title: Metabolome and transcriptome-wide effects of the carbon storage regulator A in enteropathogenic Escherichia coli.

status: Public on Dec 15 2018

city: Braunschweig

first: Michael

last: Beckstette

state: Lower Saxony

address: Inhoffenstrase 7

department: Molecular Infection Biology

institute: Helmholtz Centre for Infection Research

summary: The carbon storage regulator A (CsrA) is a conserved swivel of a global regulatory system known to regulate central carbon pathways, biofilm formation, motility, and pathogenicity. The aim of this study was to characterize changes in major metabolic pathways induced by CsrA in the human enteropathogenic Escherichia coli (EPEC) strain E2348/69. The EPEC strain E2348/69 and a csrA deletion mutant were grown under virulence factor inducing conditions and characterized by a combined analysis of their metabolomes and transcriptomes. Of the 159 metabolites identified from untargeted GC/MS and LC/MS data, 70 were significantly (fold change ≥ 1.5; p-value ≤ 0.05) regulated between the knockout and the wildtype strain. A lack of csrA led to an upregulation of upper glycolysis and glycogen synthesis pathways, whereas lower glycolysis and the citric acid cycle were downregulated. Associated pathways from the citric acid cycle like aromatic amino acid and siderophore biosynthesis were also negatively influenced. The nucleoside salvage pathways were featured by an accumulation of nucleosides and nucleobases, and a downregulation of nucleotides. In addition, a pronounced downregulation of lyso-lipid metabolites was observed. A drastic change in the morphology in the form of vesicle-like structures of the csrA knockout strain was visible by electron microscopy, which is supposed to be a consequence of a strong upregulation of colanic acid synthesis. The findings expand the scope of pathways affected by the csrA regulon and emphasize its importance as a global regulator.

overall_design: RNA of enterophatogenic E.coli csrA deletion strain and wildtype

first: Volker

last: Berndt

first: Mark

last: Brönstrup

first: Petra

last: Dersch


title: Variants of DNMT3A cause transcript-specific gene expression changes

status: Public on Dec 10 2018

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

summary: The de novo DNA methyltransferase 3A (DNMT3A) plays a pivotal role in hematopoietic differentiation. In this study, we followed the hypothesis that alternative splicing of DNMT3A has characteristic epigenetic and functional sequels. Various transcripts of DNMT3A were either knocked down or overexpressed in human hematopoietic stem and progenitor cells resulting in complementary and transcript-specific DNA methylation (DNAm) and gene expression changes. Our results demonstrate that different splice variants of DNMT3A have distinct epigenetic and functional sequels.

overall_design: Six biological replicas of cord blood-derived CD34+ hematopoietic stem and progenitor cells (HSPCs; #1-6) were isolated for the knockdown (KD; #1-3) and the overexpression (OE; #4-6) of DNMT3A transcripts. HSPCs were lentivirally infected with either shRNA or overexpression vectors 1 day after isolation. Control HSPCs were infected with a scrambled or empty vector. Genomic DNA was isolated at day 12 after infection, bisulfite converted and hybridized to the Illumina Infinium 450k Human Methylation Beadchip.

first: Tanja

last: Božić

first: Joana

last: Frobel

first: Annamarija

last: Raic

first: Fabio

last: Ticconi

first: Chao-Chung

last: Kuo

first: Stefanie

last: Heilmann-Heimbach

first: Tamme

middle: W

last: Goecke

first: Martin

last: Zenke

first: Edgar

last: Jost

first: Ivan

middle: G

last: Costa


title: Variants of DNMT3A cause transcript-specific DNA methylation changes


title: Kin competition accelerates experimental range expansion in an arthropod herbivore

status: Public on Dec 05 2018

city: Gent

first: Nicky

last: Wybouw

address: Coupure Links 653

department: Department of Crop Protection

country: Belgium

institute: University of Ghent

summary:
In this study, we show that in a spider mite species, Tetranychus urticae, genetic changes do not drive experimental range expansions.
We performed two experiments, each with two treatments, wherein mite populations were allowed to expand their habitat range.
In a first experiment, we either replaced migrating females with females from the parental stock populations (Replacement From Stock) or left the migrants unmanipulated (Control).
In a second experiment, we compared the range expansions of non-evolving, genetically inbred, populations (Iso) with those of evolving, genetically diverse, populations (Mix).
Transcriptomic analysis supported other lines of evidence showing that experimental range expansion was driven by kin competition and not by genetic changes (see also Van Petegem et al, 2017).
Only 21 differentially expressed genes were found.

overall_design:
Here, we report the transcriptomes of female mites in the Control and Mix populations that migrated to the end patch of the population range with those that stayed at the home patch.
These comparisons are referred to as: Mix-end_vs_Mix-core (5 replicates) and Control-end _vs_Control-core (6 replicates).

first: Katrien

last: Van Petegem

first: Thomas

last: Van Leeuwen

first: Dries

last: Bonte


title: Transcriptional cycle suited to daytime N2 fixation in the unicellular cyanobacterium Candidatus Atelocyanobacterium thalassa (UCYN-A)

city: Córdoba

first: Muñoz Marin

last: Maria del Carmen

state: Córdoba

address: Campus Rabanales

department: Bioquímica y Biología Molecular

country: Spain

institute: Universidad de Córdoba

summary: Investigation of whole genome gene expression level changes in two strains of the cyanobacteria Atelocyanobacterium thalasaa (UCYN-A) from environmental samples.  The diel gene expression analyzed in this study is further described in Muñoz-Marin, M., I. N. Shilova, T. Shi, H. Farnelid & J. P. Zehr. 2017. Unicellular cyanobacterial symbiosis facilitates aerobic nitrogen fixation. Science (to be submitted).

overall_design: Two 8x60K array slides and one 4x180K array slide using total RNA extracted from seawater at the Scripps Institution of Oceanography (SIO) Ellen Browning Scripps Memorial Pier in La Jolla, CA between 28th July and 1st August 2014 during diel cycles. Each chip measures the expression level of 1194 genes from UCYN-A1 and 1244 genes from UCYN-A2 with up to six 60-mer probes per gene.

first: María del Carmen

last: Muñoz-Marin

first: Irina

last: Shilova


title: Zc3h13/Flacc is required for adenosine methylation by bridging the mRNA binding factor Rbm15/Spenito to other components of the m6A machinery

status: Public on Dec 04 2018

city: Lausanne

first: Jean-Yves

last: Roignant

address: genopode building

country: Switzerland

institute: University of Lausanne

type: Expression profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

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

sample_organism:
Drosophila melanogaster
Mus musculus

platform_organism:
Drosophila melanogaster
Mus musculus

overall_design: Refer to individual Series


title: Competitive RNA Pair Controls Gastric Cancer Metastasis by Regulating EphrinA1 mRNA Translation

status: Public on Dec 03 2018

city: Hangzhou

first: Tianhua

last: Zhou

state: Zhejiang

address: 866 Yuhangtang Road

department: School of Medicine

country: China

institute: Zhejiang University

summary: EphrinA1 silencing-induced gene signature was significantly enriched in GMAN-depleted cells

overall_design: GMAN or EphrinA1 induced gene expression in BGC-823 gastric cancer cell was measured at 48h after transfection with  siRNA control or siRNAs targeting GMAN or EphrinA1.

first: Wei

last: Zhuo

first: Yiman

last: Liu


title: Transcriptome analysis of a red-flowered white clover mutant

city: Wuhan

first: Heshan

last: Zhang

state: Hubei

address: Southern Lake Street, Hongshan District, Wuhan city, China

department: Institute of Animal Husbandry and Veterinary science

institute: Hubei Academy of Agricultural Sciences

summary: Transcriptomes analysis of the petals from a red-flowered white clover mutant (red flowers) and its shade-treated counterpart (white flowers) grown under shaded conditions was performed using high-throughput sequencing. We obtained 121,626,564 and 130,577,944 clean reads in red-flowered mutant and treated counterpart, respectively. Of these clean reads, we respectively gained 125,350 and 99,638 unigene sequencces in two groups. As a result, a total of 157,964 unigenes were obtained with an average length of 728 bp and a median length of 1346 bp. These findings provideed insights into the expression profiles in red-flowered white clover mutant, and deepened our understanding of flower pigmentation in white clower.

overall_design: Petaline mRNA profiles of a red-flowered white clover mutant and its treated counterpart grown under shaded conditions by deep sequencing, in triplicate.

first: Yang


title: Characterizing the nuclease accessibility of DNA in human cells to map higher order structures of chromatin

city: Regensburg

first: Uwe

last: Schwartz

address: Universitätstraße 32

department: NGS Analysis Center

institute: University of Regensburg

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Packaging of DNA into chromatin regulates DNA accessibility and consequently all DNA-dependent processes. The nucleosome is the basic packaging unit of DNA forming arrays that are suggested, by biochemical studies, to fold hierarchically into ordered higher-order structures of chromatin. This organization has been recently questioned using microscopy techniques, proposing an irregular structure. To address the principles of chromatin organization, we applied an in situ differential MNase-seq strategy and analyzed in silico the results of complete and partial digestions of human chromatin. We investigated whether different levels of chromatin packaging exist in the cell. We assessed the accessibility of chromatin within distinct domains of kb to Mb genomic regions, performed statistical analyses and computer modelling. We found no difference in MNase accessibility, suggesting no difference in fiber folding between domains of euchromatin and heterochromatin or between other sequence and epigenomic features of chromatin. Thus, our data suggests the absence of differentially organized domains of higher-order structures of chromatin. Moreover, we identified only local structural changes, with individual hyper-accessible nucleosomes surrounding regulatory elements, such as enhancers and transcription start sites. The regulatory sites per se are occupied with structurally altered nucleosomes, exhibiting increased MNase sensitivity. Our findings provide biochemical evidence that supports an irregular model of large-scale chromatin organization.

overall_design: Differential MNase-seq (high and low MNase concentrations used) of 2 mono-nucleosome and 1 di-nucleosome extractions in HeLa cells.

first: Sarah

last: Diermeier

first: Josef

last: Exler

first: Rodrigo

last: Maldonado

first: Gernot

last: Längst


title: A distinct epigenetic profile distinguishes stenotic from non-inflamed fibroblasts in the ileal mucosa of Crohn's disease patients [methylation]

status: Public on Dec 19 2018

city: Amsterdam

first: Peter

last: Henneman

state: Noord Holland

address: Meibergdreef 9

department: Clinical Genetics

country: Netherlands

institute: Academic Medical Center Amsterdam

summary:
The Illumina Infinium EPIC Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 867,000 CpGs in ileal fibroblast samples. Samples included 5 control samples and 13 Crohn’s disease samples. The Crohn’s disease samples can be further subdivided into inflamed (2), non-inflamed (7) and stenotic (4) samples.

