title: Maturation of the 90S pre-ribosome requires Mrd1 dependent U3 snoRNA and 35S pre-rRNA structural rearrangements

status: Public on Jan 15 2018

city: Edinburgh

first: Sander

last: Granneman

address: Mayfield Road, Kings Buildings, Waddington building, room 3.06

department: Centre for Synthetic and Systems Biology

country: United Kingdom

institute: University of Edinburgh

summary: In eukaryotes, biogenesis of ribosomes requires folding and assembly of the precursor rRNA (pre-rRNA) with a large number of proteins and snoRNPs into huge RNA-protein complexes. In spite of intense genetic, biochemical and high resolution cryo-EM studies in Saccharomyces cerevisiae, information about the conformation of the earliest 35S pre-rRNA is limited. To overcome this, we performed high-throughput SHAPE chemical probing on the 35S pre-rRNA associated with 90S pre-ribosomes. We focused our analyses on external (5´ETS) and internal (ITS1) transcribed spacers as well as the 18S region. We show that in the 35S pre-rRNA, the central region of the 18S is in a more open configuration compared to 20S pre-rRNA and that the central pseudoknot is not formed. The essential ribosome biogenesis protein Mrd1 influences the structure of the 18S part locally and is involved in organizing the central pseudoknot and surrounding structures. Our results demonstrate that the U3 snoRNA dynamically interacts with the 35S pre-rRNA and that Mrd1 is required for disrupting U3 snoRNA base-pairing interactions in the 5'ETS. We propose that the dynamic U3 snoRNA interactions and Mrd1 are essential for establishing the structure of the central region of 18S that is required for processing and 40S subunit function.

overall_design:
Two different ribosomal RNA species were probed with 1M7

This series contains 4 samples re-analyzed from GSE83821. The raw data associated with these samples in this series (GSM2856218-GSM286221) include the barcodes not present in the raw data from the original samples from GSE83821 (GSM2219115-GSM2219118).


title: Interplay between genome topology and gene regulation during somatic cell reprogramming [HiC-seq]

status: Public on Jan 30 2018

city: Barcelona

first: Thomas

last: Graf

address: c/Dr. Aiguader, 88. PRBB Building

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: CRG (Center for Genomic Regulation)

summary: Studies of genome topology, chromatin state and transcriptome dynamics during highly-efficient somatic cell reprogramming

overall_design: Genome topology profiling of B cells reprogramming to pluripotent cells and (induced) pluripotent stem cells using in-situ Hi-C

first: Ralph

last: Stadhouders

first: Enrique

last: Vidal

first: Antonio

last: Gomez


title: Interplay between genome topology and gene regulation during somatic cell reprogramming [4C-seq]

overall_design: Profiling genome-wide chromatin conformation of the Nanog gene in B cells reprogramming to pluripotent cells and (induced) pluripotent stem cells using 4C-Seq


title: Defining the Nasal Transcriptome in Granulomatosis with Polyangiitis

status: Public on Aug 29 2018

city: Bethesda

first: Peter

middle: C.

last: Grayson

state: MD

address: 10 Center Dr Building 10 6N216G

department: NIAMS

country: USA

institute: NIH

summary: Objectives: To determine whether disease processes related to granulomatosis with polyangiitis (GPA) are reflected in gene expression profiles of nasal mucosa.    Methods: Nasal brushings of the inferior turbinate were obtained from 32 patients with GPA (10 with active nasal disease, 13 with prior nasal disease, 9 with no history of nasal disease) and a composite comparator group with and without inflammatory nasal disease (12 healthy people, 15 with sarcoidosis, 8 with allergic rhinitis). Differential gene expression was assessed between subgroups of GPA and comparators.    Results: 339 genes were differentially expressed between the GPA and comparator groups (absolute fold change > 1.5; false discovery rate < 0.05). Top canonical pathways upregulated in nasal brushings from patients with GPA include granulocyte adhesion and diapedesis (p=8.6 E-22), agranulocyte adhesion and diapedesis (p=1.3 E-14), interleukin 10 signaling (3.0 E-11), and TREM1 signaling (9.0 E-11). A set of genes differentially expressed in GPA independent of nasal disease activity status included genes related to epithelial barrier integrity (fibronectin 1, desmosomal proteins) and several matricellular proteins (e.g. osteonectin, osteopontin). Significant overlap of differentially expressed genes was observed between active and prior nasal disease GPA subgroups. Peripheral blood neutrophil and mononuclear gene expression levels associated with GPA were similarly altered in the nasal gene expression profiles of patients with active or prior nasal disease.    Conclusions: Profiling the nasal transcriptome in GPA reveals gene expression signatures related to innate immunity, inflammatory cell chemotaxis, extracellular matrix composition, and epithelial barrier integrity. Airway-based expression profiling is feasible and informative in GPA.

middle: C

first: Katrina

last: Steiling


title: Oxygen responsive lncRNAs in MCF-7 breast cancer cells

status: Public on Dec 31 2017

city: Taipei

first: Liang-Chuan

last: Lai

state: Taiwan

address: 1 Jen-Ai Road, Sec 1

department: Physiology

country: Taiwan

institute: National Taiwan University

type: Non-coding RNA profiling by high throughput sequencing

summary: Previous studies have identified oxygen-responsive lncRNAs as having a role in the onset of several cancers. However, the lncRNAs regulated by oxygen in breast cancer have not been identified. In this study, we hypothesized that a group of lncRNAs were regulated by oxygen in breast cancer. To identify the oxygen-responsive lncRNAs, next-generation sequencing was performed

overall_design: Cells were harvested under normoxia (O2), hypoxia (N2) and re-oxygenation (Re-O2) conditions. Each condition was done in triplicate. SRA study accession: SRP077846; BioProject accession: PRJNA327155


title: Interplay between genome topology and gene regulation during somatic cell reprogramming [RNA-seq]

type: Expression profiling by high throughput sequencing

overall_design: Gene expression profiling of B cells reprogramming to pluripotent cells and (induced) pluripotent stem cells using RNA-Seq


title: Gene expression alterations upon knock down of transcription factors

status: Public on Dec 01 2017

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

summary: To investigate the influence of PRMT3, PRMT6, TAL1 and RUNX1 on gene expression they were knocked down by shRNA in K562 cells or human CD34 cells.

overall_design: Cells were lentivirally transduced with specific shvectors or a control shvector targeted against LacZ. Transduction was monitored by GFP, only cells with more than 95% GFP positiv cells were further processed. Cells were harvested 5 days after transduction.

first: Jörn

last: Lausen


title: Gene expression profiling of Brucella abortus-infected mouse macrophages

status: Public on Nov 06 2017

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

summary:
Gene expression analysis of wild-type and STING knock-out mouse bone marrow-derived macrophages (mBMDM) infected with Brucella abortus or transfected with Brucella abortus DNA.
Genes whose expression are affected by Brucella abortus in a STING-dependent manner will be identified and signaling pathways regulated by STING will be elucidated.

overall_design: Mouse BMDMs were infected with Brucella abortus or transfected with Brucella abortus DNA for 17 hours. Total RNA was extracted for array analysis.

first: Sergio

last: Oliveira

first: Glen

last: Barber


title: Exploiting Prmt5-orchestrated intron detention signatures to treat splicing-addicted malignant glioma tumors

status: Public on Sep 29 2017

city: Rochester

first: Paul

middle: L.

last: Boutz

state: NY

address: 601 Elmwood Ave.

department: Biochemistry & Biophysics

institute: University of Rochester School of Medicine

summary: The presence of introns within otherwise completely spliced mRNA molecules has been associated with splicing errors. Recent evidence however suggests that intron-based transcript inactivation is widespread and regulates the cytoplasmic availability of productive transcript isoforms. The regulatory and functional details of this process have remained unclear. We here present the arginine methyltransferase Prmt5 as the top hit from an in vivo RNAi screen for therapeutic vulnerabilities of malignant gliomas. Inhibition of Prmt5 inactivates hundreds of pro-proliferative genes by increasing the inclusion of so-called “detained” introns (DIs) within mRNAs. DI-based inactivation of these genes causes cessation of cell proliferation and exhibits potent anti-tumor effects in vitro and in vivo. Gliomas become increasingly sensitive to Prmt5 inhibition upon tumor progression. Furthermore, DI-based gene expression regulation is not restricted to cancer, but contributes to cell differentiation by governing the expression levels of gene sets related to both cell cycle and cell identity.

overall_design: 2 experimental conditions (vehicle DMSO treatment, EPZ015666 treatment), in triplicate, for 72h, of human U-87 MG tumor cells.

first: Christian

middle: J

last: Braun

first: Monica

last: Stanciu

first: Philip

middle: A

last: Sharp

first: MIchael

middle: T

last: Hemann

first: Jacqueline

last: Lees


title: Gene expression associated with PTSD in World Trade Center responders: An RNA sequencing study

status: Public on Feb 13 2018

city: BUFFALO

first: Eduardo

last: Cortes

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

summary: The gene expression approach has provided promising insights into the pathophysiology of PTSD. However, few studies used hypothesis-free transcriptome-wide expression approach. Transcriptome-wide expression study using RNA sequencing (RNA-Seq) of whole blood was conducted in 324 World Trade Center responders (201 with never, 81 current and 42 past PTSD). The current and never PTSD samples were randomly split to form both discovery (N=195) and replication (N=87) cohorts. Differentially expressed genes identified in RNA-Seq were used in pathway analysis and to create a polygenic expression score. There were 448 differentially expressed genes in the discovery cohort, of which 99 remained significant in the replication cohort, and 5 (FKBP5, NDUFA1, CCDC85B, SNORD54, SNORD46) showed >1.2-fold difference in expression consistently between the discovery and replication cohorts. Several enriched biological pathways were found, including glucocorticoid receptor signaling and immunity-related pathways, but were not significant following FDR correction. The gene expression score achieved sensitivity of 0.917 and specificity of 0.508 for identifying PTSD cases in the replication cohort. It was similar in current and past PTSD, with both groups scoring higher than trauma-exposed controls. We confirmed the role of FKBP5 in PTSD and identified four additional differentially expressed genes that may constitute biomarkers for this condition. Together with the pathway analysis results, these findings point to HPA-axis and immune dysregulation as key biological processes underpinning PTSD. A novel polygenic expression aggregate that differentiates PTSD patients from trauma-exposed controls might be a useful screening tool for research and clinical practice, if replicated in other populations.

