title: Expression data of mouse eSZ and GP cells with or without EWS-FLI1

city: Tokyo

first: Takuro

last: Nakamura

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

department: The Cancer Institute

institute: Japanese Foundation for Cancer Research

summary: Ewing’s sarcoma is highly malignant bone tumor that involves childhood and adolescent, and its nature has not been well understood. To clarify its cellular origin and the mechanisms of tumorigenesis, we used ex vivo approach to create a murine model for Ewing’s sarcoma. The osteochondrogenic progenitors derived from the embryonic superficial zone (eSZ, designated as FZ in the data set) of murine long bones at late gestation were purified by microdissection, introduced with EWS-FLI1 or EWS-ERG retroviruses and transplanted into nude mice. Ewing’s sarcoma-like small round cell sarcoma developed at 100% penetrance, whereas tumor induction was less effective when growth place (GP)-derived cells were used. The different response of gene expression to EWS-FLI1 between eSZ and GP cells suggests importance of the specific cellular context for EWS-FLI1 to induce Ewing’s sarcoma. The Wnt/β-catenin pathway was involved in close relationship to the cellular context, with Dkk2 and Wipf1 as important downstream modulators. Furthermore, gene expression profiling revealed similarity between our models and human Ewing’s sarcoma. These results indicate that Ewing’s sarcoma originates from the embryonic osteochondrogenic progenitor.

overall_design: We purified eSZ and GP cells by microdissection from dpc 18.5 murine embryo. The purified eSZ cells were mildly digested by collagenase and their osteochondrogenic potency was confirmed by in vitro differentiation assay. Retrovirus-mediated gene transfer of EWS-FLI1 or EWS-ERG was then carried out and transduction efficiency was exhibited by FACS analyses. The relationship between cellular context and EWS-FLI1 is important, given the strict limitation for the origin of mouse Ewing’s sarcoma. Gene expression profiles were therefore compared between eSZ and GP cells in the presence or absence of EWS-FLI1.

first: M

last: Tanaka

first: Y

last: Yamazaki

last: Kanno

first: K

last: Igarashi

last: Aisaki

first: J

first: T


title: Expression data of mouse Ewing's sarcoma

status: Public on Jun 30 2014

country: Japan

summary: Ewing’s sarcoma is highly malignant bone tumor that involves childhood and adolescent, and its nature has not been well understood. To clarify its cellular origin and the mechanisms of tumorigenesis, we used ex vivo approach to create a murine model for Ewing’s sarcoma. The osteochondrogenic progenitors derived from the facial zone (FZ) of murine long bones at late gestation were purified by microdissection, introduced with EWS-FLI1 or EWS-ERG retroviruses and transplanted into nude mice. Ewing’s sarcoma-like small round cell sarcoma developed at 100% penetrance, whereas tumor induction was less effective when growth place (GP)-derived cells were used. The different response of gene expression to EWS-FLI1 between FZ and GP cells suggests importance of the specific cellular context for EWS-FLI1 to induce Ewing’s sarcoma. The Wnt/β-catenin pathway was involved in close relationship to the cellular context, with Dkk2 and Wipf1 as important downstream modulators. Furthermore, gene expression profiling revealed similarity between our models and human Ewing’s sarcoma. These results indicate that Ewing’s sarcoma originates from the embryonic osteochondrogenic progenitor.

overall_design:
Ewing's sarcoma was induced by introduction of EWS-FLI1 into murine FZ cell followed by transplantation into nude mice. Ten sarcoma samples were analyzed.
No controls are part of this experiment
For comparing with human Ewing's sarcoma, we used expression databases E-MEXP-533 (Henderson SR et al, Genome Biol 6:R76, 2005) and E-MEXP-1142 (Schaefer KL et al, Eur J Cancer 44:699, 2008).  In addition, the data sets for other sarcomas that include GSE6481 (Nakayama R et al, Mod Pathol 20:749, 2007), GSE7529 (Albino D et al, Cancer 113:1412, 2008) and GSE21122 (Barretina J et al, Nat Genet 42:715, 2010) were used for clustering analysis.

last: Yamzaka


title: Impaired revascularization in a mouse model of diabetes associated with dysregulation of angiogenic-regulatory network.

city: Boston

first: Stephan

last: Schiekofer

state: MA

address: 700 Albany Street, W611

department: Molecular Cardiology

country: USA

institute: Boston University School of Medicine

summary:
Diabetes is a risk factor for the development of cardiovascular diseases that are associated with impaired angiogenesis or increased endothelial cell apoptosis. Here is it shown that angiogenic repair of ischemic hind limbs was impaired in Lepr db/db mice, a leptin receptor deficient model of diabetes, compared to wild-type C57BL/6 (WT) mice as evaluated by laser Doppler flow and capillary density analyses. To identify molecular targets associated with this disease process, hind limb cDNA expression profiles were created from adductor muscle of Lepr db/db and WT mice before and after hind limb ischemia using Affymetrix GeneChip® Mouse Expression Set microarrays. The expression patterns of numerous angiogenesis related proteins were altered in Lepr db/db versus WT mice following ischemic injury. These transcripts included neuropilin-1, VEGF-A, placental growth factor, elastin and matrix metalloproteinases that are implicated in blood vessel growth and maintenance of vessel wall integrity. These data illustrate that impaired ischemia-induced neovascularization in type 2 diabetes is associated with the dysregulation of a complex angiogenesis-regulatory network.
Keywords: Diabetes, ischemia, angiogenesis, microarrays

overall_design: Gene expression data for adductor muscle in the ischemic limb from wild type mice and Lepr db/db mice of 4 time points (before hind limb ischemia, 1 day, 7 days and 14 days after hind limb ischemia surgery). Three independent experimental replicates of each condition for each time point.

first: Gennaro

last: Galasso

first: Kaori

last: Sato

first: Benjamin

middle: J

last: Kraus

first: Kenneth

last: Walsh


title: Cytoplasmic YAP and TAZ are intrinsic components of the b-catenin destruction complex

status: Public on Jun 26 2014

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

summary: To investigate the role of YAP/TAZ as b-catenin inhibitors, we compared the expression profiles of Rex1GFPd2 ES cells transfected with siControl#1, siControl#2, siYAP/TAZ#1, siYAP/TAZ#2 and cultured in 2i medium or PD-only medium

overall_design: We collected RNA from  Rex1GFPd2 embryonic stem (ES) cells transfected with siControl#1, siControl#2, siYAP/TAZ#1, siYAP/TAZ#2. Cells were maintained in 2i medium (2i=PD0325901+CHIR99021) or switched to PD (PD0325901)-only medium after 24 hours from siRNA transfection. Cells were harvested 72 hours post-siRNA transfection. Samples were then processed for total RNA extraction and hybridization on Affymetrix microarrays.

first: Luca

last: Azzolin

first: Michelangelo

last: Cordenonsi

first: Stefano

last: Piccolo


title: Expression data from Wild type and Wip1 knockout Hematopoietic stem cell

status: Public on Jun 25 2014

city: hangzhou

first: Hu

last: Wang

address: wenyixi road 1378

country: China

institute: hangzhou normal university

summary:
Hematopoietic stem cell (HSC) aging underlies many age-related hematopoietic disorders. Accumulation of DNA damage is a hallmark of HSC aging. Wild-type p53-induced phosphatase 1 (Wip1) is a homeostatic regulator of DNA damage response.
We used microarrays to detail the global programme of gene expression in Wip1 KO HSC

overall_design: Wild-type p53-induced phosphatase 1 (Wip1) knockout HSC and Wild type HSC were selected  for RNA extraction and hybridization on Affymetrix microarrays.

first: Zhenyu

last: Ju

first: Weiwei

last: Yi


title: Transcriptome and Molecular Pathways Analysis of CD4 T-Cells from Young NOD Mice

status: Public on Jun 20 2014

city: Memphis

first: Dorothy

middle: N.

last: Kakoola

state: TN

address: 1030 Jefferson Avenue

department: Medicine

institute: University of Tennessee Health Science Center

summary: Type 1 diabetes is a multigenic disease caused by T-cell mediated destruction of the insulin producing β-cells. Although conventional (targeted) approaches of identifying causative genes have advanced our knowledge of this disease, many questions remain unanswered. Using a whole molecular systems study, we unraveled the genes/molecular pathways that are altered in CD4 T-cells from young NOD mice prior to insulitis (lymphocytic infiltration into the pancreas). Many of the CD4 T-cell altered genes lie within known diabetes susceptibility regions (Idd), including several genes in the diabetes resistance region Idd13 and two genes (Khdrbs1 and Ptp4a2) in the CD4 T-cell diabetogenic activity region Idd9/11. Alterations involved apoptosis/cell proliferation and metabolic pathways (predominant at 2 weeks), inflammation and cell signaling/activation (predominant at 3 weeks), and innate and adaptive immune responses (predominant at 4 weeks). We identified several factors that may regulate these abnormalities: IRF-1, HNF4A, TP53, BCL2L1 (lies within Idd13), IFNG, IL4, IL15, and prostaglandin E2, which were common to all 3 ages; AR and IL6 to 2 and 4 weeks; and Interferon (IFN-I) and IRF-7 to 3 and 4 weeks. Others were unique to the various ages (e. g. MYC, JUN, and APP to 2 weeks; TNF, TGFB1, NFKB, ERK, and p38MAPK to 3 weeks; and IL12 and STAT4 to 4 weeks). Our data suggest that diabetes resistance genes in Idd13 and Idd9/11, and BCL2L1, IL6-AR and IFNG-IRF-1-IFN-I/IRF-7-IL12 pathways play an important role in CD4 T-cells in the early pathogenesis of autoimmune diabetes. Thus, the alternative approach of investigation at the molecular systems level has captured new information, which combined with validation studies, offers the opportunity to test hypotheses on the role played by the genes/molecular pathways identified in this study, to understand better the mechanisms of autoimmune diabetes in CD4 T-cells, and to develop new therapeutic strategies for the disease.

overall_design: CD4 T-cells were purified from spleen leukocytes collected from 2-, 3- and 4-week old NOD mice and two age-matched control strains, NOR, and C57BL/6, (n=5 for each strain and each age group; except NOD2wk). NOR is an insulitis- and diabetes-free control strain that shares shares ~88% of its genome with NOD mice, including the diabetogenic H2g7 MHC haplotype and several important non-MHC T1D susceptibility loci. C57BL/6 is also a diabetes-resitant strain, but it is more genetically distantly related to NOD.

middle: N

first: Anita

last: Curcio-Brint

first: Nataliya

middle: I

last: Lenchik

first: Ivan

middle: C

last: Gerling


title: Microarray profiling of STEP knockout mouse striatum

status: Public on Jun 23 2014

city: Groton

first: Thomas

middle: A

last: Lanz

state: CT

address: Eastern Point Rd

department: Multi-Omics & Biomarkers

institute: Pfizer

summary: STEP (striatal-enriched tyrosine phosphatase) is a brain-specific phosphatase named for its robust expression in striatum.   Brains from homozygous and heterozygous STEP knockout mice and wild-type littermates were harvested, and striatum microdissected.  RNA was extracted and hybridized to Affymetrix 230_2 microarray chips.

