title: RNASeq analysis of NB1691 neuroblastoma cells treated with MDM2-p53 inhibitor RG7388 alone and in combination with temozolomide

city: Newcastle

first: John

last: Casement

address: Framlington Place

department: Bioinformatics Support Unit

country: United Kingdom

institute: Newcastle University

summary: To further identify potential mechanisms involved in combining RG7388 with temozolomide, GSEA was performed and revealed that RG7388 and temozolomide act cooperatively to upregulate the p53 pathway and downregulate MYC targets, the former resulting in significantly greater induction of several apoptotic genes.

overall_design: NB1691 neuroblastoma cells were treated with DMSO, RG7388 alone, temozolomide alone, or RG7388 and temozolomide in combination for 24 and 72 hours. All experiments were performed in triplicate.

first: Deborah

last: Tweddle

first: Lindi

last: Chen


title: Gene expression responses of Ceratitis capitata (medfly) males to experimental evolution under divergent larval nutrition

status: Public on May 14 2019

city: Norwich

first: Tracey

last: Chapman

address: Norwich Research Park

department: School of Biological Sciences

institute: University of East Anglia

type: Expression profiling by high throughput sequencing

summary: The aim was to profile the gene expression responses of males to divergent selection on larval diets, using two different dietary regimes (sucrose-based ASG 'A' diet, versus starch-based Starch 'S' diet). 3 x replicated populations of medfly originating from the same base strain were set up on each of these two regimes (adult nutrition was standardised) and maintained. At generation 62, the flies were subjected to two generations of rearing on a glucose common garden diet (to standardise rearing to minimise proximate nutritional effects and minimise maternal carry over). Adult males reared under these standardised conditions were then snap frozen at 7 days post eclosion. The head-thorax and abdomen body parts of these males were then subjected to mRNA-seq. The overall aim was to describe the evolved differences in gene expression associated with the divergent larval diets.

overall_design: There were 2 nutritional regimes (ASG 'A', and Starch 'S') x 3 replicates x 2 body parts (head-thorax, abdomen) = 12 samples. Total RNA was extracted using the mirVana extraction kit. RNA-seq was conducted on pools of 17-22 individuals per treatment. mRNA-seq was single end, 50 nt, standard Illumina adapters on the HiSeq 2500 platform.

first: Will

last: Nash

first: Irina

last: Mohorianu


title: Transcriptome and Genomic DNA methylation distinguishes human FCD subtypes

status: Public on May 13 2019

city: Melbourne

first: Assam

last: El-Osta

address: 75 Commercial Road

country: Australia

institute: Baker Heart and Diabetes Institute

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Extracellular Vesicle P100 Fraction Small RNAs

city: Clemson

first: David

middle: Matthew

last: Feliciano

state: South Carolina

address: 132 Long Hall

department: Biological Sciences

country: USA

institute: Clemson University

type: Non-coding RNA profiling by high throughput sequencing

summary: Extracellular Vesicles were isolated from primary cultures of neural stem cells (NSCs) and astrocytes by performing serial centrifugation and a 100,000 x g ultracentrifugation step. The goal of this experiment is to compare EV small RNAs from two cell types.

overall_design: EVs were isolated by serial centrifugation from primary neural stem cells (NSCs) cultured from the subventricular zone or cortical astrocytes of CD1 mice. Small RNA libraries were constructed with the CleanTag Small RNA Library Preparation Kit (TriLink,Cat# L-3206) according to the manufacturer's protocol. The final purified library was quantified with High Sensitivity DNA Reagents (Agilent Technologies, PO# G2933-85004) and High Sensitivity DNA Chips (Agilent Technologies, PO# 5067-4626). The libraries were pooled, and the 140bp to 300bp region was size selected on a 8% TBE gel (Invitrogen by Life Technologies, Ref# EC6215). The size selected library is quantified with High Sensitivity DNA 1000 Screen Tape (Agilent Technologies, PO #5067-5584), High Sensitivity D1000 reagents (Agilent Technologies, PO# 5067-5585), and the TailorMix HT1 qPCR assay (SeqMatic, Cat# TM-505), followed by a NextSeq High Output single-end sequencing run at SR75 using NextSeq 500/550 High Output v2 kit (Cat #FC-404-2005, Illumina, San  Diego, CA) according to the manufacturer's instructions.

middle: M


title: Identification of the O-GlcNAc-regulated alternative splicing events by performing RNA sequencing on HeLa cells with altered O-GlcNAc level.

city: Beijing

first: Xing

address: Chengfu Road 202

country: China

institute: Peking University

summary: We performed RNA sequencing on HeLa cells treated with OGT inhibitor (Ac4-5SGlcNAc), DMSO, or OGA inhibitor (Thiamet-G) and obtained about 100 million paired-end reads (150 bp) for each replicate. Then the sequencing data was analyzed by MISO to select the O-GlcNAc-regulated alternative splicing events.

overall_design: Identify the O-GlcNAc-regulated alternative splicing events.

first: Mengting

last: Han

first: Rongbing

last: Huang


title: Maternal to zygotic transition：A two-step process with two phases of ZGA occurs in zygote right after fertilization in Arabidopsis

status: Public on May 12 2019

city: Wuhan

first: Peng

last: Zhao

address: Luojia Hill

department: College of Life Sciences

institute: Wuhan University

summary:
The goal of the present study is to analyze the characteristics of maternal to zygotic transition (MZT) in Arabidopsis.
The maternal-to-zygotic transition (MZT) is an essential developmental turning point during the alternation of generations in both plants and animals. In animals, early embryogenesis is maternally controlled and zygotic genome activation (ZGA) starts much later. However, in plants, the timing of MZT and parental contributions to the zygotic transcriptome remain unclear. To address above mentioned questions, we selected Arabidopsis as model plant for the analysis. Regarding to the characteristics of MZT, egg cells, embryos including spherical zygote, elongated zygote, 1-cell embryo and 32-cell embryo were isolated and collected for RNA sequencing. Hybrid zygotes at two representative stages from the reciprocal crosses between polymorphic Arabidopsis Columbia (Col) and Landsberg erecta (Ler) accessions were also sequenced for investigating the parental contributions. We demonstrate that plant MZT occurs during the zygote stage and is a two-step process, first involving rapid maternal transcript degradation and, second, large-scale de novo transcription. Parental contributions to the zygotic transcriptome are stage dependent over the course of zygote development; the spherical zygote is characterized by a maternally dominated transcriptome, whereas the elongated zygote genome shows equal parental contributions.

overall_design: Regarding to the characteristics of MZT, egg cells and embryos including spherical zygote, elongated zygote, 1-cell embryo and 32-cell embryo were isolated and collected for RNA sequencing (RNA-seq). Hybrid zygotes at two representative stages from the reciprocal crosses between polymorphic Arabidopsis Columbia (Col) and Landsberg erecta (Ler) accessions were also sequenced to investigate the parental contributions.

first: Mengxiang

last: Sun


status: Public on May 11 2019

city: Moscow

first: Aleksandra

middle: Vital'evna

last: Zinov'eva

address: Delegatskaya, 20

country: Russia

institute: MSMSU

summary: Analysis of retinal gene expression when exposed to laser radiation with a wavelength of 577 nm in the micropulse mode on the retina. The hypothesis tested in the present study was that laser radiation in a micropulse mode leads to a change in the expression of retinal genes. The genes whose expression level was significantly changed were identified - genes involved in the regulation of neoangiogenesis, structural cellular functions, cell proliferation, transcription, differentiation, transmembrane transport, signaling, synaptic transmission, and others.

overall_design: Total RNA obtained from the retinal pigment epithelium and retinal neuroepithelium, subjected to the introduction of PBC, VEGP and laser exposure in the micropulse mode with a wavelength of 577 nm

first: Natalia

middle: A

last: Gavrilova


title: Transcriptomic profiling of O-GlcNAcylated mRNA-protein complexes by using OG-CLAP in HeLa cells.

summary: We report the development of OG-CLAP strategy and the identification of 9840 high-confidence O-GlcNAcylated binding sites by using OG-CLAP. The sequencing depth of each replicate is about 1.3 G.

overall_design: Identification of the RNA binding sites of O-GlcNAcylated proteins by using OG-CLAP strategy.


title: Circular RNA expression profiling and selection of key circular RNAs in the hypothalamus of heat-acclimated rats

city: TianJin

first: Fan

middle: Li

last: Jun

state: TianJin

address: No. 1 Dali Road, Heping District, Tianjin

department: Academy of Military Medical Sciences, Academy of Military Medical Sciences

institute: Institute of Environmental and Operational Medicine

summary: Circular RNAs (circRNAs) play crucial roles in diverse biological processes. However, expression levels and functions of circRNAs related to heat acclimation (HA) are poorly understood. we, for the first time, used comprehensive circRNA expression profiling to investigate circRNA–miRNA interactions in HA rats, to provide a better understanding of mechanisms underlying HA. CircRNA expression profile was performed in rats’ hypothalamus of HA and control group with microarray assays. Bioinformatics analysis was conducted to predict their functions. And differential circRNAs and their regulated downstream miRNAs and mRNAs were quantitatively validated using real-time quantitative polymerase chain reaction (RT-qPCR ). Predicted proteins expression were determined using enzyme-linked immunosorbent assay (ELISA). In total, 53 circRNAs were differentially expressed between the HA and C group; 28 of these circRNAs were upregulated, while 25 were downregulated in HA (Fold change >1.5; P < 0.05). Three circRNAs and two miRNAs and three predicted mRNAs were obviously regulated after validated by RT-qPCR in HA rats. Two proteins expression were proportional to their mRNA changes. Further analysis indicated the circRNAs mostly close to HA were grouped into 3 signal pathways: including rno_circRNA_014301-vs-rno-miR-3575-vs-Hif-1α, rno_circRNA_014301-vs-rno-miR-3575-vs-Lppr4, rno_circRNA_010393-vs-rno-miR-20b-3p-vs-Mfap4 in hypoxia response pathways, substance/energy metabolism and inflammatory response pathways. Our findings implicate that many circRNAs regulate expressions of genes that interact with each other to exert their functions during HA.

first: LiJun

last: Fan

first: Jing

last: Wang


title: Transcriptomes distinguish human FCD subtypes

summary: Focal Cortical Dysplasia (FCD) is a major cause of drug-resistant focal epilepsy in children and the clinico-pathological classification remains a challenging issue in daily practice. With the recent progress in DNA methylation based classification of human brain tumors we examined, whether genomic DNA methylation and gene expression analysis can be used to also distinguish human FCD subtype

overall_design: DNA methylomes and transcriptomes were generated from massive parallel sequencing in 15 surgical FCD specimens, matched with 5 epilepsy and 8 non-epilepsy controls.

first: Katja

last: Kobow

first: Mark

last: Ziemann

first: K

middle: N

last: Harikrishnan

first: Ishant

last: Khurana

first: Angelika

last: Mühlebner

first: Martha

last: Feucht

first: Johannes

last: Hainfellner

first: Thomas

last: Czech

first: Eleonora

last: Aronica

first: Tom

last: Pieper

first: Hans

last: Holthausen

first: Manfred

last: Kudernatsch

first: Hajo

last: Hamer

first: Burkhard

middle: S

last: Kasper

first: Karl

last: Rössler

first: Valerio

last: Conti

first: Renzo

last: Guerrini

first: Roland

last: Coras

first: Ingmar

last: Blümcke

first: Antony

last: Kaspi


title: miRNAs expression profile in ischemic hindlimb muscle of normocholesterolemic (C57) vs hypercholesterolemic (Apoe-/-) mice.

