title: FLUNEXT transcriptome analysis

city: Lyon

first: Julien

last: Textoris

address: Hôpital Edouard herriot - Pavillon P; 5 place d'Arsonval

department: Medical Diagnostic Discovery Department (MD3)

country: France

institute: bioMérieux

summary: Influenza virus infections remain a major public health burden. The intrinsic ever-evolving nature of this virus, the suboptimal efficacy of recent influenza inactivated vaccines, as well as the emergence of resistance against a limited antiviral arsenal, highlight the urgent need for novel therapeutic approaches to treat influenza infections. Here, we exploited in vivo transcriptomic signatures of infection, directly obtained from a patient’s cohort to identify in silico a list of marketed drugs with signatures that counteracted that of the infection state.

overall_design: Nasal swabs were collected from patients infected with influenza H1N1 virus, either at inclusion (before any antiviral treatment, Infected status), or 3 month after recovery (Cured status). Total RNA was extracted from nasal swabs collected into RNAlater  buffer, and subsequently analyzed by microarray.

first: Olivier

last: Terrier

first: Andres

last: Pizzorno

first: Thomas

last: Julien

first: Blandine

last: Padey

first: Magali

last: Roche

first: Séverine

last: Croze

first: Vanessa

last: Escuret

first: Bruno

last: Lina

first: Catherine

last: Legras-Lachuer

first: Manuel

last: Rosa-calatrava


title: Transcriptome analysis of antigen-specific T follicular helper (Tfh) and non-Tfh cells after Bach2 overexpression

status: Public on Feb 11 2019

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

country: Germany

institute: Deutsches Rheuma-Forschungszentrum

type: Expression profiling by high throughput sequencing

summary: We identified Bach2 as factor to be expressed at low levels in Tfh cells. Induced overexpression of Bach2 in the germinal center reaction results in loss of the Tfh cell population. RNA-seq of sorted antigen-specific Tfh and non-Tfh cells 18 hours after induction of Bach2 overexpression allowed the simultaneous analysis of Bach2 regulated genes and genes differentially expressed in Tfh and non-Tfh cells.

overall_design: Smarta T cell receptor transgenic cells were retrovirally transduced with an inducible vector encoding Bach2 or an empty control vector and transferred into C57BL/6 recipients. Ectopic Bach2 overexpression was induced five days after s.c. immunization with nitrophenol and GP61-80 coupled to mouse serum albumin. After 18 hours, transgenic T cells from pooled inguinal lymph nodes were sorted for a CD44hi CXCR5+ PD-1+ Tfh and CD44hi CXCR5- PD-1- non-Tfh cell phenotype for analysis by RNA-seq.

first: Annette

last: Lahmann

first: Julia

last: Kuhrau

first: Franziska

last: Fuhrmann

first: Frederik

last: Heinrich

first: Laura

last: Bauer

first: Mir-Farzin

last: Mashreghi

first: Andreas

last: Hutloff


title: Liver Transcriptomes in C57BL/6 mice

status: Public on Feb 13 2019

city: Hangzhou

first: Shan

last: Li

state: 浙江省

address: 866 Yuhangtang Road

country: China

institute: Zhejiang University

summary:
Purpose: a transcriptome analysis was used to ascertain whether lipid metabolism disorders were induced by high-fat diet (HFD), and comparisons were made between control, HFD and DfCS-Ib(treatment) groups.
Methods: liver mRNA profiles of C57BL/6 mice were generated by deep sequencing using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.
Results: HFD could change the expression of some genes and disturb normal metabolisms.  However, there were fewer changes for genes of DfCS-Ib group mice.  According to the KEGG Pathway Database and GO analysis, genes involving in lipid biosynthesis, degradation, and transportation were changed by HFD.
Conclusions: Our study indicated that DfCS-Ib alleviated lipid disorder of HFD-fed mice in liver by normalizing the expressions of related genes.

overall_design: total liver mRNA profiles of C57BL/6 treated with sulfated oligosaccharide were generated by deep sequencing

first: Shiguo

last: Chen


title: Single cell RNA-seq data of microglia cells from normal mouse brain as well as in the context of neurodegenerative inhury models

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

institute: University Medical Center Freiburg

summary: Single cell RNA-seq data was obtained from FACS sorted microglia from different brain regions of normal 16 weeks old CD1 mice as well as from mice undergoing facial nerve axotomy or cuprizone treatment in order to elucidate microglia heterogeneity in a regional and disease model specific manner.

overall_design: 1920 cells total were sequenced with 3-4 replicate mice per condition. For normal tissue different brain regions from the same mice were obtained.

first: Takahiro

last: Masuda

first: Marco

last: Prinz


title: Single cell RNAseq data of CD1 microglia

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: The contribution of adenosine receptor 3-mediated signaling to TLR4-induced responses by human dendritic cells

status: Public on Feb 12 2019

city: Rijswijk

first: Jeffrey

last: Bajramovic

address: Lange Kleiweg 161

department: Alternatives

country: Netherlands

institute: Biomedical Primate Research Centre

summary: Human dendritic cells were exposed to LPS, in the absence and presence of adenosine receptor 3 inhibitor

overall_design: 4 donors, 4 experimental conditions. VUF concentration used was 5 µM, LPS was 500 ng/ml. Exposure times were 6 hours

first: Celine

last: van der Putten


title: Transcriptomics analysis of the impact of CSRP2 loss in human breast cancer cells

status: Public on Feb 08 2019

city: Luxembourg

first: Joshua

middle: Don

last: Brown-Clay

address: 84 Val Fleuri

department: Oncology

country: Luxembourg

institute: Luxembourg Institute of Health

summary:
CSRP2 is an actin-bundling protein essential for assembly of invadopodia. We observed that it is also present in the nucleus and its knock-down results in decreased expression of MMPs important in the invasive or metastatic process.
Therefore, we sought to examine the transcriptomic impact of loss of CSRP2 in human breast cancer cells.

overall_design: 150 000 Hs578T cells were plated in each well of a six-well plate. The following day, Lipofectamine 2000 was used to transfect the cells with non-targeting or CSRP2 siRNA. 24 hours later, 100,000 cells from each well were transferred to a 24-well plate. 48 hours later, RNA was extracted from the cells and analyzed on Affymetrix HuGene 2.0 arrays.

first: Xianqing

last: Mao

first: Tony

last: Kaoma

first: Clément

last: Thomas


title: Circulating exosomal miRNA profile during term and preterm birth pregnancies – a longitudinal study

city: Brisbane

first: Dominic

last: Guanzon

state: Queensland

address: Building 71/918 RBWH Herston

department: UQCCR

country: Australia

institute: University of Queensland

type: Non-coding RNA profiling by high throughput sequencing

summary: The objective of this study was to characterise the changes in the exosomal miRNA concentrations circulating in the maternal plasma between mothers delivering term and preterm neonates, across gestation using a longitudinal study design. A retrospective stratified study design was used to characterize the miRNA content in exosomes present in maternal plasma of term (n=20 per time point) and preterm birth (PTB) (n=10 per time point) across gestation (i.e. first, second and third trimester).