overall_design: n=4-5 per group.  Wild-type littermates were compared with STEP +/- and -/-


title: Gene expression profiling of human IL-10+ B-cells

city: Singapore

first: Michael

last: Poidinger

address: #04-06, 8A Biomedical Grove

department: Bioinformatics

country: Singapore

institute: Singapore Immunology Network

summary:
Following combined stimulation through Toll-like receptor (TLR)-9 and the B-cell receptor (BCR),  human B cells were sorted based on IL-10 expression.
Microarray analysis showed that just ~0.7% of genes were differentially expressed between IL-10- and IL-10+ B-cells.  However, connectivity map analysis revelaed that the IL-10+ cells were those undergoing differentiation to germincal centre B cells, and we identified a CD11c- B-cell subset that was enriched in cells capable of producing IL-10

overall_design: B-cells were isolated using the Dynabeads Untouched Human B-cells kit, stimulated during 48 hours and then sorted based on IL-10 using secretion assay kit and cell sorter.

first: Wenyu

last: Lin

first: Kaibo

last: Duan

first: Josephine

last: Lum

first: Francesca

last: Zolezzi

first: Sébastien

last: Calbo


title: Gene expression profiling of the mandibular arch from Alk5 mutant mouse models

status: Public on Jun 18 2014

city: Oklahoma City

first: Richard

last: Pelikan

state: Oklahoma

address: 825 NE 13th St

department: Genes & Human Disease Research Program

institute: Oklahoma Medical Research Foundation

summary: The overall goal of this project is to investigate the role of TGF-beta signaling in tissue-tissue interactions between myogenic precursors of craniofacial muscles and cranial neural crest cells (CNCCs). Here, we conducted gene expression profiling of the mandibular arch from mice at embryonic day E11.5 with a CNCC-specific conditional inactivation of the TGF-beta  receptor type 1 gene Alk5. These mice provide a model of microglossia as well as disrupted extraocular and masticatory muscle development, which are congenital birth defects commonly observed in several syndromic conditions.

overall_design: To investigate the adverse effects of dysfunctional TGF-beta signaling on tissue-tissue interactions between CNCCs and myogenic precursors of craniofacial muscles, we analyzed mandibular arch tissue of mice with a CNCC-specific conditional inactivation of Alk5 (Wnt1-Cre; Alk5 fl/fl). We performed microarray analyses of the mandibular arch  of  Alk5 fl/fl control mice and Wnt1-Cre; Alk5 fl/fl mutant mice, collected at embryonic day E11.5 (n=4 per group).

last: Zhao

first: Arum

last: Han

first: Yang

last: Chai


title: Gene expression profiling of the tongue bud from Alk5 mutant mouse models

summary: The overall goal of this project is to investigate the role of TGF-beta signaling in tissue-tissue interactions between myogenic precursors of craniofacial muscles and cranial neural crest cells (CNCCs). Here, we conducted gene expression profiling of the tongue bud from mice at embryonic day E13.5 with a CNCC-specific conditional inactivation of the TGF-beta  receptor type 1 gene Alk5. These mice provide a model of microglossia as well as disrupted extraocular and masticatory muscle development, which are congenital birth defects commonly observed in several syndromic conditions.

overall_design: To investigate the adverse effects of dysfunctional TGF-beta signaling on tissue-tissue interactions between CNCCs and myogenic precursors of craniofacial muscles, we analyzed tongue bud tissue of mice with a CNCC-specific conditional inactivation of Alk5 (Wnt1-Cre; Alk5 fl/fl). We performed microarray analyses of the tongue bud  of  Alk5 fl/fl control mice and Wnt1-Cre; Alk5 fl/fl mutant mice, collected at embryonic day E13.5 (n=4 per group).

first: Hu


title: Linking Notch signaling to ischemic stroke

status: Public on Jun 11 2014

first: Joseph

last: Arboleda-Velasquez

address: 20 Staniford st

department: Opthalmology

institute: Schepens Eye Research Institute

summary: Using a hitherto uncharacterized knockout mouse model of Notch 3, a Notch signaling receptor paralogue highly expressed in vascular SMCs, we uncover a striking susceptibility to ischemic stroke upon challenge. Cellular and molecular analyses of vascular SMCs derived from these animals associate Notch 3 activity to the expression of specific gene targets, whereas genetic rescue experiments unambiguously link Notch 3 function in vessels to the ischemic phenotype.

overall_design: Microarray Studies. Biotinylated cRNA samples from freshly sorted brain SMCs (four Notch 3 +/− mice and five Notch 3 −/− mice) were fragmented before hybridization (15 μg each) onto mouse 430 2.0 Affymetrix chips. The chips were washed, stained by using strepavidin-phycoerytrin, and scanned the next day as described in ref. 24. For data normalization, all probe sets were scaled to a target intensity of 150. Microarray data analysis was performed by using Rosetta Resolver. All cells were from 10- to 12-week-old male mice. Gene Ontology Analyses. PANTHER software was used to define over- and underrepresented functions in the list of signature genes found by microarray analysis (25). P values were calculated by using binomial statistics.

first: Spyros

last: Artavanis-Tsakonas


title: Expression data from mus musculus subjected to traumatic brain injury (TBI) for treatment with cyclophosphamide

status: Public on Jun 14 2014

city: Uppsala

first: Ted

last: Ebendal

address: Husargatan 3

department: Neuroscience

country: Sweden

institute: Uppsala University

summary:
We inflicted TBI to wildetype (wt) mice in order to establish whether the anti-inflammatory agent cyclophosphamide can be used therapeutically.
Cyclophosphamide was found to regulate distinct inflammatory cells such as activated microglia separate from invading phagocytes and dendritic cells. Cyclophosphamide postinjury selectively reduces antigen-presenting dendritic cells.  Findings show feasibility of drug development to interfere with brain inflammation.

overall_design: TBI was carried out in injured wt B6 mice for postinjury treatment with cyclophospamide i.p. using saline as a control substance for comparison with injured but untreated mice. Total RNA was prepared from injured cerebral neocortex after three days. RNA samples were also from uninjured wt mice as reference for hybridization on Affymetrix microarrays.

first: Charlotte

last: Israelsson


title: Bloom syndrome protein modulates protein-coding gene and miRNA expression as a function of G4 DNA content

status: Public on Jun 12 2014

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

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

summary: Bloom syndrome is a rare autosomal recessive genetic instability and cancer predisposition syndrome caused by loss of function mutations in the BLM RECQ helicase gene. To ask if some of the distinctive pathological features of Bloom syndrome might reflect altered gene expression, we analyzed global mRNA and miRNA expression in fibroblasts from 16 patients and 15 matched normal controls, and in control primary diploid fibroblasts depleted of the BLM protein. We document significant differential expression of both protein-coding genes and miRNAs with well-characterized cancer associations in BLM-deficient cells. Differences in expression correlated significantly with G4 motifs, which are associated with potential to form G-quadruplex structures. These results indicate that BLM helicase may modulate gene expression by regulating the in vivo stability of G-quadruplex structures, and identify sets of genes and miRNAs whose expression, when altered, may drive the pathogenesis of Bloom syndrome and associated cancers.

platform_organism:
Homo sapiens
Mus musculus

overall_design: Global profiling of mRNA and miRNA expression was analyzed in primary fibroblasts from 16 patients and 15 matched normal controls, and in 9 primary diploid fibroblasts depleted of BLM protein by BLM-specific (3), control (3) and scrambled (3) shRNA.

middle: P

last: Beyer

first: Giang

middle: H

last: Nguyen

first: Ana

last: Robles

first: Weiliang

last: Tang

first: Lucas

last: Gray

first: Judy

last: Welsh

first: Aaron

last: Schetter

first: Kensuke

last: Kumamoto

first: Xin

middle: W

last: Wang

first: Ian

middle: D

last: Hickson

first: Nancy

last: Maizels

first: Raymond

last: Monnat

first: Curtis

last: Harris


title: Expression data from chemokine-deficient mus musculus subjected to traumatic brain injury (TBI)

summary:
We inflicted TBI to chemokine-deficient mouse lines in order to establish involvement of various signalling pathways that may be addressed therapeutically.
Interacting chemokine pathways in brain regulate distinct inflammatory cells. Activated microglia are separate from invading phagocytes and dendritic cells. Findings show potential targets to interfere with specific inflammatory responses after brain injury.

overall_design: TBI was carried out in Ccl3-/- and Ccr2-/- mice, total RNA prepared from injured cerebral neocortex after three days. RNA samples were from uninjured Ccl3-/- and Ccr2-/- mice as reference for hybridization on Affymetrix microarrays.


title: Expression data from intestinal organoids altered for Tgfbeta signaling

status: Public on Jun 09 2014

city: Portland

first: Jared

middle: Michael

last: Fischer

state: OR

address: 3181 SW Sam Jackson Park Road

department: Molecular and Medical Genetics

institute: Oregon Health and Science University

summary: We treated intestinal organoids continuously for 5 days with or without TgfbR1/2 inhibitor (LY2109761) or Tgfb1 ligand

overall_design: Organoids were continuously treated for 5 days, then RNA was extracted and hybridized to Affymetrix Mouse Genome 430 2.0

middle: M


title: Environmental factors transmitted by aryl hydrocarbon receptor influence severity of psoriatic skin inflammation [Affymetrix]

city: London

first: Gitta

last: Stockinger

address: The Ridgeway

department: Division of Molecular Immunology

country: United Kingdom

institute: National Institute for Medical Research

summary: Environmental stimuli are known to contribute to psoriasis pathogenesis and that of other autoimmune diseases, but the mechanism is unknown. Here we show that the aryl hydrocarbon receptor (AhR), a transcription factor that senses environmental stimuli, modulates pathology in psoriasis. AhR-activating ligands reduced inflammation in the lesional skin of psoriasis patients, whereas AhR antagonists upregulated inflammation. Similarly, AhR signaling via the endogenous FICZ ligand reduced the inflammatory response in the imiquimod-induced model of psoriasis and AhR deficient mice exhibited a substantial exacerbation of the disease, compared to AhR sufficient controls. Non-haematopoietic cells, in particular keratinocytes, were responsible for this hyper-inflammatory response, which involved increased reactivity to IL-1beta and upregulation of AP-1 family members of transcription factors. Thus, our data suggest a critical role for AhR in the regulation of inflammatory responses and open the possibility for novel therapeutic strategies in chronic inflammatory disorders.

overall_design: Total RNA obtained from skin explants taken from AhR heterozygous or knock-out mice treated pericutaneously with imiquimod for 0 and 2d.

first: Brigitta

first: Joao

last: Duarte

first: Paola

last: Di Meglio


title: Expression profiling of KRas ablation surviving cells and matched Kras expressing spheres in pancreatic tumors

city: Houston

first: Sahil

last: Seth

state: TX

address: 1801 East Road

institute: MD Anderson

summary: In this dataset, we include the expression data obtained from KRas expressing tumors, matched Kras expressing tumor spheres, surviving cells and surviving cells after KRas re-expression for 24hs

overall_design: Data reported here are obtained from 5 independent tumors (from 1 to 5). For each tumor, expression data for the original Tumor (in vivo bulk tumor lesion), the KRas Expressing Spheres derived from the bulk tumor, the matched surviving cells after 8 days of KRas ablation (SCs) and Surviving Cells after 24 hours of KRas re-expression are reported.

