title: MST-312: a telomerase inhibitor effectively blocking MYC oncogenic functions [ChIP-Seq]

first: Julius

last: Müller

summary: Reactivation of the telomerase reverse transcriptase subunit, TERT, is linked to tumourigenesis due to well-documented telomere-dependent and independent functions. The aim of this study was to investigate the effect of the telomerase inhibitor, MST-312, on TERT functions, focusing in particular, on its effects on MYC stabilty and MYC-regulated pathways, in order to assess its potential as a therapeutic agent.  We demonstrate that MST-312 reduces MYC levels in cancer cells, leading to reduced MYC levels on chromatin, and subsequently affecting the MYC-regulated transcriptional program. As a result, MST-312 treatment increases the survival of lymphoma-bearing mice.   Mechanistically, MST-312 affects the conformation of TERT, leading to TERT/Terc dissociation, and the subsequent loss of both its telomere-dependent and independent functions.   Based on the presented data, we conclude that MST-312 treatment is a promising therapeutic strategy, in particular, in MYC-driven tumorus.

overall_design: ChIP was performed using anti-MYC (sc-764) in P493 cells and treated with MST-312.

first: Ekta

last: Khattar

first: Cheryl

middle: M

last: Koh

first: Shi

last: Leow

last: Muller

first: Wei

middle: X

last: Ang

first: Guido

last: Franzoso

first: Shang

last: Li

first: Vinay

last: Tergaonkar

first: Ernesto

last: Guccione


title: MST-312: a telomerase inhibitor effectively blocking MYC oncogenic functions [array]

status: Public on Jan 01 2020

city: Singapore

address: 61 Biopolis Drive

department: IMCB

country: Singapore

institute: A*Star Singapore

overall_design: Total RNA was extracted from P493 cells treated with MST-312 and TET for 48 h, then released into fresh TET-free media with MST-312 for 0, 4, 8 and 24 hours.

middle: C


title: Inflammatory Cytokines shape a Changing DNA Methylome in Monocytes Mirroring Disease Activity in Rheumatoid Arthritis (patients)

status: Public on Dec 31 2019

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute (IJC)

summary: Genome wide DNA methylation profiling of monocytes from healthy donors and rheumatoid arthritis patients. The Illumina Infinium MethylationEPIC Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpGs in CD11b+CD33+CD15neg monocytes isolated from PBMCs of 17 healthy donors and 47 rheumatoid arthritis patients with different disease activity scores (DAS28).

overall_design: Bisulphite converted DNA from the 64 samples were hybridised to the Illumina Infinium MethylationEPIC Beadchip.

first: Javier

last: Rodríguez-Ubreva

first: Carlos

last: de la Calle-Fabregat

first: Tianlu

first: Laura

last: Ciudad

first: Maria

middle: L

first: Francesc

last: Català-Moll

first: Octavio

last: Morante-Palacios

first: Antonio

last: García-Gómez

first: Raquel

last: Celis

first: Frances

last: Humby

first: Alessandra

last: Nerviani

last: Martín

first: Constantino

last: Pitzalis

first: Juan

middle: D

last: Cañete


title: Defining heterogeneity and biological signature in human effector memory CD8+ T cells expressing different levels of IL-7 receptor alpha by high-dimensional analysis

city: New Haven

first: Insoo

last: Kang

address: 300 Cedar Street

country: USA

institute: Yale University

type: Expression profiling by high throughput sequencing

summary: FACS-purified human effector memory (EM) CD8+ T cells were analyzed for single cell gene expression profile using single cell RNA-seq.  The relationship of IL-7 receptor alpha expression with other molecules was determined at the single cell level. The results showed heterogeneity in human EM CD8+ T cells as defined by IL-7Ra expression that has distinct but organized relationships with a set of molecules, including effector molecules, chemokine receptors, and transcription factors.

overall_design: Effector memory (EM) CD8+ T cells were FACS-sorted from peripheral blood mononuclear cells of a healthy adult donor.  Purified cells were analyzed using single cell RNA-seq.

first: Min

middle: S

last: Shin

first: Dongjoo

last: Kim

first: Rong

last: Fan


title: Gene expression analysis of astrocytes differentiated from iPS cells generated from the fibroblasts of PSEN1deltaE9 mutant AD and their isogenic control iPS lines

city: Helsinki

first: Iiris

last: Hovatta

address: Haartmaninkatu 3

department: Department of Psychology and Logopedics

country: Finland

institute: University of Helsinki

summary: Mutations in presenilin 1 (PSEN1) cause a familiar form of Alzheimer's disease (AD). We have obtained skin biopsies from two individuals carrying PSEN1 exon9 deletion and reprogrammed skin fibroblasts into induced pluripotent stem cells (iPSCs). To get controls, we have corrected PSEN1 exon9 deletion by CRISPR/Cas9 technique. Since astrocytes play role in AD pathogenesis, we further differentiated iPSCs into astrocytes. We ran RNA sequencing analysis to compare our iPSC-derived astrocytes with previously published data on human astrocytes and to identify genes and pathways affected by PSEN1 exon 9 deletion.

overall_design: Ribo-depleted RNA was sequenced with Illumina Next-seq 500 from iPS derived astrocytes

first: Jari

last: Koistinaho


title: Epicatechin metabolites exert epigenetic regulation in endothelial cells by modulating DNA methylation profile

city: Antwerp (Wilrijk)

first: Ken

last: Declerck

address: Universiteitsplein 1

country: Belgium

institute: University of Antwerp

type: Methylation profiling by genome tiling array

summary: Diets rich in flavanols are known to exert beneficial cardiovascular health effects. We previously showed that epicatechin metabolites reduce monocyte-endothelial cell adhesion by modulating expression of genes in HUVECs involved in cell adhesion signaling pathways. The aim of the present study is to examine potential epigenetic remodeling of HUVEC cells upon inflammation in presence or absence of cocoa derived epicatechin metabolites through genomewide DNA methylation profiling. Epicatechin metabolites were found to trigger DNA hypermethylation in gene bodies and intergenic genomic regions, while hypomethylation in promoter regions. In addition, pathway enrichment of differentially methylated genes demonstrates epigenetic remodeling cell adhesion and cytoskeleton signaling pathways. Finally, in silico docking supports evidence for direct regulation of DNMTs through epicatechin binding. In conclusion, our study provides evidence that epicatechin metabolites elicit vascular health effects in part through epigenetic regulation of endothelial cell adhesion functions.

overall_design: HUVEC cells were treated with single epicatechin metabolites or a mixture of epicatechin metabolites for 3h. After 18h incubation in flavanol-free medium, cells were treated with TNFalpha for 4h. DNA methylation was measured using the 450k methylation array.

first: Dragan

last: Milenkovic

first: Yelena

last: Guttman

first: Zohar

last: Kerem

first: Sylvain

last: Claude

first: Hagen

last: Schroeter

first: Christine

last: Morand

first: Wim

last: Vanden Berghe


title: Ebola virus gycoprotein (EbovGP) stimulation of whole human PBMC

city: London

first: Harry

last: Pickering

state: Greater London

address: LSHTM, Keppel Street

country: United Kingdom

institute: London School of Hygiene and Tropical Medicine

summary: EbovGP has been shown to stimulate high concentrations of innate cytokines from cells of myeloid lineage via TLR-4 engagement.

overall_design: PBMC from 6 healthy adult donors were isolated and stimulated with EbovGP in vitro for 15 hours, cells were then separated into CD14+ and remaining CD14 depleted fractions and RNA was extracted for RNA trascriptional analysis.

first: Helen

middle: R

last: Wagstaffe

first: Joanna

last: Houghton

first: Martin

middle: J

last: Holland

first: Eleanor

last: Riley

last: Goodier


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type LNCaP95 cells and Androgen receptor knocked-out clones Transcriptomes

city: Baltimore

first: Yezi

last: Zhu

state: MD

address: 600 N. Wolfe Street

institute: Johns Hopkins University

summary:
Purpose: To compare the gene expression changes in parental LNCaP95 cells when androgen receptor is knocked out in androgen depleted and androgen-enriched conditions
Methods: Cell line mRNA profiles of LNCaP95 cells and two androgen receptor knockout clones were generated by deep sequencing, using Illumina HiSeq.
Results: Using an optimized data analysis workflow, we mapped about 100 million sequence reads per sample to the human (build UCSC hg19).
Conclusions: Our study represents the overall gene expression profile changes when androgen receptor is knocked-out in androgen-sensitive prostate cancer parental LNCaP95 cells.

overall_design: Cell line mRNA profiles of LNCaP95 cells and AR-KO cell clones were generated by deep sequencing.

first: W

middle: N

last: Brennen


title: Gene expression during root nodule development in wild type and Fix- mutant of Lotus japonicus

city: Tsukuba

first: Yoshikazu

last: Shimoda

state: Ibaraki

address: 3-1-1 Kannondai

country: Japan

institute: National Agriculture and Food Research Organization

summary: RNA-seq analysis was performed to know the expression profiles of Lotus japonicus genes during nodule development and nitrogen fixation.

overall_design: RNA samples were prepared from uninoculated roots and nodules (5, 7, and 10 days after rhizobium inoculation) of wild type (MG20-miyakojima) and Fix- mutant (apn1). Deep sequencing was performed using illumina Hiseq1000.


title: LncRNA expression profiling of A549 cells with the mesenchymal-like and epithelial-like characteristics

city: Xi'an

first: Yang

last: Zhao

state: Shaanxi

address: No.157, fifth west road

department: Oncology

country: China

institute: Second affiliated hospital of Xi'an Jiaotong University

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

summary: The clinical response to chemotherapy regimen of cisplatin and paclitaxel in lung adenocarcinoma is frequently limited in magnitude and duration due to drug resistance. Recently, epithelial-mesenchymal transition (EMT) was associated with drug resistance. However, the underlying mechanisms remain elusive. To discover mechanisms of resistance, we developed the epithelial-like and mesenchymal-like A549 cell lines (lung adenocarcinoma cell line), and have their lncRNA expressions profiled and compared. Results provide insight into the molecular mechanisms underlying chemotherapy-resistance.

overall_design: According to our prior report, A549 cell presented the mesenchymal phenotype on the fibronectin-coated dish. Knockdown of Caspase-8 or c-Src impaired the process of EMT to show the epithelial-like characteristics. Hence, we stably transfected control shRNA, Caspase-8 shRNA and c-Src shRNA into A549 cell, A549+Control-meshenchymal-like A549, A549+Casp8 shRNA and A549+Src shRNA-epithelial-like A549. We designed this experiment to screen for lncRNA which is required for chemotherapy-resistance in the mesenchymal-like A549 cell.