overall_design: miRNAs were profiled from exosomes using next generation seqeuencing (Illumina NextSeq 500 platform).

first: Ramkumar

last: Menon

first: Carlos

last: Salomon


title: Human colon organoids reveal distinct physiologic and oncogenic Wnt responses II

city: Frankfurt

first: Henner

middle: F.

last: Farin

address: Paul-Ehrlich-Str. 42-44

department: Institute for Tumor Biology and Experimental Therapy

institute: DKTK/Georg-Speyer-Haus

summary: Constitutive Wnt activation upon loss of Adenoma polyposis coli (APC) acts as main driver of colorectal cancers (CRC). Targeting Wnt signaling has proven difficult because the pathway is crucial for homeostasis and stem cell renewal. To distinguish oncogenic from physiologic Wnt activity, we have performed comprehensive transcriptome and proteome profiling in human colon organoids. Culture in the presence or absence of exogenous ligand allowed us to discriminate receptor-mediated signaling from the effects of CRISPR/Cas9 induced APC loss. We could catalogue two non-overlapping molecular signatures that were stable at distinct levels of stimulation. Newly identified markers for normal colon stem/progenitor cells and adenomas were validated by immunohistochemistry and flow cytometry. We found that oncogenic Wnt signals are associated with good prognosis in tumors of the consensus molecular subtype 2 (CMS2). In contrast, receptor-mediated signaling was linked to CMS4 tumors and poor prognosis. Together, our data represent a valuable resource for biomarkers that allow more precise stratification of Wnt responses in CRC.

overall_design: Culturing normal and CRISPR/Cas9 engineered APC mutant isogenic organoid lines in the presence or absence of Wnt-stimulation, followed by transcriptome and proteome profiling allowed for the stratification of physiologic and oncogenic Wnt responses.

first: Birgitta

middle: E

last: Michels

first: Mohammed

middle: M

last: Mosa

first: Britta

last: Grebbin

first: Diego

last: Yepes

first: Tahmineh

last: Darvishi

first: Johannes

last: Hausmann

first: Henning

last: Urlaub

first: Stefan

last: Zeuzem

first: Hans

last: Kvasnicka

first: T

last: Oellerich

middle: F


title: Transforming Growth Factor β-Induced Epithelial-to-Mesenchymal Signature Predicts Metastasis-Free Survival in Non-Small Cell Lung Cancer.

city: Tampa

first: Eric

last: Welsh

state: FL

address: 12902 Magnolia Dr

department: Biostatistics and Bioinformatics

country: USA

institute: H Lee Moffitt Cancer Center

summary: 14 human Non-Small Cell Lung cancer (NSCLC) cell lines were treated with Transforming Growth Factor beta-1 (TGFβ-1) to induce epithelial-to-mesenchymal transition. Microarrays measured gene expression at baseline and at different times after treatment.

overall_design: NSCLC cells lines (NCI- H23, H292, H322, H358, H441, H522, H1395, H1437, H1648, H1944, H2122, H2347, CALU-6, and A549) were used in the study.  Cell lines were characterized in terms of their response to TGFβ-1, via measurements of: growth, morphology, migration, SMAD phosphorylation, transcriptional activity, and expression of cadherin 1 and SNAIL. Gene expression changes in NSCLC cells after TGFβ treatment were determined using Affymetrix U133 Plus 2.0 microarrays.

first: Teresita

last: Muñoz-Antonia

first: Steven

last: Eschrich

first: Edna

last: Gordian


title: Epigenetic regulation of the acute T cell leukemia

status: Public on Feb 09 2019

city: Chicago

first: Sundararajan

last: Jayaraman

state: IL

address: 909 South Wolcott Avenue

institute: University of Illinois at Chicago

summary:
Treatment of the acute T cell leukemia cell line Jurkat in vitro with the most potent histone deacetylase inhibitor, Trichostatin A induced apoptosis in a dose-dependent manner. Analysis of the drug-treated Jurkat cells using high throughput genome-wide gene expression profiling indicated the upregulation as well as downregulation of several genes crucial for cellular functions. Use of quantitative reverse transcriptase-mediated polymerase chain reaction validated the regulation of selected genes in drug-treated cells. Collectively, this study has unraveled the genes involved in epigenetic regulation of the T cell leukemia.
Microarray analysis was performed to determine the changes in global gene expression profiles during apoptosis of a T cell leukemia induced by the histone deacetylase inhibitor, Trichostatin A. Drug treatment induced the upregulation and repression of a number of genes.

overall_design: The T cell leukemia cell line Jurkat was grown in tissue culture, resuspended at 1 x 106 cells/ml and treated with Trichostatin A dissolved in dimethylsulfoxide at 50 ng/ml concentration. Controls included untreated cells and those treated with an equal amount of the vehicle. After 18 hours of culture, cells were harvested, and total RNA was extracted and hybridized to microchips in duplicate. Differential gene expression was analyzed as follows: media control vs. DMSO-treated cells, and media control vs. Trichostatin A-treated cells.

first: Jayaraman

last: Sundararajan.


title: Transcriptome analysis of swine spleen after infection with PCV2

status: Public on Feb 10 2019

city: Tai'an

first: Gen

last: Liu

state: Shandong

address: Daizong Road No.61

department: College of Animal Science and Veterinary Medicine

institute: Shandong Agricultural University

summary:
Purpose: Post-weaning multisystemic wasting syndrome (PMWS) is a disease associated with porcine circovirus type 2 (PCV2) infection. One main feature of PMWS is seriously decreased lymphocyte in lymphoid tissues. This research aims to investigate the molecular mechanism of evident lymphocyte depletion in spleen from Yorkshire x Landrace (YL) pigs after infection with PCV2.
Methods: At the age of 6 weeks, 15 piglets of Laiwu (LW) and YL pigs were assigned randomly into two groups, respectively: 10 infected pigs and 5 uninfected pigs. Spleen tissues of each group were collected at 35 days post infection with PCV2. Three PCV2-infected YL pigs with apparently pathologic characteristics and mock-infected YL pigs were selected for RNA sequencing, respectively. The RNA extraction, library construction and RNA-Seq were performed on the Illumina HiSeq2500 at Beijing BioMarker Technologies (Beijing, China).Differential expression genes (DEGs) were filtrated from the result of transcriptome. The quantitative real-time PCR was performed to validate the expression patterns of candidate DEGs between LW and YL pigs.
Results: The clean reads percolated from the raw reads were mapped to Sus scrofa genome (Sscrofa10.2) using Tophat2 software. The efficiency of alignment was about 76% between the six samples and reference genome, and approximate 50% clean reads were perfectly matched to pig genome. Two samples with high R-squared value (T1-T3: 0.98; T5-T6: 0.97) from PCV2 and mock-infected YL pigs, respectively, was performed differential expression analysis through DESeq after biologic repetition correlation detection. With the criterion of log FC (fold change) > 1.5 and of P value < 0.05, 90 significantly differentially expressed genes were identified between the two groups, of which 57 were up-regulated and 33 were down-regulated. Eleven candidate DEGs were confirmed by quantitative real-time PCR, which expression pattern were generally in accordance with the results of RNA-seq.
Conclusions: Many DEGs participate in immune response and some of them are involved in cells proliferation or apoptosis, such as CD81, HGF, CXCL13, KLF11, PSMD4, CYCS and ACTC1. The expression changes of these DEGs may cause the lymphocyte depletion in spleen after challenge with PCV2.

