title: The affect of specific ablation of Runx3 from Esam splenic dendritic cells

city: Rehovot

first: Yoram

last: Groner

state: istael

department: Molecular genetics

country: Israel

institute: Weizmann institute of science

summary: Esam/CD4+ dendritic cells are part of the innate immunity essential for priming and activating of CD4+ T cells

overall_design: To identify Runx3 responsive genes Esam dendritic cells were freshly sorted from macs enriched splenic DCs taken from 6 weeks old mice. Four samples from four mice were sorted and analyzed where in each littermates pair consisted of a control and Runx3 conditional KO. Mice lacking Runx3 specifically in the DC compartment were produced by crossing Runx3fl/fl mice onto CD11c-Cre mice. This mating scheme generated Runx3fl/fl/CD11c:Cre (CD11c-DC-Runx3Δ) mice.

first: Joseph

last: Dicken

first: Dena

last: Leshkowitz


title: Time course gene expression profiling of mouse mammary gland TEB and duct cells throughout branching morphogenesis

status: Public on Jul 07 2014

city: Irvine

first: Michael

middle: L

last: Salmans

state: CA

address: 250 Sprague Hall

country: USA

institute: University of California Irvine

summary:
Branching morphogenesis of the mammary gland is driven by the highly motile terminal end bud (TEB) throughout pubertal development. The stem cell enriched, proliferative TEB branches as it invades the mammary fat pad to create a complex network of ducts. The gene expression programs specific to the TEB and the differentiated duct are poorly understood. We conducted a time course analysis of gene expression in the TEB and duct throughout branching morphogenesis. Additionally, we determined the gene regulatory networks coordinated by the Co-factor of LIM domains (CLIM/LDB) transcriptional regulators and determined an essential function for CLIMs in branching morphogenesis by maintaining basal mammary epithelial stem cells and promoting cell proliferation.
We used laser capture microdissection to isolate TEB and duct cells throughout branching morphogenesis. We then profiled gene expression in these cells to determine gene regulatory networks involved in branching morphogenesis, and specifically those regulated by CLIM transcriptional regulators.

overall_design: Mouse mammary glands from 4, 6, 8, and 10 week old mice (early puberty through early adulthood) were used for laser capture microdissection of TEB and duct cells from WT and K14-DN-Clim transgenic mice. RNA was isolated (Qiagen) and hybridized to Affymetrix MouseGene 1.0 ST arrays. In addition, basal (CD29HiCD24+Lin-) and Luminal (CD29LoCD24+Lin-) cells were sorted and RNA collected for hybridization to Affymetrix MouseGene 1.0ST arrays.

first: Bogi

last: Andersen


title: Runx3 function in CD4+ splenic dendritic cells

status: Public on Jun 22 2014

summary: CD4+ dendritic cells are part of the innate immunity essential for priming and activating of CD4+ T cells

overall_design: To identify Runx3 responsive genes CD4+ dendritic cells were sorted from freshly isolated macs enriched splenic DCs taken from 6 weeks old mice. Six samples from six mice were sorted and analyzed where in each littermates pair consisted of a  control and Runx3 KO.


title: Expression data of wild type and C-DGCR8 KO cones at different timepoints [array]

status: Public on Jun 20 2014

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

summary: We have analyzed gene expression in cone photoreceptors isolated from wild type and C-DGCR8 (DiGeorge Syndrome Critical Region Gene 8) KO mice at five different time points to get a mechanistic inside into the altered molecular pathways after microRNAs depletion.

overall_design: Cones were isolated by FACS from wild type and C-DGCR8 KO mice expressing Cre recombinase postnatally specifically in cones (D4-Cre) and bearing conditional null Dgcr8 allele. Experiments were performed in duplicates from different time points (P30, P40, P50, P60, and P90). Total RNA was extracted and hybridization on Affymetrix array was performed.

first: Jacek

last: Krol

first: Volker

last: Busskamp

first: Botond

last: Roska

first: Witold

last: Filipowicz


title: Transcript profile comparison of Zbtb20-sufficient and Zbtb20-deficient polyclonal bone marrow plasma cells

status: Public on Jun 19 2014

city: Saint Louis

first: Yinan

last: Wang

state: Missouri

address: 660 South Euclid Avenue

department: Immunology and Pathology

institute: Washington University in St. Louis

summary:
ZBTB20 is an adjuvant-specific factor for long-term antibody responses. This factor is critical for maintaining long-lived plasma cells in alum-adjuvanted antibody responses but is dispensable for TLR ligand-adjuvanted responses.
To identify the functions of ZBTB20 in long-lived plasma cells, we performed microarray analysis on Zbtb20-sufficient and Zbtb20-deficient polyclonal bone marrow plasma cells under the assumption that ZBTB20 regulates relevant targets in all long-lived plasma cells, irrespective of their mode of formation.

overall_design: Chimeras were generated using Zbtb20-sufficient (WT) or Zbtb20-deficient (TRAP) E14.5 fetal livers. 3-4 months after reconstitution, donor bone marrow B220low/-CD138+ cells (4 replicates per genotype) were purified via FACS for microarray. In total, 8 samples, 4 for each genotype, were included in this study.

first: Deepta

last: Bhattacharya


title: Expression profiling of Aldh1l1-precursors in the developing spinal cord reveals glial lineage-specific genes and direct Sox9-Nfe2l1 interactions

city: San Francisco

first: David

last: Rowitch

address: 35 Medical Center Way, RMB 932D

department: Institute for Regenerative Medicine

institute: University of California-San Francisco

summary: Developmental regulation of gliogenesis in the mammalian CNS is incompletely understood, in part due to a limited repertoire of lineage-specific genes. We used Aldh1l1-GFP as a marker for gliogenic radial glia and later-stage precursors of developing astrocytes and performed gene expression profiling of these cells. We then used this dataset to identify candidate transcription factors that may serve as glial markers or regulators of glial fate. Our analysis generated a database of developmental stage-related markers of Aldh1l1+ cells between murine embryonic day 13.5-18.5. Using these data we identify the bZIP transcription factor Nfe2l1 and demonstrate that it promotes glial fate under direct Sox9 regulatory control. Thus, this dataset represents a resource for identifying novel regulators of glial development.

overall_design: 18 total samples consisting of three biological replicates each of flow sorted embryonic spinal cord Aldh1l1-GFP positive cells and whole cord,  spanning the radial glial to astrocyte transition

first: A

middle: V

last: Molofsky

first: M

middle: C

last: Oldham

first: D

middle: H


title: Epigenome Wide Association Study unveils differential methylation of Leukocyte cell adhesion molecules in neonatal sepsis

city: Pondicherry

first: Benet

middle: Bosco

last: Dhas

state: Pondicherry

address: Danvantri Nagar

department: Paediatrics

country: India

institute: Jawaharlal Insitute of Postgraduate Medical Education and Research

type: Methylation profiling by genome tiling array

summary: DNA methylation is the current strategy in the field of biomarker discovery due to its prognostic efficiency. Its role in prognosis and early diagnosis has been recognized in various types of cancer. Sepsis still remains one of the major causes of neonatal mortality due to the lack of sensitive diagnostic and prognostic biomarkers. Delay in sepsis diagnosis leads to treatment difficulties and poor outcomes. In this study, we have done an epigenome wide search to identify potential markers for prognosis of neonatal sepsis which may improve the treatment strategies. Illumina 450K methylation microarray revealed that the genes involved in transendothelial leukocyte migration were differentially methylated in septic newborns compared to non-septic newborns, especially the Protocadherin Beta group. Genes like ITGB2-AS1, CCS were found to be differentially methylated significantly, which gives the hope of developing novel, potential epigenetic markers for neonatal sepsis. From this study, we conclude that DNA methylation might play crucial functions in the pathophysiology of neonatal sepsis which was obvious from the difference in methylation level among septic and non-septic babies. In future, the potentiality of these epigenetic biomarkers can be studied in large scale with appropriate techniques which will give further in depth knowledge in this context.

overall_design: DNA methylation analysis of three septic newborns and three non-septic newborns were performed with  Illumina Infinium HumanMethylation450 BeadChip. Peripheral venous blood sample was collected from the babies during the third day of birth while taking blood for routine investigations. Non-septic babies are babies admitted to NICU and sampled for other minor ailments. Genomic DNA was extracted using QIAmp DNA Blood Mini kit (Qiagen, Hilden, Germany) and bisulfite treated using EZ DNA methylation kit (Zymoresearch, USA).

middle: B

first: Hiasindh

last: Ashmi

first: Vishnu

last: Bhat

first: S

last: Parija


title: Cyclosporine in patients with atopic dermatitis modulates activated inflammatory pathways and reverses epidermal pathology

status: Public on Jun 17 2014

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

summary: After 2 and 12 weeks of treatment, we observed significant reductions of 51% and 72%, respectively, in SCORAD scores. Clinical improvements were associated with significant gene expression changes in lesional but also nonlesional skin, particularly reductions in levels of TH2-, TH22-, and some TH17-related molecules (ie, IL-13, IL-22, CCL17, S100As, and elafin/peptidase inhibitor 3), and modulation of epidermal hyperplasia and differentiation measures.

overall_design: CsA's effects on AD skin pathology were evaluated by using gene expression and immunohistochemistry studies in baseline, week 2, and week 12 lesional and nonlesional biopsy specimens from 19 patients treated with 5 mg/kg/d CsA for 12 weeks.

first: Emma

last: Guttman-Yassky


title: Optic nerve crush induces spatial and temporal gene expression patterns in retina of BALB/cJ mice

city: Fort Worth

first: Tasneem

middle: Putliwala

last: Sharma

state: Texas

address: 3500 Camp Bowie Blvd

department: Cell Biology and Anatomy- Visual Sciences

institute: UNTHSC

summary:
Central nervous system (CNS) trauma and neurodegenerative disorders trigger a cascade of cellular and molecular events resulting in neuronal apoptosis and regenerative failure. The pathogenic mechanisms and gene expression changes associated with these detrimental events can be effectively studied using a rodent optic nerve crush (ONC) model. The purpose of this study was to use a mouse ONC model to: (a) evaluate changes in retina gene expression, (b) identify neurodegenerative pathogenic pathways and (c) discover potential new therapeutic targets.
Affymetrix Mouse Gene 1.0 ST arrays were utlized to detail the global gene expression profile following optic nerve crush (ONC) in the retina of BALB/cJ mice at six different days post crush (dpc) (naive, 3 dpc, 7 dpc, 14 dpc, 21 dpc and 28 dpc) to understand the pathogenic responses in relation to neuronal loss and regenerative failure.