first: Andrea

last: Viale

first: Giulio

last: Draetta


title: Expression data from mouse spleen CD11c dendritic cells, bone marrow Gr1DC11b cells, and RAW264.7 cells

status: Public on Jun 10 2014

city: Milwaukee

first: Hartmut

last: Weiler

state: WI

address: 8727 Watertown Plank Road

department: Blood Research Institute

institute: BloodCenter of Wisconsin

summary:
We investigated in mouse models how enhanced coagulation activation due to a common disease polymorphism in coagulation factor V (fV Leiden Arg506Gln) modifies the host response to infection and inflammation
We used microarrays to characterize the in vivo and in vitro inflammatory responses of mouse spleen dendritic cells, macrophage-like RAW264.7 cells, and bone marrow myeloid cells

overall_design: Samples 1-6 were generated by pooling equal amounts of RNA prepared from FACS-enriched spleen dendritic cells isolated from 6 individual mice before (control sample 1) or 16 hours after challenge with lipopolysaccharide. Samples 7-10 were generated by pooling equal amounts of RNA prepared from triplicate cultures of RAW264.7 cells. Samples 10-14 (2 replicas per condition) were prepared from RNA isolated from FACS-enriched bone marrow myeloid cells (pooled from 4 adoptively transferred animals each) 7 days after infection with S.aureus.

first: H


title: Expression data from chemically-induced skin papillomas (benign tumours)

status: Public on Jun 08 2014

city: Bruxelles

first: Cédric

last: BLANPAIN

address: 808, route de Lennik

country: Belgium

institute: ULB

summary:
Cancer stem cells (CSCs) have been reported in various cancers including skin squamous cell carcinoma (SCC). The molecular mechanisms regulating tumour initiation and stemness are still poorly characterized. Here, we found that Sox2, a transcription factor expressed in various types of embryonic and adult stem cells (SCs), was the most upregulated transcription factor in CSCs of squamous skin tumours. Sox2 is absent in normal epidermis and begins to be expressed in the vast majority of mouse and human pre-neoplastic skin tumours and continues to be expressed in a heterogeneous manner in invasive mouse and human SCCs. In contrast to other SCCs, in which Sox2 is frequently genetically amplified, the expression of Sox2 in mouse and human skin SCCs is transcriptionally regulated. Conditional deletion of Sox2 in the mouse epidermis dramatically decreases skin tumour formation following chemical induced carcinogenesis. Using Sox2-GFP knockin mice, we showed that Sox2 expressing cells in invasive SCC are greatly enriched in tumour propagating cells (TPCs) that further increase upon serial transplantations.  Lineage ablation of Sox2 expressing cells within primary benign and malignant SCCs leads to tumour regression, consistent with the critical role of Sox2 expressing cells in tumour maintenance. Conditional Sox2 deletion in pre-existing skin papilloma and SCC leads to their regression and decreases their ability to be propagated upon transplantation into immunodeficient mice, supporting the essential role of Sox2 in regulating CSC functions. Transcriptional profiling of Sox2-GFP expressing CSC and upon Sox2 deletion uncovered a gene network regulated by Sox2 in primary tumour cells in vivo. Chromatin immunoprecipitation identified several direct Sox2 target genes controlling tumour stemness, survival, proliferation, adhesion, invasion, and paraneoplastic syndrome. Altogether, our study demonstrates that Sox2, by marking and regulating the functions of skin tumour initiating cells and CSCs, establishes a continuum between tumour initiation and progression in primary skin tumours.
We used microarrays to profile tumour epithelial cells upon Sox2 deletion to uncover a gene network regulated by Sox2 in primary tumour cells in vivo.

overall_design: Microarray analysis was performed on FACS isolated Epcam+ a6+ TECs from 3 different biological experiments following TAM administration to K14CREER:SOX2fl/fl and control mice. Total RNA was analysed using Mouse whole genome 430 2.0 array from Affymetrix.

first: Soufiane

last: Boumahdi

last: Blanpain


title: Expression data from chemically-induced skin squamous cell carcinomas

summary:
Cancer stem cells (CSCs) have been reported in various cancers including skin squamous cell carcinoma (SCC). The molecular mechanisms regulating tumour initiation and stemness are still poorly characterized. Here, we found that Sox2, a transcription factor expressed in various types of embryonic and adult stem cells (SCs), was the most upregulated transcription factor in CSCs of squamous skin tumours. Sox2 is absent in normal epidermis and begins to be expressed in the vast majority of mouse and human pre-neoplastic skin tumours and continues to be expressed in a heterogeneous manner in invasive mouse and human SCCs. In contrast to other SCCs, in which Sox2 is frequently genetically amplified, the expression of Sox2 in mouse and human skin SCCs is transcriptionally regulated. Conditional deletion of Sox2 in the mouse epidermis dramatically decreases skin tumour formation following chemical induced carcinogenesis. Using Sox2-GFP knockin mice, we showed that Sox2 expressing cells in invasive SCC are greatly enriched in tumour propagating cells (TPCs) that further increase upon serial transplantations.  Lineage ablation of Sox2 expressing cells within primary benign and malignant SCCs leads to tumour regression, consistent with the critical role of Sox2 expressing cells in tumour maintenance. Conditional Sox2 deletion in pre-existing skin papilloma and SCC leads to their regression and decreases their ability to be propagated upon transplantation into immunodeficient mice, supporting the essential role of Sox2 in regulating CSC functions. Transcriptional profiling of Sox2-GFP expressing CSC and upon Sox2 deletion uncovered a gene network regulated by Sox2 in primary tumour cells in vivo. Chromatin immunoprecipitation identified several direct Sox2 target genes controlling tumour stemness, survival, proliferation, adhesion, invasion, and paraneoplastic syndrome. Altogether, our study demonstrates that Sox2, by marking and regulating the functions of skin tumour initiating cells and CSCs, establishes a continuum between tumour initiation and progression in primary skin tumours.
We used microarrays to profile Sox2-GFP expressing CSC to uncover a gene network regulated by Sox2 in primary tumour cells in vivo.

overall_design: Two different biological replicates from SOX2-GFP+ and SOX2-GFP- TECs (control) from 2 different SCC from 2 different mice were analysed. Total RNA was analysed using Mouse whole genome 430 2.0 array from Affymetrix.


title: Perinatal-Estrogen-Induced Changes in Gene Expression Related to Brain Sexual Differentiation in Mice

status: Public on Jun 07 2014

city: Nagoya

first: Yoshihisa

last: Uenoyama

address: Furo-cho, Chikusa-ku

institute: Nagoya University

summary:
Sexual dimorphism of the behaviors or physiological functions in mammals is mainly due to the sex difference of the brain.  The goal of this study is to identify genes mediating sexaul dimorphism of the brain.
The large-scale analysis with microarray in the present study is an attempt to obtain the candidate gene(s) mediating the perinatal estrogen effect causing the brain sexual differentiation.

overall_design: Thirty female mice were injected with estradiol benzoate (EB) or vehicle on the day of birth, and the hypothalamus was collected at either 1, 3, 6, 12, or 24 h after the EB injection.

first: Mototsugu

last: Sakakibara

first: Shiori

last: Minabe

first: Chikaya

last: Deura

first: Sho

last: Nakamura

first: Youki

last: Watanabe

first: Genki

last: Suzuki

first: Kei-ichiro

last: Maeda

first: Hiroko

last: Tsukamura


title: Expression data from liver of Retnla transgenic (Tg) and non-transgenic (non-Tg) mice.

status: Public on Jun 06 2014

city: Seoul

first: GooTaeg

last: Oh

address: 52, Ewhayeodae-gil

department: Department of Life Sciences

country: South Korea

institute: Ewha Womans University

summary:
We found that Retnla-Tg mice had significantly lower serum cholesterol levels than non-Tg mice on a high-fat diet (HFD). To explore the molecular mechanisms underlying the cholesterol-lowering effects of Retnla under hyperlipidemic conditions, we subjected age- and sex-matched Retnla-Tg and non-Tg mice to a HFD for 4 weeks.
Using a microarray approach, we analyzed the hepatic gene expression profiles related to cholesterol metabolism, including catabolism, biosynthesis, and transport.

overall_design: Total RNA was extracted from livers of Retnla-Tg and non-Tg mice after feeding with a HFD for four weeks, and transcriptional profiling was performed on individual samples using Affymetrix Mouse Genome chips (MG 430 2.0 array).

first: Goo Taeg

first: Mi-Ran

last: Lee


title: Impact of gamma chain cytokines on the differentiation of recently antigen-activated CD8 T cells

first: Michael

last: McNamara

state: Oregon

address: 4805 NE Glisan St

department: EACRI - Cancer Research

institute: Providence Portland Medical Center

summary: Analysis of how different gamma chain family cytokines influence CD8 T cell differentiation.

overall_design: Naïve CD8 T cells were isolated from the spleens OT-I Thy1.1 TCR Tg mice. Whole splenocytes from wild-type C57BL/6 mice were used as stimulator cells. Purified naïve wild-type OT-I (1×106/well) were stimulated with OVA peptide (SIINFEKL) pulsed (5 µg/ml) and irradiated (2,000 rads) syngeneic splenocytes (6×106/well) in 24-well plates. Forty-eight hours later, activated OT-I T cells were harvested and viable cells were enriched over a Ficoll-paque gradient and washed with cRPMI prior to being reseeded in cRPMI (5×105 cells/ml) and treated with the media supplemented with various γc cytokines (IL-2, IL-4, IL-7, IL-15 and IL-21). Experimental samples were treated with 100 ng/ml of their respective gamma chain cytokine and incubated at 37ºC for 24 hours.  RNA was isolated using either the RNeasy Mini kit, or a combination of TRIzol reagent and the Direct-zol RNA miniprep kit, all following manufacturer protocols. Two biological replicates for mRNA analysis were prepped using the RNeasy kit. The third replicate was prepped using the Trizol/Direct-zol approach. The quality and quantity of RNA samples was further analyzed on the Bioanalyzer. Labeled target cDNA was prepared from total RNA samples using the Ambion MessageAmp Premier protocol (3’IVT assay). Each sample target was hybridized to a Mouse 430 2.0 GeneChip array. Image processing and expression analysis were performed using Affymetrix GeneChip Command Console (AGCC) v. 3.1.1 and Affymetrix Expression Console v.1.1 software, respectively. Data from all biological replicates and conditions was imported into the Affymetrix Expression Console and normalized (RMA).  RNA processing and microarray hybridization were performed by the Oregon Health & Science University Gene Microarray Shared Resource core facility in Portland, Oregon.

first: Redmond

last: William


title: Gene expression profile in peritoneal macrophage infected with Listeria monocytogenes

status: Public on Jun 29 2014

city: Meguro-ku, Tokyo

first: hideo

last: negishi

address: Komaba 4-6-1

department: Molecular Immunology

institute: University of Tokyo

summary:
Several Toll-like receptors are activated by Listeria monocytogenes infection, resulting in the activation of  MyD88 dependent signaling pathway.  However, the negative role of MyD88 in gene expresson is unclear.
To address this, we performed microarray analysis of mRNAs from WT or MyD88-/- peritoneal macrophages infected with Listeria monocytogenes.

overall_design: Peritoneal macrophages from WT or MyD88-/- mice were infected with Listeria monocytogenes for 6 hours, and then subjected to microarray analysis.

first: Hideo

last: Negishi

first: Tadatsugu

last: Taniguchi


title: Expression data from mouse bone marrow-derived macrophages (BMDMs)

status: Public on Jun 24 2014

city: Sakyo-ku, Kyoto-shi

first: Hiroshi

last: Yamaguchi

state: Kyoto

address: Yoshida

department: Graduate school of medicine

institute: Kyoto University

summary:
To recruit phagocytes, apoptotic cells characteristically release ATP, which functions as a “danger” signal. Here, we found that the culture supernatant of apoptotic cells activated the macrophages to express anti-inflammatory genes such as NR4A and Thbs1. A high level of AMP accumulated in the apoptotic cell supernatant in a Pannexin1-dependent manner. A nucleotidase inhibitor and A2a adenosine receptor antagonist inhibited the apoptotic supernatant-induced gene expression, suggesting AMP was metabolized to adenosine by an ecto-5’-nucleotidase expressed on macrophages, to activate the macrophage A2a adenosine receptor. Intraperitoneal injection of zymosan into AdoR A2a- or Panx1-deficient mice produced high, sustained levels of inflammatory mediators in the peritoneal lavage. These results indicated that AMP from apoptotic cells suppresses inflammation as a “calm down” signal.
If apoptotic cells produce “danger” or “anti-danger” signal(s), we rationalized that such signals would activate gene expression in macrophages. To investigate this possibility, we examined the effect of the culture supernatant from apoptotic cells on macrophage gene expression by using microarrays.