This experiment together was performed in conjunction with a gene expression experiment (GSE99816). Use Supplemental Table 2 of the manuscript to quickly find the samples that were present in both experiments.

overall_design: Bisulphite converted DNA from 18 samples were hybridised to the Illumina Infinium EPIC Human Methylation Beadchip

first: A

middle: Y

last: Li Yim

first: J

middle: R

last: de Bruyn

first: N

last: Duijvis

first: C

last: Sharp

first: E

last: Ferrero

first: W

middle: J

last: de Jonge

first: M

middle: E

last: Wildenberg

last: Mannens

last: Buskens

first: G

last: D’Haens

first: P

middle: A

last: te Velde


title: RNA-Sequencing of Control KD and KD for Ime4-dMettl14, Fl(2)d, Vir, Nito, CG7358 in S2R+ cells

first: Jean-Yves

last: Roignant

summary: N6-methyladenosine (m6A) is an abundant RNA modification in eukaryotes, playing crucial roles in multiple biological processes. m6A is catalyzed by the activity of Mettl3, which depends on additional proteins whose precise functions remain poorly understood. Here we identified Flacc/Zc3h13 as a novel interactor of m6A methyltransferase complex components in Drosophila and mouse. Like other components, Flacc controls m6A levels and is involved in sex determination in Drosophila. We demonstrate that Flacc promotes the recruitment of the methyltransferase to mRNA by bridging Fl(2)d to the mRNA binding factor Spenito. Altogether, our work advances our molecular understanding of conservation and regulation of the m6A machinery.

overall_design: Cells were treated with corresponding double stranded RNA three times during 6 days

first: Tina

last: Lence

first: Nastasja

last: Kreim


title: Expression data of TPC-1 cells with SMAD3 knockdown

status: Public on Dec 14 2018

city: Columbus

first: Yanqiang

last: Wang

state: Ohio

address: 12th w street

country: USA

institute: The Ohio State University

summary:
The human SMAD3 gene consists of 9 exons, has 4 isoforms, is located in chromosome 15 and measures 129,339bp in size. Loss of SMAD3 expression was found in gastric cancer and T cell acute lymphoblastic leukemia. Recent genome-wide association studies (GWAS) for thyroid cancer suceptibility discovered 15q22 as one of the significantly risky loci. Two tag SNPs of this locus are located in the intronic region of SMAD3 gene.
In order to reveal the regulation gene network of SMAD3 in thyroid cells, microarray analysis was performed in TPC-1 cell line treated with si-SMAD3.

overall_design: TPC-1 cells were seeded in 6-well-plate and grown to ~85% confluence at the time of transfection.  25pmol si-SMAD3 or si-Control were transfected into the cells using 4.5ul RNAiMAX lipofectamine (Thermo Fisher SCIENTIFIC). After transfection for 24h, the cells were harvested and total RNA was extracted by using Trizol reagent (Thermo Fisher SCIENTIFIC) then treated by DNase-I (Ambion) to eliminate DNA contamination. Experiments described above were performed at three different time points in order to obtain three replicates for expression analysis.

first: Albert

last: de la Chapelle


title: Ginkgo biloba induces different gene expression signatures of oncogenic pathways in malignant and non-malignant cells of the liver

city: Mainz

first: Jens

last: Marquardt

address: Langenbeckstraße 1

department: Department of Medicine I

institute: Johannes Gutenberg University Mainz

summary: Ginkgo biloba (EGb761) is a widely used botanical drug with diverse biological properties. Several reports indicate that EGb761 confers both preventive effects as well as anti-tumorigenic properties in a variety of tumors, including hepatocellular carcinoma (HCC). We here evaluate a differential functional and mechanistic effect of EGb761 on HCC cells and non-malignant hepatocytes.    A reduced production of reactive oxygen species (ROS) in a state of oxidative stress was predominantly present in non-transformed IH. Further, EGb761 administration significantly impaired proliferation and induced apoptosis in all cell lines, but median IC50 for hepatoma cells was significantly lower than in IH confirming a differential response of EGb761 on normal and malignant cells. Consistently, EGb761 induced a significant reduction in both colony and sphere forming ability in hepatoma cells whereas treatment caused no mentionable changes in IH. Transcriptomic changes in hepatoma cells involved key oncogenic properties resembling proliferation and pro-survival signaling as well as xenobiotic and oxidative stress response. Comparative analyses of differentially affected molecular pathways centered on MAPK/ERK and PI3K/AKT/mTOR signaling.   EGb761 has a differential effect in non-transformed and cancer cells. While treatment confers protective effects in non-malignant cells, treatment significantly impaired tumorigenic properties by affecting multiple molecular pathways. Results, therefore, indicate that EGb761 could be safely used for both preventive as well as therapeutic strategies in the liver.

overall_design: Human hepatoma cell lines (Huh7, WRL68), primary human HCC cells (PItts1) and immortalized human hepatocytes (THLE5B) were exposed to various concentrations (0 - 1000 μg/ml) of EGb761. Effects on apoptosis and proliferation were evaluated after 72h of EGb761 exposure and IC50 concentration was defined for each cell line and used for further experiments. Response to oxidative stress and tumorigenic properties of the cells such as sphere and colony formation were investigated. Molecular changes were assessed by gene expression microrarrays and western blotting. Effects of EGb761 treatment was compared to non-treated controls.

first: Carolin

last: Czauderna

first: Mayrel

middle: P

last: Dominguez

first: Darko

last: Castven

first: Diana

last: Becker

first: Luis

middle: Z

last: Rodriguez

first: Monika

last: Herr

first: Dennis

last: Strand

first: Susanne

first: Stefanie

last: Heilmann-Heimbach

last: Gomez-Quiroz

last: Galle

middle: U


title: Expression profiling of extracellular long noncoding RNAs in aqueous humor of primary open-angle glaucoma patients

status: Public on Dec 18 2018

city: Changsha

first: li

middle: li

last: xie

address: No.139 Remin Middle Road

department: Ophthalmology

institute: the Second Xiangya Hospital, Central South University

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

summary: Long noncoding RNAs (lncRNAs) are emerging as important regulators in cellular processes and have been showed to be involved in the occurrence and development of various neurodegenerative diseases including glaucoma. The aim of this study is to reveal disease-related extracellular lncRNAs and message RNAs (mRNAs) in aqueous humor (AH) of individual primary open-angle glaucoma (POAG) patients, to determine the potential biomarkers for POAG diagnosis

overall_design: LncRNAs and mRNAs expression profiles in 100μl of AH from 10 POAG patients and 10 age-matched controls were determined through microarray analysis.

first: Lili

last: Xie

first: Bing

last: Jiang


title: Profiling proliferative cells and their progeny in damaged murine hearts

city: Würzburg

first: Kai

last: Kretzschmar

address: Josef-Schneider-Str. 2

institute: University Hospital Würzburg

summary: The significance of cardiac stem cell (CSC) populations for cardiac regeneration remains disputed. Here, we apply the most direct definition of stem cell function (the ability to replace lost tissue through cell division) to interrogate the existence of CSCs. By single-cell mRNA sequencing and genetic lineage tracing using two Ki67 knockin mouse models, we map all proliferating cells and their progeny in homoeostatic and regenerating murine hearts. Cycling cardiomyocytes were only robustly observed in the early postnatal growth phase, while cycling cells in homoeostatic and damaged adult myocardium represented various noncardiomyocyte cell types. Proliferative postdamage fibroblasts expressing follistatin-like protein 1 (FSTL1) closely resemble neonatal cardiac fibroblasts and form the fibrotic scar. Genetic deletion of Fstl1 in cardiac fibroblasts results in postdamage cardiac rupture. We find no evidence for the existence of a quiescent CSC population, for transdifferentiation of other cell types toward cardiomyocytes, or for proliferation of significant numbers of cardiomyocytes in response to cardiac injury.

overall_design:
We generated transciptome data from proliferative cardiac cells collected from 3, 7 or 14 days following myocardial infarction (MI) or sham surgery.

This series includes single-cell transcriptome data from (Ki67-RFP+) cardiac cells collected from neonatal murine hearts, adult homeostatic murine hearts  or adult murine hearts collected 14 days following myocardial infarction (MI), ischemic/perfusion (I/R) or sham surgery.

first: Yorick

last: Post

first: Marie

last: Bannier-Hélaouët

first: Jarno

last: Drost

first: Onur

last: Basak

first: Vivan

middle: S

last: Li

first: Maaike

last: van den Born

first: Danielle

last: Versteeg

first: Lieneke

last: Kooijman

first: Stefan

last: van der Elst

first: Johan

middle: H

last: van Es

first: Eva

last: van Rooij

first: Hans

last: Clevers


title: Large scale analysis of fruit evolution during cold storage within different apple varieties and HIVW progeny

city: Beaucouzé

first: Mathilde

last: ORSEL

address: 42, rue Georges Morel

country: France

institute: IRHS

summary: Based on sensorial analysis over 2 years, 12 apple varieties and 4 hybrides with contrasted fruit texture were selected for transcriptionnal analyses over 4 months of cold storage (harvest, 1 month, 2 and 4 months).

overall_design: The 16 genotypes were associated in 8 pairs to perform competitive hybridisations of fruit samples at each time point (harvest, 1, 2 and 4 months cold storage) from the same harvest year. A total of 44 comparisons including dye-swap repetitions were performed. Biological replicates are fruits from 2 to different harvest year. 4 additionnal comparisons were performed between 'harvest' and '2 months cold storage' for 2 genotypes from  2 different harvest year (biological replicates), including dye-swap (technical replicates).

first: Maryline

last: Bruneau

first: Jean-Marc

last: Celton

first: Marie-Charlottte

last: Guillou

first: Sandrine

last: Mikol

first: Jean-Pierre

last: Renou

last: Orsel


title: Viral infection is a risk factor for TB disease in infants

city: Oxford

first: Julius

last: Muller

state: Oxfordshire

address: ORCRB, Roosevelt Drive

department: Nuffield Department of Medicine

country: United Kingdom

institute: The Jenner Institute, University of Oxford

summary: Immune activation is associated with increased risk of tuberculosis (TB) disease in infants. We performed a prospective case–control analysis to identify the drivers of immune activation in infants and found cytomegalovirus (CMV) stimulated IFN-γ-expressing cells to be associated with CD8+ T cell activation (Spearman’s rho r = 0.241, p <0.0001). Among 49 infants who developed incident TB disease and 129 matched controls who remained healthy we found that CMV and Epstein–Barr virus (EBV) specific IFN-γ responses were associated with increased risk of developing TB (Fisher’s Exact Test, p=0.049, OR 2.14, 95% CI 1.03-4.47), and associated with a shorter time to TB diagnosis (Log Rank Mantel-Cox p=0.012).   T cell activation and CMV are associated with lower mycobacterial antigen-specific immune responses following immunization with Bacille Calmette-Guerin (BCG) and MVA85A, suggesting that increased susceptibility to TB in infants with virus infection may, in part, be due to poor responsiveness to vaccination. Understanding of the causes and impact of T cell activation could transform strategies used to protect against TB disease.

overall_design: PBMC collected pre or 28 days post vaccinated with MVA85A or Candin Placebo, stimulated with either BCG or media alone.

first: Magali

last: Matsumiya

first: Helen

last: Fletcher


title: Variants of DNMT3A cause transcript-specific DNA methylation and gene expression changes

first: Wolfgang

last: Wagner

type:
Expression profiling by array
Methylation profiling by array


title: Chromatin changes in G9a inhibited lung adenocarcinoma cells

status: Public on Dec 02 2018

city: New York

first: Hideo

last: Watanabe

state: NY

address: One Gustave L. Levy Place

department: Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine

institute: Icahn School of Medicine at Mount Sinai


title: FLIP modulates monocyte immunosuppression and selective resistance to chemotherapy

status: Public on Dec 01 2018

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

summary: To investigate the genes differentially induced by c-FLIP up-regulation by lentivirus infection in monocytes from healthy donors

overall_design: We collected RNA from CD14+ cells  isolated from buffy coats of healthy donors and infected  for 4 hours by spin-inoculation with c-FLIP or Luciferase-encoding lentiviral vectors . Samples were then processed for total RNA extraction and hybridization on Affymetrix microarrays. Seven biological replicas (A, B, C, D, E, F, G)  for Luciferase controls and four biological replicas (A, B, C, D) were used c-FLIP; for a total of eleven samples.

