title: Gene expression profiles of Calu-3 lung epithelial cells after neutrophil transmigration

status: Public on Aug 28 2011

city: Denver

first: Rachel

last: Zemans

state: CO

address: 1400 Jackson St

institute: National Jewish Health

summary: Injury to the epithelium is integral to the pathogenesis of many inflammatory lung diseases, and epithelial repair is a critical determinant of clinical outcome. However, the signaling pathways regulating such repair are incompletely understood. Herein, we used in vitro and in vivo models to define these pathways. Human neutrophils were induced to transmigrate across monolayers of human lung epithelial cells in the physiologic basolateral-to-apical direction to a gradient of fMLP.  Control wells were treated with fMLP alone.  Indicated wells were pretreated with an anti-CD47 blocking antibody, which exacerbates epithelial injury. This allowed study of the neutrophil contribution not only to the initial epithelial injury, but also to its repair, as manifest by restoration of transepithelial resistance (TER) and re-epithelialization of the denuded epithelium. Microarray analysis of epithelial gene expression revealed that neutrophil transmigration activated β-catenin signaling, and this was verified by real time PCR, nuclear translocation of β-catenin, and TOPFlash reporter activity. This pathway represents a potential therapeutic target to accelerate physiologic recovery in inflammatory lung diseases.

overall_design: Total of 20 samples: Calu-3 cells that were untreated, treated with fMLP, treated with fMLP and neutrophil transmigration, and treated with anti-CD47 antibodies, fMLP, and neutrophil transmigration; cDNA was pooled from n=3 experiments; No biological replicates

first: Natalie

last: Briones

first: Megan

last: Campbell

first: Jazalle

last: McClendon

first: Scott

middle: K

last: Young

first: Tomoko

last: Suzuki

first: Ivana

last: Yang

first: Stijn

last: de Langhe

first: Susan

middle: D

last: Reynolds

first: Robert

last: Mason

first: Michael

last: Kahn

first: Peter

middle: M

last: Henson

last: Colgan

first: Gregory

last: Downey


title: The Phytoestrogen Genistein Is a Tissue-Specific Androgen Receptor Modulator

status: Public on Aug 19 2011

city: Helsinki

first: Olli

middle: A.

last: Jänne

department: Inst. of Biomedicine/Physiology

country: Finland

institute: University of Helsinki

summary: We report that the phytoestrogen genistein acts as a tissue-specific androgen receptor modulator in mouse using a novel androgen reporter mouse line and gene expression profiling. Genistein is a partial androgen agonist/antagonist in prostate, brain, and testis but not in skeletal muscle or lung. Gene expression profiling has been done from prostates of intact and castrated male mice treated with genistein or vehicle. Gene expression profiling was also done from prostates of estradiol-treated intact male mice.

overall_design: Gene expression profiling from prostates of castrated and intact male mice after 5-day genistein- or vehicle-treatment or after 4-day estradiol- or vehicle-treatment.

first: Päivi

last: Pihlajamaa

first: Fu-Ping

last: Zhang

first: Lilli

last: Saarinen

first: Laura

last: Mikkonen

first: Sampsa

last: Hautaniemi

middle: A


title: Depletion of murine intestinal microbiota: effects on gut mucosa and epithelial gene expression

status: Public on Aug 15 2011

city: Oslo

first: Leonardo

last: Meza-Zepeda

address: Ullernchausseen 70

department: Dept. of Tumor Biology

country: Norway

institute: The Norwegian Radium Hospital

summary: Inappropriate cross talk between mammals and their gut microbiota may trigger intestinal inflammation and drive extra-intestinal immune-mediated diseases. Studies with germ-free or gnotobiotic animals represent the gold standard for research on bacterial-host interaction but they are not readily accessible to the wide scientific community. We aimed at refining a protocol that in a robust manner would deplete murine intestinal microbiota and prove to have significant biologic validity.      Previously published protocols for depleting mice of their intestinal microbiota by administering broad-spectrum antibiotics in drinking water were difficult to reproduce. We show that twice daily delivery of antibiotics by gavage depleted mice of their cultivable fecal microbiota and reduced the fecal bacterial DNA load by approximately 400 fold while ensuring the animals’ health. Mice subjected to the protocol for 17 days displayed enlarged ceca, reduced Peyer’s patches and small spleens. Antibiotic treatment significantly reduced the expression of antimicrobial factors and altered the expression of 517 genes in total in the colonic epithelium. Genes involved in cell cycle were significantly altered concomitant with reduced epithelial proliferative activity in situ assessed by Ki-67 expression, suggesting that commensal microbiota drives cellular proliferation in colonic epithelium.      We present a robust protocol for depleting mice of their cultivatable intestinal microbiota with antibiotics by gavage and show that the biological effect of this depletion is phenotypic characteristics and epithelial gene expression profile similar to those of germ-free mice.

overall_design: Comparison of genome-wide gene expression of colon intestinal epithelial cells from mice subjected to microbiota depletion protocol  against to control mice.

first: Dag

middle: H

last: Reikvam

first: Anders

last: Sandvik

first: Vedrana

last: Grcic

first: Finn-Eirik

last: Johansen


title: Human ependymoma samples [expression]

city: Heidelberg

first: Hendrik

last: Witt

state: BW

address: INF 580

department: Molecular Genetics

country: Germany

institute: German Cancer Research Center

summary: Whole-genome transcriptional profiling of human ependymoma tumors. Subgrouping based on mRNA expression profile.

overall_design: Fresh frozen tumor material was collected during tumor resection. Gene expression profiles illustrate distinct expression pattern at diagnosis.

first: Stefan

last: Pfister


title: Delineation of Two Clinically and Molecularly Distinct Subgroups of Posterior Fossa Ependymoma.

type: Genome variation profiling by genome tiling array

summary:
Despite histological similarity of ependymomas from throughout the neuraxis, the disease likely comprises multiple independent entities, each with a distinct molecular pathogenesis. Transcriptional profiling of two large independent cohorts of ependymomas reveals the existence of two demographically, transcriptionally, genetically and clinically distinct groups of posterior fossa (PF) ependymoma. Group A patients are younger, have laterally located tumors with a balanced genome, and are much more likely to exhibit recurrence, metastasis, and death as compared to Group B patients. Identification and optimization of immunohistochemical markers for PF ependymoma subgroups allowed validation of our findings on a third group of independent ependymomas using a human ependymoma tissue microarray, and provides a tool for prospective prognostication and stratification of PF ependymoma patients.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Foxo1 is a Marker of Spermatogonial Stem Cells Required for their Maintenance and the Initiation of Spermatogenesis in Mice

status: Public on Aug 10 2011

city: Dallas

first: Diego

last: Castrillon

state: TX

address: 6000 Harry Hines Blvd. NB6.126

department: Pathology

country: USA

institute: U.T. Southwestern Medical Center

summary: Foxo factors in spermatogonial stem cells

overall_design: Total RNA obtained from postnatal day 4 (pd4) Foxo1 null and wild-type testes.

first: Meredith

middle: J

last: Goertz

first: Zhuoru

last: Wu

first: Teresa

last: Gallardo

first: F

last: Hamra


title: Mesenchymal Stem Cells Promote the Sustained Expression of CD69 on Activated T-lymphocytes: Roles of Canonical and Non-Canonical NF-κB Signaling

status: Public on Aug 03 2011

city: Ribeirao Preto

first: Rodrigo

middle: Alexandre

last: Panepucci

state: São Paulo

address: R. Tenente Catao Roxo, 2501

country: Brazil

institute: Regional Blood Center of Ribeirâo Preto (FUNDHERP, HC-FMRP-USP)

summary: Mesenchymal stem cells (MSCs) are known to induce the conversion of activated T-cells into regulatory T-cells in vitro. The marker CD69 is a target of canonical NF-κB signaling and is transiently expressed upon activation; however, stable CD69 expression defines cells with immunoregulatory properties. Given its enormous therapeutic potential, we explored the molecular mechanisms underlying the induction of regulatory cells by MSCs. Peripheral blood CD3+ T-cells were activated and cultured in the presence or absence of MSCs. CD4+ cell mRNA expression was then characterized by microarray analysis. The drug BAY11-7082 and a siRNA against RELB were used to explore the differential roles of canonical and non-canonical NF-κB signaling, respectively. Flow cytometry and real-time PCR were used for analyses. Genes with immunoregulatory functions, CD69 and non-canonical NF-κB subunits (RELB and NFKB2) were all expressed at higher levels in lymphocytes co-cultured with MSCs. The frequency of CD69+ cells among lymphocytes cultured alone progressively decreased after activation. In contrast, the frequency of CD69+ cells increased significantly following activation in lymphocytes co-cultured with MSCs. Inhibition of canonical NF-κB signaling by BAY immediately following activation blocked the induction of CD69; however, inhibition of canonical NF-κB signaling on the 3rd day further induced the expression of CD69. Furthermore, late expression of CD69 was inhibited by RELB siRNA. These results indicate that the canonical NF-κB pathway controls the early expression of CD69 after activation; however, in an immunoregulatory context, late and sustained CD69 expression is promoted by the non-canonical pathway and is inhibited by canonical NF-κB signaling.

overall_design: In order to study the molecular basis by which Multipotent Mesenchymal Stromal/Stem Cells (MSC) exert their immune regulatory function, immunomagnetically purified CD3+ T-cells from the peripheral blood of 3 individuals were activated and cultured in the presence or absence of MSCs. Following 5 days, CD4+ and CD8+ T-cells were further immunomagnetically selected and their gene expression profiles were obtained by microarrays and compared. Paired samples from 3 individuals were used for this analysis.

first: Felipe

last: Saldanha-Araujo

last: Haddad

first: Kelen

middle: C

last: Malmegrim de Farias

first: Alessandra

middle: P

last: Souza

first: Patrícia

middle: V

last: Palma

first: Amélia

middle: G

last: Araujo

first: Maristela

last: Orellana

first: Julio

last: Voltarelli

first: Dimas

middle: T

last: Covas

first: Marco

last: Zago


title: Endogenous MicroRNA Activity Is Not Affected Following Infection With MicroRNA Controlled Adenovirus

status: Public on Aug 20 2011

city: Oxford

first: Dilair

last: Baban

address: Roosevelt Drive

department: Wellcome Trust Centre Human Genetics

country: United Kingdom

institute: University of Oxford

summary:
Replicating viruses have broad applications in biomedicine, notably in cancer virotherapy and in the design of attenuated vaccines, however uncontrolled virus replication in vulnerable tissues can give pathology and often restricts the use of potent strains. Increased knowledge of tissue-selective microRNA expression now affords the possibility of engineering replicating viruses that are attenuated at the RNA level in sites of potential pathology, but retain wild type replication activity at sites not expressing the relevant microRNA.

To assess the usefulness of this approach for the DNA virus, adenovirus, we have engineered a hepatocyte-safe wild type adenovirus 5 (Ad5), which normally mediates significant toxicity and is potentially lethal in mice. To do this we have included binding sites for hepatocyte-selective microRNA122a within the 3’ UTR of the E1A transcription cassette. Imaging versions of these viruses, produced by fusing E1A with luciferase, showed that inclusion of microRNA122a binding sites caused up to 80 fold decreased hepatic expression of E1A following intravenous delivery to mice. Animals administered a ten-times lethal dose of wild type Ad5 (5 x 1010 viral particles/mouse) showed substantial hepatic genome replication and extensive liver pathology, while inclusion of 4 microRNA binding sites decreased replication 50-fold and virtually abrogated liver toxicity.