overall_design: For mouse BMDMs, bone marrow cells from female C57BL/6J mice at 8 weeks of age were cultured for more than 7 days with DMEM containing 10% FCS supplemented with mouse M-CSF. We used adherent cells as BMDMs in the study. W3 cells, mouse T cell line expressing Fas, were treated with human Fas ligand at 37°C for 30 min to induce apoptosis. The cells were then washed and re-suspended at a concentration of 1 × 107 cells/ml with RPMI containing 1% FCS, and further incubated for 60 min at 37°C. Following Fas ligand treatment, more than 90% of the W3 cells were Annexin V positive, and only small percentage were positive for both Annexin V and propidium iodide (PI). The culture supernatant was collected from apoptotic W3 cells. Next, BMDMs were incubated with medium (BMDMs-Medium) or apoptotic W3 cell supernatant (BMDMs-Apoptotic cell supernatant) for 1 h. Total RNA was extracted from the cells and hybridized on Affymetrix microarrays.

first: Shigekazu

last: Nagata


title: The Anti-Aging and Tumor Suppressor Protein Klotho Affects Signaling Pathwaysin a Human Oligodendroglioma Cell Line

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

summary: Klotho functions as an aging suppressor, which, in mice, extends lifespan when overexpressed and accelerates development of aging-like phenotypes when disrupted. Klotho is mainly expressed in brain and kidney and is secreted into the serum and CSF. We have previously shown that Klotho is reduced in brains of old monkeys, rats and mice. We further reported the ability of Klotho to enhance oligodendrocyte differentiation and myelination. Here we examined the effects of Klotho on MO3.13, a human oligodendroglioma cell line in order to determine the potential role of Klotho as a tumor suppressor. We show that exogenous Klotho affects the ERK and Akt signaling pathways and decreases the proliferative abilities of MO3.13 cells. Furthermore, microarray analysis of Klotho-treated MO3.13 cells reveals a massive change in gene expression with 80% of the differentially expressed genes being downregulated. Using gene set enrichment analysis we predicted potential transcription factors involved in regulating Klotho-treated MO3.13 cells and found that these cells are highly enriched in the gene sets, that are similarly observed in cancer, cardiovascular disease, stress, aging and hormone-related chemical and genetic perturbations. Since Klotho is downregulated in all brain tumors tested to date, enhancing Klotho has therapeutic potential for treating brain malignancies.

overall_design: 6 Samples

first: Cidi

last: Chen


title: Expression data from mus musculus subjected to traumatic brain injury (TBI)

first: Ted

last: Ebendal

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

overall_design: Refer to individual Series


title: Development of the prethalamus is crucial for thalamocortical projection formationand is regulated by Olig2

status: Public on Jun 04 2014

city: Paris

first: Adrien

last: Clavairoly

address: 47 Boulevard de l'Hôpital

country: France

institute: ICM

summary: Thalamocortical axons pass through the prethalamus in the first step of their neural circuit formation  Although it has been supposed that the prethalamus is an intermediate target for thalamocortical projection formation, much less is known about the molecular mechanisms of this targeting.

overall_design: The samples were grouped into 2 sample types: Olig2-KO and the wild-type. RNA was purified from the E13.5 ventral forebrain from Olig2-KO (Olig2-/-) and the wild-type (Olig2+/+). RNA samples were prepared by pooling RNAs extracted from 3 brains to constitute one replicate and each sample type was prepared in five replicates. cRNA hybridization probes were hybridized to Affymetrix Mouse Whole Genome MOE430 2.0 arrays. The R-CRAN statistical language and Bioconductor software package (Gentleman et al., 2004) were used throughout the expression analyses. Raw image files were processed using Affymetrix GCOS and the Microarray Suite (MAS) 5.0 algorithm. The probe signal levels were quantile-normalized, summarized and then transformed to the log 2 expression using GCRMA (gcrma R-package, Irizarry et al., 2003). Gene filtering was performed using the Wilcoxon signed-rank test to select probe sets that were “consistently expressed” (p <0.04) in at least one group (mas5calls R-package; Bioconductor). All samples showed good quality control according to MAS5.0 guidelines and the AffyQC report (R-package; Bioconductor).

first: Katsuhiko

last: Ono

first: Tadashi

last: Nomura

first: Hitoshi

last: Gotoh

first: Aoi

last: Uno

first: Olivier

last: Armant

first: Hirohide

last: Takebayashi

first: Qi

last: Zhang

first: Kenji

last: Shimamura

first: Shigeyoshi

last: Itohara

first: Carlos

last: Parras

first: Kazuhiro

last: Ikenaka


title: Tpl2 promotes chemokine/chemokine receptor expression and macrophage migration during acute inflammation

status: Public on Jun 03 2014

city: Bethesda

first: Lai

last: Wei

state: MD

address: 10 Center Dr. Room 2B47

institute: NIH/NEI/NCCAM

summary: In autoimmune diseases, accumulation of activated leukocytes correlates with inflammation and disease progression, and therefore, disruption of leukocyte trafficking is an active area of research.  The protein kinase Tpl2 (MAP3K8) regulates leukocyte inflammatory responses and is also being investigated for therapeutic inhibition during autoimmunity.  Herein, we addressed the contribution of Tpl2 to the regulation of macrophage chemokine and chemokine receptor expression and subsequent migration in vivo using a mouse model of Tpl2 ablation.  We found that gene expression of the chemokine ligands CCL2, CCL7, CXCL2, and CXCL3 as well as the chemokine receptors CCR1 and CCR5 were reduced in macrophages from the bone marrow and peritoneal cavities of tpl2-/- mice following stimulation with LPS.  LPS stimulation repressed chemokine receptor expression of CCR1, CCR2 and CCR5.  Notably, LPS-induced repression of CCR1 and CCR5 was significantly enhanced in Tpl2-deficient macrophages and was observed to be dependent upon Erk activation and independent of PI3K and mTOR signaling.  Consistent with alterations in chemokine and chemokine receptor expression, tpl2-/- macrophages were defective in trafficking to the peritoneal cavity following thioglycollate-induced inflammation.  Overall, this study demonstrates a Tpl2-dependent mechanism for macrophage expression of both chemokine receptors and their ligands and provides further insight into how Tpl2 inhibition may disrupt inflammatory networks in vivo.

overall_design: microarray was used to profile the genome-wide expression patterns in Tpl2 wild-type and deficient macrophage.

first: Sean

last: Rowley

first: Lisa

last: Mielke

first: Wendy

middle: T

last: Watford


title: Expression data from mice on a high fat, high carbohydrate diet treated with exenatide

status: Public on Jun 01 2014

city: Silver Spring

first: Rodney

middle: Lamar

last: Rouse

address: 10903 New Hampshire Ave

department: DARS

institute: U. S. FDA, CDER

summary: The present study was constructed to confirm previous findings that mice on a high fat diet (HFD) treated by subcutaneous injection with exenatide (EXE) at 3µg/kg once daily for 6 weeks develop exocrine pancreatic injury (Rouse et al. 2014).  The present study included 12 weeks of EXE exposure at multiple concentrations (3, 10, or 30 μg/kg) with multiple endpoints (histopathology evaluations, immunoassay for cytokines, immunostaining of the pancreas, serum chemistries and measurement of trypsin, amylase, and, lipase, and gene expression profiles). Time- and dose-dependent exocrine pancreatic injury was observed in mice associated with EXE exposure in a HFD environment.  The time- and dose-dependent morphological changes identified in the pancreas involved acinar cell injury and death (autophagy, apoptosis, necrosis, and atrophy), cell adaptations (hypertrophy and hyperplasia), and cell survival (regeneration) accompanied with varying degrees of inflammatory response leading to secondary injury in pancreatic blood vessels, ducts, and adipose tissues.  Gene expression profiles supported the presence of increased signaling for cell survival and altered lipid metabolism.  The potential for EXE to cause acute or early chronic pancreatic injury was identified in a HFD environment.  In human disease, the influence of pancreatitis risk factors or pre-existing chronic pancreatitis on this injury potential requires further investigation.

overall_design: Male C57BL/6 mice 6 to 8 weeks of age were purchased from Harlan Laboratories (Frederick, MD). Mice were housed individually in an environmentally controlled room (18°C–21°C, 40%–70% relative humidity) with a twelve-hour light/dark cycle.  Mice were initially fed Certified Purina Rodent Chow #5002 (Ralston Purina Co., St. Louis, MO) providing 63% of calories through carbohydrates, 24% from protein, and 13% from fat.  Per the experimental design, mice were subsequently placed on a Teklad Custom Research Diet, TD.06415 (Harlan, Frederick, MD), providing 45% of calories through fats (36% saturated, 47% monounsaturated, 17% polyunsaturated), 36% from carbohydrates, and 19% from protein.  Water and food were available ad libitum.  Thorough out the experiment all mice were weighed weekly and dosing adjusted accordingly for each mouse.  A cohort of eighty 6 to 8 week-old male C57BL6 mice were received from Harlan Laboratories.  The cohort represented experimental time point of 12 weeks.  The cohort was further divided into 4 exenatide (EXE) treatment groups (0, 3, 10, or 30 μg/kg) of 20 mice each.  Initially, all mice were placed on HFD for six weeks without additional treatment and were then maintained on HFD for an additional 12 weeks while receiving daily subcutaneous injections of saline or EXE (Creative Peptides, Shirley, NY; 3, 10, or 30μg/kg).  At the 12 week timepoint, twenty-four hours following their final dose, the mice from the treatment cohort were anesthetized with isoflurane and euthanized by exsanguination with collection of blood for serum harvest.  The pancreas from 12 mice in each cohort was preserved in 10% formalin for histology processing.  The pancreas from 5 mice in each cohort was placed in RNAlater (Life Technologies, Grand Island, NY) for subsequent RNA extraction and the pancreas from 3 mice in each cohort was immediately frozen in liquid nitrogen and then stored at -80°C.  Pancreas tissue was resected, preserved in RNALater, and stored at -80 C.  After thawing, 2.5 mg of each sample were processed using  miRNeasy Mini Kits  (Cat # 217004) (Qiagen, Valencia, CA).  Samples were homogenized in 700 uL of Qiazol Lysis Reagent (Qiagen), for 5 minutes at 50 hz in a TissueLyser LT (Qiagen), and processed using the automated purification of  total RNA on a Qiacube (Qiagen), using the “Purification of total RNA, including small RNAs, from animal tissues & cells (aqueous phase), version 2 (April 2010)” standard protocol, as described in the miRNeasy Mini Handbook (1073008 07/2012) & http://www.qiagen.com/QIAcube/Standard/ProtocolView.aspx?StandardProtocolID=847.Mean yield per 2.5 mg of pancreas tissue was approximately 35 ug, determined by NanoDrop spectrophotometer (Thermo Scientific, Wilmington, DE).   Average RIN values were approximately  5.4 +/- 1.4, as assayed by a 2100 Bioanalyzer Instrument (Agilent Technologies, Santa Clara, CA), using an Agilent RNA 6000 Nano Kit (cat # 5067-1511).  This RIN mean was consistent with our previous experiences in RNA extraction from murine pancreatic tissue.  The isolated RNA was labeled and gene expression analysis performed by Expression Analysis, Inc. (Durham, NC). The 3 samples with the highest RIN from each treatment group were used to probe treatment effect on gene expression.  Total RNA samples (100 ng) were converted into cDNA using Ovation WGA FFPE System (NuGEN, Part No. 6200). The second strand cDNA is then purified with Agencourt RNAClean beads and followed by SPIA amplification. Amplified SPIA cDNA product is purified using Agencourt RNAClean beads and quantitated using a NanoDrop ND-8000 spectrophotometer. Target preparation was performed using 4 μg of amplified cDNA and the NuGEN FL-Ovation cDNA Biotin Module V2. Fragmented and biotin-labeled target was hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 microarrays.   Raw gene expression data were first analyzed using ArrayTrack bioinformatics tool with robust multichip average algorithm and quantile normalization.  Differentially expressed genes were defined by p < 0.05 and fold change > 1.3 in Welch t-test comparing treatment and control groups.  Expression data were then imported to Ingenuity Pathway Analysis (IPA) tool for further analyses of pathway, biofunction, and toxicity using general and pancreas-specific knowledge bases.