first: Stefano

last: Ugel

first: Alessandra

last: Fiore

first: Vincenzo

last: Bronte


title: Genomic Evaluation of Multiparametric Magnetic Resonance Imaging -visible and -nonvisible Lesions in Clinically Localized Prostate Cancer

city: Manchester

first: Richard

last: Marais

address: Wilmslow Road

department: Molecular Oncology

institute: Cancer Research UK Manchester Institute

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of normal and tumour prostate samples. The Illumina Infinium MethylationEPIC Human DNA methylation oligonucleotide beads was used to obtain DNA methylation profiles across approximately 850,000 CpGs. Comparative assessment was carried out.

overall_design: Bisulphite converted DNA from 42 samples (normal and tumour prostate tissue) were hybridised to the Illumina Infinium MethylationEPIC oligonucleotide beads for comparative assessment.

first: Marina

last: Parry

first: Shambhavi

last: Srivastava

first: Adnan

last: Ali

first: Alessio

last: Cannistraci

first: Jenny

last: Antonello

first: Joao

last: Barros-Silva

first: Valentina

last: Ubertini

first: Vijay

last: Ramani

first: Maurice

last: Lau

first: Jonathan

last: Shanks

first: Daisuke

last: Nonaka

first: Pedro

last: Oliveira

first: Thomas

last: Hambrock

first: Hui

last: Leong

first: Nathalie

last: Dhomen

first: Crispin

last: Miller

first: Ged

last: Brady

first: Caroline

last: Dive

first: Noel

last: Clarke

first: Esther

last: Baena


title: cIAP1 regulates the EGFR/Snai2 axis in triple negative breast cancer cells

status: Public on Dec 06 2018

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

summary: Inhibitor of apoptosis (IAP) proteins constitute a conserved family of molecules which regulate both apoptosis and receptor signaling. They are often deregulated in cancer cells and represent potential targets for therapy. In our work, we investigated the effect of IAP inhibition in vivo to identify novel downstream genes expressed in an IAP-dependent manner that could contribute to cancer aggressiveness. To this end, immunocompromised mice engrafted subcutaneously with the triple negative breast cancer MDA-MB231 cell line were treated with SM83, a pan-IAP inhibitor developed by us, and tumor nodules were profiled for gene expression. Our work suggests that IAP-targeted therapy could contribute to EGFR inhibition and the reduction of its downstream mediators. This approach could be particularly effective in cells characterized by high levels of EGFR and Snai2, such as triple negative breast cancer.

overall_design: Experiments were approved by the Ethics Committee for Animal Experimentation of the Istituto Nazionale Tumori (INT) of Milan according to institutional guidelines and by the Italian Minister of Health. NOD/SCID mice were subcutaneously engrafted with 5x10^6 MDA-MB231 and MDA-MB468 cells and, after two weeks, were treated with 5 mg/Kg SM83 injected intraperitoneally 5 times/week for 2 weeks (MDA-MB231 model).

first: Daniele

last: Lecis


title: DNA methylation profiling of Daphnia species.

status: Public on Dec 11 2018

city: Helsinki

first: Jouni

middle: Antero

last: Kvist

state: Uusimaa

address: Haartmaninkatu 8

department: Research Program for Molecular Neurology

country: Finland

institute: University of Helsinki

summary:
To profile the Daphnia species methylome and to achieve a better understanding of the level of variations in the methylome of Daphnia species, we performed whole genome bisulfite sequencing (WGBSeq) of adult Daphnia magna Bham2 strain and Daphnia pulex Eloise Butler strain (EB45 and EB31 strains). We also analysed the correlation between gene expression and methylation in the two species, using data generated in this study and RNA-seq data from Orsini, et al. 2016. We found that methylation percentage across the genome of Daphnia spp. follows a bimodal distribution. Furthermore, CpG methylation in Daphnia predominantly occurs at coding regions. Although methylation levels significantly decrease towards the 3’ end of a gene with a significant drop in methylation levels from one exon to the neighbouring intron, there is a clear spike in relative methylation levels between exon and intron boundaries, which may be linked to regulation of splicing. We further demonstrate that DNA methylation in Daphnia is responsive to intrinsic and extrinsic factors.
We also compared the methylation and gene expression correlations found in Daphnia to publicly available dataset from two other invertebrate species (Apis mellifera and Nasonia vitripennis) and two vertebrate species (Homo sapiens and Mus musculus). We observed that similar to other invertebrates, Daphnia’s genome is sparsely methylated at a lower level and the methylation is predominantly focused at gene body while in vertebrate species the genome is heavily methylated (global methylation). Although the level and distribution of methylation across CpG sites is different between vertebrates and invertebrates it is possible that methylation density at coding regions has the same function between vertebrates and invertebrates. We demonstrate evolutionary conservation of a positive correlation between high methylation density at coding regions and gene expression across vertebrates and invertebrates, leading to potentially ensuring continuous high expression of genes required throughout the life in both vertebrates and invertebrates.

sample_organism:
Daphnia pulex
Daphnia magna

platform_organism:
Daphnia pulex
Daphnia magna

overall_design:
Examination of DNA methylation in two different species of Daphnia (Daphnia magna bham2 and Daphnia pulex EB strains)
Correlation analysis between levels of gene expression and DNA methylation (Daphnia pulex EB45).

first: Camila

last: Gonçalves Athanásio

first: Leda

last: Mirbahai


title: Genome-scale chromatin interaction data for huntingtin from mouse striatal tissue

city: Seattle

first: Jocelynn

middle: Renee

last: Pearl

state: Washington

address: 401 Terry Ave N

institute: Institute for Systems Biology

summary: Transcriptional changes are an early feature of Huntington's disease (HD).  We profiled genome-wide interaction sites for the huntingtin protein (HTT) using ChIP-sequencing from mouse striatal tissue at 4 months of age.  We include replicate samples from CAG-expanded murine Htt (heterozygous Q111/+) and wildtype littermate controls.

overall_design: ChIP-seq for HTT (huntingtin) in wild type and Q111/+ CAG-expanded knock-in mouse striatum at 4 months of age.

first: Dani

last: Bergey

first: Jeffrey

last: Carroll


title: Organismal sensitivity to environmental agents induced toxicity: A comparative ecotoxicogenomics approach [Caenorhabditis elegans]

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: To understand the role of genetic makeup in organismal tolerance/susceptibility we compared the Caenorhabditis elegans transcriptome profiles with those of Drosophila melanogaster. In this study, we exposed both organisms, to a synthetic chemical and evaluated their response at the transcriptome level, to gain insights to molecular players/pathways underlying organismal tolerance/susceptibility to xenobiotics

overall_design: Organism : Caenorhabditis elegans, Agilent's C.elegans Gene Expression  8x60k Array (AMADID: 052672) designed by Genotypic Technology Private Limited

first: Nida

last: Moin

first: D

last: Kar Chowdhuri

first: Ravi

last: Ram Kristipati

first: Aruna

last: Satish


title: Integrated in vivo quantitative proteomics and nutrient tracing reveals age-related metabolic rewiring of pancreatic beta-cell function

city: La Jolla

first: Maike

last: Sander

state: CA

address: 2880 Torrey Pines Scenic Dr.

institute: UC San Diego

summary: Aging is associated with fundamental changes in pancreatic β-cell physiology; yet, the mechanisms that drive these age-related changes are poorly understood. We performed comprehensive proteomic profiling of pancreatic islets from adolescent and old mice. The analysis revealed striking differences in abundance of enzymes controlling glucose metabolism not reflected at the transcript level. We show that these changes in protein abundance are associated with increased activity of the amplifying pathway of insulin secretion. The amplifying pathway stimulates insulin secretion through coupling factors produced during glucose metabolism. Nutrient tracing and targeted metabolomics demonstrate accelerated accumulation of glucose-derived metabolites and coupling factors in aged islets, indicating that age-related changes in glucose metabolism contribute to the improved response of β-cells to glucose with age. Together, our study provides the first in-depth characterization of changes in the islet proteome during aging and establishes metabolic rewiring as an important mechanism for age-associated changes in β-cell function.

overall_design: RNA-sequencing of 3 biological replicates each of islets pooled from young 4-week-old C57Bl6 mice and old 1-year-old mice

first: Jacqueline

last: Benthuysen


title: Organismal sensitivity to environmental agents induced toxicity: A comparative ecotoxicogenomics approach [Drosophila]

overall_design: Organism : Drosophila melanogaster, Agilent's Drosophila Gene Expression 8x60k Array (AMADID: 039596) designed by Genotypic Technology Private Limited

first: Saurabh

last: Kumar


title: Transcriptome change in response to patulin stress in Rhodotorula mucilaginosa

city: Zhenjiang

first: Xiangfeng

last: Zheng

state: Jiangsu

address: 301, Xuefu Road

department: Food school

institute: Jiangsu university

summary: The yeast Rhodotorula mucilaginosa shown the capability to degrade patulin by the intracellular enzymes. However, the enzymes which risponsible for the degradation process was unkonown. Transcriptome change in response to mycotoxin patulin was analyzed. The molecular mechanism of Rhodotorula mucilaginosa withstand patulin was revealed.

overall_design: two sample was analyzed , the yeast Rhodotorula mucilaginosa amending with patulin and the control which was not amending with patulin

first: Hongyin

last: Zhang


title: ChIP-seq analysis of HeLa cancer stem cells and non-cancer stem cells using Pol II, H3K4me3 and H3K27Ac.

status: Public on Nov 29 2018

city: Suita, Osaka

first: Keisuke

last: Tamari

address: 2-2 Yamadaoka

department: Radiation Oncology

country: Japan

institute: Osaka University Graduate School of Medicine

summary: ChIP-seq analysis of HeLa cancer stem cells and non-cancer stem cells regarding Pol II, H3K4me3 and H3K27Ac.

overall_design: Epigenetic difference between HeLa nonCSC and CSCs.

first: Hideshi

last: Ishii


title: Gene expression profiles in HeLa cells exposed to spermine

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary: Analysis of gene expression profiles of HeLa cells after spermine exposure.

overall_design: Gene expression comparison of three groups


title: Gene expression profiles in HeLa cells exposed to putrescine

summary: Analysis of gene expression profiles of HeLa cells after putrescine exposure.


title: RNASeq of AlphaTC cells transfected with ARX and phosphorylation mutants

city: Adelaide

first: Cheryl

last: Shoubridge

state: SA

address: North Tce

country: Australia

institute: The University of Adelaide

summary: deficient phosphorylation of ARX results in subsequent alterations in transcriptional capacity

overall_design: Cells were transfected with either ARX-WT or phosphorylation mutants and compared to untransfected cells. For analysis each group consisted of 4 technical replicates which were collected across 4 different transfections.


title: ROS stress responses of primary human epidermal keratinocytes

status: Public on Nov 28 2018

city: Vienna

first: Marie-Sophie

last: Narzt

address: Lazarettgasse 14

department: Dermatology

country: Austria

institute: Medical University of Vienna

summary: Primary human epidermal keratinocytes were exposed to in-vitro UVA-oxidized 1-palmitoyl-2-arachidonoyl-phosphatidylcholine or to UVA in presence and absence of a commercial UVA filter.

