title: Gene expression profile of cerebral cortical cells after Rb family inactivation in progenitors and neurons

status: Public on Jan 01 2014

city: Tokyo

first: Itsuki

last: Ajioka

address: 1-5-45 Yushima, Bunkyo-ku

department: Center for Brain Integration Research

institute: Tokyo Medical and Dental University

summary: Cell cycle deregulation leads to abnormal proliferation and cell death in a context-specific manner. Cell cycle progression driven via Rb pathway forces neurons to undergo S-phase, resulting in cell death associated with the progression of neuronal degeneration. Nevertheless, some Rb- and Rb family (Rb, p107, and p130)-deficient differentiating neurons can proliferate and form tumors. Here, we found that differentiating cerebral cortical excitatory neurons underwent S-phase progression but not cell division after acute Rb family inactivation in differentiating neurons. However, the differentiating neurons underwent cell division and form tumors when Rb family members were inactivated in cortical progenitors. Differentiating neurons generated from Rb -/-; p107 -/-; p130 -/- (Rb-TKO) progenitors, but not acutely inactivated Rb-TKO differentiating neurons, activated DNA double-strand break (DSB) repair pathway without increasing the tri-methylation of histone H4 at lysine 20 (H4K20M3), which is known to protect from DNA damage. The activation of DSB repair pathway was essential for the cell division of Rb-TKO differentiating neurons. These results suggest that newly-born cortical neurons from progenitors epigenetically become protected from DNA damage and cell division in a Rb family-dependent manner.

overall_design: 3 samples of pCAG-control, pCAG-RbTKO, pMAP2-control, and pMAP2-RbTKO cells

first: Mio

last: Oshikawa


title: Comparison of gene expression between Xist KO GS cells and wild type GS

status: Public on Dec 01 2013

city: Bunkyo-ku

first: Jiyoung

last: Lee

state: Tokyo

address: 1-5-45 Yushima

country: Japan

summary: Comparison of gene expression between Xist KO germ line stem GS cells and wildtype GS cells

overall_design: The gene expression of GS cells derived from postnatal mouse testis was investigated. RNA from Xist KO-,  wildtype-GS cells, and ES cells were used for this study. 3 independent samples from each cell line were used.

first: Saori

last: Takahashi


title: Mouse ILC2 cells from wild-type or Gfi1-KO animals

status: Public on Oct 20 2013

city: South San Francisco

first: Alex

last: Abbas

state: CA

address: 1 DNA Way

department: Bioinformatics

country: USA

institute: Genentech, Inc.

summary:
Innate type-2 lymphocytes (ILC2s) are a newly described cell type whose biology and contribution to disease are poorly understood. We are interested in investigating the role of the transcription factor Gfi1 in ILC2s, which appear to be a prominent source of IL-5 and IL-13 during type-2 immune responses.
We have compelling evidence demonstrating a critical role for Gfi1 in the development and effector state of ILC2s. We would like to elucidate the molecular role of Gfi1 in ILC2s by identifying Gfi1-regulated genes by microarray analysis.

overall_design: Gfi1+/+ or Gfi1GFP/GFP (a GFP cassette has been 'knocked-in' to the Gfi1 locus and thus functions both as a surrogate for Gfi1 promoter activity and as a loss-of-function allele) mice were injected with IL-25 once daily for 4 days. On day 5, ILC2s (Lin-/Sca-1+/ICOS+/CD127+/c-Kit+) were sorted from the mesenteric lymph nodes of Gfi1+/+ (3 mice/sample were pooled together) or Gfi1-/- mice (6 mice/sample were pooled together) and cultured for 6 days in RPMI 1640, 10% FBS, Gln, P/S, 2ME, IL-2 (50ng/ml), IL-7 (10ng/ml), and IL-25 (50ng/ml). Whole RNA was harvested on day 6 via the RNeasy kit (Qiagen).

first: Alexander

middle: R

first: Chauncey

last: Spooner

first: Harinder

last: Singh


title: Transcription repressor Bach2 is required for pulmonary surfactant homeostasis and alveolar macrophage function.

status: Public on Jan 15 2014

city: Sendai

first: ari

last: itoh

state: Miyagi

address: 2-1 Seiryo-machi, Aobaku

institute: Tohoku univ.

summary: Pulmonary alveolar proteinosis (PAP) results from a dysfunction of alveolar macrophages (AMs), chiefly due to disruptions in the signaling of granulocyte macrophage colony-stimulating factor (GM-CSF). We found that mice deficient for the B lymphoid transcription repressor BTB and CNC homology 2 (Bach2) developed PAP-like accumulation of surfactant proteins in the lungs. Bach2 was expressed in AMs, and Bach2-deficient AMs showed alterations in lipid handling in comparison with wild-type (WT) cells. Although Bach2-deficient AMs showed a normal expression of the genes involved in the GM-CSF signaling, they showed an altered expression of the genes involved in chemotaxis, lipid metabolism, and alternative M2 macrophage activation with increased expression of Ym1 and arginase-1, and the M2 regulator Irf4. Peritoneal Bach2-deficient macrophages showed increased Ym1 expression when stimulated with interleukin-4. More eosinophils were present in the lung and peritoneal cavity of Bach2-deficient mice compared with WT mice. The PAP-like lesions in Bach2-deficient mice were relieved by WT bone marrow transplantation even after their development, confirming the hematopoietic origin of the lesions. These results indicate that Bach2 is required for the functional maturation of AMs and pulmonary homeostasis, independently of the GM-CSF signaling.

overall_design: WT (n=8) and Bach2KO (n=3) AMs. One expreriment was performed.

first: Atsushi

last: Nakamura

first: Risa

last: Ebina-Shibuya

first: Ari

last: Itoh-Nakadai

first: Kazuhiko

last: Igarashi


title: Gene expression profiling of mature dendritic cells from mice s. c. treated with GM-CSF-gene transduced LLC cells (LLC/SeV/GM) or control cells (LLC, LLC/SeV/GFP)

status: Public on Sep 30 2013

city: Fukuoka

first: kenzaburo

last: tani

address: 3-1-1 Maidashi

department: Medical Institute of Bioregulation

institute: Kyushu University

summary: Irradiated granulocyte macrophage-colony stimulating factor (GM-CSF)-transduced autologous tumor cells induce substantial antitumor immunity through the maturation and migration of dendritic cells (DCs). However, little is known about the key molecules involved in GM-CSF-sensitized DCs (GM-DCs) in tumor draining lymph nodes (TDLNs). We initially confirmed that mice subcutaneously injected with poorly immunogenic syngeneic Lewis lung carcinoma (LLC) cells transduced with Sendai virus encoding GM-CSF (LLC/SeV/GM) significantly rejected the tumor growth. Using microarray expression profiling, we obtained a large number of gene expression data files from GM-DCs and control DCs in TDLNs, and subjected them to network-based cluster analysis and unexpectedly unraveled the expression levels of type I IFNs-related genes specifically expressed in plasmacytoid DCs (pDC) were robustly up-regulated in GM-DCs. In vivo depletion assay showed that pDC-depleted mice treated with subcutaneous LLC/SeV/GM cells abrogated the antitumor effects observed in control mice. Moreover combination use of imiquimod for TLR7 triggering on pDC with irradiated LLC/SeV/GM cells induced a significant therapeutic antitumor effect with marked induction of CD9+ pDC with antitumor phenotype, whereas other control mice groups had only minimal to-modest antitumor responses, implicating that this combined vaccine strategy using imiquimod could be promising for improvement of GM-CSF-induced antitumor immunity.

overall_design: Mouse GM-CSF induced gene expression in mature dendritic cells in tumor draining lymph nodes from C57/BL6N female mouse  was measured at 2 days after s.c. tumor challenge with GM-CSF gene-transduced LLC cells (LLC/SeV/GM) or control cells (LLC, LLC/SeV/GFP).

first: Megumi

last: Narusawa

first: Hiroyuki

last: Inoue

first: Chika

last: Sakamoto

first: Tomoko

first: Ayumi

last: Watanabe

first: Shohei

last: Miyamoto

first: Yoshie

last: Miura

first: Yasuki

last: Hijikata

first: Makoto

first: Koichi

last: Takayama

first: Toshihiko

last: Okazaki

first: Mamoru

last: Hasegawa

first: Yoichi

last: Nakanishi

first: Kenzaburo

last: Tani


title: Dual leucine zipper kinase is required for excitotoxicity induced neuronal degeneration

status: Public on Aug 28 2013

first: Jessica

middle: Lynn

last: Larson

state: California

department: Bioinformatics and Computational Biology

institute: Genentech

summary: To investigate the role of DLK in the adult brain, we generated mice in which excision of the DLK allele can be temporally controlled to avoid the lethality observed at early postnatal ages in DLK null mice (Hirai et al., 2006). This was done by crossing mice with DLK exons 2-5 flanked by loxP sites (DLKlox/lox) to a Tamoxifen inducible Cre-ERT transgene driven by the CMV early enhancer/chicken beta actin (CAG) promoter that expresses high levels of Cre-ERT in brain and most peripheral tissues (Hayashi and McMahon, 2002). DLKlox/lox /Cre-ERTpos mice (referred to as DLKlox;Crepos) displayed minimal recombination of the DLK allele in the absence of Tamoxifen and survived to adulthood. To induce DLK recombination, 10-12 week old DLKlox;Crepos mice were put on a Tamoxifen diet for three weeks combined with three high dose injections of Tamoxifen, which resulted in efficient excision of DLK in most brain regions. Although the vast majority of DLK protein was eliminated in many brain regions one week after completion of Tamoxifen dosing, a small amount of DLK protein was still present, consistent with the levels of unrecombined DLK observed by PCR in each brain region. Nonetheless, this dosing regimen achieved a reduction in DLK levels that was adequate to assess the function of this kinase in the adult CNS and thus, avoid confounding developmental phenotypes.  To examine what changes in gene expression resulted from Tamoxifen induced excision of DLK, we performed microarray analysis on the hippocampi of five Tamoxifen treated DLKlox;Crepos (conditional knock-outs, cKO) and five DLKlox;Creneg (WT) aged matched controls.

overall_design: Gene expression of adult hippocampus was compared betwween DLK wild-type and DLK conditional knockout mice.