title: Expression data in Staphylococcus aureus-infected mice with linezolid and vancomycin treatment

status: Public on Jun 05 2014

city: Durham

first: Sun Hee

last: Ahn

state: NC

address: Stead Bldg, RM 1546A

institute: Duke University

summary: The precise mechanism and effects of antibiotics in host gene expression and immunomodulation in MRSA infection is unknown. Using a well characterized Methicillin Resistant Staphylococcus aureus (MRSA) isolate USA300 in a murine model of infection, we determined that linezolid and vancomycin induced differential production of bacterial toxins and host cytokines, differences in host gene expression, and differences in immunomodulators during MRSA bloodstream infection. A total of 35 A/J mice, categorized into seven groups (no infection;  no infection with linezolid; no infection with vancomycin; 2 hour post-infection (hpi) S. aureus; 24 hpi  S. aureus; 24 hpi S. aureus  with linezolid; and 24 hpi S. aureus with vancomycin), were used in this study. Mice were injected with USA300 (6 x 106 CFU/g via i.p. route), then intravenously treated with linezolid (25 mg/kg) or vancomycin (25 mg/kg) at 2 hpi. Control and S. aureus infected mice were euthanized at each time point (2 h or 24h) following injection.  Whole blood RNA was used for microarray; three cytokines and two S. aureus toxins [PantonValentine Leukocidin (PVL) and alpha hemolysin] were quantified in mouse serum by ELISA. S. aureus CFUs were significantly reduced in blood and kidney after linezolid or vancomycin treatment in S. aureus-infected mice. In vivo IL-1β in mouse serum was significantly reduced in both linezolid (p=0.001) and vancomycin (p=0.006) treated mice compared to untreated ones. IL-6 was significantly reduced only in linezolid treated (p<0.001) but not in vancomycin treated mice. However, another proinflammatory cytokine, TNF-α, did not exhibit altered levels in either linezolid or vancomycin treated mice (p=0.3 and p=0.51 respectively). In vivo level of bacterial toxin, Panton-Valentine leukocidin, in mouse serum was significantly reduced only in linezolid treated mice (p=0.02) but not in vancomycin treated mice. There was no significant effect of either treatment in in vivo level of alpha hemolysin production. Unsupervised hierarchical clustering using the gene expression data from 35 microarrays revealed distinct clustering based on infection status and treatment group. Study of the antibiotic-specific difference in gene expression identified the number of genes uniquely expressed in response to S. aureus infection, infection with linezolid treatment, and infection with vancomycin treatment. Pathway associations study for the differentially expressed genes in each comparison group (Control vs. 24 h S. aureus infection, 24 h S. aureus infection vs. 24 h S. aureus linezolid, and 24 h S. aureus infection vs. 24 h S. aureus vancomycin) in mice using Kyoto Encyclopedia of Genes and Genomes (KEGG) identified toll-like receptor signaling pathway to be common to every comparison groups studied. Glycerolipid metabolism pathway was uniquely associated only with linezolid treatment comparison group. The findings of this study provide the evidence that protein synthesis inhibitor like linezolid does a better job in treating MRSA sepsis compared to cell wall acting antibiotics like vancomycin.

overall_design: To identify differences in host gene expression in a murine sepsis model treated with a) linezolid and b) vancomycin, we used whole blood gene expression (RNA) signatures from A/J inbred mice infected with USA 300 MRSA to evaluate differences in host gene expression among mice treated with linezolid and vancomycin.  We used 5 RNA samples from MRSA-infected, linezolid- or vancomycin-treated mice. A total of 7 experimental groups have been employed:  1) Uninfected control group: (negative controls).    2) Uninfected, linezolid-treated group: Uninfected, linezolid-treated mice.   3) Uninfected vancomycin-treated group: Uninfected, vancomycin-treated mice.   4) Infected control group (positive control 2 h) MRSA-infected, untreated mice.   5) Infected control group (positive control 24 h): MRSA-infected, untreated mice.   6) Infected linezolid group: MRSA-infected, linezolid-treated mice.   7) Infected vancomycin group: MRSA-infected, vancomycin-treated mice.

first: Sun-Hee

first: Batu

middle: K

last: Sharma-Kuinkel

first: Yurong

first: Vance

middle: G

last: Fowler


title: Selective mRNA translation during eIF2 phosphorylation induces expression of IBTKalpha

status: Public on Jun 02 2014

city: Indianapolis

first: Ronald

last: Wek

state: Indiana

address: 6238 Brokenhurst Road

department: Biochemistry & Molecular Biology

institute: Indiana University School of Medicine

summary:
Disruption of protein folding in the endoplasmic reticulum triggers the Unfolded Protein Response (UPR), a transcriptional and translational control network designed to restore protein homeostasis. Central to the UPR is PERK phosphorylation of the alpha subunit of eIF2 (eIF2~P), which represses global translation coincident with preferential translation of mRNAs, such as ATF4 and CHOP, that serve to implement the UPR transcriptional regulation. In this study, we used sucrose gradient ultracentrifugation and a genome-wide microarray approach to measure changes in mRNA translation during ER stress. Our analysis suggests that translational efficiencies vary across a broad range during ER stress, with the majority of transcripts being either repressed or resistant to eIF2~P, while a notable cohort of key regulators are subject to preferential translation. From this latter group, we identify IBTKa as being subject to both translation and transcriptional induction during eIF2~P in both cell lines and a mouse model of ER stress. Translational regulation of IBTKalpha mRNA involves the stress-induced relief of two inhibitory uORFs in the 5'-leader of the transcript. Depletion of IBTKalpha by shRNA reduced viability of cultured cells coincident with increased caspase 3/7 cleavage, suggesting that IBTKalpha is a key regulator in determining cell fate during the UPR.
We used a genome-wide microarray approach to determine how individual mRNAs were differentially translated during endoplasmic reticulum stress.

overall_design:
A microarray analysis from our laboratory identified gene transcripts suggested to be under translation control in mouse embryonic fibroblast (MEF) cells following a 6 hour treatment with thapsigargin, a potent inducer of ER stress, or no stress. The mRNAs were separated by sucrose gradient analyses to yield three fractions, those transcripts associated with large polysomes (≥4 ribosomes per mRNA), those associated with monosome, disomes, or trisomes, and those fractionated at the top of the gradient with free ribosomes. RNA was extracted from sucrose gradients corresponding to these fractions and hybridized on Affymetrix microarrays. In parallel, we also measured total levels for each gene transcript in the presence or absence of thapsigargin treatment to address transcription regulation coincident with translational control.

Please note that the treatment plus fractionation based on association with different numbers of ribosomes did yield different populations of mRNAs, which resulted in considerable variation in normalized data across the samples.

first: Thomas

last: Baird

first: Jeanette

last: McClintick


title: Characterizing the profiles of Ebf1 in mouse fat cells.

city: Boston

first: Evan

last: Rosen

address: 3 Blackfan Cir

department: Endocrinology

institute: Beth Israel Deconess Medical Center

summary: gene expression data from mouse adipocyte, with and without Ebf1 knock-down

overall_design: To ascertain the functional targets of Ebf1 in adipocytes, we depleted Ebf1 from mature 3T3-L1 cells by transducing them with lentivirus harboring one of two different Ebf1-specific hairpins or a scrambled control. We then performed expression profiling using Affymetrix arrays with triplicate samples for each hairpin.

first: Michael

middle: J

last: Griffin

first: Yiming

last: Zhou

first: Sona

last: Kang

first: Xiaolan

first: Tarjei

middle: S

last: Mikkelsen


title: Infection of macrophages by Toxoplasma Progeny from a Type II x Type III cross

city: Stanford

first: Anjali

last: Shastri

state: CA

address: D305 Farichild Building; 299 Campus Drive

department: Microbiology & Biology

institute: Stanford University

summary:
Infection of RAW264.7 cells for 24 hours with 32 Toxoplasma Progeny from a Type II x Type III cross
To measure changes in gene expression induced in macropahges upon Toxoplasma infection, we infected RAW 264.7 macrophages in cell culture with one of 32 Toxoplasma parasite progeny from a Type II x Type III cross. RNA was harvested 24 hours post infection.

overall_design: Cells were infected with Toxoplasma parasites, in vitro

first: Melissa

last: Lodoen


title: Effect of enforced BMP4 expression on gene expression profile of 4T1.2 whole primary murine mammary tumours

city: East Melbourne

first: Cameron

middle: N

last: Johnstone

state: Vic

address: 2 St. Andrew's Place

department: Research Division

country: Australia

institute: Peter MacCallum Cancer Centre

summary:
BMP4 is down-regulated in metastatic human and murine mammary tumours. Here we determined the effect of ectopic mouse Bmp4 re-expression on global gene expression patterns in orthotopic primary mammary tumours in syngeneic Balb/c mice.
Breast cancer is a major cause of cancer related death in women, due to the development of metastatic disease in vital organs. Metastasis can be facilitated by tumor induced MDSC, which requires understanding. We have confirmed that BMP4 is a potent suppressor of breast cancer metastasis, but for potential clinical application, it is important to understand how BMP4 acts to suppress metastasis. Here, we report one mechanism by which BMP4 can inhibit metastasis. Mice bearing highly metastatic mammary tumors present with elevated numbers of myeloid derived suppressor cells (MDSC), the extent of which is markedly reduced upon exogenous BMP4 expression. Increased numbers of MDSC can also be induced directly by treatment with granulocyte-colony stimulating factor (G-CSF), leading to enhancement of metastasis. Both tumor-induced and G-CSF-induced MDSC can effectively suppress T cell activation and proliferation. BMP4 acts to reduce the expression and secretion of G-CSF through inhibition of NFkB activity in several human and mouse tumor lines. Since MDSC in breast cancer patients are correlated with poor prognosis, BMP4 treatment offers a potential new therapeutic strategy for progressive breast disease.

overall_design: Three 4T1.2 primary mammary tumours and three 4T1.2-Bmp4 primary mammary tumours were analyzed.

