title: Identification and validation of a novel 3-gene methylation classifier for HPV-based cervical screening on self-samples

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

institute: Vrije Universiteit Medical Center

summary: Background: Offering self-sampling of cervico-vaginal material for human papillomavirus (HPV) testing is an effective method to increase the coverage in cervical screening programmes. Molecular triage directly on HPV-positive self-samples for colposcopy referral opens the way to full molecular cervical screening. Here, we set out to identify a methylation classifier for detection of precancer (CIN3) or cancer, applicable to self-samples obtained by different devices.  Findings: Genome-wide DNA methylation profiling of HPV-positive self-samples revealed 12 methylation targets for CIN3 detection. Multiplex quantitative methylation-specific PCR of these targets yielded a 3-gene methylation classifier (ASCL1, LHX8 and ST6GALNAC5), showing a very good clinical performance for CIN3 detection in both lavage (AUC=0.88; sensitivity=74%; specificity=79%) and brush (AUC=0.90; sensitivity=88%; specificity=81%) self-samples in the validation set. All self-samples from women with cervical cancer scored methylation-positive.  Conclusion: By genome-wide DNA methylation profiling on self-samples, we identified a highly effective 3-gene methylation classifier for direct triage on self-samples from HPV-positive women.

overall_design: 68 self-sampled cervico-vaginal specimens were analysed by Illumina Infinium HumanMethylation450 BeadChip. This series comprised 28 HPV-positive controls, 36 from women with a CIN3 (precancer) and 4 from women with cervical squamous cell carcinoma.

first: Wina

last: Verlaat

first: Barbara

last: Snoek

first: Daniëlle

last: Heideman

first: Saskia

last: Wilting

middle: J

last: Snijders

first: Putri

last: Novianti

first: Annina

last: van Splunter

first: Carel

last: Peeters

first: Nienke

last: van Trommel

first: Leon

last: Massuger

first: Ruud

middle: L

last: Bekkers

first: Willem

last: Melchers

first: Folkert

last: van Kemenade

first: Johannes

last: Berkhof

first: Mark

last: van de Wiel

first: Chris

last: Meijer

first: Renske

last: Steenbergen


title: Bone healing in an aged murine fracture model is characterized by sustained callus inflammation and decreased cell proliferation

status: Public on Jan 01 2018

city: Philadelphia

first: Jaimo

last: Ahn

state: PA

department: Orthopaedic Surgery

country: USA

institute: University of Pennsylvania

summary:
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.
 Geriatric fractures take longer to heal and heal with more complications than those of younger patients; however, the mechanistic basis for this difference in healing is not well understood. To improve this understanding, we investigated cell and molecular differences in fracture healing between 5 month-old (young adult) and 25 month-old (geriatric) mice healing utilizing high-throughput analysis of gene expression.

overall_design: Mice aged 5 months “young” or 25 months “geriatric” underwent bilateral tibial fractures and fracture calluses were harvested at 0, 5, 10, and 20 days post fracture (DPF) for analysis, yielding a total of 41 samples.  For each time point and DPF, a group of 5 to 6 unique mice were harvested. Global gene expression analysis was performed using Affymetrix MoGene 1.0 ST microarrays. After normalization, data were compared using ANOVA and evaluated using Principal Component Analysis (PCA), CTen, heatmap, and Incromaps analysis.

first: John

last: H Hebb

first: Jason

middle: W

last: Ashley

first: Lee

last: McDaniel

first: Luke

middle: A

last: Lopas

last: Tobias

first: Kurt

middle: D

last: Hankenson


title: Expression data fron HeLa cells

city: Heidelberg

first: Julien

last: Béthune

address: Im Neuenheimerfeld 328

country: Germany

institute: Heidelberg University Biochemistry Center

summary:
The protein GIGYF2 is an RNA-binding protein that mediates repression of mRNA function when tethered to an artificial reporter mRNA. Cellular targets of GIGYF2 were not known at the time of this study.
We used microarrays to globally identify gene expression changes upon manipulating GIGYF2 expression levels.

overall_design: HeLa cells were either transfected with a control plasmid or a plasmid coding for GIGYF2 under a CMV promoter, and then processed for RNA extraction and hybridization on Affymetrix microarrays. For each condition (WT or overexpression) three biological replicate samples were prepared. Microarray analysis was performed at the EMBL GeneCore facility (Heidelberg, Germany)

first: Cinthia

last: Ramirez


title: Microarray analysis of Bone marrow derived mast cells (BMMCs) from C57BL/6 and ACKR2-/- mice

status: Public on Dec 31 2017

city: Louisville

first: Venkatakrishna

middle: R

last: Jala

state: KY

address: 505 S Hancock Street # 323

department: Dept. Microbiology and Immunology

institute: University of Louisville

summary: Mast cells have been suggested to either promote or suppress tumor progression but the mechanisms underlying these outcomes are unclear. Here, we show that mice with a heterozygous mutation in the adenomatous polyposis coli gene (ApcMin/+) displayed reduced intestinal tumor burden and increased survival in the background of the chemokine decoy receptor ACKR2 deficiency (ACKR2-/-). The ACKR2-/-ApcMin/+ tumors showed increased infiltration of mast cells. In mast cell-deficient Sash (c-kitW-sh/W-sh) ACKR2-/-ApcMin/+ mice the survival advantage was lost as the tumors grew rapidly and adoptive transfer of mast cells reduced the tumor burden in these mice. The tumor burden is also increased in Rag2-/-ACKR2-/-ApcMin/+ mice and the protection is reconstituted by adoptively transferred CD8+ T-lymphocytes. Mast cells from ACKR2-/- mice expressed elevated levels of chemokine receptors CCR2 and CCR5 and are also efficient in antigen presentation and activation of CD8+ T-cells.  Mast cell-derived leukotriene B4 is a critical mediator of CD8+ T-lymphocyte recruitment as the BLT1-/-ACKR2-/-ApcMin/+ mice are highly susceptible to intestinal tumor induced mortality. Taken together, these data demonstrate that chemokine mediated mast cell recruitment is essential for initiating LTB4/BLT1 regulated CD8+ T-cell homing and generation of effective anti-tumor immunity against intestinal tumor development.

overall_design: BMMCs were collected at 2 weeks and 10 weeks from C57BL/6 (wild type) and ACKR2-/- mice.

first: Sobha

last: Bodduluri

first: Haribabu


title: Baseline hepatic mRNA expression in three zebrafish strains

city: Portland

first: Kim

middle: H

last: Brown

state: OR

address: 1719 SW 10th Ave

department: Department of Biology

institute: Portland State University

summary: Strains of commonly used wildtype zebrafish (Danio rerio) have both shared and unique genomic features such as SNPs and copy number variants. Unfortunately, exact lab strains are often unreported in the literature and the replication of studies in zebrafish may be negatively impacted by this fact. These data were collected to assess hepatic mRNA expression patterns between three common zebrafish strains (AB, Tuebingen, and WIK) to establish baseline differences across strains and between sexes.Baseline mRNA expression was analyzed in six individuals pers strain (three males and three females) using Agilent 4x44K gene expression microarrays . These data highlight the complexity of variation that exists within zebrafish and underscore the value of this model system as a valid representation of normal variation present in other species, including humans.

overall_design: Baseline gene expression of naïve liver tissue in three wild-type zebrafish strains (AB, Tuebingen, WIK). n=3 males and n=3 females per strain; n=18 total

first: Lindsay

last: Holden


title: Myocardial reparative functions of exosomes from mouse mesenchymal stem cells (MSCs) are enhanced by hypoxia treatment

city: Hangzhou

first: Jin

middle: Yun

last: Zhu

state: zhejiang

address: Jiefang road 88

country: China

institute: Second Affiliated Hospital, College of Medicine, Zhejiang University.

summary: To determine whether hypoxia augments the activity of exosomes by modulating miRNAs, we use miRNA array profile to find the differential expression of miRNAs of exosomes in different culture conditions (normoxia, hypoxia, hypoxia supplemented with GW4869 which is an inhibitor of exosomes generation).

overall_design: Three samples were processed for each kind of exosome that derived from normoxic-MSCs, hypoxic-MSCs, and hypoxic-MSCs suppled with GW4869 (N-EXO, H-EXO, H+G-EXO). H-Exosome was isolated from conditioned medium of MSCs under hypoxia condtion 24h. The fragmentation mixtures were hybridized to an Agilent- Mouse microRNA array 21.0

first: Jinyun

first: Hong

last: Yu


title: Cord blood buffy coat DNA methylation is comparable to whole cord blood methylation

city: Ann Arbor

first: Kelly

last: Bakulski

state: MI

address: 1415 Washington Heights

department: Department of Epidemiology

institute: University of Michigan

summary: Cord blood DNA methylation is associated with numerous health outcomes and environmental exposures. Whole cord blood DNA reflects all nucleated blood cell types, while centrifuging whole blood separates red blood cells by generating a white blood cell buffy coat. Both sample types are used in DNA methylation studies. Cell types have unique methylation patterns and processing can impact cell distributions, which may influence comparability. To evaluate differences in cell composition and DNA methylation between buffy coat and whole cord blood samples, cord blood DNA methylation was measured with the Infinium EPIC BeadChip (Illumina) in 8 individuals, each contributing buffy coat and whole blood samples.

overall_design: 16 cord blood samples, 8 buffy coat and 8 whole blood paired by individual, were assayed on the Infinium EPIC BeadChip (Illumina)

last: Dou

first: Rebecca

last: Schmidt

middle: S

last: Benke

first: Craig

last: Newschaffer

first: Irva

last: Hertz-Picciotto

first: Lisa

last: Croen

first: Ana-Maria

last: Iosif

first: Janine

middle: M

last: LaSalle

first: M

last: Fallin


title: Comparison of PPIH knockdown in HeLa cells compared to scrambled shRNA control

first: Tara

last: Davis

department: Biochemistry and Molecular Biology

institute: Drexel University College of Medicine

summary:
HeLa cells transduced with shRNA from MISSION library (TRCN0000289677) using lentiviral delivery system. HeLa cells transduced with scrambled shRNA, gifted from Dr. Mauricio Reginato. Sequence is 5′-CCTAAGGTTAAGTCGCCCTCGCTCTAGCGAGGGCGACTTAACCTT-3′
Peptidyl-prolyl isomerase H (PPIH) is a cyclophilin, an enzyme that interconverts cis and trans isomers of proline. PPIH associates with the human spliceosome, the complex and dynamic machinery that removes intronic sequence from pre-messenger RNA (pre-mRNA). Although PPIH affects the ability of the spliceosome to assemble and catalyze splicing in vitro, little is known about what PPIH does to splicing in vivo. To understand the function of PPIH in the nucleus, we knocked down PPIH in human cells. We characterized a set of alternative splicing and transcriptional events that are PPIH-responsive. We used these splicing and transcriptional bioassays to show first that PPIH-responsive events are largely specific, even within the cyclophilin family. We then identified a role for proline isomerization in transcriptional regulation, but not in regulation of alternative splicing. The development of a bioassay for PPIH function can be used to answer fundamental questions about the role of spliceosomal proteins in regulating splicing and other nuclear functions.