middle: L

first: Christine

middle: D

last: Pozniak

first: Arundhati

middle: S

last: Ghosh

first: Zora

last: Mordrusan

first: Alvin

last: Gogineni

first: Jesse

last: Hanson

first: Seung-Hye

last: Lee

first: Hilda

last: Solanoy

first: Daisy

last: Bustos

first: Hong

last: Li

first: Hai

last: Ngu

first: Adrian

middle: M

last: Jubb

first: Gai

last: Ayalon

first: Jiansheng

last: Wu

first: Kimberl

last: Scearce-Levie

first: Qiang

last: Zhou

first: Robby

last: Weimer

first: Donald

last: Kirkpatrick

first: Joseph

middle: W

last: Lewcock


title: The ShcA PTB Domain Functions as a Biological Sensor of Phospho-tyrosine Signaling During Breast Cancer Progression

status: Public on Aug 07 2013

city: Montreal

first: Sean

last: Cory

state: QC

address: 3649 Promenade Sir William Osler

department: Goodman Cancer centre

country: Canada

institute: McGill

summary: The ShcA adaptor possesses two phosphotyrosine binding motifs, which include an SH2 and a PTB domain. In the majority of  cases, ShcA utilizes its PTB domain to engage activated receptor tyrosine kinases (RTKs). To establish the mportance of this domain during mammary tumorigenesis, we employed a ShcA mutant (R175Q) that no longer binds phospho-tyrosine residues via its PTB domain. We demonstrate that the ShcR175Q mutant delays mammary tumor  onset n MMTV/MT transgenic animals. Paradoxically, we observe a robust increase in the growth and angiogenesis of emerging mammary tumors. ShcR175Q-expressing breast cancer cells increase fibronectin secretion and possess elevated levels f integrin  α5/β1, the principle fibronectin receptor. Sustained integrin engagement activates Src, which in turn phosphorylates pro-angiogenic RTKs, including PDGFR, FGFR and Met, leading to increased VEGF secretion from ShcR175Q-xpressing breast cancer cells. Finally, we describe a ShcR175Q-dependent gene signature that stratifies breast cancer patients with a high microvessel density. This is the first study to demonstrate that intracellular signaling pathways ownstream of the ShcA PTB domain both positively and negatively regulate tumorigenesis during the various stages of breast cancer progression

overall_design: ShcA mutant (R175Q) vs NT/ShcA cells

first: Josie

last: Ursini-Siegel


title: 5/6 nephrectomy (5/6Nx) effect on the liver

status: Public on Aug 01 2013

city: fukuoka

first: naoya

last: matsunaga

address: maidashi 3-1-1, higashi-ku

institute: kyushu university

summary: Chronic renal failure (CRF) is associated with a decrease in drug metabolism. The present study investigated the repercussions of CRF on liver cytochrome P450 (CYPs), but the mechanisms have been little explored. On the other hand, the expression of several CYP genes exhibits circadian rhythm. Here we report that downregulation of hepatic CYP3A11 (the murine homolog to human CYP3A4; the most decrease in 5/6Nx using microarray analysis) by suppressing the expression of clock gene; D-site binding protein (DBP). In vivo experiments, the mRNA levels of hepatic CYP3A11 exhibit circadian rhythm regulated by DBP and E4BP4, and significantly decreased in 5/6Nx. Microarray analysis revealed that the general transcription factors of CYP3A11 did not changed. However, DBP were downregulated and several CYP genes controlled by DBP also significantly decreased in 5/6Nx. These downregulations were not observed in angiotensin II type 1alpha receptor (AT II R1a) deficient 5/6Nx because serum TGF-beta was not upregulate. In vitro experiments, the RNA levels of CYP3A11 and DBP were downregulated in wild-type mouse hepatocytes incubated with serum from 5/6Nx, but did not changed in Id2 (-/-) hepatocytes. In fact, hepatic Id2 was upregulated and caused the downregulation of DBP in 5/6Nx. Hepatocyte treated with SD208 (TGF-beta receptor 1 selectivity inhibitor) recovered CYP3A11, DBP and Id2 to control levels. Furthermore, 5/6Nx treated with tranilast (inhibitor of TGF-beta production or isolation) or candesartan (ARBs) also recovered CYP3A11 levels.   Our findings define that DBP has effects on downregulation of CYP3A11. In CRF conditions, TGF-beta is upregulated by angiotensin II receptor in renal and downregulates DBP and CYP3A11 levels mediated by Id2 in liver. Furthermore, downregulation of CYP3A11 can prevent by tranilast or candesartan.

overall_design: Differential gene expression between 5/6 nephrectomized and sham-operated mouse was measured on the liver.

first: Naoya

last: Matsunaga

first: Shigehiro

last: Ohdo

first: Kaori

last: Yasuda

first: Atsushi

last: Doi

first: Satoru

last: Koyanagi

first: Eriko

last: Ikeda

first: Kengo

last: Hamamura

first: Konou

last: Hideaki

first: Hironori

last: Aramaki


title: 5/6 nephrectomy (5/6Nx) effect on the brain

summary: Chronic kidney disease (CKD) is a very important problem in global health treatment. CKD increases the disease risk of apoplexy, cardiac failure and cardiac infarction. In addition, neurological complications, including depression and restless legs syndrome, occur in almost all CKD patients; however, the mechanisms of these neurological complications remain unclear. Here, we showed the disruptive effect of chronic renal failure in 5/6 nephrectomy mice on an immobility time of forced swim and tail suspension test and the 24-hr rhythm of Drd2 and clock gene expressions in the striatum. These disruptive effects were induced by abnormal signal transduction in high TGF-β1 expression from the kidney. Abnormal TGF-β signal in the striatum led to TCF7L2 expression and ID2 induced by TCF7L2 led to disruption of the 24-hr rhythm of clock gene expression. These findings suggest that neurological complications in CKD might be overcome by amelioration of the TGF-β signal.

overall_design: Differential gene expression between 5/6 nephrectomized and sham-operated mouse was measured on the brain.


title: Investigation of Alterations in Gene Expression in the Retina Induced by Intravitreal Injection of titanium dioxide nanoparticles

status: Public on Jul 20 2013

city: Seoul

first: Jeong Hun

last: Kim

address: 101, Daehak-ro, Jongno-gu

country: South Korea

institute: Seoul National University

summary: In this study, we investigated the safety of locally delivered titanium dioxide nanoaprticles at the level of gene expression in the retina. To figure out any definite dose-dependent effect, we injected titanium dioxide nanoparticles into the vitreous cavity of 8-week-old male C57BL/6 mice at the concentration of presumptive therapeutic concentration (PTC; 130.47 ng/ml) and 10 times PTC (1.30 μg/ml).

overall_design: We intravitreally injected PBS or titanium dioxide nanoparticles into the right eyes of 8-week-old male C57BL/6 mice (n = 12 per group). PBS-treated mice were regarded as negative control. Four retinal tissues were pooled into 1 test tube and prepared for further analyses.

first: Dong

middle: H

last: Jo

first: Jin

middle: G

last: Son

first: Nam

last: Song

first: Young

last: Yu

first: Tae

last: Lee

first: Jeong


title: A Toxoplasma dense granule protein, GRA24, modulates the early immune response to infection by promoting a direct and sustained host p38 MAPK activation

status: Public on Sep 01 2013

city: LA TRONCHE

first: Mohamed-ali

last: HAKIMI

state: Grenoble

address: Domaine de la Merci, Campus Santé

country: France

institute: CNRS

summary: Toxoplasma gondii, the causative agent of toxoplasmosis, is an obligate intracellular protozoan parasite that resides inside a parasitophorous vacuole. During infection, Toxoplasma actively remodels the transcriptome of its hosting cells with profound and coupled impact on the host immune response. We report that Toxoplasma secretes GRA24, a novel dense granule protein which traffics from the vacuole to the host cell nucleus. Once released into the host cell, GRA24 has the unique ability to trigger prolonged autophosphorylation and nuclear translocation of the host cell p38α MAP kinase. This noncanonical kinetics of p38α activation correlates with the up-regulation of the transcription factors Egr-1 and c-Fos and the correlated synthesis of key proinflammatory cytokines, including interleukin-12 and the chemokine MCP-1, both known to control early parasite replication in vivo. Remarkably, the GRA24-p38α complex is defined by peculiar structural features and uncovers a new regulatory signaling path distinct from the MAPK signaling cascade and otherwise commonly activated by stress-related stimuli or various intracellular microbes.

overall_design:
GRA24 = PSP7
Mouse bone marrow-derived macrophages (BMDM) were infected with the following Toxoplasma gondii strains:
- RHku80 WT versus RHku80(deltaPSP7) mutant
- Pruku80 WT versus Pruku80(deltaPSP7) mutant

first: Laurence

last: Braun

first: Marie-Pierre

last: Brenier-Pinchart

first: Manickam

last: Yogavel

first: Aurelie

last: Curt-Varesano

first: Rose-Laurence

last: Curt-Bertini

first: Tahir

last: Hussain

first: Sylvie

last: Kieffer

first: Yohann

last: Coute

first: Hervé

last: Pelloux

first: Isabelle

last: Tardieux

first: Amit

last: Sharma

first: Hassan

last: Belrhali

first: Alexandre

last: Bougdour

first: Mohamed

middle: A

last: Hakimi


title: 5/6 nephrectomy (5/6Nx) effect on the brain and liver

first: naoya

last: matsunaga

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

overall_design: Refer to individual Series


title: ZHBTc4 ES cells stably expressing EGFP vs Nr5a2-EGFP or Oct4-EGFP vs Nr5a2-EGFP

status: Public on Nov 05 2013

city: Mapo

first: kyeng

middle: won

last: choi

state: Seoul

address: Sinsu

department: Lifescience

institute: Sogang

summary: Gene expression profiles of ZHBTc4 ES cells expressing EGFP, Oct4-EGFP, Nr5a2-EGFP under CAG promoter.  Monoclonal cell lines selected by Puromycin were used for analysis. Each of the cell lines was cultured in doxycycline containing media for endogenous Oct4 knock-down. Pupose of this experiment is to investigate the possibility that forced expression of Nr5a2 can replace Oct4 function in the self-renewal of ES cells.

overall_design: Monoclonal ZHBTc4 ES cells expressing EGFP vs Nr5a2-EGFP, Oct4-EGFP vs Nr5a2-EGFP, no replication

first: Kyeng-won

last: Choi

first: Hye-rim

last: Oh

first: Junho

last: Kim


title: Mouse Uterine Transcriptome in Estrus and Proestrus: whole uterine tissue and isolated lumenal epithelial cells

status: Public on Jun 07 2013

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University


title: Changes in Mouse Uterine Lumenal Epithelial Cell Transcriptome in Estrus Compared to Proestrus

summary: The potential for xenoestrogens and other environmental chemicals to alter female reproductive function calls for the study of their affects on endogenous hormone-regulated gene expression pathways during uterine tissue remodeling which occurs as part of the menstrual/estrus cycle. However, our knowledge of these pathways is limited. Here, we characterize changes in the CD-1 mouse uterine luminal epithelial cell transcriptome during proestrus and estrus, which are regulated by estrogen and progesterone in preparation of the uterus for pregnancy. Mice were staged beginning at 6 wk of age and uterine horns were harvested at estrus and proestrus. RNA was extracted from lumenal epithelium of uterine horns. Microarray analysis identified 2,251 genes differentially expressed in estrus compared to proestrus in lumenal epithelial cells. These complement other studies where RNA was extracted from whole uterine horns of mice in estrus and proestrus (GSE43064).

overall_design: Beginning on postnatal day 41, female CD-1 mice were monitored for reproductive stage cycle and total RNA was isolated from lumenal epithelium of uterine horns at estrus or proestrus. Tissue was collected on postnatal days 41-61. Samples were pooled for microarray analysis as follows. Seven litters were used to generate 2 tissue pools for estrus and 2 tissue pools for proestrus. Each pool was comprised of uterine tissue RNA from n=4-5 individual mice and n=3-4 individual litters. Fluorescent labeling of RNA and hybridization of the Alexa 555-labeled (green) and Alexa 647-labeled (red) RNA samples to Agilent-026655 Whole Mouse Genome Microarray 4x44K v2 (Agilent Technology, Palo Alto, CA; catalog # G4846A) were carried out, with dye swapping for each estrus cycle stage comparison.

first: Alexander

last: Suvorov

first: Nicholas

last: Lodato

middle: J


title: Virus-Induced Airway Disease in Mice (C57BL/6J, d49)

status: Public on Aug 08 2013

city: St. Louis

first: Anand

middle: Champak

last: Patel

state: MO

address: Campus Box 8116, 660 S. Euclid Ave.

department: Pulmonary/Critical Care Medicine

institute: Washington University School of Medicine

summary:
Analysis of gene expression in lungs of C57BL/6J mice that develop chronic airway disease phenotypes after a single Sendai virus infection, compared with mice treated with UV-inactivated virus.
Keywords: disease state analysis

overall_design: Whole lung RNA was analyzed from 3 mice per condition per time point 49 days post infection, Sendai virus versus UV-inactivated virus, C57BL/6J mouse strain.