overall_design: BALB/cJ mice aged 2-4 months were utilized for all the experiments and were obtained from the Jackson Laboratories (Bar Harbor, ME). The mice were housed and maintained in a 12-hour light/dark cycle and fed ad libitum. All procedures were performed in accordance with Association for Research in Vision and Ophthalmology Statement on the Use of Animals in Ophthalmic and Vision Research and the University of North Texas Health Science Center (UNTHSC) Institutional Animal Care and Use Committee regulations. The ON of the left eye was crushed 0.5mm posterior from the globe for 4 seconds using the Nickell's technique. Briefly, mice were anesthetized by intraperitoneal injection of ketamine (100 mg/kg) and xylazine (10 mg/kg) and then an incision was made along the superior orbital margin. The left ON was exposed and crushed using a self-closing jeweler’s forceps to ensure reproducible and constant force. For the microarray studies, five mice were used per time-point and tissue harvested at six different times (naive, 3 dpc, 7 dpc, 14 dpc, 21 dpc and 28 dpc). After the retinal tissues were harvested, RNA was extracted and samples were all pooled for each experimental (left retina) and control (right retina) eye group to a total 2100ng of RNA/pool. Microarray hybridizations were performed at the University of Iowa DNA Core Facility. Total RNA (50ng) was converted to SPIA (Single Primer Isothermal Amplification) amplified cDNA using the WT-Ovation Pico RNA Amplification System. Biotin-labeled cDNA was placed onto Affymetrix Mouse Gene 1.0 ST arrays (Part No. 901168), and incubated at 45º C for 18 h and signals detected according to maufacturer's protocol. Arrays were scanned with the Affymetrix Model 3000 scanner with 7G upgrade, and data were collected using the using the GeneChip operating software (GCOS) v1.4. Microarray data were imported into the Partek Genomics Suite 6.6 software (Partek Inc., Louis, MO) and normalized based on the robust multi-array average (RMA). The ONC samples were contrasted against the control samples to calculate the microarray ratios and log2 fold values.

middle: P

first: Colleen

middle: M

last: McDowell

first: Yang

last: Liu

first: Alex

last: Wagner

last: Thole

first: Benjamin

last: Faga

first: Robert

middle: J

last: Wordinger

first: Terry

middle: A

last: Braun

first: Abbot

middle: F

last: Clark


title: Optic nerve crush induces spatial and temporal gene expression patterns in optic nerve of BALB/cJ mice

summary:
Central nervous system (CNS) trauma and neurodegenerative disorders trigger a cascade of cellular and molecular events resulting in neuronal apoptosis and regenerative failure. The pathogenic mechanisms and gene expression changes associated with these detrimental events can be effectively studied using a rodent optic nerve crush (ONC) model. The purpose of this study was to use a mouse ONC model to: (a) evaluate changes in optic nerve (ON) gene expression, (b) identify neurodegenerative pathogenic pathways and (c) discover potential new therapeutic targets.
Affymetrix Mouse Gene 1.0 ST arrays were utlized to detail the global gene expression profile following optic nerve crush (ONC) in the ON of BALB/cJ mice at six different days post crush (dpc) (naive, 3 dpc, 7 dpc, 14 dpc, 21 dpc and 28 dpc) to understand the pathogenic responses in relation to neuronal loss and regenerative failure.

overall_design: BALB/cJ mice aged 2-4 months were utilized for all the experiments and were obtained from the Jackson Laboratories (Bar Harbor, ME). The mice were housed and maintained in a 12-hour light/dark cycle and fed ad libitum. All procedures were performed in accordance with Association for Research in Vision and Ophthalmology Statement on the Use of Animals in Ophthalmic and Vision Research and the University of North Texas Health Science Center (UNTHSC) Institutional Animal Care and Use Committee regulations. The ON of the left eye was crushed 0.5mm posterior from the globe for 4 seconds using the Nickell's technique. Briefly, mice were anesthetized by intraperitoneal injection of ketamine (100 mg/kg) and xylazine (10 mg/kg) and then an incision was made along the superior orbital margin. The left ON was exposed and crushed using a self-closing jeweler’s forceps to ensure reproducible and constant force. For the microarray studies, five mice were used per time-point and tissue harvested at six different times (naive, 3 dpc, 7 dpc, 14 dpc, 21 dpc and 28 dpc). After the ON tissues were harvested, RNA was extracted and samples were all pooled for each experimental (left ON) and control (right ON) eye group to a total of 500ng of RNA/pool. Microarray hybridizations were performed at the University of Iowa DNA Core Facility. Total RNA (50ng) was converted to SPIA (Single Primer Isothermal Amplification) amplified cDNA using the WT-Ovation Pico RNA Amplification System. Biotin-labeled cDNA was placed onto Affymetrix Mouse Gene 1.0 ST arrays (Part No. 901168), and incubated at 45º C for 18 h and signals detected according to maufacturer's protocol. Arrays were scanned with the Affymetrix Model 3000 scanner with 7G upgrade, and data were collected using the using the GeneChip operating software (GCOS) v1.4. Microarray data were imported into the Partek Genomics Suite 6.6 software (Partek Inc., Louis, MO) and normalized based on the robust multi-array average (RMA). The ONC samples were contrasted against the control samples to calculate the microarray ratios and log2 fold values.

first: David


title: DNA methylation analysis of breast cancer cell-lines

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Recurrent mutations in histone modifying enzymes in multiple cancer types imply key roles in tumorigenesis. However, the functional relevance of these mutations remains unknown. Here we show that the JARID1B histone H3 lysine 4 demethylase is frequently amplified and overexpressed in luminal breast tumors and a somatic point mutation of JARID1B leads to the gain of luminal-specific gene expression programs. Downregulation of JARID1B in luminal breast cancer cells induces the expression of basal cell-specific genes and growth arrest, which is partially rescued by the inhibition of TGFBR thereby indicating a key role for TGFb signaling. Integrated genome-wide analysis of JARID1B chromatin binding, histone H3 lysine trimethyl (H3K4me3) and dimethyl (H3K4me2) patterns, and gene expression profiles in luminal and basal-like breast cancer cells suggest a key role for JARID1B in luminal cell-specific gene expression programs. A significant fraction of JARID1B binding-sites overlaps with CTCF in both luminal and basal-like breast cancer cells. CTCF also co-immunoprecipitates with JARID1B and it may influence its histone demethylase (HDM) activity as the H3K4me3/me2 ratio is lower at the CTCF-overlapping compared to JARID1B-unique sites. Additionally, a heterozygous JARID1B missense mutation (K1435R) in the HCC2157 basal-like breast cancer cell line is associated with unique JARID1B chromatin-binding and gene expression patterns implying gain of luminal features. In line with this, exogenous expression of this mutant in basal-like breast cancer cells leads to a gain of JARID1B binding at many luminal-specific genes. A PARADIGM score reflecting JARID1B activity in luminal breast cancer cells is associated with poor clinical outcome in patients with luminal breast tumors. Together, our data imply that JARID1B is a luminal lineage-driving oncogene and that its therapeutic targeting may represent a novel therapeutic strategy in treatment-resistant luminal breast tumors.

overall_design: Bisulphite converted DNA from 5 breast cancer cell lines were hybridised to the Illumina Infinium HumanMethylation450 BeadChip.

last: Yamamoto


title: Expression data from human embryonic stem cells(hESCs)

status: Public on Jun 30 2014

city: changsha

first: Ge

last: Lin

state: hunan

address: xiangya road

department: Institute of Reproductive & Stem Cell Engineering

country: China

institute: Central South University

summary: To detect the effect of  early culture on  hESCs, almost all initial-passaged hESCs have normal expression of DLK1-DIO3 gene cluster, the low-passaged hESCs lost the expression of DLK1-DIO3 gene cluster.

overall_design: hESCs  were  extracted for RNA with TriZOL and hybridization on Affymetrix arrays

first: Pingyuan

last: Xie

first: Guangxiu

last: Lu


title: Mtg16 regulates E protein activity and lineage specification in dendritic cell development (gene expression)

status: Public on Jun 13 2014

first: Hiyaa

middle: Singhee

last: Ghosh

address: 701 W 168th Street

institute: Columbia University Medical Center

summary: E protein transcription factors specify major immune cell lineages including lymphocytes and interferon-producing plasmacytoid dendritic cells (pDCs). Corepressors of the ETO family can bind to and block transactivation by E proteins, but the physiological role of these interactions remained unclear. We report that ETO protein Mtg16 binds chromatin primarily through the pDC-specific E protein E2-2 in human pDCs. Mtg16-deficient mice showed impaired pDC development and functionality, whereas the specification of the classical dendritic cells (cDCs) was enhanced. The deletion of Mtg16 caused aberrant expression of E protein antagonist Id2 in pDCs. Thus, Mtg16 acts as a cofactor of E2-2 to promote pDC differentiation and restrict cDC development, revealing an unexpected positive role of ETO proteins in E protein activity.

overall_design: pDC from BM of WT and mtg16-KO mice were negatively selected (lin-CD19, Tcrb, Ter119, NK1.1) and sorted as CD11c+Bst2+ population directly in Trizol. RNA was prepared and deposited for microarray processing.

middle: S

first: Boris

last: Reizis


title: Amniotic fluid RNA gene expression profiling provides insights into the phenotype of Turner syndrome

city: Medford

first: Heather

last: Wick

address: 161 College Ave

department: Department of Computer Science

institute: Tufts University

summary:
Background: Turner syndrome, a common sex chromosome aneuploidy, has characteristics and malformations associated with the phenotype.  Fetal amniotic fluid is a complex biological material that could contribute to the understanding Turner syndrome pathogenesis.  Global gene expression analysis of Turner syndrome fetal amniotic fluid supernatant was utilized to identify organ systems and specific genes that may play a role in the pathophysiologic changes that are seen in individuals with Turner syndrome.
Methods: Global gene expression analysis was performed utilizing cell-free RNA from five midtrimester fetuses with Turner syndrome matched with five euploid female fetuses.  Total RNA was extracted, amplified, hybridized onto GeneChip® Human Genome U133 Plus 2.0 arrays.  Network and pathway analysis of differentially expressed genes were completed.  Chromosomal distribution of gene expression differences, differential expression by pathway and organ system (a “Turner syndrome core transcriptome”), and candidate genes that could play a pathological role were identified.
Results: There were 470 differentially expressed genes identified in the Turner syndrome transcriptome.   The differentially expressed genes were distributed randomly across different chromosomes.  Among genes on the X chromosome, XIST was down-regulated, and SHOX not differentially expressed.  The most highly represented organ systems were hematologic/immune and neurologic.  Increased representation of differentially expressed genes in the hematologic/immune system distinguishes the Turner syndrome transcriptome from the euploid, trisomy 18 and trisomy 21 transcriptomes previously studied in our laboratory.  Manual curation of the differentially expressed gene list identified genes including NFATC3, IGFBP5, and LDLR that warrant further study.

overall_design: 2nd trimester amniotic fluid mRNA expression was compared between 5 Turners and 5 euploid fetuses.

first: Lauren

last: Massingham

first: Kirby

last: Johnson

first: Thomas

last: Scholl

first: Donna

middle: K

last: Slonim

first: Diana

middle: W

last: Bianchi


title: Gene Expression Profiling of High Altitude Polycythemia in Han Chinese migrated to Qinghai-Tibetan Plateau

status: Public on Jun 15 2014

city: Chongqing

first: jiang

last: chunhua

state: Chongqing

address: No.30 Gao Tan Yan Zheng Street, Sha Ping Ba District

institute: third military medical universtiy

summary:
Long term-exposed to high altitude, the increased numbers of red blood cells tend to stabilize to a certain extend in most people, but someone will occur over-increasing in number of red blood cells, which cause a serious of clinical symptoms and signs, and this is high altitude polycythemia. EPO-EPOR system may be the main reasons for erythroid progenitor cell proliferation and differentiation in early exposion to plateau, but, in the late, there may be other factors involved in the regulation of erythropoiesis in bone marrow, multiple factors working together lead to excessive red blood cell proliferation.
We compared gene expression profiling of leukocytes in peripheral blood from high altitude polycythemia patients with those from matched controls.