overall_design: 324 human samples; 201 never,  82 current, 41 past with PTSD. Gene expression profiling by high throughput sequencing

first: Pei

middle: F

last: Kuan

first: Benjamin

last: Luft


title: Identification of quiescence and early activation genes in satellite cells

status: Public on Nov 13 2017

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

summary: We report the transcriptional changes that occur during the isolation procedure of adult skeletal muscle stem cells (MuSCs). We have developed a protocol that is based on the in situ fixation of MuSCs before isolation. The transcriptome of the in situ fixed cells was compared to that of MuSCs isolated using the standard mechanical/enzymatic isolation protocol. The differentially expressed transcripts represent early-response genes, involved in quiescence and activation of MuSCs, but also isolation-induced artefacts.

overall_design: RNA-seq analysis of muscle stem cells that were either: fixed in situ (T0), isolated with the traditional protocols (T3) or isolated with the traditional protocols + incubated at 37C for additional 2h (T5).

first: Léo

last: Machado

first: Joana

last: Esteves de Lima

first: Odile

last: Fabre

first: Caroline

last: Proux

first: Anikó

last: Szegedi

first: Hugo

last: Varet

first: Lars

last: Ingerslev

first: Romain

last: Barrès

first: Frédéric

last: Relaix

first: Philippos

last: Mourikis


title: Time series transcriptional profiling of Ustilago maydis infecting Zea mays

status: Public on Jan 11 2018

city: Cambridge

first: Clement

last: Pellegrin

address: Downing Site

department: Plant Sciences

institute: University of Cambridge

summary: The basidiomycete fungus Ustilago maydis causes smut disease in maize and has become an important model for elucidating the strategies used for host colonization by biotrophic fungi. In this study, we performed an in-depth transcriptional profiling of the plant-associated development of a cross between U. maydis FB1 and FB2 wildtype strains. The analysis of eight different stages, including the development on the leaf surface, early colonization, tumor induction and spore maturation, offers an unprecedented view of the changes in the fungal transcriptome associated with the passage through the entirely biotrophic life cycle. In our analysis, we focus on fungal metabolism, nutritional strategies, secreted effectors and regulatory networks. Secreted proteins were enriched in three distinct expression modules corresponding to the plant surface, establishment of biotrophy and tumor formation, respectively. These modules are likely the key determinants for U. maydis virulence. With respect to nutrient utilization, we observed that expression of several nutrient transporters was tied to these virulence modules rather than being controlled by nutrient availability. We show that oligopeptide transporters likely involved in nitrogen supply during infection are important virulence determinants. By measuring the intramodular connectivity of transcription factors, we identified potential drivers for the virulence modules. While known components of the b-cascade served as inducers for the plant surface and biotrophy module, we identified a set of yet uncharacterized transcription factors as likely responsible for expression of the tumor module. We demonstrate a crucial role in effector gene expression and tumor formation for one of these transcription factors.

sample_organism:
Zea mays
Mycosarcoma maydis

platform_organism:
Zea mays
Mycosarcoma maydis

overall_design: Crossings of the compatible U. maydis wild type strains FB1 and FB2 were injected into maize seedlings of the variety EGB. Infected leaf sections were collected at 12 and 24 hours, 2, 4, 6, 8, and 12 days post inoculation. Maize plants were also mock-infected (water) and samples collected at the same time points. Additionally, the U. maydis strains FB1 and FB2 were cultivated in axenic culture and samples collected during growth in mid-log phase (OD600=1.0). All samples were subjected to RNAseq analysis with mRNA as target molecule.

first: Daniel

last: Lanver

first: André

middle: N

last: Mueller

first: Petra

last: Happel

first: Gabriel

last: Schweizer

first: Marek

last: Franitzka

first: Fabian

last: Haas

first: Clément

first: Janine

last: Altmüller

first: Stefan

last: Rensing

first: Regine

last: Kahmann


title: MLL-EB1 fusion immortalized murine bone marrow cells

status: Public on Jun 02 2017

city: TauYau

first: Yun-Shien

last: Lee

address: TauYau

department: Dept. Biotechnology

institute: Ming Chuan Univ

summary:
Background: MLL (KMT2A)-EB1 (MAPRE1) fusion was identified in a patient with de novo pro-B acute lymphoblastic leukemia. To investigate the leukemogenesis of MLL-EB1 fusion, a retroviral transduction of MLL-EB1 to murine bone marrow cells was performed. A frequent MLL fusion, MLL-AF10(OM-LZ), was used as a positive control.
Results: Two MLL-EB1 immortalized cell lines (ME1 and ME2G), and a MLL-AF10(OM-LZ) immortalized cell line (12G) were generated. Microarray results showed that many genes including  Evi1 and Ets1 were differentially expressed in ME1/ME2G and 12G cell lines.

overall_design: Total RNAs were extracted from the cell lines and used to perform microarray analysis using Affymetrix mouse 430_2.0 chip. The genes with differential expression between ME1/ME2G and 12G cell lines were selected and validated with reverse transcription-quantitative polymerase chain reaction.

first: Jen-Fen

last: Fu


title: Interplay between genome topology and gene regulation during somatic cell reprogramming [ChIP-seq]

first: Thomas

last: Graf

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Epigenome and TF binding site profiling of B cells reprogramming to pluripotent cells and (induced) pluripotent stem cells using ChIP(m)seq

first: Ralph

last: Stadhouders

first: Enrique

last: Vidal

first: Antonio

last: Gomez


title: Precise integration of inducible transcriptional elements (PrIITE) enables absolute control of inducible gene expression.

status: Public on May 09 2017

city: Copenhagen

first: Lars

last: Hansen

address: 3B Blegdamsvej

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

summary: Tetracycline-based inducible systems provide powerful methods for functional studies where  gene expression can be controlled. However, the lack of tight control of the inducible system,  leading to leakiness and adverse effects caused by undesirable tetracycline dosage  requirements, has proven to be a limitation. Here we report that the combined use of genome  editing tools and last generation Tet-On systems can resolve these issues. Our principle is  based on precise integration of inducible transcriptional elements (coined PrIITE) targeted to;  1) exons of an endogenous gene of interest (GOI) and 2) a safe harbor locus. Using PrIITE  cells harboring a GFP reporter or CDX2 transcription factor, we demonstrate discrete  inducibility of gene expression with complete abrogation of leakiness. CDX2 PrIITE cells  generated by this approach uncovered novel CDX2 downstream effector genes. Our results  provide a strategy for characterization of dose-dependent effector functions of essential genes  that require absence of endogenous gene expression.

overall_design: Transcriptome and ChIP-seq analyses of inducible CDX2 integrated expression and wt CDX2 expression in LS174T colorectal cell lines by deep sequencing. In total six transcriptome data set (LS174T_wt; LS174T_CDX+/-; LS174T_CDX2-/-; LS174T_CDX2-/-1X induced CDX2 (4ng Dox); LS174T_CDX2-/-2X induced CDX2 (0ng Dox); LS174T_CDX2-/-2X induced CDX2; 4ng Dox); LS174T_CDX2-/-2X induced CDX2 (40ngDox)) and one ChIP-seq data set (ChIP-seq CDX2 ab)

first: Eric

middle: P

last: Bennet

first: Jesper

last: Troelsen


title: Uncovering mechanisms of early human lineage specification by CRISPR/Cas9-mediated genome editing

status: Public on Sep 21 2017

city: London

first: Kathy

last: Niakan

address: Mill Hill

institute: The Francis Crick Institute

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: Epigenetic restriction of embryonic and extraembryonic lineages mirrors the somatic transition to cancer (WGBS)

status: Public on Sep 18 2017

city: Boston

first: Jiantao

last: Shi

address: 3 Blackfan Circle

institute: dana farber cancer institute

type: Methylation profiling by high throughput sequencing

summary: Concerted efforts over past decades have established a thorough understanding of the canonical somatic DNA methylation landscape as well as its systematic misregulation across most human cancers.  However, the underlying mechanism that directs this genome-scale transformation remains elusive, with no clear model for its acquisition or understanding of its potential developmental utility. Here we present base pair resolution analysis of global remethylation from the hypomethylated state of the preimplantation embryo into the early epiblast and extraembryonic ectoderm. We show that these two states acquire highly divergent genomic distributions: while the proximal epiblast establishes a canonical CpG-density dependent pattern found in somatic cells, the extraembryonic epigenome becomes substantially more mosaic.  Moreover, this alternate pattern includes specific de novo methylation of hundreds of CpG island promoter containing genes that function in early embryonic development and are orthologously methylated across an extensive cohort of human cancers.  From these data, we propose a model where the evolutionary innovation of extraembryonic tissues in eutherian mammals required cooption of DNA methylation-based suppression as an alternate pathway to the embryonically utilized Polycomb group proteins, which otherwise coordinate germ layer formation in response to extraembryonic cues at the onset of gastrulation.  Moreover, we establish that this decision is made deterministically downstream of the promiscuously utilized, and frequently oncogenic, FGF signaling pathway and utilizes a novel combination of epigenetic cofactors.  Recruitment of this silencing mechanism to developmental genes during cancer therefore reflects the misappropriation of an innate regulatory pathway that may be spontaneously sampled as an alternate epigenetic landscape within somatic cells.

overall_design: Comparison of DNA methylation patterns in Extraembryonic Ectoderm and cancer

first: Zachary

middle: D

last: Smith

first: Julie

last: Dongahey

first: Davide

last: Cacciarelli

first: Franziska

last: Michor

first: Alexander

last: Meissner


title: Uncovering mechanisms of early human lineage specification by CRISPR/Cas9-mediated genome editing [RNA-seq]

summary: Despite their fundamental biological and clinical importance, the molecular mechanisms that regulate the first cell fate decisions in the human embryo are not well understood. Here we use CRISPR?Cas9-mediated genome editing to investigate the function of the pluripotency transcription factor OCT4 during human embryogenesis. We identified an efficient OCT4-targeting guide RNA using an inducible human embryonic stem cell-based system and microinjection of mouse zygotes. Using these refined methods, we efficiently and specifically targeted the gene encoding OCT4 (POU5F1) in diploid human zygotes and found that blastocyst development was compromised. Transcriptomics analysis revealed that, in POU5F1-null cells, gene expression was downregulated not only for extra-embryonic trophectoderm genes, such as CDX2, but also for regulators of the pluripotent epiblast, including NANOG. By contrast, Pou5f1-null mouse embryos maintained the expression of orthologous genes, and blastocys  t development was established, but maintenance was compromised. We conclude that CRISPR?Cas9-mediated genome editing is a powerful method for investigating gene function in the context of human development.

