title: Aryl hydrocarbon receptor senses bacterial pigmented virulence factors and orchestrates anti-bacterial defenses (part 1)

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

summary: The aryl hydrocarbon receptor (AhR) is a highly conserved ligand-dependent transcription factor that senses environmental toxins and endogenous ligands, thereby inducing detoxifying enzymes and modulating immune cell differentiation and responses. We hypothesized that AhR not only evolved to sense pollutants from the environment, but also insults of microbial origin. We demonstrate that bacterial pigmented virulence factors, namely the phenazines pyocyanin and 1-hydroxyphenazine from Pseudomonas aeruginosa and the naphthoquinone phthiocol from Mycobacterium tuberculosis, are ligands of AhR. AhR activation leads to degradation of these virulence factors and regulated cytokine and chemokine production. The relevance of AhR to host defense is underlined by heightened susceptibility of AhR-deficient mice, both to P. aeruginosa and M. tuberculosis. Our data demonstrate that AhR senses distinct bacterial virulence factors and controls anti-bacterial responses. We provide evidence for a previously unidentified role for AhR as an intracellular pattern recognition receptor, and identify bacterial pigmented virulence factors as a new class of pathogen-associated molecular patterns.

overall_design: Microarray experiments were performed as single-color hybridizations. Quality control and quantification of total RNA amount was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies) and a NanoDrop 1000 spectrophotometer (Kisker).

first: Pedro

last: Moura-Alves

first: Erica

last: Houthuys

first: Kellen

last: Faé

first: Anca

last: Dorhoi

first: Stefan

last: Kaufmann

first: Hans


title: Homeostatic interactions between chemoprotective functions at the blood-brain barrier

status: Public on Dec 31 2013

city: San Francisco

first: Michael

last: DeSalvo

state: CA

department: Department of Anesthesia

country: USA

institute: UC San Francisco

summary:
The blood-brain barrier (BBB) is an evolutionary conserved tissue interface that possesses potent chemical protection properties functioning to strictly modulate the central nervous system (CNS) microenvironment. These same properties, including tight cellular junctions and efflux transporters, also limit access of CNS-active pharmaceuticals. For this reason, understanding the molecular mechanisms that regulate BBB chemical protection is of great biomedical interest. The BBB of Drosophila consists of two surface glia layers that completely surround the brain. This tissue interface contains both “tight” cellular junctions (termed septate junctions) and drug efflux transporters; thus, the Drosophila BBB can potentially serve as a model for understanding complex regulation of BBB physiology.
In this study, we show reciprocal compensatory responses following disruption of critical BBB genes: deletion of the septate junction regulator Moody causes increased drug efflux and up-regulation of the P-glycoprotein ortholog Mdr65; conversely, disruption of Mdr65 expression causes increased septate junction tightness and up-regulation of Moody. We reveal these homeostatic interactions with physiologic observations, gene expression data, and anatomical images of the BBB surface. Whole brain microarray data point to responses that are consistent with our physiologic observations and these responses are likely localized to the BBB. To our knowledge, this is the first observation of a reciprocal compensatory interaction at a tissue barrier. Furthermore, this study paves the way for future studies elucidating the direct pathways that link GPCR signaling and drug transporter regulation at the BBB.

overall_design: The main comparisons are between WT_new, C17 (Moody null), and PMdr65 (Mdr65 null). Since WT_new were processed on a different day than C17 and PMdr65, we also included another WT sample (WT_old) to control for genes that change depending on batch effects. Since the mutants are also in a different genetic background than WT, we also included a control that is in a similar background (UAS_control).

middle: K

first: Roland

middle: J

last: Bainton


title: Aryl hydrocarbon receptor senses bacterial pigmented virulence factors and orchestrates anti-bacterial defenses

status: Public on Jan 01 2014

country: Germany

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Transcriptome perturbation analysis from 16 hours APF Drosophila notum.

city: Paris

first: francois

last: schweisguth

address: 25 rue du Dr Roux

country: France

institute: Institut Pasteur

summary: Genome-wide transcriptome analysis of genetic pertubations induced in Drosophila notum by the over-expression of the transcription factors Achaete, Asense, E(spl)m3-HLH and Senseless.

overall_design: Transient over-expression of GFP (control), Achaete (Ac), Senseless (Sens), Asense (Ase) and E(spl)m3-HLH transcription factors in Drosophila notum using sca-Gal4, tub-Gal80ts. Transcription factorshave been over-expressed alone or in combinations. Three biological replicates were performed for each conditions.

first: K

last: Mazouni

first: F

last: Bernard

first: H

last: Rouault

first: C

last: Besson

first: L

last: Couturier

last: Schweisguth.


title: Conditional DamID and Transcriptome studies during sensory organ development in Drosophila

type: Genome binding/occupancy profiling by genome tiling array


title: An RNA-interacting protein network regulates pluripotency in mammalian primordial germ cells (in vitro, in vivo)

city: Boston

first: Niels

last: Geijsen

state: MA

address: 185 Cambridge St. CPZN 4-4256

department: Center for Regenerative Medicine

institute: Massachusetts General Hospital

summary:
Primordial germ cells (PGCs) are the embryonic precursors to egg and sperm. When removed from the embryonic gonad, PGCs can give rise to embryonic germ cell lines (EGs), pluripotent stem cells that display most of the characteristics of embryonic stem cells (ESCs) including the ability to form teratomas and to contribute to chimera formation. In mice, EG cells can be derived between E8.5 up to E12.5 of embryonic development, at which point the PGCs undergo sexual differentiation and in the male transition into unipotent gonocytes. Dazl, a germ cell-specific RNA-binding protein, is specifically expressed in developing PGCs and is required for proper germ cell development. Dazl knockout mice are infertile, but the molecular mechanisms underlying this phenotype are still unknown. Here we demonstrate that Dazl localizes in granular structures in mammalian PGCs but not in ESCs. We demonstrate Dazl plays a central role in a large mRNA/protein interactive network that includes members of Fragile-X family RNA-binding proteins. We demonstrate that Dazl and Fxr1 play a central role in these granules and directly regulate the translation of specific core pluripotency factors, including Sox2 and Suz12.

Global gene expression changes during in vitro germ cell differentiation from murine ES cells and comparison to in vivo germ cells.

overall_design: In vitro primordial germ cells differentiated from Stella-GFP ES cells and Dazl-GFP ES cells. The GFP-positive cells were isolated by FACS analysis. Dazl-GFP+ cells were isolated from transgenic E13.5 embryonic gonads and P7-P11 juvenile mouse testes. The global gene expression profiles were analyzed by Agilent Mouse Whole Genome 4X44K one-color microarrays. Two replicates per condition.

first: Hsu

middle: H

last: Chen

first: Donald

middle: B

last: Bloch

first: Edwin

last: Mientjes

first: Javier

last: Munoz

first: Xinjie

first: Cody

last: Tramp

first: Jie

last: Wu

first: Akiko

last: Yabuuchi

first: Yu

middle: F

last: Chou

first: Christa

last: Buecker

first: Maaike

last: Welling

first: Adrian

last: Krainer

first: Rob

last: Wilemsen


title: Genes regulated by ectopic expression of Sage in the entire Drosophila embryo using RNA from tub-Gal4 embryos.

city: Baltimore

first: Deborah

last: Andrew

state: MD

address: 725 N. Wolfe St., Hunterian G-1

department: Cell Biology

institute: Johns Hopkins University School of Medicine

summary: FoxA transcription factors play major roles in organ-specific gene expression. How FoxA proteins achieve specificity is unclear, given their broad expression patterns and requirements in multiple cell types. Here, we characterize Sage, a basic helix-loop-helix (bHLH) transcription factor expressed exclusively in the Drosophila salivary gland (SG). We identify Sage targets and show that not only are both Sage and the single Drosophila FoxA protein, Fork head (Fkh), required for expression of these genes, but coexpression of Sage and Fkh is sufficient to drive target gene expression in multiple other cell types. Sage and Fkh drive expression of the bZip transcription factor Senseless (Sens), which boosts expression of Sage/Fkh targets. Importantly, Sage, Fkh and Sens colocalize on salivary gland polytene chromosomes. Thus, Fkh drives cell-type specific gene expression as part of a tissue-specific transcription module that includes Sage and Sens, providing a new paradigm for how mammalian FoxA proteins acheive specificity.

overall_design: Three control samples were obtained from the tub-Gal4 strain, age matched and treated the same as the three experimental samples isolated from Stages 11-16 embryos expressing UAS-Sage controlled by the tub-Gal4 driver.

first: Rebecca

middle: M

last: Fox


title: An RNA-interacting protein network regulates pluripotency in mammalian primordial germ cells (Dazl knockdown)

summary:
Primordial germ cells (PGCs) are the embryonic precursors to egg and sperm. When removed from the embryonic gonad, PGCs can give rise to embryonic germ cell lines (EGs), pluripotent stem cells that display most of the characteristics of embryonic stem cells (ESCs) including the ability to form teratomas and to contribute to chimera formation. In mice, EG cells can be derived between E8.5 up to E12.5 of embryonic development, at which point the PGCs undergo sexual differentiation and in the male transition into unipotent gonocytes. Dazl, a germ cell-specific RNA-binding protein, is specifically expressed in developing PGCs and is required for proper germ cell development. Dazl knockout mice are infertile, but the molecular mechanisms underlying this phenotype are still unknown. Here we demonstrate that Dazl localizes in granular structures in mammalian PGCs but not in ESCs. We demonstrate Dazl plays a central role in a large mRNA/protein interactive network that includes members of Fragile-X family RNA-binding proteins. We demonstrate that Dazl and Fxr1 play a central role in these granules and directly regulate the translation of specific core pluripotency factors, including Sox2 and Suz12.

