title: Genome-wide binding sites of NF90/ILF3 in K562 erythroleukemia cells

city: Stanford

first: Mark

last: Nicolls

state: California

address: 300 Pasteur Drive

department: Pulmonary and Critical Care Medicine

institute: Stanford University School of Medicine

summary: NF90 and splice variant NF110 are DNA- and RNA-binding proteins encoded by the Interleukin enhancer-binding factor 3 (ILF3) gene that regulate RNA splicing, stabilization and export. The role of NF90 in regulating transcription as a DNA-binding protein has not been comprehensively characterized. Here, ENCODE ChIP-seq identified 9,081 genomic targets specifically bound by NF90/110 in K562 cells. One third of binding sites occurred at promoters of annotated genes. NF90/110 binding colocalized with chromatin marks associated with active promoters and strong enhancers. Analysis using ENCODE ChIP-seq experiments revealed that NF90 clustered with transcription factors exhibiting preference for promoters over enhancers (POLR2A, MYC, YY1). Differential gene expression analysis following shRNA knockdown of NF90 in K562 cells revealed that NF90 directly activates transcription factors that drive growth and proliferation (EGR1, MYC), while attenuating differentiation along erythroid lineage (KLF1). NF90/110 interacts with chromatin to hierarchically regulate transcription factors to promote proliferation and suppress differentiation.

overall_design: NF90 ChIP-seq in K562 cells

first: Ting-Hsuan

last: Wu

first: Lingfang

last: Shi

first: Jessika

last: Adrian

first: Minyi

first: Ramesh

last: Nair

first: Michael

middle: P

last: Snyder

first: Peter

middle: N

last: Kao


status: Public on Mar 01 2018

city: Montpellier

first: Gina

last: DEVAU

address: Place Eugene Bataillon

department: Universite de Montpellier CC105

country: France

institute: Inserm U1198-UM-EPHE

summary:
Parkinson disease (PD) is a neurodegenerative disease primarily associated with impaired movement affecting elderly people. To improve the understanding of the pathogenesis and to develop new therapies, we have developed a non-human primate model of PD using the lemurian Microcebus murinus (Mim). In this study, we tested the potential of canine adenovirus type 2 (CAV-2) as vector for gene transfer in the Mim brain by analyzing the gene expression changes in three regions involved in motor control: striatum, frontal cortex and midbrain. The CAV-2 viruses were injected in the right striatum of young adult females, 2 years old.
CAV-2 vectors preferentially transduce neurons in the primate brain and were carried by axonal transport to afferent structures in both hemispheres. The gene expression changes were analyzed at 2 critical times after infection by CAV-2: an acute time effect at 24h and a delayed time effect at 28 days post infection. In addition, the gene expression was compared in the ipsilateral side versus the contralateral side, and with a non-infected brain samples using human Affymetrix microarrays. The transcriptomic data were analyzed by Significance Analysis of Microarrays (SAM) to identify genes differentially expressed when comparing brain samples in the 3 conditions. The data were also analyzed by ANOVA one way and by Principal Component Analysis (PCA). The results have shown that the transduction of CAV2 in neurons induced specific changes. These changes differed during the immediate and the long-term-point. Gene expression changes were detected in transcriptional regulation, in synaptic transmission, in cellular trafficking and in immune response. More precisely, in the short term, CAV2 activated genes involved in a non-specific innate immune response. In the long term, CAV2 induced an adaptive tolerant immune response.
Gene expression changes in the striatum of Microcebus murinus induced by Canine adenovirus type 2 (CAV-2)

overall_design: Microcebus murinus brain samples were divided in 3 groups : 1- right side (ipsilateral); 2- left side (contralateral; 3- non-infected samples. All the brain samples were analyzed at 24h  post infection, to detect the acute effect of CAV-2 and at 28 days after infection to detect the long term effect in the brain.

first: Nadine

last: MESTRE-FRNACES

first: Jean-Michel

last: VERDIER

first: Eric

middle: J

last: KREMER


title: miR-550a-3-5p overexpression effect on human colon cancer cell line

city: Seoul

first: Jae-sung

last: Kim

address: 75, Nowon-ro

country: South Korea

institute: Korea Institute of Radiological and Medical Sciences

summary: To identify targets of miR-550a-3-5p in human colon cancer, HCT116 cell line expressing miR-550a-3-5p was subjected to Illumina microarrays.

overall_design: Total RNA obtained from HCT116 cells transfected with 20 nM control RNA or 20 nM miR-550a-3-5p for 48 h.

first: Seo-Young

last: Kwak

first: Min Ho

last: Choe

first: Young-Hoon

last: Han

first: Jae-Sung


title: Inflammatory Bowel Disease-specific alterations in adipose-derived stroma cell transcriptional profiles

city: Los Angeles

first: Iordanis

last: Karagiannidis

address: 675 Charles E. Young Dr. South

country: USA

institute: UCLA, David Geffen School of Medicine

summary: Transcriptional profiling of primary human mesenteric adipose-derived stroma cells isolated from control, cancer, Crohn's disease, Ulcerative colitis, and obese patients

overall_design: five-condition experiment (see summary), 6 Biological replicates per group

first: Iordanes

last: Karagiannides

first: Jill

middle: M

last: Hoffman


title: CASC15 overexpression in HuCCT1 cholangiocarcinoma cell line

city: Rennes

first: Cedric

last: Coulouarn

address: CLCC Eugène Marquis, Rue de la Bataille Flandres Dunkerque, Bat D, 1er étage

institute: INSERM

summary: The aim of the study was to characterize the transcriptional profile of cholangiocarcinoma cell line HuCCT1 after transfection with a plasmid encodind the long isoform of CASC15 (Gene ID: 401237 ; RNA sequence: NR_015410.1).

overall_design: HuCCT1 (RCB-1960) cholangiocarcinoma cell line overexpressing CASC15. Triplicate experiments were performed.


title: Transcriptomics Provides Mechanistic Indicators of Mixture Toxicology for IMX-101 and IMX-104 Formulations in Fathead Minnows (Pimephales promelas) [IMX-104]

city: Vicksburg

first: Kurt

middle: A

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

institute: US Army ERDC

summary: Abstract —  Within the US military, new insensitive munitions (IMs) are rapidly replacing conventional munitions improving safety from unintended detonation. Toxicity data for IM chemicals are expanding rapidly, however IM constituents are typically deployed in mixture formulations, and very little is known about their mixture toxicology. In the present study we sought to characterize the mixture effects and toxicology of the two predominant IM formulations IMX-101 and IMX-104 in acute (48 h) larval fathead minnow (Pimephales promelas) exposures. IMX-101 consists of a mixture of 2,4-dinitroanisole (DNAN), 3-nitro-1,2,4-triazol-5-one (NTO), and nitroguanidine (NQ) while IMX-104 is composed of DNAN, NTO, and hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). DNAN was the most potent constituent in IMX-101 eliciting an LC50 of 36.1 mg/L, whereas NTO and NQ did not elicit significant mortality in exposures up to 1040 and 2640 mg/L, respectively. Toxic unit calculations indicated that IMX-101 elicited toxicity representative of the component concentration of DNAN within the mixture. Toxicogenomic responses for the individual constituents of IMX-101 indicated unique transcriptional expression and functional responses characteristic of: oxidative stress, impaired energy metabolism, tissue damage and inflammatory responses in DNAN exposures; impaired steroid biosynthesis and developmental cell-signaling in NQ exposures; and altered mitogen-activated protein kinase signaling in NTO exposures. Transcriptional responses to the IMX-101 mixture were driven by the effects of DNAN where expression and functional responses were nearly identical comparing DNAN alone versus the fractional equivalent of DNAN within IMX-101. Given that each individual constituent of the IMX-101 mixture elicited unique functional responses, and NTO and NQ did not interact with DNAN within the IMX-101 mixture exposure, the overall toxicity and toxicogenomic responses within acute exposures to the IMX-101 formulation are indicative of "independent" mixture toxicology. Alternatively, in the IMX-104 exposure both DNAN and RDX were each present at concentrations sufficient to elicit lethality (RDX LC50 = 28.9 mg/L). Toxic-unit calculations for IMX-104 mixture formulation exposures indicated slight synergistic toxicity (ΣTU LC50 = 0.82, 95% confidence interval = 0.73-0.90). Unique functional responses relative to DNAN were observed in the IMX-104 exposure including responses characteristic of RDX exposure. Based on previous transcriptomics responses to acute RDX exposures in fathead minnow larvae, we hypothesize that the potentially synergistic responses within the IMX-104 mixture are related to interactive effects of each DNAN and RDX on oxidative stress mitigation pathways.

overall_design: Five separate microarray analyses were conducted within this study.  The five experiments investigated 5 unique chemical exposures in dose-series assays including:  1. DNAN , 2. NTO, 3. NQ, 4. IMX-101, and 5. IMX-104.  This GEO entry represents analysis number 5. IMX-104:   Fathead minnow larvae were exposed to IMX-104 at 0 (control), 24.5, 47.8, 97.3, 194.5 mg/L (measured concentrations).   Exposure and control water was dechlorinated tap water (Vicksburg, MS USA municipal dechlorinated via activated carbon filtration) amended with artificial sea salts (Instant Ocean, Blacksburg, VA, USA) to a conductivity of 600 µS/cm.  Fathead minnow larvae were exposed in static nonrenewal acute 48-h bioassays.  Exposure chambers were 250 mL beakers with a test solution volume of 200 ml.  Ten larvae were exposed in each beaker, and 4 replicate beakers were tested per treatment. Fish were fed <24-h old Artemia nauplii prior to test initiation. Surviving fish were enumerated daily and any fish found to be deceased were promptly removed from exposure chambers.  All animal testing was conducted using methods and protocols approved by the US Army, Engineer Research and Development Center’s Institutional Animal Care and Use Committee (IACUC Protocol #EL-6009-2014-1).

first: Guilherme

middle: R

last: Lotufo

first: Jacob

middle: K

last: Stanley

first: Mitchell

middle: S

last: Wilbanks

first: Pornsawan

last: Chappell

first: Natalie

middle: D

last: Barker


title: Primary melanoma cell lines vary in glycolytic activity

city: Houston

first: Zhiqiang

last: Wang

state: Texas

address: 7455 Fannin St.

department: Lymphoma and Myeloma

institute: University of Texas MD Anderson Cancer Center

summary:
Some patients with metastatic melanoma respond very well to adoptive T-cell therapy (ACT) based on re-infusion of autologous, ex vivo-expanded tumor-infiltrating T lymphocytes (TILs) plus interleukin-2 (IL-2). However, responses are highly variable.
We found that glycolysis in primary melanoma tumor cell lines, as measured by metabolic assays or expression of glycolysis genes, was strongly associated with clinical resistance of the corresponding patients' tumor to ACT.

overall_design: Primary tumors of metastatic melanoma were obtained for a phase II study (NCT00338377) evaluating autologous TILs plus high-dose IL-2. Primary tumor cell lines were established from 15 of these samples, and were used for gene expression profiling as well as for determination of extracellular acidification rate (ECAR) and oxygen consumption rate (OCR) with a Seahorse XF96 analyzer.