first: Derek

middle: E

last: Byers

first: Jennifer

last: Alexander-Brett

middle: C

first: Eugene

last: Agapov

first: Geoffrey

last: Dang-Vu

first: Xiaohua

last: Jin

first: Kangyun

last: Wu

first: Yingjian

last: You

first: Yael

last: Alevy

first: Jean-Philippe

last: Girard

first: Thaddeus

last: Stappenbeck

first: G

last: Patterson

first: Richard

last: Pierce

first: Steven

last: Brody

first: Michael

last: Holtzman


title: Changes in Mouse Uterine Transcriptome in Estrus and Proestrus

first: David

last: Waxman

summary: The potential for xenoestrogens and other environmental chemicals to alter female reproductive function calls for the study of their affects on endogenous hormone-regulated  gene expression pathways during uterine tissue remodeling which occurs as part of the menstrual/estrus cycle. However, our knowledge of these pathways is limited. Here, we characterize changes in the CD-1 mouse uterine transcriptome during proestrus and estrus, which are regulated by estrogen and progesterone in preparation of the uterus for pregnancy. Mice were staged beginning at 6 wk of age and uterine horns were harvested after monitoring two estrus cycles. Microarray analysis identified 2,429 genes differentially expressed in estrus compared to proestrus, indicating that the mouse uterus undergoes remarkable remodeling during the estrus cycle, affecting ~10% of all protein-coding genes. Changes in gene expression associated with structural alteration of the uterus include remodeling of the extracellular matrix, changes in cell keratins and adhesion molecules, activation of mitosis, MHC class II presentation, complement and coagulation cascades, and cytochrome P450 expression. Signaling pathways regulated during the estrus cycle, involving ligand-gated channels, Wnt and hedgehog signaling, and several transcription factors with poorly understood roles in reproductive tissues, include several genes and gene networks that have been implicated in pathological states. The information presented here builds a background for understanding of mechanisms involved in uterine tissue response to endocrine disruptors and the development of reproductive tract diseases.

overall_design: Beginning on postnatal day 42, female CD-1 mice were monitored for reproductive stage cycle for 2 consecutive cycles and then total RNA was isolated from uterine horns at estrus or proestrus. Samples were pooled for microarray as follows.  Six litters were used to generate 2 tissue pools for estrus and 2 tissue pools for proestrus, with estrus pool 1 and proestrus pool 1 comprised of mice from the same 3 litters, and estrus pool 2 and proestrus pool 2 comprised of mice from the other 3 litters. Each pool was comprised of uterine tissue RNA from n= 4-6 individual mice. Fluorescent labeling of RNA and hybridization of the Alexa 555-labeled (green) and Alexa 647-labeled (red) RNA samples to Agilent-026655 Whole Mouse Genome Microarray 4x44K v2 (Agilent Technology, Palo Alto, CA; catalog # G4846A) were carried out, with dye swapping for each estrus cycle stage comparison.

first: Kerri

last: Yip

first: Alexander

last: Suvorov

first: Jeannette

last: Connerney


title: Influence of G0s2 gene knockdown on primary hepatocyte

first: naoya

last: matsunaga

summary: Hepatocellular carcinoma is the third leading cause of cancer death worldwide, and it is necessary to elucidate the mechanism of hepatocarcinogenesis. Circadian clock systems have been related in cell cycle and carcinogenesis. In this study, hepatocarcinogenesis induced by DEN administration in mice was inhibited by knockdown of G0s2 at early stage in carcinogenesis. In addition, the circadian expression of G0s2 in mouse liver was regulated by RARα controlled by clock genes and ATRA. Moreover, mice administered both ATRA and DEN were not induced hepatocellular carcinoma, and decreased the expression of G0s2 at second day after the initiation of administration. These findings suggest that the control of G0s2 expression is important in carcinogenesis and G0s2 might be the novel target for prevention, diagnosis and treatment of hepatocellular carcinoma.

overall_design: Differential gene expression between G0s2 siRNA or  Control siRNA transfected primary hepatocyte was measured after 24 hr of transfection.

first: Naoya

last: Matsunaga

first: Shigehiro

last: Ohdo

first: Kaori

last: Yasuda

first: Atsushi

last: Doi

first: Keisuke

last: Kakimoto

first: Satoru

last: Koyanagi


title: Investigation of Alterations in Gene Expression in the Retina Induced by Intravitreal Injection of gold and silicate nanoparticles

status: Public on Jul 31 2013

first: Jeong Hun

last: Kim

summary: In this study, we investigated the gene expression induced by locally delivered gold and silicate nanoaprticles with the diameter of 20 and 100 nm in the retina. We injected nanoparticles into the vitreous cavity of 5-week-old male C57BL/6 mice. Au20 indicates gold nanoparticles of which diameters were 20 nm, Au100 gold nanoparticles of which diameters were 100 nm, Si20 silicate nanoparticles of which diameters were 20 nm, and Si100 silicate nanoparticles of which diameters were 100 nm.

overall_design: We intravitreally injected PBS or nanoparticles (gold and silicate) into the right eyes of 5-week-old male C57BL/6 mice (n = 12 per group). PBS-treated mice were regarded as negative control. Four retinal tissues were pooled into 1 test tube and prepared for further analyses.

first: D

last: Jo

first: J

last: Son

first: T

last: Lee


title: Max is a repressor of germ-cell-related gene expression in mouse embryonic stem cells

status: Public on May 01 2013

first: Ikuma

last: Maeda

address: 4-1 Seiryomachi, Aoba-ku

institute: Institute of Development, Aging and Cancer, Tohoku University

summary: Embryonic stem cells (ESCs) and primordial germ cells (PGCs) express many pluripotency-associated genes, but ESCs do not normally undergo conversion into PGCs. Thus, we predicted that there is a mechanism that represses PGC-related gene expression in ESCs. Here we identify genes involved in this putative mechanism, by using an ESC line with a Vasa reporter for an RNAi screen of transcription factor genes expressed in ESCs. We identify 5 genes that result in the expression of Vasa when silenced. Of these, Max is the most striking. Transcriptome analysis reveals that Max knockdown (KD) in ESCs results in selective, global derepression of germ-cell-specific genes. Max interacts with histone H3K9 methyltransferases and associates with the germ-cell-specific genes in ESCs. In addition, Max-KD results in a decrease in histone H3K9 dimethylation at their promoter regions. We propose that Max is part of a protein complex that acts as a repressor of germ-cell-related genes in ESCs.

overall_design: Gene expression profile of Vasa-positive cells isolated from Max knockdown ESCs was compared to that of normal ESCs and in vivo PGCs. As an ESCs sample, a mouse embryonic stem cell line that carries a Venus reporter driven by the Vasa gene promoter (VV3) was used for this study. VV3 ESCs were transfected with non-silencing negative control siRNA (AllStars) or siRNA against the Max gene. Vasa-positive cells were purified using fluorescence-activated cell sorting (FACS). As a PGCs sample, a mouse strain that carries a germ-cell-specific GFP reporter (Oct4ΔPE-GFP) was used. PGCs were also purified using FACS. RNA samples were isolated from each sample and labeled and hybridized to Agilent microarrays. Three biological replicates were performed for each group of samples.

first: Daiji

last: Okamura

first: Yuko

last: Tokitake

first: Makiko

last: Ikeda

first: Hiroko

last: Kawaguchi

first: Nathan

last: Mise

first: Kuniya

last: Abe

first: Toshiaki

last: Noce

first: Akihiko

last: Okuda

first: Yasuhisa

last: Matsui


title: Investigation of Alterations in Gene Expression in the Retina Induced by Intravitreal Injection of SH-42 and SH-80

status: Public on Apr 16 2013

summary: In this study, we demonstrate that SH-42 and SH-80, novel heat shock protein 90 inhibitors, suppress retinal neovascularization via inhibition of hypoxia-mediated angiogenesis. To figure out any genotoxic effect of these compounds related with heat shock protein 90 inhibition, we performed microarray analyses with retinal tissues treated with SH-42 and SH-80 for 7 days.

overall_design: We intravitreally injected PBS, SH42, or SH80 into the right eyes of C57BL/6 male mice (n = 12 per group). PBS-treated mice were regarded as negative control. Four retinal tissues were pooled into 1 test tube and prepared for further analyses.

first: Dong

first: Hongchan

last: An

first: Chang

last: Cho

first: Hyoung-Oh

last: Jun

first: Jin-Hyoung

first: Young-Ger

last: Suh

first: Jeong-Hun


title: Gene expression analysis to identify Runx1 target genes in B-cell progenitors

status: Public on May 27 2013

city: Hamburg

first: Neele

middle: Margarete

last: Kriebitzsch

address: Martinistraße 52

country: Germany

institute: Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology

summary: The t(12;21) chromosomal translocation, targeting the gene encoding the RUNX1 transcription factor, is observed in 25% of pediatric acute lymphoblastic leukemia (ALL) and is an initiating event in the disease. To elucidate the mechanism by which RUNX1 disruption initiates leukemogenesis, we investigated its normal role in murine B-cell development. Gene expression analysis and genome-wide Runx1-occupancy studies support the hypothesis that Runx1 reinforces the transcription factor network in B-cell progenitors governing early B-cell survival and development .

overall_design:
1)  To identify Runx1 target genes in early B-cell progenitors, we used a whole genome microarray for analyzing the gene expression profile in a proB-cell line [BMiFLT3(15-3)] engineered to overexpresses the Runx1 transcription factor fused to the ligand binding domain of the estrogen receptor. The use of an inducible Runx1 fusion protein allowed specific translocation of Runx1 into the nucleus activation of Runx1 target genes.
2)  To identify Runx1 target genes in early B-cell progenitors, we used a whole genome microarray for analyzing the gene expression profiles of proB-cells (CD19+/B220med/CD93+) isolated from Runx1+/+Cd79ahCre/+ and Runx1fl/flCd79ahCre/+ mice. Two independent experiments were peformed.

first: Birte

last: Niebuhr

first: Carol

last: Stocking


title: Host cell subversion by Toxoplasma GRA16,  an exported dense granule protein that targets  the host cell nucleus and alters gene expression

status: Public on Feb 06 2013

first: Mohamed-ali

last: HAKIMI

summary: After invading host cells, Toxoplasma gondii multiplies within a parasitophorous vacuole (PV) that is maintained by parasite proteins secreted from organelles called dense granules. Most dense granule proteins remain within the PV and few are known to access the host cell cytosol. We identify GRA16 as a dense granule protein that is exported through the PV membrane and reaches the host cell nucleus where it positively modulates genes involved in cell cycle progression and the p53 tumor suppressor pathway. GRA16 binds two host enzymes, the deubiquitinase HAUSP and PP2A phosphatase, which exert several functions, including regulation of p53 and the cell cycle. GRA16 alters p53 levels in a HAUSP-dependent manner and induces nuclear translocation of the PP2A holoenzyme. Additionally, certain GRA16-deficient strains exhibit attenuated virulence, indicating the importance of these host alterations in pathogenesis. Therefore, GRA16 represents a potentially emerging subfamily of exported dense granule proteins that modulate host function.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Mouse bone marrow-derived macrophages (BMDM) or Human foreskin fibroblasts (HFFs) were infected with the following Toxoplasma gondii strains:
- RHku80 WT versus RHku80(deltaGRA16) mutant (in BMDM)
- Pruku80 WT versus Pruku80(deltaGRA16) mutant (in BMDM)
- RHku80 WT versus RHku80(deltaGRA16) mutant (in HFF)

first: Alexandre

last: Bougdour

first: Eric

last: Durandau

first: Philippe

last: Ortet

first: Mohamed

last: Barakat

first: Marie-Pierre

last: Brenier-Pinchart

first: Sylvie

last: Kieffer

first: Aurelie

last: Curt

first: Rose-Laurence

first: Olivier

last: Bastien

first: Yohann

last: Coute

first: Herve

last: Pelloux

last: Hakimi


title: New protein from an unexpected ligament

status: Public on Mar 31 2013

city: Kurume

first: Michiyo

last: Tsuru

state: Fukuoka

address: 67 Asahimachi

department: Orthopardic Surgery

institute: Kurume Universuty

summary: This study describes the discovery of the gene responsible for differentiation of stem cells into ligament tissue. This important finding may lead to the development of treatments for gonarthrosis, rupture of the cruciate ligament and periodontal ligament, and ossification of the posterior longitudinal ligament.