overall_design: Spleen mRNA transcriptome of 11-week old PCV2-infected and mock-infected pigs was generated by RNA sequencing, in triplicate, using Illumina HiSeq 2500.

first: Yunliang

last: Jiang


title: A global wiring diagram of stress response signaling

first: David

last: Pincus

institute: University of Chicago

summary: We perform RNA-seq on 28 analog sensitive kinase alleles across 12 different conditions. We use this to determine condition specific kinase function on the transcriptional response.

overall_design:
392 yeast RNA-seq samples, 29 Strains, in 12 different conditions
28r was sequenced twice. The first time the sequencing quality was low so that library has been excluded.
Of the 391 samples, there are a subset of samples that did not include a kinase inhibitor, and are useful only for controlling for strain, and condition effects. These are samples [0-9]*yc, [0-9]*c, and [0-9]*k. These have been excluded from the matrices as after quality control, they were removed from downstream analysis (which includes many matrix operations).

first: Kieran

last: Mace

first: Hana

last: El-Samad


title: Single-cell RNA Sequencing Reveals Midbrain Dopamine Neuron Diversity Emerging During Mouse Brain Development

city: Uppsala

first: Asa

middle: Kristina

last: Bjorklund

address: Box 596

department: Cell and Molecular Biology

country: Sweden

institute: Uppsala University

summary: Midbrain dopamine (mDA) neurons constitute a heterogenous group of cells that have been intensely studied, not least because mDA neuron degeneration causes major symptoms in Parkinson’s disease. Diversity of mDA neurons has previously been well characterized anatomically but understanding diversity at a more complete molecular level has not previously been achieved. Here, we used single cell RNA sequencing of isolated mouse neurons expressing the transcription factor Pitx3, a marker for all types of mDA neurons. Analyses included cells isolated during development up until adulthood and was validated by histological characterization of newly identified markers. This characterization identified seven neuron subgroups divided in two major branches of developing Pitx3-expressing neurons. Five of these groups were dopaminergic, one glutamatergic and one GABAergic. Analyses also indicated evolutionary conservation of diversity in humans. This comprehensive molecular characterization will provide a molecular framework for further studies of the developing and mature mDA neuron subgroups in the mammalian brain.

overall_design: Sequencing libraries were prepared from FACS sorted individual neurons with the Smart-Seq2 protocol  (Picelli et al. Nature Methods 2013)

first: Katarina

last: Tiklova

middle: K

first: Laura

last: Lahti

first: Sara

last: Nolbrant

first: Linda

last: Gillberg

first: Nikolaos

last: Volakakis

first: Fredrik

last: Holmstrom

first: Eliza

last: Joodmardi

first: Malin

last: Parmar

first: Thomas

last: Perlmann

first: Alessandro

last: Fiorenzano

first: Chika

last: Yokota

first: Markus

last: Hilscher

last: Hauling

first: Mats

last: Nilsson


title: Mismatch-repair signature mutations activate gene enhancers across human colorectal cancer epigenomes

status: Public on Feb 07 2019

city: Cleveland Heights

first: Peter

last: Scacheri

state: OH

address: 10900 Euclid Ave; BRB 647

institute: Case Western Reserve University

summary: We show that mismatch-repair (MMR) signature mutations can activate colorectal cancer (CRC)-specific enhancers, through analysis of enhancer DNA associated with the active enhancer histone mark H3K27ac. We demonstrate that MMR mutations activate enhancers using a xenograft metastasis model, where mutations are induced naturally via CRISPR/Cas9 inactivation of MLH1 prior to tumor cell injection.

overall_design: H3K27ac profiles of LoVo cells, 2 parental WT COLO-205 subclones, 2 MLH1-/- COLO-205 subclones, and 7 xenograft tumors derived from the COLO-205 subclones.

first: Alina

middle: R

last: Saiakhova

first: Stevephen

last: Hung

middle: C


title: Chromatin profiling in HT22 hippocampal cells

city: Baltimore

first: Giovanni

middle: A

last: Carosso

state: MD

address: 733 N Broadway, MRB 426

institute: Johns Hopkins School of Medicine

summary: We conducted genome-wide analysis of KMT2D binding sites in a hippocampal cell line to define KMT2D-dependent functions in neuronal context

overall_design: ChIP-seq in wild-type HT22 cells and HT22 cells with CRISPR-Cas9 mediated deletion of the KMT2D enzymatic SET methyltransferase domain, comparing KMT2D-pulldown and input controls

first: Li

last: Zhang

first: Leandros

last: Boukas

first: Kasper

middle: D

last: Hansen


title: Genome-wide analysis of gene expression in wild-type and KMT2D-deficient HT22 cells

summary: We conducted genome wide transcription profiling by RNA-seq in a mouse hippocampal cell line (HT22), comparing cells with CRISPR-Cas9 mediated deletion of the KMT2D enzymatic SET methyltransferase domain to the parental cell line

overall_design: RNA-seq in wild-type and KMT2D-deficient (SET domain deletion) HT22 cells


title: ChIP-seq analysis of 143B cells upon mtDNA depletion and metabolic intervention [ChIP-Seq 2]

city: RTP

first: Janine

last: Santos

state: NC

address: 111 TW Alexander drive

department: GISBL

institute: NIEHS

summary: The goal of the study was to understand whether mitochondrial-driven epigenetic changes regulate gene expression. Mitochondrial metabolism has been implicated in epigenetics but the extent to which this impacts gene expression is unclear. Here we show that loss of mitochondrial DNA (mtDNA) results in locus-specific alterations in histone acetylation, DNA methylation and expression of a subset of genes. Most of these changes are rescued by restoring mitochondrial electron transport in a way that maintains the oxidative tricarboxylic acid cycle, but not reactive oxygen species or ATP production, or by modulating the mitochondrial pool of acetyl-CoA. Changes in acetyl-CoA and histone acetylation precede overt mitochondrial dysfunction and significant changes in gene expression and DNA methylation. This suggests that acetyl-CoA levels signal mitochondrial status to the nucleus. Differentially expressed genes with altered histone marks or DNA methylation regulate amino acid degradation, which likely compensates for the changes in acetyl-CoA and one carbon metabolism. These have the potential to further affect methylation reactions, redox control and nucleotide levels. These results illustrate the extent to which mitochondria impact cell physiology through epigenetic remodeling.