Global gene expression changes following Dazl knockdown in in vitro primordial germ cells.

overall_design: In vitro primordial germ cells carrying control and Dazl knockdown shRNAs were generated from Oct4-GFP ES cells and isolated by FACS analysis. The global gene expression profiles were analyzed by Agilent Mouse Whole Genome 4X44K one-color microarrays.


title: Lung conventional dendritic cells promote mucosal adjuvant activity of flagellin

first: Hans-Joachim

last: Mollenkopf

summary: The activity of the potent nasal adjuvant flagellin depends on initial activation of airway epithelilal cells. This study aims at investigating the immune cells involved in the antigen presentation within the respiratory tract. First, microarrays characterized that activation/recruitment of immune cells was the main signature of flagellin activation in lung. Neutrophils and classical monocytes were strongly recruited into the lungs and take up antigen upon nasal administration of flagellin. In contrast, the numbers of lung CD11b+ or CD103+ DC and alveolar macrophages were not enhanced although these cells were very efficient in antigen uptake. Our experiments showed that CD11b+ DC but not monocytes, PMN, CD103+ DC are not essential for the adjuvant effect. Flagellin signaling enhanced the functional activation of lung CD11b+ conventional DC and their migration to the lymph nodes. Using Cd11c-DTR mice, CD11b+ DC from lymph nodes were identified as the major stimulators of CD4 T cell activation. Finally, the migration and maturation of mucosal DC was independent of direct signaling, highlighting the contribution of epithelial factors in the mucosal adjuvant effect of flagellin. In conclusion, these data demonstrate that adjuvant activity can be dissociated from inflammatory cell recruitment an open new perpectives for improvement of vaccines.

overall_design: Female C57BL/6J (6 weeks old) mice were immunized with the TLR5 agonist Flagellin (1μg diluted in PBS) by intranasal (i.n.) administration. Blood samples of four time points post immunization were taken at 2h, 4h, 18h and 48h. Microarray experiments were performed as single-color hybridizations.

first: Jean

middle: C

last: Sirard

first: Hans


title: Retinas from the Pex1-G844D mouse model of Zellweger spectrum disorder

status: Public on Dec 15 2013

city: Los Angeles

first: Joseph

middle: Gerard

last: Hacia

address: 2250 Alcazar Street, IGM 261

department: Biochemistry and Molecular Biology

institute: University of Southern California

summary:
Gene expression analysis of retinas from a mouse model of the mild form of Zellweger spectrum disorder (ZSD). Mice homozygous for the hypomorphic Pex1-G844D allele, the murine ortholog of the human PEX1-G843D mutation found in a subset of patients with autosomal recessive ZSD,  develop  phenotypes found in humans with a milder form of ZSD, including retinal degeneration and vision loss. Similar to humans, mice heterozygous for the hypomorphic Pex1-G844D allele do not display age-related retinal abnormalities.
We conducted a comparative analysis of retinal gene expression profile from Pex1-G844D homozygous and heterozygous mice in order to investigate the pathomechanisms of vision loss in humans with mild forms of ZSD.

overall_design: Whole retinas were obtained from 4 mice homozygous and 4 mice heterozygous for the hypomorphic Pex1-G844D allele, the murine ortholog of the human PEX1-G843D mutation found in a subset of patients with autosomal recessive Zellweger spectrum disorder (ZSD).  The former group of animals show abnormal age-related related retinal degeneration due to peroxisome assembly defect resulting from having two copies of the hypomorphic Pex1-G844D allele. The latter group of animals display no evidence of abnormal age-related retinal degeneration due to the presence of one wild type copy of the Pex1 gene. The overall goal was to identify differentially expressed genes between mice homozygous and heterozygous for the hypomorphic Pex1-G844D allele that  are informative of the pathomechanisms of age-related retinal degeneration in the former group.

middle: G

first: Steven

last: Steinberg


title: Type I IFN signaling promotes local inflammation in pulmonary tuberculosis

summary: The critical role of type I IFN (IFN I ) in viral disease is thoroughly documented while their function in bacterial infection remains ambiguous. General interest in biological functions of IFN I in Mycobacterium tuberculosis (Mtb) infection was raised by the identification of a distinct IFN I gene expression signature in tuberculosis (TB) patients. Here we demonstrate that TB-susceptible mice lacking the receptor for IFN I (IFNAR1) were protected from death upon aerogenic infection with Mtb. Increased survival was accompanied by reduced bacterial burden and ameliorated lung pathology as well as diminished production of proinflammatory IL-1?, among other cytokines. IFNAR1 signaling did not affect T cell responses, but markedly altered migration of inflammatory monocytes and neutrophils to the lung during pulmonary TB. This process was orchestrated by presence of IFNAR1 in both immune and tissue-resident radioresistant cells. IFNAR1-driven TB susceptibility was initiated by CXCL5/CXCL1-driven accumulation of neutrophils into alveoli and subsequently a distinct compartmentalization of Mtb in lung phagocytes. We conclude that IFN I alters early innate events at the site of Mtb invasion leading to unleashed inflammation. Hence, our data furnish a mechanistic explanation for the detrimental role of IFN I in pulmonary TB.

overall_design: dual-color color-swap

first: Stefan

last: Kaufmann

first: Anca

last: Dorhoi

first: Vladimir

last: Yeremeev

first: January

last: Weiner


title: An RNA-interacting protein network regulates pluripotency in mammalian primordial germ cells (Dazl testis RNA-IP)

first: Niels

last: Geijsen

summary:
Primordial germ cells (PGCs) are the embryonic precursors to egg and sperm. When removed from the embryonic gonad, PGCs can give rise to embryonic germ cell lines (EGs), pluripotent stem cells that display most of the characteristics of embryonic stem cells (ESCs) including the ability to form teratomas and to contribute to chimera formation. In mice, EG cells can be derived between E8.5 up to E12.5 of embryonic development, at which point the PGCs undergo sexual differentiation and in the male transition into unipotent gonocytes. Dazl, a germ cell-specific RNA-binding protein, is specifically expressed in developing PGCs and is required for proper germ cell development. Dazl knockout mice are infertile, but the molecular mechanisms underlying this phenotype are still unknown. Here we demonstrate that Dazl localizes in granular structures in mammalian PGCs but not in ESCs. We demonstrate Dazl plays a central role in a large mRNA/protein interactive network that includes members of Fragile-X family RNA-binding proteins. We demonstrate that Dazl and Fxr1 play a central role in these granules and directly regulate the translation of specific core pluripotency factors, including Sox2 and Suz12.

RNA species interacting specifically with Dazl in juvenile testicular germ cells were identified by RNA-IP microarray analysis. This dataset contains data from native RNA-IPs from P14 Dazl-GFP transgenic mouse testes.

overall_design: Native RNA-IP (anti-V5 and anti-PABP1) experiments from juvenile testicular germ cells expressing Dazl-GFP-V5. Input Total RNA and mock IP with normal mouse IgG were used as controls. Control and IP-enriched RNA samples were analyzed by Agilent Mouse Whole Genome 4X44K one-color microarrays. Two replicates for each condition were done.

first: Hsu

last: Chen

first: Donald

last: Bloch

first: Edwin

last: Mientjes

first: Javier

last: Munoz

first: Xinjie

first: Cody

last: Tramp

first: Jie

last: Wu

first: Akiko


title: Predicting drug responsiveness in humans cancers using genetically engineered mice

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary: Anti-cancer drug testing is challenging, but genetically engineered mouse models (GEMMs) and orthotopic, syngeneic transplants (OSTs) may offer advantages for pre-clinical testing including an intact microenvironment. We examined the efficacy of six chemotherapeutic or targeted anti-cancer drugs, alone and in combination, using over 500 GEMMs/OSTs representing three distinct breast cancer subtypes: Basal-like (C3(1)-T-antigen GEMM), Luminal B (MMTV-Neu GEMM), and Claudin-low (T11/TP53-/- OST).  While a few single agents offered exceptional efficacy like lapatinib in the Neu/ERBB2 driven model, combination therapies tended to be more active and life prolonging. Using expression profiling of chemotherapy treated murine tumors, we identified an expression signature that was able to predict pathological complete response to neoadjuvant anthracycline-taxane treated human breast cancer patients, even after accounting for the common clinical variables and other genomic signatures. These results show that credentialed murine models can predict the efficacy of would-be anti-cancer compounds in humans, and that GEMMs can be used to develop new biomarkers of therapeutic responsiveness in humans.

overall_design: control X treatment

first: Jerry

last: Usary


title: Eimeria falciformis infection of the mouse caecum identifies opposing roles of IFNg-regulated host pathways for the parasite development

first: Hans-Joachim

last: Mollenkopf

summary: Intracellular parasites reprogram the host functions for their survival and reproduction. Conversely, the infected host attempts to defend the microbial insult. The extent and relevance of parasite-mediated host response in vivo remains poorly studied. We utilized Eimeria falciformis, an obligate intracellular parasite completing its entire life cycle in the mouse intestinal epithelium, to identify and validate the host determinants of the parasite infection. The most prominent mouse genes induced during the onset of asexual (24 hrs) and sexual (144 hrs) parasite cycle include IFNg-regulated factors, e.g., immunity-related GTPases IRGA6/B6/D/M2/M3, guanylate-binding proteins GBP2/3/5/8, chemokines CxCL9-11 and several enzymes of the kynurenine pathway including indoleamine 2,3-dioxygenase 1 (IDO1). These results indicated a multifarious innate defense (tryptophan catabolism, IRG, GBP, chemokines signaling) mounted by epithelial cells, and a consequential adaptive immune response (chemokines-cytokines signaling, lymphocyte recruitment). A notable increase in the inflammation- and immunity-associated transcripts correlated with the severity of infection and influx of B-cells, T-cells and macrophages to the parasitized tissue. Indeed, parasite growth was enhanced in the animals inhibited for CxCr3, a major chemokine receptor on immune cells. Interestingly, despite a prominent induction, the mouse IRGB6 failed to recognize and disrupt the parasitophorous vacuole in the parasite cultures, implying an immune evasion by E. falciformis. Likewise, the oocyst output was impaired in IFNg-R-/- and IDO1-/- mice, which signifies a subversion of IFNg-signaling by the parasite to promote its growth. In brief, the Eimeria-rodent model shows contrasting roles of IFNg-signaling for parasite development, identifies a retinue of potential host determinants, and epitomizes its efficacy for in vivo parasite-host interaction studies.

overall_design: Microarray experiments were performed as dual-color hybridizations on Agilent mouse whole genome catalog 44K arrays. To compensate for dye-specific effects, a dye-reversal color-swap was applied.

first: Manuela

last: Schmid

first: Emanuel

last: Heitlinger

first: Simone

last: Spork

first: Hans

first: Richard

last: Lucius

first: Nishith

last: Gupta


title: An RNA-interacting protein network regulates pluripotency in mammalian primordial germ cells (Dazl native RNA-IP)

first: Niels

summary:
Primordial germ cells (PGCs) are the embryonic precursors to egg and sperm. When removed from the embryonic gonad, PGCs can give rise to embryonic germ cell lines (EGs), pluripotent stem cells that display most of the characteristics of embryonic stem cells (ESCs) including the ability to form teratomas and to contribute to chimera formation. In mice, EG cells can be derived between E8.5 up to E12.5 of embryonic development, at which point the PGCs undergo sexual differentiation and in the male transition into unipotent gonocytes. Dazl, a germ cell-specific RNA-binding protein, is specifically expressed in developing PGCs and is required for proper germ cell development. Dazl knockout mice are infertile, but the molecular mechanisms underlying this phenotype are still unknown. Here we demonstrate that Dazl localizes in granular structures in mammalian PGCs but not in ESCs. We demonstrate Dazl plays a central role in a large mRNA/protein interactive network that includes members of Fragile-X family RNA-binding proteins. We demonstrate that Dazl and Fxr1 play a central role in these granules and directly regulate the translation of specific core pluripotency factors, including Sox2 and Suz12.