overall_design: This study describes the discovery of the gene (A) responsible for differentiation of stem cells into ligament tissue. The transfection of this gene into mouse mesenchymal stem cells resulted in the formation of ligament-like connective tissue composed of parallel fibres. We performed microarray analysis of four samples: stem cells (sample1),  ligament-like tissue from stem cells transfected with A (sample 4), ligament tissue from A-transgenic mice (sample 2) , and ligament tissue from wild type mice (sample 3).

first: Takashi

last: Soejima

first: Naoto

last: Shiba

first: Kimiko

last: Kimura

first: Kimiaki

last: Sato

first: Yoshiaki

last: Toyama

first: Kensei

last: Nagata


title: Leptin and the Placental Response to Maternal Food Restriction during Early Pregnancy

status: Public on Dec 07 2012

city: Columbia

first: Laura

middle: Clamon

last: Schulz

address: 1 Hospital Dr.

department: Obstetrics, Gynecology and Women's Health

institute: University of Missouri

summary: Concentrations of leptin decline during food restriction.  This study was designed to test the hypothesis that some of the effects of maternal food restriction on placental development are mediated by the loss of leptin.

overall_design: Mice were randomized to 3 treatment groups on day 1.5 of pregnancy: (1) ad libitum fed (control) (2) 50% food restriction (restricted) (3) 50% food restriction with leptin replacement (1µg/g body weight/day) (leptin). On day 11.5 placentas were collected, and two placentas from each mother were pooled for microarray analysis.

first: Gerialisa

last: Caesar

first: Jessica

last: Schlitt


title: Investigation of Alterations in Gene Expression in the Retina Induced by High-Affinity Peptides targeting vascular endothelial growth factor, AAP and HAN

status: Public on Apr 26 2013

first: Jeong Hun

last: Kim

summary: In this study, we demonstrate that high-affinity peptides targeting vascular endothelial growth factor, AAP and HAN, suppress in vivo pathologic angiogenesis in the retina. To figure out any definite toxicity at the level of gene expression, we performed microarray analyses of gene expression from retinal tissues after the treatment with AAP and HAN

overall_design: We intravitreally injected PBS, AAP, or HAN into the right eyes of C57BL/6 male mice (n = 12 per group). PBS-treated mice were regarded as negative control. Four retinal tissues were pooled into 1 test tube and prepared for further analyses.

first: Dong-Hyun

last: Jo

first: Sangyong

last: Jon

first: Jeong-Hun


title: Mechanistic analysis of the model obesogen Tributyltin in the 3T3-L1 cell line

status: Public on Feb 25 2013

city: Antwerp

first: Anna

last: Pereira-Fernandes

address: Groenenborgerlaan 171

department: Biology

country: Belgium

institute: University of Antwerp

summary:
Obesogenic compounds are chemicals that might have an influence on obesity development through in utero or chronic lifetime exposure. Tributyltin (TBT) is one of the most studied obesogenic compounds, inducing adipogenesis in vitro and increasing body fat after in utero exposure of mice. This study was designed to unravel the molecular mechanisms of TBT, using microarray analysis, and to evaluate the use of toxicogenomics for obesogen screening.
The murine 3T3-L1 cell line was used to study TBT induced adipogenesis. Lipid staining as well as gene expression measurements of an adipocyte specific marker gene were performed to select relevant concentrations (10 nM, 50 nM) and time points (day1, day10) for microarray analysis. Additionally, solvent control and positive control (MDI) treated 3T3-L1 cells were included in the analysis.   The microarray results were analysed using GO enrichment and Pathway analysis tools, which revealed enrichment of several GO terms involved in energy and fat metabolism after 10 days of TBT exposure. Pathway analysis unveiled PPAR signalling pathway as the sole pathway significantly enriched after 1 day and the most significantly enriched pathway after 10 days of exposure.  By examination of effects on both cell physiological and gene expression level we provide a detailed overview of TBT induced obesogenic mechanisms. To our knowledge, this is the first study delivering an in depth mechanistic outline of the mode of action of TBT as an obesogen. Furthermore, our results show that combining omics with 3T3-L1 cells is promising for screening of potential obesogenic compounds.

overall_design: A separate v+2 A-optimal hybridization design was used for each time-point. Using this design each exposure condition is represented by three biological replicates, with each biological replicate analysed in technical duplicate while applying the dye swap principle to correct for dye bias. Two concentrations of TBT (10 nM, 50 nM), DMSO and MDI (positive control, adipogenic hormone cocktail) were the conditions tested, at two time-points (day 1 and day10).

first: Caroline

last: Vanparys

first: Tine

last: Hectors

first: Lucia

last: Vergauwen

first: Dries

last: Knapen

first: Philippe

last: Jorens

first: Ronny

last: Blust


title: Gene expression profiles of Tet1 knockout (T1KO), Tet2 knockout (T2KO) and Tet1/Tet2 double knockout (DKO) mouse embryonic stem cells.

status: Public on Feb 01 2013

city: Cambridge

first: Inmaculada

last: Barrasa

address: Nine Cambridge Center

institute: Whitehead Institute

summary: Global gene expression profile of single and double mutant mouse ES cells were compared to wt ES cells. Two male Tet1 KO, one male Tet2 KO, two male double KO, two female double KO, two male WT and two female WT mouse ES cells were compared.

overall_design: Global gene expression profile of single and double knockout mouse embryonic stem cells were compared to that of wild type mouse ES cells. All used ES lines were derived from C57/BL/6 mixed background mice. RNA from feeder free mutant mouse ES cells was competetively hybridized against RNA from WT ES cells. Same sex lines were compared. Two independent ES line of each genotype were used, with the exception of Tet2 KO ES cells where only one male line was used.

first: M

middle: I

first: Meelad

last: Dawlaty

first: Rudolf

last: Jaenisch


title: Contribution of molecular actors from somatic origin to oocyte developmental competence acquisition, lessons from evolution

status: Public on Oct 14 2012

city: Rennes

first: Julien

last: Bobe

address: Campus de Beaulieu

institute: Institut National de la Recherche Agronomique

sample_organism:
Oncorhynchus mykiss
Xenopus laevis
Bos taurus
Mus musculus


title: Transcriptional profiling of cumulus cells differentiation throughout oocyte competence acquisition in the murine ovarian follicles.

summary:
Cumulus cells surrounding the oocyte were sampled at the following stages: developmentally incompetent or poorly competent prophase I oocytes (NC1 oocytes), developmentally competent prophase I oocytes (C1 oocytes), and developmentally competent metaphase II oocytes (C2 oocytes).
NC1 samples were collected from immature, unexpanded cumulus-oocytes complexes (COC)  from prepubertal (3-week-old) mice, C1 samples from immature, unexpanded cumulus-oocytes complexes (COC)  from adult (8-week-old) and C2 samples from mature, expanded COCs obtained from the oviduct  from 8-week-old mice after standard superovulation protocol.

overall_design: Global transcriptional profiling was performed using cumulus cells collected from murine ovarian follicles during in vivo oocyte developmental competence acquisition. Cumulus cells were collected at 3 stages: early stage follicles (prophase I arrested oocytes, meiotically competent but developmentally incompetent, n=5), late stage follicles (prophase I arrested oocytes, meiotically competent and developmentally competent, n=5) and ovulatory follicles collected in vivo (metaphase II arrested oocytes, developmentally fully competent, n=5).

first: Cathy

last: Charlier

first: Svetlana

last: Uzbekova

first: Franck

last: Chesnel


title: Factor VII activating protease (FSAP) exerts antifibrotic effects in a mouse model of experimental liver fibrosis

status: Public on Sep 19 2012

city: Bergisch Gladbach

first: Ute

last: Bissels

state: NRW

address: Friedrich-Ebert-Str. 68

department: R&D

institute: Miltenyi Biotec GmbH

summary: Background and Rationale: Factor VII activating protease (FSAP) is a circulating serine protease produced in the liver. A single nucleotide polymorphism (G534E, Marburg I, MI-SNP) in the gene encoding FSAP (HABP2) leads to lower enzymatic activity and is associated with enhanced liver fibrosis. FSAP is activated by damaged cells and its substrates include growth factors and haemostasis proteins. We have investigated the progression of liver fibrosis in FSAP deficient mice. Results: Wild type (WT) or FSAP-/- mice were subjected to bile duct ligation (BDL) and assessment of liver fibrosis. FSAP-/- mice showed enhanced liver fibrosis and accumulation of extracellular matrix as determined by Sirius Red staining and hydroxyproline content. FSAP deficient mice exhibited stronger injury as determined by higher necrosis in the liver and circulating liver enzymes. This correlated with expression of markers like α-smooth muscle actin, collagen and fibronectin that are markers of stellate cell activation. FSAP-deficient mice exhibited higher expression of PDGF-BB as well as PDGFRβ that are strong activators of liver fibrosis. In order to gain more insight into this difference microarray analysis was performed and the pattern of gene expression in WT vs. FSAP-/- mice would indicate that FSAP modulates the inflammatory /immune system. Conclusions: The results with FSAP-/- mice correlates with the human situation where lower FSAP activity, due to the MI SNP, is associated with enhanced liver fibrosis. This strengthens the concept that FSAP is a “protective factor” in liver fibrosis. A probable mechanism for this effect is likely to be related to the role of FSAP in the regulation of fibrosis/ inflammation-related processes n the liver.

overall_design: The dataset comprises 12 samples divided into four sample groups each representing a certain treatment group.

first: Erawan

last: Borkham-Kamphorst

first: Andreas

last: Bosio

first: Ralf

last: Weiskirchen

first: Sandip

last: Kanse


title: Effect of deletion of the selenium-binding protein 1 gene on gene expression in the ovary of C57BL/6J mouse

status: Public on Sep 10 2012

first: Tomoki

last: Takeda

address: 3-1-1 Maidashi, Higashi-ku

department: Pharmaceutical sciences

institute: Kyushu University

summary: Selenium-binding protein 1 (SeBP1) is a cytosolic protein expressed in various tissues such as liver, kidney and gonad. This protein is suggested to serve in tumor suppression, anti-aging, modification of oxidative stress, protein transport/degradation in cells, and other phenomena. However, the physiological function of SeBP1 remains obscure because of lack of definitive evidence. To address this issue, we compared gene expression between wild-type and SeBP1-knockout (KO) mice using DNA microarray analysis. The results obtained in this study revealed that the deletion of SeBP1 causes a lot of changes in the expression of proliferation-related genes, including a decrease in myelocytomatosis oncogene and an increase in adenomatosis polyposis coli and tumor necrosis factor. Thus, it is suggested that SeBP1 plays a role in the proliferative and/or anti-proliferative effect via the regulation of these genes.