first: Weiyi

last: Peng

first: Tina

last: Cascone

first: R

middle: E

last: Davis

first: Patrick

last: Hwu


title: Transcriptomics Provides Mechanistic Indicators of Mixture Toxicology for IMX-101 and IMX-104 Formulations in Fathead Minnows (Pimephales promelas) [IMX-101]

overall_design: Five separate microarray analyses were conducted within this study.  The five experiments investigated 5 unique chemical exposures in dose-series assays including:  1. DNAN , 2. NTO, 3. NQ, 4. IMX-101, and 5. IMX-104.  This GEO entry represents analysis number 4. - IMX-101:   Fathead minnow larvae were exposed to IMX-101 at 0 (control), 2, 7.6, 15.2, 30.2, 61.7, 85.2, and 121.9 mg/L (measured concentrations).   Exposure and control water was dechlorinated tap water (Vicksburg, MS USA municipal dechlorinated via activated carbon filtration) amended with artificial sea salts (Instant Ocean, Blacksburg, VA, USA) to a conductivity of 600 µS/cm.  Fathead minnow larvae were exposed in static nonrenewal acute 48-h bioassays.  Exposure chambers were 250 mL beakers with a test solution volume of 200 ml.  Ten larvae were exposed in each beaker, and 4 replicate beakers were tested per treatment. Fish were fed <24-h old Artemia nauplii prior to test initiation. Surviving fish were enumerated daily and any fish found to be deceased were promptly removed from exposure chambers.  All animal testing was conducted using methods and protocols approved by the US Army, Engineer Research and Development Center’s Institutional Animal Care and Use Committee (IACUC Protocol #EL-6009-2014-1).


title: Transcriptomics Provides Mechanistic Indicators of Mixture Toxicology for IMX-101 and IMX-104 Formulations in Fathead Minnows (Pimephales promelas)

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

overall_design: Refer to individual Series


title: Transcriptomics Provides Mechanistic Indicators of Mixture Toxicology for IMX-101 and IMX-104 Formulations in Fathead Minnows (Pimephales promelas) [NQ]

overall_design: Five separate microarray analyses were conducted within this study.  The five experiments investigated 5 unique chemical exposures in dose-series assays including:  1. DNAN , 2. NTO, 3. NQ, 4. IMX-101, and 5. IMX-104.  This GEO entry represents analysis number 3. NQ:   Fathead minnow larvae were exposed to NQ at 0 (control), 20.7, 41.8, 82.7, 172, 367, 693. 1390, and 2640 mg/L (measured concentrations).   Exposure and control water was dechlorinated tap water (Vicksburg, MS USA municipal dechlorinated via activated carbon filtration) amended with artificial sea salts (Instant Ocean, Blacksburg, VA, USA) to a conductivity of 600 µS/cm.  Fathead minnow larvae were exposed in static nonrenewal acute 48-h bioassays.  Exposure chambers were 250 mL beakers with a test solution volume of 200 ml.  Ten larvae were exposed in each beaker, and 4 replicate beakers were tested per treatment. Fish were fed <24-h old Artemia nauplii prior to test initiation. Surviving fish were enumerated daily and any fish found to be deceased were promptly removed from exposure chambers.  All animal testing was conducted using methods and protocols approved by the US Army, Engineer Research and Development Center’s Institutional Animal Care and Use Committee (IACUC Protocol #EL-6009-2014-1).


title: Transcriptomics Provides Mechanistic Indicators of Mixture Toxicology for IMX-101 and IMX-104 Formulations in Fathead Minnows (Pimephales promelas) [NTO]

overall_design: Five separate microarray analyses were conducted within this study.  The five experiments investigated 5 unique chemical exposures in dose-series assays including:  1. DNAN , 2. NTO, 3. NQ, 4. IMX-101, and 5. IMX-104.  This GEO entry represents analysis number 2. NTO:   Fathead minnow larvae were exposed to NTO at 0 (control), 68, 130, 265, 528, and 1040 mg/L (measured concentrations).   Exposure and control water was dechlorinated tap water (Vicksburg, MS USA municipal dechlorinated via activated carbon filtration) amended with artificial sea salts (Instant Ocean, Blacksburg, VA, USA) to a conductivity of 600 µS/cm.  Fathead minnow larvae were exposed in static nonrenewal acute 48-h bioassays.  Exposure chambers were 250 mL beakers with a test solution volume of 200 ml.  Ten larvae were exposed in each beaker, and 4 replicate beakers were tested per treatment. Fish were fed <24-h old Artemia nauplii prior to test initiation. Surviving fish were enumerated daily and any fish found to be deceased were promptly removed from exposure chambers.  All animal testing was conducted using methods and protocols approved by the US Army, Engineer Research and Development Center’s Institutional Animal Care and Use Committee (IACUC Protocol #EL-6009-2014-1).


title: Chip-chip from human epidermis with H3ac

status: Public on Feb 28 2018

city: changsha

first: Shu

last: Ding

state: hunan

address: Tongzipo street 138#

country: China

institute: The Third Xiangya Hospital

type: Genome binding/occupancy profiling by array

summary:
The UV radiation induced epigenetic changes play an important role in photoaging, but experimental evidence of histone modification to support this perspective has been scarce.
Analyse the histone H3 acetylation pattern in sun-exposed and non-exposed skin by ChIP-chip. 227 genes displayed significant histone H3 hyperacetylation and 81 genes displayed significant histone H3 hypoacetylation in sun-exposed skins.

overall_design: ChIP-chip assay with anti-acetyl-histone H3 antibody in sun-exposed Pool (combining six skin samples from the outer forearm) and non-exposed Pool (combining six skin samples from the buttock)

first: Gongping

last: Liang


title: Gene Expression Profiles in mouse lungs following 7 days post oropharyngeal aspiration exposure to different asbestos and asbestiform fibers.

city: morgantown

first: Anna

last: Shvedova

state: WV

address: 1095 willowdale Rd

department: HELD

institute: CDC/NIOSH

summary: Asbestos is the general term for a family of naturally occurring fibrous silicate minerals having commercial importance. They have been used widely for construction and for a number of industrial applications until early 70’s.  It is now well known that workers exposed to asbestos are at high risk of developing many lung diseases including asbestosis, malignant mesothelioma, bronchial adenocarcinoma; squamous cell carcinoma of the respiratory epithelium and large/ small cell lung carcinoma. However, the disease causing potential and related processes associated with various asbestos/asbestiform fiber exposures are still largely unknown. In this study, we exposed C57BL6 female mice to asbestos (crocidolite, tremolite), asbestiform fibers (erionite) and a low pathogenicity mineral fiber (wollastonite) to assess pulmonary toxicity responses along with gene expression profiles in the lungs following 7 days post pharyngeal aspiration.

overall_design: Global mRNA expression profiles in the mouse lungs exposed to various asbestos (crocidolite, Tremolite), asbestiform (Erionite) and low pathogenic (Wollastonite)  fibers.

first: Yanamala

last: Naveena

first: Shvedova

last: Anna


title: Gene expression in Sox9 progenitors in the developing mouse lung

first: Edwin

middle: Justin

last: Ostrin

address: 1515 Holcombe Blvd, Unit 1465

department: Pulmonary Medicine

institute: MD Anderson Cancer Center

type: Expression profiling by high throughput sequencing

summary: This submission consists of two experiments utilizing translating ribosome affinity purification-sequencing (TRAP-seq). The first uses TRAP-seq to isolate transcripts from Sox9 positive progenitors at E14 and an E17 lung and compares it to non-immunoprecipitated whole lung homogenate control. The second compares TRAP-seq isolated transcripts from Sox9-wild type progenitors versus mutant progenitors. Recombination was induced at E13 and cells were isolated at E16.

overall_design: Sox9-TRAP at E14 vs supernatant; Sox9-TRAP at E17 vs whole lung homogenate; duplicated Sox9-mutant versus Sox9-wild-type

first: Jichao

last: Chen


title: Generation of Tumor Antigen-Specific iPSC-Derived Thymic Emigrants (iTE) using a Novel 3D Thymic Culture System

city: Bethesda

first: Li

last: Jia

state: MD

address: 10 Clinic center

institute: NCI/NIH

summary: Induced Pluripotent Stem Cell (iPSC)-derived T cells may provide future therapies for cancer patients, but those generated by current methods, such as the OP9/DLL1 system, have shown abnormalities that pose major barriers for clinical translation. Our data indicate that these iPSC-derived CD8 single positive T cells are more similar to CD4+CD8+ double positive T cells than to mature naïve T cells, display markers of developmental arrest and exhibit characteristics of innate-like immune cells. We developed a 3D organ culture method which avoids these aberrant developmental fates, and generates a novel homogenous subset of CD8αβ+ antigen-specific T cells, iPSC-derived Thymic Emigrants (iTE). iTE exhibit phenotypic and functional similarities to naïve T cells both in vitro and in vivo, including an enormous capacity for expansion, memory formation and tumor suppression. These data illustrate the limitations of current methods and provide a blueprint for the generation of antigen-specific iTE with tremendous clinical potential.

overall_design: Comparison of iPSC-derived Thymic Emigrants vs. Extrathymic T cells generated on OP9/DLL1 system

first: Nicholas

last: Restifo

first: Raul

last: Vizcardo


title: Gene expression of macrophages and microglia from naïve or MHV infected mouse brains

city: iowa City

first: Dorthea

last: Wheeler

state: IA

address: 51 Newton Road

institute: University of Iowa


title: Role of SWEF proteins in ABC differentiation

city: New york

first: Yurii

last: Chinenov

state: New York

address: 535 E 71 str, Hospital for Special Surgery

department: Research Division

institute: Hospital for special surgery

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Age/autoimmune-associated B cells (ABCs) are a T-bet dependent B cell subset, which accumulates prematurely in autoimmune settings. The molecular pathways that regulate ABCs in autoimmunity are largely unknown. The SWEF proteins include SWAP-70 and DEF6, a newly identified SLE risk variant. SWEF-deficient mice (double knock-out=DKO) develop a lupus like syndrome, which is accompanied by a marked expansion of ABCs. The accumulation of ABCs in DKO mice provided us with a unique opportunity to gain new insights into the molecular features that characterize the ABCs that prematurely expand in autoimmune conditions. Splenic Follicular B cells (FoB, B220+CD19+CD23+CD11c-CD11b-) and ABCs (B220+CD19+CD11c+CD11b+) were FACS sorted from >20 weeks old WT or DKO female mice and RNA-seq was employed to compare the transcriptome of DKO ABCs to that of FoB cells derived from either WT or DKO mice. Here we show that loss of SWEF proteins leads to altered gene expression in B cells independently of their differentiation state. In addition, a subset of genes was uniquely regulated in ABCs from DKO mice as compared to FoB cells from either WT or DKO mice. Ananlysis of the ATAC-seq experiment show that the ABCs that expand aberrantly in the DKO autoimmune setting exhibit a unique chromatin landscape and ABC-specific accessible loci displayed enrichment in AP-1/BATF, IRF, and T-bet binding motifs. Together our findings suggest that absence of SWEF proteins affects several key processes in ABCs. In particular, we observed alterations in a number of pathways involved in the control of cellular proliferation and inflammation, a finding that may play a crucial role in the premature accumulation of ABCs in DKOs and could distinguish them from non-autoimmune ABCs.