overall_design: Subjects consisting of 5 masculine Han Chinese patients with HAPC (diagnosed according to international consensus statement on HAPC) and 5 matched controls, were migrants at River of TUOTUO area (Qinghai-Tibetan Plateau, 4550 m). Each of the five HAPC patients was matched to each of the control: gender, nationality, birthplace, duration migrating to plateau, height of location, work intensity. Peripheral blood samples were obtained at 4550m plateau from above subjects. Total RNA was extracted from peripheral blood leucocytes. The gene expression profilings were analysed by Human Genome U133 Plus 2.0 Array.

first: Chunhua

last: Jiang

first: Yuqi

last: Gao


title: Expression analysis of neurospheres generated in vitro

city: St lucia Brisbane

first: Zong-Hong

last: Zhang

state: Queensland

address: QBI Building (#79)

country: Australia

institute: QBI

summary: Neurospheres generated in vitro were treated with non-epinephrine or potassium chloride. Gene expression analysis was then carried out to identify genes that are up or down regulated due to chemical treatement.

overall_design: The microarray data for the neurosphere samples was generated at Queensland Brain Institute. Briefly, RNA was isolated from neurospheres generated in presence of either N (norepinephrine) or K (potassium chloride)and converted to cDNA using Applause WT-Amp ST kit (NuGEN). Fragmentation and biotin labelling of the cDNA was carried out using Encore Biotin module (NuGEN) for Affymetrix GeneChip Mouse Gene 1.0 ST arrays. Labelled cDNA was hybridised to arrays in an oven at 45°C. Hybridised arrays were scanned using the Affymetrix GeneChip Scanner and the scanned data (.CEL files) was transferred to the Partek Genomics Suite and data analysis was carried out as described in Narayanan RK, Mangelsdorf M, Panwar A, Butler TJ, Noakes PG, et al. (2013).


title: Early tissue responses to etanercept in psoriasis lesions

status: Public on Jun 07 2014

first: William

middle: R

last: Swindell

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard University

summary: Anti-TNF-alpha therapy has made a significant impact on the treatment of psoriasis. Despite being designed to neutralize TNF-alpha activity, the mechanism of action of these agents in the resolution of psoriasis remains unclear. The aim of this study was to better understand the mechanism of action of etanercept by examining very early changes in the lesional skin of psoriasis patients. 20 chronic plaque psoriasis patients were enrolled and received 50mg etanercept twice weekly. Skin biopsies were obtained before treatment and on days 1, 3, 7 and 14 post-treatment. Skin mRNA expression was analysed by microarray.

overall_design: Twenty individuals with chronic plaque psoriasis were enrolled (age range 18-75 years). Entry criteria included age greater than 18 years and stable plaque-type psoriasis involving at least 10% body surface area. Exclusion criteria included use of systemic psoriasis therapy within 4 weeks, topical therapy within 2 weeks, or severe co-morbid diseases. For 12 weeks, subjects received etanercept (Enbrel) 50mg twice a week subcutaneously. At baseline, 6 mm punch biopsies were obtained under local anaesthesia (lidocaine) from uninvolved skin and a target plaque. Subsequent biopsies were taken on days 1, 3, 7 and 14 of therapy from the same target plaque.

first: Andrew

last: Johnston

first: Johann

middle: E

last: Gudjonsson


title: Banking Placental Tissue: An Optimized Collection Procedure for Genome-Wide Analysis of Nucleic Acids

status: Public on Jun 09 2014

city: La Jolla

first: Rathi

middle: D

last: Thiagarajan

address: 2880 Torrey Pines Scenic Drive

department: Reproductive Medicine

institute: UCSD

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

overall_design: Refer to individual Series


title: Expression profile of stromal cells in the lymph node

city: Hirakata

first: Tomoya

last: Katakai

state: Osaka

address: 2-5-1 Shinmachi

department: Department of Molecular Genetics, Institute of Biomedical Science

country: Japan

institute: Kansai Medical University

summary:
Tissue structure of the lymph node (LN) is supported by the network of stromal cells of mesenchymal origin, which is suggested to contribute to various immunological processes.
In order to identify stromal cell–derived factors that regulate immune function, we performed gene expression profiling of stromal cells freshly isolated from collagenase digested mouse LNs, cultured stromal cell lines, and embryonic fibroblasts as a mesenchymal control.

overall_design: Total RNAs extracted from the CD45-CD31-podoplanin+VCAM-1+ stromal cell fraction was sorted from enzymatically digested mouse LNs, cultured stromal cell lines stimulated with or without lymphotoxin (LTβR agonistic antibody), and mouse embryonic fibroblasts (MEFs) were used for microarray analysis to assess relative gene expression.

first: Tatsuo

last: Kinashi


title: Gene expression data from medulloblastoma tumor samples

status: Public on Jun 02 2014

city: Heidelberg

first: Marcel

last: Kool

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

country: Germany

institute: German Cancer Research Center DKFZ

summary:
Smoothened (SMO)-inhibitors recently entered clinical trials for sonic-hedgehog driven medulloblastoma (SHH-MB). Clinical response appears highly variable. To understand the mechanism(s) of primary resistance and to identify pathways co-operating with aberrant SHH-signaling, we sequenced a large cohort of SHH-MBs across all age groups by sequencing, DNA methylation and expression profiling. Our data show that most adults but only half of the pediatric patients with SHH-MB will respond to SMO inhibition as predicted by molecular analysis of the primary tumor and tested in the SHH-xenografts, demonstrating that the next generation of SMO-inhibitor trials should be based on these predictive biomarkers.
To further dissect the biological differences between the different age groups within SHH medulloblastomas, we looked at the transcriptomic profiles of SHH medulloblastoma samples.

overall_design: 73 medulloblastoma samples from patients of various ages were selected for RNA extraction and hybridization on Affymetrix Human Genome U133 Plus 2.0 Arrays.

first: Stefan

last: Pfister


title: TET1 is a maintenance DNA demethylase that prevents methylation spreading in adult cells [cDNA microarray]

status: Public on Jun 04 2014

city: Houston

first: CHUNLEI

last: JIN

state: TX

address: 1515 Holcombe Blvd

institute: The University of Texas MD Anderson Cancer Center

summary: We report that full length TET1 (TET1-FL) overexpression fails to induce global DNA demethylation in HEK293T cells. The preferential binding of TET1-FL to hypomethylated CpG islands (CGIs) through its CXXC domain leads to its inhibited 5-hydroxymethylcytosine (5hmC) production as methylation level increases. TET1-FL-induced 5hmC accumulates at CGI edges, while TET1 knockdown induces methylation spreading from methylated edges into hypomethylated CGIs. However, TET1 can regulate gene transcription independent of its dioxygenase catalytic function. Thus, our results identify TET1 as a maintenance DNA demethylase that does not purposely decrease methylation levels, but specifically maintains the DNA hypomethylation state of CGIs in adult cells.

overall_design: HEK293T cells were transfected with wild type or catalytically mutant TET1 expression plasmids (TET1-CD, mTET1-CD, TET1-FL and mTET1-FL), or subjected to shRNA-mediated TET1 knockdown. Total RNA samples were extracted and assayed on Affymetrix microarrays

first: Chunlei

last: Jin

first: Yue

last: Lu

first: Jaroslav

last: Jelinek

first: Shoudan

last: Liang

first: Marcos

last: Estecio

first: Michelle

last: Barton

first: Jean-Pierre

last: Issa


title: Gene expression profiling of PBMC from normal individuals, chronic hepatitis B carriers and hepatocellular carcinoma patients

city: Singapore

first: Kam

last: Hui

address: 11 Hospital Drive

country: Singapore

institute: National Cancer Centre Singapore

summary: Aberrant gene expression analysis between peripheral blood mononuclear cell (PBMC) samples from healthy individuals and patients with chronic hepatitis B carriers and HCC were identified using Affymetrix gene arrays.

overall_design: Peripheral blood mononuclear cell (PBMC) from healthy individuals, patients with patients with chronic hepatitis B carriers and HCC were isolated and total RNA was extracted for Affymetrix gene microarray analysis.


title: SSEA-4 labels a subset of poor prognosis-associated osteosarcoma-initiating cells that respond to differentiation induction

status: Public on Jun 05 2014

city: Shanghai

first: WU

last: ZHANG

address: No.197,  Ruijin 2nd Road

institute: RuiJin Hospital Shanghai Jiao Tong University school of Medicine

summary: Osteosarcoma is thought of arising from the malignant transformation of osteogenic progenitors. The stage-specific embryonic antigen-4 (SSEA-4) labels a subset of TICs specially present in the high-risk subgroup.

overall_design: SSEA-4+ AND SSEA-4-

first: Wu

last: Zhang

first: Meng-lei

last: Ding

first: Wei-bin

first: Jiang

last: Zhu


title: Analysis of Liver Progenitor Cells Generated from Yap Expression [Set 1]

status: Public on Jun 06 2014

first: Dean

last: Yimlamai

address: 300 Longwood Ave

department: Medicine

institute: Boston Children's Hospital

summary:
Hippo signaling is highly associated with activity in the stem cell compartment of many epithelial tissues.  In this study, we examined if Hippo signaling inhibition (by inducing Yap expression) could convert differentiated cells into a progenitor like phenotype.  Organoid cells derived from mouse livers under various conditions, wild-type, Yap ON (Plus Dox), and Yap ON then OFF (Minus Dox) was examined.
Comparison between freshly isolated hepatocytes; Uninduced_YPF-#.cel  against Organoids grown in  wild-type conditions (WT), Yap On (in vivo) off (in vitro) -  YapOrganoidDoxMinus , and Yap On continuously - YapOrganoidDoxPlus.

overall_design: Organoids grown in culture or YFP+ sorted liver cells after the indicated time of Yap expression were collected.  These were amplified using Nugene technology and hybridized to Affymetrix MoGene1.0 st arrays.


title: Hippo Pathway Activity Influences Liver Cell Fate

type:
Expression profiling by array
Third-party reanalysis


title: Infinium Monkeys: Infinium 450K array for the Cynomolgus macaque (Macaca fascicularis) (methylation array)

first: Joanna

last: Holbrook

address: 30 Medical Drive

institute: SICS

summary:
Infinium 450K is a hybridization array designed for the human genome, but the relative conservation between the macaque and human genomes makes its use in macaques feasible.
We used the Infinium450K array to assay twelve Cynomolgus macaque muscle biopsies and compared it to Reduced Representation Bisulphite Sequencing (RRBS) data generated on the same samples.