overall_design: Total RNAs were extracted from the ovaries of wild-type and SeBP1 KO mice at 20 weeks old (each N=3), and their cDNAs were applied to the analysis using Agilent-026655 Whole Mouse Genome Oligo DNA Microarray (4x44K) version 2.

first: Sayuri

last: Tsujimoto

first: Hideyuki

last: Yamada


title: Genome-wide RNA expression in muscle-enriched embryos across different mutations.

status: Public on Jun 22 2012

city: Pasadena

first: Diane

last: Trout

address: 1200 E California Blvd M/C 156-29

institute: California Institute of Technology

type: Expression profiling by high throughput sequencing

summary: To investigate the structure of the bodywall muscle differentiation network, we sought to both identify what these transcription factors regulate in bodywall muscle. Through loss of function analysis, we identified genome-wide regulatory targets of hlh-1 and unc-120 using RNA-seq. 1445 targets of hlh-1 and 3674 targets of unc-120 were identified, with 760 of these genes being targets of both. Crosstalk was identified between the networks of hlh-1 and hlh-8, which is involved in non-bodywall muscle development. In the process, we quantified bodywall muscle RNA. Our data suggest that shared target genes and overlapping regulation buffer the hlh-1 and unc-120 mutant phenotypes.

overall_design: RNA expression genome-wide in the early embryo

first: Steven

last: Kuntz

first: Barbara

last: Wold


title: HLH-1 binding in muscle-enriched embryos and RNA expression in muscle-enriched embryos across different mutations

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Expression data from pain model: rat L5 sensory ganglia after local inflammation

city: Cincinnati

first: Judith

middle: Ann

last: Strong

state: OH

address: 231 Albert Sabin Way

department: Anesthesiology

institute: University of Cincinnati

summary:
Inflammation plays a role in neuropathic pain conditions as well as in pain induced solely by an inflammatory stimulus.  Robust mechanical hyperalgesia and allodynia can be induced by locally inflaming the L5 dorsal root ganglion (DRG) in rat.  This model allows investigation of the contribution of inflammation per se to chronic pain conditions.  Most previous microarray studies of DRG gene expression have investigated neuropathic pain models involving axon transection.  To examine the role of inflammation, we used microarray methods to examine gene expression 3 days after local inflammation of the L5 DRG in rat.
We observed significant regulation in a large number of genes (23% of observed transcripts), and examined 221 (3%) with a fold-change of 1.5-fold or more in more detail.   Immune-related genes were the largest category in this group and included members of the complement system as well as several pro-inflammatory cytokines.  However, these upregulated cytokines had no prior links to peripheral pain in the literature other than through microarray studies, though most had previously described roles in CNS (especially neuroinflammatory conditions) as well as in immune responses.

overall_design: The L5 dorsal root ganglion (DRG) was locally inflamed with zymosan/Incomplete Freund's Adjuvant.  DRG were isolated 3 days later. Each sample was RNA extracted from a single DRG.  6 samples from rats with local DRG  inflammation were compared with 6 samples from sham-operated rats.

first: Jun-Ming

last: Zhang


title: Genome-wide maps of HLH-1 binding in muscle-enriched embryos.

summary: To investigate the structure of the bodywall muscle differentiation network, we sought to both identify what role HLH-1 binding has in this regulation. We mapped the relationship between the regulatory targets and HLH-1 binding, as measured by ChIP-seq in animals enriched for bodywall muscle tissue through RNAi feeding. While regulatory targets are enriched for HLH-1 binding, the majority of HLH-1 binding actually occurs away from genes that are affected by hlh-1 loss of function. Nevertheless, HLH-1 binding is associated with both the expected E-box and, near genes belonging to specific regulatory subgroups, novel motifs that may serve as binding sites for cooperative transcription factors.

overall_design: HLH-1 binding genome-wide in the early embryo of C. elegans


title: IGF1-receptor signalling attenuates the age-related decline of diastolic cardiac function

status: Public on Aug 01 2012

city: Duesseldorf

first: Antje

last: Lindecke

address: Universitaetsstr. 1

department: BMFZ

institute: Universitaet Duesseldorf

summary: Insulin-like growth factor (IGF1R) signalling has been implicated to play an important role in regulation of cardiac growth, hypertrophy and contractile function, and has been linked to the development of age related congestive heart failure. Here we address the question to what extent cardiomyocyte specific IGF1 signalling is essential for maintenance of the structural and functional integrity of the adult murine heart. To investigate the effects of IGF1 signalling in the adult heart without confounding effects due to IGF1 over-expression or adaptation during embryonic and early post-natal development, we inactivated the IGF1R by a 4-hydroxy tamoxifen inducible Cre recombinase in adult cardiac myocytes. Efficient inactivation of the IGF1R (iCMIGF1RKO) as assessed by Western analysis and real-time PCR went along with reduced IGF1-dependent AKT and GSK3β-phosphorylation. Functional analysis by conductance manometry and magnetic resonance imaging (MRI) revealed no functional alterations in young adult iCMIGF1RKO mice (age 3 month). However, when induced in aged mice (11 month) diastolic cardiac function was depressed. To address the question if insulin signalling might compensate for the defective IGF1R signalling we inactivated β-cells by streptozotocin. However, the diabetes associated functional depression was similar in controls and iCMIGF1RKO mice. Similarly, analysis of the cardiac gene expression profile on 44K microarrays did not reveal activation of overt adaptive processes. Endogenous IGF1 receptor signalling is required for conservation of cardiac function of the aging heart, but not for the integrity of cardiac structure and function of young hearts.

overall_design: Four samples of each group: the control group, positive for Cre recombinase, but negative for the floxed IGF-1R and the experimental group with double transgenic mice (merCremer/+ IGFloxP/IGFloxP).

first: Sarah

last: Moellendorf

first: Claudia

last: Kessels

first: Lena

last: Peiseler

first: Annika

last: Raupach

first: Christoph

last: Jacoby

first: Nora

last: Vogt

first: Linda

last: Koch

first: Jens

last: Brüning

first: Jacqueline

last: Heger

first: Karl

last: Koehrer

first: Axel

last: Goedecke


title: p53 deletion induces liver carcinoma with bilineal differentiation

status: Public on Dec 29 2011

city: Ulm

first: Hans

last: Kestler

address: Albert-Einstein-Allee 11

department: Research Group Bioinformatics and Systems Biology

institute: University of Ulm

summary:
Background and Aims: p53 can limit the self-renewal of stem cells from various tissues. Experimental evidence suggests that deletion of p53 can cooperate with other oncogenic events to induce aberrant self-renewal and transformation of progenitor cells. It is not known whether p53 deletion alone can lead to liver tumor formation.

Methods: We used AlfpCre mice for liver-specific deletion of Trp53 in a conditional knockout mouse model to analyze liver carcinogenesis.

Results: Here, we show that liver-specific deletion of p53 in mice consistently induces formation of liver carcinoma depicting bilineal differentiation. Freshly isolated p53-/- liver progenitor cells and hepatocytes exhibit chromosomal imbalances and an enhanced clonogenic capacity compared to p53-positive cells or p21-deficient cells. Primary cultures of hepatocytes and liver progenitor cells from p53-/- mice formed tumors with bilineal differentiation when transplanted into immuno-compromised mice. Together, these results indicate that loss of p53 alone is sufficient to induce primary liver cancer with bilineal differentiation originating from chromosomal instable cultured liver progenitor cells or hepatocytes.

Conclusions: The study shows that p53-dependent checkpoints inhibit transformation of liver progenitor cells and hepatocytes involving p21-independent mechanisms.

overall_design: Liver tumors derived from Trp53 KO mice, liver tumors from DEN-treated wildtype mice, Trp53 KO liver and wildtype liver were isolated and RNA was extracted. Agilent-026655 Mouse 4x44K v2 arrays were used.

middle: F

last: Katz

first: André

last: Lechel

first: K

middle: L

last: Rudolph


title: Synergistic Tumor Suppressor Activity of E-cadherin and p53 in a Conditional Mouse Model for Diffuse-Type Gastric Cancer

status: Public on Dec 04 2011

city: Bunkyo-ku

first: Kaoru

last: Mogushi

address: 2-1-1 Hongo

department: Intractable Disease Research Center

institute: Juntendo University

summary: BACKGROUND & AIMS: Gastric cancer is the second most frequent cause of death from cancer in the world, diffuse-type gastric cancer (DGC) exhibiting a poor prognosis. Germline mutations of CDH1, encoding E-cadherin, have been reported in hereditary DGCs, and genetic and/or epigenetic alterations of CDH1 are frequently detected in sporadic DGCs. Genetic alterations of TP53 are also frequently found in DGCs. To examine the synergistic effect of loss of E-cadherin and p53 on gastric carcinogenesis, we established a mouse line in which E-cadherin and p53 are specifically inactivated in the stomach parietal cell lineage. METHODS: We crossed Atp4b-Cre mice with Cdh1loxP/loxP and Trp53loxP/loxP mice, and examined the gastric phenotype of Atp4b-Cre+;Cdh1loxP/loxP;Trp53loxP/loxP mice. RESULTS: Non-polarization of E-cadherin-negative parietal cells and proton pump-negative atypical foci were observed in the transgenic mice. Intramucosal cancers and invasive cancers composed of poorly differentiated carcinoma cells and signet ring cells, which were histologically very similar to those in humans, were found from 6 and 9 months, respectively. Fatal DGCs developed at 100% penetrance within a year, frequently metastasized to lymph nodes, and had tumorigenic activity in immunodeficient mice. Gene expression profiling analyses also revealed that DGCs in the E-cadherin/p53-deficient mice resembled human DGCs. CONCLUSIONS: Our mouse line is the first genetically modified mouse model of DGC and very useful for clarifying the mechanism underlying gastric carcinogenesis, and provides a new approach to the treatment and prevention of DGC because of morphological and biochemical similarities with human DGC.

overall_design: Two-condition experiment, Gastric cancer vs. normal gastric mucosal tissues. Biological replicates: pooled control sample from five normal gastric mucosal tissues, three replicates from diffuse-type gastric cancer.

first: Shu

last: Shimada

first: Ayako

last: Mimata

first: Yoshimitsu

last: Akiyama

first: Hiroshi

last: Fukamachi

first: Jos

last: Jonkers

last: Tanaka

first: Yoshinobu

last: Eishi

first: Yasuhito

last: Yuasa


title: Hepatic gene expression profiles after long-term high-fat diet feeding in wild type and Nrf2 knock-out mice.

status: Public on Nov 30 2011

city: Lausanne

first: Dionysios

last: Chartoumpekis

address: Ave de la Sallaz 8

department: Service of Endocrinology Diabetes and Metabolism

country: Switzerland

institute: Lausanne University Hospital CHUV

summary: To assess the role of the transcription factor NFE2 related factor 2 like 2 ( Nrf2) in the development of high-fat diet (HFD)-induced obesity and non-alcoholic HFD-induced fatty liver disease, 8 wild type (WT) and 8 Nrf2 knock-out (Nrf2-KO) C57BL6J male mice (obtained from Riken BRC, Tsukuba, Japan and originally developed by Prof. M. Yamamoto) were fed an HFD (60 kcal % fat) for 180 days. Whole genome microarray expression profiling was performed in pooled liver samples of WT and Nrf2-KO mice to identify genes that are differentially expressed between WT and Nrf2-KO mice under the stress conditions of HFD-induced obesity.