title: Biphasic response of Protein Kinase A to cyclic adenosine monophosphate triggers distinct epithelial phenotypes

city: San Francisco

first: Joao Pedro

last: Fons

state: CA

address: 1700 4th Street, Room BH409C

department: Biochemistry and Biopysics

institute: UCSF

summary: We postulated that the ability of bPAC-generated cAMP to induce the biphasic response of PKA might have profound and distinct effects on the cellular transcriptome. To test this hypothesis, we carried out mRNA sequencing of MDCKI and MDCKI+bPAC cells under no, low, or high cAMP inputs (0%, 1.7% and 33% blue light duty cycle)

overall_design: Examination of the effect of three light doses, for 2 hours,  in parental MDCKI and MDCKI+bPAC cells

first: Joao

middle: P

last: Fonseca

first: Hana

last: El-Samad


title: Temperature change modulates pathogenicity of Francisella noatunensis subsp. orientalis to Nile tilapia but not the expression of its virulence genes

city: Belo Horizonte

first: Henrique

middle: César Pereira

last: Figueiredo

state: Minas Gerais

address: Av. Antônio Carlos 6627, Caixa Postal 567, Pampulha

country: Brazil

institute: AQUACEN - National Reference Laboratory for Aquatic Animal Diseases

summary: Francisellosis outbreaks have been reported in the literature as occurring seasonally when water temperature is below 24°C. The aim of this study was to quantify the median lethal doses (LD50) of FNO in experimental challenges at 28°C and 22°C, and to investigate the impact of temperature changes in whole genome expression using microarray technology. The LD50 for Nile tilapia at 28°C was ~105.7, whereas at 22°C, the LD50 was ~102.2, showing that the decrease in temperature enhanced pathogen virulence. Out of 1,917 genes screened, a total of 31 and 19 genes were down- and up-regulated at 22°C, respectively. These genes were grouped by orthology into functional categories of: amino acid, inorganic ion, and carbohydrate transport and metabolism; transcription; and posttranslational modification, protein turnover, and chaperones. Expression of genes related to metabolism, oxidative stress, and thermal shock were regulated by temperature changes, reflecting an ability of FNO to adapt to the environment. Expression of virulence genes usually required for the Francisella genus was not changed between tested temperatures, including that of genes located on the Francisella Pathogenicity Island.

overall_design: The F. noatunensis subsp. orientalis FNO12 isolated from diseased fish was used in this study. Quadruplicate culture of this strain were incubated at 22°C or 28°C and harvested at the mid-exponential phase of bacterial growth (OD600 = 0.2) for RNA extraction. The RNA level expression are analyzed on Agilent Microarray platform.

first: Felipe

last: Pereira

first: Guilherme

last: Tavares

first: Alex

middle: F

last: Carvalho

first: Júlio

last: Rosa

first: Cristiana

last: Rezende

first: Carlos

middle: A

last: Leal


title: Functional stem cell aging dictated by skin tissue microenvironment

city: New York

first: Yejing

last: Ge

state: NY

address: 1230 York Ave

institute: The Rockefeller University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Organismal aging in mammals is manifested with architectural alteration and functional decline of multiple organs throughout the body. In aged skin, hairs are sparse, which has led to the hypothesis that the hair follicle stem cells (HFSCs) undergo epidermal differentiation during aging. Here, we employ single cell analysis to interrogate aging-related changes in the HFSCs. Unexpectedly, HFSCs maintain their lineage fidelity and show no signs of shifting to an epidermal fate.  Despite maintaining lineage identity, HFSCs do show prevalent transcriptional changes in extracellular matrix genes. Of importance, these HFSC changes are accompanied by profound architectural perturbations in the aging stem cell niche. Upon surveying the dermis from young and aged skin, we also observe age-related changes in many non-epithelial cell types, including resident immune cells, sensory neurons, arrector pili muscles, and blood vessels – all of which have been previously associated with abilities to modulate hair follicle regeneration. Consistent with both intrinsic and extrinsic alterations in stem cell: niche communications, we find that in response to skin wounding, aged HFSCs repair the epidermis, but are defective in hair follicle regeneration.  Intriguingly, whereas aged dermis cannot support young HFSCs, aged HFSCs can be rescued when supported by young dermis. Together, these findings favor a model where skin tissue microenvironment plays a dominant role in dictating the molecular properties and activities of HFSCs.

overall_design: Young and aged murine hair follicle stem cells and those from interfollicular epidermis in the skin were purified and assayed for their genome-wide transcriptional (RNAseq) and open chromatin (ATACseq) landscape, and 10x genomics was used to survey single cell transcriptome in young and aged skin epithelium

first: Elaine

last: Fuchs


title: Mss51 deletion enhances muscle metabolism and glucose homeostasis in mice

first: Yazmin

last: Rovira Gonzalez

address: 707 N Broadway

institute: Johns Hopkins University School of Medicine

summary: Myostatin is a negative regulator of muscle growth and metabolism and its inhibition in mice improves insulin sensitivity, increases glucose uptake into skeletal muscle, and decreases total body fat. A recently described mammalian protein called Mss51 is significantly downregulated with myostatin inhibition. In vitro disruption of Mss51 results in increased levels of ATP, β-oxidation, glycolysis and oxidative phosphorylation. To determine the in vivo biological function of Mss51 in mice, we disrupted the Mss51 gene by CRISPR/Cas9 and found that Mss51 KO mice have normal muscle weights and fiber-type distribution but reduced fat pads. Myofibers isolated from Mss51 KO mice showed an increased oxygen consumption rate compared to WT controls, indicating an accelerated rate of skeletal muscle metabolism. The expression of genes related to oxidative phosphorylation and fatty acid β-oxidation were enhanced in skeletal muscle of Mss51 KO mice compared to that of WT mice. We found that mice lacking Mss51 and challenged with a high fat diet were resistant to diet-induced weight gain, had increased whole-body glucose turnover and glycolysis rate, and increased systemic insulin sensitivity and fatty acid β-oxidation. These findings demonstrate that Mss51 modulates skeletal muscle mitochondrial respiration and regulates whole-body glucose and fatty acid metabolism, making it a potential target for obesity and diabetes.

overall_design:
RNA-seq analysis of quadriceps muscle of wild type (WT) and Mss51 knockout (Mss51 KO) mice.
Total RNA isolated from 4 WT and 4 Mss51 KO quadriceps samples of 6mo female mice were analyzed.

middle: I

first: Kathryn

last: Wagner


title: Combination Targeting of the Bromodomain and Acetyltransferase Active Site of p300/CBP

city: Boston

first: Beth

last: Zucconi

state: Massachusetts

address: 77 Avenue Louis Pasteur, NRB 164

department: Medicine

institute: Brigham & Women's Hospital

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

overall_design: Refer to individual Series


title: RNA-seq of cold stimulated inguinal fat of wild type and Rarres2-/- mice

city: Shanghai

first: Yuli

last: Lin

address: No.130, Dong'an Road, Xuhui

institute: Fudan University

summary: Although various stimuli and mediators have been identified to promote thermogenic beige fat development, less is known about the negative regulator of cold-induced beiging. We here show that lack of chemerin that is highly expressed in white adipose tissue or its receptor CMKLR1 in adipocytes enhances cold-induced beiging and thermogenesis. Our results reveal a previously unrecognized beige-inhibitory role of chemerin-CMKLR1 axis, and suggests CMKLR1 as a therapeutic target for obesity-related metabolic disorders.

overall_design: Total RNA profiles of 8-week old wild type (WT) and Rarres2-/- mice were generated by deep sequencing using Illumina Hiseq 2000.

first: Liuling

last: Xiao


title: Effect of Selective Androgen Receptor Degraders (SARDs) on Androgen Receptor (AR) Function in MR49F (LNCaP enzalutamide-resistant) Cells

city: Memphis

first: Daniel

middle: Lee

last: Johnson

state: Tennessee

address: 71 S Manassas

department: Molecular Informatics Core

institute: UTHSC

summary:
Androgen receptor (AR)-targeting prostate cancer drugs, which are predominantly competitive ligand binding domain (LBD)-binding antagonists, are inactivated by common resistance -mechanisms. It is important to develop next-generation mechanistically-distinct drugs to treat castration- and drug- resistant prostate cancers. Here, we describe a second-generation AR pan-antagonist (UT-34) that degrades the AR and AR splice variants. UT-34 inhibits the wild-type and LBD mutant ARs comparably and inhibits the in vitro proliferation and in vivo growth of enzalutamide-sensitive and resistant prostate cancer xenografts. In preclinical models, UT-34 induced the regression of enzalutamide-resistant tumors at doses when the AR is degraded; but, at lower doses when the AR is just antagonized, it inhibits, without shrinking, the tumors. This indicates that degradation might be a prerequisite for tumor regression. Mechanistically, UT-34 promotes a conformation that is distinct from the LBD-binding competitive antagonist, enzalutamide, and degrades the AR through the ubiquitin proteasome mechanism. UT-34 has a broad safety margin and exhibits no cross-reactivity with G-Protein Coupled Receptor, kinase, and nuclear receptor family members. Collectively, UT-34 exhibits the properties necessary for a next-generation prostate cancer drug.
MR49F cells (n=3-4/group) were maintained in charcoal-stripped serum containing medium for 48 hours and treated with vehicle, 0.1 nM R1881, or 10 uM of UT-34 in combination with 0.1 nM R1881. Twenty four hours after treatment, the cells were harvested, RNA was isolated and expression of genes was measured using microarray (Affymetrix Clarion S)
UT-34 is a selective androgen receptor degrader that degrades and antagonizes the AR. UT-34 binds to the AF-1 domain of the AR and degrades the AR through ubiquitin proteasome pathways. The transcriptome study was performed to evaluate the ability of UT-34 to antagonize the enzalutamide-resistant AR function.

overall_design: MR49F cells were maintained in charcoal-stripped serum containing medium for 48 hours and treated with vehicle, 0.1 nM R1881, or 10 uM of UT-34 in combination with 0.1 nM R1881. Twenty four hours after treatment, the cells were harvested, RNA was isolated and expression of genes was measured using microarray (Affymetrix Clarion S)

first: Ramesh

last: Narayanan


title: Transcriptional profiling of human epithelial cells infected with trachoma isolates of Chlamydia trachomatis

first: Harry

last: Pickering

summary: Hep-2C cells were infected with A/2497 or B/Tunis-864 strains of Chlamydia trachomatis to compare changes in host gene expression

overall_design: Hep-2C cells were incubated with media alone, media inoculated with A/2497 or media inoculated with B/Tunis-864 at 37ºC for 3 hours, including 1 hour centrifugation at 1800 RPM. Inoculum was replaced with media (plus supplement) and incubated at 37ºC for 36 hours. RNA was extracted for RNA trascriptional analysis.

first: Joanna

last: Houghton

first: Martin

last: Holland


title: Transcriptome data and CNVs for Sus scrofa

city: Chengdu

first: Song

last: Yang

address: No.211, Huimin Road, Wenjiang District, Chengdu City, Sichuan Province, P.R.China

institute: Sichuan Agricultural University College of Animal Science and Technology


title: Transcriptomic analysis of gefitinib-resistant EGFR-mutant NSCLC cells

city: Burjassot

first: Julian

last: Carretero

state: Valencia

address: Ave. Vicent Andres Estelles s/n

department: Physiology

institute: University of Valencia

summary: We have employed a transcriptomic  approach to find a molecular target that could compensate for the loss of EGFR signaling in NSCLC cell lines with acquired resistance to gefitinib with an EMT phenotype.

overall_design: Total RNA obtained from EGFR-mutant HCC4006 lung adenocarcinoma cells treated with increasing concentrations of gefitinib for 6 months (gefitinib resistant, GER), alone or in combination with the TGFB receptor inhibitor SB431542.