city: montreal

first: michel

last: desjarlais

state: quebec

address: 5415 Blvd L’Assomption

department: Department of Ophthalmology,

country: Canada

institute: Maisonneuve-Rosemont Hospital Research Center, University of Montréal, Montréal, Québec, Canada.

summary: Using NGS, we report the differential-expression profiling of miRNAs in hypercholesterolemic/atherosclerotic conditions in hindlinb ischemic muscle compare to healthy control mice. Data of total miRNA expression are presented as normalized copy number: read per millions  of read (RPM). Hindlimb ischemia was surgicaly induced by feromal artery ablation and the animal was sacrified 1 day after surgery for RNA collection.

overall_design: examination of miRNAs expression modulation in healty normocholesterolemic mice compare to hypercholesterolemic mice (Apoe-/- subjected to high fat diet).

first: Michel

last: Desjarlais

first: Alain

last: Rivard


title: Adaptive regulation of pathogenic factors by microRNA-like RNA directed mRNA cleavage in plant pathogenic fungus Valsa mali

status: Public on May 10 2019

city: Yangling

first: Ming

last: Xu

state: Shaanxi

address: No. 3, Taicheng Road

department: College of Plant Protection

institute: Northwest A&F University

summary: MicroRNAs (miRNAs) play important roles by regulating the expression of target genes in plant and animal. However, little known about mechanism of fungal miRNA-like RNAs (milRNAs) regulating target gene restricts their functional exploration. In this study, multiple omics were used to identify the milRNAs and their target genes in a phytopathogenic fungus Valsa mali. Many candidate pathogenic factors were found to be regulated by milRNA-directed cleavage way. Absence or downregulated expression of Vm-milRNAs promote expression of candidate pathogenic factors during V. mali infection. Vm-milR16 is a significantly downregulated milRNA during V. mali infection, resulting in significantly upregulated expression of three target genes: VmSNF1, VmDODA, and VmHy1. Overexpression of Vm-milR16 significantly reduces the pathogenicity of V. mali. And all the three target genes of Vm-milR16 are required for the full pathogenicity of V. mali. Further analysis revealed that VmSNF1 regulates the pathogenicity by affecting the expression of pectinase genes during V. mali infection. And all the three target genes are essential for oxidative stress response during V. mali-host interaction. Vm-milRNAs may help V. mali to intelligently use limited resources and adaptively regulate pathogenicity by enhancing expression of pathogenic factors and fitness during infection.

sample_organism:
Malus domestica
Cytospora mali

platform_organism:
Malus domestica
Cytospora mali

overall_design: miRNA-like RNAs were isolated using high-throughput sequence analysis and their corresponding target genes were identified using degradome sequencing technology.

first: Hao

last: Feng

first: Lili

last: Huang


title: Comparing transcrional changes in Plasmodium yoelii infected to uninfected primary hepatocytes

city: Iowa city

first: Samarchith

last: Kurup

state: Iowa

address: 51 Newton Rd

institute: The University of Iowa

summary: GFP expressing Plasmodium yoelii (Py-GFP) infected, or naïve cultured primary hepatocytes were FACS sorted and re-suspended in TRIzol and RNA purified with RNAeasy kit (Qiagen).RNA was assessed for purity and quality using an Agilent 2100 Bioanalyzer and transcriptome analysis performed on Affymetrix GeneChip Mouse Transcriptome array 1.0. Data output was analyzed and visualized using Affymetrix Expression Console 4.0.

overall_design: Infected hepatocytes were sorted based on the fluorescence signal from infecting Plasmodium yoelii (GFP) and compared to uninfected, sorted hepatocytes from an uninfected culture

middle: P

first: Rahul

last: Vijay

first: John

middle: T

last: Harty


title: Genomic DNA methylation distinguishes human FCD subtypes

first: Assam

last: El-Osta

overall_design: DNA methylomes and transcriptomes were generated from massive parallel sequencing in 15 surgical FCD specimens, matched with 5 epilepsy (TLE-HS) and 6 non-epilepsy controls.

first: Katja

last: Kobow

first: Mark

last: Ziemann

first: K

last: Harikrishnan

first: Ishant

last: Khurana

first: Angelika

last: Mühlebner

first: Martha

last: Feucht

first: Johannes

last: Hainfellner

first: Thomas

last: Czech

first: Eleonora

last: Aronica

first: Tom

last: Pieper

first: Hans

last: Holthausen

first: Manfred

last: Kudernatsch

first: Hajo

last: Hamer


title: Fine chromatin-driven mechanism of transcription interference by antisense noncoding transcription

city: Geneva

first: Julien

last: Soudet

address: 30 quai Ansermet

department: BICEL

country: Switzerland

institute: Université de Genève

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Eukaryotic genomes are almost entirely scanned  by RNA polymerase II (RNAPII). Consequently, the transcription of long noncoding RNAs (lncRNAs) often overlaps with coding gene promoters triggering potential gene repression through a poorly characterized mechanism of transcription interference.  In this study, we propose a global model of chromatin-based transcription interference in Saccharomyces cerevisiae (S. cerevisiae). By using a noncoding transcription inducible strain, we analyzed the relationship between antisense elongation and coding sense repression, nucleosome occupancy and transcription-associated histone modifications using near-base pair resolution techniques. We show that antisense noncoding transcription leads to -1/+1 nucleosome deacetylation via H3K36 trimethylation (H3K36me3). This results in the loss of -1/+1 nucleosome interaction with the RSC chromatin remodeler and subsequent sliding into the Nucleosome-Depleted Region (NDR) hindering Pre-Initiation Complex (PIC) binding. Finally, we extend our model by showing that natural antisense noncoding transcription significantly regulates around 20% of  S. cerevisiae genes through this chromatin-based transcription interference mechanism.

overall_design: RNA-seq, MNase-seq, MNase-ChIP-seq, ATAC-seq and ChEC-seq in a Nrd1-AA and Nrd1-AA drpd3 strains treated or not with Rapamycin for 1 hour.

first: J

middle: K

last: Gill

first: A

last: Maffioletti

first: V

last: Garcia-Molinero

first: F

last: Sutz


title: Genotoxic stress triggers the selective activation of IRE1α-dependent RNA decay to modulate the DNA damage response

city: Santiago

first: Alfredo

last: Sagredo

state: Santiago

address: Independencia Av. 1027

country: Chile

institute: University of Chile

summary:
The molecular connections between homeostatic systems that sustain genome integrity and proteostasis are poorly understood. Here we identified the selective activation of the unfolded protein response transducer IRE1α under genotoxic stress to engage repair programs and sustain cell survival. DNA damage engages IRE1 signaling in the absence of an endoplasmic reticulum (ER) stress signature, leading to the exclusive activation of regulated IRE1α-dependent decay (RIDD) and not its canonical output mediated by the transcription factor XBP1. IRE1α controls the stability of mRNAs involved in the DNA damage response, impacting DNA repair, cell cycle arrest and apoptosis. The protective role of IRE1α under genotoxic stress is conserved in evolution as demonstreated using fly and mouse models. Altogether, our results uncovered a novel intersection between the molecular pathways that ensure genome stability and proteostasis.
Affymetrix gene expression data were pre-processed using ‘affyPLM’ packages of the Bioconductor Software. Genes with the strongest evidence of differential expression were obtained using a linear model fit. Data obtained from untreated wild type or IRE1αcKO after ploy I:C treatment liver tissues were used as reference for tunicamycin (Tm) and etoposide (Eto) treatment respectively. Custom chip definition file version 22 from Brainarray based on Entrez ID’s was used. A false positive rate of a=0.05 with FDR correction and a fold change greater 1.5 was taken as the level of significance.

overall_design: Liver tissue were obteined from a conditional knockout (cKO) mice controlled by the Mx-Cre system for the deletion of IRE1a gene. Poly[I:C] was injected to induce Cre expression, and three weeks later animals were treated with a single dose of either etoposide or tunicamycin, followed by the analysis of gene expression of liver tissues. WT IRE1 = Mice with the full expression of IRE1a (ERN1), KO IRE1= Mice wiht IRE1a (ERN1) deletion, WT IRE1 Eto 50ug 16h= Mice with the full expression of IRE1a (ERN1) treated with Etoposide 50ug/kg for 16 hours, WT IRE1 Tm 1ug 16h= Mice with the full expression of IRE1a (ERN1) treated with Tunicamicyn 1ug/kg for 16 hours, Fi/Fi Cre WT Eto50ug 6h=Mice with the full expression of IRE1a (ERN1) treated with Etoposide 50ug/kg for 6 hours,Fi/Fi Cre WT Tm1ug 6h=Mice with the full expression of IRE1a (ERN1) treated with Tunicamicyn 1ug/kg for 6 hours, KO IRE1 Eto 50ug 16h= Mice wiht IRE1a (ERN1) deletion,treated with Etoposide 50ug/kg for 16 hours, KO IRE1 Tm 1ug 16h= Mice wiht IRE1a (ERN1) deletion,treated with Tunicamicyn 1ug/kg for 16 hours, Fi/Fi Cre KO Eto 50ug 6h= Mice wiht IRE1a (ERN1) deletion,treated with Etoposide 50ug/kg for 6 hours,Fi/Fi Cre KO Tm 1ug 6h=Mice wiht IRE1a (ERN1) deletion, treated with Tunicamicyn 1ug/kg for 6 hours, WT IRE1 untreat = Mice with the full expression of IRE1a (ERN1) with DMSO, KO IRE1 untreat= Mice wiht IRE1a (ERN1) deletion with DMSO, Fi/Fi Cre WT untreat= Mice with the full expression of IRE1a (ERN1) with DMSO, Fi/Fi Cre KO untreat= Mice wiht IRE1a (ERN1) deletion with DMSO

first: Estefanie

last: Dufey

first: José

last: Bravo-San Pedro

first: Cristian

last: Eggers

first: Matías

last: González-Quiroz

first: Hery

last: Urra

first: Denisse

last: Sepulveda

middle: I

first: Amado

last: Carreras-Sureda

first: Eduardo

first: Daniela

last: Gutierrez

last: Valls

first: Diego

last: Acosta-Alvear

first: Gissela

last: Campos

first: Alejandra

last: Alvarez

first: Patricio

last: Godoy

first: Peter

last: Walter

first: Alvaro

last: Glavic

first: Guido

last: Kroemer

first: Claudio

last: Hetz


title: Cell cycle plasticity driven by MTOR signaling: integral mechanism for resistance to CDK4/6 inhibition

city: Buffalo

first: Erik

last: Knudsen

state: NY

address: 665 Elm St.

department: Molecular & Cellular Biology

institute: Roswell Park Comprehensive Cancer Center

summary: Pancreatic ductal adenocarcinoma (PDAC), like many KRAS-driven tumors, preferentially loses CDKN2A to bypass the RB tumor suppressive pathway.   This finding and a gene expression profile indicative of a CDK4/6-driven cell cycle suggests that PDAC could be particularly sensitive to CDK4/6 inhibition.   Analysis of a panel of patient-derived cell lines and xenografts indicates that many pancreatic cancers have an intrinsic resistance to CDK4/6 inhibition that is not due to known molecular mechanisms.   Rather, there is a rapid and potent adaptive response that led to the upregulation of Cyclin D1 and Cyclin E proteins and compromised the suppression of a DNA replication gene expression program.  These adaptive responses are dependent on MTOR signaling both in cell and animal studies.    Strikingly, combination treatments with MTOR and CDK4/6 inhibitor had potent activity across a large number of patient derived models of PDAC underscoring the potential clinical efficacy.