overall_design: Muscle biopsies were performed on eleven adult male cynomologus macaques


title: Effect of Selective Androgen Receptor Modulator (SARM) on Gene Expression in Triple-Negative Breast Cancer Cells, MDA-MB-231-AR

status: Public on Jun 03 2014

city: Memphis

first: Ramesh

last: Narayanan

state: Tennessee

address: 19 S. Manassas, Room 120

institute: University of Tennessee Health Science Center

summary: RNA from tumors treated with vehicle or 30 mg/kg GTx-027 were pooled and subjected to microarray analysis. Genes that were increased or decreased by 2-fold or more were considered for further analyses. Unlike in prostate cancer, where AR agonists induce more genes than they repress, in MDA-MB-231-AR tumors, GTx-027 inhibited 2.5X the number of genes (1092 vs. 456) than it activated. Functional clustering of the genes indicated that GTx-027 modified more breast cancer genes than other pathway genes. Genes that regulate the function of others cancers, such as colorectal, lung, and oral, and metabolic diseases were also favorably altered by GTx-027. Breast cancer proliferative genes, such as aurora kinase, ERCC1, IGFBP3 were inhibited and growth inhibitory genes, such as NQO1, PTPRJ were activated by GTx-027. Many of the established androgen responsive-genes were also activated by GTx-027, indicating that breast cancer growth inhibitory role of GTx-027 evolved from its agonistic activity.

overall_design:
A mixture of cells was suspended in 0.05 ml RPMI+10% FBS and 0.05 ml Matrigel/animal and was injected subcutaneously.
Once the tumor size reached 200-300 mm3, the animals were randomized and treated orally with the indicated drugs formulated in Tween 80:Captex 200:water (0.8:0.2:9).
Tumor volume and body weight were measured thrice weekly. At the end of study, animals were sacrificed, tumors excised, weighed, and stored for various analyses.
RNA from tumors was isolated and verified qualitatively and quantitatively.
Samples from each group (n=8; 100 ng/µl; total 1000 ng) were pooled and hybridized to Affymetrix human ST2.0 gene array.
Data from the array were analyzed using Ingenuity Pathway Analysis software (IPA3).

first: James

middle: T

last: Dalton


title: Optic nerve crush induces spatial and temporal gene expression patterns in optic nerve and retina of BALB/cJ mice

first: Tasneem

last: Sharma

address: 3500 Camp Bowie Blvd

institute: UNTHSC


title: Expression data from progesterone receptor knockout versus heterozygous mouse oviducts

status: Public on Jun 16 2014

city: St Lucia

first: Lisa

last: Akison

state: QLD

address: Sir William MacGregor Building

department: Biomedical Sciences

institute: University of Queensland

summary:
The oviducts play a critical role in gamete and embryo transport, as well as supporting fertilization and early embryo development.  Progesterone receptor (PGR) is a transcription factor highly expressed in oviductal cells, while it’s activating ligand, progesterone (P4), surges to peak levels as ovulation approaches.  P4 is known to regulate oviduct cilia beating and muscular contractions in vitro, but how PGR may mediate this in vivo is poorly understood.  We used PGR-knockout (PRKO) mice to determine how PGR regulates oviductal function during the periovulatory period, in particular oviductal transport and embryo support.
We used microarrays to identify putative PGR-regulated genes in the oviduct during the periovulatory period, a time when the oviduct is preparing to receive the newly-ovulated COC.

overall_design: The mutant strain used in this experiment were PRlacZ knock-in mice which originated from Assoc Prof John Lydon, Baylor College of Medicine, Houston TX, USA.  The lacZ insertion results in disruption of transcription of both isoforms of PGR (Ismail et al, 2002, Mol Endocrinol 16:2475-2489), and therefore mice homozygous for the lacZ insertion are a phenocopy of the knockout strain described by Lydon et al. (1995, Genes Dev. 9:2266-2278) and are hereafter referred to as PRKO.  Heterozygous mice (PR+/-) are a phenocopy of WT and have normal fertility (Ismail et al, 2002) and are therefore appropriate controls.  Whole oviducts were collected from pre-pubertal PRKO and PR+/- mice 8 h after a standard protocol for hormonal induction of ovulation.  Day 21-23 old mice were injected i.p. with 5IU of equine chorionic gonadotropin (eCG) to stimulate follicle growth, followed 44-47 h later by i.p. injection of 5 IU of human chorionic gonadotropin (hCG) to trigger ovulatory processes.  Oviducts from 15 animals were collected per genotype, with oviducts from 3 animals pooled per sample for a total of n = 5 samples per genotype.

first: Rebecca

middle: L

last: Robker

first: Darryl

last: Russell


title: miR-28 expression in the Burkitt lymphoma cell line P3HR1

status: Public on Jun 01 2014

first: Riccardo

last: Dalla-Favera

address: 1130 St Nicholas Avenue

institute: Columbia University

summary: Burkitt lymphoma (BL) is a highly aggressive B cell non-Hodgkin lymphoma (B-NHL), which originates from germinal center (GC) B cells and harbors translocations deregulating the MYC oncogene. A comparative analysis of microRNAs (miRNAs) expressed in normal and malignant GC B cells identified miR-28 as significantly down-regulated in BL, as well as in other GC-derived B-NHL. We show that re-expression of miR-28 impairs cell growth and clonogenic properties of BL cells by modulating several targets including MAD2L1, a component of the spindle checkpoint whose down-regulation is essential in mediating miR-28-induced growth-arrest, and BAG1, an activator of the ERK pathway.

overall_design: P3HR1 Burkitt lymphoma cell line was engineered to display inducible expression of GFP alone or GFP in combination with the miR-28 precursor from the pRTS1 vector upon doxycycline treatment. Two bulk populations (A and B) were established for both the control (GFP alone) and the miR28-expressing (GFP and miR-28 precursor) cells. Cells were induced with 0.1ug/ml doxycycline for 12h or 24h. Induction was performed on each bulk population in triplicates.

first: Christof

last: Schneider

first: Katia

last: Basso

first: Antony

last: Holmes


title: Genetic targets of hydrogen sulfide in ventilator-induced lung injury

city: Freiburg

first: Sashko

last: Spassov

address: Breisacher Straße 64

department: Department of Anaesthesiology and Intensive Care Medicine

institute: UCM-Freiburg

summary:
In this study we provide evidence on potential mechanisms involved in H2S mediated protection against VILI. H2S down-regulates genes that are involved in oxidative stress and pro-inflammatory cell responses. H2S regulates ECM remodelling, a mechanism which may contribute to H2S-mediated lung protection. In addition, H2S inhalation activates anti-apoptotic and anti-inflammatory genes, and genes controlling the vascular permeability. The functional relevance of Atf3 underscores the potential of H2S to limit lung injury.
We utilized a microarray approach for large scale analysis of target genes in order to elucidate the therapeutic effects of H2S in VILI. This study demonstrates the influence of supplemental H2S on gene expression in a model of VILI. In addition to describing the genes differentially regulated in VILI, the present study focused on newly identified H2S target genes within several functional groups, including anti-inflammatory and anti-apoptotic pathways, regulation of extracellular matrix (ECM) remodelling and angiogenesis.

overall_design: Gene expression analysis of control group, allowed to breathe spontaneously synthetic air and  mice ventilated with synthetic air or synthetic air with 80 ppm H2S for 6 hours.

first: Dietmar

last: Pfeifer

first: Karl

last: Strosing

first: Stefan

last: Ryter

first: Matthias

last: Hummel

first: Simone

last: Faller

first: Alexander

last: Hoetzel


title: Analysis of Liver Progenitor Cells Generated from Yap Expression [Set 2]

first: Dean

last: Yimlamai

summary:
Hippo signaling is highly associated with activity in the stem cell compartment of many epithelial tissues.  In this study, we examined if Hippo signaling inhibition (by inducing Yap expression) could convert differentiated cells into a progenitor like phenotype.
Rosa26-lsl-YFP mice had recombination induced and cells were FACS sorted using YFP as a marker at either 1 week or 6 weeks after recombination.  YFP expression is a surrogate for Yap expression  (our protein of interest) and time was varied in vivo.  RNA was immediately extracted after sorting and labeled to be hybridized to the array.

overall_design:
FACS sorted Yap expressing liver cells were sorted one or six weeks after induction and compared to fetal liver samples as controls

The control data from fetal liver samples have been previously published and is available in the GEO database as GSE12117 (GSM305568, GSM305569, GSM305570).

The complete dataset representing: Yap Expressiong Liver samples and the fetal liver control Samples from Series GSE12117 (re-processed in this study), is linked below as a supplementary file.


title: Upregulation of immunoproteasome subunits in myositis indicates active inflammation with involvement of antigen presenting cells, CD8 T-cells and IFNγ

city: Berlin

first: Thomas

last: Häupl

address: Charitéplatz 1

department: Rheumatology

institute: Charité

summary: Objective: In idiopathic inflammatory myopathies (IIM) infiltration of immune cells into muscle and upregulation of MHC-I expression implies increased antigen presentation and involvement of the proteasome system. To decipher the role of immunoproteasomes in myositis, we investigated individual cell types and muscle tissues and focused on possible immune triggers.   Methods: Expression of constitutive (PSMB5, -6, -7) and corresponding immunoproteasomal subunits (PSMB8, -9, -10) was analyzed by real-time RT-PCR in muscle biopsies and sorted peripheral blood cells of patients with IIM, non-inflammatory myopathies (NIM) and healthy donors (HD). Protein analysis in muscle biopsies was performed by western blot. Affymetrix HG-U133 platform derived transcriptome data from biopsies of different muscle diseases and from immune cell types as well as monocyte stimulation experiments were used for validation, coregulation and coexpression analyses.   Results: Real-time RT-PCR revealed significantly increased expression of immunoproteasomal subunits (PSMB8/-9/-10) in DC, monocytes and CD8+ T-cells in IIM. In muscle biopsies, the immunosubunits were elevated in IIM compared to NIM and exceeded levels of matched blood samples. Proteins of PSMB8 and -9 were found only in IIM but not NIM muscle biopsies. Reanalysis of 78 myositis and 20 healthy muscle transcriptomes confirmed these results and revealed involvement of the antigen processing and presentation pathway. Comparison with reference profiles of sorted immune cells and healthy muscle confirmed upregulation of PSMB8 and -9 in myositis biopsies beyond infiltration related changes. This upregulation correlated highest with STAT1, IRF1 and IFNγ expression. Elevation of T-cell specific transcripts in active IIM muscles was accompanied by increased expression of DC and monocyte marker genes and thus reflects the cell type specific involvement observed in peripheral blood.   Conclusions: Immunoproteasomes seem to indicate IIM activity and suggest that dominant involvement of antigen processing and presentation may qualify these diseases exemplarily for the evolving therapeutic concepts of immunoproteasome specific inhibition.

overall_design:
Investigation of constitutive and immunoproteasomal subunit expression in muscle tissue of patients with inflammatory and non-inflammatory myopathies
These transcriptomes were used as reference signatures of different immune cell types in order to estimate the contribution of immune cell transcripts to the muscle transcriptomes investigated in the datasets GSE2044, GSE3112, GSE5370, GSE39454, GSE3307, GSE13205, GSE10685.

first: Khetam

last: Ghannam

first: Lorena

last: Martinez-Gamboa

first: Lydia

last: Spengler

first: Sabine

last: Krause

first: Biljana

last: Smiljanovic

first: Marc

last: Bonin

first: Salyan

last: Bhattarai

first: Andreas

last: Grützkau

first: Gerd-R.

last: Burmester

first: Eugen

last: Feist


title: siRNA-mediated knockdown of VAMP7 in NTERA2/D1 cells

first: Mounia

last: Tannour-Louet

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: To unravel the function of VAMP7 in the male sexual differentiation, we carried out in vitro studies of VAMP7 knockdown using siRNA, in the human embryonal carcinoma NTERA2/D1 cells.