overall_design: Liver samples were taken from 8 wild type (WT) and 8 Nrf2 knock-out (Nrf2-KO) male mice on high-fat diet (60 kcal % fat) for 180 days. Total RNA was isolated from pooled liver samples from WT or Nrf2-KO mice to produce 4 samples each using the guanidinium thiocyanate method.

first: Apostolos

last: Zaravinos

first: Ioannis

last: Habeos


title: Differentially expressed genes between oncogene-introduced wild-type and Atf4-/- cells

status: Public on Aug 17 2011

city: Fukuoka

first: Satoru

last: Koyanagi

department: Pharmaceutics

summary: During oncogenic transformation, cells acquire genetic mutations that override the normal mechanisms regulating cellular proliferation. Excessive expression of activating transcription factor 4 (ATF4) is often observed in mammalian malignant tumors. However, little is known about the role of ATF4 in the malignant transformation of normal cells. Here, we show that ATF4 promotes oncogene-induced malignant transformation of murine fibroblasts by suppressing the expression of cellular senescence-associated genes. Ectopic expression of oncogenes, H-rasV12 and simian virus 40 large T-antigen, elicited malignant transformation of embryonic fibroblasts from wild-type mice, but not from Atf4-null (Atf4-/-) mice. The oncogenic stresses induced the expression of both Atf4 and cyclin-dependent kinase inhibitor 2a (Cdkn2a), in wild-type cells. Elevated levels of ATF4 successively suppressed the expression of cdkn2a encoding the cellular senescence-associated proteins, p16INK4a and p19ARF, thereby promoting oncogenic transformation. Conversely, the loss of ATF4 caused cellular senescence resulting from the consistent expression of p16INK4a and p19ARF. These findings reveal a novel function of ATF4: that of promoting oncogenic transformation by suppressing cellular senescence.

overall_design: Total 2 samples were derived from [1] H-Ras and SV40T expressing vector-transfected wild-type mouse embryonic fibroblasts (MEFs) and [2] H-Ras and SV40T expressing vector-transfected Atf4-/- MEFs

first: Michiko

last: Horiguchi

first: Akinori

last: Okamoto

first: Satoshi

last: Suzuki

first: Naoya

last: Matsunaga

first: Shigehiro

last: Ohdo


title: Analysis of 22G siRNA triggered siRNA amplification in Caenorhabditis elegans

status: Public on Dec 10 2011

first: Taiowa

last: Montgomery

address: 185 Cambridge Street, CPZN-7250

department: Molecular Biology

institute: Massachusetts General Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: To determine if an endogenous 22G siRNA sensor transgene is subject to siRNA amplification, small RNAs were deep sequenced from the sensor and from a control transgene that is identical to the sensor but lacks an siRNA target site.

overall_design: Small RNAs were isolated from synchronized young adult C. elegans and subjected to deep sequencing.


title: Analysis of differential genetic expression by moderate-carbohydrate restriction diet with calorie restriction mimetic multiple phytochemicals (MCDmp) using a transgenic liver cancer model developed by a simple hydrodynamic transfection method.

status: Public on May 05 2012

city: Seoul

first: Jong-Doo

last: Lee

address: 250 seonsan-ro seodaemum-gu

institute: Yonsei University

summary: We performed survival analysis of control and MCDmp groups, and explored underlying tumor suppression mechanisms after dietary intervention, focused on alterations in the energy-dependent signaling pathways, and global gene expression differences on cDNA microarray study.

overall_design: Five- week- old male C57BL6 mice were randomly divided into two groups and fed control diet (control group, LabDiet, Brentwood, MO, USA) or MCDmp formula (Treat group) in a specific pathogen free zone. All procedures were approved by the institutional animal use and care committee. Following a preliminary feeding of each diet formula for two week, HrasG12V / shp53 / GFP4 gene containing transposon vector were injected into mouse tail vein by hydrodynamic injection method. After 4 weeks of diet supplementation, all mice were sacrificed. Mouse liver tissue was excised for microarray analysis.

first: Jong

middle: D

first: Min-Ah

last: Choi

first: Weon

middle: S

last: Ro


title: Mouse peritoneal macrophages at 3.5 or 48 hours, 0,0.5 or 5 μg/ml Leukocyte cell-derived chemotaxin 2 (LECT2),gene expression array, two independent biological replicates

status: Public on Dec 13 2011

city: Beijing

first: wang

last: liang

address: 7A North Yongchang Road BDA

country: China

institute: BioChainBJ

summary: LECT2 is a liver derived cytokine and involved in many pathologic conditions, especially in immune regulation. To better understand cellular and molecular mechanisms of LECT2 in immune response, mouse peritoneal macrophages were isolated from mouse peritonaeum. After treatment with 0, 0.5 or 5 μg/ml of LECT2 for 3.5 or 48 hours, gene expression profile in mouse peritoneal macrophages was measured using gene expression array. Results showed that LECT2 treatment led to the enhancement of cytokines secretion and phagocytosis in peritoneal macrophages.

overall_design: Gene expression in mouse peritoneal macrophages  isolated from mouse peritonaeum were measured after exposure to 0,0.5 or 5 μg/ml LECT2 for 3.5 or 48 hours using  gene expression array. Two independent experiments were performed using different mice for each experiment for gene expression array analysis.

first: Jiong

last: Chen

first: Xinjiang

last: Lu

first: Yuhong

last: Shi

first: Ruicheng

last: Zhang

first: Jineng

last: Lv

first: Zuoan

last: Huang


title: Essential role of gastric gland mucin in preventing gastric cancer in mice

status: Public on Sep 30 2011

city: Matsumoto

first: Jun

last: Nakayama

address: Asahi 3-1-1

department: Graduate School of Medicine

institute: Shinshu University

summary: To elucidate the molecular mechanism by which A4gnt-null mice develop gastric adenocarcinoma, gastric mucosa was isolated from the stomachs of wild-type and A4gnt-null mice, and microarray analysis was performed.

overall_design: Total RNA was isolated from the gastric mucosa stripped from the muscular layer of the glandular stomach of A4gnt-null and wild-type mice at 5, 10, and 50 weeks of age (one mouse per each group was analyzed).

first: Fumitoshi

last: Karasawa

first: Akira

last: Shiota

first: Yukinobu

last: Goso

first: Motohiro

last: Kobayashi

first: Yoshiko

last: Sato

first: Junya

last: Masumoto

first: Maiko

last: Fujiwara

first: Shuichi

last: Yokosawa

first: Takashi

last: Muraki

first: Shinichi

last: Miyagawa

first: Masatsugu

last: Ueda

first: Michiko

middle: N

last: Fukuda

first: Minoru

first: Kazuhiko

last: Ishihara


title: Gene expression profile induced by Imatinib

status: Public on Feb 08 2012

city: Tokyo

first: toyotaka

last: kawamata

department: Hematology-Oncology/Molecular therapy

institute: The Institute of Medical Science,The University of Tokyo

summary: Activation-induced cytidine deaminase (AID) is essential for class switch recombination (CSR) and somatic hypermutation (SHM). Its deregulated expression acts as a genomic mutator that can contribute to the development of various malignancies. During treatment with imatinib mesylate (IM), patients with chronic myeloid leukemia (CML) often develop hypogammaglobulinemia, the mechanism of which has not yet been clarified. Here, we provide evidence that CSR upon B cell activation is apparently inhibited by IM through downregulation of AID. Furthermore, expression of E2A, a key transcription factor for AID induction, was markedly suppressed by IM. These results elucidate not only the underlying mechanism of IM-induced hypogammaglobulinemia but also its potential efficacy as an AID suppressor.

overall_design:
We investigated that class switch recombination(CSR) upon B cell activation is apparently inhibited by imatinib mesylate(IM) through downregulation of activation-induced cytidine deaminase(AID). Furthermore, expression of E2A was markedly suppressed by IM. To elucidate the more detailed pathway, we performed the microarray analysis.
Microarray analysis was performed on splenocytes cultured for 72 h in the presence or absence of 10 µM Imatinib.
The mouse splenocytes were cultured for 72 h with or without 10 µM Imatinib (IM)  in conditioning medium containing IL-4 and LPS. RNA from 1X10^6 splenocytes used for microarray analysis was isolated using the RNeasy Mini Kit (50) (Qiagen, Hilden, Germany).　Gene expression microarray analysis was performed using one-color microarray-based gene-expression analysis (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer’s instructions. After scanning, expression values for the genes were determined using GeneSpringGX software.

first: Toyotaka

last: Kawamata

first: Lu

last: Jun

first: Tadayuki

first: Masafumi

last: Tanaka

first: Hitoshi

last: Nagaoka

first: Yasutoshi

last: Agata

first: Takae

last: Toyoshima

first: Kazuaki

last: Yokoyama

first: Naoki

last: Oyaizu

first: Naoya

last: Nakamura

first: Kiyoshi

last: Ando

first: Arinobu

last: Tojo

first: Ai

last: Kotani


title: High-throughput SuperSAGE for digital gene expression analysis of multiple samples using Next Generation Sequencing

status: Public on Oct 01 2010

city: Ueda

first: Hideo

last: Matsumura

state: Nagano

address: Tokita 3-15-1

department: Gene Research Center

summary: We established a protocol of the SuperSAGE technology combined with next-generation sequencing, coined “High-Throughput (HT-) SuperSAGE”. SuperSAGE is a method of digital gene expression profiling that allows isolation of 26-bp tag fragments from expressed transcripts. In the present protocol, index (barcode) sequences are employed to discriminate tags from different samples. Such barcodes permit to enable researchers to analyze digital tags from many transcriptomes of many samples in a single sequencing run by simply pooling the libraries. Here, we demonstrated that HT-SuperSAGE provided highly sensitive, reproducible and accurate digital gene expression data. By increasing throughput for analysis in HT-SuperSAGE, various applications were expected and several examples of its applications were introduced in the present study, including analyses of laser-microdissected cells, biological replicates or tag extraction using different anchoring enzymes.

sample_organism:
Arabidopsis thaliana
Oryza sativa
Danio rerio

overall_design: 27 different tissue samples from three different life organisms were analyzed. About 2 samples, three different anchoring enzymes were employed.

first: Kentaro

last: Yoshida

first: Shujun

last: Luo

first: Eiji

last: Kimura

first: Takahiro

last: Fujibe

first: Zayed

last: Albertyn

first: Roberto

last: Barrero

first: Detlev

middle: H

last: Krüger

first: Günter

last: Kahl

first: Gary

middle: P

last: Schroth

first: Ryohei

last: Terauchi


title: 26G endo-siRNAs regulate spermatogenic and zygotic gene expression

status: Public on May 25 2010

city: Ann Arbor

first: Arun Prasad

last: Manoharan

state: MI

address: 210 washtenaw ave

department: Bioinformatics

institute: University of Michigan

summary:
Analysis of small RNAs with 5'p, 3'OH

Raw data files are available on our FTP site:
ftp://ftp.ncbi.nlm.nih.gov/pub/geosup/Series/GSE20341

overall_design: Small RNAs (18-32nt) expressed in purified male sperm, hermaphrodite oocytes, embryos, N2, glp-4(bn2), and eri-1(mg366)  were cloned and sequenced by 454 and Illumina high-throughput sequencing.