overall_design: 1. Examination of Follicular B cells transcriptome in B cells isolated from WT or DEF6-/-SWAP70-/- (DKO) mice. 2. Examination of  Follicular B cells and ABC transcriptome in DEF6-/-SWAP70-/- (DKO) mice. 3. Analysis of chromatin landscape in Follicular B cells and ABC cells from DEF6-/-SWAP70-/- (DKO) mice by ATAC-seq

first: Michela

last: Manni

first: Alessandra

middle: B

last: Pernis

first: Sung

last: Park


title: Transcriptomics Provides Mechanistic Indicators of Mixture Toxicology for IMX-101 and IMX-104 Formulations in Fathead Minnows (Pimephales promelas) [DNAN]

first: Kurt

last: Gust

overall_design: Five separate microarray analyses were conducted within this study.  The five experiments investigated 5 unique chemical exposures in dose-series assays including:  1. DNAN , 2. NTO, 3. NQ, 4. IMX-101, and 5. IMX-104.  This GEO entry represents analysis number 1. DNAN:   Fathead minnow larvae were exposed to DNAN at 0 (control), 0.37, 0.81, 1.6, 3.3, 6.6, 13.2, 26.5, 53.0 mg/L (measured concentrations).   Exposure and control water was dechlorinated tap water (Vicksburg, MS USA municipal dechlorinated via activated carbon filtration) amended with artificial sea salts (Instant Ocean, Blacksburg, VA, USA) to a conductivity of 600 µS/cm.  Fathead minnow larvae were exposed in static nonrenewal acute 48-h bioassays.  Exposure chambers were 250 mL beakers with a test solution volume of 200 ml.  Ten larvae were exposed in each beaker, and 4 replicate beakers were tested per treatment. Fish were fed <24-h old Artemia nauplii prior to test initiation. Surviving fish were enumerated daily and any fish found to be deceased were promptly removed from exposure chambers.  All animal testing was conducted using methods and protocols approved by the US Army, Engineer Research and Development Center’s Institutional Animal Care and Use Committee (IACUC Protocol #EL-6009-2014-1).

first: Guilherme

last: Lotufo

first: Jacob

last: Stanley

first: Mitchell

last: Wilbanks

first: Pornsawan

last: Chappell

first: Natalie

last: Barker


title: Gene expression of macrophages isolated from mouse brains

summary: Hematogenous macrophages infiltrate the brain after virus infection. We use a CSF1R inhibitior, PLX5622 to deplete microglia from the brain. However, macrophages also express the CSF1R and may be affected by PLX5622-treatment of mice.

overall_design:
We used microarrays to determine the gene expression profiles of FAC-sorted macrophages from day 4 post-infection with MHV brains from control and PLX5622-treated mice. Mice treated with PLX5622 with given the drug in their food for 7 days prior to infection, continuing throughout infection.
We used 3 mice in each group

first: D

middle: L

first: Stanley

last: Perlman


title: Differential gene expression of S. aureus 04-02981 (MRSA) on exposure to AGXX®

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

summary: In general, more number of genes were differentially expressed when MRSA was exposed to AGXX® as compared to when exposed to Ag. AGXX® was found to down- regulate the key biofilm genes, and virulence- associated genes

overall_design: Two strains, two conditions.

first: A

last: Vaishampayan

last: de Jong

first: J

last: Kok

first: E

last: Grohmann


title: TAK1 is essential for growth and maintenance of skeletal muscle mass

city: Copenhagen SV

first: Shizuka

last: Uchida

email: heart.lncrna@gmail.com, suc@dcm.aau.dk

address: Frederikskaj 10B, 2. (building C)

department: Department of Clinical Medicine

country: Denmark

institute: Aalborg University

summary:
Our results demonstrate that targeted deletion of TAK1 inhibits muscle growth during post-natal development period. Inactivation of TAK1 also causes muscle wasting in adult mice.
TAK1 regulates expression of a number of molecules and signaling pathways which mediate growth and maintenance of skeletal muscle.

overall_design: Gastronemious muscle was isolated from littermate floxed TAK1 and skeletal muscle-specific TAK1-knockout mice after 3 weeks of deletion of TAK1 and processed for RNA isolation and microarray analysis.

first: Ashok

last: Kumar

first: Sajedah

last: Hindi


title: Analysis of gene expression changes in whole blood samples from young men after acute or short-term intake of probiotic yoghurt compared to acidified milk

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

summary: Fermented dairy milks have been associated with many health benefits including the regulation of metabolic dysfunction. Different circulating clinical biomarkers have been used to explore the effect of fermented milks on metabolic health but the development of whole blood transcriptomics has recently been proposed as a source of novel biomarkers for this health outcome.  In a randomised, cross-over study, we evaluate the changes in the whole blood transcriptome after the intake of a probiotic yoghurt compared to a milk acidified with gluconic acid in seven healthy young men. The effects of the dairy foods on whole blood gene expression were assessed at three time points during a 6 h postprandial test (800g single dose) and in the fasting state after a daily intake of the products over two-weeks (400g/d). RNA was extracted from Paxgene ® whole blood samples and sequenced on the Illumina HiSeq platform.

overall_design: A crossover design was used to compare the postprandial and short-term response to the intake of two dairy products in seven healthy young men. A total of 77 samples were collected. For each volunteer one samples was taken under baseline condition (run-in), four samples were taken for the postprandial assessment ('acute') of the two products (0h, 2h, 4h, 6h), and one sample was taken after two-weeks daily intake of each dairy product.

first: Kathryn

last: Burton

last: Zangger

first: Guy

last: Vergères


title: Airn isoforms are important for the functions of cardiomyocytes

type:
Other
Expression profiling by array


title: Biomodal role of H3.3 in safe-guarding and establishing cell identities during reprogramming [ATAC-Seq]

city: Singapore

first: Chadi

last: El Farran

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

summary: Determination of chromatin accessibility changes during cellular reprogramming using RNA-Seq

overall_design: ATAC-Seq of cells undergoing cellular reprogramming at several time-points

last: EL  Farran

first: Hai-Tong

last: Fang

first: Qiao

last: Xing

first: Li-Feng

last: Zhang

first: Hu

last: Li

first: Yuin-Han

last: Loh


title: Biomodal role of H3.3 in safe-guarding and establishing cell identities during reprogramming [ChIP-Seq]

summary: Identification of the genome-wide enrichment of H3.3, H3K4me3 and H3K36me3 during cellular reprogramming using ChIP-Seq

overall_design: ChIP-Seq of H3.3, H3K4me3 and H3K36me3 at seveal time-points during cellular reprogramming or transdifferentiation


title: Airn isoforms are important for the functions of cardiomyocytes (RIP-chip-Igf2bp2)

summary: To elucidate the function of Airn isoforms in the heart, we conducted RNA immunoprecipitation experiment followed by microarray (RIP-chip) in murine cardiomoycyte cell line HL-1.

overall_design: Using HL-1 cells, we performed RIP-chip assay using anti-Igf2bp2 antibody upon silencing of Airn.

first: Mohammed

last: Hosen


title: Genome-wide analysis of the histone variant H3mm7

status: Public on Feb 27 2018

city: Fukuoka

first: Yasuyuki

last: Ohkawa

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

department: Medical Institute of Bioregulation, Medical Institute of Bioregulation

country: Japan

institute: Kyushu University

summary: We identified a histone H3.3 sub-variant, H3mm7, to be specifically expressed in skeletal muscle satellite cells. H3mm7 knockout mice demonstrated an essential role of H3mm7 in skeletal muscle regeneration. Chromatin analysis revealed that H3mm7 facilitates transcription by forming an open chromatin structure around promoter regions including those of myogenic genes.

overall_design: We performed CEL-Seq2 in mouse tissues, RNA-seq and ATAC-seq in C2C12 and NIH3T3 cells, ChIP-seq in NIH3T3 cells. (BioProject: PRJDB5940, Accession: DRA005975, DRA006453)

first: Akihito

last: Harada

first: Kazumitsu

last: Maehara


title: Resistance to BET inhibitor leads to new therapeutic vulnerabilities in castration resistant prostate cancer

city: Philadelphia

first: Irfan

last: Asangani

state: Pennylvania

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania

summary: BRD4 plays a major role in the transcription networks orchestrated by androgen receptor (AR) in castration resistant prostate cancer (CRPC) cells. Bromodomain and extraterminal protein (BET) inhibitors displace BRD4 protein from chromatin, resulting in the inhibition of oncogenic transcriptional programs. Several BET inhibitors (BETi) are currently being evaluated in clinical trials for a variety of malignancies, including CRPC. Here we describe a general mechanism of acquired resistance to BETi due to modulation of cellular pathways that are amenable to targeted therapies in CRPC cells. BETi resistant CRPC cells displayed cross resistance to a variety of BETi in the absence of gatekeeper mutations or persistent drug pump activation. Resistant cells exhibited reduced chromatin bound BRD4, and were less sensitive to Proteolysis Targeting Chimeric (PROTAC) -mediated degradation or genetic knockdown, suggesting a BRD4-independent transcription program. Transcriptomic analysis revealed reactivation of AR-signaling due to CDK9-mediated serine-81 phosphorylation of AR, with a consequent increase in sensitivity to CDK9 inhibitors and enzalutamide in BETi resistant cells. Additionally, increased DNA damage associated with PRC2-mediated transcriptional silencing of DNA damage response (DDR) genes was observed due to the loss of BRD4 from their proximal promoter regions in the resistant cells, leading to PARP inhibitor sensitivity. Collectively, our results identify the therapeutic limitation of BETi as a monotherapy in CRPC. However, data showing the reactivation of AR-signaling and increased DNA damage in the BETi resistant cells provide unique opportunities for combination therapies in managing CRPC.

overall_design: Gene epxression by RNAseq in the parental vs BETi resistant 22RV1 and LNCaP cells


title: Biomodal role of H3.3 in safe-guarding and establishing cell identities during reprogramming

overall_design: Refer to individual Series


title: Transcription profiling of human neural precursors upon alcohol exposure

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: Cells were treated with 0 and 100mM of OH at 2 different stages of neurogenesis

first: Rajarshi

last: Pal


title: Snord116-dependent diurnal rhythm of DNA methylation in mouse cortex

city: Davis

first: Rochelle

last: Coulson

state: CA

address: One Shields Ave.

institute: University of California, Davis

type: Methylation profiling by high throughput sequencing

summary: Rhythmic oscillations of physiological processes depend on integrating the circadian clock and diurnal environment.  DNA methylation is epigenetically responsive to daily rhythms, as a subset of CpG dinucleotides in brain exhibit diurnal rhythmic methylation.  A major genetic effect on rhythmic methylation was identified in a mouse Snord116 deletion model of the imprinted disorder Prader-Willi syndrome (PWS).  > 23,000 diurnally rhythmic CpGs were identified in wild-type cortex, with nearly all lost or phase-shifted in PWS.  Circadian dysregulation of a second imprinted Snord cluster at the Temple/Kagami-Ogata syndrome locus was observed at the level of methylation, transcription, and chromatin, providing mechanistic evidence of cross-talk.  Genes identified by diurnal epigenetic changes in PWS mice overlapped rhythmic and PWS-specific genes in human brain and were enriched for PWS-relevant phenotypes and pathways. These results support the proposed evolutionary relationship between imprinting and sleep, and suggest possible chronotherapy in the treatment of PWS and related disorders.

overall_design:
Examination of whole genome DNA methylation in mouse cerebral cortex throughout the diurnal cycle.
Genotypes: WT, Snord116+/-
Timepoints: ZT0, ZT3, ZT6, ZT9, ZT12, ZT16
n = 3 per condition

first: Yasui

middle: H

last: Dag

first: Keith

last: Dunaway

first: Benjamin

middle: I

last: Laufer

first: Annie

last: Vogel Ciernia

first: Yihui

last: Zhu

first: Charles

last: Mordaunt

first: Theresa

last: Totah

first: Janine

last: LaSalle


title: Gene expression of microglia from naïve or MHV infected mouse brains

first: Dorthea

last: Wheeler

summary: Microglia are the brain-resident myeloid cells of the parenchyma. We study the roles microglia play in response to virus infection.