overall_design: This study was performed in biological triplicates for human neonatal keratinocytes

first: Florian

last: Gruber


title: MicroRNA expression in the cuprizone-induced demyelination mouse model

status: Public on Nov 22 2018

city: Daejeon

first: Yun Hee

last: Kang

address: 77 Gyeryong-ro 771 beon-gil, Jung-gu

department: Eulji Biomedical Science Research Institute

country: South Korea

institute: Eulji University School of Mdicine

summary: Myelin abnormalities, oligodendrocyte damage, and concomitant glia activation are common in demyelinating diseases of the central nervous system (CNS). The neurotoxicant cuprizone (CPZ) has been extensively used to create a mouse model of demyelination. However, the changes of miRNA expression and effects on behavior of cuprizone treatment have not been clearly reported. We have analyzed the behavioral changes of mice given a diet containing 0.2% cuprizone for 6 weeks. To evaluate the changes of miRNA expression in CPZ-induced demyelination compared with control, we performed the Affymetrix GeneChip® miRNA 4.0 Array. We identified 1348 and 1253 differentially expressed miRNAs for control and CPZ-treated mice, respectively. Furthermore, the expression of 240 miRNAs was significantly changed in CPZ-induced mice comparing with control mice. These results suggest that the changes of miRNA expression in vivo may provide a new potential remyelination therapeutic target.

overall_design: We analyzed cerebellum from 2 subjects using Affymetrix GeneChip® miRNA 4.0 Array (Mus musculus) platform. Array data export processing and analysis were performed using Affymetrix® GeneChip Command Console® Software (AGCC).

first: Seung Ro

last: Han

first: Myung-Shin

last: Lee

first: Seung-Hoon


title: Role of mitochondrial unfolded protein response transcription fatcor ATFS-1 in lifespan of long-lived mitochondrial mutants

status: Public on Nov 21 2018

city: Montreal

first: Jeremy

middle: Michael

last: Van Raamsdonk

state: QC

address: 1001 Decarie Boulevard

department: Neurology and Neurosurgery

country: Canada

institute: McGill University

summary: In this work, we examined the effect of the transcription factor ATFS-1 in the long lifespan of the nuo-6 mitochondrial mutant. We also examined the effect of the hypoxia transcription factor hif-1. We sequenced both atfs-1 deletion mutants and atfs-1 gain-of-function point mutants in which the mitochondrial localization sequence of ATFS-1 is disrupted. Note that sequencing batch 2 was previously uploaded as part of GSE93724.

overall_design: At least three biological replicates per genotype were sequenced across three batches and at least two biological replicates were utilized for DGE per genotype; mRNA was isolated individually from each replicate. Two genotypes (nuo6hif1 and atfs1et15) had one replicate removed due to introduction of large variation due to technical reasons as examined by PCA. The samples that were removed clustered together and not with their respective genotypes. This was deemed acceptable due to two reasons: 1) only a single genotype had fewer than three biological replicates and 2) the underlying DGE methodology for estimating gene variance in edgeR.

middle: M

first: Benjamin

middle: K

last: Johnson


title: Identification of specific microRNAs in diabetic-derived neutrophils

status: Public on Nov 26 2018

city: Kitakyushu

first: Takahiro

last: Umehara

address: 1-1 Iseigaoka Yahatanishiku

institute: University of Occupational and Environmental Health

summary: The recruitment and/or retention kinetics of neutrophils in diabetic (db) cutaneous wounds is aberrant, and inflammation is prolonged. Intrinsic factors have been shown to play an important role in aberrant myeloid cell behavior. The pathogenesis of chronic inflammation may be due to dysfunction of db-derived neutrophils. microRNAs (miRNAs) have been shown to globally regulate a large range of biological processes within a cell. Therefore, in order to clarify the molecular mechanism of regulation of inflammation in db-derived neutrophils, we screened for changes in miRNAs in db-derived neutrophils. miRNAs are differentially expressed in db-derived neutrophils, particularly members of the miR-129 family. Our results suggest that deregulation of the miR-129 family contributes to the dysfunction of db-derived neutrophils. The retention kinetics of neutrophils and chronic inflammation may be initiated via miR-129 family-regulated genes such as Casp6, Dedd2 and Ccr2.

overall_design: Neutrophils from pooled bone marrow (BM) of 3 db or 3 non-db mice were isolated using the neutrophil isolation kit, and miRNA was purified by MicroRNA isolation kit, Mouse Ago2. Microarray analysis was performed on a total of 8 pools (4 pools of 3 db BM samples and 4 pools of 3 non-db BM samples) using SurePrint G3 Mouse miRNA microarray.


title: Integrative Proteomic Profiling Reveals PRC2-Dependent Epigenetic Crosstalk Maintains Ground-State Pluripotency.

status: Public on Nov 24 2018

city: Nijmegen

first: Hendrik

last: Marks

address: Geert Grooteplein 26/28

department: Molecular Biology

institute: Radboud University Nijmegen, RIMLS

summary: The pluripotent ground state is defined as a basal state free of epigenetic restrictions, which influence lineage specification. While naive embryonic stem cells (ESCs) can be maintained in a hypomethylated state with open chromatin when grown using two small-molecule inhibitors (2i)/leukemia inhibitory factor (LIF), in contrast to serum/LIF-grown ESCs that resemble early post-implantation embryos, broader features of the ground-state pluripotent epigenome are not well understood. We identified epigenetic features of mouse ESCs cultured using 2i/LIF or serum/LIF by proteomic profiling of chromatin-associated complexes and histone modifications. Polycomb-repressive complex 2 (PRC2) and its product H3K27me3 are highly abundant in 2i/LIF ESCs, and H3K27me3 is distributed genome-wide in a CpG-dependent fashion. Consistently, PRC2-deficient ESCs showed increased DNA methylation at sites normally occupied by H3K27me3 and increased H4 acetylation. Inhibiting DNA methylation in PRC2-deficient ESCs did not affect their viability or transcriptome. Our findings suggest a unique H3K27me3 configuration protects naive ESCs from lineage priming, and they reveal widespread epigenetic crosstalk in ground-state pluripotency.

overall_design: ChIP-Seq, RNA-Seq and WGBS profiling of various types of ESCs, including serum-grown ESCs, 2i-grown ESCs, ESCs deficient for Eed (ESC Eed-/-) and ESC (Eed-/-) treated with 5-azacytidine.

first: Guido

last: van Mierlo

first: Rene

last: Dirks

first: Laura

last: De Clerck

first: Arie

middle: B

last: Brinkman

first: Michelle

last: Huth

first: Susan

last: Kloet

first: Néhme

last: Saksouk

first: Leonie

middle: I

last: Kroeze

first: Sander

last: Willems

first: Matthias

last: Farlik

first: Christoph

last: Bock

first: Joop

last: Jansen

first: Dieter

last: Deforce

first: Michiel

last: Vermeulen

first: Jérome

last: Déjardin

first: Maarten

last: Dhaenens


title: Role of interleukin 2 on gene expression in lymph node Foxp3+CD4+ regulatory (Treg) and conventional T (Tconv) cells

city: Bronx

first: Gregoire

last: Lauvau

address: 1301 Morris park

department: M&I

institute: Albert Einstein College of Medicine

summary: Interleukine 2 (IL-2) is still one of the most interesting cytokines in T cell biology with its ability to control immune homeostasis by maintaining the functional identity of Foxp3+ regulatory T (Treg) cells and the expansion of activated conventional T (Tconv) cells. Yet, how IL-2 exactly enables Treg cells to suppress autoreactive Tconv cells and to maintain their identity is unclear. Using a mouse model in which IL-2 signaling via its high affinity receptor CD25 is selectively impaired, the “Il2ramut/mut” mouse, we report that Treg cells that only receive low IL-2 signals keep Il2ramut/mut but not WT Tconv cells “in check”, suggesting equal IL-2 signals in Treg and Tconv cells is essential to safeguard immune homeostasis. Furthermore, the comparative analysis of gene expression and epigenetic landscape of Il2ramut/mut and WT Treg cells support a model in which IL-2 "locks in” Treg cell identity and functions in vivo by controlling their genome-wide chromatin accessibility.

overall_design: LNs from 6-8 weeks old aged-matched females either Il2ramut/mut (2 or 3 mice) or WT (2 or 3 mice) Foxp3-RFP+ reporter mice were harvested and RFP+ Treg or RFPneg Tconv cells were enriched by negative selection (dynabeads) and flow-sorted (Aria III) before proceeding to extraction of total RNA and cDNA RT transcription for microarray analysis.

first: Laurent

last: Chorro


title: Nano-structural analysis of engrafted human induced pluripotent stem cell-derived cardiomyocytes in mouse hearts using a genetic-probe APEX2.

city: Kyoto

first: Takeshi

last: Hatani

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

institute: Kyoto University

summary: Using APEX2, an engineered peroxidase, as an imaging tag, we successfully located iPSC-derived cardiomyocytes (iPSC-CMs) engrafted in post-myocardial infarction mouse hearts for more than 6 months. APEX2 caused clear contrast in X-ray microscopy and electron microscopy, and relatively well organized sarcomere structures were formed in iPSC-CMs. Electron microscopic tomography further found the development of T-tubules and dyads in APEX2-labelled cells, which are the signature characteristics of the maturation of cardiomyocytes.

overall_design:
APEX2 iPSCs, N=4
APEX2 iPSC-derived day7 cardiomyocytes sorted for EGFP, N=4
APEX2 iPSC-derived day14 cardiomyocytes sorted for EGFP, N=4
APEX2 iPSC-derived day21 cardiomyocytes sorted for EGFP, N=4
Control iPSCs, N=4
Control iPSC-derived day7 cardiomyocytes sorted for EGFP, N=4
Control iPSC-derived day14 cardiomyocytes sorted for EGFP, N=4
Control iPSC-derived day21 cardiomyocytes sorted for EGFP, N=4

first: Narita

last: Megumi

first: Yoshinori

last: Yoshida


title: The BET Bromodomain Inhibitor OTX015/MK-8628 modulates microRNA expression in Diffuse Large B-Cell Lymphoma

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via V. Vela 6

department: Lymphoma & Genomics Research Program

institute: IOR

type:
Expression profiling by array
Other

summary: Aberrant changes in microRNAs (miRNAs) contribute to lymphomagenesis and represent potential therapeutic targets. OTX015 (MK-8628), a bromodomain and extra-terminal domain (BET) inhibitor (BETi), has demonstrated preclinical and clinical activity in haematological tumours. To better understand the mechanism of action of OTX015 we studied its effects on miRNAs in lymphomas. We performed miRNA profiling of DLBCL cells treated with OTX015 and observed changes in the expression levels of a subset of miRNAs, including miR-92a-1-5p, miR-21-3p, miR-155-5p and miR-96-5p, which are known to play a role in lymphomagenesis and/or resistance to chemotherapy. Analysis of publicly available BRD4 ChIP-Seq data of DLBCL cells treated with the BETi JQ1 showed that BRD4 was bound to the upstream regulatory regions of multiple miRNA genes and that this binding decreased following BETi. Alignment of our miRNA profiling data with the BRD4 ChIP-Seq data revealed that many miRNAs downregulated by OTX015 also exhibited reduced BRD4 binding in their promoter regions following BETi treatment, indicating that BRD4 directly modulated miRNA expression in lymphoma. Among the miRNAs upregulated in response to OTX015 was miR-96-5p, a miRNA known to play a role in B-cell transformation. In lymphomas, miR-96-5p transcription is repressed by the arginine methyltransferase PRMT5. In turn, PRMT5 translation is inhibited by miR-96-5p. We demonstrated that BRD4 bound to the 5’ regulatory region of PRMT5 and that following BET inhibition PRMT5 expression decreased, BRD4 binding to the 5’ region of PRMT5 was reduced and enrichment of PRMT5 at the miR-96-5p promoter lessened. Our results demonstrate that BRD4 binds to the promoters of miRNA genes to directly modulate their expression in lymphoma cells and that BETi administration results in decreased binding of BRD4 to the promoters of specific miRNAs to reduce their expression. Additionally, we show that BETi treatment can affect the expression of genes that control miRNA transcription to indirectly modulate miRNA expression. The data presented here indicate that the ability of BETi to inhibit or activate specific signalling pathways and processes critical to lymphoma cell proliferation and survival is in part due to changes in miRNA expression.