This modified wild type virus retained full activity within cancer cells and provides a potent, liver-safe oncolytic virus. In addition to providing many potent new viruses for cancer virotherapy, microRNA-control of virus replication should provide a new strategy for designing safe attenuated vaccines applied across a broad range of viral diseases.

overall_design:
four groups which we had were:
WT:	RNA extracted from livers of mice treated with wild type Ad5, 3 Replicates
miR:	RNA extracted from livers of mice treated with wild type Ad5 bearing mir122-binding sites in the 3’UTR of E1A (3 Replicates)
Luc:	RNA extracted from livers of mice treated with non-replicating Ad5 (3 Replicates)
PBS:	RNA extracted from livers of mice treated with PBS only (3 Replicates)

first: Ryan

last: Cawood

first: Leonard

middle: W

last: Seymour

first: Suet

middle: L

last: Wong

first: Ying

last: Di


title: Host Regulatory Network Response to Infection with Highly Pathogenic H5N1 Avian Influenza Virus

status: Public on Sep 02 2011

city: Portland

first: Armand

last: Bankhead III

state: OR

address: 3181 SW Sam Jackson Park Rd.

department: Depatartment of Medical Informatics and Clinical Epidemiology

institute: Oregon Health and Science University

summary: Over the last decade, more than half of humans infected with highly pathogenic avian influenza (HPAI) H5N1 viruses have died, and yet virus-induced host signaling has yet to be clearly elucidated.  Airway epithelia are known to produce inflammatory mediators that contribute to HPAI H5N1-mediated pathogenicity, but a comprehensive analysis of the host response in this cell type is lacking.  Here, we leveraged a systems biology method called weighted gene correlation network analysis (WGCNA) to identify and statistically validate signaling sub-networks that define the dynamic transcriptional response of human bronchial epithelial cells after infection with influenza A/Vietnam/1203/2004 (H5N1, VN1203). A detailed examination of two sub-networks involved in the immune response and keratin filament formation revealed potential novel mediators of HPAI H5N1 pathogenesis, and additional experiments validated upregulation of these transcripts in response to VN1203 infection in C57BL/6 mice.  Using emergent network properties, we provide fresh insight into the host response to HPAI H5N1 virus infection, and identify novel avenues for perturbation studies and potential therapeutic intervention of fatal HPAI H5N1 disease.

overall_design: Calu-3 cells were infected with VN1203 influenza virus and profiled at 0, 3, 7, 12, 18, and 24 hours post infection. There are 3 mock and infected replicates for each time point.

first: Chengjun

last: Li

first: Amie

last: Eisfeld

first: Yasuko

last: Hatta

first: Sophia

last: Jeng

first: Jean

last: Chang

first: Lauri

last: Aicher

first: G

last: Law

first: Katrina

last: Waters

first: Gabriele

last: Neumann

first: Michael

last: Katze

first: Shannon

last: McWeeney

first: Yoshi

last: Kawaoka


title: Genome-wide analysis of lung antigen presenting cells gene expression from cigarette smoke exposed mice

status: Public on Aug 01 2011

city: Houston

first: Farrah

last: Kheradmand

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: Lung antigen presenting cells isolated from wild type but not Spp1-/- mice induce Th1 and Th17 cells differentiation. The goal of this study is to identify the genes differentially expressed by lung antigen presenting cells from cigarette smoke exposed mice. These genes may play crucial roles in directing Th1 and Th17 cells differentiation.

overall_design: Lung antigen presenting cells were isolated from lungs of two groups of wild type and Spp1-/- mice that have been exposed to cigarette smoke for 4 months. Total mRNA was extracted from these samples.

first: Ming

last: Shan


title: Identification of Tfeb-dependent genes downstream of mTORC1 in MEFs

first: Samuel

last: Peña-Llopis

address: 6000 Harry Hines Blvd., NB5.102

department: Internal Medicine - Oncology Division

institute: UT Southwestern Medical Center

summary: Mammalian target of rapamycin (mTOR) complex 1 (mTORC1) is a critical regulator of cell growth by integrating multiple signals (nutrients, growth factors, energy and stress) and is frequently deregulated in many types of cancer. We used a robust experimental paradigm involving the combination of two interventions, one genetic and one pharmacologic to identify genes regulated transcriptionally by mTORC1. In Tsc2+/+, but not Tsc2-/- immortalized mouse embryo fibroblasts (MEFs), serum deprivation downregulates mTORC1 activity. In Tsc2-/- cells, abnormal mTORC1 activity can be downregulated by treatment with rapamycin (sirolimus). By contrast, rapamycin has little effect on mTORC1 in Tsc2+/+ cells in which mTORC1 is already inhibited by low serum. Thus, under serum deprived conditions, mTORC1 activity is low in Tsc2+/+ cells (untreated or rapamycin treated), high in Tsc2-/- cells, but lowered by rapamycin; a pattern referred to as a “low/low/high/low” or “LLHL”. We found that mTORC1 regulated the expression of, among other lysosomal genes, V-ATPases through the transcription factor EB (TFEB, Tcfeb in the mouse). The knockdown of Tfeb resulted in the 'flattening' of the LLHL pattern and allowed the identification of genes regulated by mTORC1 through Tfeb

overall_design: Mouse embryo fibroblasts (MEFs) wild type or deficient in Tsc2 expressing a Tfeb shRNA or scrambled shRNA vector were treated with 25 nM rapamycin or vehicle (methanol) for 24 h under low serum conditions (0.1% FBS)

first: James

last: Brugarolas


title: MYCN-MB with MYCN amplification

status: Public on Sep 01 2011

city: Toronto

first: Marc

last: Remke

address: 555 University Ave. Rm 1504

department: Laboratory Medicine and Pathobiology

country: Canada

institute: The Hospital for Sick Children

summary: BACKGROUND  Focal high-level amplifications of MYC define a subset of high-risk medulloblastoma patients. However, the prognostic role of MYCN oncogene amplification remains less clear. We aimed to evaluate the prognostic value of this alteration alone and in combination with biological modifiers in a large cohort of 67 pediatric medulloblastomas with MYCN amplification (MYCN-MB).     METHODS  Twenty-one MYCN-MB with MYCN amplication  and 56 MYCN-MB were respectively examined using either gene expression profiling and array-CGH, or immunohistochemical analysis and FISH. All 67 tumors were further subject to mutational analyses. Semi non-negative matrix factorization–based and unsupervised hierarchical clustering methods were used to identify biological groups. We compared molecular, clinical, and prognostic characteristics both within biological MYCN-MB groups and with non-amplified tumors.    RESULTS  Transcriptomic analysis of this large cohort of MYCN-MBs demonstrated a significant enrichment of MYCN-MB in the SHH and group D variants. Further substantiating this biological dichotomy of MYCN-MB, respective group affiliations were also accompanied by variant-specific cytogenetic aberrations including deletion of 9q in the SHH variant, and gain of 7q and isochromosome 17q/17q gain in MYCN-MBs clustering with group D tumors. Among clinically relevant variables, SHH subtype and 10q loss for Non-SHH tumors comprised the most powerful markers of favorable prognosis in MYCN-MB.    CONCLUSION  We demonstrate considerable heterogeneity within MYCN-MB in terms of genetics, tumor biology, and clinical outcome. Thus, assessment of disease group and 10q copy-number status may improve risk stratification of this group and may delineate MYCN-MB with the same dismal prognosis as MYC amplified tumors. Furthermore, based on the enrichment of MYCN and GLI2 amplifications in SHH-driven medulloblastoma, amplification of these downstream signaling intermediates should be excluded before a patient is enrolled into a clinical trial using a Smoothened inhibitor.

overall_design:
Fresh frozen tumor material was collected during tumor resection. Gene expression profiles illustrate distinct expression pattern at diagnosis.

This submission represents the gene expression component of the study only

first: Andrey

last: Korshunov

first: Marcel

last: Kool

first: Thomas

last: Hielscher

first: Paul

last: Northcott

first: Dan

last: Williamson

first: Hendrik

last: Witt

first: David

last: Jones

first: Marina

last: Ryzhova

first: Elke

last: Pfaff

first: Yoon-Jae

last: Cho

first: Andrea

last: Wittmann

first: William

last: Weiss

first: Axel

last: Benner

first: Andreas

last: von Deimling

first: Wolfram

last: Scheurlen

last: Kulozik

first: Steven

last: Clifford

first: V

last: Collins

first: Frank

last: Westermann

last: Taylor

first: Peter

last: Lichter

first: Stefan

last: Pfister


title: Tumor-entrained neutrophils inhibit seeding in the pre-metastatic lung

status: Public on Jul 25 2011

city: New York

first: Yupu

last: Liang

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

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


title: Neutrophil expression array

summary:
Primary tumors have been shown to prepare distal organs for later colonization of metastatic cells by stimulating organ-specific infiltration of bone marrow-derived cells. Here we demonstrate that neutrophils accumulate in the lung prior to the arrival of metastatic cells in mouse models of breast cancer. Tumor-entrained neutrophils (TENs) inhibit metastatic seeding in the lungs by generating H2O2, and tumor-secreted CCL2 is a critical mediator of optimal anti-metastatic entrainment of G-CSF-stimulated neutrophils. TENs are present in the peripheral blood of breast cancer patients prior to surgical resection but not in healthy individuals. Thus, while tumor-secreted factors contribute to tumor progression at the primary site, they concomitantly induce a neutrophil-mediated inhibitory process at the metastatic site.

This experiment was designed to compare the RNA expression profile in resting (control) neutrophils vs. that of TENs (neutrophils purified from tumor-bearing mice). In addition, we also compared the expression profiles of cultured neutrophils in vitro and treated with CCL2, CCL5 and GCSF.

overall_design: Circulating neutrophils were purified from control and 4T1 tumor-bearing mice and flash frozen. For in vitro cultures, circulating neutrophils were purified from control mice, cultured in the presence of chemokines for 2 hours and flash frozen.

first: Zvi

last: Granot

first: Robert

last: Benezra


title: Modeling OPMD in myotube cultures reveals reduced accumulation of soluble mutant PABPN1 protein

city: Leiden

first: Seyed Yahya

last: Anvar

address: Einthovenweg 20

department: Center for Human and Clinical Genetics

country: Netherlands

institute: Leiden University Medical Center

summary:
Oculopharyngeal muscular dystrophy (OPMD) is an autosomal dominant disease caused by an alanine tract expansion mutation in Poly(A)-binding protein nuclear 1 (expPABPN1). To model OPMD in a myogenic and physiological context, we generated mouse myoblast cell clones stably expressing either human wild type (WT) or expPABPN1 at low levels. The transgene expression is induced upon myotube differentiation and results in formation of insoluble nuclear PABPN1 aggregates that are similar to the in vivo aggregates. Quantitative analysis of PABPN1 protein in myotube cultures revealed that expPABPN1 accumulation and aggregation is greater than that of the WT protein. In a comparative study we found that aggregation of expPABPN1 is more affected by inhibition of proteasome activity, as compared with the WT PABPN1 aggregation. Consistent with this, in myotubes cultures expressing expPABPN1 deregulation of the proteasome was identified as the most significantly deregulated pathway. Differences in the accumulation of soluble WT and expPABPN1 were consistent with differences in ubiquitination and protein turnover. This study indicates, for the first time, that in myotubes the ratio of soluble to insoluble expPABPN1 is significantly lower compared to that of the WT protein. We suggest that this difference can contribute to muscle weakness in OPMD.
Clones on IM2 mouse myotubes that stably express Ala10-PABPN1-FLAG (WTA, WTD) or Ala17-PABPN1-FLAG (D7E). The transgene expression level in D7E and WTA are similar. WTA and WTD reflects differences in expression levels.