overall_design:
We used microarrays to determine the gene expression profiles of FAC-sorted microglia from the naïve and infected mouse brain.
We used 4 mice in each group

first: D

first: Stanley

last: Perlman


title: Avian zygote activates only maternal allele to disburden high variation of supernumerary sperms contrary to mammal

city: Seoul

first: JAE

middle: YONG

last: HAN

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Agricultural Biotechnology

institute: Seoul National University

summary: Here we show that the detailed insight of the onset of zygotic transcription in chicken. Our transcriptomic analysis of early chicken embryo reveal newly expressed and primary transcripts by ZGAs at genome-wide and base resolution.

overall_design: Chicken early embryo (Oocyte, Zygote, and EGK.X) samples were investigated based on the whole transcriptome sequencing approach.

first: Jae-yong

last: Han

first: Young-sun

last: Hwang


title: Evidence that DNA polymerase δ contributes to initiation of leading strand DNA replication in Saccharomyces cerevisiae

city: Research Triangle Park

first: Marta

middle: Anna

last: Garbacz

state: NC

address: 111 T.W. alexander Dr.

department: GISBL

institute: NIEHS/NIH

summary: To investigate nuclear DNA replication enzymology in vivo, we have studied Saccharomyces cerevisiae strains containing a pol2-16 mutation that inactivates the catalytic activities of DNA polymerase δ (Pol δ). Although pol2-16 mutants survive, their spore colonies are very tiny, with increased doubling time, larger than normal cells, aberrant nuclei, and rapid suppressor mutation accumulation. These phenotypes reveal a severe growth defect that is distinct from that of strains that lack Pol δ proofreading (pol2-4), consistent with the idea that Pol δ is the major leading strand replicase. Ribonucleotides are also incorporated into the pol2-16 genome in patterns consistent with leading strand replication by Pol δ when Pol δ is absent. More importantly, ribonucleotide distributions at replication origins suggest that in strains encoding all three replicases, Pol δ contributes to initiation of leading-strand replication. We describe two possible models.

overall_design: Examination of location of ribonucleotides in multiple yeast strains bearing different DNA polymerase variants, either proficient or deficient in rnh201.

first: Scott

last: Lujan

first: Adam

last: Burkholder

first: Phillip

last: Cox

first: Qiuqin

last: Wu

first: Zhi-Xiong

middle: X

last: Zhou

first: James

last: Haber

first: Thomas

last: Kunkel


title: RNA Seq analysis of pancreatic beta cell transcriptome during dedifferentiation

status: Public on Feb 26 2018

city: Mölndal

first: Fabrice

last: CHIMIENTI

address: Pepparedsleden 1

country: Sweden

institute: AstraZeneca

summary:
We report RNA Seq analysis using Illumina nextSeq500 of human beta cells EndoC-BH1 treated with FGF2 to induce dedifferentiation.
FGF2 treatment induced dedifferentiation of EndoC-BH1 cells. Indeed, we observed a strong decrease in expression of β-cell markers, (INS, MAFB, SLC2A2, SLC30A8 and GCK).  Opposingly, we identifed positive markers of human β cell dedifferentiation, as attested by increased expression of mature β-cell disallowed transcription factors (MYC, HES1, SOX9 and NEUROG3). Interestingly, our temporal analysis revealed that loss of expression of β cell specific markers preceded the induction of β cell disallowed genes.

overall_design: human beta cells EndoC-BH1 were treated with FGF2 (100ng/L) during 4, 24, 72 and 144h. RNA was isolated post treatment, along with the non-treated controls, and RNA Seq was performed using Illumina nextSeq500  to generate a full transcriptome analysis of gene   expression during dedifferentiation of pancreatic beta cells.

last: Chimienti

first: Maryam

last: Clausen

first: Suraj

last: Menon

first: Marc

last: Diedisheim

first: Raphael

last: Scharfmann


title: RNA-dependent chromatin targeting of TET2 for endogenous retrovirus control in pluripotent stem cells [CLIP-Seq]

city: New York

first: Jianlong

last: Wang

department: Department of Medicine

institute: Columbia University Irving Medical Center

summary: Ten-eleven translocation (TET) proteins play key roles in regulating the methylation status of DNA through oxidizing methylcytosines (5mC), generating 5-hydroxymethylcytosines (5hmC) that can both serve as stable epigenetic marks and participate in active demethylation. Here we show that TET2 is recruited by the RNA-binding protein Paraspeckle component 1 (PSPC1) through transcriptionally active loci, including endogenous retroviruses (ERVs) whose long terminal repeats (LTRs) have been co-opted by mammalian genomes as stage- and tissue-specific transcriptional regulatory modules. We find that PSPC1 and TET2 contribute to ERV and ERV-associated gene regulation by both transcriptional repression via histone deacetylases and post-transcriptional destabilization of ERV RNAs through 5hmC modification. Our findings provide evidence for a functional role of transcriptionally active ERVs as specific docking sites for RNA epigenetic modulation and gene regulation.

overall_design: RNA occupancy profiling of Pspc1 was performed in mouse ESCs by crosslinking immunoprecipitation and massive parallel sequencing (CLIP-seq).

first: Xin

last: Huang

first: Diana

last: Guallar


title: RNA-dependent chromatin targeting of TET2 for endogenous retrovirus control in pluripotent stem cells [RNA-Seq]

overall_design: RNA sequencing analysis was performed in mouse embryonic stem cells (ESCs) with shEV and shPspc1 treatment.


title: Pharmacogenomic comparison between D3T- and CDDO-Im in mouse liver tissue

status: Public on Feb 25 2018

city: Memphis

last: Sutter

state: Tennessee

address: 3700 Walker Avenue Ellington Hall RM 239

department: Biological Sciences

institute: University of Memphis

summary: The Keap1/Nrf2 signaling pathway is a tractable target for the pharmacological prevention of tumorigenesis.  3H-1,2-dithiole-3-thione (D3T) and 1-[2-cyano-3,12-dioxooleana-1,9(11)-dien-28-oyl]imidazole (CDDO-Im) are representative members of two classes of Nrf2-activating chemopreventive agents.  Natural dithiolethiones have been widely used in clinical trials for cancer chemoprevention.  Synthetic triterpenoids, however, have been shown to be significantly more potent Nrf2 activators and are under clinical evaluation for the treatment of chronic kidney disease.  This study seeks to characterize the structure-activity relationship between D3T and CDDO-Im in mouse liver tissue.  To this end we treated Wt and Nrf2-null mice with 300 umol/kg bw D3T and 3, 10, and 30 umol/kg bw CDDO-Im every other day for 5 days and evaulated global gene expression changes as a product of both treamtent and genotype using Affymetrix microarray.

overall_design: Hepatic global gene expression changes in the liver tissue of Wt and Nrf2-null mice treated with vehicle (10% Cremophor-EL, 10% DMSO, and PBS), 300 umol/kg bw D3T, or 3, 10, 30 umol/kg bw CDDO-Im.  12 week old male mice were treated by gavage every other day for 5 days, resulting in 3 total administrations of treatment.  Animals were euthanized 24 hours following the 3rd treatment.  n=4/treatment/genotype, male 12 week old mice were used.

first: Ryan

last: Wible

first: Quynh

middle: T

last: Tran

first: Samreen

last: Fatima

first: Carrie

middle: W

last: Kensler


title: Zc3h10 is a novel mitochondrial regulator

city: Milano

first: Stefano

last: de Pretis

address: Via Olgettina, 58

department: Center for Omics Sciences

country: Italy

institute: IRCCS San Raffaele Institute

summary: Mitochondria are the energy-generating hubs of the cell. In spite of considerable advances, our understanding of the factors that regulate the molecular circuits that govern mitochondrial function remains incomplete. Using a genome-wide functional screen, we have identified the poorly characterized protein Zinc finger CCCH-type containing 10 (Zc3h10) as regulator of mitochondrial physiology. We show that Zc3h10 is upregulated during physiological mitochondriogenesis such as myoblasts differentiation into myotubes. Zc3h10 overexpression boosts mitochondrial function and promotes myoblasts differentiation. On the other hand, depletion of Zc3h10 results in impaired myoblasts differentiation, mitochondrial dysfunction, reduced expression of electron transport chain (ETC) subunits and blunted TCA cycle flux. Notably, we have identified a loss-of-function mutation of Zc3h10 in humans (Tyr105 to Cys105) that is associated with increased body mass index, fat mass, fasting glucose and triglycerides. Isolated peripheral blood mononuclear cells from Cys105 homozygotes display reduced oxygen consumption rate, some ETC subunit expression and decreased levels of some TCA cycle metabolites that derive in mitochondrial dysfunction. Finally, our study identifies Zc3h10 as a novel mitochondrial regulator.

overall_design: Gene expression profiling in C2C12 myotubes depleted for Zc3h10 and controls

first: Matteo

last: Audano

first: Mattia

last: Pelizzola

first: Nico

last: Mitro


title: Expression profile of Gastro-Entero-Pancreatic Neuroendocrine Tumors (GEP-NET)

first: Mariano

middle: Javier

last: Alvarez

state: NY

address: 1130 St. Nicholas ave.

department: Systems Biology

institute: Columbia University

summary: Expression profile of human GEP-NET tumors, including 113 fresh frozen biopsies of primary and metastatic tumours originating from pancreas (P-NET, 83 primary and 30 metastasis), 81 from small intestine (SI-NET, 44 primary and 37 metastasis), and 18 from rectum (RE-NET, 3 primary and 15 metastasis).

overall_design: 212 GEP-NET samples with cellularity >70% were analyzed. Total RNA was isolated and RNA integrity assayed by a 2100 Bioanalyzer (Agilent Technologies). High-quality total RNA samples, with RIN (RNA integrity number) above 7, were processed by TruSeq library preparation for RNA-Seq profiling (Illumina). For each sample, a minimum of 30 million 100bp single-end reads or 90 million 100bp paired-end reads were sequenced on the Illumina HiSeq2500 platform. RNA-Seq reads were mapped to the Homo sapiens assembly 19 reference genome, using Bowtie. Reads mapping to known genes, based on Entrez Gene identifiers, were then counted using the GenomicFeatures R-system package (Bioconductor).

middle: J


title: sRNA population in HT and AB D. melanogaster

city: Oxford

first: Irina

last: Mohorianu

address: Headington

department: Medical Sciences Division

country: United Kingdom

institute: University of Oxford

type: Non-coding RNA profiling by high throughput sequencing

summary: The aim was to profile the small RNA population in females. We observed that a very abundant rRNA fragment was present in the AB sample, but not in the HT sample.

overall_design: Females were dissected into head/thorax and abdomen and RNA extracted from both tissues. For each sample, the experiment was repeated and the flies were pooled  before RNA extraction.

first: Damian

last: Smith

first: Tracey

last: Chapman


title: Expression data from Neuroendocrine  Prostate  Cancer  and Primary Small Cell Prostatic Carcinoma

status: Public on Feb 23 2018

city: Vancouver

first: Elai

last: Davicioni

state: BC

address: 1152 Mainland St #430

country: Canada

institute: GenomeDx

summary:
Neuroendocrine prostate cancer (NEPC) is rare historically but may  be  increasingin  prevalence  as  patients  potentially  develop  resistance  to contemporary  anti-androgen  treatment  through  a  neuroendocrine  phenotype.  Diagnosis  can   be   straightforward   when  classic  morphological   features  are accompanied  by  a  prototypical  immunohistochemistry  profile,  however  there  is increasing  recognition  of  disease  heterogeneity  and  hybrid  phenotypes.    In  the primary setting, small cell prostatic carcinoma (SCPC) is frequently admixed with adenocarcinomas that may be clonally related, while a small fraction of SCPC’s express markers typical of prostatic adenocarcinoma.  Gene expression patterns may  eventually  help  elucidate  the  biology  underlying  equivocal  cases  with discordant IHC, however studies to date have focused on prototypical cases and been based on few patients due to disease rarity.
Here we  examine 16  primary  SCPC’s  and  16 primary  high  grade  adenocarcinomas  profiled  on  exon  arrays  from  archived formalin-fixed  paraffin-embedded  (FFPE)material.