overall_design:
[NanoString assay V3A] Global expression profiles of mature miRNAs in the studied cells at the baseline and in a two point time course treatment (4 h, and 24 h)
[NanoString assay v2.1] RNA was extracted using trizol from human cell lines
[Agilent] Global expression profiles of mature miRNAs in the studied cells at the baseline and in a two point time course treatment (4 h, and 8 h)

first: Afua

last: Mensah

first: Luciano

last: Cascione

first: Eugenio

last: Gaudio

first: Chiara

last: Tarantelli

first: Riccardo

last: Bomben

first: Elena

last: Bernasconi

first: Domenico

last: Zito

first: Andrea

last: Lampis

first: Jens

middle: C

last: Hahne

last: Rinaldi

first: Anastasios

last: Stathis

first: Emanuele

last: Zucca

first: Ivo

last: Kwee

first: Nicola

last: Valeri

first: Valter

last: Gattei

first: Maria

last: Riveiro


title: Global miRNA expression profiling of lung fibroblasts identifies miR-19a-19b-20a subcluster as a suppressor of TGF-beta-associated fibroblast activation in murine pulmonary fibrosis

status: Public on Nov 20 2018

city: Chiba

first: Shigeyuki

last: Shichino

address: 2641, Yamasaki, Noda-shi

department: Department of Molecular regulation of Inflammatory and Immune Diseases

institute: Tokyo University of Science

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Transcriptome profile of liver tissue in CD95 activating antibody-treated mice

city: Napoli

first: Annamaria

last: Carissimo

address: via Castellino

institute: Tigem

summary: In order to identify the effects of CD95 activating antibody on the transcriptome of liver tissue, we performed RNAseq experiments  Transcriptome analysis of the liver of mice trated with CD95 activating antibody, compared with liver of mice trated with saline.

overall_design: total RNA was extracted from liver of C57BL/6N mice; RNA extracted from liver of saline treated mice was used as control.

first: Ferriero

middle: R

last: De Cegli

first: A


title: Transcriptomic analysis of miR-19a-19b-20a subcluster-overexpressed fibroblasts in bleomycin-induced lung fibrosis

summary: Lung fibroblasts play a pivotal role in pulmonary fibrosis, a devastating lung diseases, by producing extracellular matrix. MicroRNAs (miRNAs) suppress a lot of genes posttranscriptionally, but the dynamics and the role of miRNAs in activated lung fibroblasts in fibrotic lung has been poorly understood. We found miR-19a, 19b and 20a subcluster expression increased in activated lung fibroblasts as the fibrosis progression. To elucidate whether fibroblast-specific intervention against miR-19a, 19b and 20a subcluster modulates pathogenic activation of lung fibroblasts in vivo, we intratracheally-transferred the subcluster-overexpressed fibroblasts into bleomycin-treated lungs and performed global transcriptome analysis.

overall_design: miR-19a, 19b and 20a subcluster-overexpressed fibroblasts and mock-expressed fibroblasts were intratracheally-transferred to B6 mice at day 7 post-administration of 2 mg/kg of bleomycin. Donor cells were recoverred at day 3 post-transfer by cell sotring. Global transcriptome of transferred fibroblasts was generated by 3'SAGE-seq using Ion Proton sequencer.

first: Shin-ichi

last: Hashimoto

first: Shungo

last: Deshimaru

first: Kunihiko

last: Soma

first: Satoshi

last: Ueha

first: Kouji

last: Matsushima


title: Role of interleukin 2 on Foxp3+CD4+ regulatory T (Treg) cell gene expression and chromatin modeling in thymus and lymph node, and on SATB1 DNA binding in single positive CD4 thymocytes

first: Gregoire

last: Lauvau

overall_design:
Microarrays:LNs from 6-8 weeks old aged-matched females either Il2ramut/mut (2 or 3 mice) or WT (2 or 3 mice) Foxp3-RFP+ reporter mice were harvested and RFP+ Treg or RFPneg Tconv cells were enriched by negative selection (dynabeads) and flow-sorted (Aria III) before proceeding to extraction of total RNA and cDNA RT transcription for microarray analysis

ATAC-seq:
LNs from 6-8 weeks old aged-matched females either Il2ramut/mut (2 mice) or WT (2 mice) Foxp3-RFP+ reporter mice were harvested and RFP+ Treg cells were enriched by negative selection (dynabeads) and flow-sorted (Aria III) before proceeding to extraction of nuclei, transposition and library preparation for sequencing (ATAC-seq).

Thymuses from ~20 weeks old aged-matched females either Il2ramut/mut (4 mice) or WT (4 mice) Foxp3-RFP+ reporter mice were harvested and RFP+ Treg cells were enriched by negative selection (dynabeads) and flow-sorted (Aria III) before proceeding to extraction of nuclei, transposition and library preparation for sequencing (ATAC-seq).

ChIP-seq:
Thymus from 6-8 weeks old aged-matched females either Il2ramut/mut (2 mice) or WT (2 mice) mice were harvested and 2x10e6 single positive (SP) CD4+ thymocytes were pre-enriched by negative selection (dynabeads), stained with fluorescent labeled antibodies against CD4 (GK1.5) and CD8α (53-6.7) and flow-sorted (Aria III) before proceeding to fixation (cross-linking), lysis, immunoprecipation against SATB1 and library preparation for sequencing.


title: Organismal sensitivity to environmental agents induced toxicity: A comparative ecotoxicogenomics approach

first: Genotypic

last: technology

sample_organism:
Caenorhabditis elegans
Drosophila melanogaster


title: Gene expression by TRPS1 knocked down in T47D

status: Public on Nov 19 2018

city: Jinan

first: Jing

last: Hu

address: Wenhua xi road

department: Department of Pathology

institute: Shandong University

summary: The aim of this research was to confirm the regulatory effect of TRPS1 on gene expression in the development of breast cancer.

overall_design: In this research, there were two samples examed including sample of negtive control cells (T47D-NC) and sample of TRPS1 knocked down cells (T47D-shTRPS1).


title: Role of interleukin 2 on chromatin landscapes in lymph node Foxp3+ CD4+ regulatory (Treg) cells

overall_design: LNs from 6-8 weeks old aged-matched females either Il2ramut/mut (2 mice) or WT (2 mice) Foxp3-RFP+ reporter mice were harvested and RFP+ Treg cells were enriched by negative selection (dynabeads) and flow-sorted (Aria III) before proceeding to extraction of nuclei, transposition and library preparation for sequencing (ATAC-seq).

first: Laurent

last: Chorro

first: Masako

last: Suzuki


title: Effect of Cyp3a-cluster knockout on small intestine

status: Public on Nov 15 2018

city: Sendai

first: Rumiko

last: SAITO

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

department: Department of Dermatology

institute: Tohoku University Graduate School of Medicine

summary: Analysis of small intestine with or without Cytochrome P450 (Cyp) 3a-cluster. Cyp3a family is one of the most important enzymes for drug metabolism. These results suggest the biological effects of Cyp3a-knockout on small intestine.

overall_design: We obtained total RNA of purified from small intestine that were treated with or without Cyp3a-cluster. Two independent experiments were performed using different animals.

last: Saito

first: Hiroshi

last: Ohara

first: Kaoru

last: Kobayashi

first: Yoshihiro

last: Nakajima

first: Mitsuo

last: Oshimura

first: Yasuhiro

last: Kazuki


title: Effect of Cyp3a-cluster knockout on liver

summary: Analysis of liver with or without Cytochrome P450 (Cyp) 3a-cluster. Cyp3a family is one of the most important enzymes for drug metabolism. These results suggest the biological effects of Cyp3a-knockout on liver.

overall_design: We obtained total RNA of purified from liver with or without Cyp3a-cluster. Two independent experiments were performed using different animals.


title: Copy number variation in fetal alcohol spectrum disorder

city: Toronto

first: Stephen

middle: W

last: Scherer

state: Ontario

address: 686 Bay Street

department: Genetics and Genomic Biology

institute: The Hospital for Sick Children

summary: The Illumina Human Omni2.5 array is a high resolution microarray platform for studying copy number variations in the human genome.  It is widely being used in both clinical and research settings for identifying causative variants as well as interrogating the genome for benign variants. We employed this platform to investigate the risk factor CNVs in 95 individuals diagnosed with Fetal alcohol spectrum syndrome (FASD). We also examined 87 age-matched individuals with no symptoms of FASD or any neurodevelopmental disorders. We compared their CNVs to those of 10,851 population controls, in order to identify rare CNVs (<0.1% frequency) that might be relevant to FASD.

overall_design: Three CNV calling algorithms were used to detect CNVs in cases and controls: i.e. iPattern, PennCNV, and QuantiSNP. We defined a stringent set of variants when each variant was called by at least by two algorithms. We defined the ancestry and relatedness of the samples using PLINK.

first: Mehdi

last: Zarrei


title: Endogenous gene expression profiling of Cyp3a-cluster knockout mice


title: Time-course global miRNA expression profiling on lung fibroblasts isolated from untreated, bleomycin-treated and silica-treated mice

first: Shigeyuki

last: Shichino

summary: Lung fibroblasts play a pivotal role in pulmonary fibrosis, a devastating lung diseases, by producing extracellular matrix. MicroRNAs (miRNAs) suppress a lot of genes posttranscriptionally, but the dynamics and the role of miRNAs in activated lung fibroblasts in fibrotic lung has been poorly understood. To elucidate these problems, we performed global miRNA expression profiling of lung fibroblasts of bleomycin- and silica-induced fibrotic lungs

overall_design: Global miRNA expression profile of lung fibroblasts isolated from untreated, bleomycin-treated and silica-treated mice on days 7, 14 and 28 post-treatment was generated using Ion Total RNA-seq Kit v2 and Ion PGM sequencer.

first: Shin-ichi

last: Hashimoto


title: Regulation of Tfh response by Ezh2

status: Public on Nov 14 2018

city: Washington

first: Weiqun

last: Peng

state: DC

address: 1918 F Street, NW , DC

institute: The George Washington University


title: Profiling DNA copy number alterations of liver metastases from colorectal cancer (CRCLM)

status: Public on Nov 17 2018

city: Taipei

first: yi-chiung

last: hsu

address: 128 Academia Road, Section 2

country: Taiwan

institute: academia sinica

type: Genome variation profiling by genome tiling array

summary: The formation of metastasis is a complex process and the molecular events leading to metastasis are still unclear. While several studies have focused on the clonal origin and genetic heterogeneity of CRCs, there is still no clear consensus about the origin of cancer and the genetic heterogeneity between a primary cancer and its distant metastasis. Furthermore, very few validated prognostic gene signatures have been developed to assess outcomes after hepatectomy for colorectal cancer with liver metastasis (CRCLM).