overall_design: 3 replicates of PPIH knockdown cell lines (HeLa cells, stably integrated, selected using puro, shRNA TRCN0000289677). 3 replicates of SCR control cells lines (HeLa cells, stably integrated, selected using puro, sequence 5′-CCTAAGGTTAAGTCGCCCTCGCTCTAGCGAGGGCGACTTAACCTT-3′). total RNA purified from ~1million cells, cDNA converted using random hexamer primers, quantity measured using NanoDrop, quality quantified using BioAnaylzer). Affymatrix HTA2.0 array

first: S

last: Jackson

first: Beth

last: Adams

first: Anh

last: Trinh

first: Hetty

last: Rodriguez

first: John

last: Tobias


title: Variation in transcriptional responses to salt stress in rice

city: Lincoln

first: Chi

last: Zhang

state: NE

address: 1901 Vine Street

institute: University of Nebraska - Lincoln

type: Expression profiling by high throughput sequencing

summary: The aim of this study is to assess natural variation in transcriptional responses to salt stress in rice. We utilized a diversity panel (RDP1) described in Zhao et al 2011. Eight day old rice seedlings were subjected to a gradual 6 dS·m-1 salt stress for a period of 24h. RNA seqeuncing was performed on shoot tissue using Illumina HiSeq 2500.

overall_design: RNA deep sequencing

first: Harkamal

last: Walia

first: Malachy

last: Campbell


city: Bethesda

first: Yinmeng

last: Yang

address: 10 Center Drive

institute: NCI

summary:
Chimeric antigen receptor (CAR)-expressing T-cells induce durable remissions in patients with relapsed/refractory B-cell malignancies. CARs are artificial constructs introduced into mature T-cells conferring a second, non-MHC restricted specificity in addition to the endogenous T-cell receptor (TCR). The impact of TCR activation on CAR T-cell efficacy in vivo has important implications for clinical optimization of CAR T-cell therapy, but cannot be systematically evaluated in xenograft models. Using an immunocompetent, syngeneic murine model of CD19-targeted CAR T-cell therapy for pre-B cell ALL, we demonstrate loss of CD8 CAR T-cell mediated clearance of leukemia associated with T-cell exhaustion and apoptosis when TCR antigen is present. CD4 CAR T-cells demonstrate equivalent cytotoxicity, as compared to CD8 CAR T-cells, and in contrast, retain in vivo efficacy in the presence of TCR stimulation. Gene expression profiles confirm increased exhaustion and apoptosis of CAR8 upon dual receptor stimulation compared to CAR4, and indicate inherent differences in T-cell pathways.
Chimeric antigen receptor (CAR) T cells express two activating receptors, the CAR and the endogenous T cell receptor (TCR). CAR T cells can be derived from either CD8 or CD4 T cells to generate CAR8 and CAR4 cells, respectively.  In vivo, CAR8 and CAR4 cells respond differently when simultaneously stimulated through the CAR and TCR.

overall_design:
Murine CAR8 and CAR4 cells were generated with a CAR that recognizes murine CD19 and TCRs that recognize  HY-minor histocompatibility antigens.  CAR8 and CAR4 T cells were co-incubated for 10 hours with B cells that were either possitive or negative for the expression of CD19 and/or HY-antigen.  Through this CAR8 and CAR4 T cells were stimulated through the CAR, the TCR, CAR+TCR (simultaneiously) or neither receptor (CD19 negative, HY-negative B cells).
Gene expression profiles of CD4-derived (CAR4) and CD8-derived (CAR8) chimeric antigen receptor T cells after stimulation through the CAR, TCR or both receptors

first: Terry

last: Fry


title: Meta- and cross-species analyses of insulin resistance based on gene expression datasets in human white adipose tissues

city: Goyang-si

first: Junghyun

last: Jung

state: Gyeonggi-do

address: Dongguk University Biomedi Campus 32, Dongguk-ro, Ilsandong-gu

department: Life Science

country: South Korea

institute: Dongguk Uvi.

summary: Ample evidence indicates that insulin resistance (IR) is closely related to white adipose tissue (WAT), but the underlying mechanisms of IR pathogenesis are still unclear. Using 352 microarray datasets from seven independent studies, we identified a meta-signature which comprised of 1,413 genes. Our meta-signature was also enriched in overall WAT in in vitro and in vivo IR models. Only 12 core enrichment genes were consistently enriched across all IR models. Among the meta-signature, we identified a drug signature made up of 211 genes with expression levels that were co-regulated by thiazolidinediones and metformin using cross-species analysis. To confirm the clinical relevance of our drug signature, we found that the expression levels of 195 genes in the drug signature were significantly correlated with both homeostasis model assessment 2-IR score and body mass index. Finally, 18 genes from the drug signature were identified by protein-protein interaction network cluster. Four core enrichment genes were included in 18 genes and the expression levels of selected 8 genes were validated by quantitative PCR. These findings suggest that our signatures provide a robust set of genetic markers which can be used to provide a starting point for developing potential therapeutic targets in improving IR in WAT.

overall_design: Mice were orally administered with either vehicle or metformin once a day for 12 weeks. Epididymal adipose tissue was dissected from the mice after an overnight fast, snap-frozen in liquid nitrogen, then stored at -75°C until analysis.

first: Junghun

first: Go

last: Kim

first: Wonhee

last: Jang


title: Expression data of adult quiescent and activated mouse neural stem cells

city: Fontenay-aux-Roses

first: Marc-André

last: MOUTHON

address: Route du Panorama

department: IRCM

country: France

institute: CEA

summary:
Neural stem cells were sorted according to their activated or quiescent state by flow cytometry using a set of 3 markers (LeX, CD24 and EGFR)
We used microarrays  to detail the global programme of gene expression underlying the proliferation/quiescence balance.

overall_design: Neural stem cells were freshly sorted from adult mouse subventricular zone by flow cytometry and Affymetrix GeneChip MOE 430 2.0 microarrays were hybridized.

first: Lise

last: Morizur

first: Alexandra

last: Chicheportiche

first: Mathieu

last: Daynac

first: François

last: Boussin

last: Mouthon


title: Gene Level Expression Profiling of Cardiac Progenitor Cells and Cardiomyocytes

city: Toronto

first: Peter

last: Zandstra

state: Ontario

address: 160 College Street, University of Toronto

department: Institute of Biomaterials and Biomedical Engineering

country: Canada

institute: University of Toronto

summary:
Transcriptome analysis of cardiac progenitor cells and cardiomyocytes
The identification of cell surface proteins on stem cells or stem cell derivatives is a key strategy for the functional characterization, isolation, and understanding of stem cell population dynamics. Here, using an integrated mass spectrometry and microarray based approach, we analyzed the surface proteome and transcriptome of cardiac progenitor cells (CPCs) generated from the stage-specific differentiation of mouse and human pluripotent stem cells.

overall_design: We analyzed 9 samples from differentiated mouse embryonic stem cells using the Affymetrix Mouse Exon 1.0 ST platform. Array data was processed by the Transcriptome Analysis Console (TAC) Software. No technical replicates were performed.

first: Charles

last: Yoon

first: Hannah

last: Song

first: Steven

last: Kattman

first: Nicole

last: Dubois

first: Alec

last: Witty

first: Gordon

last: Keller


title: Gene expression data from stage II and III treated and untreated colorectal cancer patients

city: Belfast

first: Wendy

last: Allen

address: 97 Lisburn Road

department: Centre For Cancer Research and Cell Biology

country: United Kingdom

institute: Queen's University Belfast

summary: Colorectal cancer (CRC) has one of the highest worldwide incidences and mortality rates. Compared to surgery alone, adjuvant 5-Fluorouracil (5FU)-based chemotherapy improves 5-year overall survival (OS) in only 3-4% of stage II and 15-20% of stage III patients in unselected populations. Significant advances have been made in the molecular stratification of CRC, with the emerging Consensus Molecular Subtype (CMS) and Colorectal Cancer Intrinsic Signature (CRIS) transcriptomics-based classification systems; however, the therapeutic impact of molecular stratification has so far been limited. In an effort to identify subgroups of patients benefitting from chemotherapy, we assessed which CMS and CRIS subgroups of stage II and III CRC benefitted from adjuvant 5FU-based chemotherapy using in-house and published datasets.

overall_design: The colorectal cancer cohort was assembled from 363 stage II and III patients from 4 European Centres (Barcelona, Dublin, Florence, Aberdeen).  Within this cohort, samples from 194 patients with 50% or more tumour content as assessed by Hematoxylin and eosin (H&E ) staining were taken forward for RNA and DNA extraction.  High quality transcriptomics data were obtained for 156 samples using the Almac  Xcel array (Almac Diagnostics, Craigavion, UK).

first: Sandra

last: van Schaeybroeck

first: Mark

last: Lawler

first: Daniel

last: Longley


title: MLL2 conveys transcription-independent H3K4me3 in the oocyte

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

type: Genome binding/occupancy profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

summary: Trimethylation of histone 3 lysine 4 (H3K4me3) is classically thought of as a mark of active promoters and yet it occurs at untranscribed domains. Partial redundancy of H3K4 methyltransferases has made it difficult to delineate the mechanisms underlying genomic targeting of H3K4me3. The oocyte provides an attractive system to investigate this, because extensive acquisition of H3K4me3 occurs in a non-dividing cell and ablation of a single H3K4 methyltransferase, Mll2, prevents most H3K4me3. We developed low-input chromatin immunoprecipitation to interrogate promoter associated histone modifications H3K4me3, H3K27ac and H3K27me3 throughout oogenesis. In non-growing oocytes, H3K4me3 was restricted to transcriptionally active promoters, but as oogenesis progresses, H3K4me3 accumulates in a transcription-independent manner: targeted to broad inter-genic regions, putative enhancers, and transcriptionally silent H3K27me3-marked promoters. Consequently, thousands of bivalent domains are established during oogenesis. Ablation of Mll2 resulted in loss of transcription-independent H3K4me3, with limited effects on transcription-coupled H3K4me3 or gene expression. Deletion of Dnmt3a/b showed that DNA methylation protects regions from acquiring H3K4me3. Our findings show that there are two independent mechanisms of targeting H3K4me3 to genomic elements, with MLL2 recruited to unmethylated CpG-rich regions independently of transcription.

overall_design: We first characterised histone modifications associated with transcriptional regulation (H3K4me3, H3K27ac, and H3K27me3) in oocytes by adapting an ultra-low input native ChIP (ULI-nChIP) sequencing method. This allowed us to obtain high-resolution chromatin maps throughout oogenesis, from non-growing oocytes (NGOs) to fully-grown germinal vesicle (GV) oocytes, and to compare these profiles to gene expression and DNA methylation.  Furthermore, this has enabled the first molecular interrogation of H3K4me3 in the conditional Dnmt3a/b and Mll2 KO oocytes.

first: Courtney

last: Hanna

first: Jiahao

last: Huang

first: Andrea

last: Kranz

first: A

middle: F

last: Stewart

first: Gavin

last: Kelsey


title: Effect of Analytic Treatment Interruption of Antiretroviral Therapy on HIV Reservoirs and Immunological Parameters

first: Jana

last: Blazkova

address: 9000 Rockville Pike

institute: NIH

summary: We compared transcriptional profiles of CD4+ and CD8+ T lymphocytes from HIV infected individuals before and 1 year after interruption of antiretroviral therapy (ART).

overall_design: CD4+ and CD8+ T lymphocytes isolated from periphral blood of 7 study participants before (pre-ATI) and 1 year after (post-ATI) analytic antiretroviral therapy interruption (ATI).