overall_design: We knocked down VAMP7 expression in the testicular teratocarcinoma cell line, NTERA2/D1. By comparing the knockdown conditions with the control scrambled samples, we are able to dissect the cellular pathways affected by alteration of VAMP7 gene expression.

first: Shuo

last: Han

first: Dolores

last: Lamb


title: Comparison of gene expression profiles of miR-142-/- primary megakaryocytes and WT primary megakaryocytes

status: Public on Jun 11 2014

city: Rehovot

first: Elik

last: Chapnik

address: Herzel st.

department: Molecular Genetics

institute: Weizmann Institute of Science

summary: Whole fetal livers were collected from mouse fetuses at embryonic day 14.5 (E14.5), and single-cell suspensions were prepared by successive passage through 18-, 21 and  23-gauge needles. Fetal liver cells were maintained in Dulbecco modified Eagle medium (DMEM; Invitrogen) supplemented with 10% fetal bovine serum (FBS; Invitrogen), 100 U/ml penicillin, 100µg/ml streptomycin, and 50ng/ml recombinant human thrombopoietin (TPO; Peprotech). After 5 days of culture, megakaryocytes were purified using a discontinuous bovine serum albumin gradient (BSA, Sigma–Aldrich; 3%, 1.5%, and 0%). Total RNA was isolated with Tri–Reagent (MRC) following manufacturer’s instructions, and its quality was assessed with ND–1000 Nanodrop (Peqlab) and on a 1.5% agarose gel.

overall_design: Gene expression was measured in primary megakaryocytes cultured from miR-142-/- fetal livers and wild type fetal livers at E14.5. Two independent experiments were performed.

first: Eran

last: Hornstein


title: Banking Placental Tissue: An Optimized Collection Procedure for Genome-Wide Analysis of Nucleic Acids [methylation]

first: Rathi

last: Thiagarajan

summary:
Banking of high-quality placental tissue specimens will enable biomarker discovery and molecular studies on diseases involving placental dysfunction. Systematic studies aimed at developing feasible standardized methodology for placental collection for genomic analyses are lacking.   To determine the acceptable timeframe for placental collection, we collected multiple samples from first and third trimester placentas at serial time points 0-120 minutes after delivery, simultaneously comparing the traditional snap-freeze technique to collection in commercial solutions designed to preserve RNA (RNAlaterTM, Ambion), and DNA (DNAgard®, Biomatrica). The performance of RNAlater for preserving DNA was also tested. Nucleic acid quality was assessed by determining the RNA integrity number (RIN) and genome-wide expression and DNA methylation microarray profiling.  We found that samples collected in RNAlater had higher and more consistent RINs compared to snap frozen tissue, with similar RINs obtained for tissue collected in RNAlater as large (1 cm3) and small (~0.1 cm3) tissue pieces.  RNAlater appeared to better stabilize the time zero gene expression pattern compared to snap freezing for first trimester placenta.  Microarray DNA methylation analysis showed that overall the DNA methylation profiles remained quite stable over a two hour time period after removal of the placenta from the uterus, with the DNAgard condition being superior to both snap freezing and RNAlater.  The collection of placental samples in RNAlater and DNAgard is simple, and eliminates the need for liquid nitrogen or a freezer on-site. Moreover, the quality of the nucleic acids and the resulting data from samples collected in these preservation solutions is actually higher than that from samples collected using the traditional snap-freeze method. Thus, this new approach to placental sample collection is both easier to implement in busy clinical environments and yields higher quality data.
48 samples

overall_design: In this study, our objective was to identify the optimal timing and mode of collection for nucleic acids of sufficient quality to perform genome-wide RNA gene expression and DNA methylation studies for downstream molecular and functional enrichment analysis. To do this, we evaluated three different placenta collection methods: snap freezing in liquid nitrogen, RNAlaterTM, and DNAgard, over a two-hour window upon removal from the uterus, to determine: 1) the optimal collection method(s) for evaluation of mRNA expression and DNA methylation; and 2) the time period after delivery during which such optimal samples should be collected.

first: Lynlee

last: Wolfe

last: Thagarajan

first: Francesca

last: Boscolo

first: Veronique

last: Tache

first: Ron

last: Coleman

first: Jessica

last: Kim

first: Wai

last: Kwan

first: Jeanne

last: Loring

first: Mana

last: Parast

first: Louise

middle: C

last: Laurent


title: Integrated epigenetic and copy-number profiling identifies three clinically and biologically relevant groups of anaplastic glioma

first: Martin

last: Sill

department: Division of Pediatric Neurooncology

institute: DKFZ

summary:
The outcome of patients with anaplastic gliomas varies considerably depending on histology and single molecular markers such as codeletion of 1p/19q and mutations of the isocitrate dehydrogenase (IDH) gene. Whether a molecularly-based classification of anaplastic gliomas based on large scale genomic or epigenomic analyses is superior to histopathology, may reflect distinct biological subtypes, predict outcome and guide therapy decisions had yet to be determined.
Epigenome-wide DNA methylation analysis, which also allows for the detection of copy-number aberrations, was performed in a cohort of 228 patients with anaplastic gliomas (astrocytomas, oligoastrocytomas and oligodendrogliomas), including 115 patients of the NOA-04 trial. We further compared these tumors with a group of 55 glioblastomas.
Unsupervised clustering demonstrated two main groups based on IDH mutation status: CpG island methylator phenotype (CIMP) positive (77.5%) or negative (22.5%). CIMP+ (IDH mutant) tumors showed a further separation based on copy-number status of chromosome arms 1p and 19q, but not based on histopathology. CIMP- (IDH wild type) tumors on the other hand showed hallmark copy-number alterations of glioblastomas. These tumors clustered together with CIMP- glioblastomas without forming separate groups based on WHO grade. There was no Tumor classification based on CIMP and 1p/19q status was significantly associated with survival allowing a better prediction of outcome than the current histopathological classification alone: Patients with CIMP+ tumors with 1p/19q codeletion had the best prognosis, followed by patients with CIMP+ but intact 1p/19q status. Patients with CIMP- anaplastic gliomas had the worst prognosis.
Collectively, our data suggest that anaplastic gliomas can be grouped into three molecular subtypes with clear association to underlying biology and clinical outcome based on IDH and 1p/19q status. The data do not provide a molecular basis for the diagnosis of anaplastic oligoastrocytoma.

overall_design: We investigated a subset of 228 anaplastic gliomas using the Illumina 450k methylation array.

first: Benedikt

last: Wiestler

first: David

last: Capper

last: Jones

first: Volker

last: Hovestadt

first: Dominik

last: Sturm

first: Christian

last: Koelsche

first: Anna

last: Bertoni

first: Leonille

last: Schweizer

first: Andrej

last: Korshunov

first: Elisa

last: Weiß

first: Maximilian

middle: G

last: Schliesser

first: Alexander

last: Radbruch

first: Christel

last: Herold-Mende

first: Patrick

last: Roth

first: Andreas

last: Unterberg

last: Hartmann

first: Thorsten

last: Pietsch

first: Guido

last: Reifenberger

first: Peter

last: Lichter

first: Bernhard

last: Radlwimmer

first: Michael

last: Platten

first: Stefan

last: Pfister

last: von Deimling

last: Weller

first: Wolfgang

last: Wick


title: Gene expression profile of C1013G/CXCR4 mutated WM cells

first: Aldo

last: Roccaro

address: 450 Brookline Av

institute: Dana-Farber Cancer Institute

summary:
C1013G/CXCR4 variant has been inserted into BCWM.1 cells, and gene expression profile has been performed on the mutated cells and on the parental cells.
Affimetrix Human Genome U133_Plus2.0 array

overall_design: We used microarrays to dissect the possible changes occurring at mRNA level in mutated cells versus the parental cellular counterpart.

first: Irene

last: Ghobrial


title: Discordant disease course in a monozygotic twin pair with Juvenile Myelomonocytic Leukemia

status: Public on May 31 2014

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

country: Italy

institute: università di padova

summary: Case report of a twin pair with concordant JMML, but with a different disease course predicted by gene expression profiling

overall_design: Different variance between a twin pair at diagnosis of JMML and at relapse

first: Silvia

last: Bresolin


title: An Epigenetic Signature in Peripheral Blood Associated with Neurodegenerative Tauopathy and the Risk-Associated Haplotype on 17q21.31

city: Los Angeles

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

summary: Progressive supranuclear palsy (PSP) and frontotemporal dementia (FTD) are two neurodegenerative diseases linked, at the pathologic and genetic level, to the macrutubule associated protein tau. We identified and replicated a dose-dependent effect of the risk-associated H1 haplotype on methylation levels within the region in independent datasets in blood and brain. These data reveal that the H1 haplotype increases risk for tauopathy via differential methylation, indicating a mediating role for methylation in dementia pathophysiology.

overall_design: We studied epigenetic changes (DNA methylation levels) in peripheral blood from patients with PSP, FTD, and unaffected controls. Analysis of genome-wide methylation patterns revealed significant differentially methylated probes in patients versus unaffected controls.

first: Yun

last: Li

first: Jason

last: Chen

first: Renee

last: Sears

first: Fuying

last: Gao

first: Eric

last: Klein

first: Anna

last: Karydas

last: Geschwind

first: Howard

last: Rosen

first: Adam

last: Boxer

first: Weilong

last: Guo

first: Matteo

last: Pellegrini

first: Steve

last: Horvath

first: Bruce

last: Miller

first: Daniel

middle: H


title: Expression data comparing Huh7 control and CD47 knockdown cells

city: Hong Kong

first: Kin Wah

last: Lee

address: 21 Sassoon Road

institute: The University of Hong Kong

summary:
To identify candidate genes regulated by CD47
Affymetrix Human Genome U133 Plus GeneChip 2.0

overall_design: HCC cell line Huh7 cells with or without CD47 repressed

first: Terence


title: Expression data from WT, E2f8 KO, Rb KO and Rb;E2f8 DKO spleen Ter19+CD71high sorted cells

status: Public on May 30 2014

city: Newark

first: Lizhao

last: Wu

address: 205 S Orange Ave

department: Microbiology and Mol. Genetics

institute: Rutgers

summary:
To understand molecular mechanisms underlying the synergy of Rb loss and E2F8 loss, we used gene expression profiling to assess molecular changes in Mx1-Cre-mediated knockout (KO) mice using RNA isolated from sorted Ter119+CD71high Erythroblasts.
The top four upregulated and enriched pathways in the DKO mice included DNA replication, DNA damage response, DNA repair, and RNA processing. Interestingly, the majority of upregulated genes in the enriched sections of the four shared pathways contain E2f binding site(s) in their promoters, suggesting that Rb and E2F8 largely repress those genes through the E2f binding sites. Collectively, our data suggest that Rb and E2F8 co-regulate E2F-responsive genes.

overall_design: Spleen Ter119+CD71high cells were sorted from WT, E2f8 KO, Rb KO and E2f8;Rb DKO mice

first: Seda

last: Ghazaryan


title: EDHB treated KYSE170

status: Public on May 29 2014

city: Beijing

first: Yang

last: Xu

address: No.17 Panjiayuan Nanli, Chaoyang district

institute: Cancer Hospital

summary: We used microarrays to detail the gene expression profiles of KYSE170 cell line to identify distinct up and down-regulated genes during treatment with ethyl-3,4-dihydroxybenzoate.