overall_design: ChIP-seq for H3K9ac and 27ac marks was performed in rho0 cells, which are chronically depleted of mtDNA, prior to and after  supplemention of the cell culture media for 4h with the cell permeable metabolite DM-α-KG. This exposure increases both the total levels of acetyl-CoA, of histone acetyltransferase activity and of histone acetylation in these cells.

first: Oswaldo

last: Lozoya

first: Inmaculada

last: Martinez-Reyes

first: Tianyuan

last: Wang

first: Dagoberto

last: Grenet

first: Taylor

last: Wolfgang

first: Pierre

last: Bushel

first: Jianying

last: Li

first: Gonzalo

last: Riadi

first: Douglas

middle: G

last: da Silva

first: Richard

middle: P

last: Woychik

middle: H


title: Co-targeting RNA Polymerases IV and V promotes efficient de novo DNA methylation in Arabidopsis [ChIP-seq]

city: Haining

first: Wanlu

last: Liu

state: Zhejiang

address: 718 East Haizhou Rd.,

department: Zhejiang University - University of Edinburgh Institute

summary: The RNA-directed DNA methylation (RdDM) pathway in plants controls gene expression via cytosine DNA methylation. The ability to manipulate RdDM would shed light on the mechanisms and applications of DNA methylation to control gene expression. Here, we identified diverse RdDM proteins that are capable of targeting methylation and silencing in Arabidopsis when tethered to an artificial zinc finger (ZF-RdDM). We studied their order of action within the RdDM pathway by testing their ability to target methylation in different mutants. We also evaluated ectopic siRNA biogenesis, RNA Polymerase V (Pol V) recruitment, targeted DNA methylation, and gene expression changes at thousands of ZF-RdDM targets. We found that co-targeting both arms of the RdDM pathway, siRNA biogenesis and Pol V recruitment, dramatically enhanced targeted methylation. This work defines how RdDM components establish DNA methylation, and enables new strategies for epigenetic gene regulation via targeted DNA methylation.

overall_design: 56 ChIP-seq

first: Javier

last: Gallego-Bartolomé


title: Parasite specific 7SL-derived small RNA is an effective target for diagnosis of active trypanosomiasis infection

city: Edinburgh

first: Liam

last: Morrison

state: Midlothian

address: Easter Bush

country: United Kingdom

institute: The Roslin Institute, The University of Edinburgh

summary: Human and animal African trypanosomiasis (HAT & AAT, respectively) remain a significant health and economic issue across much of sub-Saharan Africa. Effective control of AAT and potential eradication of HAT requires affordable, sensitive and specific diagnostic tests that can be used in the field. Small RNAs in the blood or serum are attractive disease biomarkers due to their stability, accessibility and available technologies for detection. Using RNAseq, we have identified a trypanosome specific small RNA to be present at high levels in the serum of infected cattle. The small RNA is derived from the non-coding 7SL RNA of the peptide signal recognition particle and is detected in the serum of infected cattle at significantly higher levels than in the parasite, suggesting active processing and secretion. We show effective detection of the small RNA in the serum of infected cattle using a custom qRT-PCR assay. Strikingly, the RNA can be detected before microscopy detection of parasitaemia in the blood, and it can also be detected during remission periods of infection when no parasitaemia is detectable by microscopy. However, RNA levels rapidly drop following treatment with trypanocides, demonstrating accurate prediction of active infection. While the small RNA sequence is conserved between different species of trypanosome, nucleotide differences within the sequence allow generation of highly specific assays that can distinguish between infections with Trypanosoma brucei, Trypanosoma congolense and Trypanosoma vivax. Finally, we demonstrate effective detection of the small RNA directly from serum, without the need for pre-processing, with a single step qRT-PCR assay. Our findings identify a species-specific trypanosome small RNA that can be detected at high levels in the serum of cattle with active parasite infections. This provides the basis for the development of a cheap, non-invasive and highly effective diagnostic test for trypanosomiasis.

sample_organism:
Trypanosoma congolense
Bos taurus

platform_organism:
Trypanosoma congolense
Bos taurus

overall_design: RNA was extracted from samples deriving from infected animals (n=2), an uninfected animal, an in vitro trypanosome cell pellet and subjected to small RNAseq.

first: Stephen

last: Chiweshe

first: Pieter

last: Steketee

first: Siddharth

last: Jayaraman

first: Edith

last: Paxton

first: Kyriaki

last: Neophytou

first: Heidi

last: Erasmus

first: Michel

last: Labuschagne

first: Anneli

last: Cooper

first: Annette

last: MacLeod

first: Finn

last: Grey

middle: J


title: Exosomal miRNA sequencing from KPCY mice

city: Philadelphia

first: Junhyong

last: Kim

state: PA

address: 433 S University Avenue

department: Biology

institute: University of Pennsylvania

summary: We identified exosomal miRNA biomarkers for pancreatic cancer diagnostics by isolating exosomes using a recently developed magnetic nanopore isolation technology and small RNA sequencing.

overall_design: Small RNA sequencing from three different groups of mice (control, PanIN, PDAC) in 2-6 replicates.

first: Jina

last: Ko

first: Neha

last: Bhagwat

first: Taylor

last: Black

first: Stephanie

last: Yee

first: Youngji

last: Fisher

first: Erica

middle: L

last: Carpenter

first: Ben

last: Stanger

first: Dave

last: Issadore


title: Multiplex Chromatin Interactions with Single Molecule Precision

city: Farmington

first: Zhongyuan

last: Tian

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory for Genomic Medicine

summary: Emerging 3D genome mapping efforts suggest complex chromosomal folding structures. However, the true multiplex nature of chromatin interactions has yet to be fully explored. Here, we describe a chromatin interaction analysis by droplet-based sequencing (ChIA-Drop). In ChIA-Drop, individual chromatin complexes are partitioned into droplets that contain a gel bead of DNA-barcoded primers, such that tethered chromatin DNA fragments are uniquely indexed and amplified for sequencing and mapping to demarcate multiplex chromatin contacts. Thus, ChIA-Drop can identify complex chromatin interactions with unprecedented single-molecule precision, which is not possible using methods that analyze pairwise contacts via proximity ligation. We demonstrate that multiplex chromatin interactions predominantly contribute to topologically associated domains with high heterogeneity, and that multivalent promoter-centered interactions provide a topological model for gene transcription.