title: Six2CrePRRflox FACS cells microarray

city: new orleans

first: IHOR

last: YOSYPIV

state: Louisiana

address: 1430 tulane ave.

department: PEDIATRICS

institute: Tulane University

summary: This experiment aimed to uncover the genome-wide alternation in gene expression resulting from the removal of PRR from the population of Cap Mesenchyme and successive changes to the series of events in kidney development.

overall_design: Three Wild type pooled samples and three KO pooled samples are performed for the microarray to compare the gene changes.

first: Ihor

middle: V

last: Yosypiv

first: Renfang


title: Strand-oriented RNAseq of LNCaP prostate cancer cells in culture for 24h in the presence of androgen

city: São Paulo

first: Lucas

middle: Ferreira

last: daSilva

state: São Paulo

address: Av. Vital Brasil 1500

department: Parasitology

country: Brazil

institute: Instituto Butantan

summary: The aim of this study was to use NGS RNAseq deep-sequencing in order to characterize the polyadenylated mRNAs and lncRNAs expressed in LNCaP cells treated with androgen hormone compared with untreated LNCaP cells (GSE79301). Trimmed reads were mapped using the hg19 genome with TopHat v.2.0.12 and Bowtie v.2.2.3. The assembly was guided by a custom GTF file created with transcripts fromhuman lncRNA annotations from GENCODE v19 (Harrow, Frankish et al.2012) and those already annotated as lincRNAs in (Cabili, Trapnell et al. 2011; Prensner, Iyer et al. 2011; Hangauer, Vaughn et al. 2013). The diferencial expression was calculated by the sum of exon read count per gene with HTSeq (Anders, Pyl et al. 2015), followed by a DESeq2 analysis (Love, Huber et al. 2014).

overall_design:
polyA+ RNA profiles of LNCaP prostate cancer cell line grown in culture for 24h in the presence of 1 nM of the synthetic androgen R1881 and  than  were generated by paired-end deep sequencing, in duplicate, using Illumina HiSeq2000.

This series contains re-analyzed samples from GSE79301.

first: Felipe

last: Beckedorff

first: Murilo

last: Amaral

last: Silva

first: Sergio

last: Verjovski-Almeida


title: Whole genome bisulfite sequencing of mouse neural progenitor cells and neurons from the mouse cerebral cortex at day 15.5 of embryonic development

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

summary: Global changes in DNA methylation occur during mammalian development but may be more limited during differentiation of cell lineages. The extent and specific nature of methylation changes at the time when neural progenitor cells in the brain cease proliferation and commit to become differentiated cortical neurons remains unknown. Here, we have used whole genome bisulfite sequencing to quantitate a level of modified bisulfite-resistant cytosines (5-methylcytosine and 5-hydroxymethylcytosine) at base resolution in differentiating neurons and their progenitors isolated from mouse brain at the peak of embryonic neurogenesis. We find that, during this transition, globally, modified cytosine pattern is very stable. Localized losses of modified cytosines (hypomethylation) were much more common than gains and were targeted frequently to intragenic enhancer regions marked by H3K27 acetylation. Most genes with intragenic clustered hypomethylated CpG sites were upregulated in neurons and encoded factors essential for neurogenesis. The hypomethylated regions were enriched in motifs recognized by the neuronal transcription factor NEUROD2 which become activated in differentiated neurons. NEUROD2 binding coincided with 80% of the hypomethylated intragenic enhancer regions. The data suggest that in developing neurons, the limited reorganization of the DNA methylome reflects the engagement of intragenic enhancers by NEUROD2 in parallel with activation of neuronal function-related genes.

overall_design: whole genome bisulfite sequencing of two biological replicates of the purified cortical neural progenitors from the mouse cortex at day 15.5 and  two biological replicates of the purified cortical neurons from mouse at day 15.5 embryonic development

first: M

last: Hahn

middle: X

last: Li

first: J

last: Liu

first: X

first: Y

last: Fong

first: Q

last: Lu

first: G

middle: P

last: Pfeifer


title: Gene expression signatures for bladder cancer tissues and normal adjacent tissues.

city: Guangzhou

first: Wang

last: He

state: Guangdong

address: 107th, Yanjiangxi Road

department: Urology

institute: Sun Yat-sen Memorial Hospital

summary: To identify aberrantly expressed long intergenic noncoding RNAs (lincRNAs) in muscle-invasive bladder cancer tissues compared with normal adjacent tissues, we have employed microarray expression profiling as a discovery platform to identify lincRNAs that may play important roles in bladder cancer progression. Samples of fresh frozen cancer tissues, together with normal adjacent tissues (3 cm away from the tumor), were obtained during surgical resection, and total RNA was extracted for microarray analysis.

overall_design: Three cases of muscle invasive bladder cancer and paird adjacent normal tissues were subjected to microarray analysis.

first: Tianxin

last: Lin


title: Differentially expressed genes related to inflammatory disease on nasal cavity induced by diesel exhaust particles (DEPs)

city: Goyang

first: Hyo-Jeong

last: Kim

address: 32, Dongguk-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do 10326, Republic of Korea

institute: Dongguk University

summary: Recently air pollution has become serious environmental issues effect. Contaminated air by pollutants, such as emission of diesel fuel, enter the human body through airway tract and can cause inflammatory diseases in respiratory system. The relation between air pollutant and development of respiratory diseases have well-studied, but the processes of disease outbreak were not fully studied yet. We investigated global gene expression induced by diesel exhaust particle (DEP), one of air pollutants in primary human nasal epithelial cell (PHNEC) with the purpose of identifying potential biomarkers. Furthermore, we analyzed signaling pathway among differentially expressed genes (DEGs) for elucidating signaling networks of process developing airway diseases. Consequentially, we suggested several key biomarkers that include not only the expression changes but also the meaning of relation between genes. This findings might be used for early diagnosis and prevention of upper respiratory disease, especially rhinitis.

overall_design: Two-dose of DEP treated PHNEC. Biological replicates: 4

first: Hyo


title: RNA-seq and RIP-seq of LNCaP cells treated with androgen hormone

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

overall_design: Refer to individual Series


title: microRNA expression in human keratinocytes from infant, adult and ederly skin

city: LYON

first: Jerome

last: Lamartine

address: 7 passage du Vercors

institute: Université Lyon I

summary: We want to identifiy microRNAs modulated by aging in human primary keratinocytes prepared from skin samples from individuals of various age

overall_design: Comparison of 3 groups of 4 samples from different individuals: infants, youngs adults, aged adults

first: Jérôme

last: LAMARTINE


title: Microarray analysis of ApcMin/+ and D6(ACKR2)-/-ApcMin/+ tumors

city: Louisville

first: Venkatakrishna

last: Jala

address: 505 S Hancock Street # 323

institute: University of Louisville

summary: Mast cells have been suggested to either promote or suppress tumor progression but the mechanisms underlying these outcomes are unclear. Here, we show that mice with a heterozygous mutation in the adenomatous polyposis coli gene (ApcMin/+) displayed reduced intestinal tumor burden and increased survival in the background of the chemokine decoy receptor ACKR2 deficiency (ACKR2-/-). The ACKR2-/-ApcMin/+ tumors showed increased infiltration of mast cells. In mast cell-deficient Sash (c-kitW-sh/W-sh) ACKR2-/-ApcMin/+ mice the survival advantage was lost as the tumors grew rapidly and adoptive transfer of mast cells reduced the tumor burden in these mice. The tumor burden is also increased in Rag2-/-ACKR2-/-ApcMin/+ mice and the protection is reconstituted by adoptively transferred CD8+ T-lymphocytes. Mast cells from ACKR2-/- mice expressed elevated levels of chemokine receptors CCR2 and CCR5 and are also efficient in antigen presentation and activation of CD8+ T-cells.  Mast cell-derived leukotriene B4 is a critical mediator of CD8+ T-lymphocyte recruitment as the BLT1-/-ACKR2-/-ApcMin/+ mice are highly susceptible to intestinal tumor induced mortality. Taken together, these data demonstrate that chemokine mediated mast cell recruitment is essential for initiating LTB4/BLT1 regulated CD8+ T-cell homing and generation of effective anti-tumor immunity against intestinal tumor development.

overall_design: RNA from Small Intestines & Colons of  C57BL/6 (Wild type, WT), D6-/- mice as well as small intestinal and colonic tumors of ApcMin/+, D6-/-ApcMin/+  mice were isolated and pooled the respective genotypes and performed microarray.

first: Haribabu

last: Bodduluri


title: Gene Expression of larval diapause in Wyeomyia

city: Birmingham

first: John

middle: Kenneth

last: Colbourne

state: West Midlands

address: Edgbaston

department: School of Biosciences

institute: University of Birmingham

summary:
This study measured the differential expression of genes from two populations of Wyeomyia smithii in the USA : KC in Maine and PB in New Jersey.  The study reveals differential gene expression (DGE) in diapausing and developing larvae using microarrays.  It identified the temporal and developmental pattern of DGE by showing the combined differential effects of length of day and time of day overlaid in a single plot illustrating DGE from two separate, comparative arrays.  The study identified select hormonal and cell-signaling pathways underlying this pattern.
This GEO record is for a full factorial comparison (1) between the two larval populations (KC, PB) and (2) reared under two photoperiods (SD, LD) for 13-14 days (Short-Day diapausing larvae L:D = 11:13 hours; Long-Day developing larvae L:D = 14.5:9.5 hours) and (3) sampled either during the day at 10-11h after lights on (ZT10) or at night 22-23h after lights-on (ZT22).

overall_design: We compared the gene expression patterns (EXP) for the two populations: EXP1 = LD vs SD, EXP2 = ZT10 vs ZT22 using four biological replicates for each treatement and population including balanced dye-swaps. All probes including random probes were quantile-normalized across chips, subarrays, samples and replicates.

first: William

last: Bradshaw

middle: K

first: Jacqueline

last: Lopez

first: Jeong-Hyeon

last: Choi

first: Michael

last: Pfrender


title: Evolution of biting induced Wyeomyia gene expression

summary:
This study measured the differential expression of genes from two populations of Wyeomyia smithii in the USA that differ in their propensity to bite over a geographic gradient. Population KC is a northern non-biting population from Maine; population WI is a southern low-frequency biting population from Florida.  The mosquitoes were maintained at the University of Oregon under standard rearing conditions and run through two generations to minimize maternal and field effects.  Selection for biting was conducted using ~14,000  individuals from the WI population. The environment and protocols used for selection were the same as for KC except biters were removed from their cage and placed into a separate “biting” cage with supplemental males from the same generation of the selected line. All hatch from the biting cage were used to generate the subsequent generations. This protocol was followed until the selected line had undergone 5 generation of selection.  Through all generations of selection, including those that were not offered a host, hatch were placed on short days (LL:D=10:14) at 21°C to synchronize each generation and to miigate inadvertant direct selection on development time, generation time, or the timing of reproductive allocation.  After adults of a given generation had died, their offspring were transferred to long days and reared to adulthood, as above.  During experiments, all animals were in good physical condition. Animal heads were dissected then transferred into 1.5-ml microcentrifuge tubes and shock-frozen in liquid nitrogen. Samples were short-term stored at -80°C. For all experimental conditions, four independent replicates (50 heads each) were analyzed.
This GEO record is for three comparisons among the three populations: (EXP1) non-biters in the base population (WI) versus biting individuals in the WI line selected for biting (WIOB) over 5 generations of selection (WI vs WIOB); (EXP2) WIOB versus northern obligate non-biters (KC); (3) WI versus KC (n=4 per treatment group for each population).