first: Takeshi

last: Shimamura


title: RNA seq analysis of uterine stromal cells from ovariectomized (OVX) Atg7f/f;Amhr2cre mice

city: Seoul

first: Hyunjung

middle: Jade

last: Lim

address: 120 Neungdong-ro

department: Veterinary Medicine

country: South Korea

institute: Konkuk University

summary: Uterine stromal cells were isolated from OVX Atg7f/f and Atg7d/d mice injected with oil or E2. Each group was pooled from 4 OVX mice and the experiment was run in duplicates. RNA quality was assessed by Agilent 2100 bioanalyzer using the RNA 6000 Nano Chip (Agilent Technologies, Amstelveen, The Netherlands), and RNA quantification was performed using ND-2000 Spectrophotometer (ThermoFisher Scientific). Total RNA (1 μg) was prepared and processed for high-throughput sequencing using NextSeq 500 (Illumina, San Diego, CA, USA) and data profiling was serviced by e-biogen (Seoul, Korea).

overall_design: Identification of differentially expressed genes in uterine stromal cells of Atg7f/f;Amhr2cre mice with specific deletion of Atg7 in the uterine mesenchyme

first: Bora

last: Lee


title: Dysfunctional epigenetic aging of the normal colon and colorectal cancer risk

city: Seattle

first: Ting

last: Wang

state: WA

address: 1100 Fairview Ave. N.

department: Clinical Research

institute: Fred Hutchinson Cancer Research Center

summary: Genome wide DNA methylation profiling of normal colon samples. The Illumina Infinium HumanMethylation450 and EPIC Beadchip arrays were used to obtain DNA methylation profiles across approximately 450,000 and 850,000 CpGs. Samples were from nomal colons of 334 subjects with low, medium or high CRC risk according to their personal adenoma or cancer history.

overall_design: Bisulphite converted DNA from the 334 samples were hybridised to the Illumina Infinium HumanMethylation450 and EPIC Beadchip arrays

first: William

last: Grady


title: Gene expression signatures in human prostate cancer cells PC3 with lncAPP overexpression and knockdown

first: Xiaolei

last: Shi

address: 168 Changhai Road

department: Department of Urology

institute: Shanghai Changhai Hospital

summary: To explore the gene expression signatures in human prostate cancer cells PC3 with lncAPP overexpression and knocdown, we conducted lenti viruses transfection to construct upregulation and downregulation of lncAPP in PC3 cells. Expression levels of lncAPP were detected via qRT-PCR to confirm the consistency and quality of microarray.

overall_design: Gene expression in human prostate cancer cells PC3 with overexpression and knnockdown of lncAPP were measured. Three independent replicates were performed for each sample treatment.

first: Wei

last: Zhang


title: Transcriptome analysis of gene expression  in control and  Kiaa1429Zp3cKO samples (RNA-Seq)

city: Beijing

first: Wenjie

last: Shu

address: Taiping Road 27

institute: Beijing Institute of Radiation Medicine

summary: The goals of this study are to compare transcriptome profiling (RNA-seq) data and quantitative reverse transcription polymerase chain reaction (qPCR) methods and to evaluate protocols for optimal high-throughput data analysis. The sequencing libraries from control and Kiaa1429Zp3cKO oocytes were generated according to protocols of Smart-seq2. For all samples the concentration of sequencing libraries was quantified using qPCR. All samples showed a concentration of higher than 3nM and were sequenced using HiSeq XTen (Illumina) with paired-end 150-bp sequencing.RNA-seq data were aligned to the mouse genome mm10 using STAR 2-pass mode with the annotations of Ensembl version 90 and parameter ‘--outFilterMismatchNmax 6’. SAMtools was used to extract uniquely mapped reads with mapping quality more than or equal to 20. The number of reads mapped to each gene was counted using the HTSeq  python package with the ‘union’ overlap resolution mode and –stranded = no. The expressions of genes were quantified as RPKM by edgeR . Genes with RPKM more than 1 in at least three control samples were considered as expressed. Only expressed genes were kept for the subsequent analysis. Differentially expressed genes were identified by DESeq2 using two criteria: fold change of expression should be higher than 2 and the adjusted p-value should be lower than 0.05. Enriched GO terms were obtained with P-value less than 0.05 from DAVID.The analysis of data revealed a total of 1081 genes were significant differentially expressed. 448 genes were upregulated and 633 downregulated in Kiaa1429Zp3cKO oocytes.We found that Kiaa1429 deletion altered expression pattern of many oocyte-derived factors (Ccnb1ip1, Lysmd2, Vav3, sohlh2, Id3, Anks4b, Scel, Cfap53, Olfm4, Fgf8, Susd3, Clip4, Fam124b, Gfra1, Nedd4l, Bmp15), which have been reported to be involved in signaling pathways of the oocyte-granulosa cell dialog and play important roles in oocyte survival and folliculogenesis. These oocyte-derived factors selected randomly were validated by qPCR in the GV oocytes from 20-day-old mice.

overall_design: Total 8 samples from 20-day-old control or Kiaa1429Zp3cKO mice in 4 separate experiments, each sample contained about 20 oocytes.

first: Ran

last: Huo

first: Bin

last: Shen

first: Zhangyi

last: Ouyang

first: Yue

last: Hu


title: Arsenite stress response in Thioalkalivibrio thiocyanoxidans ARh2 and Tv. jannaschii ALM2

city: Amsterdam

first: Anne-Catherine

last: Ahn

address: Science Park 904

department: IBED

country: Netherlands

institute: University of Amsterdam

summary: Transcriptional response to growth with arsenite by the haloalkaliphilic sulfur-oxidizer Thioalkalivibrio thiocyanoxidans ARh2 and Tv. jannaschii by performing RNA-seq analysis

sample_organism:
Thioalkalivibrio jannaschii
Thioalkalivibrio thiocyanoxidans ARh2

overall_design: Transcriptomic analysis was performed on cultures of Thioalkalivibrio thiocyanoxidans ARh2 and Tv. jannaschii ALM2 both grown at 0 mM and 0.1 mM arsenite and Tv. jannaschii as well at 5 mM arsenite, in triplicats, using Ion Proton platform with an Ion PI Chip v3

first: Gerard

last: Muyzer


title: Differential functional roles of fibroblasts and pericytes in the formation of tissue-engineered microvascular networks in vitro

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

summary: Aims: Formation of a perfusable microvascular network (μVN) is critical for tissue engineering of solid organs. Stromal cells can support endothelial cell (EC) self-assembly into a μVN, but distinct stromal cell populations may play different roles in this process. Here we investigated the effects that two widely used stromal cells populations, fibroblasts (FBs) and pericytes (PCs), have on μVN formation.     Methods and results: We examined the effects of adding defined stromal cell populations on the self-assembly of ECs derived from human endothelial colony forming cells (HECFCs) into perfusable μVNs in fibrin gels cast within a microfluidics chamber. ECs alone fail to fully assemble a perfusable μVN. Human lung FBs stimulate the formation of EC lined μVNs within microfluidic devices. RNA-seq analysis suggested that FBs produce high levels of hepatocyte growth factor (HGF), and addition of recombinant HGF improved μVN formation within devices. Human placental PCs could not substitute for FBs, but in the presence of FBs, PCs closely associated with ECs, formed a common basement membrane, extend microfilaments intercellularly, and reduced microvessel diameters.   Conclusions: Different stromal cell types provide different functions in microvessel assembly by ECs. FBs support μVN formation by providing paracrine growth factors whereas PCs directly interact with ECs to modify microvascular morphology.

overall_design: Examination of gene expression in pericyte and fibroblast cells.

first: Natalia

last: Kosyakova

first: Derek

last: Kao

last: López-Giráldez

first: Susann

last: Spindler

first: Morven

last: Graham

first: Kevin

last: James

first: Jee

middle: W

last: Shin

first: Xinran

last: Liu

first: Gregory

middle: T

last: Tietjen

first: Jordan

last: Pober

middle: G

last: Chang


title: Adverse Events of anti-EGFR Therapy are Triggered by Hair Eruption and Commensal Skin Microbiota

city: Vienna

first: Thomas

last: Mohr

address: Borschkegasse 8a

department: Institute of Cancer Research

country: Austria

institute: Medical University of Vienna

summary: EGFR targeted anti-cancer therapy induces severe skin toxicities, which affect life quality in patients. The lack of mechanistic details underlying these adverse events hampers their effective management. Here we identified EGFR as the epidermal master-regulator of the ERK pathway, which secures skin barrier integrity upon hair eruption. EGFR deficient epidermis displays a Th2-dominated expression signature and is permissive for excessive microbiota outgrowth. In the absence of EGFR, opening of the follicular ostia during hair eruption allows invasion of commensal microbiota aggravating barrier disruption and initiating an additional Th1 and Th17 response. Chronic folliculitis leads to Staphylococcus aureus dominated dysbiosis, further exacerbating inflammation and expanding barrier defects. Restoration of epidermal ERK signaling via therapeutic FGF7 treatment or transgenic SOS expression rescues skin barrier integrity in the absence of EGFR. These data reveal a gatekeeper function of the EGFR/ERK cascade in hair follicles securing the epidermal barrier around the erupting hair shaft.

overall_design: Examination of treatment with antibiotics vs non treatment in wildtype, EGFRΔep, and K5-SOS mice

last: Bauer


title: Clariom D expression in breast cancer samples

city: Valencia

first: Sara

last: OLTRA SANCHIS

address: Avda Menéndez Pelayo, 4 accesorio

department: Medical Oncology

institute: INCLIVA

summary: We analysed expression using Clariom D array in 42 breast cancer FFPE samples

overall_design: The RNA for the Clariom™ D study was extracted from tissue fixed in formaldehyde and embedded in paraffin, preserved at room temperature. Four sections of 20 μm from breast cancer tumour paraffin embedded were used. The extraction of the RNA material was carried out using the commercial kit RecoverAll ™ Total Nucleic Acid Isolation Kit from ambion® (Applied Biosystems ™ by Life Technologies ™, Carlsbad, California, USA). RNA was quantified by Qubit® 3.0 (InvitrogenTM by Termo Fisher Scientific, Waltham, MA, USA) y Qubit® RNA HS Assay Kit (Molecular Probes® by Life Technologies Carlsbad, California, USA). Before hybridization RNA quality was assessed using Real Time PCR (qRT-PCR).

last: Oltra

first: Maria

last: Peña-Chilet

first: Victoria

last: Vidal-Tomas

first: Kirsty

last: Flower

first: María

last: Martinez

first: Elisa

last: Alonso

first: Octavio

last: Burgues

first: Ana

last: Lluch

first: James

middle: M

last: Flanagan

first: Gloria

last: Ribas


title: Next-Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Kdm2b-/- Peritoneal Macrophage Transcriptomes

first: Xingguang

last: Liu

address: Xiangyin road 800

department: National Key Laboratory of Immunity & Inflammation

institute: Naval medical university

summary:
Purpose: The purpose of this study is to detect activated or silenced genes during Kdm2b-deficient peritoneal macrophages and the control cells. Gene expression differences between two samples could be found using transcriptome profiling (RNA-seq) analysis.
Methods: Mouse peritoneal macrophages were harvested from mice 4 days after thioglycollate (BD, Sparks, MD) injection. Macrophages RNA profiles were generated by deep sequencing, using Illumina.
Results: We mapped about 10 million sequence reads per sample to the mouse genome, identified hundreds of genes with significant mRNA variation between Kdm2b-deficient macrophages and the control cells.

overall_design: Peritoneal macrophage mRNA profiles of wild type (WT) and Kdm2b-/- mice were generated by deep sequencing.