overall_design: 21 Tumor/Normal paired samples from colon cancer with liver metastasis

first: Yi-Chung

last: Hsu

first: Cin-Di

last: Wang


title: Loss of G9a preserves mutation patterns but increases chromatin accessibility, genomic instability and aggressiveness in skin tumours

status: Public on Nov 13 2018

city: Barcelona

first: Aikaterini

last: Symeonidi

state: Barcelona

address: Baldiri i Reixac, 10

department: Oncology

institute: Institut for Research in Biomedicine (IRB-Barcelona)

summary: Mutations and expression changes of epigenetic modifiers are pervasive in human tumours, making epigenetic factors attractive as antitumour targets. However, the mutational landscape of tumours correlates with the chromatin state of their cell-of-origin, raising the concern that targeting epigenetic factors might alter the mutational burden and possibly aggravate disease progression. Nonetheless, a causal link between changes in chromatin in tissues and the mutational landscape of their cognate tumours has not yet been established. Here we show that increasing chromatin accessibility through a conditional deletion of the histone H3K9 methyltransferase G9a severely delays and reduces carcinogen-induced squamous tumour initiation and burden. Strikingly, after a prolonged latency, G9a-mutant mice develop highly aggressive tumours with an expanded cancer stem cell (SC) pool. Loss of G9a leads to extensive chromatin opening in the cells of origin of these tumours (i.e. epidermal and hair follicle SCs) . Although this does not alter the number of single-nucleotide variants, the type of substitutions, or the overall mutational topography, it significantly changes the mutational signatures (i.e. microcontext) in the tumor cells. G9a-depleted tumours also display pronounced genomic instability and a frequent accumulation of loss-of-function p53 mutations, compared to their wild-type counterparts. Our results therefore provide evidence for a causal link between chromatin modifications and mutational load in tumours and call for caution when assessing the long-term therapeutic benefits of inhibiting epigenetic factors.

overall_design: Gene expression analysis of homeostatic skin it G9a Wt and G9a cKO mice

first: Alexandra

last: Avgustinova

first: Llorenç

last: Solé

first: Mercé

last: Martín

first: Andrés

last: Castellanos

first: Neus

last: Prats

first: Fran

last: Supek

first: Ben

last: Lehner

first: Salvador

last: Aznar Benitah


overall_design: Exome sequencing of DMBA/TPA induced tumors in G9a wild-type and G9a cKO tumors


overall_design: Differential expression analysis of DMBA/TPA treated pre-neoplastic skin (bulge cells)


overall_design: Gene expression analysis of DMBA/TPA induced tumors in G9a WT and G9a cKO mice


overall_design: ATAC sequencing of homeostatic epidermis in G9a WT and cKO mice

last: Aznar


title: Epigenetic effects of vitamin C on differentiation of neural stem cells

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

institute: Korea Research Institute of Bioscience and Biotechnology

summary: Vitamin C, is an antioxidant that maintains the activity of iron and alpha-ketoglutarate-dependent dioxygenase. Vitamin C has been shown to enhance neuronal yields from cultured stem cells but the underlying molecular mechanisms are not yet elucidated. Interestingly, a few recent studies have shown that vitamin C induces widespread demethylation by activating Tet methylcytosine dioxygenase and jumonji C (JmjC) domain containing histone demethylase, suggesting an epigenetic regulation by vitamin C.

overall_design: To investigate vitamin C induced changes in DNA methylation, hydroxymethylation and enhancers in a genome-wide manner, we profiled the transcriptome, DNA methylome, hydroxymethylome and enhancer associated histone marks of rat neural stem cells (NSCs) and differentiated neuron cells treated with or without vitamin C using RNA-seq, MBD-seq, hMeDIP-seq, and Chip-seq (H3K4me1, H3K27Ac), respectively.

first: Jong-Hwan

first: Mirang

first: Xi-Biao

last: He

first: Byoung

last: Yoon

first: Dong

last: Bae

last: Huh

first: Yong

first: Sang-Hun

last: Lee

first: Seon-Young


title: DNA microarray analysis of G9a knockout embryonic stem cells

status: Public on Nov 10 2018

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

institute: Hirosaki University

summary: In embryonic stem cells (ESCs), the expression of development-related genes, including germ cell–related genes, is globally repressed. The transcription factor MAX represses germ cell–related gene expression in ESCs via PCGF6-polycomb repressive complex (PRC)1, which consists of several epigenetic factors. However, we predicted that MAX represses germ cell–related gene expression through several additional mechanisms because PCGF6-PRC1 regulates the expression of only a subset of genes repressed by MAX. Here, we report that MAX associated with DNA methyltransferases (DNMTs) and the histone methyltransferase SETDB1 cooperatively control germ cell–related gene expression in ESCs. Both DNA methylation and histone H3 lysine 9 tri-methylation of the promoter regions of several germ cell–related genes were not affected by knockout of the PRC1 components, indicating that the MAX-DNMT and MAX-SETDB1 pathways are independent of the PCGF6-PRC1 pathway. Our findings provide insights into our understanding of MAX-based repressive mechanisms of germ cell–related genes in ESCs.

overall_design: Strategy for conditional G9a-KO was described in a previous report (Tachibana et al., 2007, EMBO J. 26:3346-59). In brief, we constructed a conditional G9a KO vector, in which exons 26, fused 27/28 (cDNA-derived), and PGK-Neo cassette were flanked by two loxP sequences. The targeting vector was introduced into TT2 ES cells carrying  a G9a mutant alle (Tachibana et al., 2002, Genes Dev, 16, 1779-1791) and a wild-type allele (G9a-/+). Transfected cells were selected with medium containing G418 and ganciclovir. Successfully targeted recombinant cells, that carryed a G9a mutant allele and  G9a-flox allele (G9a-/2lox), were screened by Southern hybridization. In this strategy, Cre recombinase treatment leads the deletion of exons 26 and 27 (encoding the SET domain catalytic core) form the G9a-flox allele, thereby procucing G9a-deficient cells (G9a-/1lox).

first: Daiki

last: Tatsumi

first: Yohei

last: Hayashi

first: Mai

last: Endo

first: Hisato

last: Kobayashi

first: Takumi

last: Yoshioka

first: Kohei

last: Kiso

first: Shinichiro

last: Kanno

first: Ikuma

last: Maeda

first: Kentaro

last: Mochizuki

first: Makoto

last: Tachibana

first: Haruhiko

last: Koseki

first: Akihiko

last: Okuda

first: Akira

last: Yasui

first: Tomohiro

last: Kohno

first: Yasuhisa

last: Matsui


first: Aikaterini

last: Symeonidi

overall_design: Refer to individual Series


title: Novel Alterations in Chromatin Structure during Aging Reveal Cell-Specific Differential Expression of SUMO Proteins

status: Public on Nov 09 2018

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: We investigated the chromatin accessibility of primary human adipose-derived stem cells (ASCs) and fibroblasts during chronological aging using ATAC-seq technology.  our data suggest a significant role for nucleosome positioning in sumoylation pathway regulation in response to stress during aging of adult stem cells.

overall_design: Compared chromatin accessiblity and promoter nucleosome positioning of human ASCs and fibroblasts during aging

first: Xiaoyin

last: Shan

first: Cleresa

last: Roberts

first: Ivona

last: Percec


title: Expression data from NPM-ALK T cell lymphoma in WT or WASP-deficient background

status: Public on Nov 08 2018

city: Boston

first: Roberto

last: Chiarle

state: Massachusetts

address: 300 Longwood Avenue

institute: Children’s Hospital Boston and Harvard Medical School

summary: Total RNA was extracted from primary T cell lymphoma that spontaneously developed in either NPM-ALK or NPM-ALK/WASP-deficent transgenic mice

overall_design: NPM-ALK transgenic mice were crossed with WASP-deficient mice. Both WASP-/- females or WASP -/ males were used. T cell lymphoma developed within 4-5 months of age. Lymphoma from 5 NPM-ALK and 5 NPM-ALK/WASP-deficient mice were analyzed

first: Qi

last: Wang


title: Cis-regulated alternative splicing divergence and its potential contribution to environmental responses in Arabidopsis.

city: Beijing

first: Xuncheng

address: 5 Yiheyuan Road

institute: Peiking University

summary: Alternative splicing (AS) plays key roles in plant development and responses to environmental changes. However, the mechanisms underlying AS divergence (differential expression of transcript isoforms resulting from alternative splicing) in plant accessions and its contributions to responses to environmental stimuli remain unclear. In this study, we investigated genome-wide variation of AS in Arabidopsis thaliana accessions Col-0, Bur-0, C24, Kro-0, and Ler-1, as well as their F1 hybrids, and characterized the regulatory mechanisms for AS divergence by RNA sequencing (RNA-seq). We found that most of the divergent AS events in Arabidopsis accessions were cis-regulated by sequence variation, including those in core splice site and splicing motifs. Many genes that differed in AS between Col-0 and Bur-0 were involved in stimulus responses. Further genome-wide association analyses of 22 environmental variables showed that SNPs influencing known splice site strength were also associated with environmental stress responses. These results demonstrate that cis-variation in genomic sequences among Arabidopsis accessions was the dominant contributor to AS divergence, and it may contribute to differences in environmental responses among Arabidopsis accessions.

overall_design: Total RNA was isolated from the first leaf of 14-day-old Arabidopsis seedlings for two biological replicates RNA sequencing

first: Mei

last: Yang

first: Guangming

last: He

first: Xing

last: Deng


title: Microbiome characterization using transfer RNA sequencing

city: Chicago

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

summary: Here we report a direct tRNA sequencing protocol and software to simultaneously examine the composition and biological activity of naturally occurring microbial communities. Our analysis of mouse gut microbiome with tRNA-seq and 16S ribosomal RNA gene amplicons revealed comparable microbial community structures, and additional physiological insights into the microbiome through tRNA abundance and modifications.

sample_organism:
Escherichia coli
Staphylococcus aureus
Bacillus subtilis
Barnesiella viscericola
mouse gut metagenome

overall_design: Comprehensive analysis of high throughput sequencing data to determine microbial community structures in mouse gut microbiome (tRNA profiling dataset).

first: Michael

last: Schwartz

first: Steven

last: Cui

first: Wesley

last: Clark

first: Matthew

middle: J

last: Eckwahl

first: David

first: Marc

last: Parisien

first: Sarah

last: Owens

first: Brian

middle: L

last: Cheng

first: Kristina

last: Martinez

first: Eugene

last: Chang

first: A

last: Eren


title: Small RNA loci annotation in cacao, spinach and carrot

status: Public on Nov 01 2018

city: State College

last: Axtell

address: University Park

department: Department of Biology

institute: Penn State University

summary: Cacao, spinach and carrot are three important crops with high valuable markets. For these species there isn't already an available genome-wide annotation of small rna. Here, for the first time, we sequenced and annotated small RNAs.