first: Yuan

last: Cao

first: Belinda

last: Parker

first: Bedrich

middle: L

last: Eckhardt

first: Jason

last: Li

first: Robin

last: Anderson


title: Liver expression data from 31 mouse strains treated with vehicle or isoniazid for 3 days

city: Chapel Hill

first: Merrie

last: Mosedale

state: North Carolina

address: 301 Pharmacy Lane, Kerr Hall CB#7569

department: Division of Pharmacotherapy and Experimental Therapeutics

institute: UNC Eshelman School of Pharmacy

summary: Isoniazid induced varying degrees of hepatic steatosis in an inbred strain Mouse Diversity Panel (MDP) study. RNA was isolated from all animals for analysis of gene expression changes in the liver. The objective of this study was to identify gene expression changes that drive isoniazid-induced steatosis.

overall_design: 235 total samples from 31 strains were analyzed: N=4 per treatment and strain, except isoniazid-treated LP/J (N=3), PL/J (N=3), SM/J (N=2), NON/LtJ (N=3), LG/J (N=3), MA/MyJ (N=2), RIIIS/J (N=3), SEA/GnJ (N=2), and A/J (N=2) animals where animals that died before the completion of the study were excluded from data analysis; 13 of 31 strains exhibited findings of isoniazid-induced steatosis and were coded as responders.

first: Karissa

last: Adkins


title: Expression data from WT and R6/2 mice treated with HSP90 inhibitor NVP-HSP990

city: Lausanne

first: Tamara

last: Seredenin

address: AI2135 Station 15 EPFL

country: Switzerland

institute: EPFL

summary:
Huntington’s disease (HD) is a neurodegenerative disorder that is associated with the deposition of proteinaceous aggregates in the brains of HD patients and mouse models. Previous studies have suggested that wide-scale disruption of protein homeostasis occurs in protein folding diseases. Protein homeostasis can be maintained by activation of the heat shock response (HSR) via the transcription factor heat shock factor 1 (HSF1), the pharmacological activation of which can be achieved by Hsp90 inhibition and has been demonstrated to be beneficial in cell and invertebrate models of HD. Whether the HSR is functional in HD and whether its activation has therapeutic potential in mammalian HD models is currently unknown. To address these issues, we used a novel, brain penetrant Hsp90 inhibitor to activate the HSR in brain after systemic administration. Microarrays, quantitative PCR and western blotting showed that the HSR becomes impaired with disease progression in two mouse models of HD and that this originates at the level of transcription.
Huntington’s disease (HD) is a neurodegenerative disorder that is associated with the deposition of proteinaceous aggregates in the brains of HD patients and mouse models. Previous studies have suggested that wide-scale disruption of protein homeostasis occurs in protein folding diseases. Protein homeostasis can be maintained by activation of the heat shock response (HSR) via the transcription factor heat shock factor 1 (HSF1), the pharmacological activation of which can be achieved by Hsp90 inhibition and has been demonstrated to be beneficial in cell and invertebrate models of HD. Whether the HSR is functional in HD and whether its activation has therapeutic potential in mammalian HD models is currently unknown. To address these issues, we used a novel, brain penetrant Hsp90 inhibitor to activate the HSR in brain after systemic administration. Microarrays, quantitative PCR and western blotting showed that the HSR becomes impaired with disease progression in two mouse models of HD and that this originates at the level of transcription.

overall_design: mRNA expression analysis was performed by microarray in 12 week old R6/2 and WT mice treated with vehicle or HSP990 for 4h (12mg/kg).The following number of replicates was analysed for each genotype: 7 for WT+vehicle, 10 for WT+HSP990, 7 for R6/2+vehicle and 8 for R6/2+HSP990. Microarray quality control was performed using the software package provided on RACE (http://race.unil.ch).

first: John

last: Labbadia

first: Helen

last: Cunliffe

first: Andreas

last: Weiss

first: Elena

last: Katsyuba

first: Kirupa

last: Sathasivam

last: Seredenina

first: Ben

last: Woodman

first: Saliha

last: Moussaoui

first: Stefan

last: Frentzel

first: Ruth

last: Luthi-Carter

first: Paolo

last: Paganetti

first: Gillian

last: Bates


title: Expression profiling of isolated populations of prepachytene spermatocytes, pachytene spermatocytes and spermatids of PWD and B6 males

city: Prague

first: Petr

last: Simecek

state: Not Applicable

address: Vídeňská 1083

department: Department of Mouse Molecular Genetics

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR, v. v. i.

summary: Expression profiling of isolated populations of prepachytene spermatocytes (LP), pachytene spermatocytes (RP) and spermatids (ST) from PWD and B6 was performed to study the genome wide variation in gene expression between two mouse subspecies. To evaluate the transcriptional difference between B6 and PWD in during meiosis, we compared their transcriptomes in sorted populations of pre-pachytene primary spermatocytes (Leptonema, Zygotene and Pachytene), pachytene spermatocytes (Mid-late pachytene and diplotene) and spermatids.

overall_design: Populations of pre-pachytene spermatocytes, pachytene spermatocytes and spermatids were isolated from PWD and B6 mice. All populations were isolated in duplicates from two animals. Hence, RNA was prepared from 12 samples (= 2 strains x 3 tissues x 2 replicas) and was then subject to labeling and hybridization on microarray chips.

first: Tanmoy

last: Bhattacharyya

first: Radka

last: Reifova

first: Jiri

last: Forejt


title: Mouse hybrid sterility X2 (Hstx2) controls meiotic asynapsis of heterosubspecific homologs and probes into the dominance theory of Haldane's rule.

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

platform_organism:
Mus musculus
synthetic construct


title: Gene expression profiling in THP1 cells after PAPD5 or GLD2 knockdown

status: Public on May 24 2014

city: Yokohama-shi, Tsurumi-ku

first: Michiel

last: de Hoon

state: Kanagawa-ken

address: Suehiro-cho 1-7-22

department: Center for Life Science Technologies

institute: RIKEN

summary: Next-generation sequencing experiments have shown that microRNAs are expressed in many different isoforms (isomiRs), whose biological relevance is often unclear. We found that mature miR-21, the most widely researched microRNA because of its importance in human disease, is produced in two prevalent isomiR forms that differ by one nucleotide at their 3’ end, and moreover that the 3’ end of miR-21 is post transcriptionally adenylated by the noncanonical poly(A) polymerase PAPD5. PAPD5 knockdown caused an increase in the miR-21 expression level, suggesting that PAPD5-mediated adenylation of miR-21 leads to its degradation. Exoribonuclease knockdown experiments followed by small RNA sequencing suggested that PARN degrades miR-21 in the 3’-to-5’ direction. In accordance with this model, microarray expression profiling demonstrated that PAPD5 knockdown results in a downregulation of miR-21 target mRNAs. We found that disruption of the miR-21 adenylation and degradation pathway is a general feature in tumors across a wide range of tissues, as evidenced by data from The Cancer Genome Atlas, as well as in the non-cancerous proliferative disease psoriasis. We conclude that PAPD5 and PARN mediate degradation of oncomiR miR-21 through a tailing and trimming process, and that this pathway is disrupted in cancer and other proliferative diseases.

overall_design: Gene expression levels were profiled by Illumina microarrays using RNA produced previously (PMID 20719920). Briefly, total RNA was extracted from THP1 cells in four replicates 72 hours after transfection of siRNA against PAPD5 or GLD2, or of calibrator negative control siRNA. Gene expression levels were profiled in two of the PAPD5 knockdown replicates, two of the GLD2 knockdown replicates, and two of the negative control replicates.


title: Expression data of Tfh cells

status: Public on May 30 2014

city: Yokohama

first: Takaharu

last: Okada

address: 1-7-22 Suehiro-cho, Tsurumi

department: IMS

summary: Follicular helper T (Tfh) cells access the B cell follicle to promote antibody responses, and are particularly important for germinal center (GC) reactions. However, the molecular mechanisms of how Tfh cells are physically associated with GCs are incompletely understood. Here we report that the sphingosine-1-phosphate receptor 2 (S1PR2) gene is highly expressed in a subpopulation of Tfh cells that localizes in GCs. S1PR2-deficient Tfh cells exhibited reduced accumulation in GCs due to their impaired retention. T cells deficient in both S1PR2 and CXCR5 were ineffective in supporting GC responses compared to T cells deficient only in CXCR5. These results suggest that S1PR2 and CXCR5 cooperatively regulate localization of Tfh cells in GCs to support GC responses.

overall_design: Venus-high Tfh, Venus-low Tfh, PD1-intermediate Th, PD1-low Th and naïve CD4+ T cells were sorted on FACSAria from immunized S1pr2V/+ mice or control mice for RNA extraction and hybridization on Affimetrix microarrays.

first: Saya

last: Moriyama


title: Towards epigenetic understanding and therapy of insulin resistance by intranuclear insulin [mouse liver gene expression]

status: Public on May 21 2014

city: Hangzhou

first: Yun

last: Xiao

address: Yuhangtang Road

institute: Zhejiang University

summary:
There is evidence indicating the involvement of DNA methylation memory in maintaining gene expression patterns associated with insulin resistance. Although the exact mechanism remains unknown, it has been proved that insulin resistance is correlated to low heat shock protein (HSP) expression.
We reveal that intranuclear insulin can reduce HSP DNA methylation level to up-regulate HSP protein expression and result in long term cure of hyperglycemia.

overall_design: Type 2 diabetes KKAy mouse were selected in our experiments.Three conditions were compared with three replicates each. These are:(1) Untreated KKAy mouse (2) Insulin treated KKAy mouse(Insulin); (3) Biomineralized insulin treated KKAy mouse(BI).

first: Zheng

last: Li

first: Yiyu

last: Cheng

first: Ruikang

last: Tang


title: Changes in mouse kidney glomerular gene expression following dendrin  knockout

status: Public on May 20 2014

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

institute: Uppsala University

summary:
Glomerular podocyte cells are critical for the function of the renal ultrafiltration barrier. The highly specialized cell-cell junction of podocytes, the slit diaphragm, has a central role in the filtration barrier. Dendrin is a poorly characterized cytosolic component of the slit diaphragm in where it interacts with nephrin and Cd2ap. In this study, we have generated a dendrin knockout mouse line and explored the molecular interactions of dendrin. Dendrin-deficient mice were viable, fertile and had normal life span.
To reveal the glomerular gene expression changes in the dendrin knockout mouse, Affymetrix Mouse Genome 430 2.0 Array were used to profiling the dendrin knockout and control glomeruli.

overall_design: Three dendrin knockout and three littermate control mice at age of 13 months were used to profile glomerular transcriptomes. Total glomerular RNA was extracted and hyrbridized on the Mouse Genome 430 2.0 Array according to standard procedures.

first: Zhijie

first: Patricia

last: Rodriguez

first: Liqun

first: Christer

last: Betsholtz

first: Karl

last: Tryggvason

first: Jaakko

last: Patrakka


title: in vivo dexamethasone-induced gene expression in pediatric acute lymphoblastic leukemia patient-derived xenografts

city: Randwick

first: Duohui

last: Jing

state: NSW

address: Lowy Cancer Research Centre, UNSW

department: Leukaemia Biology

institute: Children’s Cancer Institute Australia

summary: Glucocorticoids are critical components of combination chemotherapy regimens in pediatric acute lymphoblastic leukemia (ALL). The pro-apoptotic BIM protein is an important mediator of glucocorticoid-induced apoptosis in normal and malignant lymphocytes, while the anti-apoptotic BCL2 confers resistance. The signaling pathways regulating BIM and BCL2 expression in glucocorticoid-treated lymphoid cells remain unclear. In this study, pediatric ALL patient-derived xenografts (PDXs) inherently sensitive or resistant to glucocorticoids were exposed to dexamethasone in vivo. In order to understand the basis for differential in vivo glucocorticoid sensitivity of PDXs, microarray analysis of gene expression was carried out on 5 each of dexamethasone-sensitive and resistant PDXs . This provided a global understanding of dexamethasone-induced signaling cascades in ALL cells in vivo, and especialy identified the genes that are involved in transducing the apoptotic signal, upstream of BIM/BCL2 dynamic interactions.