first: Liu

last: Xingguang

first: Zhou

last: Qingqing


title: Combination Targeting of the Bromodomain and Acetyltransferase Active Site of p300/CBP [RNA-seq]

first: Beth

last: Zucconi

summary: p300 and CBP are highly related histone acetyltransferase (HAT) enzymes that regulate gene expression, and their dysregulation has been linked to cancer and other diseases. p300/CBP is composed of a number of domains including a HAT domain which is inhibited by the small molecule A-485 and an acetyl-lysine binding bromodomain which was recently found to be selectively antagonized by the small molecule I-CBP112. Here we show that the combination of I-CBP112 and A-485 can synergize to inhibit prostate cancer cell proliferation. We find that the combination confers a dramatic reduction in p300 chromatin occupancy compared to the individual effects of blocking either domain alone. Accompanying this loss of p300 on chromatin, combination treatment predominantly leads to the reduction of specific mRNAs including androgen-dependent and pro-oncogenic prostate genes such as KLK3 (PSA) and c-Myc. Consistent with p300 chromatin binding directly affecting gene expression, mRNAs that are significantly reduced by combination treatment also exhibit a strong reduction in p300 chromatin occupancy at their gene promoters. The relatively few mRNAs that are up-regulated upon combination treatment show no correlation with p300 occupancy. These studies provide support for the pharmacologic advantage of concurrent targeting of two domains within one key epigenetic modification enzyme.

overall_design: LNCaP cells were divided into 4 different drug treatment groups (including DMSO control) and were treated with I-CBP112 and/or A-485 for 24 h after which they were analyzed for total mRNA levels.

middle: E

first: Philip

last: Cole


title: Genome-wide profiling of 5-hydroxymethylcytosine in renal cell carcinoma tissue, urine and cell line samples.

city: Columbus

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

institute: The Ohio State University

type: Methylation profiling by high throughput sequencing

summary: We performed genome-wide 5hmC Methylated DNA Capture (5hMethylCap-seq) on one pooled RCC tissue sample (n=3) and the corresponding matched normal kidney tissue (NAT) (n=3), and we also performed 5hMethylCap-seq on one pooled urine sample obtained from RCC patients (n=52) along with another pooled urine sample obtained from control patients without malignancy (n=65). Global 5hmC levels were dramatically reduced in RCC tissues compared to matched normal adjacent kidney tissues, and although we detected low levels of 5hmC in urine samples, we also observed reduction of 5hmC in urine samples compared to tissue samples. Through assessing histone marked regions we found that 5hmC levels were enriched in H3K9me3 marked repressive genomic regions of normal adjacent kidney compared to RCC tissue tissues. Given the lower 5hmC signal in other genomic regions in cancer tissues, this upregulated 5hmC levels in H3K9me3 marked regions were also clearly identified comparing urine samples from RCC patients to control patients without RCC. We used Caki1 and Caki2 RCC cells to established stable cells with low H3K9me3 expression by knocking down the SUV39H1 gene. We found that low global H3K9me3 causes major upregulation of 5hmC at H3K9me3 marked regions and minor downregulation of 5hmC at genebody regions without change global 5mC and 5hmC levels.

overall_design: Examination of 5hmC in tissue, urine and cell lines.

first: Meng

last: Wei


title: HMGA2 regulates ATF4 and the serine biosynthesis genes and reprograms metabolism in breast cancer

city: Oslo

first: Leonardo

middle: A.

last: Meza-Zepeda

address: Ullernchausseen 70

department: Department of Tumor Biology

country: Norway

institute: Oslo University Hospital

summary: The transcription regulator High Mobility Group AT-Hook 2 (HMGA2) plays an important role in many types of cancers, but the molecular mechanisms are not fully elucidated. We found by knock-down studies that HMGA2 controls expression of ATF4 and the enzymes in the serine synthesis pathway in triple negative breast cancer cells, and that HMGA2 expression correlates with poor clinical outcome in ER negative breast cancers. Furthermore, we found that the metabolism was dysregulated in cells with reduced HMGA2 expression, which affected their response to mitochondrial stressors and to changed carbon sources. Altogether, our findings demonstrate that HMGA2 is a regulator of serine biosynthesis and metabolism, consistent with the well-known role of HMGA2 as a regulator of proliferation, epithelial-mesenchymal transition and stemness.

overall_design: Investigation of HMGA2 functions.

first: Else

last: Munthe

first: Iwona

last: Grad

first: Anastassia

last: Serguienko

first: Marie

last: Rosvold

first: Vandana

last: Sandhu

first: Elin

middle: H

last: Kure

first: Eva

last: Stratford

first: Sendurai

last: Mani

first: Ola

last: Myklebost


title: Transcriptome profiling of spleen and duodenum upon lymphotoxin beta receptor (LTbR) induction

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: ETH/University of Zurich

summary: To study the effect of LTbR induction on spleen and duodenum transcriptome, we performed RNA sequencing of the spleen and intestine after Intravenous LTbR agonist AC H6 or isotype treatment. We analyzed differential gene expression.

overall_design: RNA sequencing on spleen and duodenum mRNA of wild type C57BL/6J mice treated with either AC H6 or isotype control for 24 hours (dose: 100ul of 1mg/ml solution per mouse, n=3 per genotype).

first: Caihong

last: Zhu


title: Characteristic molecular signature of pericardial effusion identifies malignant cancer in pericardial disorder patients

first: Sang Yean

last: Kim

state: Select

address: 222 BANPO-DAERO SEOCHO-GU, SEOUL

institute: The Catholic university of korea

summary: we examined 24 pericardial effusion patients and obtained pericardial fluid. To identify novel biomarker for detection cancer, detected transcriptome-based molecualr signature of compare pathologic cancer patients and non-cancer patients.

overall_design: 19 patients were dichotomized cancer group (Group 1) and non-cancer (Group 3) group. Group 1 (n=6) and Group 3 (n=5) were analyzed on whole genome expression microarray to profile pericardial fluid with cancer characteristic molecuar signature.

first: Jung

last: Eun

first: Sang

middle: Y

first: Suk

last: Nam


title: BRD4 inhibitor JQ1 increase the sensitivity of arsenic trioxide in pancreatic cancer

first: Congling

last: Xu

address: number 2 ruijin road

institute: Shanghai Institute of Hematology

summary: Pancreatic cancer is a deadliest type of malignancy, largely due to lack of effective intervention. We here report a pair of agents, ATO and JQ1, which synergistically induce apoptosis in the malignancy. Through global and molecular approaches, we have provided evidence that these agents are both able to modulate ER stress and autophagy in the cancer, probably acting in different ways. Cross-talks between ER stress and autophagy are implicated during ATO/ATO plus JQ1 induced apoptosis, in which NRF2 appears to play a central role.   of the globe transcriptional profiles of ATO regulated genes in breast, colon and lung cancer cells with different p53 status. We find p53 wild type cells are resistant to ATO induced globe dynamic transcriptional changes, thus resistant to ATO induced cell growth inhibition. P53 inhibitor PFTα releases p53 mediated transcriptional resistance and increases the sensitivity of ATO in p53 wild type tumor cells.

overall_design: Pancreatic cancer cell lines BXPC3 and MIApaca were treated with ATO 2.5μM for 0, 6, 12, 24 and 48 hours. Pancreatic cancer cell lines ASPC1 and PANC1 which were unsensitive to ATO treatment, were treated with ATO, JQ1(1μM) or ATO and JQ1 combination for 0, 6, 24 and 48 hours. Total RNA was collected and profiled to Affymetrix microarray


title: Combination Targeting of the Bromodomain and Acetyltransferase Active Site of p300/CBP [ChIP-seq]

first: Beth

last: Zucconi

address: 77 Avenue Louis Pasteur, NRB 164

institute: Brigham & Women's Hospital

overall_design: LNCaP cells were divided into 4 different drug treatment groups (including DMSO control) and were treated with I-CBP112 and/or A-485 for 24 h after which they were analyzed for p300 association.

first: Philip

last: Cole


title: Genome-wide methylation analysis on the impact of gluten-free diets using Infinium HumanMethylation 450 BeadChip

city: Penrith

first: Christine

last: Chiu

state: NSW

address: Locked Bag 1797

country: Australia

institute: Western Sydney University

summary: Genome wide DNA methylation profiling in saliva samples from individuals before and after the uptake of a gluten-free diet. The Illumina Infinium 450k Human DNA methylation BeadChip was used to obtain DNA methylation profiles across approximately 485,500 CpGs. The study investigated the impact of a short-term GFD on oral DNA methylation in healthy individuals.

overall_design: Bisulphite converted DNA from 6 individuals before and after the uptake of a gluten-free diet were hybridised to the Illumina Infinium 450k Human Methylation Beadchip. All individuals followed a Western diet before commencing the gluten-free diet, were non-smokers, had no recent medication use and were generally healthy individuals.

first: Joanne

last: Lind

middle: L

first: Nerissa

last: Hearn


title: Transcriptomic analysis of epithelial to mesenchymal transition in EGFR-mutant NSCLC cell lines.

first: Julian

last: Carretero

institute: University of Valencia

summary: We have employed a transcriptomic  approach to find a molecular target that could compensate for the loss of EGFR signaling in NSCLC cell lines with acquired resistance to EGFR TKIs with an EMT phenotype.

overall_design: Total RNA obtained from EGFR-mutant HCC827 lung adenocarcinoma cells treated with TGFB1 (10 ng/mL, 72h), infected with lentiviruses encoding shRNA against epithelial CDH1, or overexpressing the EMT transcription factor SNAIL.

first: Takeshi

last: Shimamura


title: Gene expression signatures after immunisation with MF59C adjuvanted trivalent inactivated influenza vaccine for season 2014-2015 Northern hemisphere (BIOVACSAFE protocol 305D)

city: London

first: David

last: Lewis

address: Du Cane Road

department: ICRF

institute: Imperial College London

summary: The time course of whole blood gene expression was determined in healthy adult participants who were randomised to receive either a single intramuscular immunisation with MF59C adjuvanted influenza vaccine (FLUADD) or equivalent volume saline control (PLACEBOD).

overall_design: Participants attended a single outpatient unit (CEVAC, Gent, Belgium). Pre-immunisation baseline sample was drawn on day 0, and further samples collected on days 1 and 7 for one subgroup; or 1, 3, 7 and 21 in the remainder. All samples were collected into PaxGene tubes.

first: January

last: Weiner

first: Jeroen

last: Maertzdorf


title: Next Generation Sequencing Facilitates Quantitative Analysis of CD46-KO/control vector, CD46-KO/CD46-CYT1 and CD46-KO/CD46-CYT2 EJ-1 cells’ Transcriptomes

city: Wuhan

first: Jin

last: Zeng

address: Jiefang Avenue

institute: Tongji Hospital

summary: CD46 is well known to be involved in diverse biological processes. Although several splice variants of CD46 have been identified, little is known about the contribution of alternative splicing to its tumorigenic functions. Here we found that exclusion of CD46 exon13 is significantly increased in bladder cancer samples. In bladder cancer cell lines, enforced expression of CD46-CYT2 (exon13-skipping isoform) induced cell growth and migration, and promoted tumorigenicity in a xenograft model. While enforced expression of CD46-CYT1 (exon13-containing isoform) attenuated tumorigenicity, representing an inverse phenotype of CD46-CYT2. We also used RNA sequencing to identify changes in gene expression after CD46-CYT1 or CD46-CYT2 overexpression and found KRT19 is a key CD46-CYT2 target gene. Furthermore, we applied interaction proteomics to identify exhaustively the complexes containing CYT1 or CYT2 domain in EJ-1 cells. 320 proteins were identified that interact with CYT1 or/and CYT2 domain, including some well-known CYT1 partners and most of them are new interactors. The new CYT2 partners’ translation machinery, RPL17 and EIF5A, were confirmed by coimmunoprecipitation experiments. We demonstrated that CD46-CYT2 enhances mRNA translation perhaps through an interaction with the translation machinery. Strikingly, the splicing factor SRSF1 is upregulated in bladder cancer and stimulates exclusion of exon13. Importantly, SRSF1 is highly correlated with CD46 exon13 exclusion in clinical bladder cancer samples. Taken together, our findings contribute to understanding the role of CD46 in bladder cancer development.