overall_design: Patient-derived xenografts from 10 different patient pancreatic cancer tumors were implanted in mice, which were then treated with vehicle control, palbociclib, or with palbociclib in combination with TAK228.  RNA sequencing was utilized to define differentially expressed genes.  Each model-treatment was sequenced in triplicate.

first: Agnieszka

last: Witkiewicz


title: RNA-seq analysis in ARIEL knockdown Jurkat samples

city: Lund

first: Phuong

last: Cao Thi Ngoc

address: BMC, B1222b, Klinikgatan 26

country: Sweden

institute: Lund University

summary: RNA-seq of control, shARIEL Jurkat cells

overall_design: shARIEL vs. control

first: S

middle: H

last: Tan

first: P

middle: C

last: Ngoc

first: T

last: Sanda


title: Stk40 deletion elevates c-JUN protein level and impairs mesoderm differentiation

city: Shanghai

first: Jing

last: Hu

address: 280 Chongqing road

institute: Shanghai Jiaotong university school of medicine

summary: Mesoderm development is a finely tuned process initiated by the differentiation of pluripotent epiblast cells. Serine/threonine kinase 40 (STK40) controls the development of several mesoderm-derived cell types, its overexpression induces differentiation of mouse embryonic stem cells (mESCs) towards the extraembryonic endoderm, and Stk40 knockout (KO) results in multiple organ failure and is lethal at the perinatal stage in mice. However, molecular mechanisms underlying the physiological functions of STK40 in the mesoderm differentiation remain elusive. Here, we report that Stk40 ablation impairs mesoderm differentiation both in vitro and in vivo. Mechanistically, STK40 interacts with both the E3 ubiquitin ligase mammalian constitutive photomorphogenesis protein 1 (COP1) and the transcriptional regulator proto-oncogene c-Jun (c-JUN), promoting c-JUN protein degradation. Consequently, Stk40 knockout leads to c-JUN protein accumulation, which, in turn, apparently suppresses the WNT signaling activity and impairs the mesoderm differentiation process. Overall, this study reveals that STK40, together with COP1, represents a previously unknown regulatory axis that modulates the c-JUN protein level within an appropriate range during mesoderm differentiation from mESCs. Our findings provide critical insights into the molecular mechanisms regulating the c-JUN protein level and may have potential implications for managing cellular disorders arising from c-JUN dysfunction.

overall_design: The ESCs were maintained on inactivated MEF feeders in the N2/B27 medium with 2 mM Glutamax (Gibco), 0.1 mM nonessential amino acids, 0.1 mM 2-mercaptoethanol (Sigma), 1000 U/ml LIF (Millipore), 3 uM CHIR99021, and 1 uM PD0325901 (STEMCELL Technologies) . Cell colonies were digested into single cells for regular passaging using Accutase (STEMCELL Technologies). For induced mesoderm differentiation from mESCs, cells were passaged onto gelatin-coated cell culture plates to remove feeder cells prior to the initiation of differentiation. After one passage, ESCs were dissociated with Accutase, and 150000 cells were seeded in one well of 6-well plates pre-coated with gelatin, and maintained in the N2B27 medium with addition of 1% Knock-out Serum Replacement (KSR, Gibco), 0.1% bovine serum albumin (Gibco) and BMP4 (R&D) at 10 ng/ml for 2 days. Then, the medium was replaced by a DMEM-based medium with 15% KSR, 1 uM CHIR99021 (STEMCELL Technologies), and 0.5% DMSO (Sigma) for one additional day (Chal, Jerome, et al. 2015).

first: Shuang

last: Li

first: Xiaozhi

last: Sun

first: Zhuoqing

last: Fang

first: Lina

last: Wang

first: Feng

last: Xiao

first: Min

last: Shao

first: Laixiang

last: Ge

first: Fan

last: Tang

first: Junjie

last: Gu

first: Hongyao

last: Yu

first: Yueshuai

last: Guo

first: Xuejiang

first: Bing

last: Liao

first: Ying

last: Jin


title: Inhibition of gene transcription after THZ1 treatment in HeLa

first: Shanshan

last: Zhong

address: NO.160 Road, Pudong New District

institute: Ren Ji hospital

summary: To explore the transcriptional inhibition of the CDK7 inhibitor THZ1 in cervical cancer cells,  we used gene expression miceoarray analysis to detect the gene expression profiles after THZ1 treatment in HeLa compared with negative control（DMSO）.  HeLa was trreated with 100 nM THZ1 or DMSO, and total RNA was extracted after treatment for 6 hours. Microarray analysis showed that massive oncogene transcripts, especially those associated with tumorigenesis, were preferential suppressed after THZ1 treatment.

overall_design: HeLa was treated with  treatment with THZ1 or DMSO, and then total RNA was extracted using TRIZOL after treatment for 6 hours. Each group  has three replicates.

first: Yi

last: Zhang

first: Xia

last: Yin

first: Wen

last: Di


title: Transcriptome analysis of activated fibroblasts after intratracheal transfer in bleomycin-induced lung fibrosis

city: San Francisco

first: Tatsuya

last: Tsukui

state: CA

address: 555 Mission Bay Blvd South, 282

department: Medicine

institute: UCSF

summary: Intratracheal transfer of isolated lung fibroblasts in bleomycin-induced lung fibrosis recapitulates the activation process of lung fibroblasts after epithelial injury. In order to investigate gene expression signatures of transferred fibroblasts, we purified transferred fibroblasts 2, 4, and 7 days after the transfer and performed transcriptome analysis. We also isolated Acta2 high and low cells by using Acta2-mKO1 reporter mice 4 days after the transfer.

overall_design: Lung fibroblasts were isolated from untreated Col-GFP mice after tissue dissociation and negative selection for lineage markers. Isolated lung fibroblasts were intratracheally transferred into wild type mice, which received intratracheal bleomycin treatment 7 days before the transfer. Col-GFP+ cells were purified from the host lungs by FACS sorting on 2, 4, and 7 days after the transfer. Acta2 high and low cells were prepared by transferring lung fibroblasts from Acta2-mKO1 reporter mice. mRNA was isolated from sorted cells, and gene expression profiles were acquired by next generation sequencing.

first: Shinichi

last: Hashimoto

first: Shigeyuki

last: Shichino


title: A GBM-like V-ATPase signature directs cell-cell tumor signaling and reprogramming via large oncosomes

city: Planegg-Martinsried

first: Andrea

last: Terrasi

address: Großhaderner Strasse 9

department: Biomedical Center Munich

country: Germany

institute: Ludwig-Maximilians-Universität München

summary: Glioblastoma (GBM) is the most aggressive and common malignant brain tumor in adults. GBMs are characterized by high intratumor heterogeneity and by the presence of the cancer stem cell niche. The vacuolar ATPase (V-ATPase) is a multisubunit proton pump that plays a role in multiple processes in eukaryotic cells. Altered V-ATPase activity is associated with several human diseases and in cancer may play relevant role due the acidification of cellular organelles, such as, endosomes and lysosomes. We identified overexpression of the V-ATPase V1G1 subunit in GBM derived neurospheres (NS), a cell subpopulation enriched in cancer stem cells. Interestingly GBM NS secrete different types of vesicles, including large oncosomes (LO) thereby influencing their microenvironment. Herein, we assessed the transcriptome of non-sphere forming glioma cells (n=2 pairs) cocultured with LO or empty media (mock) by microarray to identify pathways associated with the LO-induced reprogramming ability. Gene set enrichment analysis (GSEA) revealed that LO-supplemented cultures activated a number of cancer-related pathways, including those involved in glioma V-ATPase-related signaling (Notch, mTOR, and lysosomal transport), as well as cell proliferation and cell transcription programs.

overall_design: Expression data from extracted total RNA of primary human non-sphere-forming glioma cells co-cultured for 6 days with empty medium (mock) or with medium containing LO-High.

first: Irene

last: Bertolini

first: Cristina

last: Martelli

first: Gabriella

last: Gaudioso

last: Di Cristofori

first: Alessandra

last: Storaci

first: Miriam

last: Formica

first: Paola

last: Braidotti

first: Katia

last: Todoerti

first: Stefano

last: Ferrero

first: Manuela

last: Caroli

first: Luisa

last: Ottobrini

first: Thomas

last: Vaccari

first: Valentina

last: Vaira


title: Transcription factor NKX3-1 is required for reprogramming to pluripotency and can replace OCT4 in mouse and human iPSC induction [ATAC-seq]

city: Stanford

first: Thach

last: Mai

address: 269 Campus Dr

institute: Stanford University

summary: Resolution of early molecular events preceding endogenous OCT4 activation is critical to understanding the mechanism of reprogramming somatic cells to induced pluripotent stem cells (iPSCs), yet capturing transient regulators at the onset of reprogramming is difficult in heterogeneous populations of asynchronously reprogramming fibroblasts following four-factor transduction. To address this need, we used a heterokaryon system to identify an early and transiently expressed homeobox transcription factor, NKX3-1. Upon knockdown of NKX3-1, iPSC reprogramming is abrogated. Further, we identify that NKX3-1 functions downstream of the IL6-STAT3 regulatory network to activate endogenous OCT4. Importantly, we show that NKX3-1 can substitute for exogenous OCT4 to reprogram both mouse and human fibroblasts at comparable efficiencies generate fully pluripotent stem cells. Our findings establish an essential role for NKX3-1, previously known as a prostate-specific tumor suppressor, in iPSC reprogramming.

overall_design: ATAC-seq timecourse of heterokaryon reprogramming

first: Glenn

last: Markov

first: Helen

last: Blau


title: Apoptotic endothelial cells release small extracellular vesicles loaded with immunostimulatory viral-like RNAs

city: Montreal

first: Marie-Pierre

last: Hardy

state: Quebec

address: 2950 Chemin de Polytechnique

department: IRIC

institute: University of Montreal

summary:
Purpose: Compare the RNA content of apoptotic human umbilical vein endothelial cells (HUVECs)-released vesicles: 1) Apoptotics bodies and 2) Apoptotic Exo-like vesicles, which are immunogenic and promote autoimmunity.
Results: The transcriptome of ApoExos was unique with regards to its genomic origin, nucleotide composition and secondary structure. We show that ApoExos essentially contain non-ribosomal non-coding RNAs, among which 89% are derived from viral-like endogenous retroelements (EREs). ApoExos are also enriched in U-rich linear nucleotide sequences and Alus repeats.
Conclusion: Our work demonstrates that apoptotic endothelial cells release EVs loaded with RNAs recognized by RLRs and endosomal TLRs (TLR3, TLR7 and TLR8), and are therefore tailor-made for initiation of innate immune responses and autoimmunity.

overall_design: We performed whole RNA-sequencing in duplicate on normal and apoptotic human umbilical vein endothelial cells and on the two types of EVs released by these apoptotic HUVECs: apoptotic bodies and ApoExos.

first: Marie

first: Claude

last: Perreault


title: High-throughput screening for modulators of CFTR activity applying an organotypic functional assay based on genetically engineered Cystic Fibrosis disease-specific iPSCs

city: Hannover

first: Ruth

last: Olmer

address: Carl-Neuberg-Str. 1

department: HTTG

institute: Hannover Medical School

summary: Organotypic culture systems from disease-specific induced pluripotent stem cells (iPSCs) exhibit obvious advantages compared to immortalized cell lines and primary cell cultures but implementation of iPSC-based high throughput (HT) assays is still technically challenging. Here we demonstrate the development and conduction of an organotypic HT Cl-/I- exchange assay using Cystic Fibrosis (CF) disease-specific iPSCs. The introduction of a halide sensitive YFP variant enabled automated quantitative measurement of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) function in iPSC-derived intestinal epithelia. CFTR function was partially rescued by treatment with VX-770 and VX-809, and seamless gene correction of the p.Phe508del mutation resulted in full restoration of CFTR function. The identification of a series of validated primary hits that improve the function of p.Phe508del CFTR from a library of ~ 42.500 chemical compounds demonstrates that the advantages of complex iPSC-derived culture systems for disease modelling can also be utilized for drug screening at a true HT format.