overall_design:
ALL xenograft cells were inoculated by tail-vein injection into NOD/SCID mice, and engraftment was monitored weekly. When >70% %huCD45+ engraftment in the peripheral blood was apparent, which occurred 8-10 weeks post-transplantation, mice were treated with either dexamethasone (15 mg/kg) or vehicle control by intra-peritoneal (IP) injection, and culled at 8 hours following the treatment. Cell suspensions of spleens were prepared and mononuclear cells enriched to >97% human by density gradient centrifugation. RNA was extracted using the RNeasy Mini Kit (QIAGEN, Valencia, CA, USA), and RNA samples with integrity number (RIN) > 8.0 were amplified and hybridized onto Illumina HumanWG-6 v3 Expression BeadChips (6 samples/chip). All chips (with associated reagents) were purchased from Illumina, and scanned on the Illumina BeadArray Reader according to the manufacturer’s instructions. Microarray data were analyzed using the online modules in GenePattern.
10 xenografts were derived from patients of 5 dexamethasone-good responder and 5 dexamethasone-poor responder. Each xenograft was innoculated into 5-6 mice, and treated with dexamethasone (15 mg/kg) or vehicle control. In total spleen-harvest xenograft samples from 58 mice were analyzed using microarray.

first: Vivek

last: Bhadri

first: Richard

middle: B

last: Lock


title: B cell-intrinsic STAT6 controls the germinal center response in type 2 immunity

status: Public on May 26 2014

city: Erlangen

first: Adriana

last: Turqueti Neves

state: Bavaria

address: Wasserturmstrasse 3/5

department: Department of Infection Biology

country: Germany

institute: Universitätsklinikum Erlangen

summary: By investigating the germinal center (GC) formation in STAT6ko/WT bone marrow-mixed chimera we found that GC formation in type 2 immune responses is dependent on B cell intrinsic expression of IL-4/IL-13-induced genes. We therefore used microarrays to find Stat6 dependent genes that are important for germinal center formation and/or organization after infection with the nematode Nippostrongylus brasiliensis (N. brasiliensis).

overall_design: Bone marrow of STAT6ko (CD45.2+) and WT (CD45.1+) were mixed and injected in lethaly irradiated WT (CD45.1+) mice. After 8 weeks, 5 Bone marrow-mixed chimera were infected with N. brasiliensis and draining lymph nodes were collected at day 14 after the infection and pooled. RNA was isolated from sort-purified CD45.1+ or CD45.2+ GC B cells (B220+CD38loGL-7hi).

last: Turqueti-Neves

first: Manuel

last: Otte

first: Cornelia

last: Lindner

first: Olivia

last: Prazeres da Costa

first: Thorsten

last: Buch

first: Uta

middle: E

last: Höpken

first: Martin

last: Lipp

first: Oliver

last: Pabst

first: David

last: Voehringer


title: Identification of Myt1 as a subunit of the neural cell   type-specific LSD1 complex

city: Sendai

first: Atsushi

last: Yokoyama

state: Miyagi

address: seiryo-machi 2-1, Aoba-ku, Sendai

institute: Tohoku University Graduate School of Medicine

summary: Regulation of spatiotemporal gene expression in higher eukaryotic cells is critical for the precise and orderly development of undifferentiated progenitors into committed cell types of the adult. Recently, dynamic epigenomic regulation, including chromatin remodeling and histone modifications by transcriptional coregulator complexes, has been shown to be involved in transcriptional regulation. Precisely how these coregulator complexes exert their cell-type and developing stage-specific activity is largely unknown. In this study, we aimed to isolate the histone demethylase LSD1 complex from neural cells by biochemical purification. In so doing, we identified MyT1 as a novel LSD1 complex component. MyT1 is a neural cell-specific zinc finger factor and it forms a stable multiprotein complex with LSD1 through direct interaction. Target gene analysis using microarray and ChIP assays revealed several genes, including PTEN, that were directly regulated by the LSD1-MyT1 complex. Knockdown of either LSD1 or MyT1 derepressed the expression of endogenous target genes and inhibited cell proliferation of a neuroblastoma cell line, Neuro2a. We propose that formation of tissue-specific combinations of coregulator complexes is a critical mechanism for tissue-specific transcriptional regulation.

overall_design: Neuro2a cells were treated with either siControl, siLSD1 or siMyT1 for 48 h (n=3)

first: Katsuhide

last: Igarashi

first: Tetsuya

last: Sato

first: Kiyoshi

last: Takagi

first: Maky

last: Otsuka I.

first: Yurina

last: Shishido

first: Takashi

last: Baba

first: Ryo

last: Ito

first: Jun

last: Kanno

first: Yasuyuki

last: Ohkawa

first: Ken

middle: I

last: Morohashi

first: Akira

last: Sugawara


title: Expression data from murine cardiac fibroblasts and endothelial cells following Transverse Aortic Constriction

status: Public on May 19 2014

city: La Jolla

first: thomas

last: moore-morris

address: 9500 Gilman Drive #0613C

department: SSPPS

institute: University of California San Diego

summary:
Accumulation of activated cardiac fibroblasts plays a key role in heart failure progression. These cells deposit excessive extracellular matrix that leads to mechanical stiffness, myocyte uncoupling and ischemia. To investigate whether two developmentally distinct cardiac fibroblast populations exhibit distinct expression profiles in response to cardiac injury, and therefore might necessitate distinct therapeutic targeting, we performed microarray analysis on FACS sorted cells. Tie2cre lineage traced CFs, non Tie2cre lineage traced cardiac fibroblasts and endothelial cells were isolated from left ventricle of SHAM operated and banded hearts at the onset of fibrosis, one week after surgery.
We used microarrays to detail the global programme of gene expression in cardiac fibroblasts and endothelium following pressure overload. Tie2cre lineage traced, non-tie2cre lineage traced fibroblasts and endothelial cells were sorted from left ventricle of 3 SHAM operated and 3 TAC operated adult male Black Swiss mice.

overall_design: Tie2cre lineage traced, non-tie2cre lineage traced fibroblasts and endothelial cells were sorted from left ventricle of 3 SHAM operated and 3 Transaortic Constriction (TAC) operated adult male Black Swiss mice for RNA extraction and Affymetrix microarray analysis. Hypertrophy in TAC animals, an lack of hypertrophy in SHAM operated animals, was evaluated by hemodynamic measurements before surgery and one week after surgery. Cells were isolated one week after surgery.

first: Thomas

last: Moore-Morris

first: Sylvia

last: Evans


title: Expression data from B6 mouse miR-142 KO and WT T cells

status: Public on May 13 2014

city: Ann Arbor

first: yaping

last: sun

state: Michigan

address: 1500 E Medical Center Dr.

department: internal medicine

institute: university of michigan

summary:
T cells are critical for modulating immune responses. miRNAs are  small, noncoding RNAs and play a significant role in T cell responses. miR-142 is a hematopoietic specific miRNA. To explore the potential role of miR-142  in regulating T cell responses, we generated mutant mice bearing a targeted deletion of the miR-142 gene.
We used microarrays to detail the global programme of gene expression underlying the profile changes between miR-142 KO and WT T cell and identified distinct classes of up-regulated genes during this process.

overall_design: miR-142 KO mice and WT littermates (biological triplicates) matched with age and sex were selected. T cells were purified from spleens by negative selection and processed for RNA isolation and hybridization on Affymetrix microarrays.

first: Pavan

last: Reddy

first: Yaping

last: Sun


title: Gene profiling on mandibular arches (MdPA1) from Tbx1+/+ and Tbx1-/- mouse embryos

city: Bronx

first: Tingwei

last: Guo

state: NY

address: 1301 Morris Park Avenue, Room 408

department: Genetics

institute: Albert Einstein College of Medicine

summary: Velo-cardio-facial syndrome/DiGeorge syndrome/22q11.2 deletion syndrome (22q11DS) patients have a submucous cleft palate, velo-pharyngeal insufficiency associated with hypernasal speech, facial muscle hypotonia and feeding difficulties. Inactivation of both alleles of mouse Tbx1, encoding a T-box transcription factor, deleted on 22q11.2, results in a cleft palate and a reduction or loss of branchiomeric muscles. To identify genes downstream of Tbx1 for myogenesis, gene profiling was performed on mandibular arches (MdPA1) from Tbx1+/+ and Tbx1-/- mouse embryos.

overall_design: To obtain enough RNA for microarray hybridization experiments, dissected mandibular arches from three Tbx1+/+ and three Tbx1-/- E10.5 embryos were pooled according to genotype, with three microarrays performed in total per genotype. The tissue was homogenized in Buffer RLT (QIAGEN). Total RNA was isolated with the RNeasy Micro Kit according to the manufacturer’s protocol. Quality and quantity of total RNA was determined using an Agilent 2100 Bioanalyzer (Agilent) and an ND-1000 Spectrophotometer (NanoDrop), respectively. Biotinylated single-stranded cDNA targets were amplified from 100 nanograms (ng) starting total RNA using the Ovation RNA Amplification System V2 and FL- Ovation cDNA Biotin Module V2 (NuGEN). A total of 3.75 μg of cDNA from the last step was hybridized to the GeneChip Test3 array (Affymetrix) to test the quality of the labeled target. Nucleic acid samples that passed quality control were then hybridized to the GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix). Hybridization, washing, staining and scanning were performed in the Genomics Core at Einstein (http://www.einstein.yu.edu/genetics/CoreFacilities.aspx?id=23934) according to the Affymetrix manual.

first: Ping

last: Kong

first: Courtney

last: Carpenter

first: Stephania

last: Macchiarulo

first: Silvia

last: Racedo

first: Steven

last: Ola

first: Vimla

last: Aggarwal

first: Bernice

last: Morrow


title: β-Cryptoxanthin suppresses inflammatory gene expression in diet-induced nonalcoholic steatohepatitis in mice

status: Public on May 28 2014

city: Tsukuba

first: Masuko

last: Kobori

state: Ibaraki

address: 2-1-13 Kannondai

institute: Food Research Institute, National Agriculture and Food Research Organization

summary:
To evaluate the effect of β-cryptoxanthin on diet-induced NASH, we fed a high-cholesterol and high-fat diet (CL diet) with or without 0.003% β-cryptoxanthin to C56BL/6J mice for 12 weeks. After feeding, β-cryptoxanthin attenuated fat accumulation, increases in Kupffer and activated stellate cells, and fibrosis in CL diet-induced NASH in the mice.
Comprehensive gene expression analysis showed that although β-cryptoxanthin histochemically reduced steatosis, it was more effective in inhibiting inflammatory gene expression change in NASH. β-Cryptoxanthin reduced the alteration of expression of genes associated with cell death, inflammatory responses, infiltration and activation of macrophages and other leukocytes, quantity of T cells, and free radical scavenging. However, it showed little effect on the expression of genes related to cholesterol and other lipid metabolism. The expression of markers of M1 and M2 macrophages, T helper cells, and cytotoxic T cells was significantly induced in NASH and reduced by β-cryptoxanthin. β-Cryptoxanthin suppressed the expression of lipopolysaccharide (LPS)-inducible and/or TNFα-inducible genes and the antioxidant enzyme glutathione peroxidase 1 in NASH. Thus, β-cryptoxanthin suppresses inflammation and the resulting fibrosis probably by primarily suppressing the increase and activation of macrophages and other immune cells. Reducing oxidative stress is likely to be a major mechanism of inflammation and injury suppression in the livers of mice with NASH.