overall_design: EJ-1 cells' mRNA profiles of CD46-KO/control vector, CD46-KO/CD46-CYT1 and CD46-KO/CD46-CYT2  were generated by deep sequencing using Illumina GAIIx.

first: Ke

last: Chen

first: Hua


title: Transcriptome data from high density, low density and Rho0 yeast cell types

first: Cheol-Koo

last: Lee

address: Korea University, Biotechnology #318 West building, Anam-dong, Seongbuk-gu

department: Biotechnology

institute: Korea University

summary: Transcriptome data using microarray to identify difference across long-living, high-density cell type and short-living, low-density and Rho0 cell types

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: We separated high density and low density cells from budding yeast BY4741 using percoll density gradient at day 3 after cultured in YPD medium. Low density cells were prepared from Rho0 strain, also. Microarray analysis was performed as biological quintuplicate for three different cell types.

first: Young-Yon

last: Kwon


title: The profiling of gene expression in mock and fuison HBx-knockdowned cells

city: Chiba

first: Ryosuke

last: Muroyama

address: Inohana 1-8-1, Chuo-ku

department: Department of Gastroenterology

institute: Graduate School of Medicine, Chiba University

summary: To comprehensively characterize the biological function of fusion HBx, the expression level of genes in mock and fusiion HBx-knockdowned cells was investigated based on microarray.

overall_design: After establishment of cells stably knockdowned for fusion HBx, the expression level of genes in mock and fusiion HBx-knockdowned cells was investigated based on microarray.


title: RNA sequencing analysis of necroptosis related genes in TBZ treated HT-29 cells.

first: Jae whan

last: Song

address: Yonsei-ro 50

department: Department of Biochemistry

institute: College of Life Science and Biotechnology

summary: Analysis of necroptosis-induced changes in gene expression patterns from HT-29 cells

overall_design:
[Samples1..4] Total RNA was obtained from DMSO treated- and TBZ 4h treated-HT-29 cells, and DMSO treated- and TBZ 12h treated-HT-29/shMLKL cells. After that, RNA-seq was perform.
[Samples5..12] Total RNA was obtained from DMSO treated- or TBZ 5h treated-HT-29/shGFP and HT-29/shMLKL cells. After that, RNA-seq was perform.

first: Eun-Woo

first: Manhyung

last: Jeong

first: Daehyeon

last: Seong

first: Hwa-Ryeon

last: Kim

first: Jae-Seok

last: Roe

first: Jaewhan


title: Expression data from Human bone mesenchymal stem cells

city: Dalian

first: Yifan

last: Pan

address: Ganjingzi District，Ruanjianyuan street

institute: Dalian University of Technology

summary: Analysis of Human bone mesenchymal stem cells treated separately with DMSO vehicle, 100 nM perfluorooctanesulfonat(PFOS), 100 nM perfluorooctanoic acid(PFOA), 100 nM perfluorohexanesulphonate(PFHxS) or100 nM Chlorinated polyfluoroalkyl ether sulfonate(F-53B) for 7 days. Results provide insight into the molecular mechanisms by which PFASs interfere with osteogenic differentiation potential in HBMSCs.

overall_design: The expression profile of HBMSCs grown for 7 days in basic medium supplemented with DMSO vehicle, 100 nM PFOS, 100 nM PFOA, 100 nM PFHxS or100 nM F-53B, with the three biological replicates, were examined using microarray analysis.

first: Wei

last: Liu

first: Hui

last: Qin


title: ATAC-seq profiling of open chromatin with global epigenetic and transcriptional trends in two-line hybrid rice

first: jin

last: jing

state: Hubei

address: Wuhan, Hubei Province, P.R.China

department: College of Life Sciences

institute: Wuhan University

summary: The transcriptional regulatory switches responsible for the mechanism of fertility conversion in two-line system of hybrid rice remain unclear.  Here, we employed the ATAC-seq, combined with H3K9ac and H3K4me2 and gene expression analyses, in a rice PTGMS Line Wuxiang S to delineate an integrative chromatin accessibility profiling to uncover the key new regulatory modules in response to temperature fluctuation, which can provide important hypotheses regarding the mechanisms of fertility conversion. Collectively, the potentially active genes with H3K4me2 mark under the permissive state of chromatin can easily be regulated by these transcription factors (TFs). Analyzing TF binding cis-regulatory motifs in differentially accessible chromatin regions identified an ERF-driven regulatory module, that acts as an active transcriptional repressor with temperature-dependent function, specially in WXS(F), which can switch into an activator to control both cell wall development, response to temperature fluctuation, and plant architecture. On the contrary, a MADS/ERF co-regulatory module is unique to the WXS(S) at meiosis period, which tends to directly or indirectly affect various metabolic pathways-related genes to coordinate plant development and growth with proper anther development. Meanwhile, there was a unique accessibility of chromatin on the promoter of UbL40 mRNA in WXS(F), which were found to be regulated by the MADS/ERF module. Our analyses uncovered new TF control modules involved in fertility conversion and shed light on the transcriptional mechanisms as fundamental for further study of genetic manipulations of these transcription factors, in order to prove and elaborate on the specific predictions made by the key model.

overall_design: ATAC-seq was performed on nuclei of a novel PTGMS male sterile line Wuxiang S (WXS) generated by our laboratory, which is derived from a mutant tms5 locus in indica rice. All ATAC-seq experiments were performed in two biological replicates. Genome-wide integrated mapping of mRNA transcripts in three biological replicates and two select histone modifications (H3K4me2 and H3K9ac) were performed. All datasets used in the analysis were developed using the  panicle of WXS(F) and WXS(S) at meiosis period and uninucleate period.

first: Yi

last: Ding

first: Jing

last: Jin


title: RNA-seq reveals differences in liver gene expression rhythms between young and old mice

first: Xiaodong

last: Li

state: Hubei Province

address: Luojia Hill, Wuchang District

summary:
Purpose: We used RNA-seq to compare daily rhythms of gene expression in livers of young and old mice.
Methods:  Livers of young and old mice were processed for RNA-seq at 4-h interval across 2 days. Gene expression level was analyzed by hisat2 and StringTie.
Results: We obtained ~10 million high quality sequencing reads per time point per sample after quality control and alignment. Gene expression levels of ~19,000 transcripts were obtained for both age groups. We found genome-wide differenes in gene expression level as well as rhythms in gene expression.
Conclusions: Our study revealed genomwide differences in the level and rhythm of liver gene expression between young and old mice.

overall_design: Mouse livers were collected at 4-h interval across two days from both young and old mice  and RNA-seq was performed to analyze gene expression.

first: Chengwei

first: Jialou

last: Zhu

first: Changxia

last: Gong


title: The profiling of miRNA expression in mock and fuison HBx-knockdowned cells

first: Ryosuke

summary: To comprehensively characterize the biological function of fusion HBx, the expression level of miRNAs in mock and fusiion HBx-knockdowned cells was investigated based on microarray.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: After establishment of cells stably knockdowned for fusion HBx, the expression level of miRNAs in mock and fusiion HBx-knockdowned cells was investigated based on microarray.


title: Effect of long-term exercise training on lncRNAs expression in the vascular injury of insulin resistance

city: changsha

first: fan

last: zheng

state: Hunan

address: Xiangya Road 87#

institute: Xiangya hospital

summary: The present study identified a panel of dysregulated lncRNAs and mRNAs that might serve as potential biomarkers relevant to the vascular injury in insulin resistance induced by high-fat diet. Exercise might alleviate the vascular injury in insulin resistance via targeting FR402720 and FR030200.

overall_design: In this study, 24 male C57BL/6J mice were randomly divided into three groups: control group (ND, n=8), high-fat diet group (HF, n=8), and high-fat diet plus exercise training group (HE, n=8). Glucose tolerance test, insulin tolerance test, fasting plasma glucose, serum insulin level, insulin resistance index, and morphological observations with the electron microscope on the aorta endothelium were applied after 12-week intervention to evaluate the effects of exercise on insulin sensitivity and vascular injury in the three groups. An lncRNA microarray analysis was applied to investigate the global differential expressions of lncRNA and mRNA in aorta endothelium among three groups and the results were further verified by qPCR. Hypergeometric distribution analysis was further applied to figure out the possible functions of these aberrantly expressed lncRNAs.

first: Fan

last: Zheng

first: Suixin


title: The profiling of gene and miRNA expression in mock and fuison HBx-knockdowned cells

last: Muroyama

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

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

overall_design: Refer to individual Series


title: H3K27Ac ChIP-seq on Patient Dirived Xenograft (PDX) material from one T-cell acute lymphoblastic leukemia (T-ALL) patient.

city: Memphis

first: Jinghui

last: Zhang

state: TN

address: 262 Danny Thomas Place

department: Computational Biology

institute: St. Jude Children's Research Hospital

summary: ChIP-seq experiment was carried out to characterize enhancers in one T-ALL PDX sample.

overall_design: H3K27Ac ChIP-seq

first: Yu


title: High-throughput sequencing analysis of miRNAs expression profiles in the HCT116 colorectal cancer sublines resistant to oxaliplatin (Oxa) or 5-fluorouracil (5-FU).

city: Vilnius

first: Raimundas

last: Ražanskas

address: Sauletėkio al. 7

department: Institute of Biotechnology, Life Sciences Center

country: Lithuania

institute: Vilnius University

type: Non-coding RNA profiling by high throughput sequencing

summary:
In the present study, we investigated miRNA expression changes caused by aquired chemoresistance to 5-FU or Oxa. 40 and 14 miRNAs were detected as differentially expressed in 5-fluouracil- and oxaliplatin-resistant colorectal HCT116 sublines, respectively.
Differentially expressed miRNAs determined in the present study could be applied for further development of diagnostic and therapeutic applications for colorectal cancer carcinoma resistant to 5-FU or Oxa.

overall_design: miRNA expression profiles of resistant to 5-FU or Oxa colorectal carcinoma HCT116 sublines and parental HCT116 cell line were analyzed using Illumina MiSeq v2 miRNA sequencing by Illumina MiSeq system.

first: Stasė

last: Gasiulė

first: Giedrius

last: Vilkaitis


title: Genetic interaction mapping (GIM) for factors involved in RNA and protein synthesis and degradation

city: Paris

first: Cosmin

last: Saveanu

address: 25-28 rue du docteur Roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

summary:
A S. cerevisiae strain a gene of interest mutated or deleted was combined with two collections of yeast mutants: one in which non-essential genes were deleted and one in which an long 3' UTR extension has been added to the mRNA of essential genes (GIM method, Decourty et al., 2008). Combined double-mutant deletion cells growth was quantified using barcodes that are specific for each gene mutation. A reference population was obtained by mixing the results of 15 GIM screens DNA prior to barcode amplification and labeling (Decourty et al., in preparation).
The identification of genetic interactions between genes involved in different cellular pathways indicate new functions for previously characterized genes and new links between

overall_design: 312 independent experiments were tested using Agilent microarrays


title: Re-sequencing data used for calling CNVs

city: Chengdu

first: Song

last: Yang

address: No.211, Huimin Road, Wenjiang District, Chengdu City, Sichuan Province, P.R.China

institute: Sichuan Agricultural University College of Animal Science and Technology

summary: Liver tissue was used for  DNA library construction.