overall_design: We compared the gene expression patterns (EXP) for the three populations: EXP1 = WI vs WIOB. EXP2 = WIOB vs KC, EXP3 = WI versus KC using four biological replicates for each population including balanced dye-swaps. All probes including random probes were quantile-normalized across chips, subarrays, samples and replicates.


title: Epigenomic analysis of Atrx deficiency in murine glioma cells of orgin [RNA-seq]

city: Houston

first: Jason

middle: T

last: Huse

state: TX

address: 1515 Holcombe Blvd

department: Department of Pathology

institute: University of Texas MD Anderson Cancer Center

summary: The chromatin regulator ATRX is inactivated in large subsets of adult and pediatric glioma.  Whether and how ATRX deficiency promotes oncogenesis by epigenomic dysregulation remains unclear.  We found that Atrx loss, especially when coupled with Tp53 inactivation, promoted cell motility and modulated differentiation state in primary murine neuroepithelial progenitors, recapitulating characteristic disease phenotypes and molecular features.  Moreover, Atrx deficiency induced widespread shifts in chromatin accessibility, histone composition, and gene transcription at vacant Atrx binding sites distributed across the genome.  Finally, target genes mediating Atrx-deficient phenotypes in vitro exhibited similarly selective misexpression in ATRX-mutant human glioma tissues and cell lines.  These findings demonstrate that, in appropriate physiological contexts, ATRX deficiency and its epigenomic sequelae are sufficient to induce disease-defining oncogenic phenotypes.

overall_design: Transcriptional analysis of Tp53+/+ and Tp53-/- neuroepithelial progenitor cells with and without Atrx inactivation

first: Carla

last: Danussi

first: Promita

last: Bose

first: Kasthuri

last: Kannan


title: Epigenomic analysis of Atrx deficiency in murine glioma cells of orgin [ATAC-seq]

overall_design: Examination of chromatin accessibility changes acquired with Atrx deficiency in Tp53-/- neuroepithelial progenitor cells


title: Effects of organophosphate flame retardants on Atlantic cod liver cells

city: Woods Hole

first: Neelakanteswar

last: Aluru

state: MA

address: 45 Water Street

department: Biology

institute: Woods Hole Oceanographic Institution

summary: Organophosphorous flame retardants (PFRs) were first reported in the late 1970, and today they account for approximately 20 % of the total use of flame retardants in Europe. PFRs are found ubiquitously in the environment, including remote areas stretching from the Arctic to the Antarctic. Generally, similar levels of PFRs is observed between Arctic and more rural areas. The toxicity of PFRs varies depending on their chemical structure. The World Health Organization have reported LC50 values for mammals and aquatic organisms with high variation from 4.2 to 180 mg/L or 707 to 4700 mg/kg body weight, depending on substance and test species. However, little is known about the toxicity and physiological effects of PFRs to fish, particularly in the Arctic species. Hence, the objective of this study is to determine the effects of PFR exposure on hepatic gene expression patterns in Atlantic cod (Gadus morhua) using liver explants in vitro. Liver explants were exposed to 2-Ethylhexyl diphenyl phosphate (EHDPP), tris(2-chloroisopropyl)phosphate (TCPP), and a mixture of both EHDPP and TCPP for 0, 24 and 48 hours. Samples were analyzed for gene expresson profiling using RNAseq. RNAsequening results suggest that exposure to PFRs differentially expressed genes involved in xenobiotic metabolism. We did not observe any chemical-specific effects on gene expression patterns. However, temporal changes in gene expression were observed. Most of the differentially expressed genes (DE) in 24h exposed samples are related in xenobiotic metabolism, whereas in 48h samples DE genes belong to diverse physiological processes.

overall_design: Each treatment contains three replicate biological samples (liver explants) exposed to either 24 or 48 hours. The treatments include DMSO (carrier control), TCPP and EHDPP.

first: Ingeborg

last: Hallanger


title: A COUP-TFII human embryonic stem cell reporter line to identify and purify atrial cardiomyocytes

city: Enschede

first: Robert

last: Passier

address: Building Zuidhorst

department: MIRA Institute for Biomedical Technology and Technical Medicine

country: Netherlands

institute: University of Twente

summary: Here, we targeted mCherry to the COUP-TFII genomic locus in NKX2.5eGFP/+ hPSCs. Upon differentiation to atrial and ventricular cardiomyocytes (CMs) this dual atrial COUP-TFIImCherry/+-NKX2.5eGFP/+ reporter line allowed identification and selection of GFP+ (G+)/mCherry+ (M+) CMs following cardiac differentiation. These cells exhibited transcriptional and functional properties of atrial CMs, whereas G+/M- CMs displayed ventricular characteristics. Via CRISPR/Cas9-mediated knockout, we demonstrated that COUP-TFII is not required atrial specification in hPSCs.

overall_design: In total we analyzed 12 samples. 5 G+/M+ hPSC-derived atrial CMs plus 5 G+/M- ventricular samples (sample 1-10) and 2 replicates of G-/M+ non-CMs (sample 11-12). Samples with different COUP-TFII genotype were analyzed: Wildtype COUP-TFII (sample 5 and 6), heterozygotes (samples 7-12) and complete knockout (samples 1-4). Samples 1 and 2 or 3 and 4 originate from two independent hPSC lines. Samples 7 and 10, 8 and 11, as well as 11 and 12 are replicates.

first: Verena

last: Schwach


title: DNA methylome modifications and subtyping in ME/CFS

first: Patrick

last: McGowan

address: 1265 Military Trail

department: Biological Sciences

institute: University of Toronto Scarborough

summary:
Examination of DNA methylome patterns for potential subtypes in a larger cohort of ME/CFS samples using the Illumina Infinium HumanMethylation450 Beadchip Array
Bisulfite-converted DNA from 25 samples were hybridised onto the Illumina Infinium HumanMethylation450 Beadchip Array

first: Wilfred

middle: C

last: de Vega

first: Suzanne

last: Vernon

middle: O


title: Identification of micro-RNA expression profile related to recurrence in women with ESMO low-risk endometrial cancer

city: Paris

first: Céline

last: Méhats

address: 24 rue du Faubourg St jacques

institute: Inserm

summary:
The aim of this study was to evaluate whether micro-RNA signature in tumor tissues from low-risk Endometrial Cancer women can be correlated with the occurrence of recurrences
MicroRNA expression was assessed by chip analysis in 7 formalin-fixed paraffin-embedded (FFPE) LREC primary tumors from women whose follow up showed recurrences (R+) and in 14 FFPE LREC primary tumors from women whose follow up did not show any recurrence (R-), matched for grade and age.

overall_design: Total RNA was extracted using the miRNeasy FFPE Kit (Qiagen, Courtaboeuf, France), according to the manufacturer’s instructions. Microarray analysis was conducted on 21 distinct specimens: 7 specimens from R+ women, each one of them matched with 2 specimens from R- women. Microarray hybridization on Micro-RNA 4.0 chips (Affymetrix) was conducted at the genomic platform of the Institut Cochin, Paris.

first: Geoffroy

last: Canlorbe

first: Sébastien

last: Jacques


title: Exhaustive profiling in Arabidopsis reveals abundant polysome-associated 24-nt small RNAs including hitherto undescribed AGO5-associated pseudogene-derived siRNAs (psiRNAs) [RNA]

city: Zurich

first: Antonin

last: Marchais

address: Universitatstrasse 2

department: Department of Biology

country: Switzerland

institute: ETHZ

summary: The present study was primarily aimed at expanding the scope of the previous analyses, which focused largely on AGO1-miRNA interactions with total polysomes and membrane-bound polysomes (MBPs), respectively. Our larger aim was to comprehensively analyze which, among the multiple AGO effector proteins and the numerous cellular sRNA classes of Arabidopsis, interact with the translational machinery.

overall_design: 4 samples examined: duplicates of polysomal and monosomal ribosomal profiling in inflorescences.

first: Clément

last: Chevalier

first: Olivier

last: Voinnet


title: Combinatorial Reprogramming of Estrogen Signaling  by the Nuclear Receptor Family 3C

city: Chicago

first: Hari

last: Singhal

state: IL

address: 929 E 57th St

department: Ben May Department for Cancer Research

institute: University of Chicago

summary: Estrogen receptor (ER) positive breast cancers exist in a complex environment of steroid hormones and their cognate receptors. Receptors for estrogens, progestogens (PR), androgens (AR), glucocorticoids (GR) and mineralocorticoids (MR) are variably expressed in these hormone- sensitive breast cancers. Clinical translation of crosstalk among these receptors has been limited by an incomplete understanding of ER reprogramming by PR, GR, AR and MR (NR3C receptors). This study reports that each of the NR3C receptors reprograms ER chromatin binding to sites enriched for NR3C binding motifs and that hormonal co-treatment increases the likelihood of ER binding to estrogen response elements. A major overlap is observed among ER conserved sites, but not among ER sites that are lost or gained due to reprogramming by each of the NR3C receptors. This stability of ER genomic binding is reflected in the resulting transcriptomes, as there is significant overlap among genes whose expression is unaltered in response to joint hormonal interventions but not among genes whose expression is enhanced or opposed by an individual NR3C receptor. The addition of NR3C ligands can enhance or oppose estrogen-mediated induction and repression of gene transcription, resulting in net agonism or antagonism of ER-mediated actions at gene loci and of cellular pathways of interest. In addition to differential modulation of chromatin binding, differences in cofactor associations for ER, PR and GR likely contribute to the divergent functions of these receptors in breast cancer. Among the NR3C receptors, MR activation differentially reprograms ER chromatin binding and, in contrast to ligands for PR, GR or AR, the MR ligand aldosterone does not inhibit estrogen-induced cell proliferation or potentiate the anti-proliferative effect of tamoxifen in ER+ MCF7 cells. PR, GR, AR and MR may be functionally relevant in ER+ breast cancer because higher expression of these NR3C receptors; or genes whose estrogen-regulated expression is altered by each of these receptors is significantly associated with better overall and relapse-free survival. In summary, this study highlights the diverse yet overlapping activities of NR3C receptors in reprogramming ER signaling.

overall_design: Model systems were deprived of steroids by culturing them in phenol red free RPMI 1640 media that is supplemented with 10% charcoal-stripped fetal bovine serum and 1% penicillin/streptomycin. Subsequently, these steroid-deprived models were treated with either vehicle, 10 nM estradiol, 10 nM of NR3C ligand (Progesterone, Dexamethasone, DHT or Aldosterone) or 10 nM of both estradiol and NR3C ligand for the time duration mentioned in the paper. Subsequently anti-ER ChIP-seq and polyA-selected mRNA-seq was performed on the treated cells.

first: Geoffrey

last: Greene


title: Exhaustive profiling in Arabidopsis reveals abundant polysome-associated 24-nt small RNAs including hitherto undescribed AGO5-associated pseudogene-derived siRNAs (psiRNAs)

type: Non-coding RNA profiling by high throughput sequencing


title: Exhaustive profiling in Arabidopsis reveals abundant polysome-associated 24-nt small RNAs including hitherto undescribed AGO5-associated pseudogene-derived siRNAs (psiRNAs) [sRNA]

summary: The present study was primarily aimed at expanding the scope of the previous analyses, which focused largely on AGO1-miRNA interactions with total polysomes and MBPs, respectively. Our larger aim was to comprehensively analyze which, among the multiple AGO effector proteins and the numerous cellular sRNA classes of Arabidopsis, interact with the translational machinery.