RNA species interacting specifically with Dazl in primordial germ cells were identified by RNA-IP microarray analysis. This dataset contains data from native RNA-IPs without UV-crosslinking.

overall_design: Two independent native RNA-IP (anti-V5 and anti-GFP) experiments from in vitro derived primordial germ cells expressing Dazl-GFP-V5. Input Total RNA and mock IP using normal mouse IgG were used as controls. Control and IP-enriched RNA samples were analyzed by Agilent Mouse Whole Genome 4X44K one-color microarrays.

first: Hsu

last: Yabuuchi

first: Yu

last: Chou

first: Christa

last: Buecker

first: Maaike

last: Welling

first: Adrian

last: Krainer

first: Rob

last: Wilemsen


title: An RNA-interacting protein network regulates pluripotency in mammalian primordial germ cells

last: Geijsen


title: Murine E9.5 embryo PSM and newly formed somites: Paraxis-/- vs WT

status: Public on Dec 05 2013

city: Tempe

first: Megan

last: Rowton

state: AZ

department: School of Life Sciences

institute: Arizona State University

summary: Transcriptional profiling of E9.5 mouse embryo tissue from the presomitic mesoderm (PSM) and somites I-IV. Tissue from embryos lacking a functional Paraxis gene (Paraxis-/-) was compared to identical tissue from E9.5 Wild Type embryos. The goal was to identify genes that had become deregulated in the absence of the transcription factor, Paraxis.

overall_design: Two-condition experiment: WT vs Paraxis-/- tissue. Biological replicates: 3 pools of 5 WT samples, 3 pools of 5 Paraxis-/- samples. Technical replicates: 3 dye swaps.

first: Alan

last: Rawls


title: An RNA-interacting protein network regulates pluripotency in mammalian primordial germ cells (Dazl UV RNA-IP)

summary:
Primordial germ cells (PGCs) are the embryonic precursors to egg and sperm. When removed from the embryonic gonad, PGCs can give rise to embryonic germ cell lines (EGs), pluripotent stem cells that display most of the characteristics of embryonic stem cells (ESCs) including the ability to form teratomas and to contribute to chimera formation. In mice, EG cells can be derived between E8.5 up to E12.5 of embryonic development, at which point the PGCs undergo sexual differentiation and in the male transition into unipotent gonocytes. Dazl, a germ cell-specific RNA-binding protein, is specifically expressed in developing PGCs and is required for proper germ cell development. Dazl knockout mice are infertile, but the molecular mechanisms underlying this phenotype are still unknown. Here we demonstrate that Dazl localizes in granular structures in mammalian PGCs but not in ESCs. We demonstrate Dazl plays a central role in a large mRNA/protein interactive network that includes members of Fragile-X family RNA-binding proteins. We demonstrate that Dazl and Fxr1 play a central role in these granules and directly regulate the translation of specific core pluripotency factors, including Sox2 and Suz12.

RNA species interacting specifically with Dazl in primordial germ cells were identified by RNA-IP microarray analysis. This dataset contains data from UV-crosslinked RNA-IPs from in vitro PGC lysates.

overall_design: UV-crosslinked RNA-IP (anti-GFP and anti-PABP1) experiments from in vitro derived primordial germ cells expressing Dazl-GFP-V5. Input Total RNA and polyA-binding protein 1 (PABP1) IP were used as controls. Control and IP-enriched RNA samples were analyzed by Agilent Mouse Whole Genome 4X44K one-color microarrays. Two replicates for each condition were done.

last: Chen

first: Donald

last: Bloch

first: Edwin

last: Mientjes

first: Javier

last: Munoz

first: Xinjie

first: Cody

last: Tramp

first: Jie

last: Wu

first: Akiko


title: Gene expression signatures of Meis1 conditional knockout hematopoietic stem cells

status: Public on Dec 01 2013

city: Tokyo

first: Takuro

last: Nakamura

address: 3-8-31 Ariake, Koto-ku

department: The Cancer Institute

country: Japan

institute: Japanese Foundation for Cancer Research

summary: Meis1 encodes a TALE family homeodomain protein that was first identified as a common retroviral integration site in mouse BHX2 myeloid leukemia. It functions as a DNA binding co-factor of Hox proteins through interacting with Pbx, a member of another TALE family protein. Moreover, Meis1 homozygous knockout mice are embryonic lethal, showing significant defects in vasculogenesis, eye development and hematopoiesis. Severe defects were also observed in adult hematopoiesis by conditional inactivation of Meis1 in vivo. Meis1 is critical to maintain the balance between enter and exit from cell cycles of hematopoietic stem cells (HSCs), indicating that Meis1 regulates self-renewal and quiescence of HSCs.

overall_design: Total RNA was isolated from KSL cells obtained from poly(I:C)-treated Mx1-Cre Meis1fl/fl and sham-treated Meis1fl/fl mice.

first: R

last: Ariki

first: S

last: Morikawa

last: Hidano

first: M

last: Nakatake

first: Y

last: Matsuzaki

first: H

last: Nakauchi

first: T

last: Goitsuka


title: Expression profiling of isolated dendritic arborization (da) neurons of Drosophila

status: Public on Nov 27 2013

city: Kyoto

first: Yukako

last: Hattori

address: Sakyo-ku

department: Graduate School of Biostudies

institute: Kyoto University

summary: Paper abstract: The transcription factors Abrupt (Ab) and Knot (Kn) act as selectors of distinct dendritic arbor morphologies in two classes of Drosophila sensory neurons, termed class I and class IV, respectively. We performed binding-site mapping and transcriptional profiling of isolated these neurons. Their profiles were similarly enriched in cell-type-specific enhancers of genes implicated in neural development. We identified a total of 429 target genes, of which 56 were common to Ab and Kn; these targets included genes necessary to shape dendritic arbors in either or both of the two sensory subtypes. Furthermore, a common target gene, encoding the cell adhesion molecule Ten-m, was expressed more strongly in class I than IV, and this differential was critical to the class-selective directional control of dendritic branch sprouting or extension. Our analyses illustrate how differentiating neurons employ distinct and shared repertoires of gene expression to produce class-selective morphological traits.

overall_design: da neurons were isolated by magnetic bead sorting from larvae of the following three genotypes and obtained genome-wide expression profiles: larvae expressing a cell-surface marker mCD8:GFP alone (Control), and larvae ectopically expressing Abrupt (Ab ME) or Knot (Kn ME) together with mCD8:GFP in all classes of da neurons. 3 biological replicates were collected.

first: Tadao

last: Usui

first: Daisuke

last: Satoh

first: Sanefumi

last: Moriyama

first: Kohei

last: Shimono

first: Takehiko

last: Itoh

first: Katsuhiko

last: Shirahige

first: Tadashi

last: Uemura


title: Gene Expression Analysis of spinal cord obtained from a mouse model of severe Spinal Muscular Atrophy (SMA)

city: Milan

first: Stefania

last: Corti

address: via F. Sforza 35

department: Neurological Sciences

country: Italy

institute: University of Milan

summary:
Spinal Muscular Atrophy (SMA) is an autosomal recessive motor neuron disease and is the second most common genetic disorder leading to death in childhood. No effective therapy is currently available. It has been suggested that β-lactam antibiotics such as ceftriaxone may offer neuroprotection in motoneuron disease. We investigated the therapeutic effect of ceftriaxone in a murine model of SMA.
Microarray technology was used to assess the global gene expression profile of spinal cord obtained by ceftriaxone-treated and vehicle treated SMA mice.

overall_design: Comparative Gene Expression Analysis. The microarray data derived from three different groups: wildtype controls, transgenic SMA (vehicle treated) and ceftriaxone-treated SMA mice. Each population consists of four RNA profiling samples.

first: Dario

last: Ronchi


title: Environmental pollution assessment using Mus spretus

city: Córdoba

first: Julia

last: Ruiz-Laguna

address: Campus Rabanales, Edif. Severo Ochoa 2ª pl.

country: Spain

institute: University of Córdoba

summary: We evaluated the suitability of high-throughput transcriptomics approach to monitor terrestrial ecosystems. Free-living Mus spretus from several polluted sites of Huelva (Andalusia, SW Spain) were compared with mice from Doñana Biological Reserve (“Santa Olalla” lagoon (SOL) used as negative control). As most popular bioindicators, M. spretus is poorly represented in gene databases, therefore limiting the use of genomics in ecotoxicological studies. To solve this problem, we used microarrays produced from mRNAs of M. musculus. Specifically we used the One-Color Gene Expression Platform commercialized by Agilent.

overall_design: Gene expression in Mus spretus liver was assessed in mice from 5 sites of the Spanish Southwest. Five independent experiments were performed. The arrays were hybridized with labelled cRNA samples made from pooled livers of 9 mice per sampling site. We made 4 technichal repetitions per sample.

first: J

first: N

last: Abril

first: C

last: Pueyo


title: The THO complex regulates pluripotency gene mRNA export to control embryonic stem cell self-renewal and somatic cell reprogramming (microarray)

status: Public on Nov 30 2013

city: Durham

first: Li

last: Wang

address: 111 T.W. Alexander Dr

institute: NIH

summary: Embryonic stem cell (ESC) self-renewal and differentiation are governed by a broad-ranging regulatory network. Although the transcriptional regulatory mechanisms involved have been investigated extensively, post-transcriptional regulation is still poorly understood. Here we describe a critical role of the THO complex in ESC self-renewal and differentiation. We show that THO preferentially interacts with pluripotency gene transcripts through Thoc5, and is required for self-renewal at least in part by regulating their export and expression. During differentiation, THO loses its interaction with those transcripts due to reduced Thoc5 expression, leading to decreased expression of pluripotency proteins that facilitates exit from self-renewal. THO is also important for the establishment of pluripotency, as its depletion inhibits somatic cell reprogramming and blastocyst development. Together, our data indicate that THO regulates pluripotency gene mRNA export to control ESC self-renewal and differentiation, and therefore uncover a role for this aspect of post-transcriptional regulation in stem cell fate specification.

overall_design: mouse J1 cells were transfected with non-targeting (NT), Thoc2, and Thoc5 siRNAs. Total RNA was isolated 96 hours after transfection.

first: James

last: Ward

first: Guang

last: Hu


title: Niche-independent high-purity cultures of Lgr5+ intestinal stem cells and their progeny

status: Public on Nov 22 2013

city: Frankfurt

first: Henner

middle: F.

last: Farin

address: Paul-Ehrlich-Str. 42-44

department: Institute for Tumor Biology and Experimental Therapy

institute: DKTK/Georg-Speyer-Haus

summary: Although Lgr5+ intestinal stem cells have been expanded in vitro as organoids, homogeneous culture of these cells has not been possible so far. Here we show that two small molecules, CHIR99021 and valproic acid, synergistically maintain self-renewal of mouse Lgr5+ intestinal stem cells, resulting in nearly homogeneous cultures. The colony-forming efficiency of cells from these cultures is ~100-fold greater than that of cells cultured in the absence of CHIR99021 and valproic acid, and multilineage differentiation ability is preserved. We made use of these homogeneous cultures to identify conditions employing simultaneous modulation of Wnt and Notch signaling to direct lineage differentiation into mature enterocytes, goblet cells and Paneth cells. Expansion in these culture conditions may be feasible for Lgr5+ cells from the mouse stomach and colon and from the human small intestine. These methods provide new tools for the study and application of multiple intestinal epithelial cell types.

overall_design: Total RNA was isolated from two independently established wild-type mouse small intestinal organoid lines after culture for 6 days in control condition or in the presence of CHIR99021, Valproic Acid (VPA) or both compounds. cRNA was labeled with Cy5 and hybridized against Cy3 labeled cRNA from control organoids (as an internal reference) on 4X44K Agilent Whole Mouse Genome dual colour Microarrays (G4122F), resulting in eight individual arrays.