overall_design: We sequenced Northeast min pig breed liver tissue using illumina Hiseq 2500 platform

first: Yan

first: Yang

last: Song

first: Mingzhou


title: Nitrate fertilizer alleviates ammonium toxicity by enhancing ACLA-3 in Panax notoginseng roots

city: Kunming

first: Yun

state: Yunnan

address: 452 Fengyuan Road

institute: Yunnan Agricultural University

summary: Nitrogen is one of the essential elements for plant growth. NH4+ and NO3- are two major forms of absorbing element N for higher plants. In this study we found that the growth of Panax notoginseng is inhibited when only adding ammonium nitrogen fertilizer, and adding nitrate fertilizer can alleviate the toxicity caused by ammonium. We use RNA-seq to identify genes that are related to the alleviated phenotypes after introducing NO3- to Panax notoginseng roots under NH4+ stresses. Twelve RNA-seq profiles in four sample groups, i.e., control, samples treated with NH4+, samples treated with NO3- only, and treated with both NH4+ and NO3- were obtained and analyzed to identify deregulated genes in samples with different treatments. ACLA-3 gene is downregulated in NH4+ treated samples, but is upregulated in samples treated with NO3- and with both NH4+ and NO3-, which is further validated in another set of samples using qRT-PCR. Our results suggest that unbalanced metabolism of nitrogen and nitrogen is the main cause of ammonium poisoning in roots of Panax notoginseng, and NO3- may significantly upregulate the activity of ACLA-3 which subsequently enhances the citrate cycle and many other metabolic pathways in Panax notoginseng root. These potentially increase the integrity of the Panax notoginseng roots. Our results suggest that introducing NO3- fertilizer is an effective means to prevent the occurrence of toxic ammonium in Panax notoginseng root.

overall_design: Illumina sequencing of RNA-seq libraries from 3-day-old seedlings

first: Ye

first: Dahui

last: Liu


title: mRNA expression of tumor-promoting molecules treated KYSE410 cells

city: Beijing

first: Jie

last: Chen

address: No. 52 Fucheng Road Haidian District Beijing

institute: Peking University Cancer Hospital

summary:
KYSE410 cells were tranfected with NOX5 plasmid in the presence or absence of HIF-1α inhibitor-BAY87-2243 and mRNA expression of tumor-promoting molecules were assayed by RiboArray Human mRNA Array
investigation of the critical gene participating in the process of NOX5/HIF-1α-mediated ESCC progression.

overall_design: We designed this experiment to srceen for mRNA whose expressions are regulated by NOX5/HIF-1α axis in KYSE410 cells

first: Qimin

last: Zhan


title: miRNA expression profiling of murine LPS-stimulated dendritic cells exposed to quercetin

city: Castellana Grotte (BA)

first: Grazia

last: Serino

address: Via Turi, 27

country: Italy

institute: National Institute of Gastroenterology “S. de Bellis”, Research Hospital

summary: Dendritic cells (DCs) are the most potent antigen-presenting cells that play an important role in the crosstalk between the innate and the adaptive immune response. We identified quercetin exposure as an effective strategy to suppress DCs inflammatory response induced by LPS. In this study, using NGS analysis, we examined the effect of quercetin on miRNAs expression in DCs. We defined a signature of 113 miRNAs differentially regulated in LPS-stimulated DCs after quercetin exposure. Among them, we observed an upregulation of miR-369-3p that potentially regulated C/EBP-beta. We functionally demonstrate that the loss of function of miR-369-3p in LPS-stimulated DCs during quercetin exposure led to an increase of C/EBP-beta and its downstream targets TNFα and IL6. Conversely, we showed that the ectopic induction of miR-369-3p even without quercetin suppresses the inflammatory response of LPS reducing C/EBP-beta, TNFα and IL6 production. In vivo, oral administration of quercetin induces miR-369-3p expression. These data demonstrate that a key mediator of immunosuppressive effect of quercetin is miR-369-3p. These findings could have potentially therapeutic implications since the induction of miR-369-3p expression may have anti-inflammatory effect.

overall_design: miRNA profiling of bone-marrow dendritic cells isolated from 4 wild-type mice. Dendritic cells were analyzed before and after quercetin exposure with and without LPS stimulation

first: Vanessa

last: Galleggiante

first: Stefania

last: De Santis

first: Marina

last: Liso

first: Marcello

last: Chieppa


title: G-protein coupled receptor kinase 2 safeguards epithelial phenotype in Head and Neck Squamous Cell Carcinomas.

city: Madrid

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

country: Spain

institute: CIEMAT

summary: Head and neck squamous cell carcinoma (HNSCC) arises from the mucosal lining of the upper aerodigestive tract and display few treatment options in advanced stages. Despite increased knowledge of HNSCC molecular biology, the identification of new players involved in triggering HNSCC recurrence and metastatic disease is needed. We uncover that G-protein-coupled receptor kinase-2 (GRK2) expression is reduced in undifferentiated, high-grade human HNSCC tumors, whereas its silencing in model human HNSCC cells is sufficient to trigger epithelial-to-mesenchymal transition (EMT) phenotypic features, an EMT-like transcriptional program and enhanced lymph node colonization from orthotopic tongue tumors in mice. Conversely, enhancing GRK2 expression counteracts mesenchymal cells traits by mechanisms involving phosphorylation and decreased functionality of the key EMT inducer Snail1. Our results suggest that GRK2 safeguards the epithelial phenotype, whereas its downregulation contributes to the activation of EMT programs in HNSCC

overall_design: Differential expression analysis between Cal27 and Cal27-shGRK2 cancer cells

first: Julia

last: Palacios-Garcia

first: Federico

last: Mayor Jr

first: Catalina

last: Ribas


title: Transcriptional signature of human placental mast cells

city: marseille

first: Amira

last: Ben Amara

address: 27  Boulevard Leï Roue

institute: IHU-CRCM

summary: Uterine Mast cells (MCs) are essential for placentation, implantation and growth of fetus. In contrast, the functions of placental MCs are poorly investigated. The objective of the study was to evaluate the transcriptional profile of human placental MCs using whole genome microarray. We isolated MCs from placenta from healthy at term donors with CD117 and IgE antibodies, and used HMC-1.2 cell lines as controls. Data analysis revealed 16,468 genes modulated in human placenta MCs as compared with HMC-1.2 cell lines; most of them (83%) were up-regulated. The differentially expressed genes in placental MCs were enriched with three biological categories: immune response, FcReI signaling and reproduction processes. The two first categories revealed the importance of immune gene expression including chemokines, cytokines, interferon, and major histocompatibility complex antigens in placental MCs. A set of genes were modulated in FcReI process suggesting a role of IgE-mediated activation. Finally, in pregnancy category, we identified specific genes of WNT pathway and those involved in response to estrogen and progesterone. Taken together, human placental MCs exhibited a unique transcriptional profile enriched with immune response and pregnancy genes, which reflects the impact of placenta environment on MC functions.

overall_design: Uterine mast cells (MCs) were isolated from human term placenta with positive selection using CD117 and IgE antibodies coupled with magnetics beads and HMC-1.2 cell lines were used as controls. For each condition ( MCS and HMC-1), each microarray is a replicate of the same biological sample.

first: Soraya

last: Mezouar

first: Joana

last: Vitte

first: Christian

last: Devaux

first: Jean-Louis

last: Mege


title: Whole kidneys at embryonic day 17.5: wildtype (WT) vs. various combinations of the conditional homozygous Ezh2-knockout (Ezh2-KO) from Six2-positive nephron progenitor cells (NPC) and/or germline Ezh1-knockout (Ezh1-KO)

city: New Orleans

first: Samir

middle: S

last: El-Dahr

state: LA

address: 1430 Tulane Ave

department: Pediatrics

country: USA

institute: Tulane University School of Medicine

summary: Transcriptional profiling of whole kidneys from Six2CreEGFP mice without (WT) or with (KO) homozygously floxed Ezh2 alleles at the age of embryonic day 17.5. This experiment aimed to uncover the genome-wide alternation in gene expression resulting from the removal of Ezh2 gene in the nephron progenitor population (Six2 positive) in combination with the removal of Ezh1 gene from germline, and successive changes to the series of events in kidney development.

overall_design: Two-condition experiment, WT vs. KO kidneys. Biological replicates: 4 for each of 4 different genotypes

first: Hongbing

last: Liu


title: Chemical nucleoside conversion-based measurement of RNA stability by targeted and untargeted mRNA 3´ end sequencing

city: Vienna

first: Brian

last: Reichholf

address: Doktor-Bohr-Gasse 3

institute: IMBA

summary: Gene expression profiling by high-throughput sequencing determines changes in gene expression only at steady state but prevents our understanding of the underlying gene expression kinetics. Here, we describe a protocol that combines metabolic RNA labeling with thiol-specific chemical nucleoside conversion to determine the stability of polyadenylated RNA transcripts. And we provide a targeted mRNA 3   end library preparation protocol that enable to robustly determine the stability even of RNA transcripts that escape robust detection in untargeted libraries. The described methods enable cost-effective insights into the kinetics underlying steady-state gene expression in order to study the mechanisms underlying the regulation of gene expression at a transcript-specific and genomic scale.

overall_design: Mouse embryonic stem cells (mES cells) were subjected to s4U metabolic RNA labeling for 12h, followed by washout and chase using non-thiol-containing uridine. Total RNA was prepared at various time points along the chase (0h, 0.5h, 1h, 3h, 6h, and 12h). Total RNA was then subjected to alkylation and targeted RNA-seq using custom-designed primers.

first: Veronika

last: Herzog

first: Nina

last: Fasching

first: Stefan

last: Ameres


title: Gene expression data of glioblastoma multiforme U-87 cells exposed to targeted electromagnetic fields

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

summary:
A novel application of a non-invasive, electromagnetic field technology has a significant inhibitory effect on the proliferation of glioblastoma multiforme U-87 MG cells in culture. This study reports the cellular and molecular responses of U-87 MG cells to the effects of a tunable, non-ionizing radiation technology that does not induce the serious side effects commonly observed with chemotherapy. The broadband (RF/Low Microwave) electromagnetic field is tuned by means of oscillating wave forms, selected reference materials and a positive feedback loop (RGFIELDS™). By simultaneously targeting specific molecules (oligonucleotides and proteins) that contribute to pathogenesis of glioblastoma with this technology, the continuous exposure of cells for 54 h results in the inhibition of cell growth and a concurrent increase in cell death.
We used microarrays to elucidate the cellular processes involved in the response of U-87 MG cells to exposure to RGFIELDS™ and identified mRNA and non-coding RNA sequences that are differentially modulated 1.5 fold or more.

overall_design: Total RNA was isolated from three independent biological replicates of U-87 MG cells exposed continuously for 54 h to RGFIELDS™ targeting selected reference materials (oligonucleotides and proteins), and from unexposed control cells cultured under identical conditions.