overall_design: For detailed analysis of the differentiated hiPSC cell populations on day 15 of differentiation 32 samples in total were analyzed.  Three independent donor lines were utilized (donor 1 and 6 CFTR WT, donor 2 (p.Phe508del)) and one isogenic gene corrected control line (donor 2 gene corrected-CFTR WT.) Samples from undifferentiated and differentiated cells represent biological replicates (n=3). As controls RNA from adult intestine, liver and colon was. Tissue samples are represented as technical replicates.

first: Sylvia

last: Merkert

first: Madline

last: Schubert

first: Lena

last: Engels

first: Silke

last: Radetzki

first: Mieke

last: Veltman

first: Bob

last: Scholte

first: Janina

last: Zöllner

first: Nicoletta

last: Pedemonte

first: Luis

last: Galietta

first: Jens

last: von Kries

first: Ulrich

last: Martin


title: Epigenetic bookmarking of H2S exposure in Caenorhabditis elegans

status: Public on May 09 2019

city: Seattle

first: Dana

last: Miller

state: United States (1)

address: 1705 NE Pacific St. HSB J-587 Box 357350

department: Biochemistry

institute: University of Washington

summary: Physiological memories of environmental stress can serve to predict future environmental changes, allowing the organism to initiate protective mechanisms and survive. Although physiological memories, or bookmarks, of environmental stress have been described in a wide range of organisms, from bacteria to plants to humans, the mechanism by which these memories persist in the absence of stress is still largely unknown. We have discovered that C. elegans transiently exposed to low doses of hydrogen sulfide (H2S) survive subsequent exposure to otherwise lethal H2S concentrations and induce H2S-responsive transcripts more robustly than naïve controls. H2S bookmarking can occur at any developmental stage and persists through cell divisions and development but is erased by fasting. We show that maintenance of the H2S bookmark requires the SET-2 histone methyltransferase and the CoREST-like demethylase complex. We propose a model in which exposure to low doses of H2S generates a long-lasting, epigenetic memory by modulating H3K4me2 modifications at specific promoters. Understanding the fundamental aspects of H2S bookmarking in this tractable system can provide mechanistic insight into how environmental exposures are translated into the epigenetic landscape in animals.

overall_design: RNA was collected by Trizol prep from larval stage 4 (L4) animals. 4 samples of 3 treatment groups: Unexposed control, Naïve animals exposed to 1 hr high (>150 ppm) hydrogen sulfide, and Bookmarked (exposed to approx. 50 ppm hydrogen sulfide for approx 8 hr as embryos) exposed to 1 hr high hydrogen sulfide. Standard unstranded mRNA library prep and paired-end sequencing were used.

first: Emily

last: Fawcett

first: Jenna

last: Johnson

first: Chris

last: Braden

first: Ellie

last: Garcia


title: Pro-angiogenic transcriptome of zebrafish endothelial cells

city: Manchester

first: Shane

last: Herbert

address: Michael Smith Building, OXford Road

department: Faculty of Biology, Medicine and Health

institute: University of Manchester

summary:
To identify previously unknown determinants of endothelial cell sprouting, we defined and exploited a pharmacological strategy for the manipulation of angiogenic cell behavior in vivo. Whereas high vascular endothelial growth factor receptor (Vegfr) signaling is known to promote tip cell (TC) specification, activation of the Notch receptor via its ligand Delta-like 4 (Dll4) represses the TC phenotype to promote stalk cell (SC) fate. Conversely, suppression of Notch activity upon antagonistic interaction with its ligand Jagged1 pro- motes TC formation. Hence, specification of TCs involves tight spatiotemporal control of Vegfr/Notch signaling.
Consequently, we hypothesized that the pharmacological manipulation of Vegfr/Notch signaling selectively during zebrafish intersegmental vessel (ISV) angiogenesis would enable the precise control of angiogenic EC behavior and sprouting- associated gene expression in vivo. For more information, see Herbert et al., 2012, PMID 22921365.

overall_design: Zebrafish embryos were treated with DMSO (Control), DAPT (hypersprouting condition), SU5416(inhibition of sprouting) or both from 22hpf to 30hpf.At 30hpf, cells were dissociated and endothelial cells were isiolated for further RNA extraction

first: Didier

middle: R

last: Stainier


title: Prognostic and Biologic Relevance of Clinically Applicable Long Non-Coding RNA Profiling in Older Patients with Cytogenetically Normal AML

city: Columbus

first: Hatice Gulcin

last: Ozer

state: OH

address: 1800 Cannon Dr

department: Biomedical Informatics

institute: The Ohio State University

summary:
We have previously shown that expression levels of 48 long non-coding RNAs (lncRNAs) can generate a prognostic lncRNA score that independently associates with outcome of older patients (aged ≥ 60 years) with cytogenetically normal acute myeloid leukemia (CN-AML). However, the techniques that were used to identify and measure prognostic lncRNAs are not tailored for real-life clinical testing. Herein we report on an assay (based on the nCounter platform), which is designed to produce targeted measurements of prognostic lncRNAs in a clinically friendly manner. We analyzed an independent cohort of 76 older CN-AML patients and found that the nCounter assay yielded reproducible measurements and that the lncRNA score retained its prognostic value; patients with favorable lncRNA scores were more likely to achieve a complete remission (CR, P=0.009) and have longer diseased-free (DFS, P=0.05), overall (OS, P=0.02) and event-free survival (EFS, P=0.002) than patients with unfavorable lncRNA scores. In multivariable analyses, lncRNA score status independently associated with CR rates (P=0.02), as well as OS (P=0.02) and EFS (P=0.02) duration.
To gain biological insights, we examined a dataset of older CN-AML patients, previously analyzed with RNA sequencing. We found genes involved in immune response and B cell receptor signaling (for which targeted inhibitors are currently available) to be enriched in patients with unfavorable lncRNA scores. We conclude that clinically applicable lncRNA profiling is feasible and potentially useful for risk stratification of older CN-AML patients. In addition we identify potentially targetable molecular pathways that are active in the high-risk patients with unfavorable lncRNA scores.

overall_design: Samples of 76 older de novo CN-AML patients were measured with the nCounter platform in five independent experiments. Of these samples, a total of 16 were measured multiply; 11 samples measured twice in separate batches, 3 samples measured 3 times in the same batch, and 2 samples measured 4 times in the same batch

first: Dimitrios

last: Papaioannou

first: Deedra

last: Nicolet

first: Hatice

last: Gulcin Ozer

first: Krzysztof

last: Mrózek

first: Stefano

last: Volinia

first: Paolo

last: Fadda

first: Andrew

middle: J

last: Carroll

first: Jessica

last: Kohlschmidt

first: Richard

last: Stone

first: Ramiro

last: Garzon

first: Clara

middle: D

last: Bloomfield


title: RNA-seq of maize seeds at different filling stages

city: Yangzhou

first: Shuangyi

last: Yin

address: 88 daxue south road

institute: Yangzhou University

summary: We study the expression level change of candidate genes associated with seed filling in maize, through RNA-seq for maize seeds in different filling stages. The results show that the change of the expression of these candidate genes would lead to the change of grain filling trajectory.

overall_design: A total of 40 samples, including 4 maize inbred lines. Each inbred line is detected at 5 time points with 2 replicates.


title: RNA-Seq of PRMT1 overexpression ECA109 cells

first: Yue

last: Zhao

address: 168 Changhai Road, Shanghai 200433, China

department: Department of Thoracic Surgery

institute: Changhai Hospital

summary: RNA-seq was performed on three biological replicates. Total RNA from ECA109 LV-GFP/LV-PRMT1.Differentially expressed genes were considered to be significant between groups when the P-value was <0.05 and the fold change of expression was ≥2-fold or ≤0.5-fold.  By this way, the RNA-Seq data showed the differential expression genes in PRMT1 overexpression ECA109 cells compared with NC cells. Furthermore, Gene ontology (GO) analysis was performed to facilitate elucidating the biological implications of the differentially expressed genes in the experiment. Pathway analysis was used to find out the significant pathway of the differentially expressed genes according to KEGG database.  In conclusion, our study represents the first detailed analysis of PRMT1 transcriptomes in esophageal squamous cell carcinoma cells.

overall_design: Exploring changes of transcriptome in in PRMT1 overexpression ECA109 cells compared with control ECA109 cells


title: Sex-Dependent Sensory Phenotypes and Related Transcriptomic Expression Profiles Are Differentially Affected by Angelman Syndrome

city: Haifa

first: Avi

last: Titievsky

address: Abba Khoushy Ave 199

department: Department of Evolution

country: Israel

institute: University of Haifa

summary: Angelman syndrome (AS) is a genetic disorder which entails autism, intellectual disability, lack of speech, motor deficits, andseizure susceptibility. It is caused by the lack of UBE3A protein expression, which is an E3-ubiquitin ligase. Despite AS equalprevalence in males and females, not much data on how sex affects the syndrome was reported. In the herein study, we thoroughlycharacterized many behavioral phenotypes of AS mice. The behavioral data acquired was analyzed with respect to sex. Inaddition, we generated a new mRNA sequencing dataset. We analyzed the coding transcriptome expression profiles with respectto the effects of genotype and sex observed in the behavioral phenotypes. We identified several neurobehavioral aspects,especially sensory perception, where AS mice either lack the male-to-female differences observed in wild-type littermates oreven show opposed differences. However, motor phenotypes did not show male-to-female variation between wild-type (WT) andAS mice. In addition, by utilizing the mRNA sequencing, we identified genes and isoforms with expression profiles that mirrorthe sensory perception results. These genes are differentially regulated in the two sexes with inverse expression profiles in ASmice compared to WT littermates. Some of these are known pain-related and estrogen-dependent genes. The observed differ-ences in sex-dependent neurobehavioral phenotypes and the differential transcriptome expression profiles in AS mice strengthenthe evidence for molecular cross talk between Ube3a protein and sex hormone receptors or their elicited pathways. Theseinteractions are essential for understanding Ube3a deletion effects, beyond its E3-ligase activity.

overall_design: mRNA sequencing data from ventral hippocampi of three WT females, three WT males, three AS females, and three AS male mice.

first: Lee

last: Koyavski

first: Lilach

last: Simchi

first: Lital

last: Sharvit

first: Hanoch

last: Kaphzan

first: Julia

last: Panov

first: Prudhvi

last: Rayi

first: Yonatan

last: Feuermann


title: A Western-type Dietary Pattern Induces an Atherogenic Gene Expression Profile in the Coronary Arteries of the Ossabaw Pig

city: Boston

first: Alice

last: Lichtenstein

state: MA

address: 711 Washington St

department: Jean Mayer USDA Human Nutrition Research Center on Aging

institute: Tufts University

summary: We investigated the effect of 2 food-based dietary patterns and statin therapy on the transcriptome of the left anterior descending coronary artery of the Ossabaw pig.

overall_design: Thirty-two Ossabaw miniature pigs (16 boars, 16 gilts) were randomized using a 2x2 factorial design into four groups: Hearty Healthy diet (HHD); Heart Healthy diet + atorvastatin (HHD+S); Western diet (WD); and Western diet + atorvastatin (WD+S). Heart Healthy diet (high in unsaturated fat, unrefined grain, fruits/vegetables [HHD]) or Western diet (high in saturated fat, cholesterol, refined grain [WD]), with or without atorvastatin.