overall_design: KYSE170 cell line were treated with 50μg/ml EDHB for 12 hrs and selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to gene expression profiles of KYSE 170 cell line treated with ethyl-3,4-dihydroxybenzoate.

first: Bo

last: Han


title: Human DNA methylation profiles for the HBV vaccine responses study

first: Weili

last: Yan

address: 399 Wanyuan Road

institute: Department of Clinical Epidemiology, Children's Hospital of Fudan University

summary: Twenty five infants received HBV vaccination and were classified as good or poor responders according to their responses, the number being 12 and 13 respectively. PBMC cells were extracted and epigenome-wide DNA methylation levels were measureed using Illumina Infinium 450K HumanMethylation beadchips.

overall_design: Bisulphite converted DNA from the 25 samples were hybridised to the Illumina Infinium 450K Human Methylation Beadchip v1.2


title: Altered gene expression in blood and sputum from COPD patients with frequent exacerbations

city: Stevenage

first: steve

middle: matthew

last: fox

address: Gunnels Wood Road

department: Statistics

country: United Kingdom

institute: GlaxoSmithKline

summary: Investigation of gene expression profiles among patients with COPD frequent exacerbations and to find gene targets as predictors of exacerbations

overall_design: COPD patient samples analysed by microarray, followed by PCR testing to identify gene predictors

first: David

last: Singh

last: Fox

first: Ruth

last: Tal-Singer

first: Steward

last: Bates

first: John

last: Riley

first: Bartolome

last: Celli


title: Transcriptional responses of wild-type and Gcn2-/- Th17 cells to halofuginone and rapamycin

city: Cambridge

first: Scott

last: Davis

address: 200 Technology Square, Suite 602

department: Tempero DPU

institute: GSK

summary: This study was designed to evaluate similarities and differences between transcriptional responses of developing Th17 cells to the prolyl-tRNA synthetase inhibitor, halofuginone, and the mTOR inhibitor, rapamycin. Further comparisons between wild-type and Gcn2-/- Th17 cells allow for investigation into which gene modules regulated by halofuginone or rapamycin treatment require Gcn2.

overall_design:
Murine CD4+ CD25- T cells were magnetically isolated from wild-type or Gcn2-/- T cells. These cells were activated through anti-CD3/ anti-CD28 antibodies and polarized into Th17 cells using TGFb plus IL-6. 10 nM halofuginone, 10 nM rapamycin, or vehicle control (DMSO) were added to cultures at the time of activation. Cells were harvested at 4, 18, or 72 hours post-activation and differentiation. RNA was isolated from each sample and used for microarray analysis. Each culture condition and time-point was repeated twice in independent experiments using cells isolated from different wild-type or Gcn2-/- mice.

Vehicle versus halofuginone, vehicle versus rapamycin, halofuginone versus rapamycin. Gcn2-/- versus wild-type T cells treated with vehicle, halofuginone, or rapamycin.

first: Mark

last: Sundrud

first: Thaddeus

last: Carlson


title: Gene expression changes in Itpr triple conditional knockout T cell progenitors

status: Public on May 28 2014

city: La Jolla

first: Sylvia

last: Evans

address: 9500 Gilman Drive

institute: University of California San Diego

summary:
Calicum plays critical roles in developing T cells, promoting survival, proliferation, and differentiation at multiple stages of maturation. Calcium release from intracellular stores due to T cell receptor and pre-T cell receptor signaling is thought to require the inositol triphosphate receptors (Itpr), however the requirement for these receptors has not been investigated. We used microarrays to examine gene expression differences between control and Itpr deficient T cell progenitors.
We used microarrays to identify changes in the transcriptional programme of developing T cells prior to acquisition of a mature T cell receptor and identified several developmentally important genes altered in the absence of Itpr.

overall_design: Thymocyte progenitors at DN4 or ISP were harvested for RNA extraction from three independent control Itpr1/Itpr2/Itpr3 triple homozygous floxed (CTL) or Tie2-Cre Itpr1/Itpr2/Itrp3 triple homozygous floxed (KO)  thymii, pooled, and hybridized on Affymetrix microarrarys. To obtain a homogenous population of thymocyte progenitors, we FACS purified cells and collect RNA from only DN4 or ISP T cells. ISP T cells were defined as CD4- CD8+ CD24+ CD3-. DN4 T cells were defined as CD45+ CD24+ CD3- CD4- CD8- CD25- CD44- CD19- B220- gdTCR- Ter119- Mac1- Gr1-. Thymocytes were harvested from neonatal mice, ranging from 7 to 10 days of age and lacked any signs of malignancy or disease.

first: Rafael

last: Gomez-Amaro

last: Stachura

first: Kunfu

last: Ouyang

last: Traver

first: Ju

last: Chen


title: Expression data from periplaque regions in multiple sclerosis spinal cord

city: Lyon

first: Serge

last: Nataf

address: 8 Rue Guillaume Paradin

department: Inserm U1028 - CNRS UMR5292

country: France

institute: Neuroscience Research Center of Lyon

summary:
There have been few studies that have focused on the periplaque regions surrounding demyelinated plaques, especially in spinal cords. Areas of incomplete demyelination have been demonstrated but poorly studied. The present study aimed to analyze the molecular immunopathology of periplaque demyelinated lesions (PDLs) in the spinal cord of patients with secondary progressive multiple sclerosis (MS).
To achieve this goal, the transcriptomic profiles of PDLs were analyzed in post-mortem tissues derived from the cervical spinal cord of 8 patients with primary or secondary progressive MS.

overall_design: Sixteen spinal cord samples were microdissected for RNA extraction and hybridization on Affymetrix microarrays. Eight periplaque samples (P) were compared to normal appearing white matter (N) from the same patient.

first: Alice

last: Lieury


title: Defining Differentiated Methylation Regions Especial for Pluripotency Acquisition and Maintenance in Human Stem Cell

city: Guangzhou

first: Wenyin

last: HE

state: Guangdong

address: No.63, Duobao road

institute: The third affiliated hospital of Guangzhou medical university

type: Non-coding RNA profiling by genome tiling array

summary: Here, we determined the DNA methylation profiles of 12 human cell lines, including 2 ESC lines, 2 pESC lines,4 virally-delivered iPSC lines, 2 episomal-delivered iPSC lines, and 2 parent cell lines that iPSCs derived from using Illumina’s Infinium HumanMethylation450. The iPSCs exhibited a hypermethylation status similarly to ESCs but distinct differences from the parent cells. Genes of common methylation pattern between iPSCs and ESCs were regarded as critical factors for stemness, while differences existing between iPSCs and ESCs implied that iPSCs partly retained the parental characteristics and gained de novo methylation aberrances during cell reprogramming. No significant variant was identified between virally- and episomal- systems. De novo differentiated methylation regions as the signature of particular stem cell lines were figured out in detail in this study.

last: He

first: Yong

last: Fan

first: Xiaofang

last: Sun


title: Seminoma and embryonal carcinoma footprints identified by analysis of integrated genome-wide epigenetic and expression profiles of germ cell cancer cell lines (methylation data).

city: Rotterdam

first: Martin

middle: Anne

last: Rijlaarsdam

address: Wytemaweg 80

department: Pathology

country: Netherlands

institute: Erasmus MC

summary:
Background: Germ Cell Cancers (GCC), originating from Primordial Germ Cells /gonocytes, are the most common cancer in young men, subdivided in seminoma (SE) and non-seminoma (NS, stem cell component: embryonal carcinoma (EC)). Somatic mutations are rarely found in GCC. It has been proposed that disruption of the epigenetic constitution, either primarily or secondary (e.g. environmental influences), is involved in cancer, and specifically in GCC.
Results: This study aims at identifying epigenetic footprints of SE and EC cell lines in genome-wide profiles by studying the interaction between gene expression, DNA CpG methylation and histone modifications, and their function in GCC and related disruption of germ cell maturation. Two well characterized GCC-derived cell lines were compared, one representative for SE (TCam-2) and the other for EC (NCCIT). Data was acquired using the Illumina HumanHT-12-v4 (gene expression) and HumanMethylation450 BeadChip (methylation) microarrays as well as ChIP sequencing (activating histone modifications (H3K4me3, H3K27ac)). The data show that known germ cell markers are not only present and differentiating between SE and NS at the expression level, but also in the epigenetic landscape.
Conclusion: The overall similarity between TCam-2 / NCCIT supports an erased embryonic gem cell arrested in early gonadal development as common origin. Subtle difference in the (integrated) epigenetic and expression profiles indicated TCam-2 to exhibit a more germ cell like profile (enrichment Androgen regulation) while NCCIT proved more pluripotent. The results provide insight into an integrated analysis of the functional genome in GCC cell lines.

overall_design: Two wildtype germ cell cancer (type II germ cell tumor) cell lines were analyzed. TCam-2 (representative for the seminomatous subtype of germ cell cancer) , [1, 2]) and NCCIT (representative of the non-seminomatous (embryonal carcinoma) subtype of germ cell cancer, [3]).   1. Mizuno, Y., et al., [Establishment and characterization of a new human testicular germ cell tumor cell line (TCam-2)]. Nihon Hinyokika Gakkai Zasshi, 1993. 84(7): p. 1211-8.  2. de Jong, J., et al., Further characterization of the first seminoma cell line TCam-2. Genes Chromosomes Cancer, 2008. 47(3): p. 185-96.  3. Teshima, S., et al., Four new human germ cell tumor cell lines. Lab Invest, 1988. 59(3): p. 328-36.

first: Yvonne

last: van der Zwan

first: Ad

last: Gillis

first: Lambert

last: Dorssers

first: Leendert

last: Looijenga


title: MMP3 treatment of Panc-2 cells

city: Jacksonville

first: Derek

middle: Charles

last: Radisky

state: Florida

address: 4500 San Pablo Road

department: Cancer Biology

institute: Mayo Clinic

summary: Response of pancreas cancer cells to treatment with recombinant MMP3

overall_design: Cells were treated with 100U/ml MMP3 for 4 days, then isolated for RNA.  The submitted experiments represent two different experiments performed at different times

first: D


title: Expression data comparing chemoresistant (cisplatin and doxorubicin) hepatospheres and differentiated HCC cells

first: Kin Wah

last: Lee

summary:
To identify candidate genes that are up-regulated in chemoresistant (cisplatin and doxorubicin) hepatospheres as compared with their differentiated counterparts
Affymetrix Human Genome U133 Plus GeneChip 2.0

overall_design: PLC/PRF/5 HCC cells were grown as spheroids and treated with cisplatin and doxorubicin combination. Differentiated counterparts were generated by addition of FBS in the spheroids and allowed to attach.