overall_design: The microfluidics device (10X Genomics’ Chromium instrument) produces Gel beads in Emulsion (GEM) with chromatin complexes for complex-specific DNA barcoding and amplification. Barcoded DNA amplicons from all GEMs (droplets) are pooled for DNA sequencing and mapping for identifying chromatin interactions.

first: Meizhen

last: Zheng

first: Simon

middle: Z

first: Yijun

last: Ruan


title: Co-targeting RNA Polymerases IV and V promotes efficient de novo DNA methylation in Arabidopsis [WGBS]

first: Wanlu

last: Liu

institute: Zhejiang University

type: Methylation profiling by high throughput sequencing

overall_design: 45 WGBS

first: Javier

last: Gallego-Bartolomé


title: The nuclear lamina maintains global spatial organization of chromatin in Drosophila

city: Skolkovo

first: Ekaterina

last: Khrameeva

state: Moscow region

address: Novaya St., 100

country: Russia

institute: Skolkovo Institute of Science and Technology

summary: The nuclear lamina (NL) is a meshwork of lamins and lamin-associated proteins lining the nuclear envelope (NE). Chromatin adjoining the NL in lamina-associated domains (LADs) is densely packed and contains predominantly silent genes. However, how the NL impacts on global chromatin architecture is poorly understood. Here, we show that NL disruption in Drosophila S2 cells leads to bulk chromatin compactization and repositioning from the NE. This increases the chromatin density in the topologically-associating domains (TADs) harboring active genes, and enhances inter-TAD interactions resulting in the intermingling of active and inactive compartments. Importantly, upon NL disruption, a fraction of TADs strongly overlapping with LADs becomes less compact, whilst resident genes are derepressed. Two-color FISH confirms that a a TAD is more decompacted following its release from the NL. Finally, polymer simulations show that chromatin binding to the NL can per se compact attached TADs. Collectively, our findings demonstrate a dual function of the NL in shaping the 3D genome. Attachment of TADs to the NL makes them more condensed but decreases the overall chromatin density in the nucleus by stretching interphase chromosomes.

overall_design: Hi-C analysis of chromatin spatial structure in cultured Drosophila cell line S2 upon lamin Dm0 knock-down.

first: Sergey

middle: V

last: Ulianov


title: Epigenetic signatures associated with paternally-expressed imprinted genes in the endosperm

first: Juan

last: Santos-González

state: Uppsala

address: Almas Allé 5

department: Department of Plant Biology and Forest Genetics

institute: SLU

summary: Genomic imprinting is an epigenetic phenomenon causing parental alleles to be active depending on their parent-of-origin. In plants, imprinted genes are mainly confined to the endosperm, an ephemeral tissue supporting embryo development. Differential methylation of histone H3 on lysine 27 (H3K27me3) established by the Polycomb Repressive Complex 2 (PRC2) is a major regulatory mechanism determining activity of paternally expressed imprinted genes (PEGs) in animals and plants.  Here, we show that the coding region of many PEGs is marked by an epigenetic signature of H3K27me3, H3K9me2 and CHG methylation and that the combination of these three modifications correlates with paternally-biased gene expression in the endosperm. The maternal alleles of PEGs are marked by CHG methylation in the central cell, indicating that the repressive epigenetic signature of PEGs is established before fertilization. We use the presence of the three modifications to predict novel PEGs and propose that genomic imprinting is substantially more common than previously estimated based on expression data.

overall_design: Col × Ler reciprocal crosses were performed using Arabidopsis lines expressing PHE1::NTF and PHE1::BirA. 4DAP siliques were collected and tissue homogenization and nuclei purification were performed from three biological replicates for LerxCol and two for ColxLer  using INTACT. Total RNA was extracted from purified nuclei using the mirVana Isolation Kit Protocol (Ambion). mRNA extraction was performed using NEBNext Poly(A) mRNA Magnetic Isolation and the Libraries were prepared with the NEBNext Ultra II RNA Library Prep Kit from Illumina. Samples were sequenced at the National Genomic Infrastructure (NGI) from SciLife Laboratory (Uppsala, Sweden) on an Illumina HiSeq2500 in paired-end 125bp read length.

first: Jordi

last: Moreno-Romero

first: Gerardo

last: Del Toro-De León

first: Vikash

last: Yadav

first: Claudia

last: Köhler


title: Genome-wide methylation profiles in saliva and intestinal mucosa using Infinium HumanMethylation 450 BeadChip

city: Penrith

first: Christine

last: Chiu

state: NSW

address: Locked Bag 1797

institute: Western Sydney University

type: Genome binding/occupancy profiling by genome tiling array

summary: Genome wide DNA methylation profiling in paired saliva and intestinal mucosa samples from individuals undergoing gastroscopies. The Illumina Infinium 450k Human DNA methylation BeadChip was used to obtain DNA methylation profiles across approximately 485,500 CpGs. The aim of the study was to determine the utility of saliva as a surrogate for intestinal mucosa in DNA methylation studies.

overall_design: Bisulphite converted DNA from saliva and intestinal mucosa samples from 10 individuals were hybridised to the Illumina Infinium 450k Human Methylation Beadchip. All individuals were non-smokers and caucasian.

first: Joanne

last: Lind

first: Nerissa

last: Hearn


title: Co-targeting RNA Polymerases IV and V promotes efficient de novo DNA methylation in Arabidopsis

overall_design: 66 BS-PCR-seq samples, 39 small RNA-seq, 45 WGBS, 40 RNA-seq, 56 ChIP-seq


title: RNA-seq analysis of pro-B cells from RAG, double RAG/Emu, double RAG/3'RR and double RAG/KOKI deficient mice.