overall_design: Single-Cell RNA-seq

first: Paul

last: Blakeley

first: Norah

middle: M

last: Fogarty


title: Satellite Cells

first: Rachel

last: Legendre


title: Genome-wide gene expression analysis of neurofibroma-derived NF1+/- and NF1-/- Schwann cells

status: Public on Dec 22 2016

city: Turku

first: Eeva-Mari

last: Jouhilahti

address: Kiinamyllynkatu 10

department: Department of Cell Biology and Anatomy

country: Finland

institute: University of Turku

summary: Analysis of the effect of NF1 second hit mutation to the reading of the whole human genome by comparing the gene expression profiles of neurofibroma derived Schwann cell cultures representing two different NF1 genotypes (NF1+/- and NF1-/-).

overall_design: Schwann cell cultures representing two different NF1 genotypes (NF1+/- and NF1-/-) were established from a total of nine tumors from three different NF1 patients (E8, E27 and S34 corresponding patients 1, 2 and 3 respectively). Total RNA was isolated from cells in passage 4. Furthermore, NF1+/- cells from 6 tumors (from patients E27 and S34) were passaged into fifth passage to test the effect of growth factor forskolin which is the separating factor between NF1+/- and NF1-/- Schwann cell culture conditions. TotalRNA samples from each culture were harvested in passage 5 (referred as Forskolin sample). For the remaining cultures, the medium was changed into proliferation medium without forskolin and after 24 hours, totalRNA samples from each culture were collected (woForskolin samples). The proliferation medium containing forskolin was given back to the remaining cultures, and after 24 hours total RNA samples from each culture were collected (ForskolinBack samples).

first: Sirkku

last: Peltonen

first: Juha


title: Generation of human microglia-like cells to study neurological disease

status: Public on Apr 19 2017

city: Irvine

first: Ricardo

middle: Noel

last: Ramirez

state: California

address: 2300 Biological Sciences III

department: Developmental and Cell Biology

institute: University of California Irvine

summary: Microglia play important roles in developmental and homeostatic brain function, and influence the establishment and progression of many neurological disorders. Here, we demonstrate that renewable human iPSCs can be efficiently differentiated to microglial-like cells (iMGL) to study neurological diseases, such as Alzheimer's disease (AD). We find that iMGLs develop in vitro similarly to microglia in vivo and whole transcriptome analysis demonstrates that they are highly similar to adult and fetal human microglia. Functional assessment of iMGLs reveal that they secrete cytokines in response to inflammatory stimuli, migrate and undergo calcium transients, and robustly phagocytose CNS substrates. We also show novel use of iMGLs to examine the effects of fibrillar Aβ and brain-derived tau oligomers on AD-related gene expression and to interrogate mechanisms involved in synaptic pruning. Taken together, these findings demonstrate that iMGLs can be used in high-throughput studies of microglial function, providing important new insight into human neurological disease.

overall_design: Human cells were collected and analyzed for gene expression using RNA-seq.

first: Edsel

last: Abud

first: Matthew

last: Blurton-Jones


title: Inefficient DNA-DSB repair via the homologous recombination pathway in prostate cancer patients with late radiation toxicity

status: Public on Jan 30 2017

city: Amsterdam

first: Perry

last: Moerland

address: Meibergdreef 9

department: Epidemiology and Data Science

country: Netherlands

institute: Amsterdam UMC

summary: Purpose: Severe late normal tissue damage limits radiotherapy treatment regimens. This study aims to validate γ-H2AX foci decay ratios and induced expression levels of DNA double strand break (DSB) repair genes, found in a retrospective study, as possible predictors for late radiation toxicity.   Methods and Materials: Prospectively, decay ratios (initial/residual γ-H2AX foci numbers) and genome-wide expression profiles were examined in ex vivo irradiated lymphocytes of 198 prostate cancer patients. All patients were followed ≥2 years after radiotherapy, clinical characteristics were assembled and toxicity was recorded using the Common Terminology Criteria (CTCAE) v4.0.    Results: No clinical factors were correlated with late radiation toxicity. Analysis of γ-H2AX foci uncovered a negative correlation between the foci decay ratio and toxicity grade. Significantly smaller decay ratios were found in grade≥3 compared to grade 0 patients (p=0.02), indicating less efficient DNA-DSB repair in radio-sensitive patients. Moreover, utilizing a foci decay ratio threshold determined in our previous retrospective study correctly classified 23 of the 28 grade≥3 patients (sensitivity, 82%) and 9 of the 14 grade 0 patients (specificity, 64%). Grade of toxicity also correlated with a reduced induction of the homologous recombination (HR) repair gene-set. The difference in average fold induction of the HR gene-set was most pronounced between grade 0 and grade≥3 patients (p=0.008).   Conclusions: Reduced responsiveness of HR repair genes to irradiation and inefficient DSB repair correlate with an increased risk of late radiation toxicity. Using a decay ratio classifier, we could correctly classify 82% of the patients with grade≥3 toxicity. Additional studies are required to further optimize and validate the foci decay assay and to assess its predictive value for late radiation toxicity in patients prostate cancer

overall_design: Between 2009 and 2013, we prospectively accrued 200 patients diagnosed with prostate cancer receiving curative external beam radiotherapy in combination with hormonal therapy at the Academic Medical Center (AMC) of the University of Amsterdam, with a follow-up of ≥2 years. After written informed consent, 40 ml whole blood was collected of all patients before start of treatment. Peripheral lymphocytes were isolated using Ficoll (Ficoll-Paque PLUS, GE Healthcare) gradient separation, and stored in liquid nitrogen. Development of late toxicities was monitored over more than 2 years after treatment using the National Cancer Institute Common Terminology Criteria for Adverse Events (CTCAE) version 4.0. Toxicity grade was determined mainly focusing on late gastrointestinal (GI) and genitourinary (GU) toxicities. Lymphocytes were cultured stimulated by phytohemagglutinin (concentration of 1μg/ml). After two weeks, half of the cells were irradiated at room temperature with 2Gy gamma rays from a 137Cs source, dose rate of approximately 0.5Gy/min and the other half of the cells was left untreated.  Total cellular RNA was isolated and gene expression levels were measured using the Affymetrix HT HG-U133+ PM Array platform for 400 samples (2 per patient) and 12 technical replicates (all labelled as 'prospective' below). Samples were also included for 7 patients [4 with (overresponding, R) and 3 without (non-responding, NR) severe late radiation toxicity] from a previous retrospective study (International Journal of Radiation Oncology, Biology, Physics, 88(3):664-70; 2014) using total RNA isolated following an identical experimental protocol from whole-blood samples collected at least 2 years after radiation treatment. This was done either using previously isolated RNA stored at –80°C (14 samples, labelled as 'retrospective (old)' below) and freshly isolated RNA from newly collected whole-blood samples (14 samples, labelled as 'retrospective (new)' below). Samples were hybridized in two batches, the first batch consisting of 104 arrays on five array plates (2x16, 3x24) and the second batch of 336 arrays on five plates (2x24, 3x96). For all patients the irradiated (2Gy) and the control sample (0Gy) had by design been hybridrized in the same batch and, for the second and largest batch, on the same plate. Genes and genesets were determined that respond differently to irradiation between the four toxicity CTCAE 4.0 score-based patient groups. For 198 of the 200 patients from the prospective study the induction and decay of radiation-induced DNA–DSB breaks was monitored in ex vivo irradiated lymphocytes by detecting γ-H2AX foci 30min and 24h post radiation.

first: Bregje

last: van Oorschot

first: Nicolaas

last: Franken


title: Transcriptomic analysis of purified human cortical microglia reveals age-associated changes

status: Public on May 19 2017

city: Ann Arbor

first: Antonio

middle: Marcondes

last: Lerario

state: MI

address: 109 Zina Pitcher Place, 1528 BSRB

department: MEND

institute: University of Michigan

summary:
Purpose: Microglia are essential for central nervous system (CNS) homeostasis and innate neuroimmune function, and play important roles in neurodegeneration and brain aging. Here, we present gene expression profiles of purified microglia isolated at autopsy from the parietal cortex of 39 human subjects with intact cognition. We identified an age-associated gene signature in human microglia that was enriched for genes involved in cell adhesion, axonal guidance, cell surface receptor expression, and actin disassembly.
Methods: mRNA profiles of 39 human microglia samples isolated from subjects with intact cognition, 16 corresponding superior parietal cortex tissue and 10 epilepsy surgical samples were generated in a Illumina HiSEQ 2500 sequencer. mRNA profiles of 6 parietal cortex from mice were prepared with a Quantseq 3’mRNA-Seq kit (Lexogen, USA). Reads were aligned to the hg38 assembly of the human genome using STAR and quantified at the gene level by featureCounts. Differential expression between whole brain tissue, surgical samples and isolated microglia was assessed with limma.
Results: Overall, genes expressed by human microglia are similar to those in mouse, including established microglia genes CX3CR1, P2YR12, and ITGAM/CD11B. However, a number of immune genes, not identified as part of the mouse microglial signature, were abundantly expressed in human microglia, including TLR, Fc-gamma and SIGLEC receptors, as well as TAL1 and IFI16, regulators of proliferation and cell cycle. Age-associated changes in human microglia were enriched for genes involved in cell adhesion, axonal guidance, cell surface receptor expression, and actin (dis)assembly. Limited overlap was observed in microglial genes regulated during aging between mice and humans, indicating that human and mouse microglia age differently.
Conclusions: Here we present the an extensive human microglia gene expression profile. Critical differences with mouse microglia, especially in the context of aging, were observed which highlight the necessity to independently study human microglia. These data and analyses serve as a starting point to address human-specific microglia genes and functions under physiological and neuropathological conditions.

first: Thais

last: Galatro

first: Inge

middle: R

last: Holtman

first: Ilia

last: Vainchtein

first: Nieske

last: Brower

first: Paula

last: Sola

first: Mariana

last: Veras

first: Tulio

last: Pereira

first: Renata

last: Leite

first: Thomas

last: Möller

last: Wes

first: Mari

last: Sogayar

first: Jon

last: Laman

first: Wilfred

last: denDunnen

first: Carlos

last: Pasqualucci

first: Sueli

last: Oba-Shinjo

first: Erik

middle: W

last: Boddeke

first: Suely

last: Marie

first: Bart

last: Eggen


title: RNA-seq analysis of Drosophila melanogaster posterior midguts

status: Public on Dec 18 2016

city: Los Angeles

first: Martin

last: RESNIK DOCAMPO

state: CA

address: 610 Charles E young Dr East

department: MCDB

institute: UCLA


title: miRNA expression data from pediatric high grade gliomas

status: Public on Nov 01 2016

city: New Delhi

first: Dr. Chitra

last: Sarkar

state: Delhi

address: Ansari Nagar

department: Dept of Pathology

country: India

institute: All India Institute of Medical Sciences

summary: miRNA expression analysis was performed on 14 cases of high grade gliomas and 4 controls obtained from age-matched epileptic patients. After this differentially miRNA analysis has been done among T53,H3F3A,normal and pediatric high grade glioma patient and try to identify the highly altered  miRNA expression as well as sno expression pattern.