sample_organism:
Spinacia oleracea
Theobroma cacao
Daucus carota

overall_design: Small RNA profile of cacao leaf, spinach leaf and carrot leaf and root. grown in control conditions

first: Alice

last: Lunardon

first: Nathan

last: Johnson


title: Epigenetic correction of defective plasticity in a tauopathy mouse model with an acetyltransferase activator [ChIP-Seq]

status: Public on Nov 05 2018

city: Strasbourg

first: Anne-Laurence

last: Boutillier

address: 12 rue Goethe

department: LNCA

summary: In the adult brain, histone acetylation is associated with activity-regulated transcriptional changes that are required for synaptic plasticity and memory. These processes are dismantled in neurodegenerative diseases. Here, we demonstrate that synaptic plasticity and memory deficiencies can be restored in a mouse model of tauopathy following treatment with CSP-TTK21, a small molecule activator of CBP/p300 histone acetyltransferases (HAT). CSP-TTK21 normalized the H2B acetylation levels in many genes, including a series of super-enhancer –regulated genes, associated with plasticity and neuronal function in resting tauopathic mice. CSP-TTK21 re-established part of the learning-induced hippocampal transcriptome, including the induction of immediate early genes and memory-related genes, and the down-regulation of neuronal identity genes that bear super-enhancers. This study is the first to provide in vivo proof-of-concept evidence that direct activation of CBP/p300 HAT efficiently and selectively reverses epigenetic, transcriptional, synaptic plasticity, and behavioral deficits associated to Alzheimer’s disease lesions in mice.

overall_design: Examination of H2Bac and H3k27ac in the dorsal hippocampus by deep sequencing


title: The Peril DNA locus acts as an in vivo enhancer for distal but not proximal genes

status: Public on Nov 02 2018

city: Cambridge

first: Abbie

last: Groff

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology;

institute: Harvard University

summary: (1) We have performed a massively parallel reporter assay (MPRA) in C2C12 cells. Additionally, we have (2) sequenced wildtype and mutant ganglionic emminence and olfactory bulb (GE/OB), and kidney from E14.5 mouse pups, as well as mESC from the mutant strain Periltm1.1Vlcg.

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct

overall_design: (1) Analysis of tag counts from RNA or DNA input control from the MPRA experiment in C2C12s. (2) Comparison between wildtype and mutant organ transcriptomes in the Periltm1.1Vlcg strain.

middle: F

first: J

last: Rinn


title: Epigenetic correction of defective plasticity in a tauopathy mouse model with an acetyltransferase activator

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


title: Elevation in cell cycle and protein metabolism gene transcription in inactive colonic tissue from Icelandic patients with ulcerative colitis

city: London

first: Tony

last: Segal

address: 5 University Street

department: Medicine

institute: UCL

summary:
BACKGROUND & AIMS:
Ulcerative colitis (UC) is a chronic relapsing inflammatory disorder that affects the colonic epithelium. A combination of genetic and environmental factors is thought to be involved in the pathogenesis, resulting in an abnormal immune response and destruction of the colonic epithelium. In Iceland, the incidence of UC is one of the highest in the world and is three times more common than Crohn’s disease.  Previous studies have suggested a genetic component may have an influence on the increased incidence. The aim of this study was to characterise a cohort of patients with UC and identify potential germ line mutations and pathways which could be associated with UC in this population.
METHODS:
We performed exome sequencing of genomic DNA and genome-wide microarray analysis on macroscopically non-inflamed colonic mucosa from Icelandic patients with UC and age and sexed matched controls. Gene-ontology analysis was used to identify common processes and pathways differentially expressed in tissue from UC cases. Exome sequence data were examined for very rare or novel mutations which might be over represented in the UC cohort. Combined matching of variant analysis and downstream influence on transcriptomic expression in the rectum was also analysed.
RESULTS:
Non-inflamed colonic tissue from patients with UC demonstrated a significant alteration in the transcriptomic profile compared to controls. Over 2,000 genes were differentially expressed in rectal tissue from UC patients and gene ontology analysis identified an up-regulation in genes associated with cell cycle control and protein processing in the endoplasmic reticulum. Exome sequencing identified two missense mutations in thiopurine S-methyltransferase (TPMT) with a minor allele frequency of 0.22 in the UC patients compared to a reported 0.062 in the Icelandic population and 0.03 in the non-Finnish European populations. A predicted damaging mutation in the inflammatory bowel disease associated gene SLC26A3 was identified which was associated with increased expression of DUOX2 and DUOXA2 in UC rectal tissue.
CONCLUSIONS:
In patients with UC, the colonic mucosa demonstrates a clear alteration in gene expression compared to control subjects. There is evidence of an elevation in genes involved with cell proliferation and the processing of proteins within the endoplasmic reticulum. Exome sequencing identified an increased prevalence of two damaging TPMT variants within the Icelandic UC population, which would suggest screening the UC population prior to initiation of therapy is warranted in order to avoid the serious toxicity associated with these mutations and azathioprine treatment.

overall_design: The original expression data contained 47,198 probes and 57 samples: 27 ascending colon and 30 rectal taken from the 35 individuals.  For ascending colon samples, there were 12 cases and 15 controls, and for rectal samples, 15 cases and 15 controls.  Probes with a minimum detection P-value of < 0.01 in at least 2 biopsies were retained (n = 22,716). Two case samples (1 ascending colon HCA12, 1 rectal HCR10) with significantly lower numbers of detected probes were excluded. Retained probes were mapped to gene IDs by the illuminaHumanv4.db package. Adjustment of the expression data for chip-level batch effects was done by the empirical Bayes method ComBat24 (sva R package25). The recorded bowel sites were verified by examining expression of genes known to significantly differ between the ascending colon and rectum and through a PCA on all probes: 1 ascending colon (UCA20) and 2 rectal samples (UCR11, UCR18) demonstrated discordant expression from expected and were removed. Post-QC, there were 52 samples (24 cases, 28 controls), of which 25 were ascending colon (11 cases, 14 controls), and 27 were rectal (13 cases, 14 controls). These data were log2 transformed, quantile normalised and analysed in R using various Bioconductor packages.

first: Andrew

last: Smith


title: Pain-driven transcriptome changes in synovium of knee osteoarthritis patients

city: Zurich

first: Francesc

last: Castro-Giner

address: Otto-Stern-Weg 7

institute: ETH Zurich

summary:
Objectives : Joint pain causes a significant morbidity in osteoarthritis (OA). The synovium as an innervated joint structure might contribute to the peripheral pain in OA.
Methods : We used a hypothesis-free next generation RNA sequencing to study protein coding and small non-coding transcriptomes in knee synovial tissues of OA patients (n=10) with high and low knee pain (evaluated by visual analogue scale) followed by Gene Ontology (GO) and pathway analyses and integration of mRNAs and small RNAs data sets.
Results : We showed that 33 protein-coding genes and 35 small RNAs were differentially expressed in the knee synovium of patients with high compared to low intensity knee pain, with 30 mRNAs and 14 small RNAs being upregulated and 2 mRNAs and 21 small RNAs being downregulated. Top enriched genes, such as SDIM1 and CPE encode neuronal proteins that share molecular properties with neurotrophic factor BDNF and promote neuronal survival under cellular stress, and OTOF participates in calcium-dependent synaptic exocytosis and modulation of GABAergic activity. TrkB was enriched in several gene networks, suggesting its key role in pain-related transcriptional changes in OA joint. Downregulation of PTX3 in high pain group supports an argument that inflammation and pain are independent processes in symptomatic knee OA. MiR-146a-3p and miR150 appeared as the microRNA candidates in the pathogenesis of OA-related knee pain.
Conclusions : Here we uncovered the molecular complexity of pain-related transcriptome changes in the synovium of knee joints in osteoarthritis. We identified new molecular candidates in OA pain setting a firm ground for future mechanistic studies and drug discovery in OA.

overall_design: RNA-seq of mRNA and small non-coding RNA of 10 patients with high and low knee pain

first: Anna

last: Bratus-Neuenschwander


title: The absolute gut microbiome alters host physiology, varies by gut architecture and disease, and predicts response to therapy

city: New York

first: Eduardo

middle: Jose

last: Contijoch

state: NY

address: 1 Gustave L Levy Pl

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: To study the effect of alterations in microbial density on the host, conventional C57Bl6 mice were treated with polymyxin B, ciprofloxacin, vancomycin, clindamycin, or ampicillin for 4 weeks. These antibiotic regimens result in a differential reduction in fecal microbial density. RNA-seq of whole tissue from the proximal colon was performed on the antibiotic treated mice, germ free controls, and non-antibiotic treated controls to interrogate transcriptional changes in the host.

overall_design: colonic gene expression in mice given one of four antibiotics (ampicillin, clindamycin, polymyxin B, vancomycin; n = 3 per group), compared to control mice (n = 5) and germ-free mice (n = 4)

first: Edaurdo

first: Jeremiah

last: Faith


title: Comparative analysis of skin- and gut-homing CD8+ T cells in aHSCT patients developing acute graft versus host disease (aGvHD)

city: Budapest

first: Zoltan

last: Pos

address: 4 Nagyvarad ter

department: Dept. of Genetics, Cell- and Immunobiology

country: Hungary

institute: Semmelweis University

summary:
Patients diagnosed with cutaneous and/or gastrointestinal aGvHD provide a unique opportunity to perform an in-depth comparison of  activated human CD8+ T cells homing to the gut and skin, in some cases even within the same host, at the same time, acting as key players in the same human disease, and exerting their effector functions in these two tissue environments.
This study aims at the identification of novel biomarkers associated with skin- and gut-homing CD8+ T cells in general, and CD8+ T cell markers possibly linked to CTL-mediated skin- and gut damage in aGvHD in particular.

overall_design: Skin- and gut-homing CD8+ T cell subsets were isolated from aHSCT patients developing cutaneous aGvHD, gastrointestinal aGvHD, both cutaneous and GI aGvHD simultaneously, or none (reference). To this end, patients’ PBMCs were sorted into CD8b+/CLA+ (skin-homing CTL), CD8b+/ITGB7+ (gut-homing CTL), and CD8b+/CLA-/ITGB7- subsets (reference) by three-way FACS sorting. Cell purity was >98% in all cases. Next, skin-homing, gut homing and reference CD8+ T cells were analyzed by comparative gene expression profiling.

first: Nikolett

last: Lupsa

first: Barbara

last: Érsek

first: Andor

last: Horváth

first: András

last: Bencsik

first: Zoltán

last: Pós


title: Mechanisms of (photo)toxicity of TiO2 nanomaterials (NM103, NM104, NM105): using high-throughput gene expression in Enchytraeus crypticus

status: Public on Nov 07 2018

city: Aveiro

first: Susana

middle: Isabel Lopes

last: Gomes

address: Campus Universitário de Santiago, Departement of Biology, University of Aveiro

department: Biology

country: Portugal

institute: CESAM & University of Aveiro

summary: Titanium dioxide (TiO2) based nanomaterials (NMs) are among the most produced NMs worldwide. When irradiated with light, particularly UV, TiO2 is photoactive, a property that is explored for several purposes. There is an increasingly number of reports on the negative effects of photoactivated TiO2 to non-target organisms. We have here studied the effect of a suite of reference type TiO2 NMs i.e. NM103, NM104, NM105 and compared these to the Bulk) with and without UV radiation to the oligochaete Enchytraeus crypticus. High-throughput gene expression was used to assess the molecular mechanisms, while also anchoring it to known effects at organism level (i.e., reproduction). Results showed that the photoactivity of TiO2 (UV exposed) played a major role in enhancing TiO2 toxicity, activating transcription of oxidative stress, lysosome damage and apoptosis mechanisms. For non-UV activated TiO2, where toxicity at organism level (reproduction) was lower, results showed the potential for long-term effects (i.e., mutagenic and epigenetic). NM specific mechanisms were identified: NM103 affected transcription and translation, NM104_UV negatively affected reproductive system/organs; and NM105_UV activated superoxide anion response. Results provided mechanistic information for UV-related phototoxicity of TiO2 materials and evidences of the potential long-term effects.