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: By their impact on nuclear organisation, enhancers are master regulators of cell fate. We thus developed double Emu-RAG-deficient, 3’RR-RAG-deficient mice and KOKI-RAG-deficient mice to investigate a potential transcriptional cross-talk between Emu and 3'RR enhancers at the pro-B cell stage.

overall_design: Femoral pro-B cells were recovered with the EasySepTM mouse B-cell isolation Kit (STEMCELL Technologies, France). It is designed to isolate B cells from single-cell suspensions by negative selection. Pro-B cells were obtained from 10 RAG-deficient, 10 double 3’RR-RAG-deficient mice, 10 double KOKI-RAG deficient and 10 double Emu-RAG-deficient mice. Two pooled RNA (with five samples) were obtained for each genotype.

first: F

last: Boyer

first: V

last: Magnone

first: Y

last: Denizot


title: Nascent-protein ubiquitination is required for heat shock-induced gene downregulation in human cells.

city: Freiburg

first: Barbara

last: Hummel

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: Proteotoxic stress such as heat shock causes heat-shock factor (HSF)-dependent transcriptional upregulation of chaperones. Heat shock also leads to a rapid and reversible downregulation of many genes, a process we term stress-induced transcriptional attenuation (SITA). The mechanism underlying this conserved phenomenon is unknown. Here we report that enhanced recruitment of negative transcription elongation factors to gene promoters in human cell lines induces SITA. A chemical inhibitor screen showed that active translation and protein ubiquitination are required for the response. We further find that proteins translated during heat shock are subjected to ubiquitination and that p38 kinase signaling connects cytosolic translation with gene downregulation. Notably, brain samples of subjects with Huntington's disease also show transcriptional attenuation, which is recapitulated in cellular models of protein aggregation similar to heat shock. Thus our work identifies an HSF-independent mechanism that links nascent-protein ubiquitination to transcriptional downregulation during heat shock, with potential ramifications in neurodegenerative diseases.

overall_design: Examination of stress-induced gene attenuation

first: Fernando

last: Aprile Garcia

first: Parul

last: Tomar

first: Ritwick

last: Sawarkar


title: KMT2D loss disrupts cell cycle and hypoxic responses in neurodevelopmental models of Kabuki syndrome

first: Giovanni

last: Carosso

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

overall_design: Refer to individual Series


title: Wnt/β-catenin signaling pathway safeguards epigenetic stability and homeostasis of mouse embryonic stem cells.

city: Barcelona

first: Maria

middle: Pia

last: Cosma

address: C/ Dr Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: CRG

summary: Wnt/β-catenin signaling regulates both mouse embryonic stem cell (mESC) self-renewal and differentiation. Here we show that the activity of the Wnt/β-catenin signaling pathway safeguards normal DNA methylation of mESCs. Indeed, loss of Wnt activity correlated with loss of DNA methylation, especially at the imprinting control regions (ICRs) in prolonged in vitro mESC cultures. To address the role of Wnt signaling on ICR methylation we performed Reduced Representation Bisulfite Sequencing (RRBS) on both “Young” and “Old” mESCs, being at early and late passages, respectively. We found that several ICRs (both maternal and paternal) showed loss of methylation in “Old” cells that correlates with lower Wnt downstream target expression and lower β-catenin protein level, when compared to “Young” mESCs. In parallel, we analyzed the ICR methylation level also in two Wnt mutant clones after prolonged in vitro culture (O-S33Y #1 and #2). The mutant clones maintained high Wnt activity with passages, similar to “Young” mESCs and ICR methylation level at around 50%, further supporting the beneficial role of Wnt/β-catenin pathway on mESC epigenetic stability and homeostasis.

overall_design: Methylation levels of E14 mESCs displaying different levels of Wnt/β-catenin activity and β-catenin protein, analyzed by RRBS, in duplicate.

first: Ilda

last: Theka

first: Marco

last: Cammisa

first: Andrea

last: Riccio


title: Cyclical quasispecies re-equilibration of dual-tropic measles virus

status: Public on Feb 06 2019

city: Rochester

first: Ryan

last: Donohue

state: Minnesota

address: 200 First Street SW

department: Molecular Medicine

institute: Mayo Clinic

summary: RNAseq analysis of purified measles virus ribonucleocapsids after adaptation to lymphocytes (Granta-519) or epithelial cells (H358)

overall_design: 10 samples: MeV-IC323-mCherry ribonucleocapsid RNA from unpassaged (p1), seven or fourteen times passaged on Granta-519 cells (L7 and L14), seven or fourteen times passaged on H358 cells (E7 or E14), or sequentially seven times passaged on Granta-519 and seven times passaged on H358 cells (S14); MeV-IC323-mCherry-uN ribonucleocapsid RNA from one or fourteen times passaged on Granta-519 (L1-2nd or L14-2nd), or one or fourteen times passaged on H358 cells (E1-2nd or E14-2nd)

first: Christian

last: Pfaller

first: Roberto

last: Cattaneo


title: Genome-wide analysis of gene expression in proliferative dentate gyrus (DG) nuclei of adult wild-type and KMT2D-deficient mice

summary: We conducted genome wide transcription profiling by RNA-seq in proliferating neuronal progenitors after purifying EdU+ nuclei from micro-dissected DG of adult wild-type and KMT2D-deficient mice (Kmt2d +/Bgeo)

overall_design: RNA-seq in EdU+ dentate gyrus nuclei of adult wild-type and KMT2D-deficient mice (Kmt2d+/Bgeo)

first: Gabrielle

last: Cannon


title: LncRNA HAND2-AS1 controls liver cancer stem cell functions and serves as a potential therapy target

city: Beijing

first: Runsheng

last: Chen

address: 15 Datun Road, Chaoyang District

department: CAS Key Laboratory of RNA Biology

institute: Institute of Biophysics, Chinsese Academy of Sciences

type:
Expression profiling by array
Other


title: Transcriptome Analysis Reveals a Role for Myc in Constitutive and Antiestrogen-resistant Proliferation of Breast Cancer Cells Expressing ERαY537S and ERαD538G Mutations

city: Urbana

first: David

last: Shapiro

address: 600 South Mathews Avenue

department: Biochemistry

institute: University of Illinois Urbana-Champaign

summary: Approximately 30% of metastatic breast cancers harbor estrogen receptor α (ERα/ESR1) mutations that are associated with resistance to endocrine therapy and shorter patient survival. How these ERα mutations elicit an aggressive tumor phenotype was largely unknown. Recently, we reported cell lines in which the wild-type ESR1 gene is replaced by the two most common ERα mutations, ERαY537S and ERαD538G. Here we use transcriptome analysis to demonstrate that ERαY537S cells exhibit a unique expression profile and phenotype, and identify an important role for Myc in the increased growth rate, ligand independent cell proliferation, and partial resistance to tamoxifen and fulvestrant of cells expressing the ERαY537S and ERαD538G mutations. Notably, the T47DERαY537S (TYS) cells exhibit a markedly different phenotype and transcriptome than the parental T47D cells and T47DERαD538G (TDG) cells. Consistent with their estrogen-independent proliferation, RNAseq shows the TYS and TDG cells exhibit estrogen independent gene expression patterns. Gene set enrichment analysis showed Myc target pathways are highly induced in both mutant cell lines. Unlike the parental T47D cells, in TYS and TDG cells Myc mRNA and protein exhibit constitutive, fulevestrant-resistant expression. Moreover, chromatin immunoprecipitation (ChIP) showed that ERαY537S and ERαD538G exhibit constitutive, fulvestrant-resistant, recruitment to the Myc enhancer region. Myc knockdown showed that Myc protein is required for ligand independent proliferation of TYS and TDG cells. Constitutive MYC expression in T47D cells, to levels similar to those in TYS and TDG cells, partially recapitulated the aggressive phenotypes of the TYS and TDG cells. Our study demonstrates a previously undescribed role for constitutive and antiestrogen resistant Myc expression in the aggressive phenotype exhibited by breast cancer cells expressing ERα mutations and provides powerful tools for identifying pathways that contribute to the ERα mutant phenotype.