first: Xialoei

last: Yin

first: Hans

last: Clevers

first: Robert

last: Langer

first: Jeffrey

last: Karp


title: Effect of c-Maf mutation on Mafb-GFP-positive FACS-purified cells in the E12.5 mouse gonad

status: Public on Nov 20 2013

city: Cincinnati

first: Tony

last: DeFalco

state: OH

address: 3333 Burnet Avenue, MLC 7045

department: Division of Reproductive Sciences

institute: Cincinnati Children's Hospital Medical Center

summary:
Morphogenesis of the gonad requires cell-cell adhesion changes between diverse cell types. In the Drosophila gonad, the gene traffic jam regulates cell adhesion changes required for gonad formation and germ cell development (Li et al., 2003. Nature Cell Biol). To determine if the mammalian homologs of traffic jam in mammals, c-Maf and Mafb, also play a role in the transcription regulation of cell adhesion molecules in the mouse gonad, we performed a microarray analysis of FACS-purified Mafb-GFP-positive cells in E12.5 male control and c-Maf/Mafb mutant gonads.
We used microarrays to determine genes affected by c-Maf mutation in E12.5 mouse gonad/mesonephros interstitial cells and macrophages

overall_design: E12.5 XY control (c-Maf+/-;Mafb-GFP+/-) and c-mutant (c-Maf-/-;Mafb-GFP+/-) gonad/interstitial interstitial cells and macrophages were obtained by FACS sorting of Mafb-GFP-positive cells. RNA was extracted for subsequent hybridization on Affymetrix microarrays.

first: Blanche

last: Capel


title: Expression data of wild type, dDP mutant, and de2f1, deleted in the posterior, Drosophila 3rd instar larval eye imaginal discs

status: Public on Nov 25 2013

city: Chicago

first: Aaron

last: Ambrus

state: IL

address: 900 S. Ashland Ave.

institute: University of Illinois at Chicago

summary: Apoptosis is an important process to eliminate cells from tissue which have incurred irreparable DNA damage. While dE2F1/dDP complexes respond to such damage by transcriptionally activating apoptotic genes, previous data suggests that activation of the previously characterized apoptotic target genes of dE2F1/dDP alone may not be the only gene regulation important for gamma irradiation-induced apoptosis. Here we report that following irradiation in dDP mutant 3rd instar larval eye imaginal discs, many genes important for oxidative phosphorylation are down-regulated, which are not down-regulated following irradiation in wild type eye discs.

overall_design: Biological triplicates of wild type, dDP mutant and de2f1, deleted in the posterior, eye discs were untreated or irradiated with 40Gy of gamma radiation. Total RNA was extracted by Trizol from untreated eye discs and from irradiated eye discs 4h after irradiation. RNA was column purified. PCR amplified RNAs were hybridized on Affymetrix Drosophila Genome 2.0 Array.

first: Abul

last: Islam

first: Maxim

last: Frolov


title: Transcriptome analysis of testicular cells in wild type (VRK1+/+) and mutant (VRK1-/-) Mus musculus

status: Public on Nov 21 2013

city: Singapore

first: Hua

last: Ling

address: 62 Nanyang Drive

department: Department of Chemical and Biomolecular Engineering, SCBE

country: Singapore

institute: Nanyang Technological University

summary: Transcriptome analysis of testicular cells in VRK1+/+ and VRK1-/- Mus musculus

overall_design: Gene expression in whole testicular cells from wild type (VRK1+/+) and VRK1-/- mutant Mus musculus, respectively, was measured. Four independent experiment for wild type and mutant, respectively, were performed.

first: Aram

last: Kang

first: Matthew

last: Chang

first: Kyong

middle: T

last: Kim


title: The effect of imatinib therapy on tumor associated macrophages (TAMs) in murine gastrointestinal stromal tumor (GIST)

city: New York

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

summary:
The gene expression profile of TAMs sorted from vehicle control tumors in GIST mice (Sommer et al, PNAS 2003) was compared to TAMs sorted from mice after 2 weeks of imatinib therapy
The Affymetrix Mouse Genome 430A 2.0 platform was used

overall_design: Each treatment group had 8 mice. After 2 weeks of treatment, mice were sacrificed and tumors digested with collagenase. TAMs were then FACS sorted and pooled by group. Pooled groups were run in duplicate for the gene expression array.

first: Michael

last: Cavnar

first: Shan

last: Zeng

first: Teresa

middle: S

first: Eric

last: Sorenson

first: Lee

last: Ocuin

first: Vinod

middle: P

last: Balachandran

first: Adrian

last: Seifert

first: Jonathan

last: Greer

first: Rachel

last: Popow

first: Megan

last: Crawley

first: Noah

middle: A

last: Cohen

first: Benjamin

middle: L

last: Green

first: Ferdinand

last: Rossi

first: Peter

last: Besmer

first: Cristina

middle: R

last: Antonescu

first: Ronald

last: DeMatteo


title: Seeking genes responsible for developmental origins of health and disease from the fetal mouse liver following maternal food restriction

status: Public on Nov 19 2013

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

institute: University of Tsukuba

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Gene expression change in Gata2 conditional knockout mice adult renal collecting duct

city: Sendai

first: Takashi

last: Moriguchi

address: Seiryo

institute: Tohoku University

summary:
We would like to know the gene expression pattern in absence of transcription factor GATA2 in adult renal collecting duct
We used Gata2 flox::Pax8-rtTA::Tet-Cre to make a doxycycline induced Gata2 renal tubule cell specific knockout mice

overall_design: We performed microarray analyses using DBA-lectin and magnetic beads purifed collecting duct cells from WT (n=3) or Gata2 CKO mice (n=3) at 4-weeks after doxycycline induction

first: Lei

last: Yu

first: Masayuki

last: Yamamoto


title: Transcriptomic Classification of Genetically Engineered Mouse Models of Breast Carcinoma Identifies Human Subtype Counterparts

status: Public on Nov 04 2013

first: Charles

last: Perou

summary:
Background: Human breast cancer is a heterogeneous disease consisting of multiple molecular subtypes. Genetically engineered mouse models (GEMMs) are useful resources for studying breast cancers in vivo under genetically controlled and immune competent conditions. Identifying murine models with conserved human tumor features will facilitate etiology determinations, highlight the effects of mutations on pathway activation, and improve preclinical drug validation.

Results: Transcriptomic profiles of 27 murine models of mammary carcinoma and normal mammary tissue were determined using gene expression microarrays. Hierarchical clustering analysis identified 17 distinct murine subtypes (classes). Across species analyses using three independent human breast cancer datasets identified eight murine classes that represent specific human breast cancer subtypes. Multiple models were associated with human basal-like tumors including TgC3(1)-Tag, TgWap-Myc, and Trp53-/-. Interestingly, the TgWAPCre-Etv6 model mimicked the HER2-enriched subtype, a group of human tumors without a murine counterpart in previous comparative studies. Gene signature analysis identified hundreds of commonly expressed pathways between linked mouse and human subtypes, highlighting potentially common genetic drivers of tumorigenesis and candidate pathways for therapeutic intervention.

Conclusion: This study consolidates murine models of breast carcinoma into the largest comprehensive transcriptomic dataset to date to identify human-mouse disease subtype counterparts. This approach illustrates the value of comparisons between species to identify murine models that faithfully mimic the human condition and indicates that multiple GEMMs are needed to represent the diversity of human breast cancers. These trans-species associations should guide model selection during preclinical study design to ensure appropriate representatives of the human disease subtypes are used.

Keywords: breast cancer, comparative genomics, genetically engineered mouse models, and molecular pathway signatures

overall_design: reference x sample

first: Adam

middle: D

last: Pfefferle

first: Jason

middle: I

last: Herschkowitz

first: Jerry

last: Usary

first: J

last: Harrell

last: Spike

first: Geoff

last: Wahl

first: Jeffrey

last: Rosen


title: Dose- and time- dependent ionizing ratidation effect on mice peripheral blood

status: Public on Nov 15 2013

city: durham

first: lingling

last: zheng

address: research dr

institute: duke university

summary:
Gene expression profiles of peripheral blood samples from C57BL/6 mice exposed with ionizing radiation.
We used mice as model animal to study biologial recovery response after radiation damage. Therefore, we obtained gene expression profiles from C57BL/6 mice exposed with various levels of ionizing radiation, including low and high doses and control groups. In order to measure recovery rate, we collected peripheral blood samples at different time durations after the exposure. In order to obtain robust signatures specific to radiation response, we are interested in knowing if the radiation signarures will be present in the presence of confounders. Therefore, mice were given intraperitoneal injections of lipopolysaccharide endotoxin (LPS),  or treated with granulocyte colony-stimulating factor (GCSF), otherwise no treatment after ionizing radiation exposure. The underlying mechanism of confounder treatment is that LPS induces strong immune response resembling the effect of infection, and GCSF stimulates mobilization of HSCs. Exploratory analysis shows that the confounding effects did affect the radiation signature to some extent. This study provides insights into the molecular basis of time- and dose- dependent response to ionizing radiation in mice hematopoietic system.

overall_design: A total of 536 C57BL/6 mice peripheral blood gene expression profiles were measured in 3 different batches using the Affymetrix mouse 430A 2.0 microarray. The experiment is designed to assess blood gene expression changes after exposure to ionizing radiation of 0, 100, 150, 200, 300, 450, 600, 800 and 1050 cGy. Samples were collected at 6, 24, 48, 72, 120 and 168hrs after a single dose exposure.

first: Lingling

last: Zheng

first: Xiao

last: Yan

first: Sunil

last: Suchindran

first: Holly

last: Dressman

first: John

last: Chute

first: Joseph

last: Lucas


title: Effect of Pnpla6 gene silencing in D3 mouse embryonic stem cells

city: ELCHE

first: MIGUEL

last: SOGORB

state: ALICANTE

address: AVENIDA DE LA UNIVERSIDAD S/N

department: INSTITUTO DE BIOINGENIERÍA

institute: UNIVERSIDAD MIGUEL HERNÁNDEZ DE ELCHE

summary: Pnpla6 gene was silenced in D3 mouse embryonic stem cells and the cells were allowed to spontaneously differentiate. Transcription of the whole genome was analyzed 96 days afterwards and compared against control cells differentiated during the same time without previous silencing.

overall_design: Comparimg two experimental conditions: control differentiated cells versus Pnpla6 silenced differentiated cells.

first: David

last: Pamies

first: Eugenio

last: Vilanova

first: Miguel

last: Sogorb


title: Global microarray analysis of changes of gene expression in the epidermis of K14-caSmad1 mice

status: Public on Nov 01 2013

city: Bradford

first: Natalia

middle: V.

last: Botchkareva

address: Richmond Road

country: United Kingdom

institute: University of Bradford

summary: Bone morphogenetic protein (BMP) signalling plays a key role in the control of skin development and postnatal remodelling by regulating keratinocyte proliferation, differentiation and apoptosis. To study the role of BMPs in wound-induced epidermal repair, we used transgenic mice overexpressing the BMP downstream component Smad1 under the control of a K14 promoter as an in vivo model, as well as ex vivo and in vitro assays. K14-caSmad1 mice exhibited retarded wound healing associated with significant inhibition of proliferation and increased apoptosis in healing wound epithelium. Furthermore, microarray and qRT-PCR analyses revealed decreased expression of a number of cytoskeletal/cell motility-associated genes including wound-associated keratins (Krt16, Krt17) and Myo5a, in the epidermis of K14- caSmad1 mice versus wild-type controls during wound healing. BMP treatment significantly inhibited keratinocyte migration ex vivo, and primary keratinocytes of K14-caSmad1 mice showed retarded migration compared to wild-type controls. Finally, siRNA-mediated silencing of Bmpr-1B in primary mouse keratinocytes accelerated cell migration and was associated with increased expression of Krt16, Krt17 and Myo5a compared to controls. Thus, this study demonstrates that BMPs inhibit keratinocyte proliferation, cytoskeletal organization and migration in regenerating skin epithelium during wound healing, and raises a possibility for using BMP antagonists for the management of chronic wounds.