first: J

middle: K

last: Kim


title: Genomics of Estradiol-3-Sulfate Action in the Ovine Fetal Hypothalamus

status: Public on Aug 03 2011

city: Gainesville

first: Maria

middle: Belen

last: Rabaglino

state: FL

address: 326 University Village Apt 6

institute: University of Florida

summary: In the fetal sheep during late gestation sulfoconjugated estrogens in plasma reach a concentration 40-100 times greater than unconjugated estrogens. The objective of the present study was to determine the genomics of estradiol-3-sulfate (E2S) action in the fetal brain. The hypothesis was that E2S stimulates genes involved in the neuroendocrine pathways in the hypothalamus that direct or facilitate fetal development at the end of gestation. Four sets of chronically-catheterized ovine twin fetuses were studied (gestational age: 120-127 days gestation) with one infused with E2S intracerebroventricularly (1 mg/day) and the other remained untreated (control). After euthanasia, mRNA samples were extracted from the 8 hypothalami, corresponding to the four treatment and four control fetuses. Microarray analysis was performed following the Agilent protocol for 1-color 8x15 microarrays, designed for Ovis aries.

overall_design: A total of 4 sets of chronically-catheterized ovine twin fetuses were studied with one infused with estradiol-3-sulfate intracerebroventricularly (1 mg/day) for 7-12 days, using an osmotic mini-pump implanted in the fetus, and the other served as an untreated control.  The gestational age at the time of surgery was 120-127 days of gestation.  Twin fetuses were randomly assigned to the two groups at the time of surgery. After 7-12 days of infusion, twin fetuses of known gestational age (130 to 134 days) were euthanized and mRNA samples were extracted from the 8 hypothalami, corresponding to the four treatment and four control fetuses.

middle: B

first: Elaine

middle: M

last: Richards

first: Nancy

last: Denslow

first: Maureen

last: Keller-Wood

first: Charles

last: Wood


title: Phenotypic and Molecular Characterization of the Claudin-low Intrinsic Subtype of Breast Cancer

status: Public on Jun 15 2010

city: Chapel Hill

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: In breast cancer, gene expression analyses have defined five tumor subtypes, each of which has unique biologic and prognostic features. Here, we characterize the recently identified claudin-low tumor subtype as showing low to absent expression of luminal differentiation markers, high enrichment for epithelial-to-mesenchymal transition markers, immune response genes, and cancer stem cell–like features. Clinically, most claudin-low tumors are poorprognosis estrogen receptor–negative, progesterone receptor–negative, and human epidermal growth factor receptor 2–negative (triple-negative) invasive ductal carcinomas with a high frequency of metaplastic and medullary differentiation. They also have a response rate to standard preoperative chemotherapy that is intermediate between that of basal-like and luminal tumors. Moreover, we show that a group of highly used breast cancer cell lines, and several genetically engineered mouse models, express the claudin-low phenotype. Finally, we confirm that a prognostically relevant differentiation hierarchy exists across all breast cancers in which the claudin-low subtype most closely resembles the mammary epithelial stem cell. These results should help to improve our understanding of the biologic heterogeneity of breast cancer and provide tools for the further evaluation of the unique biology of claudin-low tumors and cell lines.

overall_design: We created a large genomic data set by combining three of our previously published data sets (Herschkowitz et al., Hennessy et al., Parker et al.) and included 39 new tumor samples [n = 337; UNC337). In addition, we expression profiled mammospheres (MMS) obtained from 14 reduction mammoplasties. Finally, we FAC sorted and expression profiled subpopulations from the following cell lines: MCF-7, SUM149PT and SUM159PT.

first: Aleix

last: Prat


title: Genomic analysis identifies unique signatures predictive of brain, lung, and liver relapse

status: Public on Jun 20 2011

summary: The ability to predict metastatic potential is of clinical and biological importance. Numerous metastasis/relapse predictors exist for breast cancer patients; however, what is less well established is whether predicting metastasis to specific organs sites is feasible. In this study we sought to determine: 1) the degree to which gene signatures vary across tumors and their metastases, 2) if genomic intrinsic subtypes associate with particular organs of relapse, and 3) if other genomic signatures can predict spread to specific organs.  Using a gene expression microarray data set of >1000 breast tumors and metastases, we observed that >90% of 298 gene signatures were similarly expressed between matched pairs of breast tumors and metastases; those most altered were reflective of cell types including fibroblasts and immune cells. Significant associations were identified between tumor subtypes and organ of first relapse. Among these, HER2-enriched tumors were significantly associated with liver, and Basal-like and Claudin-low tumors with brain and lung. Correspondingly, previously published brain and lung metastasis signatures, along with embryonic stem cell and tumor initiating cell signatures, were also associated with Basal-like and Claudin-low subtypes. These signatures strongly correlated with low Differentiation Scores (DS) and, to a lesser extent, high proliferation.  Interestingly, within Basal-like and Claudin-low tumors, low DS further predicted for brain and lung metastases.  In total, intrinsic subtype and DS provide clinically useful information that identifies the distant organ sites that should be most closely monitored for signs of disease recurrence.

overall_design: 414 samples profiled on Agilent microarrays.

first: Chuck

middle: J

last: Harrell


title: Endo-siRNAs in C. elegans spermatogenesis and their requirement for the RdRP RRF-3

status: Public on Jan 13 2010

city: Piscataway

first: Sam

middle: Guoping

last: Gu

state: NJ

address: Nelson Labs A125, 604 Allison Road

department: Molecular Biology and Biochemistry

institute: Rutgers University

summary: Short interfering RNAs (siRNAs) are a class of regulatory effectors that enforce gene silencing though formation of RNA duplexes. While progress has been made in identifying the capabilities of siRNAs in silencing of foreign RNA and transposable elements, siRNA functions in endogenous gene regulation have remained mysterious. In certain organisms, siRNA biosynthesis involves novel enzymes that act as RNA-directed RNA polymerases (RdRPs). Here we analyze the function of a C. elegans RdRP, RRF-3, during spermatogenesis. We found that loss of RRF-3 function resulted in pleiotropic defects in sperm development, and that sperm defects led to embryonic lethality. Notably, sperm nuclei in mutants of either rrf-3 or another component of the siRNA pathway, eri-1, were frequently surrounded by ectopic microtubule structures, with spindle abnormalities in a subset of the resulting embryos. Through high-throughput small RNA sequencing, we identified a population of cellular mRNAs from spermatogenic cells that appear to serve as templates for antisense siRNA synthesis. This set of genes includes the majority of genes known to have enriched expression during spermatogenesis, as well as many genes not previously known to be expressed during spermatogenesis. For a subset of these genes, we found that RRF-3 was required for effective siRNA accumulation. These and other data suggest a working model in which a major role for the RRF-3/ERI pathway is to generate siRNAs that set patterns of gene expression through feedback repression of a set of critical targets during spermatogenesis

overall_design: Sequencing of small RNAs from a population of C. elegans isolated spermatogenic cells and from two paired sets of rrf-3 mutant and control whole males

first: Andrew

middle: Z

last: Fire


title: Distinct phases of siRNA synthesis in an endogenous RNAi pathway in C. elegans soma

status: Public on Feb 01 2010

city: Stanford

first: Ayelet

last: Lamm

address: 300 Pasteur Drive, Lane Bldg Room L302

department: Pathology

institute: Stanford University School of Medicine

summary: Endogenous RNA-directed RNA polymerases (RdRPs) are cellular components capable of synthesizing new complementary RNAs from existing RNA templates. We present evidence for successive engagement of two different RdRPs in an endogenous siRNA-based mechanism targeting specific mRNAs in C. elegans soma. In the initiation stage of this process, a group of mRNA species are chosen as targets for downregulation, leading to accumulation of rare 26-nt 5'-phosphorylated antisense RNAs that depend on the RdRP homolog RRF-3, the argonaute ERGO-1, DICER, and a series of associated (ERI) factors. This primary process leads to production of a much more abundant class of 22-nt antisense RNAs, dependent on a secondary RdRP (RRF-1) and associating with at least one distinct Argonaute (NRDE-3).  The requirement for two RdRP/Argonaute combinations and initiation by a rare class of uniquely-structured siRNAs in this pathway illustrate the caution and flexibility used as biological systems exploit the physiological copying of RNA.

overall_design: 24 small RNA and 2 polyA RNA samples

middle: T

first: Jonathan

middle: I

last: Gent


title: An integromic analysis reveals that metaplastic carcinomas are distinct from basal-like tumors.

status: Public on Apr 01 2009

summary: Metaplastic breast cancers (MBC) are aggressive, chemoresistant tumors characterized by lineage plasticity. To advance understanding of their pathogenesis and relatedness to other breast cancer subtypes, 28 MBCs were compared with common breast cancers using comparative genomic hybridization, transcriptional profiling, and reverse-phase protein arrays and by sequencing for common breast cancer mutations. MBCs showed unique DNA copy number aberrations compared with common breast cancers. PIK3CA mutations were detected in 9 of 19 MBCs (47.4%) versus 80 of 232 hormone receptor-positive cancers (34.5%; P = 0.32), 17 of 75 HER-2-positive samples (22.7%; P = 0.04), 20 of 240 basal-like cancers (8.3%; P < 0.0001), and 0 of 14 claudin-low tumors (P = 0.004). Of 7 phosphatidylinositol 3-kinase/AKT pathway phosphorylation sites, 6 were more highly phosphorylated in MBCs than in other breast tumor subtypes. The majority of MBCs displayed mRNA profiles different from those of the most common, including basal-like cancers. By transcriptional profiling, MBCs and the recently identified claudin-low breast cancer subset constitute related receptor-negative subgroups characterized by low expression of GATA3-regulated genes and of genes responsible for cell-cell adhesion with enrichment for markers linked to stem cell function and epithelial-to-mesenchymal transition (EMT). In contrast to other breast cancers, claudin-low tumors and most MBCs showed a significant similarity to a "tumorigenic" signature defined using CD44(+)/CD24(-) breast tumor-initiating stem cell-like cells. MBCs and claudin-low tumors are thus enriched in EMT and stem cell-like features, and may arise from an earlier, more chemoresistant breast epithelial precursor than basal-like or luminal cancers. PIK3CA mutations, EMT, and stem cell-like characteristics likely contribute to the poor outcomes of MBC and suggest novel therapeutic targets.

overall_design: Comparison of reference samples against treatment

first: Bryan

last: Hennessy

first: Gordon

last: Mills


title: Breast Carcinomas arising at a Young Age:  A Unique Biology or a Surrogate for Aggressive Intrinsic Subtypes.

status: Public on Sep 01 2010

summary:
Breast cancer is no longer viewed as a homogenous disease, but rather a compilation of several distinct subtypes as defined by microarray or other large scale genomic analyses.  Based on prior reports, we hypothesized that younger women’s breast tumors would be enriched for more aggressive subtypes (i.e. Basal-like) and higher grade, and that age-specific gene expression differences may be highly dependent on subtype classification and/or grade.  Using two independent datasets, our current analysis shows that breast tumors arising in women aged = 45 years are enriched for the Basal-like subtype (and higher grade) while those aged = 65 years are enriched for Luminal tumors.  Moreover, when evaluating gene expression differences between age-defined groups, sizable gene lists were identified which diminished to few, if any, age-specific genes when statistically correcting for significant clinical factors (i.e. subtype, grade, etc).