overall_design: 6 samples examined: translating-ribosome affinity immunopurification (TRAP) and duplicates of polysomal and monosomal ribosomal profiling in inflorescences, and small RNA-seq in seedlings.


title: Ginsenoside Rg3 epigenetically regulates cell-mediated immune pathway to inhibit proliferation of the MCF-7 breast cancer cell

city: goyang

first: seungyeon

last: lee

address: dongguk-ro 32

department: life science

institute: dongguk unversity

summary: Genome wide DNA methylation profiling of estrogene receptor postive breast cancer cell line MCF-7, treating Ginsoenoside Rg3. The Illumina Infinium Human Methylation EPIC v1.0 B2 Bead chip was used to obtain DNA methylation profiles across approximately 850,000 CpGs. This profiling indicates that Ginsenoside Rg3 induces epigenetic and cellular changes.

overall_design: Genomic DNA obtained from  MCF-7 treated Ginsenoside Rg3

first: Seungyeon

last: Lee

first: Sunjung

last: Kim


title: Reduced diploidization and survival improvement of semi-cloned mice produced from androgenetic haploid embryonic stem cells

city: Shanghai

first: Xiaobai

last: Zhang

address: 1239 Siping Road

institute: Tongji University

summary: We found that the overall DNA methylation and hydroxymethylation in AG-haESCs are extremely low, and the downregulation of both de novo methyltransferase Dnmt3b and methylation maintenance enzyme Dnmt1was discovered responsible for this DNA hypomethylation. Further, our study discovered that the correction of DNA methylation can greatly reduce the incidence of diploidization and further improve the survival of semi-cloned mice produced from AG-haESCs.

overall_design:
Gene expression profiles by RNA-Seq were analyzed to investigate transcriptional changes between AG-haESCs and other samples.

Transcriptional profiling of 2i cultured ESC XX.

first: Wenteng

last: He

first: Zeyu

last: Xiong

first: Yalin

first: Weisheng

last: Zheng

first: Xinjie

last: Hu

first: Mo

last: Chen

first: Hua

last: Huang

first: Lei

last: Yang

first: Xiaochen

last: Kou

first: Yanhong

last: Zhao

first: Jiqing

last: Yin

first: Qianshu

last: Zhu

first: Yonghua

last: Jiang

first: Linfeng

first: Ruimin

last: Xu

first: Yinglu

last: Tang

first: Chong

last: Li

first: Hong

last: Wang

first: Zhiming

last: Han

first: Cizhong

first: Jiayu

first: Shaorong

last: Gao


title: Microarray expression profiling of dysregulated mRNAs between ccRCC tumor tissues and corresponding adjacent normal tissues

city: Beijing

first: yijun

last: qi

address: You an men,Xi tou tiao

department: Biochemistry

institute: Capital Medical university

summary: Renal cell carcinoma (RCC) is the most common and lethal cancer of the adult kidney. Its incidence is increasing and outcomes remain poor. Accurate discrimination of RCC patients with poor prognosis was very important for the appropriate and effective patient management. ccRCC originated from dysregulation of different gene expression. To screen novel prognosis markers, a dysregulated mRNA expression profile was identified by microarray in some pairs of different stages ccRCC.

overall_design: Gene expression of ccRCC tissues in different stages was compared with gene expression of corresponding adjacent normal tissues.

first: Zhiqiang

last: Peng

first: Junqi

last: He

first: Junfang


title: Alteration in gene expression of HUVECs infected by HTNV

city: Xi'an

first: Xuyang

last: Zheng

state: Shaanxi

address: No. 569 Xinsi Road, Baqiao District

department: Department of Infectious Diseases

institute: The Fourth Military Medical University

summary: Hantaan virus (HTNV) causes hemorrhagic fever with renal syndrome (HFRS). Previous studies have identified interferon stimulate genes (ISGs) play important roles in viral infection. However, the role of ISGs in HTNV infection is unclear. In this study, we observed the alteration of gene expression in HUVECs infected with HTNV compared with mock infected control and found considerable changes in mRNA and lncRNA profiles.

overall_design: HUVEC cells (ScienCell Research Laboratories, Carlsbad, CA, USA) were grown in ECM BulletKit (ScienCell Research Laboratories, Carlsbad, CA, USA) in a 5% CO2 incubator. Cells were used within passage 10 after primary culture. HTNV strain 76-118 was cultured in Vero E6 cells (ATCC Cat# CRL-1586) in our laboratory and titrated using an immunofluorescence staining assay for HTNV nucleocapsid protein (NP) as previously described. HUVECs were mock infected or infected by incubation with HTNV (moi=1) at 37 ℃ for 60 mins. Subsequently, the virus solution was removed and fresh medium added to the cell culture. 48 hours after infection, total RNA from cells were extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and were sent for RNA microarray. Three independent experiments were conducted.

first: Peiyu

last: Bian


title: 4 or 14-Day Food Restriction Study in Sprague Dawley Rats

city: Thousand Oaks

first: Scott

last: Taylor

address: One Amgen Center Drive

institute: Amgen Inc.

summary: This study is designed to determine effects on parameters routinely measured in toxicology studies

overall_design: Rats historically have been used in safety evaluation/toxicity studies. Animals will be male Sprage Dawley rats, approximately 8-10 weeks of age at initiation of treatment and weigh approximately 250-350 grams. Powdered feed will be provided either ad libitum, reduced 15%, reduced 30% or reduced 60% according to study group. All animals will be fasted overnight prior to necropsy.

first: Christine

last: Karbowski

first: Yudong

first: Hisham

last: Hamadeh


title: Progesterone Receptor Isoforms, Agonists and Antagonists Differentially  Reprogram Estrogen Signaling.

first: Hari

last: Singhal

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

overall_design: Refer to individual Series


title: Comparative Epigenomics Reveals Hierarchical Regulation of Non-CG Methylation in Arabidopsis

city: Cambridge

first: C. Jake

last: Harris

address: Downing Street

department: Department of Plant Sciences

institute: University of Cambridge

summary: Background: Genome-wide characterization by next-generation sequencing has greatly improved our understanding of the “landscape” of epigenetic modifications. Since 2008, whole-genome bisulfite sequencing (WGBS) has become the gold standard for DNA methylation analysis and a tremendous amount of WGBS data has been generated by the research community. However, methods for the systematic comparison of DNA methylation profiles to identify novel regulatory mechanisms have yet to be established.Results: Here we developed a standardized pipeline and re-analyzed over three hundred publicly available Arabidopsis WGBS libraries from various mutant backgrounds, tissue types, and stress treatments. In total this collection included more than 3,700 Gb (Giga base-pairs) of sequencing data and a large number of wild-type controls. This enabled us to identify “high-confidence Differentially Methylated Regions” (hcDMRs) with high reliability by comparing each ‘test’ library to each of the 54 controls. We adopted two statistical methods, Statistical Measurements on Overlapping of DMRs (S-MOD) followed by Quantitative Measurements on Overlapping of DMRs (Q-MOD), to compare and cluster libraries based on their impacts on DNA methylation. In addition to confirming existing relationships using this unbiased approach, we revealed novel connections between methylation pathways. For instance, MET1 and CMT3 were found to be required for maintenance of asymmetric CHH methylation at non-overlapping regions of CMT2 targeted heterochromatin.Conclusions: Our comparative methylome approach has established a framework for extracting biological insights via large-scale comparison of methylomes, and can also be adopted for other omics datasets. Together, the results demonstrate the effectiveness of data-driven, hypothesis-generating epigenetic research.

overall_design: this dataset includes 7 RNA-seq and 1 BS-seq libraries

first: C

middle: J


title: Expression data from rice roots treated with NH4NO3

city: Taipei

first: Ming-Hsiun

last: Hsieh

address: 128 Academia Road, Section 2

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

summary:
We used GeneChip Rice Genome Array (Affymetrix, Santa Clara, CA, USA) to identify genes that were rapidly induced by NH4NO3 in rice roots.
Transcriptomic analysis of rice roots revealed that the expression of at least 158 genes involved in metabolism, transport, signal transduction, and stress responses was rapidly induced by NH4NO3 within 30 minutes.

overall_design: Total RNA from –N and NH4NO3-treated roots (1.43 mM NH4NO3, 30 min) was extracted using a phenol extraction protocol. RNA samples from two biological repeats were sent to the Affymetrix Gene Expression Service Lab at Academia Sinica, Taipei, Taiwan (http://ipmb.sinica.edu.tw/affy/) for target preparation, and hybridization to the GeneChip Rice Genome Array.

first: Chia-Cheng

last: Kan

first: Tsui-Yun

last: Chung


title: Epigenomic analysis of Atrx deficiency in murine glioma cells of orgin

first: Jason

last: Huse


title: Identification of specifically activated angiogenic molecules in HMGB-1-induced angiogenesis

status: Public on Dec 29 2017

city: Seoul

first: YUJIN

last: KWON

address: 50 Yonsei-fo, Seodaemun-gu

institute: YONSEI UNIVERSITY

summary: High-mobility group box-1 (HMGB-1), a nonhistone chromosomal protein, is expressed in almost all types of cells with nucleus, and dysregulation of its expression correlates with pathological conditions such as inflammatory diseases, ischemia and cancers. Some of these conditions accompany abnormal angiogenesis induced by HMGB-1 mediated activation of downstream signaling pathways. So far, the underlying mechanism by which HMGB-1 induces angiogenesis remains largely unknown. In this study, we performed time-dependent gene expression microarray in endothelial cells (ECs) after HMGB-1 or VEGF treatment. By pathway analysis using each gene set up-regulated by HMGB-1 or VEGF, we found that most of HMGB-1 induced angiogenic pathways were also commonly activated by VEGF, while activation time and gene sets belonging to the pathways were different. In addition, HMGB-1 up-regulated some VEGFR signaling related conventional angiogenic factors including EGR1 and importantly, novel angiogenic factors such as ABL2, CEACAM1, KIT and VIPR1 which have been reported to independently promote angiogenesis in physiological and pathological conditions. Our gene expression profiling suggests that HMGB-1 is capable of independently inducing angiogenesis through activation of HMGB-1 specific angiogenic factors and also functions as an accelerator for VEGF mediated conventional angiogenesis according to physiological and pathological condition.

overall_design: Primary human umbilical vein endothelial cells (HUVECs) were treated with recombinant HMGB-1 at 1 µg/mL and recombinant VEGF at 50 ng/mL for 20 minutes, 45 minutes, 2 hours, 6 hours, or 12 hours.

first: Won-Kyu

last: Kim

first: Yujin

last: Kwon

first: Hoguen


title: Expression profiling in breast cancer brain metastases compared to breast cancers and primary brain tumors

city: Jeddah

first: Hans-Juergen

last: Schulten

department: Center of Excellence in Genomic Medicine Research

country: Saudi Arabia

institute: King Abdulaziz University

summary: Experiment: Expression profiling in breast cancer brain metastases (BC) compared to breast cancers (BC) and primary brain tumors (prBT). The objectives are to identify expression profiles that are specific to BCBM in order to identify new molecular biomarkers. The characterization of the BCBM samples included adjacent genetic techniques.