overall_design: Two-condition experiment, Wild type vs. Smad1 overexpressing mice. Biological replicates: 2 replicates.

first: Christopher

middle: J

last: Lewis

first: Andrei

middle: N

last: Mardaryev

first: Tatyana

middle: Y

last: Sharova

first: Krzysztof

last: Poterlowicz

last: Sharpe

middle: V

first: Andrey

last: Sharov


title: Expression data from skin of mice treated subcutaneously with TGF-beta, IL-13 or TSLP for 7 days

status: Public on Oct 31 2013

city: Boston

first: Romy

middle: B

last: Christmann

state: MASSACHUSETTS

address: 715 Albany Street E5

institute: Boston University School of Medicine

summary:
Gene expression in mice skin stimulated with 3 different cytokines
We used microarrays to detail the global programme of specific or common gene expression by 3 cytokines: TGF-beta, IL-13 and TSLP

overall_design: Mice skin were taken from the outlet of the 7-day pump (subcutaneous) and RNA was extracted.

first: Christmann

last: Romy

first: Lafyatis

last: Robert


title: HDAC inhibition by TSA and Butyrate In Flt3L-elicited DC

status: Public on Oct 15 2013

first: Nicholas

last: Arpaia

address: 701 W 168TH ST HHSC 910C

department: Microbiology & Immunology

institute: Columbia University Irving Medical Center

summary: Butyrate induces Treg via HDACi activity

overall_design: Microarray of DC treated with TSA or Butyrate over untreated

first: Alexander

last: Rudensky


title: Total lung gene expression data of Pneumocystis-infected wildtype and IFN-gamma knockout mice.

status: Public on Oct 27 2013

city: Bozeman

first: Steve

last: Swain

state: MT

address: 560 Technology Blvd

department: Immunology & Infectious Disease

institute: Montana State University

summary:
Pulmonary hypertension (PH) is a disease of diverse etiology. While primary PH can develop in the absence of prior disease, PH more commonly develops in conjunction with other pulmonary pathologies. We previously reported a mouse model in which PH occurs as a sequelae of Pneumocystis infection in the context of transient CD4 depletion. Here, we demonstrate that instead of the expected Th2 pathways, the Th1 cytokine IFN-γ was essential for the development of PH, as wild type mice developed PH, but not IFN-γ knockout mice.
Because gene expression analysis showed few strain differences that were not immune function related, we focused on those responses as potential pathologic mechanisms. While there were several differences in cellular and cytokine response that warrant further examination, we focused on three important aspects. First, if CD4 cells were continuously depleted, but the infection was limited by antibiotic treatment, then PH did not occur, confirming that CD4 T-cells are required for PH development. Second, although CD8 T-cells are implicated in the pathology of unabated Pneumocystis pneumonia, they did not have a role in the onset of PH. Finally, although there are differences in the amounts of the pulmonary immune cells, differences existed in phenotypes of immune cells that correlated with PH, such as elevated CD204 expression in lung CD11c+ cells.

overall_design: Two groups of BALB/c mice (3 per group) were infected i.t. with 10e7 Pneumocystis; one of those groups also received 4 injections of CD4 T-cell depleting antibodies beginning 3 days prior to infection and ending 7 days after infection. A third group was IFN-gamma knockout mice infected with Pneumocystis and depleted of CD4 cells in the same way. A fourth group of control non-treated BALB/c mice were also used. AT 38 days post infection, lung tissues were taken, and RNA was extracted to allow for differential gene expression analysis

first: Dan

middle: W

last: Siemsen

first: Rebecca

last: Pullen

first: Soo

last: Han


title: CSF-1R inhibition alters macrophage polarization and blocks gliomagenesis

status: Public on Sep 20 2013

city: Philadelphia

first: Robert

last: Bowman

state: PA

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania School of Medicine

summary: Glioblastoma multiforme (GBM), the most common and aggressive primary brain tumor in adults, can be divided into several molecular subtypes including proneural GBM. Most clinical strategies aimed at directly targeting glioma cells in these tumors have failed. A promising alternative is to target stromal cells in the brain microenvironment, such as tumor-associated microglia and macrophages (TAMs). Macrophages are dependent upon colony stimulating factor (CSF)-1 for differentiation and survival; therefore, we used an inhibitor of its receptor, CSF-1R, to target macrophages in a mouse proneural GBM model. CSF-1R inhibition dramatically increased survival in mice and regressed established GBMs. Tumor cell apoptosis was significantly increased, and proliferation and tumor grade markedly decreased. Surprisingly, TAMs were not depleted in tumors treated with the CSF-1R inhibitor. Instead, analysis of gene expression in TAMs isolated from treated tumors revealed a decrease in alternatively activated/ M2 macrophage markers, consistent with impaired tumor-promoting functions. These gene signatures were also associated with better survival specifically in the proneural subtype of patient gliomas. Collectively, these results establish macrophages as valid therapeutic targets in proneural gliomas, and highlight the clinical potential for CSF-1R inhibitors in GBM.

overall_design:
RNA was isolated from sorted tumor associated macrophages (TAMs) from murine gliomas following either 7 days of vehicle or BLZ945 treatment.  Samples were collected from 16 total tumor burdened mice, with 8 replicates for each treatment group.
BLZ945: a Colony-Stimulating Factor 1 Receptor (CSF-1R) inhibitor

first: Stephanie

middle: M

last: Pyonteck

first: Leila

last: Akkari

first: Alberto

last: Schuhmacher

first: Joyce

last: Joyce


title: Expression data from murine sarcomas

status: Public on Oct 11 2013

first: Jordan

last: Blum

address: 450 Research Dr LSRC RmB232

institute: Duke University Medical Center

summary: The cell of origin for rhabdomyosarcoma (RMS) and undifferentiated pleomorphic sarcoma (UPS) remains to be determined.  We utilized two skeletal muscle specific inducible Cre mouse lines to transform both skeletal muscle stem cells and progenitors to determine which cells give rise to RMS and UPS.

overall_design: Both P7KP and MDKP derived mice were injected with systemic tamoxifen and mice were euthanized after tumor development.  Sections of resected tumor were placed in RNAlater and placed at -80 until RNA isolation.  RNA was isolated by grinding up tumor sections in liquid nitrogen and using the Qiagen RNEasy Micro kit.

first: David

middle: G

last: Kirsch

first: Sayan

last: Mukherjee

first: Brian

last: Bennett

first: Leonor

last: Añó


title: A transcriptional and metabolic signature of primary aneuploidy is present in chromosomally-unstable cancer cells and informs clinical prognosis

status: Public on Oct 01 2013

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

summary: In all primary cells analyzed to date, aneuploidy is associated with poor proliferation.  Yet, how abnormal karyotypes affect cancer – a disease characterized by both aneuploidy and heightened proliferative capacity – is largely unknown.  Here, I demonstrate that the transcriptional alterations caused by aneuploidy in primary cells are also present in chromosomally-unstable cancer cell lines, but are not common to all aneuploid cancers.  Moreover, chromosomally-unstable cancer lines display increased glycolytic and TCA-cycle flux, as is also observed in primary aneuploid cells.  The biological response to aneuploidy is associated with cellular stress and slow proliferation, and a 70-gene signature derived from primary aneuploid cells is a strong predictor of increased survival in several cancers.  Inversely, a transcriptional signature derived from clonal aneuploidy in tumors correlates with high mitotic activity and poor prognosis.  I speculate that there are two types of aneuploidy in cancer: clonal aneuploidy, which is selected during tumor evolution and is associated with robust growth, and sub-clonal aneuploidy, which is caused by chromosomal instability (CIN) and more closely resembles the stressed state of primary aneuploid cells.  Nonetheless, CIN is not benign: a subset of genes upregulated in high-CIN cancers predict aggressive disease in human patients in a proliferation-independent manner.

overall_design: The mRNAs from 3 different mouse embryo fibroblast (MEF) lines that are chromosomally stable were compared with mRNAs from 3 different MEF lines that were chromosomally unstable due to mutations in either BUBR1 or CDC20

first: J

last: Sheltzer


title: Different developmental trajectories of ovaries in Siberian hamsters raised in long and short day lengths

status: Public on Sep 14 2013

city: Ithaca

first: Ned

last: Place

address: 240 Farrier Road

department: Population Medicine & Diagnostic Sciences

institute: Cornell University

summary: A genome-wide association study was performed on ovaries from Siberian hamsters raised in either long or short photoperiod. Few differences between long and short photoperiod were noted at 3 wk of age, when ovarian histology was identical, whereas many differences in gene expression were noted at 8 wk of age, when ovarian histologies were markedly different.

overall_design: Hamsters were gestated and maintained in 16 or 10 hours of light per day, the latter short photoperiod delays sexual maturity and alters ovarian histology. Differences in gene expression were evaluated by microarray at 3 and 8 wk of age, as were changes between 3 and 8 wk of age in each photoperiod.

first: Sung-Un

last: Park


title: Hepatocellular carcinomas (HCC) in mice transduced in utero with feline immunodeficiency virus-based vectors (expression)

status: Public on Sep 11 2013

city: Jerusalem

first: Reba

last: Condiotti

department: Goldyne Savad Institute of Gene Therapy

country: Israel

institute: Hadassah Medical Center

summary:
Fetal mice (16 days gestation) were administered feline immunodeficiency virus (FIV)-based lentiviral viral particles containing the gene encoding GFP.  Six liver tumors developed in three mice between the ages of 273 and 484 days, each mouse developed 2 tumors. These tumors and non-tumorous liver tissue from the same animals and animals that did not develop tumors and untransduced controls were harvested and microarrays were performed on total RNA extracted from these samples. We were interested in investigating the link between lentiviral integration and gene expression.