overall_design: A  total  of  33  FFPE  samples diagnosed  as  16 small cell carcinomas, 16 high-grade adenocarcinomas (majority Gleason 9), and 1   adenocarcinoma   with   neuroendocrine   differentiation   were   retrieved   from surgical pathology and consultation files  of Johns Hopkins Hospital from  1999-2013  and  successfully  processed  for  gene  expression profiling withHuman  Exon  1.0  ST  GeneChips  (Affymetrix). Samples came from 28 patients: on   pathologic   classification, 6   had evidence   of   SCPC alone,   10   had adenocarcinoma  alone,  1  had adenocarcinoma with  NE  differentiation,  and  11 had  mixed  histology  tumors  containing separate  adenocarcinoma  and  SCPC components, with 4   matched   pairs.

first: Tsai

last: Harrison

first: Lehrer

last: Jonathan

first: Alshalalfa

last: Mohammed

first: Erho

last: Nicholas

first: Davicioni

last: Elai

first: Lotan

last: Tamara


title: Expression data from C57/6J mice (Normal), APP/PS1 mice and APP/PS1 mice treatment with HPYD

city: Tianjin

first: Weiying

last: Liu

address: Qi-Xiang-Tai Road 42

institute: Tianjin Medical University

summary:
Aβ is a peptide of 39-42 amino acid residues that derived from putative intramembranous processing of amyloid precursor protein (APP) at the proposed active site of the γ-secretase/PS1 aspartyl. Aβ has been shown to aggregate and accumulate abnormally in the brain of AD (Alzheimer's disease), and extracellular amyloid plaques of Aβ peptides aggregation can trigger a cascade of pathologic events leading to nerve fiber entanglement and neuronal apoptosis protease.
We used microarrays to investigate the effects of HPYD on the gene expression of APP/PS1 transgenic mice, the brain tissues of control group, model group and HPYD group mice.

overall_design: The brain tissues of control group (Normal mice), model group (APP/PS1 mice) and HPYD group mice were obtained from the mice at the end of the Morris water maze experiment. The total RNAs from these brain tissues were isolated for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain the expression profiles of control group , model group and HPYD group mice, and found the dysregulated expression of many genes in model mice that could be restored to normal level after treatment with HPYD according to three groups:control group, model group and HPYD group.

first: Shumei

last: Xu


title: Identification of a neutrophil-related gene expression signature that distinguishes between adult patients with and without nephritis in active systemic lupus erythematosus

city: Toronto

first: Stephenie

last: Prokopec

state: Ontario

address: 661 University Avenue, Suite 510

institute: Ontario Institute for Cancer Research

summary: Both a lack of biomarkers and relatively ineffective treatments constitute impediments to management of lupus nephritis (LN). Here we used gene expression microarrays to contrast the transcriptomic profiles of active SLE patients with and without LN to identify potential biomarkers for LN. RNA isolated from whole peripheral blood of active SLE patients was used for transcriptomic profiling and the data analyzed by linear modeling, with corrections for multiple testing. Results were validated in a second cohort of SLE patients, using NanoString technology. The majority of genes demonstrating altered mRNA abundance between patients with and without LN were neutrophil-related. Findings in the validation cohort confirmed this observation and showed that the levels of gene expression in renal remission were similar to active patients without LN. In secondary analyses, gene expression correlated with disease activity, hematuria and proteinuria, but not renal biopsy changes. As expression levels of the individual genes correlated strongly with each other, a composite neutrophil score was generated by summing all levels before examining additional correlations. There was a modest correlation between the neutrophil score and the blood neutrophil count, which was largely driven by the dose of steroids and not the proportion of low density and/or activated neutrophils. Analysis of longitudinal data revealed no correlation between baseline neutrophil score or changes over the first year of follow-up with subsequent renal flare or treatment outcomes, respectively. The findings argue that although the neutrophil score is associated with LN, its clinical utility as a biomarker may be limited.

overall_design: Blood samples were collected from 38 patients satisfying 4 or more of the revised 1997 American College of Rheumatology classification criteria for SLE and 17 controls recruited from the University Health Network.

first: Joan

last: Wither

first: Babak

last: Noamani

first: Nan-Hua

last: Chang

first: Dennisse

last: Bonilla

first: Zahi

last: Touma

first: Carmen

last: Avila-Casado

first: Heather

middle: N

last: Reich

first: James

last: Scholey

first: Paul

middle: R

last: Fortin

middle: C

last: Boutros

first: Carolina

last: Landolt-Marticorena


title: Reduction of rRNA during sRNA library construction using a set of blocking oligos, in Drosophila melanogaster

first: Irina

last: Mohorianu

summary: This experiment was designed to improve the proportion of miRNA mapping reads from sRNA library sequencing, by reducing the amount of particularly abundant rRNA fragments.

overall_design: We extracted the sRNA fraction from 50 pooled male D. melanogaster accesory glands and constructed 4 cDNA libraries from the resultant RNA (blocked vs not-blocked with 2 biogical replicates). For the blocked libraries  we introduced several blocking oligos, with sequences complentary to the most abundant contaminating rRNA fragments, with the aim of preventing ligation of that rRNA to library adapters. The other libraries (unblocked) were constructed according to standard HD protocol. The libraries were sequenced on a HighSeq2500 platform.

first: Emily

last: Fowler

first: Tracey

last: Chapman


title: Reduction of rRNA during sRNA library construction using a complementary blocking oligo, in Drosophila melanogaster

summary: This experiment was designed to improve the percentage of miRNA mapping reads from sRNA library sequencing, by reducing the amount of one particularly abundant rRNA 30mer sequence.

overall_design:
We extracted the sRNA fraction from 50 pooled male D. melanogaster abdomens, and constructed 2 cDNA libraries from the resultant RNA. For one library (blocked), we introduced a 30nt blocking oligo, with a sequence complentary to the most abundant contaminating rRNA fragment, with the aim of preventing ligation of that rRNA to library adapters. The other library (unblocked) was constructed according to standard protocol. Both libraries were sequenced using a HighSeq2500.

We extracted the sRNA fraction from 50 pooled male D. melanogaster accessory glands and testes and constructed 2 cDNA libraries from the resultant RNA. For one library (blocked), we introduced a 30nt blocking oligo, with a sequence complentary to the most abundant contaminating rRNA fragment, with the aim of preventing ligation of that rRNA to library adapters. The other library (unblocked) was constructed according to standard protocol. Both libraries were sequenced using a HighSeq2500.


title: Dual Blockade of the Lipid Kinase PIP4Ks and Mitotic Pathways Leads to Cancer-selective Lethality

first: Manvendra

middle: K.

last: Singh

address: 8 College Road

department: Programme in Cardiovascular & Metabolic Disorders

institute: Duke-NUS MEDICAL SCHOOL

summary:
We discover drugs with a dual-inhibitory mechanism provides a unique pharmacological strategy against cancer and evidence of cross-activation between the Ras/Raf/MEK/ERK and PI3K/AKT/mTOR pathways via a Ras˧PIK3IP1˧PI3K signaling network
Achieving robust cancer-specific lethality is the ultimate clinical goal. Here we identify a compound with dual-inhibitory properties, named a131, that selectively kills cancer cells, while protecting normal cells. Through an unbiased CETSA screen, we identify the PIP4K lipid kinases as the target of a131. Ablation of the PIP4Ks generates a phenocopy of the pharmacological effects of PIP4K inhibition by a131. Notably, PIP4Ks inhibition by a131 causes reversible growth arrest in normal cells by transcriptionally up-regulating PIK3IP1, a suppressor of the PI3K/Akt/mTOR pathway. Strikingly, Ras activation overrides a131-induced PIK3IP1 up-regulation and activates the PI3K/Akt/mTOR pathway. Consequently, Ras-transformed cells override a131-induced growth arrest and enter mitosis where a131’s ability to de-cluster supernumerary centrosomes in cancer cells eliminates Ras-activated cells through mitotic catastrophe. Our discovery of drugs with a dual-inhibitory mechanism provides a unique pharmacological strategy against cancer and evidence of cross-activation between the Ras/Raf/MEK/ERK and PI3K/AKT/mTOR pathways via a Ras˧PIK3IP1˧PI3K signaling network.

overall_design: Isogenic BJ human foreskin fibroblast cell lines, including non-transformed (normal) and transformed BJ cells, were treated with DMSO (n=4), a131 (n=7), a166 (n=3), control siRNA (n=3), PIP4K siRNA #1 (n=3), PIP4K siRNA #2 (n=3).

first: Mayumi

last: Kitagawa

first: Sujoy

last: Ghosh

first: Sang

last: Lee


title: RNA-dependent chromatin targeting of TET2 for endogenous retrovirus control in pluripotent stem cells

first: Jianlong

last: Wang

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

overall_design: Refer to individual Series


title: Microarray analysis of CCAR2-responsive gene expression in the presence of hydrogen peroxide

first: Ja-Eun

last: Kim

address: 26 Kyungheedae-ro, Dongdaemun-gu

institute: Kyung Hee University

summary: The hypothesis tested in the present study was that CCAR2 is one of factors to regulate gene expression under the oxidative condition. Results provide the information that specific genes are regulated in a CCAR2-dependent manner following hydrogen peroxide treatment.

overall_design: Total RNA obtained from hydrogen peroxide-treated CCAR2 siRNA-transfected cells compared to untreated control HeLa cells

first: Ja

middle: E

first: Wootae

first: Jaehyuk

last: Pyo


title: Expression data from mucosa of pigs

status: Public on Feb 22 2018

city: Frederiksberg C

first: Andrew

last: Williams

state: --- Select One ---

address: Dyrlægevej 100

institute: University of Copenhagen

summary: We aimed to determine the infect of Ascaris suum infection on mucosal immune pathways in pigs

overall_design: Pigs were infected or not with Ascaris suum. At days 56 post-infection the jejunum mucosa was sampled for microarray analysis


title: Characterization of a novel breast cancer cell line derived from a metastatic bone lesion of a breast cancer patient [gene expression]

city: Herston

first: Fares

last: Al-Ejeh

state: QLD

address: 300 Herston Road

department: Cancer

country: Australia

institute: QIMR Berghofer

summary: As organ-specific models of breast cancer bone metastasis do not exist, we established a novel breast cancer line was established from the ER-/PR-/HER2- bone metastasis from a breast cancer patient. This cell line was characterized and compared to the primary tumour and/or normal mammary epithelial cells with regards to phenotypes (i.e. marker expression), gene expression and copy number variation.

overall_design: Total RNA was isolated from the P7731 cell line (3 replicates) and compared to that isolated from the primary tumour (2 replicates).