Keywords: reference x sample

overall_design: 344 breast tumor samples hybridized with Stratagene common reference and profiled on Agilent microarrays.

first: Carey

last: Anders


title: DNA accessibility profile of three C. elegans tissues during development

status: Public on Apr 16 2011

summary: We show there is minimal genome-wide chromatin rearrangements (as measured by DNA accessibility) during tissue differentiation in C. elegans

overall_design:
transgenic expression of E. coli DAM (DNA Adenine Methyltransferase) from tissue-specific promoters followed by mapping of methylated sites using a procedure that captures 20bp sequences flanking methylated sites for Illumina sequencing
PD3994 = transgenic line expressing DAM from myo-3 promoter
PD3995 = transgenic line expressing DAM from rol-6 promoter
PD3997 = transgenic line expressing DAM from vit-2 promoter
N2dam = wildtype (N2) line; its genomic DNA was in vitro DAM-methylated
parsed = Solexa reads in which linker sequences were successfully parsed out by the authors
WS170DAMtags_ALL.txt = the set of all in_silico-generated DAM tags from C. elegans genome version WS170

first: Ky

last: Sha


title: Encyclopedia of C. elegans 3' UTRs and their regulatory elements

status: Public on Sep 02 2009

city: New York

first: Kristin

middle: C

last: Gunsalus

state: NY

department: Biology

institute: NYU Center for Genomics and Systems Biology

summary:
The 3' untranslated region (3'UTR) constitutes a major site of post-transcriptional regulation of gene expression. Sequence elements in the 3'UTR interact with trans-acting regulators such as microRNAs that affect translation and stability. The overall aim is to use a 3'RACE cloning-sequencing stragety to identify the 3'UTRs of C. elegans transcripts and explore their heterogeneity in different developmental stages and tissues.

Keywords: Transcriptome analysis

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

Raw data files are available on our FTP site:
ftp://ftp.ncbi.nlm.nih.gov/pub/geosup/Series/GSE17781

overall_design:
pilot study [GSM443959..GSM443964]: N2 wildtype worms staged at embryo, L1, L2, L3, L4, and adult
full experiment [GSM446651..GSM446661]: N2 wildtype worms staged at embryo, L1, L2, L3, L4, dauer, and adult.
Illumina Genome Analyzer sequencing of isolated clones [GSM469439]
454 sequencing of RACE clones [GSM469976]

first: Kris

first: Arun

last: Manoharan

first: Marco

last: Mangone

first: John

last: Kim

first: Fabio

last: Piano


title: Estrogen-regulated genes predict survival in estrogen receptor and/or progesterone receptor-positive breast cancers

status: Public on Dec 01 2005

first: Charles

summary:
The prognosis of a patient with Estrogen Receptor (ER) and/or Progesterone Receptor (PR)-positive breast cancer is highly variable. Therefore, we developed a gene-expression based outcome predictor for ER+ and/or PR+ (i.e. Luminal) breast cancer patients using biological properties of the tumors. First, we identified estrogen-regulated genes using the ER+ MCF-7 breast cancer cell line treated with estrogen. The estrogen-induced gene set was then used to hierarchically cluster a training set of 65 ER+ and/or PR+ tumors into 2 group, which showed survival differences (p=0.0004). Next, supervised analyses based upon these two groups was performed and identified 822 genes that optimally defined these two groups, with the poor prognosis Group IIE tumors showing a proliferation signature and high expression of anti-apoptosis genes and the good outcome Group IE showing the high expression of estrogen and GATA3-induced genes. Centroids were created for each group and applied to ER+ and/or PR+ tumors from three published datasets. For all datasets, Kaplan-Meier survival analyses showed a statistically significant difference in Relapse-Free Survival (and Overall) between Group IE and IIE tumors. Multivariate Cox analysis of the largest test dataset also showed that this predictor was adding independent information. This study provides new biological information concerning differences within Luminal/ER+ breast cancers and a means of predicting long term outcomes in ER+ and/or PR+ breast cancer patients.
Keywords: other

overall_design: cell lines Vs. Tumors

first: Daniel

last: Oh


title: Breast Tumor's study

status: Public on Nov 23 2005

last: Perou

summary:
Microarray analysis has been shown to improve risk stratification of breast cancer. Breast tumors analyzed by hierarchical clustering of expression patterns of "intrinsic" genes have been reported to subdivide into at least four molecular subtypes that are associated with distinct patient outcomes. Using a supervised method, a 70-gene expression profile has been identified that predicts the later appearance or absence of clinical metastasis in young breast cancer patients. Here, we show that distant metastases display both the same molecular breast cancer subtype as well as the 70-gene prognosis signature as their primary tumors. Our results suggest that the capacity to metastasize is an inherent feature of most breast cancers. Furthermore, our data imply that poor prognosis breast carcinomas classified either by the intrinsic gene set or the 70 prognosis genes represent distinct disease entities that seem sustained throughout the metastatic process.
Keywords: other

overall_design: Tumor Vs. Cell line


title: EGFR signaling varies with breast tumor subtype

status: Public on Aug 20 2007

summary:
Our research data suggest that almost all basal-like tumors have an EGFR-activation profile, however, few may respond to the direct inhibition of EGFR due to ligand independent activation of the EGFR-RAS-MEK pathway via CRYAB or KRAS function. Thus, for those tumors that show a ligand independent EGFR-activation profile, alternative strategies that target downstream components like MEK may prove to be viable alternatives.
Keywords: reference x sample

overall_design: Will be updated soon

first: Katherine

middle: A

last: Hoadley


title: A New Breast Tumor Intrinsic Gene List Identifies Novel Characteristics that are Conserved Across Microarray Platforms

status: Public on Dec 08 2005

summary:
Breast cancer is a difficult disease to manage because it is comprised of a spectrum of tumor subtypes with different biological characteristics. Previous gene expression studies using breast tumor “intrinsic” gene lists identified five distinct subtypes of breast tumors: Luminal A, Luminal B, Normal Breast-like, HER2+/ER- and Basal-like. Using a training data set of 102 unique breast tumors, we derive a new “intrinsic” gene list based upon 26 paired samples. This Intrinsic/UNC gene set recapitulates the old classifications and extends the analysis to include a large proliferation signature, which was lacking before. Using Distance Weighted Discrimination, we next created a true “test set” of 311 tumors by combining together three different publicly available breast tumor microarray data sets (1-3), which was then analyzed using the newly derived Intrinsic/UNC gene set. The test set analysis identified the same five intrinsic subtypes seen before and a new one (Luminal I), and we show that the intrinsic subtype classifications are independent predictors of relapse-free survival when adjusting for age, node status, tumor size, grade and ER status. We also developed a “Single Sample Predictor” that is able to assign an intrinsic subtype to one sample at a time, which was also shown to be predictive of outcomes on another independent test set of tamoxifen-treated ER+ patients. These analyses demonstrate that 1) common patterns of expression can be identified across different microarray platforms, 2) the breast tumor “intrinsic” subtypes are present in all breast tumor data sets studied, and 3) this classification is adding value to the existing repertoire of clinical markers for breast cancer patients.
Keywords: parallel sample

first: Zhiyuan

last: Hu


title: Identification of conserved gene expression features across human and murine mammary tumors

status: Public on May 01 2007

summary:
Mice have been used as models for human breast cancers for many years, however, it is still unclear which murine models faithfully represent human tumor phenotypes.  To address this question, we used DNA microarrays to characterize 10 different murine mammary models and compared these data to the expression patterns from primary human breast tumors. Hierarchical clustering analysis of the murine samples showed that the WAP-Myc, MMTV-Neu, MMTV-PyMT, WAP-Int3, and C3(1)-Tag tumors were highly correlated within each model. Other models, including the WAP-T_121 , MMTV-Wnt1, and DMBA-induced tumor model, did not show this consistency and gave rise to tumors with potentially different cell types of origin.  A combined clustering analysis of the murine tumors with 102 human breast tumors showed many shared expression features.  These features included a proliferation signature, an Interferon-regulated pattern, and patterns reflective of the presence of lymphocytes and fibroblasts. Murine tumors could be categorized according to their presumed cellular origins; the C3(1)-Tag, BRCA1+/-; p53+/-;IR, and DMBA-treated models displayed expression characteristics of human basal-like breast tumors; the MMTV-Neu, MMTV-PyMT, and WAP-Myc models shared features with human luminal breast tumors including the high expression of GATA3 and XBP1. In some cases, single mouse models did not reproduce the entire expression pattern seen in a specific human subtype; rather portions of a subtype’s expression profile were captured/represented by different murine models.  The presence of shared patterns of expression between mice and humans provides a common framework for the direct comparison and integration of animal models with human breast
Keywords: reference x sample

overall_design: 122 microarrays consisting of 108 unique mammary tumors and 10 normal mammary gland samples and 232 Human breast tumor and normal tissue arrays

first: Jason

last: Herschkowitz


title: Transcriptional Activation of Mitochondria Respiratory Chain by UV irradiation

status: Public on Nov 17 2006

city: Hsinchu

first: ChengWei

last: Chang

address: 101, Section 2 Kuang Fu Road

department: bmes

country: Taiwan

institute: nthu

summary:
A fuller study of UV-induced biological effects lies beyond the scope of this paper. I will focus on the genetic interaction of cells irradiated by UV. Accordingly, in respect to genomic, the regulation of the gene expressions in cells represents how they response to the stress and repair themselves. In the past, Northern Blot has been used to detect the expression level of a few genes in one experiment. Thus, this assay is always limited to a small scope of a huge unknown network of gene expression. However, to investigate gene expression networks made of thousands of genes, a powerful tool must be implemented. As anticipated, the interactions between regulated genes in UV irradiation time-course experiment can be analyzed by cDNA microarray analysis with experimental loop design. This study provides a platform to investigate the gene networks regulated by UV irradiation.
Keywords: UV, cDNA microarray, mitochondria respiratory chain, ROS, carcinogenesis

overall_design:
We used a loop design in this study, cDNA microarray experiment consisted of eight RNA samples, including UV-treated samples and their corresponding controls of 4 time points after UV irradiation.

***WARNING***  All samples have identical data.

first: Kun-Yu

first: Tsai-Jiuan

last: Weng

first: ChihYing

last: Hsu


title: A Snapshot of Copy Number Variation in the pig genome

status: Public on Mar 19 2009

city: Tjele

first: Jakob

last: Hedegaard

address: PO-box 50

department: Department of Genetics and Biotechnology

country: Denmark

institute: Aarhus University, Faculty of Agricultural Sciences

type: Genome variation profiling by genome tiling array

summary:
Recents studies in mammalian genomes have uncovered the extent of copy number variation (CNV) that contributes to phenotypic diversity, including health and disease status. Here we report the first glimpse of CNVs in the pig genome covering part of the chromosomes 4, 7, 14 and 17 already sequenced and assembled. We used a custom tiling oligonucleotide array with a median probe spacing of 409 bp to screen 12 unrelated Duroc boar founders of a vast-family material. After a strict CNV calling pipeline it was identified 40 copy number variable regions covering all the four chromosomes, with some overlapping segmental duplications and pig unigenes. This CNV snapshot analysis lays the groundwork for a better understanding of porcine phenotypes and genotypes for the identification of important economic traits.
Keywords: comparative genome hybridization, CNV, Sus Scrofa, Nimblegen tiling array

overall_design:
A custom 385k tiling-path array CGH was designed (Nimblegen Systems) to cover the preliminary Sus Scrofa assembly for chromosomes 4, 7, 14 and 17, from the August 2007 release (http://www.sanger.ac.uk/Projects/S_scrofa/), which was the newest version at the time of the experiment.

From a pig family-material comprising 14 boar founders, 700 sows and about 12.000 offspring, 12 Duroc boar founders (A, B, C, D, E, G, H, J, K, L, M and N) were selected to function as test animals. An unrelated boar of the Hampshire breed was selected as the common reference.
Each of the 12 boars were hybridized twice (technical replicates, 24 arrays) against the common reference.

first: João

last: Fadista

first: Marianne

last: Nygaard

first: Lars-Erik

last: Holm

first: Bo

last: Thomsen

first: Christian

last: Bendixen