overall_design: Hormone depleted T47D, TYS and TDG cells were treated with 10nM E2 or ethanol, as vehicle control, for 4 hours or 24 hours with 3 biological replicates. RNAseq was carried out using Illumina Hiseq 4000.

first: Liqun

last: Yu


title: Co-targeting RNA Polymerases IV and V promotes efficient de novo DNA methylation in Arabidopsis [small RNA-seq]

first: Wanlu

last: Liu

overall_design: 39 small RNA-seq

first: Javier

last: Gallego-Bartolomé


title: Transcriptome analysis of pulmonary CCR2+ inflammatory monocytes challenged with Cryptococcus neoformans

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

summary: The encapsulated yeast Cryptococcus neoformans can cause a fatal meningoencephalitis in immunocompromised patients. C. neoformans infection is acquired through the respiratory tract, but the cellular and molecular mechanisms of the pulmonary innate immune response are still not well defined. To investigate the response of CCR2+ inflammatory monocytes to C. neoformans, we compared the transcriptomes of CCR2+ inflammatory monocytes from the lungs of naïve versus infected mice.

overall_design: Sorted pulmonary CCR2+ inflammatory monocytes were pooled from 6-7 CCR2-GFP reporter mice per group, including naïve mice and mice challenged with intratracheal Cryptococcus neoformans on days 5 and 10 post-infection.

first: Lena

last: Heung

first: Tobias

last: Hohl


title: Co-targeting RNA Polymerases IV and V promotes efficient de novo DNA methylation in Arabidopsis [RNA-seq]

overall_design: 40 RNA-seq


title: Co-targeting RNA Polymerases IV and V promotes efficient de novo DNA methylation in Arabidopsis [BS-PCR-seq]

overall_design: 66 BS-PCR-seq samples


title: Mir-146a wild-type 3ʹ sequence identity is dispensable for proper innate immune function in vivo (miRNA-Seq)

city: Ithaca

first: Andrew

last: Grimson

address: 445 Biotech Bldg

department: Molecular Biology and Genetics

institute: Cornell University

summary: A long-prevailing model has held that the “seed” region (nucleotides 2-8) of a microRNA is typically sufficient to mediate target recognition and repression. However, numerous recent studies, both within the context of defining miRNA/target pairs by direct physical association and by directly assessing this model in vivo in C. elegans have brought this model into question. To test the importance of miRNA 3' pairing in vivo, in a mammalian system, we engineered a mutant murine mir-146a allele in which the 5' half of the mature microRNA retains the sequence of the wild-type mir-146a but the 3ʹ half has been altered to be anti-complementary to the wild-type miR-146a sequence. Mice homozygous or hemizygous for this mutant allele are phenotypically indistinguishable from wild-type controls and do not recapitulate any of the immunopathology previously described for mir-146a-null mice. Our results strongly support the conclusion that 3ʹ pairing is dispensable in the context of the function of a key mammalian microRNA.

overall_design: Small-RNA expression profiling of resting bone marrow derived macrophages (BMDMs) from miR-146 wild-type (WT), knock-out (KO) and non-seed swap (3'F) mice

first: Joel

last: Neilson


title: Mir-146a wild-type 3' sequence identity is dispensable for proper innate immune function in vivo


title: Activation of IGFBP7 Drives Resistance to Epidermal Growth Factor Receptor Tyrosine Kinase Inhibition in Lung Cancer

city: Taipei

first: Tzu-Hua

last: Chang

address: No. 7, Chung-Shan South Road

department: Department of Internal Medicine

country: Taiwan

institute: National Taiwan University Hospital

summary:
Previous study has demonstrated that HCC827/gef cells are resistant to gefitinib-induced aspoptosis. To investigate the regulators contributed to gefitinib resistance in lung cancer, we analyzed the gene expression profiles between HCC827 andHCC827/gef cells.
Reduced IGFBP7 in TKI-resistant cells reversed resistance to EGFR-TKIs, and increased EGFR-TKI-induced apoptosis through up-regulation of BIM and activation of caspases. Suppression of IGFBP7 attenuated phosphorylation of IGF-IR and downstream AKT in TKI-resistant cells.

overall_design: RNAs extracted from gefitinib-sensitive HCC827 cells and gefitinib-resistant HCC827/gef cells were hybridized on Affymetrix microarrays. We tried to compare the differential gene expression profiles between HCC827 and HCC827/gef cells to identify the possible regulators in gefitinib resistance.

first: Shang-Gin

last: Wu

first: Meng-Feng

last: Tsai

first: Yi-Nan

first: Chia-Lang

last: Hsu

first: Yih-Leong

first: Chong-Jen

first: Jin-Yuan

last: Shih


title: Mir-146a wild-type 3' sequence identity is dispensable for proper innate immune function in vivo (RNA-Seq)

overall_design: Gene expression profiling of either stimulated (1 ng/ml LPS for 16 hours) or resting bone marrow derived macrophages (BMDMs) from miR-146 wild-type (WT), knock-out (KO) and non-seed swap (3'F) mice, in triplicate.


title: Gat1- and Dal80-sensitive genes in budding yeast

city: Paris

first: Maxime

last: Wery

address: 26 rue d'Ulm

institute: Institut Curie

summary: GATA transcription factors are highly conserved among eukaryotes and play roles in transcription of genes implicated in cancer progression and hematopoiesis. However, although their consensus binding sites have been well defined in vitro, the in vivo selectivity for recognition by GATA factors remains poorly characterized. Using ChIP-Seq, we identified the Dal80 GATA factor targets in yeast. Our data reveal Dal80 binding to a large set of promoters, sometimes independently of GATA sites, correlating with nitrogen- and/or Dal80-sensitive gene expression. Strikingly, Dal80 was also detected across the body of promoter-bound genes, correlating with high expression. Mechanistic single-gene experiments showed that Dal80 spreading across gene bodies requires active transcription. Consistently, Dal80 co-immunoprecipitated with the initiating and post-initiation forms of RNA Polymerase II. Our work suggests that GATA factors could play dual, synergistic roles during transcription initiation and post-initiation steps, promoting efficient remodeling of the gene expression program in response to environmental changes.

overall_design: Strand-specific RNA-Seq analysis in gat1 and dal80 mutants grown in glutamine- or proline-containg medium.