overall_design: RNA was extracted from myotubes of WTA, WTD and D7E in triplicates. cDNA synthesis and lebeling was preformed with the Illumina cDNA labeling kit.

first: Vered

last: Raz

first: Samantha

last: Routledge

last: Venema

first: Hellen

last: Buijze

first: Erik

last: van der Wal

first: Seyed

last: Yahya Anvar

first: Kirsten

middle: R

last: Straasheijm

first: Rinse

last: Klooster

first: Michael

last: Antoniou

first: Silvere

last: van der Maarel


title: Establishment of Enhancer Repertoires that Orchestrate the Myeloid and Lymphoid Cell Fates (gene expression dataset 2)

city: La Jolla

first: Yin

middle: Chun

last: Lin

state: CA

address: 9500 Gilman Drive

department: Division of Biological Sciences

institute: UCSD

summary: Recent studies have documented genome-wide binding patterns of transcriptional regulators and their associated epigenetic marks in hematopoietic cell lineages. In order to determine how epigenetic marks are established and maintained during developmental progression, we have generated long-term cultures of hematopoietic progenitors by enforcing the expression of the E-protein antagonist Id2. Hematopoietic progenitors that express Id2 are multipotent and readily differentiate upon withdrawal of Id2 expression into committed B lineage cells, thus indicating a causative role for E2A in promoting the B cell fate. Genome-wide analyses revealed that a substantial fraction of lymphoid and myeloid enhancers are pre-marked by H3K4me1 in multipotent progenitors. However, H3K4me1 levels at a subset of enhancers are elevated during developmental progression, resulting in evolving enhancer repertoires that we propose orchestrate the myeloid and B cell fates.

overall_design:
ChIP-Seq and gene expression profiling were performed in an inducible hematopoietic pluripotent cell line that can be differentiated into multiple lymphoid lineages. This submission contains gene expression profiling data.

To compare the expression signatures from differentiated B- and myeloid-cells derived from hematopoietic progenitors that express Id2, Id2-HPCs were differentiated into either CD19+ B cells or CD11b+ myeloid cells. The gene expression profiles of differentiating B cells at 6-, 12-, 24-, 48-, 72-, 120-, and 240-hour time points were also investigated. RNA was isolated from the cultures and analyzed by microarray gene expression analysis. Id2-HPCs were cultured in IMDM medium supplemented with 10% FCS/2% PSG/β-me and IL7, Flt3-ligand, and SCF cytokines on S17 feeder cells in a humidified incubator at 37 degrees C with 5% CO2. Id2-HPC expanded cells were depleted of small (<1-5%) numbers of CD19-, CD25- and CD11b-positive cells by auto-MACS. For myeloid differentiation, cells were cultured for up to 6 days in IMDM medium supplemented with 10% FCS/2% PSG/β-me and IL3, Flt3L, GMCSF and MCSF cytokines. To promote B-cell differentiation, cells were cultured for up to 10 days in IMDM medium supplemented with 10% FCS/2% PSG/β-me and IL-7 and SCF cytokines on S17 feeder cells in the presence of 1 ug/mL doxycycline.

first: Elinore

last: Mercer

first: Christopher

last: Benner

first: Suchit

last: Jhunjhunwala

first: Janusz

last: Dutkowski

first: Martha

last: Flores

first: Mikael

last: Sigvardsson

first: Trey

last: Ideker

last: Glass

first: Cornelis

last: Murre


title: The roles of ppar-delta and ppar-gamma in regulating the metabolic switch between oxidation and storage of fats in white adipose tissue

status: Public on Jul 14 2011

city: Cambridge

first: Julian

last: Griffin

address: Tennis Court Road

department: Biochemistry

institute: University of Cambridge

summary: Obesity is a major risk factor for the development of insulin resistance and type II diabetes. The nuclear receptors PPAR-delta and PPAR-gamma play a central role in regulating metabolism in adipose tissue, as well as being targets for the treatment of insulin resistance. The metabolic effects of PPAR-delta and PPAR-gamma activation have been examined both in vivo in white adipose tissue from ob/ob mice and in vitro in cultured 3T3-L1 adipocytes using a combined 1H NMR spectroscopy and mass spectrometry metabolomic methodology to understand the contrasting roles of these receptors. These steady state measurements were supplemented with 13C-stable isotope substrate labeling to assess fluxes, respirometry and transcriptomic microarray analysis. The metabolic effects of the two receptors were readily distinguished, with PPAR-gamma activation characterised by increased fat storage and fat synthesis/elongation, while activation of PPAR-delta caused increased fatty acid beta-oxidation, TCA cycle rate and oxidation of extracellular branch chain amino acids. Stimulated glycolysis and increased desaturation of fatty acids were the only common pathways. PPAR-delta has a role as an anti-obesity target as well as an anti-diabetic.

overall_design: Total RNA obtained from cultured 3T3-L1 cells treated for 48 hours with either DMSO control, GW610742 PPARd agonist or GW347845 PPARg agonist and compared.

first: Lee

last: Roberts

first: Andrew

last: Murray

first: David

last: Menassa

first: Tom

last: Ashmore

last: Nicholls


title: Investigation of griffithsin's interactions with human cells confirms its outstanding safety and efficacy profile as a microbicide candidate

city: Louisville

first: joseph

middle: calvin

last: kouokam

state: KY

address: 505 S. Hancock St.

department: Pharm  Tox

institute: U of L

summary: Treatment of cells by  different concentrations of Griffithsin resulted in minor alterations in gene expression

overall_design: Cells were treated with Griffithsin or controls (Cyanovirin-N, lectin deficient Griffithsin termed mGRFT and PBS) and incubated overnight (16 h). Gene expression was compared to that of the PBS treated cells to derive fold changes. Each treatment was done in triplicates. Benjammini and Hochberg  correction was used and we considered a fold change of at least 2.0 compared to the PBS treated samples to represent a meaningfully altered gene expression.

first: J

last: Kouokam

first: K

middle: E

last: Palmer


title: Transcriptional Profiling of Human Liver Identifies Sex-Biased Genes Associated with Polygenic Dyslipidemia and Coronary Artery Disease

status: Public on Aug 17 2011

city: Boston

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

summary: Sex-differences in human liver gene expression were characterized on a genome-wide scale using a large liver sample collection, allowing for detection of small expression differences with high statistical power. 1,249 sex-biased genes were identified, 70% showing higher expression in females. Chromosomal bias was apparent, with female-biased genes enriched on chrX and male-biased genes enriched on chrY and chr19, where 11 male-biased zinc-finger KRAB-repressor domain genes are distributed in six clusters. Top biological functions and diseases significantly enriched in sex-biased genes include transcription, chromatin organization and modification, sexual reproduction, lipid metabolism and cardiovascular disease. Notably, sex-biased genes are enriched at loci associated with polygenic dyslipidemia and coronary artery disease in genome-wide association studies. Moreover, of the 8 sex-biased genes at these loci, 4 have been directly linked to monogenic disorders of lipid metabolism and show an expression profile in females (elevated expression of ABCA1, APOA5 and LDLR; reduced expression of LIPC) that is consistent with the lower female risk of coronary artery disease. Female-biased expression was also observed for CYP7A1, which is activated by drugs used to treat hypercholesterolemia. Several sex-biased drug-metabolizing enzyme genes were identified, including members of the CYP, UGT, GPX and ALDH families. Half of 879 mouse orthologs, including many genes of lipid metabolism and homeostasis, show growth hormone-regulated sex-biased expression in mouse liver, suggesting growth hormone might play a similar regulatory role in human liver. Finally, the evolutionary rate of protein-coding regions for human-mouse orthologs, revealed by dN/dS ratio, is significantly higher for genes showing the same sex-bias in both species than for non-sex-biased genes. These findings establish that human hepatic sex differences are widespread and affect diverse cell metabolic processes, and may help explain sex differences in lipid profiles associated with sex differential risk of coronary artery disease.

overall_design: A first set of randomized liver RNA pools (WS9) was generated by randomly distributing 112 male and 112 female liver RNA samples into 8 pools comprised of 14 male liver samples (pools M1 to M8), and 8 pools of 14 female liver samples each (pools F1 to F8).  A second set of 16 pools (WS10) was prepared from the same set of 224 liver samples in the same way (pools M9 to M16 and F9 to F16). The 16 liver RNA pools of each sex were used in a total of 16 male vs.  female two-color hybridization microarrays by pairing pool M1 and pool F1, pool M2 with pool F2, etc.  Fluorescent labeling of RNA and hybridization of the Alexa 555-labeled and Alexa 647-labeled amplified RNA samples to Agilent Whole Human Genome oligonucleotide microarrays (4 x 44K format; Agilent Technology, Palo Alto, CA; catalog # G4112F) were carried out, with dye swaps to eliminate dye bias.

first: Yijing

last: Zhang

first: Kathrin

last: Klein

first: Aarathi

last: Sugathan

first: Najlla

last: Nassery

first: Alan

last: Dombkowski

first: Ulrich

middle: M

last: Zanger


title: Gene expression profiling of the Se-Ax cell line following E2A reconstitution

status: Public on Jul 07 2011

city: Berlin

first: Reinhard

last: Ullmann

department: Human Molecular Genetics

institute: MPIMG

summary: The transcription factor E2A is essential for lymphocyte development. In this study, we describe a recurrent E2A gene deletion in at least 70% of patients with Sézary syndrome (SS), a subtype of T cell lymphoma. Loss of E2A results in enhanced proliferation and cell cycle progression via derepression of the proto-oncogene MYC and the cell cycle regulator CDK6. Furthermore, by examining the gene expression profile of SS cells following restoration of E2A expression, we identify a number of E2A-regulated genes that interfere with oncogenic signaling pathways including the Ras pathway. Several of these genes are down-regulated or lost in primary SS tumor cells. These data demonstrate a tumor suppressor function of E2A in human lymphoid cells and could help to develop new treatment strategies for human lymphomas with altered E2A activity.

overall_design: The E2A-deficient Sézary cell line Seax was transiently transfected with the E2A-expression constructs E47myc (a myc-tagged E47 construct) or E47-forced dimer (a construct coding for two covalently linked E47 molecules), respectively. Every experiment was performed as two replicates accompanied by control transfections with a Mock plasmid.

first: Karl

last: Köchert

first: Stephan

last: Mathas

first: Anne

last: Steininger


title: Gene expression of polyoma middle T antigen induced mammary tumors [AKXD x PyMT]

status: Public on Jul 22 2011

city: Rockville

first: Ying

last: Hu

email: yhu@mail.nih.gov, hunterk@mail.nih.gov

state: MD

address: 9609 Medical Center Dr.

department: NCI/CCR

institute: NIH

summary: Mouse genetic crosses were established between the PyMT model of metastatic breast cancer and AKXD strain.  Tumors were harvested from the animals for gene expression analysis to identify genes and network modules associated with progression to distant metastatic disease.

overall_design: Gene expression of  56 samples from the AKXD crosses were assayed on Affymetrix chips

first: Kent

last: Hunter


title: Genomic loss of the putative tumor suppressor gene E2A promotes cutaneous T-cell lymphoma in human


title: Whole-genome gene expression profiling of Pik3cg-depleted mice

status: Public on Jul 01 2011

city: Hinxton

first: Dirk

middle: Stefan

last: Paul

address: Wellcome Trust Genome Campus

department: Human Genetics

institute: Wellcome Trust Sanger Institute

summary:
We performed whole-genome gene expression profiling in Pik3cg-/- mice and subsequent gene ontology clustering of differentially expressed genes compared to wild type mice, in order to investigate the role of Pik3cg in platelet membrane biogenesis and blood coagulation.
Pik3cg-deficient mice were obtained from sources previously described (T. Sasaki et al, 2000, Science 287, 1040-1046), backcrossed onto the C57BL/6J Jax genetic background for eight generations (B6J;129-Pik3cg-tm1Pngr) and then maintained as a closed colony by intercrossing from within the colony (C57BL/6J Jax contribution: 99.6%).