first: Julie

last: Johnson

first: Darrell

last: Bessette

first: Jodi

middle: M

last: Saunus

first: Chanel

last: Smart

first: Sarah

last: Song

first: Rebecca

last: Johnston

first: Sibylle

last: Cocciardi

first: Esdy

last: Rozali

first: Cameron

last: Johnstone

first: Ana Christina

last: Vargas

first: Katia

last: Nones

first: Peter

last: MacCallum

first: Kum Kum

last: Khanna

first: Sunil

last: Lakhani

first: Georgia

last: Chenevix-Trench

last: Simpson

first: Nic

last: Waddell


title: A seven-helix protein acts as a key regulator of translation during human-to-mosquito transmission of Plasmodium falciparum

city: University Park

first: Manuel

last: Llinas

state: Pennsylvania

address: Millennium Science Complex, Pollock Rd

department: Biochemistry and Molecular Biology

institute: Penn State University

summary: Plasmodium falciparum is a unicellular parasite responsible for the majority of 440,000 death due to malaria every year. Due to their essential role for malaria transmission, gametocytes represent prime targets for transmission-blocking strategies intended to prevent spread of the deadly disease. In this study, we explored the signaling pathways leading to gametogenesis and identified a hitherto unknown protein, which structurally belongs to the class of seven-helix proteins and which thus was termed 7-helix-1. The protein is specifically expressed in female gametocytes and gene disruption leads to impaired gamete formation and thus reduced transmission of malaria parasites to mosquitoes. The loss of 7-helix-1 caused significant changes in the expression of components of the molecular machinery needed by eukaryotic cells to synthesize proteins. We thus propose that 7-helix-1 is a key regulator needed to coordinate the increased need of proteins at the onset of gametogenesis.

overall_design: Plasmodium falciparum parasite strains WT NF54 and 7-Helix-1-KO 2E6 were Percoll-enriched for mature (stage V) gametocytes were activated with 100 µM Xanthurenic acid for 30 minutes at RT. Total RNA was isolated using the Trizol reagent (Invitrogen) according to the manufacturer’s protocol. The extracted RNA was then hybridized on a DNA microarray against a common reference pool.

first: Sandra

last: Bennink

first: Andreas

last: von Bohl

first: Che

last: Ngwa

first: Leonie

last: Henschel

first: Andrea

last: Kühn

first: Nicole

last: Pilch

first: Tim

last: Weißbach

first: Alina

last: Rosinski

first: Matthias

last: Scheuermayer

first: Urska

last: Repnik

first: Jude

last: Przyborski

first: Lindsey

last: Orchard

first: Gareth

last: Griffiths

last: Llinás

first: Gabriele

last: Pradel


title: Global transcriptome analysis of colon tissues from AOM/DSS mouse models treated with anti-S100a9 antibody

city: Changsha

first: Jian

last: Ma

state: Hunan

address: 110  Xiangya  Road

department: Cancer  Research Institute

institute: Central South University

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are using transcriptome profiling (RNA-seq) to evaluate the effects of anti-S100a9 antibody on the global transcriptome of the colon tissues of the AOM/DSS mouse model (a model that mimics the human colitis-associated colon cancer development).
Methods: 36 five-week-old male ICR mice were randomized divided into three groups: control (i.e. no AOM/DSS and antibody treatment), AOM/DSS+IgG Ab (1.5 mg/kg), and AOM/DSS+anti-S100a9 Ab (1.5 mg/kg). Mice were intraperitoneal injected with a single dose of 10 mg/kg azoxymethane (AOM) (A5486; Sigma) on day 1. One week after the AOM injection, mice were given three cycles of DSS (cycle 1: 2%, 7 days; cycle 2: 1.5%, 5 days; and cycle 3: 1.5%, 5 days, DSS: 36–50 kDa; MP Biomedicals, CA, USA) in their drinking water, and then distilled water until the end of the experiment. Antibodies were administrated intravenously every two days during the three cycles of DSS treatment. Mice were sequentially killed randomly at the end of the 18th week, and at least five mice were killed for each group at each time point. RNAs were extracted by Trizol and sequenced by Solexa high-throughput sequencing service (Oebiotech, Shanghai, China). Data were extracted and normalized according to the manufacturer’s standard protocol.Each group has three mices' colon tissues be tested.
Results: Log-fold changes of up- or down-regulated mRNAs between the control and experiment group were selected with a significance threshold of p<0.05. There are 1017 mRNAs were up-regulated and 815 were down-regulated in “AOM/DSS+IgG Ab" group comparing to “control" group. There are 385 mRNAs were up-regulated and 163 were down-regulated in “AOM/DSS+anti-S100a9 Ab" group comparing to “control" group. There are 1314 mRNAs were up-regulated and 968 were down-regulated in “AOM/DSS+anti-S100a9 Ab" group comparing to “AOM/DSS+IgG Ab".
Conclusions: Our study describes the global transciptome changes of colon tissues of the AOM/DSS mouse model induced by anti-S100a9 antibody treatment.

overall_design: Mice colon tissues mRNA profiles of “control" (no AOM/DSS and antibody treatment), “AOM/DSS+IgG Ab", and “AOM/DSS+anti-S100a9 Ab" were generated by RNA sequecning, using Solexa high-throughput sequencing service (Oebiotech, Shanghai, China).

first: Xuemei

last: Zhang


title: Expression data for the molecular signature of TF1a acute myeloid leukaemia cell line

city: Nottingham

first: Marios

last: Georgiou

address: Queen's Medical Centre

department: School of Life Sciences

institute: University of Nottingham

summary:
TF1a AML cell line was selected for in vitro modelling of dormancy in AML. TF1-a were subjected to AML-niche-mimicking in vitro conditioning by culture with TGFB1 and the mTOR inhibitor rapamycin. Also TF1a cells were in vitro cultured with prolonged sublethal doses of Etoposide.
The molecular signature of untreated, dormancy induced and genotoxicity-surviving TF1a cells were investigated using global human genome GEP to identify drivers of dormancy in different conditioning scenarios in comparison to untreated counterparts.

overall_design: TF1a cells were cultured for 3 days with TGFB1 or rapamycin (mTOR inhibitor that mimickes scarcity of neutrients) or combination of the tow dormancy inducer. Also TF1a cells were cultured with IC20 doses of Etoposide for 6 days. At the end of the treatmnt incubation duration, TF1a were harvested and total RNA were extracted for the GEP analysis.

first: Mazin

middle: G

last: Al-Asadi

first: Monica

last: Pallis


title: RNA-Seq analysis of murine splenic B cells with deletion of YY1

city: Edmonton

first: Guanxiang

last: Liang

state: Alberta

address: 410 Agriculture/Forestry Centre

institute: University of Alberta

summary: X chromosome inactivation (XCI) in female lymphocytes is uniquely regulated, as the inactive X (Xi) chromosome lacks localized Xist RNA and heterochromatin modifications. Epigenetic profiling reveals that Xist RNA is lost from the Xi at the pro-B cell stage and that additional heterochromatic modifications are gradually lost during B cell development. Activation of mature B cells restores Xist RNA and heterochromatin to the Xi in a dynamic two-step process that differs in timing and pattern, depending on the method of B cell stimulation. Finally, we find that DNA binding by YY1 maintains XCI in activated B cells, as ex-vivo YY1 deletion results in loss of Xi heterochromatin marks and up-regulation of X-linked genes. Ectopic expression of the YY1 zinc finger domain is sufficient for Xist RNA localization during B cell activation. Together, our results indicate that Xist RNA localization is critical for maintaining XCI in female lymphocytes, and that chromatin changes on the Xi during B cell development and the dynamic nature of YY1-dependent XCI maintenance in mature B cells predisposes X- linked immunity genes to reactivation.

overall_design: Follicular B cells were isolated from the spleens of six (three males and three females) C57Bl/6 yy1 fl/fl mice. For each spleen, 1/3 of the cells were not treated with any reagent (naive cells), 1/3 the cells received mock treatment (mock cells) and 1/3 received TATCRE (tatcre cells). The mock and tatcre samples were then grown in RPMI medium along with anti-IgM and 20% FBS for 48 hours. All cells were lysed and RNA was isolated for library preparation. Expression differences between Mock and TATCRE treated cells were determined to understand the role of yy1 in B cell activation.

first: Michael

last: Atchison


title: Human primary macrophages derived in vitro from circulating monocytes comprise adherent and non-adherent subsets with differential expression of Siglec-1 and CD4 and permissiveness to HIV-1 infection

city: Silver Spring

first: Mangala

last: Rao

state: MD

address: 503 Robert Grant Avenue

institute: WRAIR

summary: Macrophages are a major target for human immunodeficiency virus type 1 (HIV-1) infection. However, macrophages are largely heterogeneous and may exhibit differences in permissiveness to HIV-1 infection. This study highlights the interplay of macrophage heterogeneity in HIV-1 pathogenesis. We show that monocyte-derived macrophages (MDM) could be divided into two distinct subsets: CD14+Siglec-1hiCD4+ (non-adherent MDM), and CD14+Siglec-1LoCD4- (adherent MDM). The CD14+Siglec-1hiCD4+MDM subset represented the smaller proportion in the macrophage pool, and varied among different donors. Fractionation and subsequent exposure of the two MDM subsets to HIV-1 revealed opposite outcomes in terms of HIV-1 capture and infection. Although the CD14+Siglec-1hiCD4+MDM captured significantly more HIV-1, infection was significantly higher in the CD14+Siglec-1LoCD4-MDM subset. Thus, CD14+Siglec-1hiCD4+MDM were less permissive to infection. Depletion of CD14+Siglec-1hiCD4+MDM or a decrease in their percentage, resulted in increased infection of MDM, suggestive of a capacity of these cells to capture and sequester HIV-1 in an environment that hinders its infectivity. Increased expression of innate restriction factors and cytokine genes were observed in the non-adherent CD14+Siglec-1hiCD4+MDM, both before and after HIV-1 infection, compared to the adherent CD14+Siglec-1LoCD4-MDM. The differential expression of gene expression profiles in the two macrophage subsets may provide an explanation for the differences observed in HIV-1 infectivity.

overall_design: Adherent and non-adherant MDM that were either uninfected or infected with HIV-1 from 3 different PBMC donors were evaluated.


title: Reduction of rRNA during sRNA library construction using blocking oligos

first: Irina

last: Mohorianu


title: Expression data from HPV 11E6 and HPV18E6 infected cells

city: Cape Town

first: Lamech

last: Mwapagha

address: Anzio Road Observatory

department: Medical Biochemistry

country: South Africa

institute: University of Cape Town/ICGEB

summary:
The aim of this study was to compare the roles of the E6 proteins from HPV18 and HPV11, a high-risk and low-risk type, and to evaluate the effect of these two types of E6 proteins on gene expression
We used microarrays to detail the  gene expression patterns during the early stages of cellular transformation

overall_design: HPV 11 and HPV 18 E6 genes were cloned into adenoviral vectors for transformation of HaCaT cell lines to induce intense, high-level expression of these genes. RNA isolated from these cells were used in DNA microarray analysis to study and compare the effects that the E6 gene from the low-risk and high-risk type HPVs have on gene expression patterns during the early stages of transformation.Once data had been collected from the microarray study, further analysis of important genes and pathways was done by qRT-PCR and western blotting. Signalling pathways involved in E6-mediated transformation were identified, and the effect of inhibiting these pathways was investigated.