first: Maura

middle: E

last: Walker

first: Nirupa

last: Matthan

first: Gloria

last: Solano-Aguilar

first: Saebyeol

last: Jang

first: Sukla

last: Lakshman

first: Aleksey

last: Molokin

first: Tyler

last: Faits

first: Joseph

middle: F

last: Urban Jr

first: W

last: Johnson

first: Stefania

last: Lamon-Fava


title: RNA-sequencing reveals a distinct transcriptomic signature of chicken embryonic stem cells (cESC) infected with recombinant vaccine vectors

city: London

first: Michael

last: Skinner

address: St Mary's Campus, Norfolk Place

department: Faculty of Medicine, Section of Virology

institute: Imperial College London

summary: In this study, we used RNA-sequencing to compare the transcriptional programmes in cESC, elicited either by stimulation with recombinant interferon-α or by infection with the attenuated Fowlpox virus vaccine strain (FP9), the canarypox virus vaccine strain (CNPV), the Modified Vaccinia Ankara (MVA) virus or PBG98, a mild vaccine strain of infectious bursal disease virus.

overall_design: Examination of the transcriptome of cESC following stimulation with recombinant IFN-a or infection with recombinant vaccine viral vectors (Fowlpox virus FP9, MVA, Canarypox virus CNPV, Infectious bursal disease virus PBG98)

first: Efstathios

last: Giotis


title: Circadian gene expression in mouse gastrocnemius muscle after deletion of SIRT1 in SF1 neurons

city: irvine

first: Siwei

last: Chen

address: 66304 Verano Road South

department: Computer Science

institute: University of California, Irvine

summary: Loss of synchrony between geophysical time and insulin action predisposes to metabolic diseases.  Yet,  the brain and peripheral pathways linking proper insulin effect to diurnal changes in light/dark and feeding/fasting inputs are poorly understood. Here, we show that insulin sensitivity of several metabolically relevant tissues fluctuates during the 24-hour period. For example, in mice insulin sensitivity of skeletal muscle, liver, and adipose tissue is lowest during the light period. Mechanistically, by performing loss- and gain-of-light-action and food-restriction experiments, we demonstrate that SIRT1 in steroidogenic factor 1 (SF1) neurons of the ventromedial hypothalamic nucleus (VMH) conveys  photic inputs toentrain the biochemical and metabolic action of insulin in skeletal muscle. These findings uncover a critical light-SF1-neuron-skeletal-muscle axis that acts to finely tune diurnal changes in insulin sensitivity and reveal a light regulatory mechanism of skeletal muscle function.

overall_design: Gastrocnemius muscle was dissected from 10-week old mice with deletion of SIRT1 in SF1 neurons (Sf1-Cre; Sirt1loxP/loxP) and intact controls (Sirt1loxP/loxP) at different Zeitgebers (0, 6, 12, 18).

first: Ebru

last: Aras

first: Giorgio

last: Ramadori

first: Roberto

last: Coppari

first: Paolo

last: Corsi

first: Pierre

last: Baldi

first: Kenichiro

last: Kinouchi

first: Yu

last: Liu


title: Ets1 suppresses atopic dermatitis by suppressing pathogenic T cell responses

city: Pohang

first: Sin-Hyeog

last: Im

state: Gyeongsangbuk-do

address: POSTECH Biotech Center Rm. 428-431, Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Nam-gu, Pohang, Republic of Korea

department: Academy of Immunology and Microbiology

country: South Korea

institute: Institute for Basic Science

summary: To identify the molecular mechanisms responsible for enhanced atopic dermatitis (AD) pathogenesis upon Ets1 deficiency in CD4+ T cells, we compared transcriptome profile between CD4+ T cells from littermate control (LMC) and Ets1ΔdLck mice at the peak of AD progression by performing RNA-seq.

overall_design: Skin-draining lymph nodes near sites of inflammation under AD were excised from LMC and Ets1ΔdLck mice and prepared into single cell suspensions. CD4+ T cells were purified by CD4+ negative selection method.

first: Choong-Gu

last: Lee


title: Fatty acid transporter 2 regulates lipid metabolism and suppressive function of neutrophils in cancer

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Polymorphonuclear myeloid derived suppressor cells (PMN-MDSC) are pathologically activated neutrophils that accumulate in cancer and many other pathologic conditions. PMN-MDSC are critically important for the regulation of immune responses in cancer, promotion of tumor progression, and metastases. Despite the recent advances in understanding of the PMN-MDSC biology, the mechanisms responsible for pathological activation of neutrophils are not well defined, which limit selective targeting of PMN-MDSC. Here, we report that mouse and human PMN-MDSC exclusively up-regulate fatty acid transporter protein 2 (FATP2). Over-expression of FATP2 in PMN-MDSC was controlled by GM-CSF, through the activation of STAT5 transcription factor. Genetic ablation of FATP2 abrogated the suppressive activity of PMN-MDSC in spleens and tumors. FATP2 in neutrophils promoted accumulation of oxidized lipids. However, the main mechanism of FATP2 mediated suppressive activity of PMN-MDSC involved uptake of arachidonic acid and synthesis of prostaglandin E2. The selective pharmacological inhibition of FATP2 abrogated activity of PMN-MSC and substantially delayed tumor progression. In combination with check-point inhibitors it blocked tumor progression in mice. Thus, FATP2 mediates acquisition of immune suppressive activity by PMN-MDSC and represents a new target to inhibit the functions of PMN-MDSC and improve the effect of immunotherapy of cancer.

overall_design: RNA-seq for WT and FATP2 KO PMN-MDSC cells

first: Dmitry

last: Gabrilovich

first: Filippo

last: Veglia


title: Expression Characteristics of Genes Hypermethylated and Downregulated in Rat Liver Specific to Non-genotoxic Hepatocarcinogens

city: Kitakatsushika-gun

first: Kyosuke

last: Yamashita

state: Saitama

address: Sugito-machi Shimotakano1600

department: Tokyo

country: Japan

institute: Chemicals Evaluation and Research Institute Japan

summary: The present study examined hypermethylated and downregulated genes specific to carbon tetrachloride (CCl4) by Methyl-Seq analysis combined with expression microarray analysis in the liver of rats treated with CCl4 or N-nitrosodiethylamine (DEN) for 28 days, by excluding those with DEN.

overall_design: Gene expression microarray analysis was performed using total RNA from liver tissue samples of untreated controls, DEN (4 mg/5 mL/kg body weight, dissolved in saline) and CCl4 (100 mg/5 mL/kg body weight, dissolved in corn oil) groups (n = 3/group) after repeated treatment by oral gavage for 28 days.

first: Yuko

last: Ito

first: Kota

last: Nakajima

first: Yasunori

last: Masubuchi

first: Satomi

last: Kikuchi

first: Fumiyo

last: Saito

first: Yumi

last: Akahori

first: Meilan

last: Jin

first: Toshinori

last: Yoshida

first: Makoto

last: Shibutani


title: Global brain transcriptome analysis of a Tpp1 Neuronal Ceroid Lipofuscinoses Mouse Model

city: Chicago

first: WEN-CHING

last: CHAN

state: IL

department: Biological Sciences Division

institute: The University of Chicago

summary: We analyzed expression changes in the Tpp1-/- forebrain/midbrain and cerebellum of 4 mo. mutants compared to strain-related controls RNA-sequencing technology.

overall_design: The objective of this study was to perform, for the first time in a classical late-infantile form of Neuronal ceroid lipofuscinoses model, a transcriptome wide characterization by RNA-seq of two macro-areas mostly affected in the 4-mo.-old Tpp1-/- (cerebellum (Cb) and forebrain/midbrain (F/M)).  We used a mouse model previously developed by the Lobel laboratory (J. Neurosci. 2004, 24(41)9117). Four-mo.-old males Tpp1-/- homozygous mice were compared to male wild type siblings.

first: Miriam

last: Domowicz

first: Nancy

last: Schwartz


title: Immune parameters and outcome during Ebola virus disease

city: Paris

first: Hugo

last: Varet

address: 28 rue du Docteur Roux

country: France

institute: Institut Pasteur

summary: Immune patterns in Ebola patients were characterized depending on the outcome of the illness. Non-healthy controls were compared to Ebola patients to define the specificity of the immune response against Ebola virus infection.

overall_design: RNA from leukocytes were used for microarray analysis

first: S

last: Reynard

last: Baize

first: H

first: N

last: Pietrosemoli


title: Three Transcription Factor Functions Empower Formative Transition from Naïve Pluripotency [ChIP-Seq]

city: Cambridge

first: Susanne

last: Bornelöv

address: Tennis Court Road

department: WT-MRC Cambridge Stem Cell Institute

institute: University of Cambridge

summary: The gene regulatory network in naïve mouse embryonic stem cells (ESC) is reconfigured to enable lineage commitment. Tcf3 sanctions rewiring to formative pluripotency by suppressing components of the ESC transcription factor circuitry. However, Tcf3 depletion only delays, and does not prevent transition. Here we delineate major contributions of Ets-family transcription factor Etv5 and the repressor Rbpj. ERK signalling triggers genome relocation of Etv5 to commission formative pluripotency enhancers. Concomitant up-regulation of Rbpj prevents reversion by repressing potent naïve factors, Nanog and Tbx3. Triple deletion of Etv5, Rbpj and Tcf3 disables naïve ESC, such that they remain undifferentiated and locked in self-renewal even in the presence of differentiation stimuli. Thus, pluripotency dynamics are driven by combined action of two repressors that respectively dissolve and extinguish the naive network, and an activator that initiates transcription of formative network genes. Similar tripartite modality might be a general requirement for robust cell state transitions.

overall_design: ChIP-seq of Etv5-3xFlag knock-in (KI) RGd2 ESCs cultured in 2i and withdrawn from 2i inhibitors for 16hrs (N16h) using M2-Flag Antibody (Sigma). 2 Etv5-3xFlag knock-in (KI) clonal ESC lines (clones 20 and 32) were used as biological replicates per condition. Wild type RGd2 ESCs were used as negative control.   ChIP-seq of RGd2 ESCs cultured  in 2i and withdrawn from 2i inhibitors for 16hrs (N16h), and 25hrs (N25h) FACS-sorted for Rex1-GFPd2 (Rex1-high, Rex1-low) for H3K4me3.

first: TÃ¼zer

last: Kalkan

last: Bornelov

first: Evangelia

last: Diamanti

first: Tim

last: Lohoff

first: Carla

last: Mulas

first: Meryem

last: Ralser

first: Sjors

last: Middelkamp

first: Patrick

last: Lombard

first: Jennifer

last: Nichols

first: Austin

last: Smith


title: Three Transcription Factor Functions Empower Progression from Naïve to Formative Pluripotency

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

overall_design: Refer to individual Series


title: Transcriptional profile of zebrafish eyes after exposure to 350 mg/L Propylthiouracyl (PTU)

city: Heidelberg

first: Lisa

middle: Annie

last: Baumann

address: Im Neuenheimer Feld 504

department: COS

institute: University of Heidelberg

summary: Vertebrate eye devlopment is partially regulated by thyroid hormones. Propylthiouracyl is a pharmaceutical that lowers thyroid hormone levels. We investigated the effects of PTU on eye development of zebrafish. We expected PTU exposure to cause transcriptional changes of visual-system-related genes, which find their phenotypic anchoring in eye malformations and dysfunction, as observed in our previous studies. Additionally, the reversibility of effects after recovery in clean water for three days was investigated.