first: Terence


title: RNA-Seq and expression microarray highlight different aspects of the fetal amniotic fluid transcriptome [microarray]

status: Public on May 27 2014

city: Boston

first: Lillian

last: Zwemer

address: 800 Washington St, Box 394

department: Mother Infant Research Institute

institute: Tufts Medical Center

summary:
The second trimester fetal transcriptome can be assessed based on cell-free RNA found within the amniotic fluid supernatant. The objective of this study was to compare the suitability of two technologies for profiling the human fetal transcriptome: RNA-Seq and expression microarray. Comparisons were based on total numbers of gene detected, rank-order gene expression, and functional genomic analysis.
Fewer gene transcripts were observed using RNA-Seq than microarray (4,158 vs 8,842). Correlation of total expression within each sample ranged from R=0.43 to R=0.57. On average, there was 59% concordance in gene identity among the top 10% of genes ranked by expression. The RNA-Seq data yielded more significant pathways enrichment within the ?Physiological Systems Development and Function? categories of IPA. Alternative splicing of many well-known genes, including those previously studied in fetal development, such as H19 and IGF2  is detected by RNA-Seq. Also included in this paper is discussion of the technical challenges inherent to working with cell-free fetal RNA and possible solutions.

overall_design: Cell-free fetal RNA from the amniotic fluid supernatant of five second trimester fetuses was divided and prepared in tandem for analysis using either the Illumina HiSeq 2000 or Affymetrix HG-U133 Plus 2.0 GeneChip microarray.

middle: M

first: Lisa

last: Hui

first: Heather

last: Wick

first: Diana

last: Bianchi


title: DNA methylation alteration and gene expression sigature in brainstem, thalamic, and supratentorial gliomas

city: Durham

first: Hai

last: Yan

state: NC

address: 199B-MSRB, Research Drive

institute: Duke University

type:
Expression profiling by array
Methylation profiling by array

summary: Gliomas arising in the brainstem and thalamus are devastating tumors that are difficult to surgically resect due to their proximity to eloquent brain structures. Here, we performed a comprehesive genomic and epigenomic study, using gene expression and methylation microarrays, to research on th different genomic and epigenetic signatures between brainstem, thalamic, and supratentorial gliomas.

overall_design: Comparison of brainstem, thalamic and supratentorial gliomas

first: Liwei

last: Zhang

first: Lee

last: Chen

first: Hong

last: Wan

first: Weixin

last: Zhou

first: Jie

last: Feng

first: Shaohua

last: Yang

first: Sian

last: Jones

first: Rui

first: Patrick

middle: J

last: Killela

first: Junting

first: Zhen

last: Wu

first: Guilin

last: Li

first: Shuyu

last: Hao

first: Yu

last: Wang

first: Joseph

middle: B

last: Webb

first: Roger

last: McLendon

first: Yiping

first: Zachary

last: Reitman

first: Darell

last: Bigner


title: Expression data from skeletal muscle satellite cells at different development stages

status: Public on May 26 2014

city: Ottawa

first: Hang

last: Yin

state: Ontario

address: 501 Smyth Road, CCW 5113

department: Sprott Centre for Stem Cell Research

country: Canada

institute: Ottawa Hospital Research Institute

summary:
Satellite cells are responsible for the long-term regenerative capacity of adult skeletal muscle. The diminished muscle performance and regenerative capacity of aged muscle is thought to reflect progressive fibrosis and atrophy. Whether this reduction in muscle competency also involves a diminishment in the intrinsic regulation of satellite cell self-renewal remains unknown.
We used microarray to identify gene expression changes underlying the marked reduction in the capacity of satellite cells to self-renew, contribute to regeneration and repopulate the niche as they age.

overall_design: Skeletal muscles from heterozygous Pax7-ZsGreen mice were isolated at defined stages: E17.5 (fetal - whole forelimb and hindlimb), postnatal day 21 (adolescent - hindlimb), 2-3 month old (adult - hindlimb) and >1 year old (Aged - hindlimb) mice. ZsGreen-positive skeletal muscle satellite cells were isolated by FACS and pooled (fetal n=4, adolescent n=6, adult n=8 and aged n=8 mice).

first: Feodor

last: Price

first: Michael

middle: A

last: Rudnicki


title: Comparative analysis of gene expression in Fra-1+/+ and Fra-1-/- mice lung

status: Public on May 22 2014

city: Chicago

first: Rajasekaran

last: Subbiah

state: IL

address: 909, South Wolcott Ave, Room # 7160

department: Pediatrics

institute: University of Illinois at Chicago

summary: We hypothesized that gene expression in lungs of Fra-1+/+ and Fra-1-/- mice are divergent thus contributing fibrosis. More specifically, Fra-1-/- mice are increased susceptible to fibrosis. In order to test these hypotheses at the gene expression level, we utilized microarray analysis to examine transcriptional differences between Fra-1+/+ and Fra-1-/- mice at early time point.

overall_design: This study utilizes microarray analysis to test these hypotheses. 5 days PBS and bleomycin treated lung samples from both Fra-1+/+ and Fra-1-/- mice were used. RNA was isolated and used for global gene expression profiling (Affymetrix MoGene 1.0ST v1 Array). The raw probe signal intensities were quantile normalized over all samples, summarized with the robust multi-array average (RMA) algorithm and log2 transformed with a median polish, using the Affymetrix Power Tools. We considered a transcript cluster (gene-level) to be reliably expressed in a sample if the Affymetrix implemented DABG (detection above ground) p-value was less than 0.05. We used local-pooled-error (LPE) estimates and robust statistical tests for evaluating significance of each gene's differential expression in a comparison.

first: Subbiah

last: Rajasekaran

first: Narsa

last: Reddy

first: Wei

last: Zhang

first: Sekhar

middle: P


title: Gene expression in diploid and evolved tetraploid RPE-1 and BJ-1 cells

first: Neil

last: Ganem

address: 72 E. Concord St

department: Pharmacology and Medicine

institute: Boston University School of Medicine

summary: Both diploid RPE-1 and BJ-1 cells were made tetraploid by transient treatment with the cytokinesis inhibitor DCD. Proliferating tetraploids from both BJ-1 and RPE-1 were selected and isolated. The gene expression profiles of the proliferating tetraploid cells were then compared to the diploids from which they originated.

overall_design: Triplicate biological samples were collected and analyed.


title: Towards epigenetic understanding and therapy of insulin resistance by intranuclear insulin [DNA methylation]

status: Public on May 23 2014

city: Hangzhou

first: Yun

last: Xiao

address: Yuhangtang Road

institute: Zhejiang University

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

overall_design: Insulin resistance HepG2 cell were selected in our experiments.Two conditions were compared with three replicates each. These are:(1) Insulin resistance HepG2(R-HepG2) and (2) Biomineralized insulin treated HepG2 (BI).

first: Zheng

first: Yiyu

last: Cheng

first: Ruikang

last: Tang


title: The effect of Crem absence on gene expression in mouse adrenal glands.

status: Public on May 25 2014

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana

summary:
CREM (cAMP responsive element modulator) together with CREB and ATF-1 belong to the CREB family of transcriptional factors, that respond to cyclic AMP signaling and bind to cAMP responsive element (CRE) sites in promoters of selected genes. CREM can produce isoforms that have either activating or repressing functions, depending on the transcription of specific exons. In adrenal glands it is involved in the regulation of expression of genes for steroid hormone synthesis.
In this dataset, we include the expression data obtained from wild-type and Crem knock-out mouse adrenal glands.

overall_design: 2 condition experiment: 2 strains (WT, Crem-/-). 5 biological replications per condition.

first: Rok

last: Košir

first: Martina

last: Perše

first: Gregor

last: Majdič

last: Fink

first: Damjana

last: Rozman


title: Myocilin regulates cell proliferation and survival by activating the ERK pathway

status: Public on May 21 2014

city: Rockville

first: Radu

last: Cojocaru

state: MD

address: 5635 Fishers Lane, Suite 510

institute: Elsevier

summary: Myocilin, a causative gene for open-angle glaucoma, encodes a secreted glycoprotein of unknown function. To elucidate its function(s), we produced a stably transfected HEK293 cell line expressing myocilin and compared the expression profiles between the myocilin-expressing cell line and a vector control cell line using Affymetrix GeneChip U133 plus 2.0 array. A significant portion of differentially-expressed genes in the myocilin-expressing cells was associated with cell growth and cell death, suggesting that myocilin may have an important role regulating cell growth/survival..

overall_design: We developed vector control and myocilin-expressing Tet On HEK293 cell lines. The gene expression profiles in two stable cell lines were compared.

first: Myung

middle: K

last: Joe

first: Heung

middle: S

last: Kwon

first: Stanislav

middle: I

last: Tomarev


title: Global gene expression analysis in macrophages treated with Nutlin-3

city: RTP

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: The goal of the study is to identify p53 target genes specific to macrophages using the p53 stabilizer, Nutlin-3.

overall_design: Macrophages were differentiated x-vivo from monocytes obtained from healthy volunteers either left untreated or treated for 2 hours with 100 ng/mL of lipopolysaccharide (LPS), 0.1%v/v of DMSO (vehicle control for Nutlin-3) or 10 micromolar Nutlin-3. Three replicates were included for each treatment group.

first: Julie

last: Lowe

first: Daniel

last: Menendez

first: Michael

last: Resnick


title: Integrated bioinformatic and wet-lab approach to identify potential oncogenic networks in neuroblastoma: MSX1

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

institute: msterdam UMC and University of Amsterdam

summary: mRNA profiles of thousands of human tumors are available, but methods to deduce oncogenic signaling networks from these data lag behind. It is especially challenging to identify main-regulatory routes, and to generalize conclusions obtained from experimental models. We designed the bioinformatic platform R2 (http://r2.amc.nl) in parallel with a wet-lab approach of neuroblastoma. Here we demonstrate how R2 facilitates an integrated analysis of our neuroblastoma data. Analysis of the MYCN pathway suggested important regulatory connections to the polyamine synthesis route, the Notch pathway and the BMP/TGFβ pathway. A network of genes emerged connecting major oncogenes in neuroblastoma. Genes in the network carried strong prognostic values and were essential for tumor cell survival.

overall_design: Triplicate time course experiments of MSX1 induction, with 4 timepoints.

first: Dirk

last: Geerts

first: Jan

last: Koster

first: Rogier

last: Versteeg


title: Towards epigenetic understanding and therapy of insulin resistance by intranuclear insulin

first: Yun

last: Xiao

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Epigenome analysis of normal and preeclamptic placenta samples

status: Public on May 20 2014

city: Philadelphia

first: Lauren

last: Anton

state: PA

address: 421 Curie Blvd, 1349 BRB II/III

department: Obstetrics and Gynecology

institute: University of Pennsylvania

summary: Preeclampsia (PE), a hypertensive disorder of pregnancy, is hypothesized to be associated with, if not mechanistically related to abnormal placental function. However, the exact mechanisms regulating the pathogenesis of PE remain unclear. While many studies have investigated changes in gene expression in the PE placenta, the role of epigenetics in PE associated placental dysfunction remains unclear.  Using the genome-wide Illumina Infinium Methylation 450 BeadChip array, we analyzed gene-specific alterations in DNA methylation in placental biopsies collected from normal pregnant women delivering at term (n=14), with term PE (≥37 weeks; n=19) or with preterm PE (<37 weeks, n=12).  Of the 485,582 gene loci on the array, compared to controls, 229 loci were differentially methylated in PE placentas and 3411 loci were differentially methylated in preterm PE (step up p-value <0.05 and >5% methylation difference). Functional annotation of the differentially methylated genes in preterm PE placentas revealed a 32 gene cluster in the cadherin and cell adhesion functional groups (Benjamini p<0.00001). Hypermethylation of CDH11 (p=0.0143), COL5A1 (p=0.0127) and TNF (p=0.0098) and hypomethylation of NCAM1 (p=0.0158) was associated with altered mRNA expression in preterm PE placentas. These studies demonstrate aberrant methylation, correlating with disease severity, in PE placentas.