first: Iqbal

last: Parker


title: Bivalent complexes of PRC1 with orthologs of BRD4 and MOZ/MORF target developmental genes in Drosophila

city: Boston

first: Mitzi

last: Kuroda

state: MA

address: 77 Ave. Louis Pasteur

institute: Brigham & Women's Hospital

summary: Regulatory decisions in Drosophila require Polycomb group (PcG) proteins to maintain the silent state and Trithorax group (TrxG) proteins to oppose silencing. Since PcG and TrxG are ubiquitous and lack apparent sequence specificity, a long-standing model is that targeting occurs via protein interactions; for instance, between repressors and PcG proteins. Instead, we found that Pc-repressive complex 1 (PRC1) purifies with coactivators Fs(1)h [female sterile (1) homeotic] and Enok/Br140 during embryogenesis. Fs(1)h is a TrxG member and the ortholog of BRD4, a bromodomain protein that binds to acetylated histones and is a key transcriptional coactivator in mammals. Enok and Br140, another bromodomain protein, are orthologous to subunits of a mammalian MOZ/MORF acetyltransferase complex. Here we confirm PRC1-Br140 and PRC1-Fs(1)h interactions and identify their genomic binding sites. PRC1-Br140 bind developmental genes in fly embryos, with analogous co-occupancy of PRC1 and a Br140 ortholog, BRD1, at bivalent loci in human embryonic stem (ES) cells. We propose that identification of PRC1-Br140 "bivalent complexes" in fly embryos supports and extends the bivalency model posited in mammalian cells, in which the coexistence of H3K4me3 and H3K27me3 at developmental promoters represents a poised transcriptional state. We further speculate that local competition between acetylation and deacetylation may play a critical role in the resolution of bivalent protein complexes during development.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design:
36 samples in total:
human data set: 8 samples; HUES64 cells IP for BRD1 and RING1B
fly data set: 28 samples; Genomic binding/occupancy profiling of Fs(1)h, Br140, H3K27ac and H3K27me3 by high throughput sequencing

first: Jessica

middle: L

last: Woolnough

first: Hyuckjoon

last: Kang


title: Effect of benzoxazolyl compound mBMG290 on Mycobacterium tuberculosis

status: Public on Feb 24 2018

city: Saranac Lake

first: Brian

last: Weinrick

address: 154 Algonquin Avenue

institute: Trudeau Institute

summary: Transcriptional profiling of Mycobacterium tuberculosis H37Rv after 4 hours of treatment with benzoxazolyl compound mBMG290 relative to untreated

overall_design: Two condition experiment, 4 hour mBMG290 treated vs. untreated. Biological replicates: 3 of each condition, independently grown and harvested. One replicate per array, third array is a dye-flip.


title: KH-type splicing regulatory protein (KHSRP) is involved in esophageal squamous cell carcinoma progression through regulating a subset of microRNAs [mRNA]

city: Tokushima

first: Kiyoshi

last: Masuda

address: 3-18-15 Kuramoto-cho

department: Department of Human Genetics

institute: Institute of Biomedical Sciences, Tokushima University Graduate School

summary: KH-type splicing regulatory protein (KHSRP) is a multifunctional RNA-binding protein (RBP), which is involved in many post-transcriptional aspects of RNA metabolism including microRNA (miRNA) biogenesis, affects distinct cell functions in different tissues and can impact on various pathological conditions. However, the function and underlying mechanisms of KHSRP in esophageal squamous cell carcinoma (ESCC) remain largely unknown. In the present study, we uncover a novel oncogenic function of KHSRP in esophageal tumorigenesis, and implicate its use as a marker for prognostic evaluation and as a putative therapeutic target in ESCC.

overall_design: To investigate the molecular pathways involved by KHSRP-knockdown, the expression levels of mRNAs in KHSRP-knockdown cells were analyzed using microarray.

first: Yuji

last: Fujita

first: Issei

last: Imoto


title: KH-type splicing regulatory protein (KHSRP) is involved in esophageal squamous cell carcinoma progression through regulating a subset of microRNAs [miRNA]

overall_design: To investigate the molecular pathways involved by KHSRP-knockdown, the expression levels of miRNAs in KHSRP-knockdown cells were analyzed using microarray.


title: Electrochemically active bacteria sense electrode potentials for regulating catabolic pathways

city: Hachioji

first: Atsushi

last: Kouzuma

state: Tokyo

address: 1432-1 Horinouchi

institute: Tokyo University of Pharmacy and Life Sciences

summary: Electrochemically active bacteria (EAB) receive considerable attention for their utility in bioelectrochemical processes. Although electrode potentials are known to affect the metabolic activity of EAB, it is unclear whether EAB are able to sense and respond to electrode potentials. Here, we show that, in the presence of a high-potential electrode, a model EAB Shewanella oneidensis MR-1 can utilize NADH-dependent catabolic pathways and a background formate-dependent pathway to achieve high growth yield. We also show that an Arc regulatory system is involved in sensing electrode potentials and regulating the expression of catabolic genes, including those for NADH dehydrogenase. We suggest that these findings may facilitate the use of EAB in biotechnological processes and offer the molecular bases for their ecological strategies in natural habitats.

overall_design: A single-chambered EC (electrochemical cell) was used for analyzing transcriptomes of wild-type (WT) and ∆arcS strains. The working electrode was poised at +0.2 V until the electric current became stable (for approximately 15 h), and then the potential was changed to +0.5 V (high potential; HP) or –0.1 V (low potential; LP). After further cultivation in the ECs for 2 h, the bacterial cells attached to the working electrode were collected and subjected to RNA extraction. For the transcriptome analysis of WT strain, five biological replicates were prepared from independent ECs (n = 5). For the analysis of ∆arcS, three biological and two technical replicates were prepared (n = 6). Transcriptomic profiles in each strain were compared between the two potential conditions (HP and LP; total 22 samples).

first: Atsumi

last: Hirose

first: Kazuya

last: Watanabe


title: KH-type splicing regulatory protein (KHSRP) is involved in esophageal squamous cell carcinoma progression through regulating a subset of microRNAs

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


title: Epigenetic activation during Th17 cell differentiation is impaired after TRIM28 deletion

city: Beijing

first: Huiping

last: Lu

address: Tsinghua university

institute: Tsinghua university

summary: Cell fate decision is mediated by epigenetic mechanisms. We have analyzed naive T cell differentiation into Th17 cells, which is regulated by environmental cytokines and their downstream transcription factors. RORγt is a lineage-specific master transcription factor for Th17 cells. Although epigenetic mechanisms have been implicated in Th17 cell differentiation, how transcription factors interact to activate epigenetic program is unclear. Here we show that tripartite motif containing 28 (TRIM28) expression in Th17 cells is required for cytokine production and autoimmune diseases. Genome-wide occupancy analysis reveals that TRIM28 bound regions contain many super-enhancers, which are impaired after TRIM28 or STAT3 but not RORγt deletion. Importantly, TRIM28 exists in a complex with STAT3 and RORγt; TRIM28 recruitment to the Il17 gene requires STAT3, and further promotes RORγt recruitment. TRIM28 thus is a key player in the epigenetic activation during T cell differentiation.

overall_design: 8 samples in total: 2 RNA-seq samples; 6 ChIP-seq samples, including 3 control samples(input)

first: Yu

last: Jiang

first: Ying

last: Liu

first: Shao-cong

last: Sun

first: Wei

last: Jin

first: Xiaohu

last: Wang

first: Chen

last: Dong


title: CD300E is activated by Helicobacter pylori macrophages infection

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

institute: University of Padova

summary: Macrophages are important cells involved in infections responses. They are mediators of gastritis in acute Helicobacter pylori (Hp) infection. After macrophages infection with Hp one of the most up-regulated protein is CD300E. To identify effects of CD300E activation in macrophages an agonistic antibody was used to activate CD300E and effects on gene expression were monitored.

overall_design: A time serie experiment was performed to identify effects of CD300E activation. 23 samples were profiled. Macrophages monocytes derived using M-CSF  for 6 days. They were cultured for 1 d in culture medium without M-CSF and then infected with Helicobacter pylori for 48h. After infection macrophages were treated with an antibody to activate CD300E for 3 hours (3 biological replicates), 6 hours (4 biological replicates) and 24 hours (4 biological replicates). As controls were used macrophages not treated with the activacting CD300E antibody: 3, 6, and 24 hours four biological replicates each.

first: Matteo

last: Pagliari

first: Fabio

last: Munari

first: Silvia

last: Lonardi

first: Francesco

last: Chemello

first: Gaia

last: Codolo

first: Caterina

last: Millino

first: Beniamina

last: Pacchioni

first: William

last: Vermi

last: Fassan

first: Marina

last: de Bernard

first: Stefano

last: Cagnin


title: Gene expression profiling of skin melanophages and macrophages positive or negative for MHC class II expression

status: Public on Feb 21 2018

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

institute: CIML

summary: The lack of mouse models permitting the specific ablation of tissue-resident macrophages and monocyte-derived cells complicates understanding of their contribution to tissue integrity and to immune responses. Here we use a new model permitting diphtheria-toxin (DT)-mediated depletion of those cells and in which dendritic cells are spared. We showed that the myeloid cells of the mouse ear skin dermis are dominated by a population of melanin-laden macrophages, called melanophages, that has been missed in most previous studies. By using  gene expression profiling, DT-mediated ablation and parabiosis, we determined their identity including their similarity to other skin macrophages, their origin and their dynamics. Limited information exist on the identity of the skin cells responsible for long-term tattoo persistence. Benefiting of our knowledge on melanophages, we showed that they are responsible for retaining tattoo pigment particles through a dynamic process which characterization has direct implications for improving strategies aiming at removing tattoos.

overall_design: Immune cells were isolated from the skin of C57BL/6 mice as previoulsy described (Tamoutounour et al. Immunity. 2013). Melanophages and macrophages were sorted by flow cytometry according to the marker combinations (i.e., phenotype) for each sample.

first: Anna

last: Baranska

first: Alaa

last: Shawket

first: Marc

last: Dalod

first: Sandrine

last: Henri

first: Bernard

last: Malissen


title: Transcriptomic study of bronchoalveolar lavage cells in the local environment of non-small cell lung cancer

city: London

first: Chih-hsi

middle: Scott

last: Kuo

address: South Kensington Campus

department: Department of Computing

institute: Imperial College London

summary: Background: Lung-resident immune cells around local environment of non-small cell lung cancers implicate the balance of pro- and anti-tumor immunity; however the transcriptomic profiles of these cells remain poorly understood. Methods: Transcriptomic microarray study of lung-resident immune cells, harvested by bronchoalveolar lavage, was performed in the discovery group and the findings were validated in published microarray datasets and in an independent group by RT-qPCR

overall_design: Bronchoalveolar lavage was performed from the lung segment in which tumor located (n=13) and from the normal controls (n=6) to harvest lung-resident immune cells. All non-small cell lung cancer subjects were in advanced or metastatic stage without central airway invasion confirmed by bronchoscopic examination.

first: Chihhsi

middle: S


title: Natural and molecular history of prolactinoma: insights from a Prlr -/- mouse model

city: le Kremlin-Bicêtre

first: Nadine

last: Binart

address: 63 rue Gabriel Péri

department: Faculté de médecine Paris Sud

institute: INSERM 1185

summary: Mouse models of prolactinoma can be useful to better understand molecular mechanisms involved in abnormal lactotroph cell proliferation and secretion. We have previously developed a prolactin receptor deficient (Prlr -/-) mouse, in which Prlr -/- females develop large secreting prolactinomas from 12 months of age with a penetrance of 100%, mimicking human aggressive densely granulated macroprolactinoma, a highly secreting subtype.

overall_design: In order to gain molecular insights into the pathogenesis of prolactinoma in Prlr-/- mice, we performed a microarray analysis at 2 and 4 months of age, before the overt appearance of the tumors. Two and four months-old wild-type (n=6 and 6 respectively) and Prlr KO (n=6 and 6 respectively) mice were sacrified by decapitation. Pituitaries were removed, pooled three by three to form duplicates for each genotype, and frozen at -80°C before RNA extraction and subsequent analysis. The whole experiment was replicated with another set of animals (12 wild-type and 12 Prlr -/-  mice) (Note : in the replication experiment (array2), the second duplicate for 4 months-old mice did not hybridize correctly and therefore was removed before analysis, both in the WT and the Prlr KO conditions)

first: Valérie

last: Bernard

first: Chiara

last: Villa

first: Aurélie

last: Auguste

first: Sophie

last: Lamothe

first: Anne

last: Guillou

first: Agnès

last: Martin

last: Caburet

first: Jacques

last: Young

first: Reiner

middle: A

last: Veitia


title: Genome-wide profiling of Ixr1 binding to the chromatin in Saccharomyces cerevisiae and the changes associated to cisplatin treatment.