overall_design: The data was used for identifying TP53 and H3F3A mutation specific miRNA profile

first: Prerana

last: Jha

first: Rahul

last: Agarwal

first: Ritu

last: Kulshreshtha

first: Chitra


title: RNA-seq analysis of young vs. old Drosophila melanogaster posterior midguts

summary: The goal of this study is to compare changes in gene expression between young (5 days old) and old (45 days old) flies posterior midguts.

overall_design: Seventy-five female WT posterior midguts per condition (5do and 45do) were dissected. Each condition was sequenced in triplicate, using Illumina HiSeq 2000.

last: Resnik-Docampo

first: D

middle: L

last: Jones


title: Motility and stem cell properties induced by the epithelial-mesenchymal transition require destabilization of lipid rafts

status: Public on Oct 29 2016

city: Houston

first: Jeffrey

last: Chang

address: 6431 Fannin St

institute: University of Texas

summary:
The epithelial-mesenchymal transition provides cells with the characteristics needed to metastasize.  We hypothesized that it does so through changes in the organization of the plasma membrane.
We found that the EMT leads to destabilization of the membrane concomitant with transcriptional reprogramming.  However, treatment with DHA stabilizes the membrane and reverts the transcriptional program toward an epithelial state.

overall_design: HMLE cells are treated with a combinations of Snail expression, TGF-b ligand, or DHA.

first: Michael

last: Tisza

first: Weina

middle: S

last: Zhao

first: Jessie

last: Fuentes

first: Sara

last: Prijic

first: Xiaoling

last: Chen

first: Ilya

last: Levental


title: Wnt5A signaling in human coronary artery endothelial cells

status: Public on Oct 03 2016

city: Zürich

first: TOM

last: SKARIA

address: Rämistr. 100

department: INTERNAL MEDICINE

country: Switzerland

institute: UNIVERSITY HOSPITAL ZURICH

summary:
Inflammatory Wnt5A signalling in human macrophages was found to be critically involved in severe systemic inflammatory response. However, the targets of Wnt5A in endothelial cells and downstream mechanisms by which Wnt5A might induce endothelial inflammation still remain unclear.
We show that Wnt5A principally regulate genes involved endothelial cytoskeleton rearrangements and impairs the barrier function of cultured endothelial monolayer causing hyper permeability. We further prove that Wnt5A neither affects the expression of adhesion molecules nor induces cytokine storm in endothelial cells. These findings suggest that Wnt5A, secreted by activated macrophages during septic inflammation, paracrinically act on the endothelial wall, causing endothelial barrier breakdown and subsequent vascular leakage in sepsis.

overall_design: A two color competitive hybridization design was chosen.  Samples from respective treatments are labelled with Cy5  and hybridized against a Cy3 labelled non-treated reference sample from the same experiment.

first: Tom

last: Skaria

first: Gabriele

last: Schoedon


title: Exon Array Expression data from fershly isolated human peripheral blood NK cells (pNK),  deciudual NK cells (dNK)  and induced decidual NK-like cells (i-dNK)

status: Public on Oct 14 2016

first: Hernan

last: Kopcow

state: MA

address: 330 Brookline Ave Rn 359

department: Medicine

institute: BIDMC

summary: pNK treatment with a combination of TGFb, 5-aza-2’-deoxycytidine and hypoxia yields cells with functional and phenotypic similarities to human dNK cells, called induced dNK-like cells (idNK)

overall_design: This dataset includes the expression data of 3 CD56Bright CD16- pNK samples, 3  CD56Dim CD16+ pNK samples,  3 dNK csamples, 3  CD56Bright CD16- idNKsamples  and 3  CD56Dim CD16+ idNK samples

first: Ana

last: Cerdeira

first: Manoj

last: Bhasin

first: Ananth

last: Karumanchi


title: The HLA-B*35 allele modulates ER stress, inflammation and proliferation in PBMCs from Limited Cutaneous Systemic Sclerosis patients

status: Public on Nov 02 2016

summary:
The goal of this study was to assess whether the presence of HLA-B*35 contributes to activation of ER stress/UPR and inflammation in lcSScPAH PBMC.
HLA-B*35 is associated with increased risk of developing PAH in lcSSc patietns. Also we previously reported that HLA-B*35 induces ECs dysfunction via activation of ER stress/UPR and upregulation of the inflammatory response. Our study demonstrates that HLA-B*35 contributes to the dysregulated expression of selected ER stress, inflammation and proliferation related genes in lcSSc patient PBMCs, as well as healthy individuals, thus supporting a pathogenic role of HLA-B*35 as a risk factor for developing PAH in SSc patients.

overall_design: In this study, PBMCs from 3 healthy controls were investigated.

first: Stefania

last: Lenna

first: Shervin

last: Assassi

first: Alessandra

middle: G

last: Farina

first: Julio

last: Mantero

first: Raffaella

last: Scorza

first: Robert

last: Lafyatis

first: Harrison

last: Farber

first: Maria

last: Trojanowska


title: MiR-26 dampens IL-6 production by down-regulating TNF-a/NF-kB signaling through silencing HMGA1 and MALT1 and not by directly targeting IL-6 mRNA

status: Public on Mar 31 2016

first: Jeffrey

last: Chang

summary: We found NF-kB signaling as a major target of miR-26 based on an analysis of the changes in gene activation by TNF-a in response to alteration of miR-26 levels.

overall_design: Transcriptional profiling of genes in response to either a miR-26 mimic or miR-26 antagomir.

first: Chyi-Ying

last: Chen

first: Yi-Fang

last: Ho

first: Ann-Bin

last: Shyu


title: ChIP-seq from liver (ENCSR136GMT)

status: Public on Jun 22 2016

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
H3K27ac ChIP-seq on embryonic 12.5 day mouse liver

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Spatial differentiation of gene expression in Aspergillus niger colonies grown for sugar beet pulp utilization

status: Public on Mar 04 2016

city: Utrecht

first: miaomiao

last: Zhou

address: Uppsalalaan 8

department: fungal physiology

institute: centre of fungal biodiversity, Utrecht, KNAW

summary: Filamentous fungi are ubiquitous organisms and major plant biomass degraders. As a single colony, some fungal species can colonize large areas as up to five soccer stadia. During growth, the mycelium encounters heterogeneous carbon sources. Here we assessed whether substrate heterogeneity is a main determinant of spatial gene expression in colonies of Aspergillus niger. This question was addressed by analyzing whole-genome gene expression in five concentric zones of 5-day-old sugar beet pulp grown colonies. Growth, protein production and secretion were occurring throughout the whole colony. Carbon and nitrate utilization were constant from the centre to the periphery whereas genes encoding plant cell wall degrading enzymes were expressed with a different pattern across the colony. Finally our results demonstrate a fine-tuning of the different enzymatic tools available in A. niger and expand the knowledge on how this fungus adapts as it colonizes complex environments.

overall_design: We aim to discover differentially expressed genes accross in A.niger wild type strain N402 colony (five zones) while growing on sugar beet pulp as carbon source.  Biological duplicates were made for RNA extraction. The RNAs were pooled for transcriptome studies. The strains were grown O/N in complete medium with 2% frunctose and mycelium was then washed and transferred to minimal medium with 25 mM D-galactose and incubated for 2 hours. Affymetrix microarray experiments were performed RNA isolated from these samples.

first: Miaomiao

first: Isabelle

last: Benoit

first: Alexandra

last: Vivas Duarte

first: Damien

last: Downes

first: Richard

middle: B

last: Todd

first: Wendy

last: Kloezen

first: Harm

last: Post

first: Albert

last: Heck

first: A

last: Maarten Altelaar

first: Ronald

last: de Vries


title: ChIP-seq from limb (ENCSR737QWV)

summary:
H3K27ac ChIP-seq on embryonic 12.5 day mouse limb

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Mechanism of Ikaros tumor suppression in Leukemia

status: Public on Nov 03 2015

city: Hershey

first: chunhua

last: song

state: PA

address: 500 University Drive

department: Pediatrics

institute: Pennsyvania  State University College of Medicine

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


title: Proinflammatory isoforms of IL-32 as novel and robust biomarkers for control failure in HIV-infected slow-progressors.

status: Public on Dec 31 2015

city: Montréal

first: Jean-Philippe

last: Goulet

state: Québec

address: C.P. 6128, succursale Centre-ville

country: Canada

institute: Université de Montréal

summary:
HIV-infected slow-progressors (SP) represent a heterogeneous group of subjects who spontaneously control HIV infection without treatment for several years while showing moderate signs of disease progression.
Here we determined the frequency of SP subjects who showed loss of HIV control within our Canadian Cohort of HIV+ Slow-Progressors and identified the proinflammatory cytokine IL-32 as a robust biomarker for control failure.

overall_design: Total cellular RNA was extracted from PBMC from 5 donors at two time points ('V1' before and 'V2' after loss of control, and only Long Term Non Progressors (LTNP) were part of the case study), along with 2 control Leuka914 and Aging106032 samples.

first: Mohamed

last: El-Far

first: Pascale

last: Kouassi

last: Sylla

first: Yuwei

last: Zhang

first: Ahmed

last: Fouda

first: Thomas

last: Fabre

first: Julien

last: van Grevenynghe

first: Terry

last: Lee

first: Joel

last: Singer

first: Marianne

last: Harris

first: Jean-Guy

last: Baril

first: Benoit

last: Trottier

first: Petronela

last: Ancuta

first: Jean-Pierre

last: Routy

first: Nicole

last: Bernard

first: Cécile

last: Tremblay


title: Mechanisms of Ikaros Tumor Suppression with HDAC1 through distinct histone markers in Pre-B ALL Leukemia

first: chunhua

last: song

summary: Ikaros functions as a master regulator of lymphocyte differentiation and a tumor suppressor. Ikaros binds DNA and regulates gene expression by chromatin remodeling. Mechanisms of Ikaros-mediated tumor suppression are unknown. Here we examined genome-wide occupancy of Ikaros and histone deacetylase 1 (HDAC1) and  Histone midificaition markers in human leukemia, and found that the Ikaros and HDAC1 showed similar binding partern  and HDAC1–DNA interactions are associated with the presence of bivalent chromatin, and the recruitment of HDAC1 by Ikaros is associated with bivalent chromatin at Ikaros target genes.

overall_design: Examine the genome-wide binding of Ikaros, HDAC1, H3K9me3, H3K9ac, H3K27me3, H3K4me3 and H3K36me3 in Nalm6 ALL leukemia cells.