overall_design: Whole blood from three Pik3cg-/- and three C57BL/6J Jax wild type mice (all females, age: 13-16 weeks, Mouse Breeders Diet (Lab Diets 5021-3)) was collected from terminally anaesthetized mice via the retro-orbital sinus. For each RNA extraction, in vitro transcription (IVT) reactions were performed in duplicates.

middle: S

first: Panos

last: Deloukas


title: Response of the EPI-200 human 3-D skin model to high and low doses of protons

first: Sally

last: Amundson

department: Center for Radiological Research

institute: Columbia University

summary: Accumulating data suggest that the biological responses to high and low doses of radiation are qualitatively different, necessitating the direct study of low dose responses. Most such studies have utilized 2-dimensional culture systems, which may not fully represent responses in 3-dimensional tissues.  To gain insight into low dose responses in tissue, we have profiled global gene expression in EPI-200, a 3-dimensional tissue model from MatTek that imitates the structure and function of human epidermis, at 4, 16 and 24 hours after exposure to high (2.5 Gy) and low (0.1 Gy) doses of low LET protons.

overall_design: Untreated controls and samples exposed to 10 cGy or to 2.5 Gy were analyzed at three different times (4, 16 or 24 hours after  exposure).  Three biological repeats were performed for each condition

middle: A

first: Alexandre

last: Mezentsev


title: IL13 and CCL2 Drive Disease in an Inflammatory Subset of Scleroderma

status: Public on Jun 30 2011

city: Hanover

first: Jennifer

last: Sargent

state: NH

address: Dartmouth College; HB7400

department: Genetics

institute: Dartmouth Medical School

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Genetic and pharmacologic approach to identify genes regulated by mTORC1

first: Samuel

last: Peña-Llopis

summary: Mammalian target of rapamycin (mTOR) complex 1 (mTORC1) is a critical regulator of cell growth by integrating multiple signals (nutrients, growth factors, energy and stress) and is frequently deregulated in many types of cancer. We used a robust experimental paradigm involving the combination of two interventions, one genetic and one pharmacologic to identify genes regulated transcriptionally by mTORC1. In Tsc2+/+, but not Tsc2-/- immortalized mouse embryo fibroblasts (MEFs), serum deprivation downregulates mTORC1 activity. In Tsc2-/- cells, abnormal mTORC1 activity can be downregulated by treatment with rapamycin (sirolimus). By contrast, rapamycin has little effect on mTORC1 in Tsc2+/+ cells in which mTORC1 is already inhibited by low serum. Thus, under serum deprived conditions, mTORC1 activity is low in Tsc2+/+ cells (untreated or rapamycin treated), high in Tsc2-/- cells, but lowered by rapamycin; a pattern referred to as a “low/low/high/low” or “LLHL”, which allowed the identification of genes regulated by mTORC1 by performing the appropriate comparisons

overall_design: Mouse embryo fibroblasts (MEFs) wild type or deficient in Tsc2 were treated with 25 nM rapamycin or vehicle (methanol) for 24 h under low serum conditions (0.1% FBS)

first: James

last: Brugarolas


title: SMAD3 targets in A549 lung epithelial cells

status: Public on Jun 24 2011

city: Pittsburgh

first: Kusum

middle: Vijay

last: Pandit

state: PA

address: 200, Lothrop street, W1200-25A Biomedical Science Tower

department: Medicine-PACCM

institute: University of Pittsburgh

summary: TGFβ activates a signal transduction cascade that results in the transcription of genes, primarily through the DNA-binding transcription factor SMAD3. The objective of this study is to identify SMAD3 binding targets and the molecular pathways affected by the TGFβ1/SMAD3 signal transduction on a genome-wide scale.

overall_design: Cultured A549 cells at 30-50% confluence were treated with 10 uM SIS3 in dimethyl sulfoxide (DMSO), or DMSO (vehicle-only) 30 min prior to TGFβ1 treatment. Cells were treated with 2 ng/mL recombinant TGFβ1 for 0, 2, 12, and 24 h.

first: Yingze

last: Zhang

first: Daniel

last: Handley

first: Naftali

last: Kaminski


title: Genes downstream of p53 mediating its effect on megakaryopoiesis

status: Public on Jul 27 2011

city: Newark

first: Eleftherios

middle: Terry

last: Papoutsakis

state: DE

address: 15 Innovation Way

department: Chemical Engineering

institute: University of Delaware

summary: In order to examine genes whose expression is altered as a result of the knock-down (KD) of p53, we used gene expression microarray analysis based on the CHRF cell line, a human megakaryoblastic cell line, which upon PMA stimulation undergoes polyploidization, and extends proplatelet-like cytoplasmic protrusions combined with apoptosis. The CHRF cell line has been validated in our laboratory as a good model of in vitro megakaryopoiesis by comparison to hematopoietic stem cells undergoing Mk differentiation. As described, we have previously generated stable p53-KD CHRF cell lines by lentiviral delivery of microRNA-adapted-short hairpin sequences targeting p53 as well as a suitable scrambled-control cell line.

overall_design: For the microarray analysis we utilized the 4x44K whole human genome microarrays from Agilent. This analysis compared the p53-KD CHRF cells against the control CHRF cells in the absence of PMA treatment and on days 1, 3, 5 and 7 after PMA treatment (5 time-points). p53-KD and control samples were hybridized against each other (direct comparison). We carried out two biological replicate experiments, i.e., 10 measurements of gene expression for each microarray probe. Probes from which >50% of measurements were missing were discarded and not included in the analysis of differential expression. Differentially expressed genes were identified using the significance analysis of microarrays (SAM) with a false discovery rate (FDR) of less than 5%, as implemented in the MultiExperiment Viewer (MeV) tool.

first: Pani

last: Apostolidis

last: Lindsey

first: William

last: Miller


title: Expression data from human naïve (TN), stem cell memory (TSCM), central memory (TCM) and effector memory (TEM) CD8+ T cells

status: Public on Jul 13 2011

city: Budapest

first: Zoltan

last: Pos

address: 4 Nagyvarad ter

department: Dept. of Genetics, Cell- and Immunobiology

country: Hungary

institute: Semmelweis University

summary:
An early-differentiated CD8+ memory T cell subset with stem cell-like properties (TSCM) can be identified within the naïve-like T cell population by the expression of CD95/Fas. Based on experiments including exon- and gene-level expression analysis, we provide evidence that this subset of antigen-specific cells represents an early precursor of conventional central (TCM) and effector (TEM) memory CD8+ T cells with enhanced self-renewal capacity and proliferative potential.
We identified 900 genes differentially expressed between major T cell subsets defined along with memory T cell commitment. Based on the analysis of these genes, CD95+ naïve T cells (TSCM) cluster closer to the CD8+ T memory compartment than to classical (CD95-) naïve T (TN) cells, and display an intermittent phenotype between classical TN and TCM cells in terms of all major T cell differentiation markers analyzed.

overall_design:
Three healthy human blood donors provided lymphocyte-enriched apheresis blood for this study after informed consent. From all samples, total RNA was isolated using an RNEasy Micro kit (Qiagen), processed by Ambion’s WT expression kit, fragmented and labeled with a WT Terminal Labeling Kit (Affymetrix), hybridized to WT Human Gene 1.0 ST arrays (Affymetrix) and stained on a Genechip Fluidics Station 450 (Affymetrix), all according to the respective manufacturer's instructions.

Samples represent "exon-level" and "gene-level" analyses.

first: Luca

last: Gattinoni

first: Enrico

last: Lugli

first: Yun

last: Ji

first: Chrystal

last: Paulos

first: Maire

last: Quigley

first: Jorge

last: De Almeida

first: Zhiya

last: Yu

first: Carmine

last: Carpenito

first: Ena

last: Wang

first: Barney

last: Graham

first: Steven

last: Rosenberg

first: Carl

middle: H

last: June

first: Francesco

last: Marincola

middle: C

last: Douek

first: David

last: Price

first: Mario

last: Roederer

first: Nicholas

middle: P

last: Restifo


title: MKK2 is sufficient but not necessary for proliferation and anchorage-independent growth of SK-MEL-28 cells.

city: Grand Rapids

first: Karl

last: Dykema

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

summary: Though mitogen activated protein kinase kinases (MKK or MEK) 1 and 2 are widely assumed to be functionally redundant some reports indicate they possess distinct biologic activities.  To test the hypothesis that MEK1 and MEK2 signaling pathways are interchangeable we used two complementary approaches to determine the necessity and sufficiency of individual MEK1 and MEK2 signaling pathways for human melanoma SK-MEL-28 cell proliferation.  To test the necessity we targeted MEK1 and/or MEK2 using specific siRNAs.  An effect on proliferation was observed only when both MEK1 and MEK2 were knocked down indicating that neither of the individual MEK isoforms is necessary for SK-MEL-28 cell proliferation.  To test the sufficiency we inhibited multiple MEK and MKK signaling pathways in SK-MEL-28 cells with anthrax lethal toxin (LeTx) a MEK/MKK-specific protease and rescued individual MEK signaling pathways by expressing a cleavage-resistant form of MEK (MEKcr).  In this fashion ERK activation was retained only in MEK2cr-expressing cells but not in MEK1cr-expressing cells following LeTx treatment.  Microarray analysis revealed groups of non-overlapping downstream transcriptional targets of MEK1 and MEK2 and indicated a substantial rescue effect of MEK2cr on proliferation pathways.  Furthermore LeTx efficiently inhibited the cell proliferation and anchorage-independent growth of SK-MEL-28 cells expressing MKK1cr but not MEK2cr.  These results not only indicate that in this cellular context MEK2 signaling pathway alone is sufficient for ERK activation melanoma cell proliferation and anchorage-independent growth but MEK1 is not but also demonstrate that MEK1 and MEK2 signaling pathways are not redundant and interchangeable for melanoma cell proliferation.  We conclude that while MEK2 alone is sufficient for SK-MEL-28 cell proliferation MEK1 can conditionally compensate for loss of MEK2.

overall_design: SK-MEL-28 melanoma cells +/- cleavage resistant MKK1/MKK2


title: Expression data from mouse model of Ecoli mastitis

city: Kearneysville

first: Roger

middle: Luis

last: Vallejo

state: WV

address: 11861 Leetown Rd.

department: NCCCWA

institute: USDA-ARS

summary:
We performed a genome-wide transcriptional analysis in the mammary gland in a mouse model of E. coli mastitis using high-density mouse oligonucleotide microarrays.
This global transcription analysis revealed that about 7% of tested genes are mobilized in the mouse mammary gland to E. coli endotoxin. We identified 1402 differentially expressed genes that were associated with physiological system development/function and molecular/cellular functions and metabolic/signalling pathways that are highly relevant to host immune-inflammatory defense response against E. coli infection.
The mouse differentially expressed genes through the use of comparative mapping/genomics and positional information on reported QTL for bovine mastitis allowed identifying 293 potential candidate genes for bovine mastitis.
This study will enable other researchers to combine our mRNA expression data with genetic association studies to discover genomic variation underlying variation of susceptibility to mastitis in dairy cows.