overall_design: Bisulphite converted DNA from the 45 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip v1.2

first: Michal

last: Elovitz


title: Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes as an In Vitro Model for Coxsackievirus B3-Induced Myocarditis and Antiviral Drug Screening Platform

status: Public on May 19 2014

city: Stanford

first: Jared

last: Churko

state: CA

address: 265 Campus Dr G1105 SIM1

department: Radiology

institute: Stanford

summary:
ABSTRACT  Background: Viral myocarditis is a life-threatening illness that may lead to heart failure or cardiac arrhythmias. This study examined whether human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) could be used to model the pathogenic processes of coxsackievirus-induced viral myocarditis and to screen antiviral therapeutics for efficacy.   Methods and Results: Human iPSC-CMs were infected with a luciferase-expressing mutant of the coxsackievirus B3 strain (CVB3-Luc). Brightfield microscopy, immunofluorescence, and calcium imaging were used to characterize virally infected hiPSC-CMs. Viral proliferation on hiPSC-CMs was subsequently quantified using bioluminescence imaging. For drug screening, select antiviral compounds including interferon beta 1 (IFNβ1), ribavirin, pyrrolidine dithiocarbamate (PDTC), and fluoxetine were tested for their capacity to abrogate CVB3-Luc proliferation in hiPSC-CMs in vitro. The ability of some of these compounds to reduce CVB3-Luc proliferation in hiPSC-CMs was consistent with the reported drug effects in previous studies. Finally, mechanistic analyses via gene expression profiling of hiPSC-CMs infected with CVB3-Luc revealed an activation of viral RNA and protein clearance pathways within these hiPSC-CMs after IFNβ1 treatment.   Conclusions: This study demonstrates that hiPSC-CMs express the coxsackievirus and adenovirus receptor, are susceptible to coxsackievirus infection, and can be used to confirm antiviral drug efficacy. Our results suggest that the hiPSC-CM/CVB3-Luc assay is a sensitive platform that could be used to screen novel antiviral therapeutics for their effectiveness in a high-throughput fashion.
For this experiment, human induced pluripotent stem cell derived cardiomyocytes were infected with coxsackievirus at multiplicity of infection (MOI) of 5 for 8 hours. Cells were treated with and without interferon beta 1 in order to determine if treatment activates antiviral response genes and/or viral clearance pathways.

overall_design: 4 total samples (2 for each condition) were analyzed

first: Arun

last: Sharma

first: Joseph

last: Wu


title: Novel strategies to enforce an epithelial phenotype in mesenchymal cells

city: New Haven

first: Beile

last: Gao

state: CT

address: 295 Congress Ave

department: Microbial Pathogenesis

institute: Yale University

summary:
E-cadherin downregulation in cancer cells is associated with epithelial-to-mesenchymal transition (EMT) and metastatic prowess, but the underlying mechanisms are incompletely characterized. In this study, we probed E-cadherin expression at the plasma membrane as a functional assay to identify genes involved in E-cadherin downregulation. The assay was based on the E-cadherin-dependent invasion properties of the intracellular pathogen Listeria monocytogenes. On the basis of a functional readout, automated microscopy and computer-assisted image analysis were used to screen siRNAs targeting 7,000 human genes. The validity of the screen was supported by its definion of several known regulators of E-cadherin expression, including ZEB1, HDAC1 and MMP14. We identified three new regulators (FLASH, CASP7 and PCGF1), the silencing of which was sufficient to restore high levels of E-cadherin transcription. Additionally, we identified two new regulators (FBXL5 and CAV2), the silencing of which
was sufficient to increase E-cadherin expression at a post-transcriptional level. FLASH silencing regulated the expression of E-cadherin and other ZEB1-dependent genes, through post-transcriptional regulation of ZEB1, but it also regulated the expression of numerous ZEB1-independent genes with functions predicted to contribute to a restoration of the epithelial phenotype. Finally, we also report the identification of siRNA duplexes that potently restored the epithelial phenotype by mimicking the activity of known and putative microRNAs. Our findings suggest new ways to enforce epithelial phenotypes as a general strategy to treat cancer by blocking invasive and metastatic phenotypes associated with EMT

overall_design: The experiment is designed to compare gene expression in a mock treated HeLa229 cells versus FLASH-depleted and ZEB1-depleted cells in order to asses the specific role of ZEB1 and FLASH in epithelial-to- mezenchymal transition.

first: Ana-Maria

last: Dragoi

first: Rachel

last: Swiss

first: Herve

last: Agaisse


title: Identification of beta-cetenin/TCF4 target genes in LS174T colorectal cancer cells using gene expression arrays

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB Barcelona

summary: Aberrant activation of WNT signaling and loss of BMP signals represent the two main alterations leading to the initiation of colorectal cancer (CRC). Here we screen for genes required for maintaining the tumor stem cell phenotype and identify the zinc-finger transcription factor GATA6 as key regulator of the WNT and BMP pathways in CRC. GATA6 directly drives the expression of LGR5 in adenoma stem cells while it restricts BMP signaling to differentiated tumor cells. Genetic deletion of Gata6 in mouse colon adenomas increases the levels of BMP factors, which signal to block self-renewal of tumor stem cells. In human tumors, GATA6 competes with beta-catenin/TCF4 for binding to a distal regulatory region of the BMP4 locus that has been previously linked to increased susceptibility to develop CRC. Hence, GATA6 creates a permissive environment for tumor stem cell expansion by controlling the major signaling pathways that influence CRC initiation.

overall_design: A 4-hydoxy tamoxifen inducible system was used to inducibly block beta-catenin/TCF activity for a period of 36h. Briefly, the ERT2 domain from the pCMV-CRE-ERT2 (Feil et al., 1996) was amplified by PCR and cloned into a modified FUGW lentiviral vector backbone (Lois et al., 2002). NTCF was then amplified byPCR from the pCDNA3.1-NTCF-NLS (van de Wetering et al., 2002) and cloned in frame upstream of the ERT2 from the FUW-CMV-ERT2 (ET) to create the FUW-CMV-NTCF-ERT2 (NET). Total RNA was extracted using the TRIzol® Plus RNA Purification Kit (Life Technologies).

first: Gavin

last: Whissell

last: Stephan-Otto Attolini

first: Eduard

last: Batlle


title: The effect of Crem absence on gene expression in mouse liver.

first: Peter

last: Juvan

summary:
CREM (cAMP responsive element modulator) together with CREB and ATF-1 belong to the CREB family of transcriptional factors, that respond to cyclic AMP signaling and bind to cAMP responsive element (CRE) sites in promoters of selected genes. CREM can produce isoforms that have either activating or repressing functions, depending on the transcription of specific exons.
In this dataset, we include the expression data obtained from wild-type (WT) and Crem knock-out (KO) mouse liver. Several comparisons were made. KO<WT at 0h, KO<WT at 12 h, 0h<12h in WT and 0h<12h in KO.

overall_design: 4 condition experiment: 2 strains (WT, Crem-/-), 2 time points (0h and 12h). 5 biological replications per condition.

first: Rok

last: Košir

first: Martina

last: Perše

first: Gregor

last: Majdič

last: Fink

first: Damjana

last: Rozman


title: Expression profiles of sorted murine lung Eosinophils following allergen challenge

city: Cincinnati

first: Marc

middle: E

last: Rothenberg

state: OH

address: 3333 Burnet Ave. MLC-7028

department: Allergy

institute: Cincinnati Children's Hospital Medical Center

summary: The eosinophil transcriptome analysis indicated a robust transcription change in eosinophils following allergen challenge in the lung.

overall_design: Eosinophils were FACS-sorted from Saline or OVA challenged lung with high purity and then subjected to genome-wide RNA microarray

first: Ting

last: Wen

first: Ben

last: Wahl

first: Oliver

last: Pabst


title: PBMCs exposed to the Mycobacterium tuberculosis H37Ra strain

city: Cartagena

first: Niradiz

last: Reyes

address: Campus de Zaragocilla. Facultad de Medicina

country: Colombia

institute: Universidad de Cartagena

summary: Human peripheral blood mononuclear cells were cultured in presence of H37Ra strain at 37oC, 5%CO2. Cellular aggregates were collected at 24h, and RNA extracted and hybridized to Affymetrix microarrays (HG-U133). Raw data from microarray experiments was analyzed with dCHIP and SAM programs to determine the significance of changes at the biological context.

overall_design: PBMCs were exposed in triplicate to H37Ra strain. PBMCs from the same donor were cultured in triplicate at the same conditions than treated samples. RNA was extracted from each sample and hybridized to Affymetrix Human arrays.

first: Ismael

first: Alfonso

last: Bettin

first: Jan

last: Geliebter


title: Gene profiling on mandibular arches (MdPA1) from Tbx1+/+ and Tbx1-/- mouse embryos E9.5

city: Bronx

first: Tingwei

last: Guo

state: NY

address: 1301 Morris Park Avenue, Room 408

department: Genetics

institute: Albert Einstein College of Medicine

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

overall_design: To obtain enough RNA for microarray hybridization experiments, dissected mandibular arches from three Tbx1+/+ and three Tbx1-/- E9.5 embryos were pooled according to genotype, with three microarrays performed in total per genotype.  Affymetrix Mouse Gene ST 1.0 arrays (Affymetrix) were used. Hybridization, washing, staining and scanning were performed in the Genomics Core at Einstein (http://www.einstein.yu.edu/genetics/CoreFacilities.aspx?id=23934) according to the Affymetrix manual.

first: Ping

last: Kong

first: C

last: Carpenter

first: S

last: Macchiarulo

last: Racedo

last: Ola

first: V

last: Aggarwal

first: Bernice

last: Morrow


title: Calcium and Magnesium responses in Brassica rapa

city: Loughborough

first: Neil

last: Graham

state: Leicestershire

address: Sutton Bonington Campus

department: Plant and Crop Sciences

institute: University of Nottingham

summary: A mapping population of Brassica rapa (BraIRRI, IMB211xR500) was grown under four external calcium and magnesium concentrations in controlled conditions. RNA was extracted and hybridised to the Affymetrix Brassica Exon 1.0 ST array. The aim of the experiment was to identify cis- and trans- expression quantitative trait loci.

overall_design:
In total 279 samples were analysed. The parents of the mapping population were grown at all four treatment levels (LL, HL, LH, HH) with three biological replicates per treatment, plus 12 technical replicates (n=36).
A 2x2 combination of external calcium and magnesium concentrations were imposed to give four treatments (LL, HL, LH, HH) as follows: the high (H) concentrations were 3.5 g L-1 (24 mM) CaCl2 and 3.04 g L-1 (15 mM) MgCl2 and the low (L) concentrations were 0.44 g L-1 (3 mM) CaCl2 and 0.2 g L-1 (1 mM) MgCl2
For the mapping population (total = 85 lines), 85 lines were analysed for the LL treatment, 81 lines were analysed for the LH treatment and 65 lines were analysed for the HL treatment. Twelve technical replicates were also analysed.

first: John

last: Hammond

first: Seosamh

last: O Lochlainn

first: Martin

middle: R

last: Broadley