (Ebioscience, 1D3), I-A/I-E-PECy7 (Biolegend, M5/114.15.2), CD11c-PE (Ebioscience, N418) and CD11b-PerCpCy5.5 (BD, M1/70). Live CD45+CD3-CD19-MHCIIhiCD11c+ dendritic cells were sorted directly into RLT Buffer (Qiagen) using FACSAriaIII (BD) and stored immediately on dry ice.  Total RNA was isolated using RNeasy® Micro kit (Qiagen).  RNA was submitted to the Functional Genomics Facility at the University of Chicago for gene expression profiling.  RNA integrity and concentration were assessed using an Agilent Bioanalyzer 2100, and all RNA samples used for microarray analysis had an RNA Integrity Number > 9.0.  Total RNA was processed into biotinylated cRNA using the Epicentre TargetAmp™ 2-Round Biotin-aRNA Amplification Kit 3.0 (TAB2R71024).  The cRNA was hybridized to Illumina MouseRef8v2 arrays using Illumina provided protocols and scanned using an Illumina HiScan.  Quantile normalized and background subtracted values were subsequently analyzed using R.

first: Sivan

last: Ayelet

first: Gajewski

last: Thomas


title: Gene expression profiling of mouse salivary gland cancer stem cells treated with Wnt inhibitors

status: Public on Oct 06 2015

city: Berlin

first: Liang

last: Fang

address: Robert-Rössle-Str. 10

institute: Max Delbrück Center for Molecular Medicine

summary:
To analyze whether Wnt inhibitors LF3 and ICG-001 have similar influence on the gene expression of mouse salivary gland cancer stem cells
Wnt/β-catenin signaling is a system that is essential for embryogenesis and tissue homeostasis which has been highly conserved through evolution. A deregulation of Wnt/β-catenin signals can initiate and promote human cancers, specifically of the colon, head and neck. As such, Wnt/β-catenin signaling represents an attractive target for cancer therapy. So far, however, no rationally developed compound targeting Wnt signaling has found clinical use. The interaction between β-catenin and TCF4 is necessary in the transduction of the signal; here we performed a High-Throughput-Screening (HTS) using AlphaScreen and ELISA techniques to identify small molecules that specifically disrupt this interaction. We identified compound LF3, a 4-thioureido-benzenesulfonamide derivative, as a robust inhibitor of β-catenin/TCF4 interactions and thus a good starting point for drug discovery, as suggested by Lipinski's “rule of five.” LF3 inhibited Wnt/β-catenin signaling in cells with exogenous reporters and in colon cancer cells with endogenously high Wnt activity. Medicinal chemistry identified an essential core structure and residues that could not be modified in LF3. Compound LF3 inhibited a number of features of cancer cells related to Wnt signaling, including high cell motility in Boyden chamber assays, hyperproliferation through induction of cell cycle arrest at the G1 phase, and the overexpression of key Wnt target genes. LF3 does not cause apoptosis or cell death or interfere with cadherin-mediated cell-cell adhesion. Remarkably, the self-renewal capacity of cancer stem cells was blocked by LF3 in concentration-dependent manners, as demonstrated by examination of sphere formation of colon and head and neck cancer stem cells in serum-free, non-attached conditions. LF3 also reduced tumor growth and induced differentiation in colon tumors in mouse xenografts. LF3 is thus a specific inhibitor of canonical Wnt signaling with a significant potential for further development for preclinical and clinical studies in cancer treatment.

overall_design: Mouse salivary gland cancer stem cells were treated with LF3 and ICG-001 for 24 h and harvested in trizol for total RNA isolation.

first: Qionghua

last: Zhu


title: Effects of ursolic acid and tomatidine on skeletal muscle mRNA expression in aged mice.

status: Public on Sep 03 2015

city: Iowa City

first: Scott

last: Ebert

state: IA

address: 500 Newton Rd

department: Int Med

institute: University of Iowa

summary: For additional details see Ebert et al, Identification and Small Molecule Inhibition of an ATF4-dependent Pathway to Age-related Skeletal Muscle Weakness and Atrophy.

overall_design: Weight-matched cohorts of 22-month-old male C57BL/6 mice were provided ad libitum access to standard chow (control) or standard chow supplemented with 0.27% ursolic acid (UA) or 0.05% tomatidine (TM) for 2 months.  After the 2 month treatment period, quadriceps femoris muscles were harvested.  mRNA levels in muscles harvested from ursolic acid or tomatidine fed mice were normalized to levels in muscles fed control diet.

first: Christopher

last: Adams


title: Genome-wide RNA expression analysis of mouse spleens in parent-into-F1 lupus immune response

status: Public on Sep 02 2015

city: Bethesda

first: Clifton

middle: Lee

last: Dalgard

state: Maryland

address: 4301 Jones Bridge Road B2038

department: Anatomy Physiology & Genetics

institute: Uniformed Services University

summary: Analysis of whole spleen tissue expression signature in divergent responses from two parent-into-F1 lupus mouse model systems.  The hypothesis is that strain differences of CD4 T cells exhibit difference lupus-inducing proclivity.

overall_design: Total RNA obtained from recipient mouse spleen at day 14 post-engraftment were profiled by Illumina BeadArray expression analysis

first: Charles

middle: S

last: Via