city: A Coruña

first: Angel

last: Vizoso-Vázquez

address: Púa da Fraga, 10

department: Cellular and Molecular Biology Department

country: Spain

institute: University of A Coruña

type: Genome binding/occupancy profiling by genome tiling array

summary: Ixr1 is a Saccharomyces cerevisiae HMGB protein that regulates the transcription of genes related to the response to changes normoxia-hypoxia, oxidative stress response or in the readaptation of catabolic and anabolic fluxes during oxygen limitation. Besides, Ixr1 binds to cisplatin-DNA adducts with high affinity. It is known that cancerous cells usually acquire resistance against the drug after the initial treatment, thus limiting its effectiveness. Yeast has been used as an easy-handled eukaryotic model to find genes related to cisplatin responsiveness and IXR1 is one among those that increase sensitivity. In this work, transcriptome analyses have been done to understand the regulatory roles of Ixr1 in absence or presence of cisplatin. Ixr1 behaves in yeast as a master regulator of other transcriptional factors, which respond to external stimuli and control cell growth, and proliferation. Diverse approaches including qPCR, ChIP and measure of 18S and 25S rRNAs confirm a function of Ixr1 in the control of ribosome biogenesis.  Furthermore, several connections between this control, the TOR signaling pathway and cisplatin resistance in ixr1Δ mutants were found.

overall_design: In total 10 arrays: 6 samples  (2 different conditions; 3 biological replica) with their corresponding input controls (2 biological replica).

first: Ángel

first: Mónica

last: Lamas-Maceira

first: M

middle: I

last: González-Siso

last: Cerdán


title: Assessment of DNA methylation patterns in osteoarthritic baboon bone and cartilage using the 450K array

city: Chicago

first: Genevieve

last: Housman

state: IL

address: 920 East 58th Street, CLSC 317

department: Genetic Medicine

institute: University of Chicago

type: Methylation profiling by genome tiling array

summary: The aim of this study was to identify DNA methylation patterns in femur trabecular bone and cartilage of age-matched female baboons, five with and five without knee osteoarthritis. The Illumina Infinium Human Methylation450 BeadChip was used to assess these genome-wide methylation patterns.

overall_design:
Bisulphite converted DNA from the 10 baboons (n=10 bone samples, n=10 cartilage samples) were hybridized to the Illumina Infinium Human Methylation450 BeadChip.

Please note that the sample data table contain the 'matrix_norm_alignmentfilter_beta' data. However, the study's conclusions are based on both norm_*_beta.csv data (linked as Series supplementary files).  It compares and contrasts both filtering criteria.


title: Genome-wide maps of HIC1 binding sites in human induced regulatory T (iTreg) cells after 72h post polarization

city: Turku

first: Kartiek

last: Kanduri

address: Tykistokatu 6

country: Finland

institute: Turku Centre for Biotechnology

summary: CD4+ T cells were cultured in iTreg cell polarizing condition for 72h. ChIP was performed as previously described (Tripathi et al., Cell Reprot 2017) with slight modifications. The cells were subjected to sonication using Bioruptor® Pico sonication device (Diagenode) to attain 100–500 bp chromatin fragments size. A total of 250 ug of sonicated chromatin fragments were incubated with 10ug of HIC-1 antibody (Santa Cruz, sc-271499) and incubated for crosslinking with magnetic beads (no. 11201D, Dynabeads® M-280 Sheep Anti-Mouse IgG, Dynal Biotech, Invitrogen). The crosslink samples were reversed at 65oC overnight and precipitated DNA was treated with Rnase A and Proteinase K and purified with QIAquick PCR purifica-tion kit (QIAGEN). The DNA libraries were prepared as per the guidelines from Illumina by Fasteris Life Sciences (Plan-les-Ouates, Switzerland). Input DNA was sequenced and used as a control. DNA libraries were sequenced on Illumina HiSeq2500 producing from 25 to 35 million reads per sample. The 50 nucleotide reads were aligned to hg19 build of human reference genome using bowtie2 (ver-sion 2.2.9). Uniquely mapped reads were retained (~20-25 million reads per sample) for further analysis. HIC-1 binding sites relative to input DNA were identified using MACS2 (version 2.1.1.20160309) with the default parameter settings. De novo motifs from HIC-1 ChIP-seq peaks were discovered using Homer (version 4.8). The binding sites were annotated in terms of genomic annotations using the “annotatePeaks.pl” script supplied as part of Homer. HIC-1 motif locations in ChIP-Seq peaks were scanned using Homer with default parameters (with the addition of –local argument).

overall_design: Identification of genome wide HIC1 binding sites  in human induced regulatory T (iTreg) cells at 72h post differentiation from naive CD4+ T cells.

first: Ubaid

last: Ullah

first: Syed

middle: B

last: Ahmad Andrabi

first: Subhash

last: Tripathi

first: Obaiah

last: Dirasantha

first: Sini

last: Rautio

first: Catharina

last: Gross

first: Sari

last: Lehtimäki

first: Kanchan

last: Bala

first: Johanna

last: Tuomisto

first: Urvashi

last: Bhatia

first: Deepankar

last: Chakroborty

first: Laura

last: Elo

first: Harri

last: Lähdesmäki

first: Heinz

last: Wiendl

first: Omid

last: Rasool

first: Riitta

last: Lahesmaa


title: Activation of the pyruvate dehydrogenase complex dictates tumour progression in prostate cancer

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via V. Vela 6

department: Lymphoma & Genomics Research Program

institute: IOR

summary: Metabolism in cancer serves to provide energy and key biomolecules that sustain cell growth, a process that is frequently accompanied by decreased mitochondrial use of glucose. Importantly, metabolic intermediates including mitochondrial metabolites are central substrates for post-translational modifications at the core of cellular signalling and epigenetics. However, the molecular means that coordinate the use of mitochondrial metabolites for anabolism and nuclear protein modification are poorly understood. Here, we unexpectedly found that genetic and pharmacological inactivation of Pyruvate Dehydrogenase A1 (PDHA1), a subunit of pyruvate dehydrogenase complex (PDC) that regulates mitochondrial metabolism16 inhibits prostate cancer development in different mouse and human xenograft tumour models. Intriguingly, we found that lipid biosynthesis was strongly affected in prostate tumours upon PDC inactivation. Mechanistically, we found that nuclear PDC controls the expression of Sterol regulatory element-binding transcription factor (SREBF) target genes by mediating histone acetylation whereas mitochondrial PDC provides cytosolic citrate for lipid synthesis in a coordinated effort to sustain anabolism. In line with the oncogenic function of PDC in prostate cancer, we find that PDHA1 and the PDC activator, Pyruvate dehydrogenase phospatase 1 (PDP1), are frequently amplified and overexpressed at both gene and protein level in these tumours. Taken together, our findings demonstrate that both mitochondrial and nuclear PDC sustains prostate tumourigenesis by controlling lipid biosynthesis thereby pointing at this complex as a novel target for cancer therapy.

overall_design:
We evaluated that the PDHA1 knockdown in a series of human prostate cancer cell lines relying on elevates PDC activity induced growth arrest
GEP analysis of mice Pdha1*pc-/pc-, mice Pten*pc-/pc- *Pdha1*pc-/pc- and mice Pten*pc-/pc- CTRL

first: Jingjing

last: Chen

first: Andrea

last: Rinaldi

last: Alimonti


title: Prepubertal vs pubertal lung gene expression during influenza in male mice

first: Lester

last: Kobzik

address: 665 Huntington Ave

department: Environmental Health

institute: Harvard T.H. Chan School of Public Health

summary:
During the 1918 influenza pandemic, children experienced substantially lower mortality than adults, a striking but poorly understood finding. Whether this was due to enhanced resistance (reduced virus load) or better tolerance (reduced impact of infection) has not been defined. We found that prepubertal mice infected with H1N1 influenza virus also showed greater survival than infected pubertal mice, despite similar virus loads.
To explore mechanisms for the survival differences, we compared gene expression profiles in lung tissue from mice of both age groups during the course of influenza pneumonia.

overall_design: Male C57Bl/6 mice were infected with PR8 H1N1 influenza (100 PFU)  at age 25 days (pre-pubertal) or age 28 days (pubertal) and lung tissue was collected on days 3, 6, and 9 after infection, as well as from vehicle-treated control mice for each age group, with 3-4 mice/group.

first: Suber

last: Freeman

first: Kobzik

last: Lester


title: Prepubertal vs pubertal lung gene expression during influenza in female mice

overall_design: Female C57Bl/6 mice were infected with PR8 H1N1 influenza (87.5 PFU)  at age 25 days (pre-pubertal) or age 28 days (pubertal) and lung tissue was collected on days 3, 6, and 9 after infection, as well as from vehicle-treated control mice for each age group, with 3-4 mice/group.


title: Modulation of human dendritic cell (DC) activity by Ascaris suum body fluid or cocoa procyanidins

city: Frederiksberg C

first: Andrew

last: Williams

address: Dyrlægevej 100

institute: University of Copenhagen

summary: The hypothesis was that A. suum body fluid or cocoa procyandins downregulate LPS-induced inflammatory pathways in human DCs

overall_design: DCs were cultured with either LPS, LPS with PC or LPS with A. suum adult body fluid for 6 hours


title: The SALT HYPERSENSITIVE MUTANT 9, a nucleolar APUM23 protein, is essential for salt sensitivity in association with ABA signal pathways in Arabidopsis thaliana

status: Public on Feb 20 2018

city: Taipei

first: KaiChao

last: Huang

address: 128 Academia Road, Section 2, Nankang

department: IPMB

country: Taiwan

institute: Academia Sinica

summary: High salinity is one of the major environmental factors, which hampers plant growth, development and productivity. To better understand the regulatory mechanisms by which plants cope with salt stress, we used genetic approaches to identify salt hypersensitive mutant 9 (sahy9), a new allele of apum23, in Arabidopsis thaliana. The sahy9/apum23 mutant seedlings display postgemination developmental arrest and later become bleached under agar plates supplemented with various salt stressors. Transcriptomic and proteomic analyses of the salt-treated sahy9/apum23 and wild-type seedlings revealed differential expression of genes with similar functional categories, primarily including cellular and metabolic processes, and abiotic and biotic stress responses. However, the consistency of gene expression at both transcript and protein levels is low (), suggesting the involvement of posttranscriptional processing in salt response. Furthermore, the altered gene/protein expression mediated by SAHY9/APUM23 in salt sensitivity is involved in several functional groups, particularly in ABA biosynthesis and signaling, abiotic stress response, LEA proteins, and ribosome biogenesis-related genes. Importantly, NCED3, a key gene involved in ABA biosynthesis, and major ABA responsive marker genes, such as RD20 and RD29B, are down-regulated at both transcript and protein levels in sahy9/apum23 under salt stress. Consistently, lower contents of ABA and proline, and expression changes of a subset of LEA proteins also support the nature of sahy9/apum23 showing salt hypersensitivity. Collectively, these data suggest that SAHY9/APUM23-mediated salt response is associated with ABA signaling pathway and its downstream stress responsive or tolerant genes.

overall_design: 150 mM NaCl treatment 1 day for Col-0 and sahy9-1 after 10 days germination.  Two independent experiments were performed.

first: Kai-Chau

first: Wan-Hsing

last: Cheng