Keywords: time course, disease state analysis

overall_design: This study was conducted using a split-plot design. We measured levels of gene expression in healthy (saline injected) and diseased (E. coli injected) mammary gland tissue (treatment = 2, in sub-plots). The mammary tissue samples were collected at two-time points: 24 hr and 48 hr post-injection (time = 2, in main-plots). Each inbred mouse was injected with both treatments: the 4th left mammary gland was injected with saline solution and the 4th right mammary gland was injected with E. coli solution (mice = 4). The expression profiling was carried out using two biological replications (replication = 2) at each time point.


title: Gene expression profiles of mouse splenic macrophages and CD8+ and CD8- conventional dendritic cells

status: Public on Jun 17 2011

city: Parkville

first: Priyanka

last: Sathe

state: Victoria

address: 1G Royal Parade

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

summary: The close functional relationship between macrophages and dendritic cells has long been recognised. Here, we have examined the gene expression profiles of splenic macrophages and the splenic resident dendritic cell subsets, and demostrate that macrophages and DC show different gene expression profiles. Further, we show that the DC subsets are closer to one another in gene expression profile than they are to macrophages. We here identify a list of differentially expressed genes between the DC subsets, and between DC and macrophages

overall_design: Splenic macrophages, CD8+ and CD8- cDC were analyzed

first: Wei

last: Shi

first: Gordon

middle: K

last: Smyth

first: Ken

last: Shortman


title: Development of a xenograft model for clinical oligo- and poly-metastatic progression

status: Public on Jun 14 2011

city: Chicago

first: Xinan

middle: "Holly"

last: Yang

state: IL

institute: universty of Chicago

summary: We previously proposed a clinically meaningful intermediate metastatic state defined by a limited number of new metastases (≤5) after 3 months of follow-up, termed oligometastasis that has the curative potential by local cancer treatments as in contrast to the incurable widespread polymetastatic dissemination. While animal models of polymetastasis exist and this phenotype can be further enhanced upon serial in vivo passage, animal models of oligometastasis are not available. Here, we report the creation of an oligometastasis model of MDA-MB-435 human tumor in nude mice in which the oligometastatic phenotype exhibits stability during successive in vivo testing, and satisfies the criteria of ≤ 5 total body macroscopic metastases definition of the human cancer oligometastatic state. In parallel, we also developed an MDA-MB-435 polymetastatic model in which the polymetastatic dissemination pattern was either poly-foci at lung, or involved multiple anatomic sites including lung, heart, muscle, ovaries, kidney, brain and pleura. We have conducted microRNA expression profiling of cell lines derived from distinct lungs of oligo- and poly-metastatic animals. Animal model-derived microRNA expression features that discriminate oligometastatic cell lines from those of polymetastases accurately identify oligometastatic patients who failed to develop widespread metastases (P=0.005). These results demonstrate the clinical relevance of the oligo- and polymetastatic animal models we have developed and their potential in elucidating the molecular underpinnings of oligometastasis progression.

overall_design:
We developed a stable human tumor (MDA-MB-435-GFP) xenograft model of oligometastatic and polymetastatic progression by conducting three consecutive rounds of experimental lung colonization assays.  In the first round, we generated oligometastases-like lung derivative MDA-MB-435-L1-GFP (L1) or polymetastases-like MDA-MB-435-L1Mic-GFP (L1Mic) cell lines.   We subsequently generated three oligometastatic L1-R2 lung cell lines as well as four polymetastatic L1Mic-R2 lung cell lines from seven distinct animals of the second in vivo passage for further biological characterization and for microRNA expression analysis. We eatracted total RNAs from four distinct lungs harvested from oligometastatic animals (L1-R3) and from polymetastatic animals (L1Mic-R3).

The pairwise microRNA profiles are stored in GEO by the accession numbers GSE29430 for the xenograft samples and GSE25967 for the cell line samples.

first: H

last: Xing

first: Yves

last: Lussier

first: Qingbei

last: Zhang


title: Cancer-related epigenome changes associated with reprogramming to induced pluripotent stem cells

status: Public on Jun 16 2011

city: Ghent

first: Leander

last: Van Neste

address: Coupure Links 653

department: Molecular Biotechnology

country: Belgium

institute: Ghent University

type:
Expression profiling by array
Methylation profiling by array

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


title: A comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants (Human1Mv1_C)

city: Toronto

first: Stephen

middle: W

last: Scherer

state: Ontario

address: 686 Bay Street

department: Genetics and Genomic Biology

institute: The Hospital for Sick Children

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: Systematic evaluation of eleven array platforms commonly used for CNV detection to address parameters of quality and CNV calling.

overall_design: 36 Samples

first: Dalila

last: Pinto

first: Jeffrey

middle: R

last: MacDonald


title: Human amnion and chondrosarcoma

status: Public on Jun 07 2011

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

country: Japan

institute: National Center for Child Health and Development

summary: Cellular differentiation and lineage commitment are considered to be robust and irreversible processes during development. Recent work has shown that mouse and human fibroblasts can be reprogrammed to a pluripotent state with a combination of four transcription factors. This raised the question of whether transcription factors could directly specify somatic cell fates in cells such as pancreatic β cells, contractile cardiomyocytes and neurons. We hypothesized that combinatorial expression of chondrocyte-specific transcription factors could directly convert human amnion cells into chondrosarcoma. Starting from a pool of candidate genes, we identified a combination of only five genes (5F pool), BCL6, T (also called BRACHYURY), c-MYC, MITF and BAF60C (also called SMARCD3) that rapidly and efficiently convert postnatal human amnion into chondrosarcoma. The cells generated expressed multiple cartilage-specific genes such as collagen type II α1, link protein-1 and aggrecan, and exhibited characteristics of cartilage both in vivo and in vitro.   Expression of the endogenous genes for T and MITF was initiated, implying that the cell conversion is due to not only the forced expression of the transgenes, but also the cellular reprogramming by the transgenes. The same set of genes converted human placental artery-derived endothelial (hPAE) cells and menstrual blood-derived cells into chondrosarcoma cells, implying that this conversion is independent of cell types. Direct conversion system from non-cartilage tissue to cartilaginous tissue contributes substantially to a major advance toward cartilage development, oncogenesis of chondrocytes, and cell-based therapy.

overall_design: We hypothesized that combinatorial expression of chondrocyte-specific transcription factors could directly convert human amnion cells into chondrosarcoma. Starting from a pool of candidate genes, we identified a combination of only five genes that rapidly efficiently convert postnatal human amnion into chondrosarcoma.

first: Ryuga

last: Ishii

first: Daisuke

last: Kami

first: Masashi

last: Toyoda

first: Hatsune

last: Makino

first: Toshiharu


title: Effect of Glis1 on human iPS cell generation

status: Public on Jun 10 2011

city: Kyoto

first: Shinya

last: Yamanaka

address: 53 Kawahara-machi, Shogoin, Sakyo-ku

institute: Center for iPS Cell Research and Applicaton (CiRA), Kyoto University

summary:
Induced pluripotent stem cells (iPSC) are generated from somatic cells by the transgene expression of three transcription factors Oct3/4, Sox2, and Klf4 (OSK), albeit at a low efficiency. The protooncogene c-Myc enhances the efficiency of iPSC generation by OSK, but it also increases the tumorigenicity of the resulting iPSC.
In the current study, we found the Gli-like transcription factor Glis1, when expressed together with OSK, to markedly enhance the generation of iPSC from both mouse and human fibroblasts. Mouse iPSC generated by OSK and Glis1 can form germline-competent chimeras. Glis1 is enriched in unfertilized oocytes and one cell-stage embryos. DNA microarray analyses revealed that Glis1 promotes multiple pro-reprogramming pathways, including Myc, Nanog, Lin28, Wnt, mesenchymal-epithelial transition (MET), and Esrrb. These results therefore demonstrated that oocyte transcription factor Glis1 effectively promote direct reprogramming during iPSC generation.

overall_design: Adult human fibroblasts were transduced with OSKM and OSK+Glis1 and were used for microarray analyses.

first: M

last: Maekawa

first: T

last: Nakamura

last: Nrita


title: Cancer-related epigenome changes associated with reprogramming to induced pluripotent stem cells (expression data)

summary: The ability to induce pluripotent stem cells from committed, somatic human cells provides tremendous potential for regenerative medicine. However, there is a defined neoplastic potential inherent to such reprogramming that must be understood and may provide a model for understanding key events in tumorigenesis. Using genome-wide assays, we identify cancer-related epigenetic abnormalities that arise early during reprogramming and persist in induced pluripotent stem cell (iPS) clones. These include hundreds of abnormal gene silencing events, patterns of aberrant responses to epigenetic-modifying drugs resembling those for cancer cells, and presence in iPS and partially reprogrammed cells of cancer-specific gene promoter DNA methylation alterations. Our findings suggest that by studying the process of induced reprogramming, we may gain significant insight into the origins of epigenetic gene silencing associated with human tumorigenesis, and add to means of assessing iPS for safety.

overall_design: Direct expression comparison of iPS lines, cultured stem cell lines and normal differentiated cells. Re-expression experiments with 5-aza-2′-deoxycytidine (AZA) and trichostatin A (TSA) to identify hypermethylated genes.

first: Joyce

last: Ohm

middle: B

last: Baylin


title: iPS cell generation


title: Human medulloblastoma samples

first: Marc

last: Remke

address: 555 University Ave. Rm 1504

department: Laboratory Medicine and Pathobiology

summary:
Purpose
Integrated genomics approaches have identified at least four distinct biological variants in medulloblastoma: WNT, SHH, group C, and group D. Non-WNT/Non-SHH tumors are associated with metastatic dissemination and an unfavorable prognosis. Additional markers may enhance outcome prediction in Non-WNT/Non-SHH medulloblastomas.

Experimental Design
We combined transcriptomic and DNA copy-number analyses for 64 primary medulloblastomas. Bioinformatic tools were applied to discover marker genes of molecular variants. Differentially expressed transcripts were evaluated for prognostic value in the screening cohort. Immunopositivity for FSTL5 was correlated with molecular and prognostic subgroups for 235 non-overlapping medulloblastoma samples on two independent tissue microarrays (TMA).

Results
Unsupervised clustering analyses of transcriptome profiles confirmed four distinct molecular variants. Stable subgroup separation was achieved using only the 300 most varying transcripts. Specific distributions of clinical and molecular characteristics were noted for each cluster. Distinct expression patterns of FSTL5 in each molecular subgroup were confirmed by quantitative real-time PCR. Immunopositivity of FSTL5 identified a large cohort of patients (84 of 235 patients; 36%) at high risk for relapse and death. Importantly, over 50% of Non-WNT/Non-SHH tumors displayed FSTL5 negativity, delineating a large patient cohort with an excellent prognosis who would be considered intermediate/high-risk based on current molecular subtyping.

Conclusions
Comprehensive analyses of transcriptomic and genetic alterations delineate four distinct variants of medulloblastoma. The addition of FSTL5 immunohistochemistry to existing molecular stratification schemes can effectively identify those Non-WNT/Non-SHH tumors with a poor outcome. Immunohistochemical staining for FSTL5 could be a high-quality and practical tool for stratification and prognostication in future clinical trials of medulloblastoma.

overall_design:
Whole-genome transcriptional profiling of human medulloblastomas. Subgrouping based on mRNA expression profiles.

Fresh frozen tumor material was collected during tumor resection. Dye-swap design used for expression profiling. Reference was a pool of normal cerebellum tissue from 24 donors. Gene expression profiles illustrate distinct expression pattern at diagnosis.