Keywords: Comparison of HCC with non-tumorous liver tissue adjacent to tumor.

overall_design: Fourteen samples were analyzed in total: Two tumors from each of three mice (6 samples); surrounding non-tumorous liver tissue from each of these three mice (3 samples); two female mice and one male mouse that were transduced and did not develop tumors (3 samples); one female and one male untransduced mouse (2 samples). The samples were performed in two runs: one containing the samples from female mice and the second containing samples from male mice.

first: Daniel

last: Goldenberg

first: Temima

last: Schnitzer-Perlman

first: Simon

last: Waddington

first: Suzanne

last: Buckley

first: Alina

last: Simerzin

first: Assaf

last: Bester

first: Batsheva

last: Kerem

first: Hilla

last: Giladi

first: Eithan

last: Galun

first: Michael

last: Themis


title: Gene expression of p53 null vs. p53 wild-type mouse kidneys at embryonic day 15.5

status: Public on Sep 05 2013

city: New Orleans

first: Yuwen

last: Li

address: 1430 Tulane Ave SL37 RM5534

department: Pediatrics

institute: Tulane University

summary: Gene expression microarray analysis was performed on E15.5 p53+/+ and p53-/- litter-matched kidneys. We have previously shown that p53 is expressed in both UB and MM lineages in the kidney, and that p53-null embryos on C57B6L background exhibit a range of congenital abnormalities of the kidney and urinary tract such as duplicated ureters, reduced nephron numbers, and compromised nephron progenitor renewal and differentiation. Here our goal was to reveal the p53 transcriptome in mouse embryonic kidneys at E15.5.

overall_design: This is a two-condition experiment comparing gene expression between p53 null vs. p53 wild-type mouse kidneys at embyronic day 15.5. Three biological replicates (rep1-3) and their dye-swapped experimental replicates are included, in which rep1 has a duplicate and a duplicate dye-swap experiments.

first: Jiao

last: Liu

first: Nathaniel

last: McLaughlin

first: Dimcho

last: Bachvarov

first: Zubaida

last: Saifudeen

first: Samir

last: El-Dahr


title: Gene expression profile in the livers of insulin-resistant mice treated with all-trans retinoic acid

status: Public on Sep 12 2013

city: Kyoto

first: Hiroyuki

last: Tsuchiya

state: Kyoto

address: Nakauchi-cho 5, Misasagi, Yamashina-ku

department: Department of Biophysical Chemistry

institute: Kyoto Pharmaceutical University

summary: Therapeutic effect of all-trans retinoic acid on diet-induced insulin resistance was found. To explore molecules involved in this pharmacological effect, the hepatic transcriptome was analyzed.

overall_design: RNA samples were prepared from the liver biopsies of control, HFHFr-N, HFHFr-NA, HFHFr-F, and HFHFr-FA groups (five mice in each group). The samples were pooled and analyzed using Whole Mouse Genome Microarray 4x44K (G4122F).

first: Goshi

last: Shiota


title: Unlimited in vitro expansion of adult bi-potent pancreas progenitors through the Lgr5/Rspondin axis

status: Public on Sep 17 2013

city: Dresden

first: Meritxell

last: Huch

address: Pfotenhauerstrasse 108

institute: Max Planck Institute of Molecular Cell Biology and Genetics

summary: Lgr5 marks adult stem cells in multiple adult organs and is a receptor for the Wnt-agonistic R-spondins (RSPOs). Intestinal, stomach and liver Lgr5+ stem cells grow in 3D cultures to form ever-expanding organoids, which resemble the tissues of origin. Wnt signaling is inactive and Lgr5 is not expressed under physiological conditions in the adult pancreas. However, we now report that the Wnt pathway is robustly activated upon injury by Partial Duct Ligation (PDL), concomitant with the appearance of Lgr5 expression in regenerating pancreatic ducts. In vitro, duct fragments from mouse pancreas initiate Lgr5 expression in RSPO1-based cultures, and develop into budding cyst-like structures (organoids) which expand 5-fold weekly for >40 weeks. Single isolated duct cells can also be cultured into pancreatic organoids, containing Lgr5 stem/progenitor cells that can be clonally expanded. Clonal pancreas organoids can be induced to differentiate into duct as well as endocrine cells upon transplantation, thus proving their bi-potentiality

overall_design: We generated arrays from whole pancreas, islet, acinar and duct (Sox9+ sorted) cells and pancreas derived cultures maintained in our defined medium. For the clustering analysis we substracted the pancreas array to all arrays. Genes 2 fold differentially expressed in the ductal array were used for the analsyis. For the genes enriched in organoid cultures compared to pancreas we substracted the organoid culture arrays to the pancreas array. Genes >2-fold differentially expressed were used for the analysis.

first: Hans

last: Clevers


title: Mbd2 promotes Foxp3 demethylation and T-regulatory cell function

status: Public on Sep 01 2013

first: Wayne

last: Hancock

address: 916B ARC, 3615 Civic Ctr Blvd

institute: CHOP/UPenn

summary: The proposed use of Foxp3+ T-regulatory (Treg) cells as potential cellular therapy in patients with autoimmune diseases, or post-hemopoietic stem cell or organ transplantation, requires a sound understanding of the transcriptional regulation of Foxp3 expression. Conserved CpG dinucleotides in the Treg-specific demethylated region (TSDR) upstream of Foxp3 are demethylated only in stable, thymic-derived Foxp3+ Tregs. Since methyl-binding domain (Mbd) proteins recruit histone-modifying and chromatin-remodeling complexes to methylated sites, we tested whether targeting of Mbd2 might promote demethylation of Foxp3 and thereby promote Treg numbers or function. Surprisingly, while ChIP analysis showed Mbd2 binding to the Foxp3-associated TSDR site in Tregs, Mbd2 targeting by homologous recombination or siRNA decreased Treg numbers and impaired Treg suppressive function in vitro and in vivo. Moreover, we found complete TSDR demethylation in WT Tregs but >75% methylation in Mbd2-/- Tregs, whereas re-introduction of Mbd2 into Mbd2-null Tregs restored TSDR demethylation, Foxp3 gene expression and Treg suppressive function. Lastly, Mbd2-/- Tregs had markedly binding of the DNA demethylase enzyme, Tet2, in the TSDR region. These data show that Mbd2 has a key role in promoting TSDR demethylation, Foxp3 expression and Treg suppressive function.

overall_design: RNA from three independent samples from magnetically separated CD4+CD25+ Treg of MBD2–/– mice, compared to wild type control (all Balb/c background).

first: Liqing

last: Wang

first: Yujie

first: Rongxiang

last: Han

first: Ulf

middle: H

last: Beier

first: Rajan

last: Thomas

first: Andrew

last: Wells


title: Pdm1/nub repression of innate immunity

status: Public on Sep 06 2013

city: Solna

first: Jessica

middle: Margareta

last: Lindvall

address: Tomtebodavägen 23A

department: NBIS

country: Sweden

institute: SciLifeLab. Stockholm University

summary:
Innate immune responses rely on expression of potent effector molecules, such as antimicrobial peptides, which have the capability to kill invading microorganisms. The presence and recognition of microbial components triggers several signaling pathways, such as the Toll and IMD pathways, which in turn activate NF-kB/Rel transcription factors to induce transcription of a large number of immune system genes. Not much is known how these genes are kept silent in healthy flies in the presence of commensal microorganisms, and how the expression of immune defense genes is turned off. We found that several immune defense genes are constitutively active in nub[1] mutants, indicating that the POU domain transcription factor Pdm1/Nubbin may act as a repressor of immune gene expression.
We used microarrays to analyze the global changes in gene expression in nub[1] mutants compared to wild type. To analyze changes in gene expression in the gut distinctly from other immune-responsive tissues, such as fat body and hemocytes, flies were dissected and the gut was analyzed separately from the rest of the fly (carcass). A large number of genes were differentially expressed in nub[1] mutants compared to wild type. The differentially expressed transcripts are dominated by genes involved in Immune system processes and in Metabolism/Catabolism processes. The gut samples were dominated by genes involved in biological processes linked to Metabolism/Catabolism, but also here, genes involved in Response processes were enriched among the differentially expressed genes.

overall_design: The following Drosophila melanogaster strains were used: OregonR was used as wild type control and nub[1] b[1] pr[1] was used as the nub[1] mutant. Flies were dissected so that gut tissue was analyzed separately (gut) from the rest of the fly, minus head and gut (carcass). In total, 12 samples consisting of four different sample types:  wt gut, wt carcass, nub[1] gut and nub[1] carcass, and three samples of each type.

first: Ylva

last: Engström

first: Monica

last: Davis

first: Widad

last: Dantoft


title: Inhibition of astroglial NF-kB regulates oligogenesis following spinal cord injury.

city: Miami

first: John

middle: R.

last: Bethea

state: FL

address: 1095 NW 14th Terrace

department: The Miami Project to Cure Paralysis

institute: University of Miami

summary: Astrocytes are taking the center stage in neurotrauma and neurological disease as they appear to play a dominant role in the inflammatory processes associated with these conditions. Previously, we reported that inhibiting nuclear factor kappa B (NF-kB) activation in astrocytes, by using a transgenic mouse model (GFAP-IκBα-dn mice), results in improved functional recovery following spinal cord injury (SCI), with increased white matter preservation and axonal sparing. In the present study we sought to determine whether this improvement, due to inhibiting NF-k-B activation in astrocytes, could be the result of enhanced oligogenesis in our GFAP-IκBα-dn mice. To gain insight into the underlying molecular mechanisms, we performed microarray analysis in naïve and 3 days, 3 and 6 weeks following SCI in GFAP-IκBα-dn and wild type (WT) littermate mice. Surprisingly, we found the largest number of genes differentially regulated between GFAP-IκBα-dn and WT mice 6 weeks post-injury. Interestingly, the data suggested that inhibiting astroglial NF-kB alters the inflammatory environment to support oligogenesis. Furthermore, confirmation of microarray data with qPCR and western blotting analysis and using BrdU labeling along with cell specific immunohistochemistry, confocal microscopy and quantitative cell counts, we demonstrate a significant increase in oligogenesis in GFAP-IκBα-dn following SCI. These studies suggest that therapeutic strategies targeting NF-kB activation in the CNS following SCI may promote oligogenesis and remyelination.

overall_design: Wild type (WT) mice - time points naïve, 3 days, 3 weeks, 6 weeks. Transgenic mice (TG) - time points naïve, 3 days, 3 weeks, 6 weeks.

first: Valerie

last: Bracchi-Ricard

first: Kate

last: Lambertsen

first: Jerome

last: Ricard

first: Lubov

last: Nathanson

first: Shaffiat

last: Karmally

first: Joshua

last: Johnstone

first: Ditte

last: Ellman

first: Beata

last: Frydel

first: Dana

last: McTigue


title: The Autonomous Hepatocyte Clock Controls Acetaminophen Bioactivation and Chronotoxicity [Kidney]

status: Public on Aug 30 2013

city: Madison

first: Brian

middle: P

last: Johnson

state: WI

address: 1400 University Ave

department: Oncology

institute: UW-Madison

summary: The diurnal variation in acetaminophen (APAP) hepatotoxicity (“chronotoxicity”) is thought to be due to oscillations in xenobiotic metabolism that are influenced by the circadian phases of feeding or fasting.  Because of APAP’s relevance to human poisoning, we set out to determine the relative contributions of the central clock in the SCN and the autonomous clock in the hepatocyte in modulating the chronotoxicity of APAP. Using a conditional null allele of Mop3 (ArntL, Bmal1) we are able to delete the clock from hepatocytes while keeping the central and other peripheral clocks intact (eg, those controlling food intake).  Our data from this hepatocyte-null mouse model suggests that, while the central circadian clock modulates some detoxification pathways indirectly by driving activity patterns and feeding rhythms, the autonomous hepatocyte circadian clock controls major aspects of APAP bioactivation independent of feeding rhythms, possibly through transcriptional regulation of cytochrome p450-oxidoreductase (Por).

overall_design: 10-20 week old Mop3fxfx mice positive or negative for Cre-recombinase driven by the albumin promoter, housed in 12 hour light:12 dark, ad lib feeding and drinking conditions were sacrificed every four hours over two separte days beginning at ZT0.  A two color, reference design experiment in which kidney RNA from at least 3 mice per timepoint were pooled and labeled with Cy3 and hybridized according to Agilent protocols against a reference pool of RNA madeup from respective tissue taken from 10 week Mop3fxfx and Mop3fxfxCreAlb mice  which was labeled with Cy5.