overall_design: We extracted RNA from BCBM and prBT. RNA samples were processed and hybridized to Affymetrix microarrays. Microarray expression samples from BC were used from one of our previous study. Bioinformatics tools and adjacent techniques were employed to display BCBM specific expression profiles and other genetic characteristics.

first: Sajjad

last: Karim


title: Greater transiency in modulation of gene expression is the predominant difference between the actions of bryostatin 1 and phorbol ester in LNCaP and U937 cells [set 1]

status: Public on Dec 30 2017

city: Bethesda

first: Noemi

last: Kedei

state: MD

address: 37 Convent drive 4048

department: NCI

institute: NIH

summary: Bryostatin 1, like the phorbol ester PMA, activates protein kinase C (PKC) in vitro but paradoxically blocks many phorbol ester responses in vivo.  Results with a limited panel of genes suggested that transiency of action was an important mechanism contributing to this differential cellular response.  Here, we examined global gene expression in LNCaP and U937 cell lines to probe the extent to which transiency of action captures the difference in response. While different genes showed different patterns of relative response, the overall pattern was reflective of an initial PMA-like response to bryostatin 1 followed by variable transiency of the continued response. This conclusion was further strengthened by detailed time course measurements by qPCR of selected genes. Merle 23, a bryostatin derivative with biological behavior intermediate between that of bryostatin 1 and PMA, was likewise intermediate for transiency of action.  Both the LNCaP and U937 cell lines behaved similarly, but the extent of transiency in response to bryostatin 1 was greater in the LNCaP cells.

overall_design: Forty samples were  analyzed in the study; Univariate one-way analysis of variance with planned contrasts (Partek® Genomics Suite 6.5) was used to identify significant changes in gene expression due to bryostatin 1, PMA, and merle 23 treatments in LNCaP and U937 cells. The ANOVA p-values were converted to false discovery adjusted q-values with the method of Storey [Storey 2002] implemented in the R package qvalue [R core team 2013, Dabney and Storey]

first: Blumberg

last: Peter

first: Kedei

last: Noemi

first: Michalowski

last: Aleksandra


title: Greater transiency in modulation of gene expression is the predominant difference between the actions of bryostatin 1 and phorbol ester in LNCaP and U937 cells [set 2]

overall_design: Forty seven samples were  analyzed in the study; Univariate one-way analysis of variance with planned contrasts (Partek® Genomics Suite 6.5) was used to identify significant changes in gene expression due to bryostatin 1 and PMA 1-hour and 6-hour treatments in LNCaP and U937 cells. The ANOVA p-values were converted to false discovery adjusted q-values with the method of Storey [Storey 2002] implemented in the R package qvalue [R core team 2013, Dabney and Storey]. Gene co-expression network was built with the R package WGCNA  (Langfelder and Horvath, 2012).


title: Greater transiency in modulation of gene expression is the predominant difference between the actions of bryostatin 1 and phorbol ester in LNCaP and U937 cells


title: Asymmetrical changes of gene expression, small RNAs and chromatin in two resynthesized wheat allotetraploids

city: Nanjing

first: Wu

last: Jiao

address: 1 Weigang Road

institute: Nanjing Agricultural University

summary: Polyploidy occurs in some animals and all flowering plants including important crops such as wheat. The consequences of polyploidy on crops remain elusive partly because their progenitors are unknown. Using two resynthesized wheat allotetraploids SSAA and AADD with known diploid progenitors, we analyzed mRNA and small RNA transcriptomes in the endosperm, compared transcriptomes between endosperm and root in AADD, and examined chromatin changes in the allotetraploids. In the endosperm, there were more nonadditively expressed genes in SSAA than in AADD. In AADD, nonadditively expressed genes were developmentally regulated, and the majority (62-70%) were repressed. The repressed genes in AADD included a group of histone methyltransferase gene homologs, which correlated with reduced histone H3K9me2 levels and activation of various transposable elements in AADD. In SSAA, there was a tendency of expression dominance of S over A homoeologs, but the histone methyltransferase gene homologs were additively expressed, correlating with insignificant changes in histone H3K9me2 levels. Moreover, more 24-nt small inferring RNAs (siRNAs) in the A subgenome were disrupted in AADD than in SSAA, which were associated with expression changes of siRNA-associated genes. Our results indicate that asymmetrical changes in siRNAs, chromatin modifications, transposons, and gene expression coincide with unstable AADD genomes and stable SSAA genomes, which could help explain evolutionary trajectories of wheat allotetraploids formed by different progenitors.

sample_organism:
Aegilops longissima
Triticum urartu
Aegilops tauschii
Triticum urartu x Aegilops tauschii
Aegilops longissima x Triticum urartu

overall_design:
We have submitted RNA-seq and small RNA-seq libraries of the endosperm of two synthetic wheats SSAA and AADD, and their diploid progenitors, RNA-seq libraries of the seedling root of AADD and its progenitors AA and DD.
Tetraploid AT2 (AADD) was resynthesized by pollinating T. urartu (AA, accession TMU38) with pollen of Ae. tauschii (DD, accession TQ27), while TLTU (SSAA) was derived from the pollination of Ae. longissima (SS, accession TL05) with pollen of T. urartu (AA, accession TMU06).

first: Jingya

last: Yuan

first: Shan

last: Jiang

first: Yanfeng

last: Liu

first: Lili

last: Wang

first: Mingming

first: Dewei

last: Zheng

first: Wenxue

last: Ye

first: Xiue

first: Z

last: Chen


title: Plasmodium falciparum association study of decreased piperaquine sensitivity

status: Public on Dec 28 2017

city: Baltimore

first: Shannon

last: Takala-Harrison

address: 685 W Baltimore St

department: Division of Malaria Research

institute: Institute for Global Health, University of Maryland School of Medicine

type: Genome variation profiling by genome tiling array

summary:
A genome wide association study (GWAS) testing association of parasite genotypes with clinically decreased piperaquine sensitivity phenotype
Submission of genotypes from all microarray genotyped samples

overall_design:
Genotyped 183 Plasmodium falciparum isolates from different sites in Cambodia and Thailand
---------------------------------------------
The authors state "We do not have permission to release the clinical phenotype data for these samples."

first: Sonia

last: Agrawal


title: Gene expression in human (h)T-ALL isolated from NSG mice as a function of the bone marrow microenvironment

first: Franck

last: Letourneur

address: 22 rue mechain

institute: INSERM

summary:
Comparative expression between hT-ALL cells isolated from NSG mouse thorax vertebrae (adipocyte poor) bone marrow and from tail vetretbrae (adipocyte rich) bone marrow
We used microarrays to understand the global program of gene expression underlying hT-ALL behaviour in two different bone marrow sites

overall_design: 3 hT-ALL were used in this study. For each sample we xenografted immunodeficient mice. When bone marrow sampling was more than 90 % of chimerism, mice were sacrified and we recovered human leukemic cells from thoracic vertebrae and from tail vertebrae. Leukemic cells were purified by immunomagnetic selection then RNA were extracted.

first: Julien

last: Calvo

first: Xavier

last: Cahu

first: Francoise

last: Pflumio


title: A bright side of Zika: potent and selective oncolytic properties against aggressive human CNS embryonal tumors

status: Public on Dec 25 2017

city: São Paulo

first: Carolini

last: Kaid Dávila

state: SP

address: Rua Corinto, 512

department: Department of Genetics

institute: Instituto de Biociências - USP

summary: Zika virus (ZIKV) is largely known for causing brain abnormalities due to its ability to infect neural progenitor stem cells (NPC) during early development. Here we show that ZIKV is also capable of infecting and destroying stem-like cancer cells from aggressive human embryonal tumors of the central nervous system (CNS). When evaluating the oncolytic properties of Brazilian Zika virus strain (ZIKVBR) against human breast, prostate, colorectal and embryonal CNS tumor cell lines, a selective infection of CNS tumor cells, followed by a massive necrotic tumor cell death, was verified. Notably, ZIKVBR was more efficient in destroying CNS tumorspheres than normal stem cell neurospheres. A single intracerebroventricular injection of ZIKVBR in BALB/c nude mice bearing orthotopic human embryonal CNS tumor xenografts resulted in a significantly longer survival, reduced tumor burden, fewer metastasis and complete remission in some animals. Tumor cells closely resembling neural stem cells at the molecular level were more susceptible to ZIKVBR oncolytic effects. Altogether, these preclinical findings indicate that ZIKV could be an efficient oncolytic agent to treat aggressive forms of embryonal CNS tumors. Considering the poor effectiveness and severe side effects of available treatments for these tumors and that most ZIKV infections are asymptomatic, our findings open new avenues for novel therapies.

overall_design: Cell lines Daoy, USP13-MED, USP7-ATRT, hiPS, NPC and Neuron were compared against normal human cerebellum.

last: Kaid


title: Telomere repeats induce domains of H3K27 methylation in Neurospora

city: Eugene

first: Eric

last: Selker

state: Oregon

address: 1370 Franklin Blvd.

institute: University of Oregon

type: Genome variation profiling by high throughput sequencing

summary: Development in higher organisms requires selective gene silencing, directed in part by di-/tri-methylation of lysine 27 on histone H3 (H3K27me2/3). Knowledge of the cues that control formation of such repressive Polycomb domains is extremely limited. We exploited natural and engineered chromosomal rearrangements in the fungus Neurospora crassa to elucidate the control of H3K27me2/3. Analyses of H3K27me2/3 in strains bearing chromosomal rearrangements revealed both position-dependent and position-independent facultative heterochromatin. We found that proximity to chromosome ends is necessary to maintain, and sufficient to induce, transcriptionally repressive, subtelomeric H3K27me2/3. We ascertained that such telomere-proximal facultative heterochromatin requires native telomere repeats and found that a short array of ectopic telomere repeats, (TTAGGG)17, can induce a large domain (~225 kb) of H3K27me2/3. This provides an example of a cis-acting sequence that directs H3K27 methylation. Our findings provide new insight into the relationship between genome organization and control of heterochromatin formation.

overall_design:
RNA-seq: We analyzed the effects of chromosomal translocations on gene expression changes in Neurospora crassa by poly-A+ mRNA-sequencing performed in duplicate. A wild type strain (N3752) serves as the reference strain (deposited in GSE82222).
ChIP-seq: We analyzed the effects of chromosomal rearrangements and transgenic strains on the distribution of histone H3 lysine 27 methylation (H3K27me2/3) in Neurospora crassa by chromatin immunoprecipitation. Strains were grown, crosslinked, lysed, modified nucleosomes were immunopurified, and associated DNA was sequenced.
Whole-genome-seq: Genomic DNA from chromosomal translocation strains were sequenced and computationally analyzed with LUMPY to identify possible chromosome breakpoints.