first: Carmen

middle: J

last: Narvaez

first: Samantha

middle: K

last: Mall

first: Aaron

last: Fountain

last: Parr

first: Boris

last: Kokorin

first: Stephen

last: Botsford

first: Joseph

last: Startari


title: Expression data of Familial adenomatous polyposis (FAP) organoids

city: Koto-ku

first: Ryoji

last: Yao

state: Tokyo

address: 3-8-31 Ariake

institute: The JFCR-Cancer Institute

summary:
FAP is an autosomal-dominant inherited disease caused by germline mutations in the APC gene 1. Two major FAP phenotypes, CFAP and AFAP, can be distinguished based on polyp numbers and age of onset. CFAP is characterized by the presence of hundreds to thousands of polyps. About half of these patients develop adenomas by age 15, and 95% develop adenomas by age 35. AFAP patients exhibit a milder phenotype than CFAP patients; AFAP is characterized by fewer polyps, later adenoma onset, and lower CRC risk.
We used microarrays to analyze the expression profiles of organoids established from three CFAP and two AFAP patients.

overall_design: Organoids were collected for RNA extraction and hybridization on Affymetrix microarrays. Each sample represents an independent organoid established from a patient. HCT number represents patient and 5 patients were analyzed in this study.


title: Difference of gene expression between colorectal tumor tissues with and without metastasis

city: Guangzhou

first: wang

middle: yi

last: qing

institute: South Medical University

summary: To identify the difference of genes expression bewteen colorectal tumor tissues with and without metastasis

overall_design: Either of the tissues,C1,C2,C3,CM1,CM2 and CM3,is collected in Department of pathology , Nanfang Hospital(Guangzhou,China)

first: Shuang

last: Wang

first: Yiqing


title: SNP data of Familial adenomatous polyposis (FAP) organoids

summary:
FAP is an autosomal-dominant inherited disease caused by germline mutations in the APC gene 1. Two major FAP phenotypes, CFAP and AFAP, can be distinguished based on polyp numbers and age of onset. CFAP is characterized by the presence of hundreds to thousands of polyps. About half of these patients develop adenomas by age 15, and 95% develop adenomas by age 35. AFAP patients exhibit a milder phenotype than CFAP patients; AFAP is characterized by fewer polyps, later adenoma onset, and lower CRC risk.
We used microarrays to analyze chromosome abberation of organids established from FAP patients.

overall_design: Organoids were collected for DNA extraction and hybridization on Affymetrix microarrays. Each sample represents an independent organoid established from a patient.  HCT number represents patient


title: Expression data and SNP data of Familial adenomatous polyposis (FAP) organoids


title: Impaired Cell Fate by Gain-of-function Mutations in a Chromatin Reader

status: Public on Jan 03 2020

city: Grand Rapids

first: Hong

last: Wen

state: Michigan

address: 333 Bostwick Ave. N.E.

department: Center for Epigenetics

institute: Van Andel Research Institute

summary: We previously identified the YEATS domain-containing protein ENL as a reader of histone acetylation. Recently, hotspot mutations in ENL were frequently found in Wilms’ tumor, the most common type of pediatric kidney cancer. Here, we report that these cancer-associated mutations in the ENL YEATS domain confer gain of functions in transcriptional control and impair kidney differentiation by driving self-reinforced chromatin targeting. Ectopic expression of ENL mutants in kidney cell lines resulted in transcriptional changes of genes enriched in embryonic nephron progenitors and Wilms’ tumor. When tested in a nephrogenesis assay, ENL mutant expression led to undifferentiated structures resembling those observed in human Wilms’ tumor. Genome-wide analyses revealed that while mutant ENL bound to largely similar genomic loci as wild-type ENL, they exhibited increased occupancy at a subset of targets, including developmentally critical genes such as the HOXA cluster. The cancer-associated mutations enabled self-reinforced recruitment of ENL on chromatin by promoting self-association, resulting in the formation of discrete nuclear puncta that are characteristic of phase-separated biomolecular condensates. Enhanced occupancy of ENL mutants led to a marked increase in the recruitment and activity of transcription elongation machinery that enforces active transcription from target loci. Collectively, our studies represent, to our knowledge, the first discovery that cancer-associated mutations in a chromatin reader drive self-reinforced chromatin targeting, which in turns, perturbs developmental programs and derails normal cell fate control during mammalian development towards an oncogenic path.

overall_design: Established stable cell lines to ectopic express either wild type or mutant human ENL in HEK293 and HK2 cell lines, and used these cell lines for Flag, CDK9 and Pol II S2P ChIP-seq and RNA-seq analysis.

first: Xiaodong

last: Cui

first: Liling

last: Wan


title: Frataxin deficiency in Friedreich?s Ataxia is associated with reduced levels of HAX-1, a regulator of cardiomyocyte death and survival.

city: Rome

first: Silvia

last: Gioiosa

address: Via dei Tizii,6

department: Supercomputing Applications and Innovation

institute: CINECA

summary: Friedreich's Ataxia (FRDA), a rare, inherited, progressive degenerative disease, is caused by a defective expression of mitochondrial protein frataxin (FXN), due to homozygous hyper-expansion of GAA triplets in the gene which severely reduce its transcription. FXN is crucial for cell survival and its deficiency in humans critically affects viability of neurons, cardiomyocytes and pancreatic beta cells. Around two thirds of individuals with FRDA show typical manifestation of hypertrophic cardiomyopathy, that can progress in heart failure and death. Except for FXN, very few genes have been correlated with ataxia and cardiac disease in FRDA. To identify other genes involved in pathogenesis of FRDA, a microarray analysis on FRDA patient's lymphoblastoid cells stably reconstituted with FXN was performed. HS-1 associated protein X-1 (HAX-1), a family of proteins playing important roles in the protection of cardiomyocytes from apoptosis, is the highest up-regulated transcript (FC=+2, p<0.0006). HAX-1 is highly expressed in heart and HAX-1 heterozygous-deficient hearts exhibit increases in infarct size.  The microarray result was further assessed with qRT-PCR and western blot analysis performed on HEK293 stably transfected with empty vector or FXN-vector and lymphoblasts from FRDA patients compared to clinically unaffected heterozygous parents, confirming a strong co-expression of HAX-1 and FXN both at mRNA and protein level. Moreover, analysis of FXN and HAX-1 in peripheral blood mononuclear cells (PBMCs) of FRDA patients (n=13), heterozygous parents (n=6) and non-correlated healthy controls (n=13) revealed that their expressions are correlated. The positive correlation is more significant in FRDA patients showing a cardiac disease (10/13).  The positive correlation between frataxin and HAX-1 expression level suggests a potential link of HAX-1 expression to pro-survival or protective cellular pathways related to frataxin. Thus, HAX-1 may be considered a specific biomarker of cardiomyopathy in FRDA and may represent a prognostic implement in these patients. Moreover, the discovery of novel genetic "risk" or "protective" factors in cardiomyopathy is crucial to improve risk stratification strategies and to identify new therapeutic targets.

overall_design: A microarray analysis was performed on FRDA patient's lymphoblastoid cells GM15850 stably reconstituted with FXN. As control, the patient's lymphoblastoid cells were transfected with an empty vector. The experiment was repeated with a dye swap.

first: F

last: Amati

last: Malisan

first: S


title: Glycosylation-related gene expression in gastrointestinal cell line HT29 in response to infection by Campylobacter jejuni

city: Galway

first: Michael

last: Cairns

address: University Road

department: NCBES

country: Ireland

institute: NUI Galway

summary:
HT29 cells were infected with C. jejuni 11168 and the transcriptome of infected and uninfected HT29 were compared by micoarray analysis (Affymetrix).
The study focused on glycosylation related genes as these regulate the structures that have a major role to play in pathogen-host cell interaction. This experiment is related to another experiment where the parental cell line (HT29) is replaced by the derivative cell line (E12). E12 cells secrete an adherent mucus layer whereas HT29 cells do not.

overall_design: Two control uninfected HT29 replicates are compared to two C. jejuni (11168) infected HT29 replicates

first: Ananya

last: Gupta

first: Lokesh

last: Joshi


title: A mosaic renal myeloid subtype linked to immune escape correlates with poor patient survival in clear cell renal cell carcinoma [ex vivo]

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

country: Germany

institute: LMU Munich

summary: Mononuclear phagocytes moderate tissue repair, immune activation and tolerance. In the renal tubulo-interstitium, specialized DCs help maintain homeostasis and protect tubuli from immune injury. Human renal cell carcinoma is immunogenic; yet immunotherapies that target T-cell dysfunction show limited clinical efficacy suggesting additional mechanisms of immunoinhibition. We previously described “enriched-in-renal cell carcinoma” (erc)DCs. In tumor tissue, they are found in tight contact with T cells which are dysfunctional. Here we describe that ercDCs exhibit a distinct polarization state imparted by tissue-specific signals characteristic for ccRCC and renal tissue homeostasis. The resulting mosaic transcript signature includes features associated with host defense activity, angiogenesis/invasion and T-cell inhibition. An ercDC-specific profile was predictive for patient survival and suggests potential therapeutic targets for improved immunotherapy.

overall_design: RNA isolated from FACS-sorted donor cells.

first: Dorothee

last: Brech

first: Evangelos

last: Kokolakis

first: Martin

last: Irmler

first: Johannes

last: Beckers

first: Florian

last: Buettner

first: Elke

last: Schaeffeler

first: Stefan

last: Winter

first: Matthias

last: Schwab

first: Peter

last: Nelson

first: Elfriede

last: Noessner


title: Genome-wide mapping of CTCF binding in asynchronous and mitotic cells

city: Bloomington

first: Gabriel

last: Zentner

state: IN

address: 915 E 3rd St

department: Biology

institute: Indiana University

summary: CCCTC-binding factor (CTCF), a conserved and essential regulator of genome architecture bearing a unique complement of 11 zinc fingers (ZFs), has been reported to remain associated with chromatin throughout mitosis and has thus been proposed to act as a bookmark to ensure rapid reestablishment of chromatin structure after cell division. However, little is known about how CTCF is regulated during mitosis. Using a phospho-specific antibody, we found that phosphorylation of CTCF threonine 431, contained within an atypical ZF linker unique to vertebrate CTCF, is highly enriched in mitotic cells and that this phosphorylated form of CTCF is preferentially localized to mitotic chromosomes. We show that T431 mutations abolish the association of CTCF with mitotic chromatin, arguing that T431 phosphorylation is necessary for CTCF mitotic retention. Furthermore, mutation of the CTCF paralog BORIS to accommodate phosphorylation at the residue corresponding to CTCF T431 induces mitotic retention of BORIS. Our data support previous work demonstrating mitotic retention of CTCF and provide new insight into how CTCF remains associated with chromatin during mitosis. Furthermore, our results indicate that phosphorylation of ZF linkers is not exclusively associated with dissociation of ZF-containing proteins from DNA during mitosis.

overall_design: Examination of CTCF binding in asynchronous and mitotic cells

first: Sungyun

last: Kang


title: Gene expression analysis of the hippocampus in Il18+/+ and Il18-/- mice at 12 weeks of age

city: Nichinomiya

first: Kyosuke

last: Yamanishi

state: Hyogo

address: 1-1, Mukogawa

department: Neuropsychiatry

institute: Hyogo College of Medicine

summary: Interleukin-18 (IL-18) was one of the inflammatory cytokines and related to major depressive disorder (MDD) and dementia. Compared with Il18+/+ mice, IL-18 knockout (Il18−/−) mice developed impaired learning and memory, more anxiety, and less motivation. To reveal the mechanism, the microarray was performed.