first: Chris

middle: A

last: Bradfield


title: The Autonomous Hepatocyte Clock Controls Acetaminophen Bioactivation and Chronotoxicity

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

overall_design: Refer to individual Series


title: Expression profiles from Drosophila melanogaster scrib and lgl mutant wing imaginal disc and brain complexes at day 9 after egg deposition (AED) versus wild type at day 5 AED

status: Public on Jan 31 2014

city: East Melbourne

first: Helena

middle: Elizabeth

last: Richardson

state: Victoria

address: 7 St Andrew's place

department: Research Division

country: Australia

institute: Peter MacCallum Cancer Center

summary:
mRNA microarray of Drosophila wing imaginal discs or brain complexes from lgl27S3/lglE2S31 (lgl-null), scrib1/scrib2 or wild-type 3rd instar larvae
RNA was isolated from 20 pairs of wing discs/brain complexes per sample (i.e 20 individuals). Samples were from 5 day AED wildtype and 9 day AED mutant tissue

overall_design: Samples were prepared in triplicate from lgl27S3/lglE2S31 (lgl-null) and scrib1/scrib2 samples and in duplicate from the wild-type 3rd instar larvae

middle: E

first: Jason

last: Ellul


title: Effect of adiponectin deficiency on pulmonary responses to subacute ozone exposure in mice

status: Public on Aug 27 2013

first: Stephanie

last: Shore

address: 665 Huntigton Av Bld1 room 307

department: Environmental Health

institute: Harvard School of Public Health

summary: Adiponectin is an adipose-derived hormone with anti-inflammatory activity.  Following subacute ozone exposure (0.3 ppm for 24-72 h), pulmonary neutrophilic inflammation is augmented in adiponectin deficient mice.  The purpose of this study was to use microarrays to examine the impact of adiponectin deficiency on changes in pulmonary gene expression induced by ozone, a common air pollutant.

overall_design: Lungs were harvested from wildtype and mice that were genetically deficient in adiponectin.  Mice were exposed either to room air or to ozone (0.3 ppm) for 72 h.  RNA was extracted and microarray analysis of gene expression performed. Both male and female mice were used.

first: David

middle: I

last: Kasahara


title: Inhibition of p300 impairs Foxp3+ T-regulatory cell function and promotes anti-tumor immunity

status: Public on Aug 18 2013

first: Wayne

last: Hancock

summary: Foxp3+ T-regulatory (Treg) cells maintain immune homeostasis and limit autoimmunity, but can also curtail host responses to cancers. Tregs are therefore promising targets to enhance anti-tumor immunity. Histone/protein acetyltransferases (HATs) promote chromatin accessibility, gene transcription and the function of multiple transcription factors and non-histone proteins. We found that conditional deletion or pharmacologic inhibition of one specific HAT, p300, in Foxp3+ Tregs, increased TCR-induced apoptosis in Tregs, impaired Treg suppressive function and iTreg peripheral conversion, and limited tumor growth in immunocompetent, but not in immunodeficient, hosts. Our data demonstrate that p300 is important for Foxp3+ Treg function and homeostasis in vivo and in vitro, and identify a novel mechanism to diminish Treg function without overtly impairing effector Tcell responses or inducing autoimmunity. Collectively, these data suggest a new approach for cancer immunotherapy.

overall_design: RNA from three independent samples from magnetically separated CD4+CD25+ Treg of fl-p300/Foxp3cre mice, compared to wild type (Foxp3cre) control (all C57Bl/6 background).

first: Yujie

last: Liu

first: Liqing

last: Wang

first: Jarrod

last: Predina

first: Rongxiang

last: Han

first: Ulf

last: Beier

first: Liang-Chuan

middle: S

first: Veena

last: Kapoor

first: Tricia

middle: R

last: Bhatti

first: Tatiana

last: Akimova

first: Sunil

last: Singhal

first: Paul

middle: K

last: Brindle

first: Philip

last: Cole

first: Stephen

last: Albelda


title: The Autonomous Hepatocyte Clock Controls Acetaminophen Bioactivation and Chronotoxicity [Liver]

first: Brian

last: Johnson

summary: The diurnal variation in acetaminophen (APAP) hepatotoxicity (“chronotoxicity”) is thought to be due to oscillations in xenobiotic metabolism that are influenced by the circadian phases of feeding or fasting.  Because of APAP’s relevance to human poisoning, we set out to determine the relative contributions of the central clock in the SCN and the autonomous clock in the hepatocyte in modulating the chronotoxicity of APAP. Using a conditional null allele of Mop3 (ArntL, Bmal1) we are able to delete the clock from hepatocytes while keeping the central and other peripheral clocks intact (eg, those controlling food intake).  Our data from this hepatocyte-null mouse model suggests that, while the central circadian clock modulates some detoxification pathways indirectly by driving activity patterns and feeding rhythms, the autonomous hepatocyte circadian clock controls major aspects of APAP bioactivation independent of feeding rhythms.

overall_design: 10-20 week old Mop3fxfx mice positive or negative for Cre-recombinase driven by the albumin promoter, housed in 12 hour light:12 dark, ad lib feeding and drinking conditions were sacrificed every four hours over two separte days beginning at ZT0.  A two color, reference design experiment in which liver RNA from at least 3 mice per timepoint were pooled and labeled with Cy3 and hybridized according to Agilent protocols against a reference pool of RNA madeup from respective tissue taken from 10 week Mop3fxfx and Mop3fxfxCreAlb mice  which was labeled with Cy5.

first: Chris

last: Bradfield


title: Sexual dimorphisms in zonal gene expression in mouse liver

status: Public on Aug 10 2013

city: RTP

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary:
Zone 1 and zone 3 areas were captured from mouse liver sections by laser capture microdissection
Total RNA was isolated and gene expression profiles were determined using microarrays

overall_design: Six C3H/HeNCrlBR (C3H) mice, 3 male and 3 female mice were used. They were not treated in any way.

first: Kosuke

last: Saito

first: James

last: Squires

first: Masahiko

last: Negishi


title: Expression Data from 12 week old APCmin/+ and littermate matched Wildtype B6 mouse Terminal Ileum (TI)

status: Public on Aug 20 2013

city: Buffalo

first: Allen

middle: Yicheng

last: Chung

address: 3435 Main Street

department: Microbiology and Immunology

institute: University at Buffalo

summary:
APCmin/+ mice develop spontaneous gastrointestinal polyposis due to a dominantly inhereited germline loss-of-function mutation in the tumor suppressor adenomatous polyposis coli (APC). Changes in intestinal immune activity have been documented to occur prior to the development of fulminate polyposis. Such changes are thought to contribute to disease development.
We used microarrays to describe the changing intestinal transcriptional landscape in APCmin/+ mice. Whole transcriptome profiling from polypotic and nonpolypotic intestinal sections of  APC/min+ mice were examined in the early stages of disease, and compared to  normal intestinal sections from littermate matched wildtype B6 mice.

overall_design: Nonpolypotic  (wildtype and APCmin/+) and Polypotic (APCmin/+) sections of terminal ileum were identified by visual inspection, and subsequently selected for RNA isolation and hydridzation to Affymetrix Mouse Genome 430A 2.0 Arrays. Interference from bacterial RNA was selected against using a probeset enriched in oligos extending into 3’-poly-A tails.

middle: Y

first: Nejat

last: Egilmez


title: Mouse whole kidney, Dot1lAC vs. Dot1lf/f mice

status: Public on Aug 14 2013

city: Houston

first: Wenzheng

last: Zhang

state: TX

address: 6431 Fannin

department: Internal Medicine

institute: University of Texas Medical School at Houston

summary: Transcriptional profiling of whole kidneys of adult Dot1lAC mice  comparing control kidneys of their littermates Dot1lf/f mice fed a normal pellet Na+ diet. Goal was to determine the effects of inactivation of histone H3 K79 methyltransferase Dot1l in Aqp2-expressing cells in Dot1lAC on global kidney gene expression.

overall_design: Two-condition experiment, Dot1lAC vs. Dot1lf/f. Biological replicates: Total kidney RNAs from 4 mice/genotype were mixed within the same genotype.

first: Hongyu

last: Wu

first: Lihe

last: Chen


title: Expression profile of cortices, hippocampi and brainstems of Nrf2 knockout mice under unstressed conditions

status: Public on Aug 05 2013

city: Sendai

first: Masayuki

last: Yamamoto

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

department: Medical Biochemistry

institute: Tohoku University Graduate School of Medicine

summary: Microarray analysis of cortices, hippocampi and brainstems of Nrf2 knockout mice,

overall_design: Three independent RNAs from cortices, hippocampi and brainstems of Nrf2 knockout and wild-type control mice were used for the microarray analyses.

first: Hiroyuki

last: Muramatsu

first: Fumiki

last: Katsuoka

first: Katsuo

last: Toide

first: Yusuke

last: Shimizu

first: Shoji

last: Furusako


title: Seeking genes responsible for developmental origins of health and disease from the fetal mouse liver following maternal food restriction [Expression]

city: Tsukuba

first: RANDEEP

last: RAKWAL

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

institute: University of Tsukuba

summary: Non-optimal fetal environments resulting in low birth weight have epidemiologically been associated with adult diseases. In animal models, maternal undernutrition has successfully demonstrated increased risks for adult diseases. In the present study, we treated pregnant mice with 50% food restriction (FR), and performed global gene expression and promotor DNA methylation profiling on the fetal livers. Considering that effects of food restriction is opposite between before and after birth, we further searched genes which are regulated oppositely against adult calorie restriction and commonly against aging. Searched genes were included in groups related to the immune system, obesity and heart disease. Among these genes, trib1 has already been demonstrated to contribute to an increased risk of cardiovascular disease. The present result suggests that trib1 is a target of DOHaD. In addition, lepr was also dow-regulaed by maternal FR, suggested a potential role of this gene in induction of obesity. Promotor DNA methylation profiling as well as gene expression profiling revealed glucocorticoid target genes were regulated by maternal FR, supported previous reports suggesting important role of glucocorticoid in DOHaD.

overall_design: C57BL/6J mice were purchased from Japan SLC Co. Ltd. (Hamamatsu, Japan).  The animals were housed at the Animal Institution in Showa University. They were maintained in cages in a ventilated animal room with controlled temperature and relative humidity with a 12 h light: 12 h dark schedule (lights turned on at 8:00 AM) and had access to chow (CE-2, CLEA Japan) and tap water ad libitum. As per the supplier’s (CLEA) information, CE-2 includes 51.4% nitrogen free extracts, 24.9% crude protein, 8.6% moisture, 6.7% crude ash, 4.6% crude fat, and 3.7% crude fiber. The physiological fuel value is 346.7 kcal per 100 g chow. All animal experiments were started after a period of acclimation of at least one week. Pregnant animals were obtained by housing females with males (1-2 females/male). The day the vaginal plug was observed was designated embryonic day 0 (ED0) and gestation day 0 (GD0). Pregnant mice were exposed to 50% food restriction (FR) from GD 10 to 17 and caesarean section was performed between 10:00-12:00 AM on GD18. Amount of CE-2 chow supplied FR group was calculated as 50% of CE-2 consumed by control group each gestation day. Control group was supplied with chow ad libitum. Pregnant mice were sacrificed by cervical dislocation, and the fetuses were taken out and anesthetized on ice cold phosphate buffered saline.   The fetuses were dissected under a dissection microscope, and fetal tissues were carefully removed avoiding any other tissues contamination. The liver was collected from six mothers in each group. Fetal liver was collected from two male fetuses from each mother. The liver was also collected from mothers to compare with fetal one in gene expression analysis. The harvested livers were immediately immersed in liquid nitrogen (N2) and stored at -80ºC. In all combinations, total RNA (1000 ng) was labeled with either Cy3 or Cy5 dye using an Agilent Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies Inc., CA, USA). Fluorescently labeled targets of control as well as treated samples were hybridized to the same microarray slide with 60-mer probes (4 x 44K (41,090 gene probes), mouse whole genome, Agilent). A flip labelling (dye-swap or reverse labelling with Cy3 and Cy5 dyes) procedure was followed to nullify the dye bias associated with unequal incorporation of the two Cy dyes into cDNA. Hybridization and wash processes were performed according to the manufacturer’s instructions, and hybridized microarrays were scanned using an Agilent Microarray scanner. For the detection of significantly differentially expressed genes between control and exercise samples each slide image was processed by Agilent Feature Extraction software (version 9.5.3.1).