overall_design: Eight-week old male C57BL/6J mice were fed for 12 weeks on a CRF-1 standard chow (control), a high-cholesterol and high-fat diet (CL diet; 38.23% CRF-1, 60% cocoa butter, 1.25% cholesterol, 0.5% sodium cholate) or a CL diet containing 0.003% β-cryptoxanthin.


title: Stability of gene expression and epigenetic profiles highlights the utility of patient-derived paediatric acute lymphoblastic leukaemia xenografts for investigatoing molecular mechanisms of drug resistance (expression)

status: Public on May 14 2014

city: Clayton

first: Nicholas

middle: C

last: Wong

state: Victoria

address: Wellington Road

department: Monash Bioinformatics Platform, Central Clinical School

institute: Monash University

summary: Background: Patient-derived tumour xenografts are an attractive model for preclinical testing of  anti-cancer drugs. Insights into tumour biology and biomarkers predictive of responses to  chemotherapeutic drugs can also be gained from investigating xenograft models. As a first step  towards examining the equivalence of epigenetic profiles between xenografts and primary tumours  in paediatric leukaemia, we performed genome-scale DNA methylation and gene expression  profiling on a panel of 10 paediatric B-cell precursor acute lymphoblastic leukaemia (BCP-ALL)  tumours that were stratified by prednisolone response.  Results: We found high correlations in DNA methylation and gene expression profiles between  matching primary and xenograft tumour samples with Pearson’s correlation coefficients ranging  between 0.85 and 0.98. In order to demonstrate the potential utility of epigenetic analyses in BCPALL  xenografts, we identified DNA methylation biomarkers that correlated with prednisolone  responsiveness of the original tumour samples. Differential methylation of CAPS2, ARHGAP21, ARX  and HOXB6 were confirmed by locus specific analysis. We identified 20 genes showing an inverse  relationship between DNA methylation and gene expression in association with prednisolone  response. Pathway analysis of these genes implicated apoptosis, cell signalling and cell structure  networks in prednisolone responsiveness.  Conclusions: The findings of this study confirm the stability of epigenetic and gene expression  profiles of paediatric BCP-ALL propagated in mouse xenograft models. Further, our preliminary  investigation of prednisolone sensitivity highlights the utility of mouse xenograft models for  preclinical development of novel drug regimens with parallel investigation of underlying gene  expression and epigenetic responses associated with novel drug responses.

overall_design: 20 samples were analysed using Illumina Infinium WG-6 V3 Expression Chips. This consisted of 10 matched primary tumour and low passage xenografts. Of which, 5 were prednisolone good responders and 5 were prednisolone poor responders. Two Samples were eliminated due to not passing qc.

first: Vivek

last: Bhadri

first: Richard

last: Lock


title: Gene expression analysis of WT and Flt3-ITD multipotent progenitors

status: Public on May 16 2014

city: Oxford

first: Sten Eirik

last: Jacobsen

address: Headington

department: Weatherall Institute

institute: University of Oxford

summary: FLT3-ITDs Introduce a Myeloid Differentiation and Transformation Bias in Lympho-myeloid Multipotent Progenitors

overall_design: WT multipotent progenitors were compared with FLT3-ITD multipotent progenitors

first: Sten

first: Adam

last: Mead

first: Iain

last: Macaulay


title: Stability of gene expression and epigenetic profiles highlights the utility of patient-derived paediatric acute lymphoblastic leukaemia xenografts for investigatoing molecular mechanisms of drug resistance

type:
Expression profiling by array
Methylation profiling by array

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

overall_design: Refer to individual Series


title: Role of Blimp-1 in programing Th effector cells into IL-10 producers

status: Public on May 08 2014

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

institute: Deutsches Rheuma-Forschungszentrum

summary: Gene expression profiling on IL-10-secreting and non-secreting murine Th1 cells, stimulated in the presence or absence of the Notch ligand Delta-like 4 (Dll4), was performed to identify transcription factors co-expressed with IL-10.

overall_design:
Primary naïve T helper cells were isolated from lymph nodes and spleens of C57BL/6 wildtype mice. Cells were enriched using the Multisort Kit from Miltenyi Biotec for CD25-CD4+CD62L+, and afterwards cultured under Th1 polarizing conditions. For activation, 0.25E06 naïve T cells were co-cultured with 0.75E06 MACSi Beads in 96-well flat bottom plates. MACSi Beads were coated with anti-CD3 and anti-CD28 (30 µg of total primary IgG antibody per 1.0E08 beads) prior to seeding. Notch activation via Dll4 was induced by additional co-culture with MACSi Beads covalently coated with recombinant mouse Dll4.
After 5 days in culture, the cells were restimulated with PMA/Ionomycin and subjected to an IL-10-secretion assay (Miltenyi Biotec) to separate IL-10-secreting and non-secreting cells. Using a BD Aria or DIVA cell sorter (Becton Dickinson), living CD4+ IL-10-secreting and non-secreting cells, with (co-culture with Dll4; 'TH1Notch') or without ('TH1Control') activation of the Notch signaling pathway, were isolated.
Total RNA was extracted using the RNeasy Mini kit (Qiagen). The integrity and amount of isolated RNA was assessed for each sample using an Agilent 2100 Bioanalyzer (Agilent, Waldbronn, Germany) and a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). The preparation for the hybridization to the chip was done using the GeneChip 3' IVT Express Kit. Fifteen micrograms of fragmented cRNA of each sample were hybridized to a total of 4 mouse genome 430 2.0 GeneChips (Affymetrix). Hybridization was performed in a Hybridization Oven 640, and chips were washed and stained in the Fluidics Station 400 (both Affymetrix). Finally, the arrays were scanned with a GeneChip Scanner 3000 using the GCOS software, version 1.1.1., both Affymetrix. The data was analyzed using the original GCOS CHP-file Signals, Excel and AmiGO website.

first: Christian

last: Neumann

first: Frederik

last: Heinrich

first: Katrin

first: Victoria

last: Junghans

first: Mir

middle: F

last: Mashreghi

first: Jonas

last: Ahlers

first: Marko

last: Janke

first: Christine

last: Rudolph

first: Nadine

last: Mockel-Tenbrinck

first: Anja

middle: A

last: Kühl

first: Markus

last: Heimesaat

first: Charlotte

last: Esser

first: Sin

middle: H

last: Im

first: Andreas

last: Radbruch

first: Sascha

last: Rutz

first: Alexander

last: Scheffold


title: Expression data from common myeloid progenitor cells (CMP) of C57BL6 mouse

status: Public on May 09 2014

city: Bunkyo-ku

first: Akihito

last: Shinohara

state: Tokyo

department: Hematology and Oncology, Graduate school of medicine

institute: The University of Tokyo

summary:
Common myeloid progenitor cells from murine bone marrow were sorted according to ROS content using FACS with H2-DCFDA staining.
We compared gene expression profile between CMP with low-ROS levels and those with high-ROS levels.

overall_design: We analysed function of ROS in differentiation step from CMP to MEP.

first: Yoichi

last: Imai

first: Masahiro

last: Nakagawa

first: Tsuyoshi

last: Takahashi

first: Motoshi

last: Ichikawa

first: Mineo

last: Kurokawa


title: Transcriptional profiles of macrophages in resolving inflammation

city: CARDIFF

first: Peter

last: Giles

address: Heath Park

institute: Cardiff University

summary: We have performed a comprehensive transcriptional analysis of specific monocyte and macrophage (MØ) subsets during an acute self-resolving inflammatory insult. Following initial induction of acute inflammation, tissue resident (Resident) MØ are rapidly ‘cleared’ from the inflammatory foci, only becoming recoverable as inflammation resolves. Monocytes are recruited to the inflammatory lesion where they differentiate into MØ. We term these monocyte-derived MØ ‘inflammation-associated’ to distinguish them from Resident MØ which are present throughout the inflammatory response and can renew during the resolution of inflammation by proliferation. Comparative analysis of the Mo and MØ populations (both ‘inflammation-associated’ and Resident MØ) identifies select genes expressed in subsets of ‘inflammation-associated’ and Resident MØ that play important roles in the resolution of inflammation and/or for immunity, including molecules involved in antigen presentation, cell cycle and others associated with ‘immaturity’ and MØ activation.

overall_design: We purified monocyte and macrophage populations from the peritoneal cavity of C57BL/6 mice 4, 18, 72 and 168 hours after the induction of inflammation with intraperitoneal administration of zymosan (2x10^7 particles). We also purified tissue resident macrophages and Ly-6B+ bone marrow monocytes from naive mice as reference populations.

first: Philip

middle: R

last: Taylor

first: Marcela

last: Rosas


title: Gene expression profiles of PIK3CA knockdown by shRNA in lung cancer cells

status: Public on May 02 2014

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: To gain insight into EMT-independent biological processes through which PI3K promotes invasion, RNA samples from 344SQ_p110α shRNA cells and 344SQ_scr cells were subjected to global transcriptional profiling.

overall_design:
Two groups, control and PIK3CA shRNA, in 344SQ lung cancer cell line
Two group comparison

first: Jon

last: Kurie

first: Yiqun

last: Zhang


title: Transcriptional Atlas of Cardiogenesis Maps Congenital Heart Disease Interactome

city: Rochester

first: XING

last: LI

state: MN

address: 200 1st street SW

department: Health Sciences Research

institute: Mayo Clinic

summary: Mammalian heart development is built on highly conserved molecular mechanisms with polygenetic perturbations resulting in a spectrum of congenital heart diseases (CHD). However, the transcriptional landscape of cardiogenic ontogeny that regulates proper cardiogenesis remains largely based on candidate-gene approaches. Herein, we designed a time-course transcriptome analysis to investigate the genome-wide expression profile of innate murine cardiogenesis ranging from embryonic stem cells to adult cardiac structures. This comprehensive analysis generated temporal and spatial expression profiles, prioritized stage-specific gene functions, and mapped the dynamic transcriptome of cardiogenesis to curated pathways. Reconciling the bioinformatics of the congenital heart disease interactome, we deconstructed disease-centric regulatory networks encoded within this cardiogenic atlas to reveal stage-specific developmental disturbances clustered on epithelial-to-mesenchymal transition (EMT), BMP regulation, NF-AT signaling, TGFb-dependent induction, and Notch signaling. Therefore, this cardiogenic transcriptional landscape defines the time-dependent expression of cardiac ontogeny and prioritizes regulatory networks at the interface between health and disease.

overall_design: To interrogate the temporal and spatial expression profiles across the entire genome during mammalian heart development, we designed a time-course microarray experiment using the mouse model at defined stages of cardiogenesis, starting with embryonic stem cells (ESC, R1 stem cell line), early embryonic developmental stages: E7.5 whole embryos, E8.5 heart tubes, left and right ventricle tissues at E9.5, E12.5, E14.5, E18.5 to 3 days after birth (D3) and adult heart (Figure 1A). At each time point, microarray experiments were performed on triplicate biological samples. Starting at E9.5, tissue samples from left ventricles (LV) and right ventricles (RV) were microdissected for RNA purification and microarray analysis to determine spatially differential gene expression between LV and RV during heart development.

first: Xing

last: Li

first: Almudena

last: Martinez-Fernandez

first: Andre

last: Terzic

first: Timothy

last: Nelson