first: Chunhua

last: Song

first: Xiaokang

last: Pan

first: Chandrika

last: Gowda

first: Yali

last: Ding

first: Hui

last: Li

first: Marie

last: Bulathsinghala

first: Gregory

last: Yochum

first: Markus

last: Muschen

first: Kimberly

last: Payne

first: John

last: Stamatoyannopoulos

first: Sinisa

last: Dovat


title: Gene expression profiling in Nalm6 ALL leukemia cells

summary: Identify the expression intensity for all genes in Nalm6 cells and all the genes are divided into 4 equal groups with group 1 containing the 25% of genes that were expressed at the highest levels, and group 4 containing the 25% of genes that were expressed at the lowest levels.

overall_design: Total RNA are isolated from 3 lots of Nalm6 cells and gene expression are determined by microarray gene expression analysis with Nimblegen Human 385K array.


title: Sp7/Osterix is restricted to bone-forming vertebrates where it acts as a Dlx co-factor in osteoblast specification

status: Public on Apr 28 2016

city: Bunkyo-ku

first: Hironori

last: Hojo

state: Tokyo

address: 7-3-1 Hongo

department: Center for Disease Biology and Integrative Medicine

country: Japan

institute: The University of Tokyo

overall_design: Refer to individual Series

first: Shinsuke

last: Ohba

first: Xinjun

last: He

first: Lick

last: Lai

first: Andrew

last: McMahon


title: Sp7/Osterix is restricted to bone-forming vertebrates where it acts as a Dlx co-factor in osteoblast specification [RNA-Seq]

summary: Sp7/Osterix is a master regulator of osteoblast specification. To identify transcripts profile in Sp7 positive osteoblast, we performed RNA-seq on primary mouse calvarial cells obtained from Sp7-GFP reporter mice at P1. By hierarchical clustering using transcriptional profiles for chondrocytes and mouse embryonic fibroblasts (MEFs) together with the osteoblast data, we identified cell-type enriched gene expression signatures in osteoblasts, chondrocytes and MEFs. In conjunction with Sp7 ChIP-seq in osteoblast, we identified putative Sp7 targets which underlie the osteoblast regulatory program.

overall_design: RNA-seq experiments with GFP-sorted Sp7 positive osteoblasts and chondrocytes isolated from wild-type rib cartilage at P1


title: Novel long non-coding RNAs in breast cancer

status: Public on Feb 09 2017

city: Shanghai

first: Ji-Gang

last: Wang

address: 138 Yixueyuan Road

country: China

institute: Fudan University

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

summary:
Five matched breast cancer and normal tissues were used for microarray.
Ther were 224 lncRNAs increased and 324 decreased in breast cancer tissues

overall_design: Microarray experiments were performed to determine the lncRNA expression in corresponding normal and malignant breast tissues

first: Ping

last: Zhou


title: Sirt1 is essential for Aire-mediated induction of central immunological tolerance

status: Public on May 25 2015

city: Nantes

first: Matthieu

last: Giraud

address: 30 bd Jean Monnet

department: CRTI

institute: INSERM _ Université de Nantes

summary: Autoimmune regulator (Aire) is a unique transcriptional regulator that induces promiscuous expression of thousands of tissue-restricted antigens (TRAs) in medullary thymic epithelial cells (mTECs), a step critical for induction of immunological self-tolerance. Although several recent studies provided very important molecular insights into how Aire operates, a more comprehensive understanding of this process still remains elusive. Here we demonstrate that a lysine deacetylase Sirtuin-1 (Sirt1) is predominantly expressed in mature Aire+ mTECs, where it is required for expression of Aire-dependent TRA genes and a subsequent induction of immunological self-tolerance. Our study elucidates a previously unknown molecular mechanism for Aire-mediated transcriptional regulation and uncovers a unique functional role for Sirt1 in preventing organ-specific autoimmunity.

overall_design: ~100ng of total RNA isolated by Trizol extraction from MHC-II low and high mTECs (pool of 3 mice) was used to generate poly-A-selected transcriptome libraries using the non-directionnal TruSeq V3 RNA Sample Prep Kit (without additional pre-amplification) following the manufacturer's protocols.  Enrichment of DNA fragment with adapter molecules on both ends was done using 15 cycles of PCR amplification using the Illumina PCR mix and primer cocktail. Paired-end (2 × 100 bp) sequencing was performed using the Illumina HiSeq2000 machine.

first: Jakub

last: Abramson


title: Chronic growth factor signaling in Acute Myeloid Leukemia is connected to a specific chromatin signature

status: Public on Jul 03 2015

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

institute: University Medical Center Freiburg


title: Identification of a novel cofactor, SH3YL1, that functions through interaction with the androgen receptor N-terminal polyproline domain

status: Public on Aug 20 2015

first: Jeffrey

last: Chang

summary: Nuclear receptor (NR)-mediated transcription is a dynamic process that is regulated by the binding of distinct ligands that induce conformational changes in the NR. These molecular alterations lead to the recruitment of unique cofactors (coactivators or corepressors) that control the expression of NR-regulated genes. Here, we show that a stretch of proline residues located within the N-terminus of AR is necessary for maximal androgen-mediated prostate cancer cell growth and migration. Furthermore, this polyproline domain is necessary for the expression of a subset of AR-target genes, but is dispensable for classical AR-mediated gene transcription. Using T7 phage display, we subsequently identified a novel AR-interacting protein, SH3YL1, whose interaction with AR is dependent upon this polyproline domain. Like the AR polyproline domain, SH3YL1 was required for maximal androgen-mediated cell growth and migration. Microarray analysis revealed that SH3YL1 also regulated a subset of AR-modulated genes. Correspondingly, we identified ubinuclein1 (UBN1), a key member of a histone H3.3 chaperone complex, as a transcriptional target of AR/SH3YL1. Moreover, UBN1 was necessary for maximal androgen-mediated proliferation and migration. Collectively, our data link a specific surface located within AR’s N-terminus to the recruitment of a novel cofactor, SH3YL1, which is required for the androgen-mediated expression of UBN1. Importantly, this signaling network was important for both androgen-mediated prostate cancer cell growth and migration. This work is significant because it could aid in the development of selective androgen receptor modulators (SARMs) and have therapeutic implications for AR-driven diseases.

overall_design: Inducible LNCaP stable cell lines were created using lentivirus that with the addition of doxycycline, cells express an shRNA directed against SH3YL1. Cells were treated with vehicle (EtOH), 100pM R1881 or 10nM R1881 for 24 or 72 hours +/- doxycycline (12 conditions). Triplicate samples were used for each group.

first: Alicia

last: Blessing

first: Ganesan

last: Sathya

first: Emily

middle: Y

last: Lu

first: Ying

last: Sung

first: Lakshmi

last: Bollu

first: Yan

last: Shi

first: Fatima

last: Merchant

first: Edwin

last: Cheung

first: Jeffery

first: Donald

last: McDonnell

first: Daniel

middle: E

last: Frigo


title: The hypoxia marker pimonidazole reflects a transcriptional program associated with aggressive prostate cancer.

status: Public on Jan 05 2015

city: Oslo

first: Heidi

last: Lyng

address: Montebello

department: Department of Radiation Biology

country: Norway

institute: Oslo University Hospital

summary:
We aimed to investigate the transcriptional program associated with pimonidazole staining in prostate cancer.
A pimonidazole gene signature was identified that showed positive correlation to Ki67 labeling index, indicating increased proliferation in pimonidazole positive tumors. A positive correlation to clinical tumor stage and presence of lymph node metastasis was also found, consistent with associations between pimonidazole staining and clinico-pathological parameters. Moreover, the gene signature was associated with high Gleason score in a validation cohort of 59 patients and showed prognostic impact independent of Gleason score and other clinical markers in a watchful waiting validation cohort of 281 patients. Our work reveals the molecular basis of an aggressive prostate cancer phenotype reflected by pimonidazole staining, and suggests that genes involved in proliferation, DNA repair and hypoxia response contribute to this phenotype.

overall_design: We combined pimonidazole immunohistochemistry data and expression profiles to identify transcriptional program activated in pimonidazole positive tumors. Whole-genome gene expression profiles were determined in tumor biopsies from an investigation cohort of 46 patients, where 39 patients had received pimonidazole prior to surgery. Gene ontology analysis of 1046 genes upregulated in pimonidazole positive tumors, as defined by a staining fraction above 10%, showed significant enrichment of the biologic processes cell cycle, translation and cellular response to stress. Gene set analysis based on this result identified gene expressions in proliferation, DNA repair and hypoxia response as major parts of the transcriptional program associated with pimonidazole staining. Gene expression data of four prostate cancer cell lines were used to generate hypoxia response gene sets for this analysis. A signature of the 32 most essential genes in the program was constructed and shown to be associated with prostate cancer aggressiveness in two independent validation cohorts.

first: Harald

last: Ragnum

first: Ljiljana

last: Vlatkovic

first: Agnes

middle: K

last: Lie

first: Karol

last: Axcrona

first: Cathinka

middle: H

last: Julin

first: Kari-Anne

last: Frikstad

first: Knut

last: Hole

first: Therese

last: Seierstad


title: Neural gene expression in Pten knock-in mice at 6-weeks of age

status: Public on Mar 12 2015

city: Cleveland

first: Charis

last: Eng

state: OH

address: 9500 Euclid Ave., NE-50

department: Genomic Medicine Institute

institute: Cleveland Clinic

summary: The goal of this study was to assess the changes in the neural transcriptome of Ptenm3m4 mice, in order to better understand their ASD-related phenotypes. For our initial cellular and behavioral characterization of this mouse line, see Tilot, et al., Human Molecular Genetics, 2014

overall_design: Comparison of mice heterozygous and homozygous for the Ptenm3m4 mutation to Wt littermates at 2 and 6 weeks of age

first: Amanda

last: Tilot


title: Transcriptome analysis of apoplastic reactive oxygen species signaling and dissection of its regulatory pathways

status: Public on Feb 10 2015

city: Beijing

first: Yuxin

last: Hu

address: No.20 Nanxincun, Xiangshan

department: Key Laboratory of Plant Molecular Physiology

institute: Institute of Botany, CAS

summary: As sessile organism, plants evolved a highly complicated signaling system to cope with unfavorable and fluctuating environmental conditions. Rapid and transient Reactive Oxygen Species (ROS) burst is a common response to both biotic and abiotic stresses. Plants exposed with O3 could trigger extracellular similar ROS production through cell wall peroxidases and NPADPH oxidases, resulting in changes in the gene expression and cell death. Whereas ROS induced cell death is not simply due to its toxicity, rather due to interplay with several other signaling pathways, such as salicylic acid (SA), jasmonic acid (JA) and ethylene signaling pathways. Furthermore, the three hormones have both synergistic and antagonistic interactions, where the suppression of JA signaling by SA is the mostly studied. In addition, ethylene promotes cell death while JA has a protective role upon O3 exposure. The role of SA is more complicated; depending on the genetic background it can have either cell death promoting or protecting roles. Hence, a clean system to deliver apoplastic ROS is required to study the role of ROS apart from con-current activation of other signaling pathways. Arabidopsis thaliana offer a convenient system to study apoplastic ROS signaling due to the availability of hormone signaling or biosynthesis mutants including the JA receptor mutant coi1-16 (CORONATINE INSENSITIVE1), the essential ethylene signaling mutant ein2 (ETHYLENE INSENSITIVE2), the SA biosynthesis mutant sid2 (SALICYLIC ACID INDUCTION DEFICIENT2 also known as ISOCHORISMATE SYNTHASE1), and essential regulators in SA/JA/ethylene-induced defense response triple mutant tga2 tga5 tga6 (Clade II TGA transcription factors). Here we used a combination of transcriptome analysis, cell death assays and mutant analysis to systematically quantified the contribution of hormone signaling in relation to apoplastic ROS signaling, identified transcription factors (TFs) involved in ROS regulation and dissected the components involved in defense hormones associated cell death.