overall_design:
We used an n + 2 A-optimal design (Kerr and Churchill, 2001, PMID 12933549).  See microarray_set-up.pdf linked at the foot of the superSeries GSE121338 record.
Zebrafish eggs were exposed to 0 (C, control) or 350 mg/L PTU (E, exposure) from 0 to 5 days post fertilization (dpf) in 6 replicates each (= 12 plates, 24 eggs per plate). At 5 dpf , 3 replicate plates of each treatment were sampled (C: control 5 dpf and E: PTU 5 dpf), resulting in 6 samples that were further analysed (exposure 5 dpf vs. control 5 dpf). The 3 remaining replicates were further raised in clean water (R: recovery) and sampled at 8 dpf (CR: recovery control 8 dpf and ER: recovery PTU 8 dpf), again resulting in 6 samples for further analyses (recovery exposure 8 dpf vs. recovery control 8 dpf; exposure 5 dpf vs. recovery exposure 8 dpf).

first: L

last: Segner

first: A

last: Ros

first: D

last: Knapen

last: Vergauwen


title: Therapeutic targeting of BRD4 in head neck squamous cell carcinoma

city: Nanjing

first: Jie

last: Cheng

state: Jiangsu

address: 136 Hanzhong Road

institute: Nanjing Medical University

summary: The bromodomain and extraterminal family members are epigenetic readers and transcriptional coactivators which are critically involved in various biological processes including tumorigenesis. BRD4 has been increasingly appreciated as a key oncogene and promising anticancer target. Here, we sought to characterize the expression of BRD4 and its tumorigenic roles as well as therapeutic targeting in HNSCC. Expression of BRD4 mRNA and protein was determined by bioinformatics interrogation of public available databases, primary HNSCC samples and 4NQO-induced HNSCC animal model. The tumorigenic roles of BRD4 in HNSCC were evaluated by genetic and pharmacological approach in vitro and in vivo. Therapeutic efficiency of BRD4 targeting by JQ1 was assessed in three preclinical models including xenograft model, 4NQO-induced model and patients-derived xenograft model. Gene candidates responsible for therapeutic effects of JQ1 were identified by transcriptional profiling in HNSCC cells after JQ1 exposure. Significant upregulation of BRD4 was found in primary HNSCC samples and 4NQO-induced HNSCC model. Its overexpression associated with aggressive clinicopathological features and inferior overall and disease-free survival. BRD4 depletion by genetic silencing or pharmacological inhibition impaired cell proliferation, migration and invasion and reduced tumor growth and metastasis in vivo. Transcriptional profiling of HNSCC cells following JQ1 exposure identified hundreds of genes which might mediated its antitumor effects and enriched in cancer-relevant pathways. A novel prognostic risk score derived from JQ1-regualted genes was developed to stratify patients into subgroups with favorable or inferior prognosis. Our findings reveal that BRD4 serves as a novel oncogene driving cancer progression and a robust prognostic biomarker in HNSCC. Therapeutic targeting of BRD4 represents a potent and promising strategy against HNSCC.

overall_design: JQ1 induced gene expression in human head neck squamous cell carcinoma cells were detected at 24 hours after exposure to dose of 0, 0.5 μM. Two different kinds of HNSCC cells Cal27 and Fadu were utilized in this study.

first: Yaping

last: Wu

first: Yanling

last: Wang

first: Pengfei

last: Diao

first: Wei

last: Zhang

first: Jin

last: Li

first: Han

last: Ge

first: Yue

last: Song

first: Zhongwu

first: Dongmiao

first: Laikui

last: Liu

first: Hongbing

last: Jiang


title: Sensory experience remodels genome architecture in neural circuit to drive motor learning

city: Evanston

last: Yang

address: 2200 Campus Dr

department: Neurobiology

institute: Northwestern University

summary: Neuronal activity-dependent transcription couples sensory experience to adaptive responses of the brain including learning and memory. Mechanisms of activity-dependent gene expression including alterations of the epigenome have been characterized. However, the fundamental question of whether and how sensory experience remodels chromatin architecture in the adult brain in vivo to induce neural code transformations and learning and memory remains to be addressed. Here, in vivo calcium imaging, optogenetics, and pharmacological approaches reveal that granule neuron activation in the anterior dorsal cerebellar vermis (ADCV) plays a crucial role in a novel delay tactile startle learning paradigm in mice. Strikingly, using large-scale transcriptome and chromatin profiling, we have discovered that activation of the motor learning-linked granule neuron circuit reorganizes neuronal chromatin including through long-distance enhancer-promoter and transcriptionally active compartment interactions to orchestrate distinct granule neuron gene expression modules. Conditional CRISPR knockout of the chromatin architecture regulator Cohesin in ADCV granule neurons in adult mice disrupts activity-dependent transcription and motor learning. These findings define how sensory experience patterns chromatin architecture and neural circuit coding in the brain to drive motor learning.

overall_design: Two to four replicates of the histone modifications (H3K27ac, H3K27me3, and H3K4me3), histone variant (H2A.z), transcriptional regulator (CTCF), in situ chromosome conformation capture (HiC), and proximity ligation assisted ChIP (PLAC) from ADCV of 6-8 weeks old mice subjected to optogenetic stimulation or the homecage control were examined using libraries prepared with the NEBNext Ultra™ II DNA Library Prep Kit. Two to five replicates of chromatin-bound RNA, nucleocytoplasmic RNA, or total RNA were extracted from ADCV, lobule VI, or total cerebella of 6-8 weeks old mice subjected to optogenetic stimulation, pharmacological treatment, sensorimotor stimulation, or control conditions using Trizol and the NEBNext rRNA Depletion Kit were examined using libraries prepared with the NEBNext Ultra™ Directional RNA Library Prep Kit. Two replicates of DNase hypersensitive sites from total cerebella of P22 mice were examined using libraries prepared with the Illumina DNA Sample Prep Kit. All samples were sequenced on the Illumina NextSeq 500 platform, except for DHS samples that were sequenced on the Illumina HiSeq 2000 platform.

first: Tomoko

last: Yamada

first: Pamela

last: Valnegri

first: Ivan

last: Juric

first: Armen

last: Abnousi

first: Kelly

last: Markwalter

first: Arden

last: Guthrie

first: Abigail

last: Godec

first: Anna

last: Oldenborg

first: Ming

last: Hu

first: Timothy

last: Holy

first: Azad

last: Bonni


title: Transcriptional profile of zebrafish eyes after exposure to 200 ug/L Tetrabromobisphenol A (TBBPA)

first: Lisa

last: Baumann

summary: Vertebrate eye devlopment is partially regulated by thyroid hormones. TBBPA is a chemical that interacts with thyroid receptors. We investigated the effects of TBBPA on eye development of zebrafish. We expected TBBPA exposure to cause transcriptional changes of visual-system-related genes, which find their phenotypic anchoring in eye malformations and dysfunction, as observed in our previous studies. Additionally, the reversibility of effects after recovery in clean water for three days was investigated.

overall_design:
We used an n + 2 A-optimal design (Kerr and Churchill, 2001, PMID 12933549).  See microarray_set-up.pdf linked at the foot of the superSeries GSE121338 record.
Zebrafish eggs were exposed to 0 (C, control) or 200 ug/L TBBPA (E, exposure) from 0 to 5 days post fertilization (dpf) in 6 replicates (24 eggs per plate) each. At 5 dpf , 3 replicate plates of each treatment were sampled (control 5 dpf and TBBPA 5 dpf). The 3 remaining replicates were further raised in clean water and sampled at 8 dpf (control 8 dpf and TBBPA 8 dpf).

first: L

first: H

last: Segner

first: A

last: Ros

first: D

last: Knapen

last: Vergauwen


title: Bovine pituitary gland gene expression database of Polish-HF, Polish-Red and Hereford cattle breeds.

city: Torun

first: CHANDRA

middle: SHEKHAR

last: PAREEK

state: Kuj. Pom.

address: ul. Wilenska 4

department: Centre for Modern Interdisciplinary Technologies

country: Poland

institute: Nicolaus Copernicus University

summary: We reported the bovine pituitary gland gene expression database of Polish-HF, Polish-Red and Hereford cattle breeds.

overall_design: Examination of bovine pituitary gland gene expression in Polish-HF, Polish-Red and Hereford cattle breeds.

first: Chandra

last: Shekhar Pareek

first: Dibyendu

last: Kumar


title: Thyroid disruptors interfere with molecular pathways of eye development and function in zebrafish


title: Transcriptome Analyses of Loss of Pitx2 Gene Function at Fetal/Neonatal Mouse Muscle

city: Corvallis

first: Chih-Ning

last: Chang

state: OR

address: 1601 SW Jefferson Ave., RM 115

department: Pharmacy

institute: Oregon State University

summary: Ablation of the homeobox gene Pitx2 in skeletal muscles resulted in abnormally elevated levels of blood glucose and insulin as animals became morbidly obese. Grasping defects, abnormal accumulation of inter-myofiber connective tissue, deformed ultrastructure of the contractile apparatus, vestigial mitochondria accompanied by increased FoxO3-mediated mitophagy, and multiple disrupted metabolic pathways were apparent at the onset of blood-measurable metabolic disease. The respiration rate of mutant muscle cells was reduced, due to problems with both the electron transport chain (complex I, II and IV) and ATP synthase (complex V), and was consistent with the vestigial mitochondria and disruption in fatty acid metabolism observed in mutant muscle. Pitx2 influences expression of components of the contractile apparatus and the molecular machinery that assembles it. Similarly, Pitx2 influences the expression of genes encoding metabolic enzymes and genes encoding the molecular machinery that will be needed after birth for facultative adaptation of muscle energy metabolism.

overall_design: Tibialis mRNA profiles of 30-day old control (Pitx2fl/z) and mutant (MCKcrePitx2fl/z) mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000.

first: Arun

last: Singh

first: Chrissa

last: Kioussi

first: Kelli

middle: A

last: Lytle

first: Donald

middle: B

last: Jump

first: Sean

last: Newsom

first: Jaewoo

last: Choi

first: Jan

last: Stevens

first: Michael

last: Gross


title: Reducing astrocyte calcium signaling in vivo alters striatal microcircuits and causes repetitive behavior I

city: Los Angeles

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

summary: Astrocytes tile the central nervous system, but their functions in neural microcircuits in vivo and their roles in mammalian behavior remain incompletely defined. We used 2-photon laser scanning microscopy (2PLSM), electrophysiology, MINIscopes, RNA-seq and a new genetic approach to characterize the effects of reduced striatal astrocyte Ca2+ signaling in vivo. In wild type mice, reducing striatal astrocyte Ca2+-dependent signaling increased repetitive self-grooming behaviors by altering medium spiny neuron (MSN) activity. The mechanism involved astrocyte-mediated neuromodulation mediated by ambient GABA and was corrected by blocking astrocyte GABA transporter 3 (GAT-3). Furthermore, in a mouse model of Huntington’s disease, dysregulation of GABA and astrocyte Ca2+ signaling accompanied excessive self-grooming, which was relieved by blocking GAT-3. Assessments with RNA-seq revealed astrocyte genes and pathways regulated by Ca2+ signaling in a cell autonomous and non-cell autonomous manner, including Rab11a, a regulator of GAT-3 functional expression. Thus, striatal astrocytes contribute to neuromodulation controlling obsessive-compulsive-like behavior in mice.

overall_design: Total 16 samples were used in this data set. Whole striata were extraced from 8 adult mice: 4 mice received RiboTag AAV and AAV encoding a control protein and 4 mice received RiboTag AAV and AAV encoding a protein that suppresses calcium signals named hPMCA2w/b. After homogenization, RNA was purified from (i) cleared lysate as the input and control, and (ii) astrocyte-specific ribosome-associated RNA precipitated via a hemagglutinin (HA) tag.