This submission represents the gene expression component of the study.

first: Thomas

last: Hielscher

first: Andrey

last: Korshunov

first: Paul

last: Northcott

first: Sebastian

last: Bender

first: Marcel

last: Kool

first: Frank

last: Westermann

first: Axel

last: Benner

first: Huriye

last: Cin

first: Marina

last: Ryzhova

first: Dominik

last: Sturm

first: Hendrik

last: Witt

first: Daniel

last: Haag

first: Grischa

last: Toedt

first: Andrea

last: Wittmann

first: Anna

last: Schöttler

first: Andre

middle: O

last: von Bueren

first: Stefan

last: Rutkowski

first: Wolfram

last: Scheurlen

first: Andreas

middle: E

last: Kulozik

first: Michael

middle: D

last: Taylor

first: Peter

last: Lichter

last: Pfister


title: Microarray analysis of CaSki cell line grown as spheroids and adherent conditions

status: Public on Jun 09 2011

city: Bangalore

first: Sudhir

last: Krishna

state: Karnataka

address: UAS-GKVK Campus, Bellary Road

country: India

institute: National Centre for Biological Sciences, TIFR

summary: Microarry based whole genome expression analysis was done for the more tumorigenic CaSki spheroids cultures and the less tumorigenic CaSki adherent cultures to identify signaling mechanisms that vary between the two populations. Subsequent to this, an independent array was done to characterize the differences in gene expression between the cancer stem cell-like Lin-CD66+ and the bulk Lin- CD66- cells isolated from primary human cervical carcinomas. The second array was custom-designed and had genes implicated in stemness, epithelial differentiation, signaling pathways implicated in stemness (Notch and Wnt) and cell cylce-regulation.

first: Jeevisha

last: Bajaj

first: Eric

last: Vivien


title: Identification of genes upregulated by methyl-CpG targeted transcriptional activation (MeTA) in 293T

status: Public on Jun 03 2011

city: Sendai

first: Shinichi

last: Fukushige

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

department: Department of Diabetes, Metabolism and Endocrinology

institute: Tohoku University Graduate School of Medicine

summary: The identification of genes transcriptionally silenced by DNA hypermethylation is important in understanding the molecular basis of epigenetically regulated biological processes such as X chromosome inactivation, genomic imprinting, and cancer development. Our previously developed methyl-CpG targeted transcriptional activation (MeTA) method reactivates epigenetically silenced genes by using a methyl-CpG binding domain from MBD2 with a transcriptional activation domain. We applied either MeTA or a conventional DNA demethylating agent, 5-aza-cytidine (Aza-CR), to a human embryonic kidney cell line 293T and analyzed gene expression profiles by microarray; 138 and 202 genes that are upregulated 5-fold or more were identified by MeTA and Aza-CR, respectively. The top ten upregulated genes detected by MeTA were further analyzed. We found associations between expressional restorations by MeTA, methylation status, and NFkB(AD)-MBD fusion protein bindings in CpG islands (CGIs) around the transcription start site of the genes. Importantly, MeTA can upregulate genes meeting the stringent criteria of CGIs defined by Takai and Jones at the promoter region at higher frequency; 109 of 138 (79.0%) genes in MeTA vs. 121 of 202 (59.9%) genes in Aza-CR. Interestingly, only 27 genes were upregulated by both methods; MeTA may identify methylated genes that show low levels of induction by the DNA demethylating agents; demethylating agents may also induce factors that help re-expression of genes that harbor less stringent or no CGIs. These results suggest that microarray coupled with MeTA (MeTA-array) is an efficient alternative way to identify transcriptionally silenced genes by DNA hypermethylation.

overall_design: 293T cells were transfected with pcDNA6/myc-His vector or pcDNA6-3xFLAG-NFkB (AD)-MBD and were harvested 48 h after transfection. In contrast, 293T cells were treated with 5-aza-cytidine (Aza-CR, 25 uM) or the same volume of PBS for 96 h and medium replaced every 24 h.

first: Yuko

last: Sato


title: Genomic Analysis of wig-1 Pathways

status: Public on Jun 06 2011

city: Carlsbad

first: Mahyar

last: Sabripour

address: 1896 Rutherford Ave.

institute: Isis Pharmaceuticals

summary: Analysis of wig-1 pathways via suppression of Wig-1 by antisense oligonucleotides

overall_design: Total RNA obtained from  mouse brain subjected to antisense oligonucleotide (ASO) treatement compared to PBS (control), and negative control ASO brain treatment.

first: Yalda

last: Sedaghat

first: Curt

last: Mazur

first: Gene

last: Hung

first: Brett

last: Monia


title: The transcription factor cyclic AMP–responsive element–binding protein H regulates triglyceride metabolism

status: Public on Jun 04 2011

city: Boston

first: Ann-Hwee

last: Lee

address: 651 Huntington Ave, FXB/205

institute: Harvard School of public health

summary: Here we report that the transcription factor cyclic AMP–responsive element–binding protein H (CREB-H, encoded by CREB3L3) is required for the maintenance of normal plasma triglyceride concentrations. CREB-H–deficient mice showed hypertriglyceridemia secondary to inefficient triglyceride clearance catalyzed by lipoprotein lipase (Lpl), partly due to defective expression of the Lpl coactivators Apoc2, Apoa4 and Apoa5 and concurrent augmentation of the Lpl inhibitor Apoc3. We identified multiple nonsynonymous mutations in CREB3L3 that produced hypomorphic or nonfunctional CREB-H protein in humans with extreme hypertriglyceridemia, implying a crucial role for CREB-H in human triglyceride metabolism.

overall_design: Total RNAs were isolated from the liver of three WT and three Creb3l3 deficient mice after a 24-h fasting. Littermates were used. Gene expression profiles were examined using Illumina WG-6 microarray chips.

first: Ann

first: Jung

first: Laurie

last: Glimcher

first: Stephen

last: Duncan


title: Expression data from mouse B16-F10 cells treated with heat shock (HS), Lipofectamine 2000 (LA), and benzyl alcohol (BA)

city: Gliwice

first: Katarzyna

middle: Marta

last: Lisowska

address: ul. Wybrzeże Armii Krajowej 15

department: Center for Translational Research  and Molecular Biology of Cancer

country: Poland

institute: MSC Memorial Cancer Center and Institute of Oncology, Gliwice Branch

summary: Three types of stimuli -- heat shock, Lipofectamine 2000 and benzyl alcohol -- induce activity of some stress genes (hsp) in mouse B16-F10 cells. Besides hsp genes induction, each stimulus causes gene expression changes of different sets of genes. We used microarrays to analyze global gene expression changes in mouse B16-F10 cells treated with elevated temperature (heat shock, HS), with Lipofectamine 2000 (LA) or with 40mM benzyl alcohol (BA).

overall_design: In order to study how lipofection may affect cellular homeostasis, we used Affymetrix microarrays to analyze the whole transcriptome of mouse B16-F10 cells treated with Lipofectamine 2000. To find out which genes are affected, we compared the cells treated with Lipofectamine (LA1, LA2, LA3), the cells treated with 40mM benzyl alcohol (BA1, BA2, BA3), heat-shocked cells (HS1, HS2, HS3) and control, untreated cells (C1-5). RNA was extracted from cells 30 min after treatment.


title: Notch signaling in CD66+ cells drives the progression of human cervical cancers

summary:
Microarry based whole genome expression analysis was done for the more tumorigenic CaSki spheroids cultures and the less tumorigenic CaSki adherent cultures to identify signaling mechanisms that vary between the two populations. Subsequent to this, an independent array was done to characterize the differences in gene expression between the Lin-CD66+ and the Lin- CD66- cells isolated from primary human cervical carcinomas. The second array was custom-designed and had genes implicated in stemness, epithelial differentiation, signaling pathways implicated in stemness (Notch and Wnt) and cell cylce-regulation.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series.


title: Probucol ameliorates renal and metabolic sequelae of primary CoQ deficiency in Pdss2 mutant mice

city: Philadelphia

first: Marni

middle: J

last: Falk

address: 3615 Civic Center Blvd

department: Pediatrics/ Human Genetics

institute: CHOP

summary: To discern whether the same transcriptional signature of mitochondrial dysfunction previously reported in B6.Alb/cre,Pdss2loxP/loxP liver-conditional knockout mice (Peng, Falk et al. PLoS Genetics, 2008 [PMID 18437205]) was present regardless of Pdss2 mutation type, as well as to assess whether pharmacologic therapies modulate expression of particular pathways, genome-wide transcriptional profiling was performed in liver from B6.Pdss2(kd/kd) missense mutant mice on standard chow or supplemented long-term with either probucol or CoQ10.

overall_design:
For analysis of lifelong probucol and CoQ10 supplementation effects in B6.Pdss2(kd/kd) missense mutant mice, total RNA was isolated from the livers of B6 mice and from Pdss2(kd/kd) missense mutant mice fed a normal diet, or a diet supplemented with Probucol or CoQ10. Total RNA was individually hybridized to 20 total Illumina Mouse WG-6 v2.0 arrays, which included 5 biological replicates from each of the 4 groupings: untreated B6.Pdss2(kd/kd) missense mutant mice, probucol-treated B6.Pdss2(kd/kd) mice, CoQ10-treated B6.Pdss2(kd/kd) mice, and untreated B6 wild-type mice.
Total RNA

first: Zhe

last: Zhang


title: Microarray analysis of heart gene expression in wild type and JMJD2A heart specific transgenic mice after sham and thoracic aortic constriction surgery

status: Public on Jun 02 2011

city: Dallas

first: Qingjun

address: 5323 Harry Hines Blvd,NB11.110

institute: UT Southwestern

summary: Cardiac hypertrophy and failure are accompanied by a reprogramming of gene expression that involves transcription factors and chromatin remodeling enzymes.  Little is known about the role of histone methylation and demethylation in this process. To understand the role of JMJD2A, a trimethyl demethylase for histone 3 lysine 9 and 36, in cardiac hypertrophy, we generated heart specific JMJD2A deletion (JMJD2A hKO) and overexpression (JMJD2A-Tg) mouse lines. JMJD2A hKO and JMJD2A-Tg mice are viable and have no overt baseline phenotype. However, they have altered responses to cardiac stresses. While inactivation of JMJD2A in hKO mice resulted in an attenuated hypertrophic response to transverse aortic constriction (TAC)-induced pressure overload compared to that of control littermates, JMJD2A-Tg mice have exacerbated cardiac hypertrophy after TAC.  We identified four-and-a-half LIM domains 1 (FHL1) as a novel target of JMJD2A.  JMJD2A binds to the FHL1 promoter in response to TAC and upregulates the expression of FHL1. Binding of JMJD2A to the FHL1 promoter is associated with downregulation of trimethylated H3K9.  Upregulation of FHL1 by JMJD2A is mediated through SRF and myocardin, and requires its demethylase activity. The expression of JMJD2A is upregulated in human hypertrophic cardiomyopathy patients.  Our studies reveal that JMJD2A promotes cardiac hypertrophy by synergistically upregulating SRF/myocardin-targeted genes and suggest a novel mechanism of reprogramming of gene expression involved in cardiac hypertrophy.

overall_design: Six to eight years old wildtype and JMJD2A heart specific transgnic mice were undergone either sham or TAC surgery. After 3 weeks, mice were sarcirificed to harvest heart. RNA was extracted from heart samples and treated with DNase, followed by biotin-labeling and microarray hybridization.

first: Qing-jun

first: Zhi-ping

last: Liu


title: The transcriptional repressor Blimp1/Prdm1 regulates post-natal reprogramming of intestinal enterocytes

city: Oxford

first: Arne

middle: Wyndham

last: Mould

state: Oxfordshire

address: Warneford Hospital

department: Psychiatry

institute: Oxford University

summary: Expression profiling of Prdm1 mutant E18.5 small intestine was performed using Illumina whole genome V2 arrays. The hypothesis tested in the present study was that Blimp1 regulates the transcription of key genes involved in enterocyte differentiation and survival. Results identify substantial and premature activation of key components of the adult enterocyte biochemical signature.