overall_design: Transcriptome profiling of ozone response using two arabidopsis triple mutants coi1-16 ein2 sid2 and tga2 tga5 tga6 related to Jasmonic acid, salicylic acid and ethylene signaling to identify hormone-independant apoplastic ROS signaling

first: Enjun

last: Xu

first: Lauri

last: Vaahtera

first: Mikael

last: Brosché


title: Gene expression profile of duodenal follicular lymphoma

status: Public on Mar 01 2014

city: Okayama city

first: Katsuyoshi

last: Takata

address: 2-5-1, Kita-ku, Shikata-cho

department: Pathology

institute: Okayama University

summary:
To clarify the molecular pathogenesis of DFL pathogenesis using GEP.
DFL shares characteristics of both NFL and MALT lymphoma.

overall_design: 55 total samples were examined; 10 DFL, 18 NFL, 10 gastric MALT lymphoma, 5 normal duodenal mucosa, 8 nodal reactive lymphoid hyperplasia, and 4 normal gastric mucosa.

first: Motohiko

last: Tanino

first: Daisuke

last: Ennishi

first: Akira

last: Tari

first: Yasuharu

last: Sato

first: Hiroyuki

last: Okada

first: Yoshinobu

last: Maeda

first: Naoe

last: Goto

first: Hiroshi

last: Araki

first: Mai

last: Harada

first: Midori

last: Ando

first: Masaya

last: Iwamuro

first: Mitsune

last: Tanimoto

first: Kazuhide

last: Yamamoto

first: Randy

last: Gascoyne

first: Tadashi

last: Yoshino


title: Interrelationships between replication infidelity and genome composition

status: Public on Aug 25 2014

city: Research Triangle Park

first: Scott

middle: Alexander

last: Lujan

state: NC

address: 101 T.W. Alexander Drive

department: LMG/LSB

institute: NIEHS

summary: An enduring issue in evolutionary and cancer biology is how replication infidelity influences genome composition and vice versa. Here we examine this issue by sequencing the genomes of diploid budding yeast strains that are either mismatch repair (MMR) proficient or deficient and encode wild type or mutator variants of the three major nuclear DNA replicases. Analysis of over 43,000 mutations that accumulated in the absence of selective pressure demonstrates that the nuclear DNA replication machinery generates less than one mismatch per genome and in combination with MMR, achieves a genome-wide per base error rate of 1.7 x 10-10. Absent both MMR and purifying selection, replication error patterns strongly depend on replication origin proximity, replication fork direction, and the local DNA sequence. Preferred sequences were observed for base substitutions and deletions. Error rates also vary with replication time, in linker versus nucleosome-bound DNA, in 5'- and 3'-untranslated regions, in coding regions and in intergenic DNA. This genome-wide view shows that replication fidelity is amazingly high but heterogeneous, in patterns that suggest the underlying mechanisms by which replication modulates genome stability and composition and vice versa.

overall_design: Six to ten isolates were sequenced for each combination of DNA polymerase (WT, pol1-L868M, pol2-M644G, pol3-L612M) and mismatch repair (proficient, deficient) genotypes.  A single WT isolate was sequenced following micrococcal nuclease digestion.

middle: A

first: Anders

last: Clausen

first: Alan

last: Clark

first: Heather

last: MacAlpine

first: David

first: Ewa

last: Malc

first: Piotr

last: Mieczkowski

first: Adam

last: Burkholder

middle: C

last: Fargo

first: Dmitry

last: Gordenin

first: Thomas

last: Kunkel


title: mRNA expression profiles in YT and NK92 cells

status: Public on Jan 21 2014

city: Taipei

first: Chung-Wu

last: Lin

address: 7 South Chung-Shan Road

institute: National Taiwan University

summary: YT and NK92 cells are EBV-infected lymphoma cells of NK- cell origin. YT cells have weaker expression of T-bet and IFNg than NK92 cells. However, this data set shows that both cell lines have similar mRNA levels, implying post-transcriptional regulations.

overall_design: Affymetrix chips (Human Genome U133 plus 2.0) were used for a genome-wide screen of transcriptional profiles on YT and NK cells. Hybridization and washing of the arrays were done according to the GeneChip® Expression Analysis Technical Manual from Affymetrix. The arrays were scanned with GenePix 4000B (Molecular Devices, Sunnyvale, CA.), and the data were extracted with Affymetrix Microarray suite (MAS) software.


title: Targets of the bHLH transcription factor, Sage

status: Public on Dec 31 2013

city: Baltimore

first: Deborah

middle: J

last: Andrew

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

department: Cell Biology

institute: Johns Hopkins University School of Medicine

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

overall_design: Three wild type (reference) samples were obtained from the Oregon R strain, age matched and treated the same as the three experimental samples isolated from Stages 11-16 sage mutant embryos.

first: Rebecca

last: Fox


title: DNA Methylation Signature of Childhood Chronic Physical Aggression in T Cells of Both Men and Women (Illumina)

status: Public on Dec 11 2013

city: Montreal

first: Moshe

last: Szyf

state: Quebec

address: McIntyre Medical Building, 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology

institute: McGill University

summary: High frequency of physical aggression is the central feature of severe conduct disorder and is associated with a wide range of social, mental and physical health problems. We have previously tested the hypothesis that differential DNA methylation signatures in peripheral T cells are associated with a chronic aggression trajectory in males. Despite the fact that sex differences appear to play a pivotal role in determining the development, magnitude and frequency of aggression, most of previous studies focused on males, so little is known about female chronic physical aggression. We therefore tested here whether or not there is a signature of physical aggression in female DNA methylation and, if there is, how it relates to the signature observed in males.

overall_design: Genome-wide promoter methylation profiles of T cell DNA from adult males and females on a Chronic Physical Aggression (CPA) trajectory during childhood and adolescence were compared to adults on a normative physical aggression trajectories (NPA). Each sample was bisulphite converted gDNA pooled in equimolar amounts. Three different pools of genomic DNA were made per group: male CPA (2 or 3 different subjects per pool), male NPA (4 different subjects per pool), female CPA (2 different subjects per pool) and female NPA (4 or 5 different subjects per pool) . The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles of the 2 groups in both sex.

first: Claire

last: Guillemin

first: Nadine

last: Provencal

first: Matthew

last: Suderman

first: Sylvana

middle: M

last: Cote

first: Frank

last: Vitaro

first: Michael

last: Hallett

first: Richard

last: Tremblay

first: Szyf

last: Moshe


title: Cross-platform prediction of gene expression signatures.

status: Public on Aug 21 2013

city: Houston

first: Jeffrey

last: Chang

address: 6431 Fannin St

institute: University of Texas

summary: We developed a method to convert gene expression signatures across the Illumina and Affymetrix platforms.

overall_design:
We generated an E2F1 signature.
We processed RNA for E2F1, MYC, and Ras signatures on the Illumina platform.  16 Melanoma samples are also included for validation.

first: Shu-Hong

first: Lauren

last: Beane

first: Dawn

last: Chasse

first: Kevin

last: Zhu

first: Bernard

last: Mathey-Prevot

first: Joseph

last: Nevins

middle: T


title: Chronic growth factor signaling in Acute Myeloid Leukemia is connected to a specific chromatin signature [ChIP-Seq]

first: Pierre

last: Cauchy

summary: We performed genome-wide DNaseI hypersensitive site in FLT3-ITD and WT patient samples. We report corresponding gene expression, promoter methylation patterns of differential DHSs as well as differentially occupied TF binding motifs using surrounding DNAseI cut profiles. We examined association patterns of FLT3 ITD and WT AMLs and found that FLT3-ITD signaling is associated with common gene expression and chromatin signature.

overall_design: Examination of Runx1 binding sites in FLT3 ITD AML.

first: Sally

last: James

first: Anetta

last: Ptasinska

first: Joaquin

last: Zacarias-Cabeza

first: Maria

middle: R

last: Imperato

first: Salam

last: Assi

first: Jason

last: Piper

first: Sascha

last: Ott

first: Constanze

last: Bonifer

first: Peter

last: Cockerill


title: DNA Methylation Signature of Childhood Chronic Physical Aggression in T Cells of Both Men and Women (Agilent)

first: Moshe

last: Szyf

type: Methylation profiling by genome tiling array

overall_design: Genome-wide promoter methylation profiles of T cell DNA from adult females on a Chronic Physical Aggression (CPA, n=5) trajectory during childhood and adolescence were compared to those on normative physical aggression trajectories (NPA, n=14). Two technical replicates were generated for each individual.

first: Claire

last: Guillemin

first: Nadine

last: Provencal

first: Matthew

last: Suderman

first: Sylvana

last: Cote

first: Frank

last: Vitaro

first: Michael

last: Hallett

first: Richard

last: Tremblay

first: Szyf

last: Moshe


title: Gene expression in whi3 and WHI3x4 in YPD and YPE

status: Public on Sep 26 2013

city: Stony Brook

first: Ying

last: Cai

state: New York

address: Life Sciences Building Rm 363

department: Molecular Genetics and Microbiology

institute: Stony Brook University

summary: Measurement of the change in steady state mRNA level in cells with whi3 deletion or WHI3 overexpression relative to wildtype cells. In the overexpression experiment, WHI3 is moderately overexpressed by integrating four copies of WHI3 at its endogenous locus. This was performed in YEP glucose medium and YEP ethanol medium. Goal was to measure the effects of WHI3 on global gene expression at RNA level.