first: Xinzhu

last: Yu

first: Anna

middle: W

last: Taylor

first: Jun

last: Nagai

first: Peyman

last: Golshani

first: Christopher

last: Evans

first: Baljit

last: Khakh


title: Reducing astrocyte calcium signaling in vivo alters striatal microcircuits and causes repetitive behavior


title: Analyses of circRNA profiling during the development from pre-receptive to receptive phases in goat endometrium

city: Yangling District

first: Lei

last: Zhang

state: Province, State or Region

address: No.22 Xinong Road,  Yangling District

department: College of Animal Science and Technology

institute: Northwest A&F University

summary: In the present study, RNA-seq technique was used to compare the expression profiles of circRNAs from goat endometrium samples at gestational day 5 (pre-receptive endometrium, PE) and day 15 (receptive endometrium, RE). A total of 21,813 circRNAs were identified in goat endometrium, of which only 31.22% (6,810) circRNAs were co-expressed at both stages, and 5,925 circRNAs were identified specifically in RE and 9,078 in PE, suggesting high stage specificity in the circRNAs in dairy goats. Further analysis found that there were 334 DECs (differentially expressed circRNAs) in RE compared to PE (P< 0.05), and circRNA8077 was up-regulated with the highest FPKM value in RE. It was noteworthy that half of the up-regulated circRNAs with top 10 highest FPKM value in RE were come from CRIM1. Moreover, GO and KEGG analysis of the hgDEGs (hosting genes of DECs) revealed some circRNAs, genes and pathways that may involve in the formation of the receptive endometrium in dairy goats. In a word, our data provided an endometrium circRNA expression atlas related to the biology of the goat receptive endometrium during embryo implantation, and the results suggested that a subset of circRNAs might involve in the processes of the formation and development of endometrial receptivity.

overall_design: A total of 20 healthy 24-month-old multiparous dairy goats (Xinong Saanen) were induced to estrous synchronization for this study. The first day of mating was considered to be Day 0 of pregnancy. Gestational days 5 and 15 were important time points for the embryo implantation in goats. The experimental goats were observed 3 times daily to ascertained estrous sign and mated naturally twice in estrus. And then the goats were euthanized when the goats lost consciousness caused by intravenous injection of barbiturate (30mg/kg) at gestational day 5 (pre-receptive endometrium) and gestational day 15 (receptive endometrium). Endometrium samples from 10 goats at gestational day 5 and 10 goats at gestational day 15 were obtained from the anterior wall of the uterine cavity.

first: Bin-yun

last: Cao


title: Reducing astrocyte calcium signaling in vivo alters striatal microcircuits and causes repetitive behavior II

overall_design: Total 16 samples were used in this data set. Whole striata were extraced from 8 adult Aldh1l1-Cre/ERT2 x Ribotag mice: 4 mice received AAV encoding a control protein and 4 mice received AAV encoding a protein that suppresses calcium signals named hPMCA2w/b. After homogenization, RNA was purified from (i) cleared lysate as the input and control, and (ii) astrocyte-specific ribosome-associated RNA precipitated via a hemagglutinin (HA) tag.

middle: S


title: Sequencing of smallRNAs of fish embryos in somite stage

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

institute: Leibniz Institute on Aging - FLI

summary: Sequencing of smallRNA of different Nothobranchius furzeri (Nfu) strains and 8 further anual and not anual fish species for investigation of its differential expression with and without diapause.

sample_organism:
Rivulus cylindraceus
Aplocheilus lineatus
Callopanchax occidentalis
Iconisemion striatum
Nothobranchius furzeri
Austrofundulus leohoignei
Nematolebias papilliferus
Epiplatys dageti monroviae

overall_design: Sequencing of: Nfu (Strain: MZM0403, MZM0410, GRZ x MZZW), Callopanchax occidentalis, Nematolebias papilliferous, Austrofundulus leohoignei, Aphyosemion striatum, Aplocheylus lineatus, Rivulus cylindraceus, Epiplatys dageti monroviae

first: Alessandro

last: Cellerino

first: Mario

last: Baumgart

first: Luca

last: Dolfi

first: Auroa

last: Savino

first: Roberto

last: Ripa

first: Matthias

last: Platzer


title: Next Generation Sequencing Facilitates Quantitative Analysis of primary myoblast cell treated with different concentration glycine Transcriptomes

status: Public on May 08 2019

city: Tianjin

first: GANG

last: HAN

address: No.22 Qi Xiang Tai Road

institute: Tianjin medical university

summary:
Purpose: The goals of this study are to analyze primary myoblast cell from mdx mice skeletal muscle transcriptome profiling (RNA-seq) treated with different concentration glycine.
Methods: primary myoblast cell isolated from 6-8-week-old mdx mice limb skeletal muscle and the primary myoblast treated with 0.2mM or 0.8mM glycine 24-hour. Primary myoblast mRNA profiles of 0.2mM glycine treated(3 replicates) and 0.8mM glycine treated(6 replicates) were generated by deep sequencing, using Illumina HiSeq 2500. The sequence reads that passed quality filters were analyzed at the gene level using HISAT2 and StringTie followed by DESeq2.

first: Gang

last: Han

first: Haifang

last: Yin


title: Three Transcription Factor Functions Empower Progression from Naïve to Formative Pluripotency [RNA-Seq]

first: Susanne

last: Bornelöv

summary: The gene regulatory network in naïve mouse embryonic stem cells (ESCs) must be reconfigured for lineage competence. Tcf3 enables rewiring to formative pluripotency by repressing components of the ESC transcription factor circuitry. However, elimination of Tcf3 only delays, and does not prevent, state transition. Here we delineate distinct contributions of the Ets-family transcription factor Etv5 and the repressor Rbpj. Downstream of Erk1/2 signalling, Etv5 activates enhancers for formative pluripotency. Concomitant up-regulation of Rbpj ensures irreversible exit from the naïve state by extinguishing reversal factors, Nanog and Tbx3. Triple deletion of Etv5, Rbpj and Tcf3 incapacitates ESCs, such that they remain undifferentiated and locked in self-renewal even in the presence of differentiation stimuli. Thus, pluripotency progression is driven hierarchically by two repressors, that respectively dissolve and extinguish the naive network, and an initiator that commissions the formative network. Similar tripartite action may be a general mechanism for efficient cell transitions.

overall_design: RNA-seq analysis of parental Rex1-GFPd2 ES cells (RGd2), and deletion mutants generated in this background (Etv5-KO, RbpJ-KO, Etv5-RpbJ-dKO, Etv5-RbpJ-Tcf3-tKO) cultured in 2i, N2B27 or supplemented with Chiron, 3 biological replicates per condition.

first: Tüzer

last: Kalkan

first: Evangelia

last: Diamanti

first: Tim

last: Lohoff

first: Carla

last: Mulas

first: Meryem

last: Ralser

first: Sjors

last: Middelkamp

first: Patrick

last: Lombard

first: Jennifer

last: Nichols

first: Austin

last: Smith


title: QBiC-Pred: Quantitative Predictions of Transcription Factor Binding Changes Due to Sequence Variants V

city: Durham

first: Raluca

last: Gordan

state: NC

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

institute: Duke University

summary: Non-coding genetic variants/mutations can play functional roles in the cell by disrupting regulatory interactions between transcription factors (TFs) and their genomic target sites. For most human TFs, a myriad of DNA-binding models are available and could be used to predict the effects of DNA mutations on TF binding. However, information on the quality of these models is scarce, making it hard to evaluate the statistical significance of predicted binding changes. Here, we present QBiC-Pred, a web server for predicting quantitative TF binding changes due to nucleotide variants. QBiC-Pred uses regression models of TF binding specificity trained on high-throughput in vitro data. The training is done using ordinary least squares (OLS), and we leverage distributional results associated with OLS estimation to compute, for each predicted change in TF binding, a p-value reflecting our confidence in the predicted effect. We show that OLS models are accurate in predicting the effects of mutations on TF binding in vitro and in vivo, outperforming widely-used PWM models as well as recently developed deep learning models of specificity. QBiC-Pred takes as input mutation data sets in several formats, and it allows post-processing of the results through a user- friendly web interface. QBiC-Pred is freely available at http://qbic.genome.duke.edu.

overall_design: Universal protein-binding microarray (PBM) experiments were performed for recombinant, epitope-tagged transcription factors from human, mouse, and A. thaliana. Briefly, universal PBMs involved binding of GST-tagged, His-tagged, or Flag-tagged transcription factors to double-stranded Agilent microarrays containing a DNA library designed to cover all possible 10-bp sequences, with every 8-mer occurring in at least 16 different spots on the array. This design allows comprehensive and unbiased characterization of the binding specificity of transcription factors for all possible 8-bp sequences.


title: QBiC-Pred: Quantitative Predictions of Transcription Factor Binding Changes Due to Sequence Variants IV


title: QBiC-Pred: Quantitative Predictions of Transcription Factor Binding Changes Due to Sequence Variants III


title: QBiC-Pred: Quantitative Predictions of Transcription Factor Binding Changes Due to Sequence Variants II


title: QBiC-Pred: Quantitative Predictions of Transcription Factor Binding Changes Due to Sequence Variants I

sample_organism:
Homo sapiens
Mus musculus


title: PRDM16 orchestrates neuron-vascular communication for angiogenesis during brain development

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary:
Purpose:To gain a deeper insight into how PRDM16 regulates neuron-vascular communication for angiogenesis, RNA-sequencing (RNA-seq) was performed to analyze the genome-wide changes by PRDM16 deletion at E15.
Methods: Total RNA was extracted from E15 telencephalic tissue of Prdm16cKO and Prdm16fl/fl mice. Then total RNA was quality controlled and quantified using an Agilent 2100 Bioanalyzer. After converting to cDNA and building library, high-throughput sequencing was performed using the Illumina HiSeq 2500 platform in Annoroad Genomics.
Results: Approximately approximately one thousand transcripts showed differential expression between the Prdm16fl/fl and Prdm16cKO brain cortex, with a fold change ≥1.5 and p value <0.05. Gene ontology (GO) analysis showed that the down-regulated genes were enriched in the terms related to neurogenesis, blood vessel development and secretion by cells. Up-regulated genes showed a significant enrichment of terms involved in negative regulation of cell communication and negative regulation of angiogenesis. These results reflected the importance of PRDM16 in cortical development.
Conclusions: We conclude that RNA-seq based transcriptome characterization would provide a framework for understanding how Prdm16 gene contribute to brain cortical development.

overall_design: Total RNA was extracted from E15 telencephalic tissue of  Prdm16cKO and  Prdm16fl/fl mice and generated by deep sequencing, in triplicate, using Illumina HiSeq 2500.

first: Libo

last: Su


title: Highly-motile versus unsorted MDA-MB-231 breast cancer cells

city: Baltimore

first: Konstantinos

last: Konstantopoulos

state: MD

address: 3400 N Charles St

department: Chemical and Biomolecular Engineering

institute: Johns Hopkins University

summary: The challenge of predicting which patients with breast cancer will develop metastases leads to the overtreatment of patients with benign disease and to the inadequate treatment of the aggressive cancers. Here, we report the development and testing of a microfluidic assay that quantifies the abundance and proliferation of migratory cells in breast-cancer specimens, for the assessment of their metastatic propensity and for the rapid screening of potential antimetastatic therapeutics. On the basis of the key roles of cell motility and proliferation in cancer metastasis, the device accurately predicts the metastatic potential of breast-cancer cell lines and of patient-derived xenografts. Compared to unsorted cancer cells, highly motile cells isolated by the device exhibited similar tumourigenic potential but markedly increased metastatic propensity in vivo. RNA sequencing of the highly motile cells revealed an enrichment of motility-related and survival-related genes. The approach might be developed into a companion assay for the prediction of metastasis in patients and for the selection of effective therapeutic regimens.