overall_design: Gene expression profile of Enchytraeus crypticus was analysed after 5 days of exposure to: i) TiO2 NMs under standard lab illumination (No-UV) and ii) TiO2 NMs + UV radiation. To maximise exposure, the test media was reconstituted water (ISO 1). The concentration tested was 1 mg/L (known to cause effects at reproduction - 3 weeks - after transference to clean soil). Three biological replicates per test treatment/NM and controls (standard laboratory light or UV) were used.

first: Carlos

middle: P

last: Roca

first: Janeck

last: Scott-Fordsmand

first: Mónica

last: Amorim


first: Aikaterini

last: Symeonidi

country: Spain

overall_design: Differential expression analysis of DMBA/TPA treated pre-neoplastic skin (interfollicular epidermis cells)

first: Alexandra

last: Avgustinova

first: Llorenç

last: Solé

first: Mercé

last: Martín

first: Andrés

last: Castellanos

first: Neus

last: Prats

first: Fran

last: Supek

first: Ben

last: Lehner

first: Salvador

last: Aznar Benitah


title: Impact of Ezh2 deficiency on differentiation of follicular helper T (Tfh) cells

first: Weiqun

last: Peng

address: 1918 F Street, NW , DC

summary: Comparison of transcriptome between control and Ezh2-deficient follicular helper T cells

overall_design: Control mice or those are deficient for Ezh2 (deleted by CD4-Cre) were infected with vaccinia virus. Eight days later, CD44-high, CD62L-negative CD4+ T cells were further stained, and CXCR5+, SLAM-low follicular helper T cells were sorted cells and used for RNAseq analysis.

first: Hai-Hui

last: Xue


title: APA modulator_U2OS_3'-seq

city: Fujisawa

first: Yusuke

last: Nakayama

address: 26-1, Muraoka-Higashi 2-chome

department: Pharmaceutical Research Division

institute: Takeda Pharmaceutical Company Limited

summary: 3'-seq data treated with small molecule compounds that modulate alternative polyadenylation

overall_design: polyA RNA profiles treated with APA modulator (T4 or T5) for 6 h in U2OS cells

first: Shinsuke

last: Araki


title: Functional difference in the HTLV-1 subgroup specific viral transcriptional regulators Tax and HBZ

status: Public on Oct 31 2018

city: Kurashiki

first: Tadasuke

last: Naito

state: Okayama

address: 577 Matsushima

department: Microbiology

institute: Kawasaki Medical School

summary: Among HTLV-1-infected individuals, the lifetime risk of developing HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) is associated with the HTLV-1 gene subgroup (i.e., subgroup-A or -B) in Japan. The purpose of this study is to understand the molecular mechanism responsible for this association.

overall_design: Jurkat Tet-On 3G cells were transfected with each indicated plasmids (i.e., pTRE3G-IRES-empty, pTRE3G-Tax-A, pTRE3G-Tax-B, pTRE3G-HBZ-A, and pTRE3G-HBZ-B) using an electroporator and then cultured at 37ºC in RPMI1640 without antibiotics. After 24 h transfection, Tax or HBZ protein expression were induced by adding Dox (final concentration: 3 ng/ml) to the culture medium. After 24 h induction, cells were collected, and total RNA was extracted with the RNeasy Mini Kit (QIAGEN) following the manufacture’s instructions. We synthesize cDNA and performed microarray analysis according to the manufacturer's instructions (Agilent Tecnologies). Data were analyzed using GeneSpring GX (Agilent Technologies).

first: Mineki

last: Saito


title: Lipid bilayer stress-activated IRE-1 modulates autophagy during endoplasmic reticulum stress

city: Singapore

first: Guillaume

last: Thibault

state: Outside the US or Canada

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

summary: Metabolic disorders such as obesity and nonalcoholic fatty liver disease (NAFLD) are emerging disorders that affect the global population. One facet of the disorders is attributed to the disturbance of membrane lipid homeostasis. Perturbation of endoplasmic reticulum (ER) homeostasis through changes in membrane phospholipid composition results in activation of the unfolded protein response (UPR) and causes dramatic translational and transcriptional changes in cell. To restore cellular homeostasis, the three highly conserved UPR transducers ATF6, IRE1, and PERK mediate cellular processes upon ER stress. The roles of the UPR in proteostatic stress caused by the accumulation of misfolded protein is well understood but lipid perturbation-induced UPR remains elusive. We found that genetically attenuated PC synthesis in C. elegans causes lipid droplets accumulation if not for the intervention of the UPR program. Transcriptional profiling of lipid perturbation-induced ER stress animals shows a unique subset of genes modulated in an UPR-dependent manner that are unaffected by proteostatic stress. Among these, we identified IRE1-modulated autophagy genes that trigger liberation of free fatty acids from excess lipid droplets suggesting a stress release mechanism by which free fatty acids are rechannelling to restore lipid homeostasis. Considering the important role of lipid homeostasis and how its impairment contributes to the pathologies in metabolic diseases, our data uncovers the indispensable role of a fully functional UPR program in regulating lipid homeostais in the face of chronic ER stress.

overall_design: Total of 30 samples (triplicates of different experimental conditions (10 conditions) stated below)

first: Jhee Hong

last: Koh

first: Lei

last: Wang

first: Caroline

last: Chabot


title: 3'-seq and RNA-seq of APA modulator_U2OS

overall_design: Refer to individual Series


title: Transcriptomic analysis of neuroblastoma cells in response to stable over-expression of Ets-1 promoter-associated noncoding RNA (pancEts-1)

status: Public on Oct 30 2018

city: Wuhan

first: Qiangsong

last: Tong

state: Hubei

address: 1277 Jiefang Avenue

department: Department of Surgery

country: China

institute: Union Hospital of Tongji Medical College

summary: Neuroblastoma (NB), a malignant embryonic tumor arising from primitive neural crest cells, accounts for more than 7% of malignancies and around 15% of cancer-related mortality in childhood. Better elucidating the mechanisms of tumorigenesis and aggressiveness is important for improving the therapeutic efficiencies of NB. Through mining of a public microarray dataset and rapid amplification of cDNA ends, we identified v-ets erythroblastosis virus E26 oncogene homolog 1 (Ets-1) promoter-associated noncoding RNA (pancEts-1) as a novel lncRNA associated with the progression of NB. To investigate the mechanisms underlying the oncogenic functions of pancEts-1, we employed the Illumina HiSeq X Ten as a discovery platform to analyze the transcriptome profiling changes of human SH-SY5Y cells in response to stable over-expression of pancEts-1. The results showed that stable over-expression of pancEts-1 led to altered expression of 1912 human mRNAs, including 1035 up-regulated genes and 877 down-regulated genes. Then we found the possible roles of these differentially regulated mRNAs in selected pathways including cell cycle/proliferation, invasion, and metastasis by Bioinformatic analysis. Furthermore, we validated the RNA-seq results by real-time RT-PCR with high identity. Overall, our results provided fundamental information about the transcriptomic changes in response to pancEts-1 over-expression in human NB cells, and these findings will help us understand the pathogenesis of NB.

overall_design: Total RNA of cells stably transfected with empty vector or pancEts-1 was extracted using the TRIzol® reagent according to the manufacturer's instructions. RNA concentration was measured using a Qubit® RNA Assay Kit with a Qubit® 2.0 Fluorometer (Life Technologies, Inc.), and integrity was assessed using the RNA Nano 6000 Assay Kit with a Bioanalyzer 2100 system (Agilent Technologies, CA). Library preparation and transcriptome sequencing on an Illumina HiSeq X Ten platform were performed by Novogene Bioinformatics Technology Co., Ltd. (Beijing, China), and 100 bp paired-end reads were generated. HTSeq v0.6.0 was used to count the reads numbers mapped to each gene.

first: Tong

last: Qiangsong

first: Zheng

last: Liduan


title: Transcriptomic analysis of neuroblastoma cells in response to stable over-expression of FOXD3 antisense RNA 1 (FOXD3-AS1)

first: Liduan

last: Zheng

department: Department of Pathology

institute: Union Hospital, Tongji Medical College

summary: Neuroblastoma (NB), a malignant embryonic tumor arising from primitive neural crest cells, accounts for more than 7% of malignancies and around 15% of cancer-related mortality in childhood. Better elucidating the mechanisms of tumorigenesis and aggressiveness is important for improving the therapeutic efficiencies of NB. Through mining of publically available microarray datasets, we discovered a novel 963-bp lncRNA, named FOXD3 antisense RNA 1 (FOXD3-AS1), as an independent prognostic marker for favorable clinical outcome of NB patients. To investigate the mechanisms underlying the oncogenic functions of FOXD3-AS1, we employed the Illumina HiSeq PE125/PE150 as a discovery platform to analyze the transcriptome profiling changes of human BE(2)-C cells in response to stable over-expression of FOXD3-AS1. The results showed that stable over-expression of FOXD3-AS1 led to altered expression of 3191 human mRNAs, including 1542 up-regulated genes and 1650 down-regulated genes. Then we found the possible roles of these differentially regulated mRNAs in selected pathways including cell cycle/proliferation, apoptosis, and cytokine/chemokine responses by Bioinformatic analysis. Furthermore, we validated the RNA-seq results by real-time RT-PCR with high identity. Overall, our results provided fundamental information about the transcriptomic changes in response to FOXD3-AS1 over-expression in human NB cells, and these findings will help us understand the pathogenesis of NB.

overall_design: Total RNA of cells stably transfected with empty vector or FOXD3-AS1 was extracted using the TRIzol® reagent according to the manufacturer's instructions.RNA concentration was measured using a Qubit® RNA Assay Kit with a Qubit® 2.0 Fluorometer (Life Technologies, Inc.), and integrity was assessed using the RNA Nano 6000 Assay Kit with a Bioanalyzer 2100 system (Agilent Technologies, CA). Library preparation and transcriptome sequencing on an Illumina HiSeq 2000 platform were performed by Novogene Bioinformatics Technology Co., Ltd. (Beijing, China), and 100 bp paired-end reads were generated. HTSeq v0.6.0 was used to count the reads numbers mapped to each gene.


title: Gene expression data of murine CD90- and CD90+ fibroblasts  in the colon.

status: Public on Oct 27 2018

city: Amsterdam

first: Olga

middle: N

last: Karpus

address: Meibergdreef 69-71

department: Tytgat Institute for Liver and Intestinal research

country: Netherlands

institute: Academic Medical Center

summary:
We described differential expression of CD90 in gp38+ fibroblasts in murine colon. We functionally characterized CD90- and CD90+ fibroblasts by co-culturing with intestinal organoids.
CD90+ colon fibroblasts were able to support organoid growth while CD90- did not.

overall_design: Fibroblasts from colon tissue from wild-type mice were isolated and Epcam-CD45-CD31-gp38+ fibroblasts were flow-sorted based on expression of CD90 generating 2 populations CD90- and CD90+ from 4 different mice

first: O

first: G

last: van den Brink


title: Transcriptional profiles of human CD14+ monocytes conditioned with melanoma exosomes

status: Public on Oct 26 2018

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

institute: IRCCS Ospedale San Raffaele