overall_design: The hippocampus of mice Il18+/+ and Il18-/- C57BL/6 N mice at 12 weeks of age was extracted. We mixed tatal RNA from 7 mice prefrontal cortex per each.

first: Hisato

last: Matsunaga


title: Genome-wide mRNA expression profiling of WT MEFs and NSD2 KO MEFs

city: New York

first: Mahesh

last: Bachu

email: bmahesh07@gmail.com, bachum@hss.edu

state: New York

address: 535 E 70th St 6th Floor

institute: Hospital For Special Surgery

summary: NSD2 (also known as Whsc1, MMSET) play a role in H3K36 methyl transferase. Here we showed that 199 ISGs of the total 393 ISGs after 2h IFN treatment were up regulated in NSD2 KO MEFs, suggesting negatively regulate ISGs induction. IFN pretreatment creates transcriptional memory. In this study we identified 129 ISGs were memory ISGs and 40 ISGs were non-memory ISGs.

overall_design: RNA-seq WT MEFs and NSD2 KO MEFs

first: Ryota

last: Ouda


title: NSD2 negatively regulate innate immune response through Zmynd11

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

overall_design: Refer to individual Series


title: Genome-wide analysis of H3.3, H3K36me2, H3K36me3 and ZMYND11 accumulation in WT MEFs and NSD2 KO MEFs.

summary: We found that the incorporation of histone H3 variant H3.3 was impaired and the accumulation of ZMYND11, which specifically binds to H3.3K36me3, was decreased in NSD2 KO MEFs. About H3K36me2, the average gene body profiles of H3K36me2 showed preferential enrichment of H3K36me2 at the promoter and first half of the genic regions. We examined H3K36me2 mark in super enhancer regions using the ROSE super enhancer prediction program and identified of the 519 super enhancer islands of H3K36me2 in WT MEFs the H3K36me2 signals were decreased in NSD2 KO MEFs

overall_design: Chip-seq WT MEFs and NSD2 KO MEFs


title: Identification of resistance mechanisms to anti-HER2 antibody in breast cancer cell line BT-474

first: Juan

last: Madoz-Gúrpide

address: Avda. Reyes Católicos, 2

department: Anatomical Pathology

institute: Health Research Institute Fundación Jiménez Díaz

summary:
Background: The addition of the anti-HER2 antibody pertuzumab to trastuzumab/chemotherapy treatment in HER2+ breast cancer significantly improves clinical outcome. Concomitantly, the drug-antibody conjugate T-DM1 (trastuzumab-emantasine) has demonstrated efficacy, at least equal, to the combination of trastuzumab/chemotherapy. Scientific, economic and health challenges emerge from the clinical use of these novel anti-HER2 antibodies, aimed to identify new resistance mechanisms and to select the target breast cancer population.
Objectives: (1) To identify primary resistance mechanisms to anti-HER2 antibodies trastuzumab, pertuzumab, and to the combined trastuzumab/pertuzumab or pertuzumab/T-DM1 therapy, (2) To identify acquired resistance mechanisms to anti-HER2 antibodies trastuzumab, pertuzumab, and to the combined trastuzumab/pertuzumab or pertuzumab/T-DM1 therapy, (3) To develop new combinations of anti-HER2 antibodies with other targeted therapies.

overall_design: Samples: Breast cancer cell line BT-474. Treatments: trastuzumab-conditioned cultures. Control samples: same cell lines with no treatment. Triplicates.

first: Federico

last: Rojo

first: Sandra

last: Zazo

first: Paula

last: González-Alonso


title: Genome-wide mRNA expression profiling of ZMYND11 crispr KO in NIH3T3 cells upon IFN treatment.

summary: ZMYND11 is a ‘reader’ protein, which specifically recognizes H3.3K36me3 and regulate RNA polymerase II elongation. Our RNA-seq data showed that 93 ISGs were up regulated, 47 ISGs were down regulated and 48 ISGs were not changed in ZMYND11 KO.

overall_design: RNA-seq WT NIH3T3 and ZMYND11 crispr KO NIH3T3


title: Expression data from Jaridon 6 on the human esophageal cancer cells

city: Zhengzhou

first: Ling

last: Fu

address: 100# Science Road

department: School of Pharmaceutical Sciences

institute: Zhengzhou University

summary: Jaridon 6, an ent-kaurene diterpenoid derivative from Rabdosia rubescens (Hemsl.) Hara, possesses strong antitumor activity in esophageal cancer cells. This study explored the underlying molecular events of Jaridon 6’s anti-tumor activity in esophageal cancer cells through the cDNA microarray.

overall_design: We wanted to obtain early changes of RNA by Jaridon 6's action on the esophageal cancer 109 cells, especially in early apoptosis stage. The IC50 of Jaridon 6 is 15 µM. When the esophageal cancer 109 cells were acted by 15 µM Jaridon 6 for 16h, the apoptosis rate is approximately 40%, near to the early apoptosis stage. So the esophageal cancer 109 cells were treated with 15 µM Jaridon 6 for 16 h for RNA extraction and hybridization on Affymetrix microarrays.

first: Hong-min

last: Liu


title: Identification and comprehensive analysis of microRNAs and phased small interfering RNAs in Rosa rugosa Thunb [degradome]

city: Kunming

first: Yun

last: Zheng

address: 452 Fengyuan Road

institute: Yunnan Agricultural University

summary: MicroRNAs (miRNAs) are small non-coding RNAs that regulate target mRNAs by inducing degradation or preventing translation of their target mRNAs. Rose, Rosa rugosa Thunb., is an important ornamental and edible plant, yet there are only a few studies on the miRNAs of rose. Here we carried out computational and experimental analysis of miRNAs and phased small interfering RNAs (phasiRNAs) in rose by analyzing 10 small RNA profiles from roots, petals, pollens, stamens, and leaves. To identify the targets of miRNAs and phasiRNAs, we generated a degradome profile for rose leaf which is analyzed using the SeqTar algorithm. This study identified 25 conserved pre-miRNAs, of which 24 have not been reported previously. We also found 22 novel pre-miRNAs. Three hundred and thirty nine 21 nucleotide (nt) PHAS loci, and forty nine 24 nt PHAS loci were also identified. We identified more than 4000 putative targets of the conserved miRNAs using a criteria of less than 4 mismatches between miRNA and targets. Among these targets, at least 171 have shown significant accumulation of degradome reads. Our results demonstrate that the miR482 family triggers the generations of phasiRNAs by targeting nucleotide-binding, leucine-rich repeat (NB-LRR) disease resistance genes in rose. These results significantly enhanced our knowledge of the miRNAs and phasiRNAs, as well as their potential functions in rose.

overall_design: Identification and comprehensive analysis of conserved microRNAs, phased small interfering RNAs and their targets in rose using Illumina HiSeq 2000 sequencer.


title: Expression data from ALDOA overexpression in CL1-0 lung cancer cell line and ALDOA knockdown in CL1-5 lung cancer cell line.

city: Taipei

first: Michael

last: Hsiao

address: Academia Road, Section 2, Nankang, Taipei, 115, Ta

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

summary:
We demonstrate that ALDOA down-regulation shRNAs significantly reduced cell migration and invasion in highly invasive lung cancer cell lines in vitro, as well as in lung metastases in vivo
We used microarrays to analyze the ALDOA regulated gene expression underlying invasion-metastasis cascade.

overall_design: CL1-0 lung adenocarcinoma cells with ALDOA overexpression and CL1-5 cells with ALDOA knockdown were selected for RNA extraction and hybridization on Affymetrix microarrays.

first: Yu-Chan

last: Chang


title: Glycosylation-related gene expression in the mucous-secreting gastrointestinal cell line HT29-MTX-E12 in response to infection by Campylobacter jejuni

last: Cairns

summary:
The HT29 derivative cell line HT29-MTX-E12 (E12) produces an adherent mucus layer predominantly of the gastric MUC5AC mucin when grown on transwells. E12 cells were infected with C. jejuni and the transcriptome of infected and uninfected E12 were compared.
The study focused on glycosylation related genes as these regulate the structures that have a major role to play in pathogen-host cell interaction. This experiment is related to another experiment where the cell line (E12) is replaced by the parental cell line (HT29) and importantly HT29 cells do not produce an adherent mucus layer.

overall_design: Three control uninfected E12 replicates were compared to two C. jejuni (11168) infected E12 replicates

first: Ananya

last: Gupta

first: Lokesh

last: Joshi


title: A mosaic renal myeloid subtype linked to immune escape correlates with poor patient survival in clear cell renal cell carcinoma

first: Tobias

last: Straub


title: A mosaic renal myeloid subtype linked to immune escape correlates with poor patient survival in clear cell renal cell carcinoma [in vitro]

overall_design: Pooled RNA isolated from in vitro cultured cells.

first: Dorothee

last: Brech

first: Evangelos

last: Kokolakis

first: Martin

last: Irmler

first: Johannes

last: Beckers

first: Florian

last: Buettner

first: Elke

last: Schaeffeler

first: Stefan

last: Winter

first: Matthias

last: Schwab

first: Peter

last: Nelson

first: Elfriede

last: Noessner


title: Genome-wide Investigation of Population Structure in Myanmar

first: Ya-ping

last: Zhang

address: 32 Jiaochang Donglu

department: State Key Laboratory of Genetic Resources and Evolution

institute: Kunming Institute of Zoology, Chinese Academy of Sciences

summary: Myanmar locates in the crossroads of South Asia, Southeast Asia, and East Asia, and is known for high culture diversity in different ethnic groups. It is considered to be important for understanding human evolutionary history and genetic diversity in East Eurasia. However, relatively few studies have examined the population structure and demographic history in Myanmar to date. In this study, we analyzed more than 220,000 genome-wide SNPs in 175 new samples of five ethnic groups from Myanmar and compared them with the published data. Our results showed that the Myanmar population is intricately substructured, with the main observed clusters corresponding roughly to western/northern highlanders (Chin, Naga, and Jingpo) and central/southern lowlanders (Bamar and Rakhine). The gene flow inferred from South Asia has a substantial influence (~11%) on the gene pool of central/southern lowlanders rather than western/northern highlanders. The genetic admixture is dated around 650 years ago. These findings suggest that the genome-wide variation in Myanmar was likely shaped by the linguistic, cultural, and historical changes.

overall_design: To investigate the genetic structure of Myanmer populations, we genotyped 240 samples of four different ethnic groups (i.e. Bamar also Burman, Chin, Naga, and Rakhine) in Myanmar, neighboring Chinese minor ethnic groups (Jingpo), and Africans from Nigeria conducted on Illumina HumanOmniZhongHua-8 BeadChip. Three Africans here were used as out group. Sample type is normal blood. For general population genetics analysis, we filtered out 4 samples for duplication, 2 for wrong gender information, and 56 samples for close genetic relationship (using IBD test). Finally, 175 genetic-independent individuals data were used to reflect the genetic structure of Myanmar.

first: Min-Sheng

last: Peng

first: Wen-Zhi

last: Wang

first: Quan-Kuan

last: Shen

first: Jun-Dong

last: He

first: Shi-Fang

last: Wu

first: Chun-Ling

last: Zhu

first: Robert

last: Murphy

first: Haipeng

last: Li

first: Ya-Ping