overall_design: RNA was isolated from samples of 1000 migratory or unsorted cells in triplicate

first: Christopher

middle: L

last: Yankaskas

first: Keyata

middle: N

last: Thompson

first: Colin

last: Paul

first: Michele

last: Vitolo

first: Panagiotis

last: Mistriotis

first: Ankit

last: Mahendra

first: Vivek

last: Bajpai

first: Daniel

last: Shea

first: Kristen

middle: M

last: Manto

first: Andreas

last: Chai

first: Navin

last: Varadarajan

first: Aikaterini

last: Kontrogianni-Konstantopoulos

first: Stuart

last: Martin


title: Malignant transformation of normal mature mouse B cells into myeloma-like cells in vitro using defined genetic elements

city: Solna

first: Jessica

middle: Margareta

last: Lindvall

address: Tomtebodavägen 23A

department: NBIS

institute: SciLifeLab. Stockholm University

summary:
Expression of MYC+BMI1+BCLXL in normal mature mouse B cells results inmalignant transformation into  lymphoma-like cells
Expression of MYC+BMI1+BCLX+IRF4 in normal mature mouse B cells results in malignant transformation into myeloma-like cells

overall_design: Retroviral transduction of lipopolysaccharide-stimulated B cells in vitro. The 7 cells tested are biological replicates.

first: Alf

last: Grandien

first: Kari

last: Högstrand

first: Anne

last: Sundblad


title: CDK11 loss induces cell cycle dysfunction and death of BRAF and NRAS melanoma cells

city: Minneapolis

first: Todd

middle: P

last: Knutson

state: MN

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota

summary: Cyclin dependent kinase 11 (CDK11) is a protein kinase that regulates RNA transcription, pre-mRNA splicing, mitosis, and cell death. Targeting of CDK11 expression levels is effective in the experimental treatment of breast and other cancers, but these data are lacking in melanoma. To understand CDK11 function in melanoma, we evaluated protein and RNA levels of CDK11, Cyclin L1 and Cyclin L2 in benign melanocytes and BRAF- as well as NRAS-mutant melanoma cell lines. We investigated the effectiveness of reducing expression of this survival kinase using RNA interference on viability, clonal survival, and tumorsphere formation in melanoma cell lines. We examined the impact of CDK11 loss in BRAF-mutant melanoma on more than 700 genes important in cancer signaling pathways. Follow-up analysis evaluated how CDK11 loss alters cell cycle function in BRAF- and NRAS-mutant melanoma cells. We present data on CDK11, CCNL1 and CCNL2 mRNA expression in melanoma patients, including prognosis for survival. In sum, we found that CDK11 is necessary for melanoma cell survival, and a major impact of CDK11 loss in melanoma is to cause disruption of the cell cycle distribution with accumulation of G1- and loss of G2/M-phase cancer cells.

overall_design: The study included six A375 melanoma cell lines samples. Three sample replicates were treated with an siRNA targeting both the CDK11A and CDK11B transcripts and three sample replicates were treated with an non-targeting siRNA control. RNA was harvested 48 h post-transfection and gene expression levels were measured using the NanoString platform with the PanCancer codeset, plus additional custom gene codesets (CSNK2A1; CSNK2A2; CSNK2B; CDK11A; CDK11B; CCNL1; CCNL2; MCL1; STAT5A; STAT5B).

first: Rehana

last: Ahmed

last: Shaughnessy

first: Rachel

middle: I

last: Vogel

first: Khalil

first: Betsy

middle: T

last: Kren

first: Janeen

middle: H

last: Trembley


title: mRNA sequencing of PPD3 over expression in Col-0 background in Arabidopsis

city: University Park

first: Hardik

last: Kundariya

address: 361 N. Frear

institute: The Pennsylvania State University

summary: The PPD3 genomic DNA was cloned in the binary vector pCAMBIA1302C with its native promoter of about 1.5 kb and was tagged with  GFP. Wild type Col-0 plants were transformed by the dipping method and screened for positive plants by hygromycin and also by PCR primers for presence of the transgene.

overall_design: Two plants each for both PPD3 over expression and Col-0 wild-type control were sequenced

first: Jesus

last: Beltran

first: Sally

last: Mackenzie


title: C/EBPβ regulates the M2 transcriptome in β-adrenergic-stimulated macrophages

first: Donald

middle: M.

last: Lamkin

state: CA

address: 300 UCLA Medical Plaza, Room 3160

department: Semel Institute for Neuroscience

summary: We screened RNAseq results from RAW 264.7 macrophages for previous empirically-defined M2 genes in the whole transcriptome that followed the Arg1 pattern of up-regulation by β-adrenergic-signaling with inhibition by Cebpb gene knockdown. We also screened RAW 264.7 macrophages for empirically-defined M1 genes that exhibited the orthogonal pattern of Arg1 regulation (i.e., down-regulation by β-adrenergic signaling, with rescue of this effect by Cebpb knockdown).

overall_design: Total RNA was purified from RAW 264.7 macrophage cells that were incubated in one of four experimental conditions: Control siRNA, Cebpb siRNA, Control siRNA+Isoproterenol, Cebpb siRNA+Isoproterenol; four biological replicates per condition


title: Expression profile of NIH3T3 cells overexpressing FOXP2 or a FOXP2 arrangement (FOXP2-CPED1)

first: Yanyang

last: Zhao

state: Not required for this country

address: No.1, Dahua Road,Dongdan

institute: Genetics Medicine

summary: To study the underlying mechanism of tumor initation driven by FOXP2, we performed transcriptome analysis of transformed NIH3T3 overexpressing FOXP2 or FOXP2-CEPD1 and control cells to explore the FOXP2-related transcriptome in tumorigenesis.

overall_design: mRNA profiles of NIH3T3 cells overexpressing FOXP2 or FOXP2-CPED1 were generated by deep sequencing, using Illumina HiSeq 2500. Four independent cell clones for NIH3T3 cells overexpressing FOXP2, four independent cell clones for NIH3T3 cells overexpressing FOXP2-CPED1, NIH3T3 parental cells and NIH3T3 cells overexpressing vector as the controls.

first: Xiaoquan

last: Zhu


title: Sir2 suppresses transcription-mediated displacement of Mcm2-7 replicative helicases at the ribosomal DNA repeats

city: Seattle

first: Eric

middle: Jan

last: Foss

state: WA

address: 1100 Fairview Ave N

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

summary: Repetitive DNA sequences within eukaryotic heterochromatin are poorly transcribed and replicate late in S-phase. In Saccharomyces cerevisiae, the histone deacetylase Sir2 is required for both transcriptional silencing and late replication at the repetitive ribosomal DNA arrays (rDNA). Despite the widespread association between transcription and replication, it remains unclear how transcription might impinge on replication, or vice versa. Here we show that, when silencing of an RNA polymerase II (RNA Pol II)-transcribed non-coding RNA at the rDNA is disrupted by SIR2 deletion, RNA polymerase pushes and thereby relocalizes replicative Mcm2-7 helicases away from their loading sites to an adjacent region with low nucleosome occupancy, and this relocalization is associated with increased rDNA origin efficiency. Our results suggest a model in which two of the major defining features of heterochromatin, transcriptional silencing and late replication, are mechanistically linked through suppression of polymerase-mediated displacement of replication initiation complexes.

overall_design: sonication (replication profiling), MNase (MNase-seq), and calcium (MCM2-ChEC)

first: Antonio

last: Bedalov

middle: J


title: RNA-Seq Analysis of TCDD-Elicited Changes in Circadian Hepatic Gene Expression in Male Mice

city: East Lansing

first: Timothy

last: Zacharewski

state: Michigan

address: 603 Wilson Road

department: BMB

institute: Michigan State University

summary: Hepatic gene expression was examined every 3 hours for 24 hours following repeated exposure (every 4 days for 28 days) to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). These data were used to examine the effect of repeated TCDD exposure on the circadian rhythmicity of hepatic gene expression in C57BL/6 male mice.

overall_design: Three biological replicates for each timepoint (ZT0, ZT3, ZT6, ZT9, ZT12, ZT15, ZT18, ZT21) of TCDD and sesame oil vehicle.

first: Kelly

last: Fader

first: Rance

last: Nault

first: Claire

last: Doskey

first: Russell

middle: R

last: Fling


title: A revised model of clonal evolution of intraductal papillary mucinous neoplasm-related pancreatic carcinogenesis

city: Asahikawa

first: Yusuke

last: Mizukami

state: Hokkaido

address: 2-1 Modorigaoka Higashi

department: Medicine

institute: Asahikawa Medical University

type: Methylation profiling by genome tiling array

summary: Similarity of DNA methylation profile observed in the multi-regions from the branch-off subtype intraductal papillary mucinous neoplasm-related pancreatic adenocarcinoma

overall_design: DNA methylation profile

first: Yuko

last: Omori

last: Ono

first: Katsuro

last: Enomoto

first: Jun

last: Ueda

first: Kenzui

last: Taniue


title: Gene expression profiles in CYP2C19-deficient human iPS cell-derived hepatocyte-like cells

status: Public on May 07 2019

city: Suita

first: Tomoki

last: Yamashita

state: Osaka

address: 1-6 Yamadaoka

department: Graduate School of Pharmaceutical Sciences

institute: Osaka University

summary: Cytochrome P450 family 2 subfamily C member 19 (CYP2C19), in liver, plays important roles in terms of drug metabolism. It is known that CYP2C19 poor metabolizers (PMs) lack CYP2C19 metabolic capacity. Thus, unexpected drug-induced liver injury or decrease of drug efficacy would be caused in CYP2C19 substrate-treated CYP2C19 PMs. However, it is difficult to evaluate the safety and effectiveness of drugs and candidate compounds for CYP2C19 PMs because there is currently no model for this phenotype. Here, using human iPS cells and our highly efficient genome editing and hepatocyte differentiation technologies, we generated CYP2C19-knockout human iPS cell-derived hepatocyte-like cells (CYP2C19-KO HLCs) as a novel CYP2C19 PM model for drug development and research. The gene expression levels of hepatocyte markers were similar between WT HLCs and CYP2C19-KO HLCs, suggesting that CYP2C19 deficiency did not affect the hepatic differentiation potency. We also examined CYP2C19 metabolic activity by measuring S-mephenytoin metabolites using LC-MS. The CYP2C19 metabolic activity was almost eliminated by CYP2C19 knockout. Additionally, we evaluated whether clopidogrel (CYP2C19 substrate)-induced liver toxicity could be predicted using our model. Unexpectedly, there was no significant difference in cell viability between clopidogrel-treated WT HLCs and CYP2C19-KO HLCs. However, the cell viability in clopidogrel- and ketoconazole (CYP3A4 inhibitor)-treated CYP2C19-KO HLCs was significantly enhanced as compared with that in clopidogrel- and DMSO-treated CYP2C19-KO HLCs. This result suggests that CYP2C19-KO HLCs can predict the clopidogrel-induced liver toxicity. We succeeded in generating CYP2C19 PM model cells using human iPS cells and genome editing technologies for pharmaceutical research.

overall_design: We generated CYP2C19-deficient human iPS cells based on a human iPS cell line, FCL-iPS (Takayama et al., 2014). Each CYP2C19-deficient iPS cells and wild type iPS cells were differentiated into hepatocyte-like cells (CYP2C19-KO HLCs and WT HLCs, respectively). CYP2C19-KO HLCs and WT HLCs were pooled from triplicate samples of one independent experiments, and then microarray analysis was performed.

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