overall_design: Villin-Cre and Prdm1BEH/+ animals were intercrossed to generate heterozygous Villin-Cre, Prdm1BEH males that were then mated with homozygous Prdm1 CA/CA females carrying the R26R allele to generate Prdm1+/+ (Prdm1CA/+) or Prdm1-/- (Villin-Cre, Prdm1CA/BEH) offspring. Total RNA obtained from 11 Prdm1+/+ and 10 Prdm1-/- E18.5 small intestine samples was hybridized to Illumina WG6_V2 beadchips.

first: James

last: Harper

first: Robert

last: Andrews

first: Elizabeth

last: Bikoff

last: Robertson


title: Expression data from Pou4f3-Rb1 cKO and control inner ear

status: Public on Jun 01 2011

first: Zheng-Yi

last: Chen

address: 243 Charles Street

department: Otolaryngology

institute: MEEI

summary: Retinoblastoma gene (Rb1) is required for proper cell cycle exit in the developing mouse inner ear and its deletion in the embryo leads to proliferation of sensory progenitor cells that differentiate into hair cells and supporting cells. In the Pou4f3-Cre:Rb1 flox/flox (Rb1 cKO) inner ear, utricular hair cells differentiate and survive into adulthood whereas differentiation and survival of cochlear hair cells are impaired. To comprehensively survey the pRb pathway in the mammalian inner ear, we performed microarray analysis of Rb1 cKO cochlea and utricle.

overall_design: P6 or 2-month control and Rb1 cKO littermates were euthanized and the inner ear tissues were dissected. Total RNA was extracted from the pooled samples. Technical duplicates of the pooled RNA were used for microarray.

first: Mingqian

last: Huang


title: Functional genomics of human bronchial epithelial cells interacting with conidiospores of Aspergillus fumigatus

city: Vancouver

first: Scott

last: Tebbutt

state: BC

address: St. Paul's Hospital - Rm 166 - 1081 Burrard St.

institute: UBC - iCAPTURE Centre

summary: The cells of the airway epithelium play critical roles in host defense to inhaled irritants, and in asthma pathogenesis. These cells are constantly exposed to conidiospores of the ubiquitous mould Aspergillus fumigatus, which are small enough to reach the alveoli. This exposure is asymptomatic in most individuals but can be associated with a spectrum of diseases ranging from asthma and allergic bronchopulmonary aspergillosis to aspergilloma and invasive aspergillosis. Airway epithelial cells have been shown to internalize A. fumigatus conidiospores in vitro, but the implications of this process for pathogenesis remain unclear. We have developed a cell culture model for this interaction using the 16HBE cell line and a transgenic A. fumigatus strain expressing green fluorescent protein. Comparing the transcriptional profiles of control cells and cells exposed to A. fumigatus conidiospores using Agilent Whole Human Genome microarrays revealed significant changes in gene expression in response to the presence of conidiospores. The identification of biologically relevant responses validates this methodology, and motivates further work to characterize the interactions between A. fumigatus conidiospores and primary airway epithelial cells of normal and asthmatic origins.

overall_design: Gene expression levels were investigated in 16HBE cells incubated in the presence or absence of A. fumigatus conidiospores for 6 hours. Four independent cell samples were analysed for each of these conditions, using Agilent Whole Human Genome microarrays, with a one-colour experiemntal design.

first: Pol

last: Gomez

first: Tillie

middle: L

last: Hackett

first: Margo

middle: M

last: Moore

first: Darryl

middle: A

last: Knight


title: A2780 and OVCAR-3 Cells:Control vs. LS-98 treated

city: Shanghai

first: Tau

address: Rm 429, No. 41 Building, 320 Yueyang Road, Shanghai, China (200031)

country: China

institute: Institute for Nutritional Sciences (INS)

summary: Transcriptional profiling of human ovarian cancer cells comparing control vehicle-treated A2780 and OVCAR-3 (Human ovarian cancer cell lines) cells with A2780 and OVCAR-3 cells treated with 5μM LS-98 for 24 hours.Goal was to determine the effects of LS-98 compound  on the global A2780 and OVCAR-3 cells gene expression.

overall_design: One-condition experiment, control vehicle-treated A2780 and OVCAR-3  vs. LS098 treated-A2780 and OVCAR-3 cells. Biological replicates: 2 replicates.

first: Tao


title: Transcriptomic analysis of interactions between Aspergillus fumigatus conidiospores and human bronchial epithelial cells

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

sample_organism:
Homo sapiens
Aspergillus fumigatus

platform_organism:
Homo sapiens
Aspergillus fumigatus

overall_design: Refer to individual Series


title: Gene induction by Dex, IL-9 and CCL-1 in BW5147 mouse T cell lymphoma

status: Public on May 25 2011

city: Brussels

first: Amel

last: Tounsi

address: 74 avenue hippocrate

institute: LICR

summary:
The aim of this work was to determine the genes and mechanisms involved in IL-9- and CCL1-mediated protection against glucocorticoid-induced apoptosis. We made the hypothesis that the expression of the really critical mediators could be regulated in a reciprocal way by Dex on the one hand and anti-apoptotic cytokines such as IL-9 and CCL1 on the other hand.Therefore, we performed a comprehensive study of the genes expressed by BW5147 cells stimulated with or without Dex, IL-9 and CCL1, taking advantage of the Affymetrix microarray technology.

Keywords: cytokine and dexamethasone stimulation

overall_design: One million BW5147 cells were stimulated with 100 ng/ml of dexamethasone and/or with 100 U/ml of IL-9 or CCL1 for eight hours. RNA was then extracted for  hybridization on Affymetrix microarrays. This experiment was performed in duplicates .

first: Laure

last: Dumoutier

first: Jean-Christophe

last: Renauld


title: Mechanistic Rationale for Inhibition of Poly(ADP-Ribose) Polymerase in ETS Gene Fusion Positive Prostate Cancer

status: Public on May 18 2011

city: Ann Arbor

first: Christopher

last: Maher

address: 1500 E. Medical Center Drive

institute: Michigan Center for Translational Pathology

summary: To identify commonly altered genes between ERG, PARP1, and DNA-PKcs.

overall_design: Two-condition experiment: Each siRNA, targeting either DNA-PKcs or PARP1, was compared to a control RNA.

first: Christophe


title: Nickel Chloride (NiCl2) effect on human T cells from whole blood

first: Rumiko

last: SAITO

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

department: Department of Dermatology

summary: Analysis of anti-CD3/anti-CD28 stimulated T cells treated with or without nickel chloride. Nickel is the most important contact allergen in the general population of the industrialized world. Results provide insight into the biological effects of nickel on human CD3+ T cells.

overall_design: We obtained mRNA of purified human CD3+ T cells from 3 different donors that were treated with or without 1000 μM nickel chloride for 1 h and then stimulated with anti-CD3/anti-CD28 for 6 h.

last: Saito

first: Satoshi

last: Hirakawa

first: Hiroshi

last: Ohara

first: Makoto

last: Yasuda

first: Tomomi

last: Yamazaki

first: Shigeaki

last: Nishii

first: Setsuya

last: Aiba


title: Deficiency in the multicopy Sycp3-like X-linked genes Slx and Slxl1 causes major defects in spermatid differentiation

status: Public on May 11 2011

city: Canterbury

first: Peter

middle: James

last: Ellis

state: Kent

address: Stacey Building

department: School of Biosciences

institute: University of Kent

summary: The gene Sly is present in multiple copies on the mouse Y chromosome and encodes a protein that is required for the epigenetic regulation of postmeiotic sex chromosome expression. The X chromosome carries two multicopy genes related to Sly: Slx and Slxl1. Here we investigate the role of Slx/Slxl1 using transgenically-delivered small interfering RNAs to disrupt their function. We show that Slx and Slxl1 are important for normal sperm differentiation and male fertility. Slx/Slxl1 deficiency leads to delay in spermatid elongation and sperm release. A high proportion of delayed spermatids are eliminated via apoptosis, with a consequent reduced sperm count. The remaining spermatozoa are abnormal with impaired motility and fertilizing abilities. Microarray analyses reveal that Slx/Slxl1 deficiency affects the metabolic processes occurring in the spermatid cytoplasm but does not lead to a global perturbation of sex chromosome expression; this is in contrast with the effect of Sly deficiency which leads to an up-regulation of X and Y chromosome genes.

overall_design: Total RNA isolated from separated round spermatids of young adult males (8 weeks postpartum) with shSLX or shSLY targeted knockdown, compared to age- and strain-matched controls.

first: Julie

last: Cocquet

first: Yasuhiro

last: Yamauchi

first: Jonathan

last: Riel

first: Thomas

last: Karacs

first: Aine

last: Rattigan

first: Obah

last: Ojarikre

first: Nabeel

last: Affara

first: Monika

last: Ward

first: Paul

middle: S

last: Burgoyne


title: The Multicopy Gene Sly Represses the Sex Chromosomes in the Male Mouse Germline after Meiosis part 2

summary: Studies of mice with Y chromosome long arm deficiencies suggest that the male-specific region (MSYq) encodes information required for sperm differentiation and postmeiotic sex chromatin repression (PSCR). Several genes have been identified on MSYq, but because they are present in more than 40 copies each, their functions cannot be investigated using traditional gene targeting. Here, we generate transgenic mice producing small interfering RNAs that specifically target the transcripts of the MSYq-encoded multicopy gene Sly (Sycp3-like Y-linked). Microarray analyses performed on these Sly-deficient males and on MSYq-deficient males show a remarkable up-regulation of sex chromosome genes in spermatids.

overall_design: Total RNA isolated from testis of young adult males (4-8 weeks postpartum) with Yq deletions or shSLY targeted knockdown, compared to age- and strain-matched controls.

first: Shantha

last: Mahadevaiah


title: Expression data from P4 and P10 mouse optic nerves

status: Public on May 16 2011

city: Montreal

first: Hana

middle: C.

last: Friedman

address: 687 Pine Ave. West

institute: McGill University

summary: Optic nerves are an accessible part of the CNS, providing a source of glia without the presence of neuronal cell bodies.  Therefore, an analysis was carried out of gene expression in optic nerves at P4, before myelination begins and at P10, when myelination is very actively proceeding.  The goal was to obtain a profile of the changing gene expression that accompanies this transition from unmyelinated CNS nerve to myelinated nerve.

overall_design: Two microarray experiments were combined here.  In the first, RNA was prepared from the optic nerves of 75 P4 C57BL/6J mice and 70 P10 C57BL/6J mice. In the second experiment, RNA was prepared from the optic nerves of 55 P4 C57BL/6J mice and two groups of 50 P10 C57Bl/6J mice. In total, there are 2 P4 RNA samples and 3 P10 RNA samples being hybridized to Affymetrix GeneChip 430A for Mouse Expression.