first: Junko

last: Shibato

first: Tetsuo

last: Ogawa

first: Randeep

last: Rakwal

first: Tomomi

first: Makiko

last: Kuwagata

first: Seiji

last: Shioda


title: Comparison of gene expression profiles of p45-/- primary megakaryocytes and WT primary megakaryocytes

status: Public on Aug 07 2013

first: Hozumi

last: Motohashi

state: Miyagi

department: Center for Radioisotope Science

summary: Whole livers were collected from mouse fetuses at embryonic day 13.5 (E13.5), and single-cell suspensions were prepared by successive passage through 25-gauge needles. Fetal liver cells were maintained in RPMI1640 (Wako, Osaka, Japan) supplemented with 20% charcoal-stripped fetal bovine serum (FBS), 100 U/ml penicillin, 100µg/ml streptomycin, and 50ng/ml recombinant human thrombopoietin (TPO) (generously provided by Kyowa Hakko Kirin Co. Ltd.). Megakaryocytes were harvested for RNA purification from a day-3 culture.  CD41+ cells were enriched using biotinylated anti-CD41 antibody (Serotec; clone MWReg30) and streptavidin-coupled Dynabeads (Dynal Biotech ASA) from a culture of E13.5 fetal liver cells of WT and p45–/– mice.  Total RNA was purified from the sorted CD41+ cells.

overall_design: Gene expression was measured in primary megakaryocytes cultured from p45-/- fetal livers and wild type fetal livers at E13.5.  Three independent experiments were performed.

first: Rie

last: Fujita


title: Angiotensin converting enzyme inhibition attenuates insterstitial injury in a murine model of chronic glomerulonephritis

status: Public on Jul 30 2013

city: Syracuse

first: Frank

last: Middleton

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

summary: Evolution of glomerulonephritis (GN) to tubulointerstitial disease is a universal antecedent to the development of chronic kidney disease (CKD).  There is also evidence that angiotensin converting enzyme (ACE) inhibition may attenuate the development of CKD in some forms of glomerulonephritis.  We tested the role of ACE inhibition in a model of GN in which complement-dependent tubulointerstitial disease develops. GN was induced in C57BL/6 mice with intraperitoneal injections of horse spleen apoferritin (HSA) using lipopolysaccharide (LPS) as an adjuvant.  Four groups of six animals were studied:  saline-injected control mice treated with captopril or water, and GN mice treated with captopril or water. GN developed in all HSA-treated animals.  In those receiving captopril, however, proteinuria (albumin/creatinine ratio) was significantly reduced by captopril treatment.  Array screening was used to examined the expression of collagen-related genes and determine if these effects could be mediated by regulation of collagen genes.  Six genes were identified for further analysis by quantitative RT-PCR.  This model demonstrates that tubulointerstitial disease can be attenuated by ACE inhibition, with clinical, histologic, and gene expression measures.

overall_design: All protocols were approved by the Institutional Animal Care and Use Committee at SUNY Upstate Medical University. We employed four groups of six mice each:  saline-injected control mice with and without captopril, and GN with and without captopril.  C57BL/6 mice were purchased from The Jackson Laboratories (Bar Harbor, ME).  Glomerulonephritis (GN) was induced by intraperitoneal (i.p.) injection of 10 mg of apoferritin from horse spleen (HSA, Sigma, St. Louis, MO) five days per week, with i.p. injection of 100 micrograms lipopolysaccharide (LPS, from Salmonella minnesota; EMD Biosciences, La Jolla, CA), as adjuvant, three times per week.  Control animals received equal volumes of 0.15 M NaCl by i.p. injection.  Injections were begun when the mice were approximately eight weeks of age and were continued for six weeks.  Captopril, at 100 mg/kg/day was given in the drinking water.  After 9 weeks, the animals were euthanized and kidneys were removed for RNA purification and analysis.

first: Thomas

last: Welch

first: Lisa

middle: W

last: Blystone

first: Karen

middle: L

last: Gentile


title: Juvenile hormone regulation of Drosophila aging

status: Public on Jul 26 2013

city: Providence

first: Hua

last: Bai

state: RI

address: 34 Olive St, BMC502

department: EEB

institute: Brown University

summary:
Background. Juvenile hormone (JH) has been demonstrated to control adult lifespan in a number of non-model insects where surgical removal of the corpora allata eliminates the hormone’s source. In contrast, little is known about how juvenile hormone affects adult Drosophila melanogaster.  Previous work suggests that insulin signaling may modulate Drosophila aging in part through its impact on juvenile hormone titer, but no data yet addresses whether reduction of juvenile hormone is sufficient to control Drosophila life span.  Here we adapt a recent genetic approach to knock out the corpora allata in adult Drosophila melanogaster and characterize adult life history phenotypes produced by reduction of juvenile hormone. With this system we test potential explanations for how juvenile hormone modulates aging.
Conclusions. Reduced juvenile hormone alone is sufficient to extend lifespan of Drosophila melanogaster. Reduced juvenile hormone limits reproduction by inhibiting the production of yolked eggs, and this may arise because juvenile hormone is required for the post-eclosion development of vitellogenin-producing adult fat body. Our data do not support a mechanism for juvenile hormone control of longevity simply based on reducing the physiological costs of reproductive. Nor does the longevity benefit appear to function through mechanisms by which dietary restriction extends longevity. We identify transcripts that change in response to juvenile hormone independent of reproductive state and suggest these represent somatically expressed genes that could modulate how juvenile hormone controls persistence and longevity.

overall_design: Four genotypes were analyzed. They are CA knockout (CAKO), wildtype (wDah/w1118 ), CAKO with OvoD1 mutation and control (wDah/w1118) with OvoD1 mutation. Three biological replicates for each genotype.

first: Rochele

last: Yamamoto

first: Marc

last: Tatar


status: Public on Aug 01 2013

city: Brussels

first: Olivier

last: Feron

address: Avenue E. Mounier, 52 - FATH5349

department: IREC

country: Belgium

institute: UCL

summary:
Hypoxia-driven alterations in the B16 melanoma cell transcriptome account for a higher metastatic potential: evidence for a role of Ero1L

We analyzed transcriptomic adaptations to hypoxia/reoxygenation in B16 melanoma cells. By Ero1L over- and down-expression in vivo, we identified this ER oxidase as an actor of tumor growth and metastasis take.

overall_design: In vitro culture of B16 submitted to hypoxia (oxygen rate less than 1%)

first: Géraldine

last: Daneau

first: Julie

last: De Wever

first: Florence

last: Defresne

first: Ahlame

last: Saidi


title: miR expression profiling of mouse hematopoietic stem and progenitor populations [mRNA]

status: Public on Jul 24 2013

city: Baltimore

first: Curt

last: Civin

state: Maryland

address: BRB 14-021, 655 W Baltimore St

department: Center for Stem Cell Biology & Regenerative Medicine

institute: University of Maryland School of Medicine

summary: Several individual miRNAs (miRs) have been implicated as potent regulators of important processes during normal and malignant hematopoiesis.  In addition, many miRs have been shown to fine-tune intricate molecular networks, in concert with other regulatory elements.  In order to study hematopoietic networks as a whole, we first created a comprehensive map of global miR expression during early murine hematopoiesis.   Next, we determined the copy number per cell for each miR in each of the examined stem and progenitor cell types.  As data is emerging indicating that miRs function robustly mainly when they are expressed above a certain threshold (~100 copies per cell), our database provides a resource for determining which miRs are expressed at a potentially functional level in each cell type.   Finally, we combine our miR expression map with matched mRNA expression data and external prediction algorithms, using a Bayesian modeling approach to create a global landscape of predicted miR-mRNA interactions within each of these hematopoietic stem and progenitor cell subsets.  This approach identifies several interaction networks comprising a “stemness” signature in the most primitive hematopoietic stem cell (HSC) populations, as well as “myeloid” patterns associated with two branches of myeloid development.

overall_design: Six populations of mouse hematopoietic stem and progenitors have been analyzed (LT-HSC, ST-HSC, MPP, CMP, GMP, MEP).  2-3 replicates are included for each sample.

first: Diane

middle: J

last: Heiser

first: Brian

last: Godsey

first: Ian

middle: M

last: Kaplan

first: YeeSun

last: Tan

first: Sebastien

last: Morisot

first: Wen-Chih

last: Cheng

first: Donald

last: Small


title: miR expression profiling of mouse hematopoietic stem and progenitor populations

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


title: Gene expression profile of isolated splenic NK cells from mice treated with ptaquiloside and/or selenium

city: Sao Paulo

first: Andreia

middle: Oliveira

last: Latorre

state: SP

address: 87, Prof. Dr. Orlando Marques de Paiva

department: Pathology

country: Brazil

institute: University of Sao Paulo

summary: To better understand the immunosuppressor mechanism of ptaquiloside in splenic NK cells and the reversion of this effect by selenium, we have employed whole genome microarray expression profile to identify genes associated with immunosuppression. Among 89 genes induced by ptaquiloside treatment in splenic NK cells only two genes (Mt1 and Mt2) were identified as related with its immunosuppressor effect. Moreover this augmented expression of Mt1 and Mt2 was totally abrogated by selenium co-treatment. These results were confirmed by flow cytometry in splenic cells harvested from other six mice and treated in vitro for 1 hour with ptaquiloside and/or selenium.

overall_design: Twenty mice were separated randomly into four groups as Control (water), Pt (ptaquiloside 5.3 mg/kg), PtSe (ptaquiloside 5.3 mg/kg and selenium 1.3 mg/kg) and Se (selenium 1.3 mg/kg) and were treated daily by gavage for 14 days. After treatment, untouched NK cells were isolated using the NK cell isolation kit, LS columns, and QuadroMACS cell separator system (Miltenyi Biotec, Inc.) to perform RNA isolation and whole-genome gene expression profile. Thereby, five independent experiments were performed per group using different donors for each experiment. To confirm the increase of metallothionein protein induced by ptaquiloside, splenic cells were harvested from other six mice and treated in vitro for 1 hour with ptaquiloside [4.4 µg/mL] and/or selenium [0.1 mM] and analyzed by flow cytometry.