first: Kirsty

last: Jamieson

first: Kevin

last: McNaught

first: Neena

middle: A

last: Leggett

first: Tereza

last: Ormsby

first: Shinji

last: Honda

middle: U


title: Adult hepatocytes direct liver organogenesis through non-parenchymal cell recruitment in the kidney

city: Chiba

first: Rie

last: Utoh

state: Chiba

address: 1-33 Yayoi-cho, Inage-ku

department: Department of Applied Chemistry and Biotechnology

country: Japan

institute: Chiba University

summary:
Background & Aims: Since the first account of the myth of Prometheus, the amazing regenerative capacity of the liver has fascinated researchers due to its enormous medical potential. Liver regeneration is promoted by multiple types of liver cells, including hepatocytes and liver non-parenchymal cells (NPCs), through the complex intercellular signaling. However, the liver organogenetic mechanism, especially the role of adult hepatocytes at ectopic sites, remains unknown. In this study, we demonstrate that hepatocytes alone spurred liver organogenesis to form an organ-sized complex 3D liver that exhibited native liver architecture and functions in the kidneys of mice.
Methods: Isolated hepatocytes were transplanted under the kidney capsule of monocrotaline (MCT) and partial hepatectomy (PHx)-treated mice. To determine the origin of NPCs in neo-livers, hepatocytes were transplanted into MCT/PHx-treated green fluorescent protein (GFP) transgenic mice or wild-type mice transplanted with bone marrow (BM) cells isolated from GFP mice.
Results: Hepatocytes engrafted at the subrenal space of mice underwent continuous growth in response to a chronic hepatic injury in the native liver. More than 1.5 yrs later, whole organ-sized liver tissues having a greater mass than those of the injured native liver had formed. Most remarkably, we revealed that at least three types of NPCs with similar phenotypic features to the liver NPCs were recruited from the host tissues including BM. The neo-livers in the kidney exhibited liver-specific functions and architectures, including sinusoidal vascular systems, zonal heterogeneity, and emergence of bile duct cells. Furthermore, the neo-livers successfully rescued the mice with lethal liver injury.
Conclusion: Our data clearly showed that adult hepatocytes play a leading role as organizer cells in liver organogenesis at ectopic sites via NPC recruitment.

overall_design: Donor hepatocytes were isolated from FVB/N-human α1-antitrypsin (hA1AT) transgenic (Tg) mice (8−20 weeks old).  Wild-type FVB/N mice (7−9 weeks old) were used to develop a chronic hepatic injury model; these mice served as the recipients for hepatocyte donation.  The recipient mice received two doses of monocrotaline (MCT) (70 mg/kg) into the intraperitoneal space at intervals of 2 weeks.  Two weeks after the last injection of MCT, 1 × 10(6) isolated hepatocytes from FVB/N-hA1AT Tg mice were transplanted under the kidney capsule of the FVB/N mice.  The total RNA was isolated from the recipient injured liver and kidney tissues, ectopic neo-livers microdissected from the kidneys on days 250−300, and the livers of normal mice (20-week-old).

first: Junji

last: Komori

first: Hiroyuki

last: Kuge

first: Kohei

last: Tatsumi

first: Masumi

last: Yamada

last: Hirohashi

first: Masahiro

last: Tsutsumi

first: Toshihiro

last: Amanuma

first: Akira

last: Yoshioka

first: Yoshiyuki

last: Nakajima

first: Kenjiro

last: Wake

first: Teruo

last: Okano

last: Lagasse

first: Kazuo

last: Ohashi


title: Transcripotome analysis of different locations of hair follicles (bulb, bulge) in androgenetic alopecia

city: GuangZhou

first: Qian

last: Qu

address: 1838 North Guangzhou AV

institute: Nanfang Hospital of Southern Medical University

summary: To fully interrogate location-specific variations of the hair follicle in AGA and normal persons, we sought to perform a thorough and comprehensive transcripotome profiling of different locations of hair follicles (bulb  portions, bulge  portions) in balding and non-balding areas of AGA, with normal comparisons.

overall_design: Hair follicles harvested by follicular unit extraction came respectively from vertex (balding) and occipital (nonbalding) areas from 12 patients and occipital areas from 12 control subjects. Using microdissection, hair follicle was separated into two parts(bulb and bulge portion) for further study.

first: Zhi-Qi

last: Hu

first: Yong

last: Miao


title: Effects of PSF knockdown in castration-resistant prostate cancer cells

status: Public on Dec 24 2017

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

institute: Tokyo Metropolitan Institute of Gerontology

summary:
Prostate cancer is the most common cancer in men and AR downstream signalings promote prostate cancer cell proliferation. Androgen-deprivation therapy is the first-line treatment strategy for advanced prostate cancer. However, many tumors develop to castration-resistant prostate cancer (CRPC) and relapse. Thus, analyzing key factors for development of  CRPC is important. We found PSF functions as RNA binding protein and transcription factor to promote castration-resistant tumor growth. High expression of PSF in metastatic prostate cancer tissue indicates the clinical relevance.
In order to investigate the PSF function in CRPC cells, we performed gene expression in CRPC model cells derived from AR-positive prostate cancer cell lines after siPSF treatment.

overall_design: Observation of gene expression changes after treatment with siRNAs targeting PSF wiith microarray.

first: K


title: Drosophila melanogaster developmental transcriptome of whole body thorugh embryogenesis

city: Okazaki

first: Shuji

last: Shigenobu

state: Aichi

address: Nishigonaka 38, Myodaiji

institute: National Institute for Basic Biology

summary: To understand dynamics of embryonic transcriptome in a high resolution, whole bodies of embryos were collected at 12 time points during the embryogenesis and were subjected to microanalyses. These data were originally obtained aiming to compare to our other microarray data [GSE83460] of PGCs (primordial germ cells; pole cells).

overall_design: RNA from whole body collected at 12 different time points were hybridized to a microrray after Cy3/Cy5 labeling.  A pooled total RNA purified from whole embryos at early to late stage was used as a common reference in all hybridizations.

first: Satoru

last: Kobayashi

first: Kayo

last: Arita


title: A role of Polycomb in the maintenance of hypomethylation for DNA methylation valley

first: Yuanyuan

last: Li

address: Tsinghua University, Qinghua Yuan, Haidian District

institute: Tsinghua Universary

summary: DNA methylation valleys (DMVs) are large loci that are devoid of DNA methylation in the genome. We show that DMVs are hypomethylated at most stages in development and are highly conserved across vertebrates. Importantly, DMVs are hotspots of regulatory regions for key developmental regulator genes. 4C-seq analyses indicate that DMVs are insulated and self-interacting domains. By analyzing a panel of DNA methylomes for the mouse tissues, we have identified a subset of DMVs that are dynamically methylated. These DMVs are strongly enriched by Polycomb and their histone substrate H3K27me3 when the associated genes are silenced, and surprisingly show elevated DNA methylation upon gene activation. In support of a role of Polycomb in DMV hypomethylation, we observed aberrant methylation in DMVs in mESCs deficient for Eed.  Finally, we showed that Polycomb regulates hypomethylation of DMVs likely through TET proteins.

overall_design: Through a global survey DMVs in different species and different developmental stages , we validated DMVs play important role in gene regulation and development. Further studying different types of DMVs in vivo, Polycomb-target DMVs are more enriched TFs. Next, we continue to finding out what roles Polycomb plays in maintenance hypomethylation of DMVs and how it regulates DNA methylation in DMVs.

first: Hui

last: Zheng

first: Wei

last: Xie


title: GFZF, a glutathione S-transferase protein implicated in cell cycle regulation and hybrid inviability, is a transcriptional co-activator

status: Public on Dec 22 2017

city: University Park

first: David

last: Gilmour

state: Pennsylvania

address: 465 North Frear

institute: Penn State University

summary: The core promoter of protein-encoding genes plays a central role in regulating transcription. M1BP is a transcriptional activator that associates with a core promoter element known as Motif 1 that resides at thousand of genes in Drosophila. To gain insight into how M1BP functions, we identified an interacting protein called GFZF. GFZF had been previously identified in genetic screens for factors involved in maintenance of hybrid inviability, the G2-M DNA damage checkpoint, and RAS/MAPK signaling but its contribution to these processes was unknown. Previous evidence indicated that GFZF resides in the cytoplasm. Here, we show that GFZF resides in the nucleus and functions as a transcriptional co-activator. In addition, we show that GFZF is a glutathione S-transferase(GST). Thus, GFZF is the first transcriptional co-activator with intrinsic GST activity, and its identification as a transcriptional co-activator provides an explanation for its role in numerous biological processes.

overall_design: 2 M1BP, 3 GFZF, 3 controls (this includes 2 Preimmune, 1 NoIgG)

first: Douglas

middle: G

last: Baumann

first: Mu-Shui

last: Dai

first: Hua

last: Lu


title: Spatial reconstruction of immune niches by combining photoactivatable reporter and single-cell RNA-seq

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: Cellular function is strongly dependent on surrounding cells and environmental factors. Current technologies are limited in characterizing the spatial location and unique gene-programs of cells in less structured and dynamic niches. Here we developed a method (NICHE-seq) that combines photoactivatable fluorescent reporters, two-photon microscopy and single-cell RNA-seq to infer the cellular and molecular composition of niches. We applied NICHE-seq to examine the high-order assembly of immune cell networks. NICHE-seq is highly reproducible in spatial tissue reconstruction, enabling identification of rare niche-specific immune subpopulations and unique gene-programs, including natural killer cells within infected B cell follicles and distinct myeloid states in the marginal zone. This study establishes NICHE-seq as a broadly applicable method for elucidating high-order spatial organization of cell types and their molecular pathways.

overall_design: Transcriptional profiling of single cells from the specific immune niches in the lymph node and spleen, generated from deep sequencing of tens of thousands of cells, sequenced in several batches on illumina Nextseq500

first: Ziv

last: Shulman

first: Matteo

last: Iannacone

first: Chiara

last: Medaglia

first: Amir

last: Giladi

first: Liat

last: Stoler Barak

first: Marco

last: De Giovanni


title: Mucositis in patients with tonsil squamous cell carcinoma: gene expression profile of oral mucosa before, during, and after radiation therapy

city: Aalborg

first: Julie

middle: Støve

last: Bødker

address: Sdr. Skovvej 15

department: Department of Heamatology

country: Denmark

institute: Aalborg University Hospital

summary:
Objectives: In patients with tonsil squamous cell cancer (TSCC), radiation-therapy (RT) induce mucositis, which is clinically challenging with limited prophylactic interventions and no predictive tests. In a pilot study set-up, we performed global gene-expression analysis on human oral mucosa tissue and blood cells to identify differential expressed genes involved in mucositis pathogenesis.
Materials and Methods: Eight patients with TSCC had consecutive buccal biopsies and blood samples taken before, after 7 days of RT, and 20 days following RT. We monitored clinical  mucositis and applied gene-expression analysis to the tissues. Single biopsies and blood tests from 9 healthy individuals served as controls (CON).
Results: In response to RT, we did not register changes in the blood cells, but we found upregulation of both apoptosis inducers and inhibitors in the mucosa: EDA2R and MDM2; and POLH, encoding a polymerase that replicates UV-damaged DNA. Six members of the histone cluster family, e.g., HIST1H3B, involved in nucleosome structure, were downregulated. Genes related to proliferation were also altered: MKI67 (downregulated), encoding Ki-67-proliferation; and KRT16 (upregulated), encoding keratin16, characteristic in early differentiated epithelial cells. None of these alterations were associated to mucositis severity. However, before treatment, LY6G6C, which encodes a surface immunoregulatory protein, was upregulated in NM compared to UM, although not significantly.
Conclusion: RT caused divergent changes in genes expression related to DNA damage and proliferation, all independently altered of mucositis severity. LY6G6C may be a potential predictive biomarker for UM following RT. Based on these result, we will design a prospective clinical validation trial, including more patients.