middle: C

first: Alan

last: Peterson


title: Cell Type-Specific DNA Methylation at Intragenic CpG Islands in the Immune System (gene expression data)

status: Public on May 23 2011

city: Edinburgh

first: Adrian

last: Bird

address: Mayfield Road

department: WTCCB

institute: The University of Edinburgh

summary: Human and mouse genomes contain a similar number of CpG islands (CGIs), which are discrete CpG-rich DNA sequences associated with transcription start sites. In both species, about 50% of all CGIs are remote from annotated promoters, but nevertheless often have promoter-like features. To document the role of CGI methylation in cell differentiation, we analysed DNA methylation at a comprehensive CGI set in cells of the mouse hematopoietic lineage. Using a method that potentially detects ~33% of genomic CpGs in the methylated state (>7 million) we found that large differences in gene expression were accompanied by surprisingly few DNA methylation changes. There were, however, many DNA methylation differences between hematopoietic cells and a distantly related tissue, brain. Altered DNA methylation occurred predominantly at CGIs within gene bodies, which have the properties of cell type-restricted promoters, but infrequently at annotated gene promoters or CGI flanking sequences. Elevated intragenic CGI methylation correlated with silencing of the associated gene. Differentially methylated intragenic CGIs tended to lack H3K4me3 and associate with a transcriptionally repressive environment regardless of methylation state. Our results indicate that DNA methylation changes play a relatively minor role in the late stages of differentiation, but point to a distinct role for intragenic CGIs.

overall_design: Mouse immune cells (dendritic cells, B cells, CD4 T cells, Th1 and Th2 cells) were isolated and DNA methylation and gene expression profiled. Methylation and expression patterns were compared to those in brain. For gene expression analysis three biological replicates were used for each cell type.

first: Aimée

last: Deaton

first: Shaun

last: Webb

first: Alastair

last: Kerr

first: Robert

last: Illingworth

first: Jacky

last: Guy

last: Andrews


title: The Multicopy Gene Sly Represses the Sex Chromosomes in the Male Mouse Germline after Meiosis

first: Peter

last: Ellis

overall_design: Two sets of samples were examined: (1) Total RNA isolated from separated round spermatids of young adult males (8 weeks postpartum) with Yq deletions or shSLY targeted knockdown, compared to age- and strain-matched controls. (2) Total RNA isolated from whole testis of juvenile males (17 days post partum) with shSLY targeted knockdown, compared to age- and strain-matched controls.

first: Julie

last: Cocquet

first: Yasuhiro

last: Yamauchi

middle: K


title: Systems biology approach to identify transcriptional reprogramming and microRNA targets during the progression of Polycystic Kidney Disease

status: Public on Apr 30 2011

first: Priyanka

last: Pandey

address: Children's Hospital Boston, 300 Longwood avenue

department: Medicine/Nephrology

institute: Children's Hospital Boston

summary: Autosomal dominant polycystic kidney disease (ADPKD) is characterized by cyst formation throughout the kidney parenchyma. It is caused by mutations in either of two genes, PKD1 and PKD2. Mice that lack functional Pkd1 (Pkd1null/null), develop rapidly progressive cystic disease during embryogenesis, and serve as a model to study human ADPKD.  We examined the molecular pathways that modulate renal cyst growth in the Pkd1null/null model by performing global gene-expression proﬁling in embryonic kidneys at day 14 and 17. Gene Ontology and gene set enrichment analysis were used to identify overrepresented signaling pathways in Pkd1null/null kidneys. We found dysregulation of developmental, metabolic, and signaling pathways (e.g. Wnt, calcium, TGF-b and MAPK) in Pkd1null/null kidneys.

overall_design: Total RNA were obtained from kidneys of wild-type and Pkd1null/null animals at embryonic ages 14.5 and 17.5.

first: Jordan

last: Kreidberg


title: Coxsackievirus B3 (CVB3) infection of AJ, B10.A, CSS3 and B6.chr3AJ (heart tissue day 4)

status: Public on May 01 2011

first: Sean

last: Wiltshire

address: 3649 Sir william Osler, Rm 356

department: Human Genetics

summary: The pathogenesis of viral myocarditis is a multifactorial process involving host genetics, viral genetics and the environment in which they interact. Here, we used a model of infection with Coxsackievirus B3 to characterize the contribution of host genetics to viral myocarditis. We determined heart CVB3 load in mice from a classical intercross between progenitors A/J (H2a) and  B10.A-H2a (B10.A) of different genetic backgrounds but with a common H2 haplotype. Here we compare whole genome expression patterns in infected and uninfected A/J and B10.A mice in order to determine which gene expression programs are common or distinct to each strain.

overall_design: Total RNA obtained from hearts of 3 AJ, 3 B10.A(H2a), 3 CSS3 and 3 B6.chr3AJ that were infected or uninfected with CVB3(CG) at 400pfu/g and collected at day 4 post infection.

first: Silvia

last: Vidal


title: Glucocorticoid receptor (GR) target genes in C2C12 myotubes

status: Public on Apr 25 2011

city: Berkeley

first: Jen-Chywan

last: Wang

state: CA

address: 315 Morgan Hall, UC Berkeley

department: Nutritional Sciences & Toxicology

institute: UC Berkeley

summary: Analysis of C2C12 myotubes treated with dexamethasone (Dex) for 6 or 24 hours.  Dex is a synthetic glucorticoid receptor agonist. Results provide insight to the effect of glucocorticoids on myotubes.

overall_design: C2C12 myotubes  were cultured in DMEM supplemented with 2% horse serum, and treated with 1 uΜ Dex or an equal volume (0.01% v/v of media) of vehicle control ethanol for 6 or 24 hours.  Total cellular RNA was isolated utilizing the NucleoSpin RNA II kit (Macherey-Nagel).  RNA isolates were first quantified by standard spectrophotometry, and then qualitatively evaluated by capillary electrophoresis employing the Bio-Rad Experion system per manufacturer’s instruction.  The final labeled cRNA samples were hybridized overnight to Illumina mouseWG-6 BeadChip arrays, which was performed at UCSF Genomic Core.   All treatments were done in triplicates and the same batch of microarrays were used for all treatments.  The Illumina expression arrays were pre-processed using lumi package.  The differential expression analysis was performed using the Limma package.


title: Human skin fibroblast mitochondrial depletion, 0.5 Gy alpha-particle

status: Public on Apr 04 2011

city: New York

first: Shanaz

middle: Adi

last: Ghandhi

state: NY

address: 630, W 168th street

department: Center for Radiological Research

institute: Columbia University Medical Center

summary: Mitochondrial DNA depleted (ρ(0)) human skin fibroblasts (HSF) with suppressed oxidative phosphorylation were characterized by significant changes in the expression of 2100 nuclear genes, encoding numerous protein classes, in NF-κB and STAT3 signaling pathways, and by decreased activity of mitochondrial death pathway, compared to the parental ρ(+) HSF. In contrast, the extrinsic TRAIL/TRAIL-Receptor mediated death pathway remained highly active, and exogenous TRAIL in a combination with cycloheximide (CHX) induced higher levels of apoptosis in ρ(0) cells compared to ρ(+) HSF. Global gene expression analysis using microarray and qRT-PCR demonstrated that mRNA expression levels of many growth factors and their adaptor proteins (FGF13, HGF, IGFBP4, IGFBP6, and IGFL2), cytokines (IL6, ΙL17Β, ΙL18, ΙL19, and ΙL28Β) and cytokine receptors (IL1R1, IL21R, and IL31RA) were substantially decreased after mitochondrial DNA depletion. Some of these genes were targets of NF-κB and STAT3, and their protein products could regulate the STAT3 signaling pathway. Alpha-irradiation further induced expression of several NF-κB/STAT3 target genes, including IL1A, IL1B, IL6, PTGS2/COX2 and MMP12, in ρ(+) HSF, but this response was substantially decreased in ρ(0) HSF. Suppression of the IKK-NF-κB pathway by the small molecular inhibitor BMS-345541 and of the JAK2-STAT3 pathway by AG490 dramatically increased TRAIL-induced apoptosis in the control and irradiated ρ(+) HSF. Inhibitory antibodies against IL6, the main activator of JAK2-STAT3 pathway, added into the cell media, also increased TRAIL-induced apoptosis in HSF, especially after alpha-irradiation. Collectively, our results indicated that NF-κB activation was partially lost in ρ(0) HSF resulting in downregulation of the basal or radiation-induced expression of numerous NF-κB targets, further suppressing IL6-JAK2-STAT3 that in concert with NF-κB regulated protection against TRAIL-induced apoptosis.

overall_design: There are 12 total samples, 3 biological replicates each of HSF rho+ and rho0 cells that were not irradiated (control=C) or irradiated (alpha=A). Cells were harvested at 4 hours after treatment.

first: Sally

last: Amundson


title: DNA Methylation Dynamics in Human Induced Pluripotent Stem Cells over Time (Agilent)

status: Public on Apr 14 2011

city: Setagaya-ku

first: Akihiro

last: Umezawa

institute: National Center for Child Health and Development

summary: We examined genome-wide gene expression with human iPSC lines derived from different cell types, and human ESC lines using Agilent Whole Human Genome Microarray chips G4112F.

overall_design: Total RNA from 16 samples.

first: Koichiro

last: Nishino

first: Masashi

last: Toyoda

first: Mayu

last: Yamazaki-Inoue

first: Yoshihiro

last: Fukawatase

first: Emi

last: Chikazawa

first: Hironari

last: Sakaguchi

first: Hidenori

last: Akutsu


title: Seminiferous tubule degeneration and infertility in mice with sustained activation of WNT/CTNNB1 signaling in sertoli cells

status: Public on Apr 05 2011

city: Saint-Hyacinthe

first: Derek

last: Boerboom

state: QC

address: 3200 Sicotte

department: Département de biomédecine Vétérinaire

institute: Université de Montréal, Faculty of veterinary medicine

summary: To elucidate the role(s) of WNT/CTNNB1 signaling in the testis, transgenic Ctnnb1 tm1Mmt/+;Amhr2 tm3(cre)Bhr/+ mice were generated to obtain sustained activation of the WNT/CTNNB1 pathway in Sertoli cells. Male Ctnnb1 tm1Mmt/+;Amhr2 tm3(cre)Bhr/+ mice were sterile because of testicular atrophy starting at 5 wk of age, associated with degeneration of seminiferous tubules and the progressive loss of germ cells. Sustained WNT/CTNNB1 pathway activation was obtained in Ctnnb1 tm1Mmt/+;Amhr2 tm3(cre)Bhr/+ Sertoli cells. Sertoli cells often exhibited morphological characteristics suggestive of incomplete differentiation that appeared in a manner coincident with germ cell loss, accompanied by an increase in the expression of the immature Sertoli cell marker AMH. Microarray analyses performed on cultured Sertoli cells showed that CTNNB1 induces the expression of genes associated with the female sex determination pathway as well as cell-cycle associated genes . Together, these data suggest that the WNT/CTNNB1 pathway regulates Sertoli cell functions critical to their capacity to support spermatogenesis and to proliferate in the postnatal testis.

overall_design: Sertoli cells were obtained from 3wks-old Ctnnb1(tm1Mmt/tm1Mmt) mice. Cells were infected with adenoviruses to express eGFP or Cre in serum-free medium, and subsequently harvested for RNA extraction. Preliminary experiments demonstrated that an infection efficiency of nearly 100% could be obtained at an MOI of 50 (as determined by analysis of fluorescent signal in Ad-eGFP-infected cells) and that the Ad-Cre virus produced complete recombination of the floxed Ctnnb1 allele after 12 hours. Microaaray analyses were done using triplicate RNA samples from each adenoviral treatment using MouseRef-6 v.2.0 expression BeadChips technology (Illumina, San Diego, CA).

first: A

last: Boyer

first: J

middle: R

last: Yeh

first: X

last: Zhang

first: M

last: Paquet

last: Gaudin

last: Nagano

first: D


title: A comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants

status: Public on Jun 30 2011

city: Toronto

first: Stephen

middle: W

last: Scherer

address: 686 Bay Street

institute: The Hospital for Sick Children

overall_design: Six HapMap samples and 13 genotyping array platform: comparison of multiple platforms, run at multiple sites, analysed with multiple algorithms to assess and compare the performance of each