overall_design: Two testing mutants whi3 vs WHI3, WHI3x4 vs WHI3 in two conditions YPD and YPE. Biological replicates: 2 whi3 in YPD, 2 WHI3x4 in YPD, 2 whi3 in YPE, 2 WHI3x4 in YPE.

first: Hong

last: Wang


title: WHI3

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

overall_design: Refer to individual Series


title: Skin gene expression correlates of severity of interstitial lung disease in systemic sclerosis

status: Public on Jul 12 2013

first: Jeffrey

last: Chang

summary:
We identified eighty two skin transcripts significantly correlated with the severity of interstitial lung disease (ILD) in systemic sclerosis.
These genes separated patients with more sever ILD in unsupervised hierarchical clustering.  Pathway analysis revealed pathways involved in extravasation and adhesion of inflammatory cells to endothelium.

overall_design: Skin biopsy samples from 59 patients enrolled in the GENISOS cohort or an open label imatinib study were examined by global gene expression studies.

first: Shervin

last: Assassi

first: Minghua

last: Wu

first: Filemon

last: Tan

first: Tiffany

last: Graham

first: Daniel

last: Furst

first: Dinesh

last: Khanna

first: Julio

last: Charles

first: Emma

last: Ferguson

first: Carol

last: Feghali-Bostwick

first: Maureen

middle: D

last: Mayes


title: Ribosome profiling of whi3 mutant yeast

summary: In general, RNA-binding proteins act to modulate gene expression at transcript level through degradation or at protein level through translation.  To elucidate the effect of Whi3, a yeast RNA binding protein, on gene expression, we performed ribosome profiling experiment on whi3 mutant and wildtype cells.

overall_design: Comparison ribosome profiling and RNA-seq data between whi3 mutant and wildtype cells


title: Gene expression from bone-marrow derived macrophages.

status: Public on Jan 20 2012

city: Barcelona

first: Cristina

last: Lopez-Rodriguez

address: Carrer Dr. Aiguader, 88

department: Medicine and Life Sciences

institute: Universitat Pompeu Fabra

summary:
Gene expression from WT and NFAT5 KO primary macrophage cultures.

Keywords: Bone-marrow derived macrophages.

overall_design: We analyzed 4 arrays from each condition: unstimulated WT BMDMs, LPS stimulated WT BMDMs, unstimulated KO BMDMs, LPS stimulated KO BMDMs.

first: Maria

last: Buxade

first: Jose

last: Aramburu


title: HMLER cells expressing either FOXC2 or a vector control

status: Public on Feb 15 2013

summary: We used microarrays to investigate the transcription profile of FOXC2 expression in a human mammary epithelial cell line.

overall_design: HMLER cells were infected with either a control vector or a retroviral vector expressing FOXC2.

first: Sendurai

last: Mani


title: Gene expression Classification of Colon Cancer defines six molecular subtypes with distinct clinical, molecular and survival characteristics

status: Public on May 22 2013

city: Paris

first: Nabila

last: Elarouci

address: 14 rue Corvisart

department: Recherche

institute: Ligue Nationale contre le Cancer

type: Genome variation profiling by genome tiling array


title: Gene expression Classification of Colon Cancer defines six molecular subtypes with distinct clinical, molecular and survival characteristics [Expression]

summary: From a clinical and molecular perspective, colon cancer (CC) is a heterogeneous disease but to date no classification based on high-density transcriptome data has been established. The aim of this study was to build up a robust molecular classification of mRNA expression profiles (Affymetrix U133Plus2) of a large series of 443 CC and 19 non-tumoral colorectal mucosas, and to validate it on an independent serie of 123 CC and 906 public dataset. We identified and validated six molecular subtypes in this large cohort as a combination of multiple molecular processes that complement current disease stratification based on clinicopathological variables and molecular markers. The biological relevance of these subtypes was consolidated by significant differences in survival. These insights open new perspectives for improving prognostic models and targeted therapies.

overall_design: Among a large series of colon cancers collected for the Cartes d'Identité des Tumeurs (CIT) program from the French Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net), 598 were analyzed for mRNA expression profiles using Affymetrix U133plus2 chip and, among theses, 463 could also be analyzed for DNA alteration profiles using the CGH Array (CIT-CGHarray V6). The 585 tumors was divided into a discovery dataset of 443 CC and a validation dataset of 123 CC and 19 non-tumoral dataset.

first: Laetitia

last: Marisa

first: Aurélien

last: de Reyniès

first: Alex

last: Duval

first: Janick

last: Selves

first: Marie-Pierre

last: Gaub

first: Laure

last: Vescovo

first: Marie-Christine

last: Etienne-Grimaldi

first: Renaud

last: Schiappa

first: Dominique

last: Guenot

first: Mira

last: Ayadi

first: Sylvain

last: Kirzin

first: Maurice

last: Chazal

first: Jean-François

last: Fléjou

last: Benchimol

first: Erwan

last: Pencreach

first: Arnaud

last: Lagarde

first: Françoise

last: Piard

last: Elias

first: Sylviane

last: Olschwang

first: Gérard

last: Milano

first: Pierre

last: Laurent-Puig

first: Valérie

last: Boige


title: DNA methylation in the malignant transformation of meningiomas

status: Public on Jan 10 2013

city: Los Angeles

first: Fan

last: Gao

address: 1501 San Pablo St. ZNI 245

department: ZNI

institute: USC

summary: Genome wide DNA methylation profiling of malignant, atypical and benign meningiomas samples. The Illumina infinium HumanMethylation450 beadchip kit was used, which assayed 450,000 potential methylation sites.

overall_design: Bisulphite converted DNA from the 23 samples were hybridised to the Illumina Infinium 450 Human Methylation Beadchip.

first: Kai

last: Wang


title: Epigenetic portraits of human breast cancers

status: Public on Oct 19 2011

city: Toronto

first: Benjamin

last: Haibe-Kains

state: Ontario

address: 610 University Avenue

department: Princess Margaret Research

institute: Princess Margaret Cancer Centre

type:
Expression profiling by array
Methylation profiling by array


title: An Integrated genomic and expression analysis of 7q deletion in SMZL

status: Public on Jan 27 2012

city: Scottsdale

first: Esteban

last: Braggio

state: AZ

address: 13400 E. Shea Blvd, MCCRB-300

institute: Mayo Clinic Arizona

summary: Splenic marginal zone lymphoma (SMZL) is an indolent B-cell lymphoproliferative disorder characterised by 7q32 deletion, but the target genes of this deletion remain unknown.  In order to elucidate the genetic target of this deletion, we performed an integrative analysis of the genetic, epigenetic, transcriptomic and miRNomic data.  High resolution array comparative genomic hybridization of 56 cases of SMZL delineated a minimally deleted region (2.8Mb) at 7q32, but showed no evidence of any cryptic homozygous deletion or recurrent breakpoint in this region.  Integrative transcriptomic analysis confirmed significant under-expression of a number of genes in this region in cases of SMZL with deletion, several of which showed hypermethylation.   In addition, a cluster of 8 miRNA in this region showed under-expression in cases with the deletion, and three (miR-182/96/183) were also significantly under-expressed (P <0.05) in SMZL relative to other lymphomas.   Genomic sequencing of these miRNA and IRF5, a strong candidate gene, did not show any evidence of somatic mutation in SMZL.

overall_design: Twenty seven SMZL patients were included in this study.  All cases were reviewed prior to study on paraffin sections with immunohistochemistry.  Sections of each frozen tissue used for study were also reviewed by histological examination and immunohistochemistry before was submitted for the study.

first: Rafael

last: Fonseca

first: Ahmet

last: Dogan


title: Epigenetic portraits of human breast cancers (expression data)

summary: Breast cancer is a molecularly, biologically and clinically heterogeneous group of disorders. Understanding this diversity is essential to improving diagnosis and optimising treatment. Both genetic and acquired epigenetic abnormalities participate in cancer, but information is scant on the involvement of the epigenome in breast cancer and its contribution to the complexity of the disease. Here we used the Infinium Methylation Platform to profile at single-CpG resolution (over 14,000 genes interrogated) the methylomes of 119 breast tumours. It emerges that many genes whose expression is linked to the ER status are epigenetically controlled (or/ we show that the two major phenotypes of breast cancers determined by ER status are widely involving epigenetic regulatory mechanisms), offering the prospect of a novel approach to treating ER-positive tumours. We have distinguished methylation-profile-based tumour clusters, some coinciding with known “expression subtypes” but also new entities that may provide a meaningful basis for refining breast tumour typology. We show that methylation patterns may reflect the cellular origins of tumours. Having highlighted an unexpectedly strong epigenetic component in the regulation of key immune pathways, we show that a set of immune genes have high prognostic value in specific tumour categories. By laying the ground for better understanding of breast cancer heterogeneity and improved tumour taxonomy, the precise epigenetic portraits drawn here should contribute to better management of breast cancer patients.

overall_design: 92 bgene expression profiling reast cancer patients. Study of epigenetic variation (methylation) linked to gene expression. No replicate, no reference sample.  Two samples (Breast tumor from patient P_64 and Normal breast tissue N6) were of poor quality and were not processed for a final of 90 gene expression Samples.

first: Sarah

last: Dedeurwaerder

first: Christine

last: Desmedt

first: Emilie

last: Calonne

first: Sandeep

last: Singhal

first: Judith

last: Luciani

first: Pascale

last: Putmans

last: Lallemand

first: Denis

last: Larsimont

first: Jérôme

last: Toussaint

first: Sandy

last: Haussy

last: Rothé

first: Ghizlane

last: Rouas

first: Otto

last: Metzger

first: Michel

last: Georges

first: Christos

last: Sotiriou

first: François

last: Fuks


title: Snapshots of pre-rRNA structural flexibility reveal eukaryotic 40S assembly dynamics at nucleotide resolution

status: Public on Nov 14 2014

city: Edinburgh

first: Sander

last: Granneman

address: Mayfield Road, Kings Buildings, Waddington building, room 3.06

department: Centre for Synthetic and Systems Biology

institute: University of Edinburgh

summary: Ribosome assembly in eukaryotes involves the activity of hundreds of assembly factors that direct the hierarchical assembly of ribosomal proteins and numerous ribosomal RNA folding steps. However, detailed insights into the function of assembly factors and ribosomal RNA folding events are lacking. To address this, we have developed ChemModSeq, a method that combines structure probing, high throughput sequencing and statistical modeling, to quantitatively measure RNA structural rearrangements during the assembly of macromolecular complexes. By applying ChemModSeq to purified 40S assembly intermediates we obtained nucleotide-resolution maps of ribosomal RNA flexibility revealing structurally distinct assembly intermediates and mechanistic insights into assembly dynamics not readily observed in cryo-electron microscopy reconstructions. We show that RNA restructuring events coincide with the release of assembly factors and predict that completion of the head domain is required before the Rio1 kinase enters the assembly pathway. Collectively, our results suggest that 40S assembly factors regulate the timely incorporation of ribosomal proteins by delaying specific folding steps in the 3’ major domain of the 20S pre-ribosomal RNA.