overall_design: Consecutive mucosa biopsies from 8 patients with tonsil squamous cell carcinoma one biopsy and blood test before radiotherapy (RT), one biopsy and blood test after 5 days of RT (2 Gy each day) and three weeks after the last exposure to RT

first: Mette

last: Marcussen

first: Mads

last: Sønderkær

first: Maria

last: Andersen

first: Søren

last: Nielsen

first: Ilse

last: Christiansen

first: Olav

last: Bergmann

first: Martin

last: Bøgsted

first: Karen

last: Dybkær

first: Mogens

last: Vyberg

first: Hans

middle: E

last: Johnsen


title: HCFC2 needed for IRF1- and IRF2-dependent Tlr3 transcription, and for survival during viral infections

status: Public on Dec 23 2017

city: Dallas

first: Gokhul

middle: Krishna

last: Kilaru

state: TEXAS

address: 6000 Harry Hines Boulevard

department: Department of Neuroscience

institute: University of Texas Southwestern Medical Center

summary: IRF1 and IRF2 are transcription factors for interferon stimulated genes. HCFC2 facillitates their assoication with DNA targets and maintains the proper transcitpion of target genes.

overall_design: IRF2 assoicated DNA sequences were recovered from mouse embryonic fibroblasts (MEFs), comparing cells of wildtype and Hcfc2 knockout

first: Lei

last: Sun

first: Victoria

last: Acosta-Rodríguez

first: Zhengfan

last: Jiang

first: Michael

last: Berger

first: Xin

last: Du

first: Jin

middle: H

last: Choi

first: Jianhui

last: Wang

first: Kuan-wen

first: Jennifer

last: Mohawk

first: Jiexia

last: Quan

first: Lindsay

last: Scott

first: Sara

last: Hildebrand

first: Xiaohong

last: Li

first: Miao

last: Tang

first: Xiaoming

last: Zhan

first: Anne

middle: R

last: Murray

first: Diantha

last: LaVine

first: Eva

middle: M

last: Moresco

first: Joseph

middle: S

last: Takahashi

first: Bruce

last: Beutler


title: Identification of candidate genes for generalized tonic–clonic seizures in Noda Epileptic Rat

status: Public on Dec 27 2017

city: Kyoto-shi

first: Takashi

last: Kuramoto

state: Kyoto

address: yoshida-konoe-cho,sakyo-ku

department: Graduate School of medicine

institute: Kyoto University

summary: The Noda epileptic rat (NER) exhibits generalized tonic–clonic seizures (GTCS). A genetic linkage analysis demonstrated two GTCS-associated loci, Ner1 on Chr 1 and Ner3 on Chr 5. In single-locus congenic lines, neither wild-type Ner1 nor Ner3 allele suppressed GTCS, but both wild-type alleles suppressed GTCS when they were combined in double-locus congenic lines. Global expression analysis showed that Cckbr and St5 locating within Ner1 and Phf24 locating within Ner3 were significantly　downregulated. De novo BAC sequencing detected an insertion of an endogenous retrovirus sequence in intron 2 of the Phf24 gene in the NER genome. PHF24 protein was almost absent in the NER brain. It has been known that the Phf24 gene encodes Gαi-interacting protein which is involved in GABAB receptor signaling pathway. Together, we concluded that Cckbr, St5, and Phf24 were strong candidate genes for GTCS in NER.

overall_design: NER (6 and 18 weeks of age, n=6 each) and GTCS-resistant NF-Chr1e/5d congenic (6 and 18 weeks of age, n=6 each) were used for gene expression analysis. Brain sampling was conducted under interictal conditions with no observable seizures for at least 2 h before sampling. Rats were deeply anesthetized with pentobarbital (80 mg/kg, i.p.), and brains were removed and chilled in ice-cold saline. The amygdala, cortex (Left and Right) and hippocampus were then dissected immediately and stored in RNAlater (Qiagen, Tokyo, Japan). Total RNA was isolated using ISOGEN II (Nippon Gene Co., Ltd, Tokyo, Japan). To reduce variations, RNA samples from 3 rats in each group were pooled. Two-color microarray-based gene expression analyses were conducted using SurePrint G3 Rat GE 8×60K Microarray Kit (Agilent Technologies, Santa Clara, CA, USA). Mean values with standard deviation were calculated in each probe and compared between NER and the age-matched NF-Chr1e/5d. Differences in gene expression levels were evaluated by t-test. To eliminate the Type 1 false positive errors, we interpreted that the P value less than 0.01 was significant.

first: Birger

last: Voigt

first: Satoshi

last: Nakanishi

first: Kazuhiro

last: Kitada

first: Tadashi

last: Nakamura

first: Kaori

last: Wakamatsu

first: Risa

last: Uemura

first: Miyuu

last: Tanaka

first: Mitsuru

last: Kuwamura

first: Minako

last: Yoshihara

first: Mikita

last: Suyama

first: Saki

last: Shimizu

first: Yukihiro

last: Ohno

first: Masashi

last: Sasa

first: Tadao

last: Serikawa


title: c-MYC drives a subset of high-risk pediatric neuroblastomas and is activated through mechanisms including enhancer hijacking and focal enhancer amplification (ATAC-Seq)

city: Cambridge

first: Richard

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: Childhood neuroblastoma is known for MYCN gene amplification, and here we show that in a separate subset of cases MYC-itself is activated due to enhancer hijacking from chromosomal translocations or duplications, thus defining a unique subset of high-risk disease.

overall_design: ATAC-seq in high MYC expressing neuroblastoma cell types

first: Mark

middle: W

last: Zimmerman

first: Yu

last: Liu

first: Shuning

last: He

first: Adam

middle: D

last: Durbin

first: Brian

last: Abraham

first: Nina

last: Weichert-Leahey

first: Shizhen

last: Zhu

first: Amish

last: Khan

first: Xiaoling

last: Zhang

first: Jinghui

first: A

last: Look


title: The Impact of Osteoarthritis on the Biology of the Meniscus:

city: Saint Louis

first: Bo

state: MO

address: 660 S. Euclid Avenue

department: Developmental Biology

institute: Washington University School of Medicine

summary: Objectives: To identify novel gene transcripts and biological processes in meniscus from patients with and without osteoarthritis (OA).  Methods: We used microarrays to identify gene transcripts differentially expressed in meniscus tissues obtained from OA and non-OA patients (N=12 each). Real-time PCR was performed on selected gene transcripts. Biological processes and gene networking was examined computationally. Transcriptome signatures from OA and non-OA meniscus were mapped with 37 previously published gene transcripts differentially expressed between healthy and OA cartilage to evaluate how meniscus gene expression relates to cartilage with this disease. Results: We identified 168 gene transcripts that were significantly differentially expressed between OA (75 elevated, 93 repressed) and non-OA samples (≥1.5-fold). Among these, CSN1S1, COL10A1, WIF1, SPARCL1 and DEFA3 were the most prominent gene transcript elevated in OA meniscus and POSTN, VEGFA, CEMIP, COL6A3 and SOX11 were repressed in OA meniscus. Gene transcripts elevated in OA meniscus represented response to external stimuli, cell migration and localization while those repressed in OA meniscus represented histone deacetylase activity and skeletal development. Numerous long lncRNAs were differentially expressed between the two samples. When segregated by OA-associated gene transcripts, we observed three distinct clustering patterns of OA and non-OA meniscus. Conclusions: These data provide novel evidence for a role of epigenetically regulated histone deacetylation in meniscus tears as well as expression of lncRNAs. Patient clustering based on OA-associated gene transcripts confirmed that the meniscus in OA knees exhibited OA phenotype while injured meniscus demonstrated some signs towards OA.

overall_design: We used Agilent microarrays to identify gene transcripts differentially expressed in meniscus tissues obtained from 12 patients with osteoarthritis and from 12 patients without osteoarthritis (arthroscopic partial meniscectomy.

first: Muhammad

middle: F

last: Rai

first: Linda

last: Sandell

first: Robert

last: Brophy


title: A TAD boundary at the HoxD locus segregates opposing limb regulatory landscapes and their target genes [4C-Seq]

city: Geneva

first: Eddie

last: Rodríguez-Carballo

address: 4, Boulevard d'Yvoy

department: Department of Genetics and Evolution

institute: Université de Genève

summary: The mammalian HoxD cluster is positioned at the boundary between two topologically associating domains (TADs), each of them matching a distinct, enhancer-rich regulatory landscape. During limb development, the telomeric TAD controls the early phase of Hoxd gene transcription in future forearm cells, whereas the centromeric TAD subsequently regulates transcription of more posterior Hoxd genes in presumptive digit cells. The TAD boundary is essential as it prevents the terminal Hoxd13 gene to respond to potent forearm enhancers, thereby allowing the formation of proper proximal limb structures. Here we apply chromosome conformation capture onto embryonic proximal and distal limb bud cells micro-dissected from a set of nested deletions involving part- or all- of this boundary region to try to understand the nature and function of this CTCF- and cohesin-rich DNA region. We document a progressive release of the boundary effect, allowing for inter-TAD contacts to be established, which were favoured by the functional status of the newly accessed enhancers. However, the boundary was highly resilient and only a 400kb large deletion including the whole gene cluster was eventually able to merge the two neighbouring TADs into a single structure. We propose that the whole HoxD cluster is a dynamic transcriptional boundary, showing slight variations depending on both the transcriptional status and the ontogenetic context

overall_design: 4C-seq analysis of Hoxd4, Hoxd13, Evx2, CS38, Island-4, Island-2, Cs65, LacZ 3D interactions in proximal and distal limbs from E12.5 wt or serial HoxD-deleted alleles

first: E

last: Rodriguez-Carballo

first: L

last: Lopez-Delisle

last: Beccari

first: D

last: Duboule


title: Transcriptional patterns of pigs divergent in feed efficiency traits

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

department: Genome Biology

institute: FBN Dummerstorf

summary: in vivo microarray study to detect transcriptional changes in muscle tissue (M. longissimus) derived from pigs divergent in feed efficiency.

overall_design: Muscle tissue of ten female pigs per residual food intake (RFI) group was collected for expression profiling.

first: Justyna

last: Horodyska

first: Peadar

last: Lowlor

first: Ruth

last: Hamill


title: expression data from human lung adenocarcinoma cells A549

city: Beijing

first: HONG

last: WANG

address: No.8 East Avenue, Fengtai District,

department: Department of Lung Cancer

institute: The Affiliated Hospital of Military Medical Sciences, The 307th Hospital of Chinese People’s Liberation Army

summary:
GMDS is important for human lung adenocarcinoma progression, detailed molecular mechanisms remain elusive.
We used microarray to detail the global gene expression changes in A549 cells with GMDS knockdown as compared to control cells

overall_design: A549 cells infected with lentivirus expressing either Scr-shRNA (n=3) or GMDS-shRNA (n=3) were cultured and then total RNA was extracted using Trizol reagents. RNA quantity and quality were determined using NanoDrop 2000 and Agilent Bioanalyzer 2100. For gene expression analysis, Affymetrix human GeneChip primeview was used according to the manufacturer’s instructions. In brief, GeneChip 3’ IVT Expression Kit was used for first-strand complementary DNA synthesis, double-stranded DNA template conversion, in vitro transcription for aRNA synthesis and labelling. Microarray hybridization, washing and staining were done using GeneChip Hybridization Wash and Stain Kit.

first: Hong

last: Wang