overall_design: Three datasets of yeast ribosomal samples subjected to different chemical modifications; 1M7 dataset contains 8 different modified samples and 2 control samples; NAI dataset contains 3 different modified samples and 2 control samples; DMS dataset contains 1 modified sample and 1 control sample. Each sample consists of at least two replicates.

first: Ralph

last: Hector


title: DNA Methylation Signature of Childhood Chronic Physical Aggression in T Cells of Both Men and Women

first: Moshe

last: Szyf


title: Active Creb3L1 can upregulate secretory pathway genes in HeLa cells

status: Public on Oct 18 2010

first: Deborah

last: Andrew

state: MD

summary:
Abstract: Secretion occurs in all cells, with relatively low levels in most cells and extremely high levels in specialized secretory cells, such as those of the pancreas, salivary and mammary glands.  Here, we report that the CrebA/Creb3-like family of bZip transcription factors functions to upregulate expression of both the general protein machinery required in all cells for secretion and of cell-type specific secreted proteins.  Drosophila CrebA directly binds the enhancers of secretory pathway genes and is both necessary and sufficient to activate expression of every secretory pathway component gene examined thus far.  Microarray profiling reveals that CrebA also upregulates expression of genes encoding cell type specific secreted components.  Finally, we find that the human CrebA orthologues, Creb3L1 and Creb3L2, have the ability to upregulate the secretory pathway in non-secretory cell types.
Goals:  Creb3L1 is the closest related human orthologue of Drosophila CrebA.  CrebA is required to upregulate genes encoding the protein machinery and cargo in specialized secretory cells.  To determine if the human orthologues of CrebA, Creb3L1 and Creb3L2, perform the same function, we expressed the truncated active form of Creb3L1 in non-secretory HeLa cells.  We then performed microarray experiments and found that active Creb3L1 is sufficient to upregulate genes encoding the protein machinery of the secretory pathway, as observed with Drosophila CrebA.

overall_design: HeLa cells were transiently co-transfected with truncated Creb3L1 (Creb3L1 T) and GFP.  Following 20 hours in culture, GFP positive cells were isolated by FACS and RNA was extracted using the Rneasy kit (Qiagen).  As a control, mock transfected cells were also subjected to cell sorting and RNA was extracted using the same protocols.  At least three replicates were obtained for each group.

first: Rebecca

last: Fox

first: Caitlin

last: Hanlon


title: CrebA is a major and direct regulator of secretory pathway gene expression

summary:
Abstract: Secretion occurs in all cells, with relatively low levels in most cells and extremely high levels in specialized secretory cells, such as those of the pancreas, salivary and mammary glands.  Here, we report that the CrebA/Creb3-like family of bZip transcription factors functions to upregulate expression of both the general protein machinery required in all cells for secretion and of cell-type specific secreted proteins.  Drosophila CrebA directly binds the enhancers of secretory pathway genes and is both necessary and sufficient to activate expression of every secretory pathway component gene examined thus far.  Microarray profiling reveals that CrebA also upregulates expression of genes encoding cell type specific secreted components.  Finally, we find that the human CrebA orthologues, Creb3L1 and Creb3L2, have the ability to upregulate the secretory pathway in non-secretory cell types.
Goals:  The goals of the microarray experiments were to identify additional targets of the CrebA transcription factor to learn the range of genes regulated by this transcription factor during embryogenesis.  Previous work had indicated that CrebA upregulates the protein machinery of the early secretory pathway.  Our new data now shows that in addition to the protein machinery, CrebA also upregulates genes encoding the protein cargo that is secreted from specialized secretory organs.

overall_design: RNA was isolated from stage 11-15 wild type Drosophila embryos and compared to RNA from CrebA null mutant embryos of the same age; all samples were hybridized to the Drosophila Genome 2.0 Affymetrix array.  Three individual replicates were obtained for each sample.


title: CCRF-CEM Prednisolone treatment at 4h

status: Public on Mar 22 2011

city: Athens

first: George

middle: I

last: Lambrou

state: Attiki

address: Thivon & Levadeias

department: First Department of Pediatrics

country: Greece

institute: National and Kapodistrian University of Athens

summary:
Background: Glucocorticoids are important pharmaceutical agents in the treatment of acute lymphoblastic leukemia in children. Resistance or sensitivity to glucocorticoids is considered to be of crucial importance for disease prognosis. Prednisolone is a first-line chemotherapeutic agent in the treatment of acute lymphoblastic leukemia. Here, the effects of prednisolone on the resistant CCRF-CEM leukemic cell line were studied.
Methods: Prednisolone’s cytotoxic and cell cycle effects were studied with flow cytometry. NF-κB translocation was studied with Western Blotting and differential gene expression was studied with cDNA microarrays.
Results: Prednisolone exerted a delayed biphasic effect, necrotic at low doses and apoptotic at higher doses. At low doses, prednisolone exerted a pre-dominant mitogenic effect despite its induction on total cell death, while at higher doses, prednisolone’s mitogenic and cell death effects were counterbalanced. NF-κB was constitutively present in the nucleus. Early gene microarray analysis revealed 40 differentially expressed genes upon 4 hours of prednisolone’s exposure. Notable differences in gene regulation were observed between the lowest and the highest glucocorticoid doses. Prednisolone activated genes related to apoptosis/tumor suppression, cell cycle progression, metabolism and intra-/ extra-cellular signaling pathways.
Conclusions: The mitogenic/biphasic effects of prednisolone are of clinical importance in the case of resistant leukemic cells. This approach might lead to the identification of gene candidates for future molecular drug targets in combination therapy with glucocorticoids, along with early markers for glucocorticoid resistance.

overall_design:
Elucidation of the mechanisms of GC action may lead to identification of gene targets responsible for GC resistance. Key tools in this process are high-throughput technologies such as microarray-based gene expression analysis.
For this purpose, the parental CCRF-CEM cell line was chosen as the system of study for the effects of prednisolone treatment. This is a T-cell leukemia cell line characterized by a mutation (L753F) on one GR gene allele that impairs ligand binding (Thompson and Johnson 2003). It is known that both the DNA and ligand binding domains of the GR are required in order to repress NF-κB transactivation (Wissink, van Heerde et al. 1997). Interestingly, concerning the question whether this mutation would affect GC resistance, it has been reported previously that both the GC-resistant as well as the GC-sensitive CCRF-CEM subclones express heterogeneous populations of the GR (GRwt/GRL753F) (Palmer and Harmon 1991; Powers, Hillmann et al. 1993). The CCRF-CEM cell line has been reported to be resistant to GCs, presumably due to the accumulation of more resistant variants after long periods of prolonged culture (Norman and Thompson 1977). It is possible that these cells are clonally inhomogeneous, as possibly the cells obtained in vivo by patients. Moreover, the large number of the CCRF-CEM subclone studies in the literature makes it difficult to choose an appropriate resistant cell model. In addition, the utilization of an in vitro system for this study offered reproducibility, an opportunity to closely examine intracellular signals and avoid interference from other in vivo-participating systems. Thus, the cell line used for this study was considered to be useful in studying GC action and resistance in leukemic cells.
The aim of this work was to determine the cytotoxic, cell cycle phase distribution and early cancer-specific gene expression effects of prednisolone in CCRF-CEM cells, as an in vitro model of ALL resistance to glucocorticoids. The early gene expression profile allowed identification of genes initiating pivotal, early onset regulatory mechanisms activated by GC and excluded ensuing feedback responses and further downstream signals.
Samples tested were in the form of a loop-design i.e. control vs. 10nM prednisolone (designated 0vs1) , 10nM prednisolone vs.700uM prednisolone (designated 1vs3) and control vs. 700uM prednisolone (designated 0vs3), the sum of the logarithms of the first two should equal the third. In other words if Rj,i is the ratio of the ith gene in the jth experiment then R0vs1,i+R1vs3,i=R0vs3,i. We tested this using a statistical test. We have applied an intensity-dependent z-score where the sum of the ratios was compared to the ratio of the third experiment. If the difference was significant genes, in a standard deviation threshold of ±1.5 in relative units, were rejected from further analysis (Kerr and Churchill 2001; Kerr and Churchill 2001; Altman and Hua 2006; Kerr and Churchill 2007).


title: Comparative Transcriptional and Phenotypic Peripheral Blood Analysis of Kidney Recipients under Cyclosporin A or Sirolimus Monotherapy

status: Public on Oct 01 2010

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

institute: CIBEREHD

summary: Due to its low level of nephrotoxicity and capacity to harness tolerogenic pathways, sirolimus (SRL) has been proposed as an alternative to calcineurin inhibitors in transplantation. The exact mechanisms underlying its unique immunosuppressive profile in humans, however, are still not well understood. In the current study we aimed to depict the in vivo effects of SRL in comparison with cyclosporin A (CSA) by employing gene expression profiling and multiparameter flow cytometry on blood cells collected from stable kidney recipients under immunosuppressant monotherapy. SRL recipients displayed an increased frequency of CD4+CD25highFoxp3+ T cells. However, this was accompanied by an increased number of effector memory T cells and by enrichment in NFkB-related pro-inflammatory expression pathways and monocyte and NK cell lineage-specific transcripts. Furthermore, measurement of a transcriptional signature characteristic of operationally tolerant kidney recipients failed to detect differences between SRL and CSA treated recipients. In conclusion, we show here that the blood transcriptional profile induced by SRL monotherapy in vivo does not resemble that of operationally tolerant recipients and is dominated by innate immune cells and NFkB-related pro-inflammatory events. These data provide novel insights on the complex effects of SLR on the immune system in clinical transplantation.

overall_design: The complete database comprised the expression measurements of 54 675 genes for kidney trasplant recipient PBMC treated with SRL (n=23) and CSA (n=14) monotherapy. 9 healthy controls were also included.

first: Sophie

last: Brouard

first: Isabel

last: Puig-Pey

first: Juan

first: Annaick

last: Pallier

first: Christophe

last: Braud

first: Magali

last: Giral

first: Marina

last: Guillet

first: Federico

last: Oppenheimer

first: Josep

last: Campistol

first: Jean-Paul

last: Soulillou

first: A

last: Sanchez-Fueyo