first: Aria

last: Ronsmans

first: Ugo

last: Szachnowski

first: Camille

last: Gautier

first: Marc

last: Descrimes

first: Evelyne

last: Dubois

first: Antonin

last: Morillon

first: Isabelle

last: Georis


title: LncRNA HAND2-AS1 controls liver cancer stem cell functions and serves as a potential therapy target (ChiRP-Seq)

first: Runsheng

last: Chen

summary: Hepatocellular carcinoma (HCC) is the most prevalent liver cancer, characterized by a high rate of recurrence and heterogeneity. Liver cancer stem cells (CSCs) may well contribute to both of these pathological properties, but the mechanism underlying their self-renewal and maintenance are poorly understood. Here we identified a long noncoding RNA (lncRNA) termed HAND2-AS1 that is highly expressed in liver CSCs. Human HAND2-AS1 is highly conserved to its mouse ortholog lncHand2. HAND2-AS1 is required for the self-renewal maintenance of liver CSCs to initiate HCC development. Mechanically, HAND2-AS1 recruits the INO80 complex onto BMPR1A promoter to trigger its expression, leading to the activation of BMP signaling. Importantly, targeting HAND2-AS1 by antisense oligonucleotides (ASOs) and BMPR1A by siRNAs have synergistic anti-tumor effects on humanized HCC models. Moreover, knockout of lncHand2 or Bmpr1a in mouse hepatocytes impairs BMP signaling and suppresses the initiation of liver cancer. Our findings reveal that HAND2-AS1 promotes the self-renewal of liver CSCs and drives liver oncogenesis, which may be a potential target for HCC therapy.

overall_design: Investigation the genome wide enrichment of lncRNA HAND2-AS1 via ChIRP-seq in Hepatocellular carcinoma cells

first: Yanying

last: Wang

first: Pingping

last: Zhu

first: Jianjun

last: Luo

first: Jing

first: Zhiwei

last: Liu

first: Ying

last: Du

first: Wei

first: Lei

last: He

first: Yong

last: Tian

first: Zusen

last: Fan


title: Effects of HSP90 inhibitors on airway goblet cell metaplasia

city: Iowa City

first: Alejandro

last: Pezzulo

state: IA

address: 169 Newton Rd 6334 PBDB

department: Internal Medicine

institute: University of Iowa

summary: Goblet cell metaplasia and mucus hypersecretion are disabling hallmarks of chronic lung diseases for which no curative treatments are available. Therapies targeting specific upstream drivers of asthma have had variable results. We hypothesized that an a priori-knowledge independent approach would point to new therapies for airway goblet cell metaplasia. We analyzed the transcriptome of an organotypic model of human goblet cell metaplasia. We combined our data with previously published datasets from IL13-exposed in vitro and asthmatic in vivo human airway epithelial cells. The drug perturbation-response connectivity approach identified the heat shock protein 90 (HSP90) inhibitor geldanamycin as a candidate for reverting airway goblet cell metaplasia. We found that geldanamycin not only prevented but reverted IL13-induced goblet cell metaplasia. Geldanamycin did not induce goblet cell death, did not solely block mucin synthesis, and did not block IL13 receptor-proximal signaling. Moreover, the transcriptional effects of geldanamycin were absent in unstimulated cells and became evident only after stimulation with IL13. The predicted mechanism of action suggested that geldanamycin should also revert IL17-induced goblet cell metaplasia, a prediction confirmed by our data. Our findings suggest HSP90 activity may be required for persistence of goblet cell metaplasia driven by various mechanisms in chronic lung diseases.

overall_design: For both batches, airway epithelia cultures from the lungs of eight different humans were studied, therefore, there are eight biological replicates. Comparisons should be made within batches. In batch 1 (XAM1), epithelia were exposed to vehicle (DMSO 0.5%),   geldanamycin 25 uM, or the HDAC6 inhibitor ISOX 10 uM for 48 hours. In batch 2 (XAM3), the epithelia were exposed to vehicle (DMSO 0.5%), IL13 (20 ng/mL) or IL13 plus geldanamycin (10 uM) for 48 hours.

first: Joseph

last: Zabner


title: The effect of anthelmintic drugs on human leukocyte gene expression in vitro

city: Athens

first: Adrian

middle: J.

last: Wolstenholme

state: GA

address: 501 DW Brooks Dr.

department: Infectious Diseases

institute: University of Georgia

summary: Ivermectin and Diethylcarbamizine (DEC) are used in the elimination programs for lymphatic filariasis and onchocerciasis. It has been proposed that the drugs may have an effect on the host immune system that aids in parasite killing/elimination. We tested this directly by exposing human neutrophils and monocytes to the drugs in vitro.

overall_design: Five biological replicates were performed. Neutrophils and peripheral blood mononuclear cells were purified from five different human donors and exposed to ivermectin or DEC, or a DMSO vehicle control for 1 hour (neutrophils) or 16 hours (PBMC) in vitro. RNA was then extracted and transcriptional profiles of each cell type were analyzed by RNA-Seq.


title: Gene expression profiles in Norad+/+ and Norad-/- brains and spleens [RNA-seq]

status: Public on Feb 05 2019

city: Dallas

first: Joshua

last: Mendell

state: TX

address: 6000 Harry Hines Blvd., NA6.200A

department: Molecular Biology

institute: UT Southwestern Medical Center

summary: Although numerous long noncoding RNAs (lncRNAs) have been identified, our understanding of their roles in mammalian physiology remains limited. Here we investigated the physiologic function of the conserved lncRNA Norad in vivo. Deletion of Norad in mice results in genomic instability and mitochondrial dysfunction, leading to a dramatic multi-system degenerative phenotype resembling premature aging. Loss of tissue homeostasis in Norad-deficient animals is attributable to augmented activity of PUMILIO proteins, which act as post-transcriptional repressors of target mRNAs to which they bind. Norad is the preferred RNA target of PUMILIO2 (PUM2) in mouse tissues and, upon loss of Norad, PUM2 hyperactively represses key genes required for mitosis and mitochondrial function. Accordingly, enforced Pum2 expression fully phenocopies Norad deletion, resulting in rapid-onset aging-associated phenotypes. These findings provide new insights and open new lines of investigation into the roles of noncoding RNAs and RNA binding proteins in normal physiology and aging.

overall_design: Gene expression profiles were determined by RNA-seq.

first: Florian

last: Kopp

first: Beibei

first: He

last: Zhang

first: Sungyul

last: Lee

first: Yang

last: Xie

middle: T


title: Identification of RNAs bound to PUM2 in Norad+/+ and Norad-/- brains [CLIP-seq]

overall_design: RNAs bound to PUM2 were identified using enhanced UV crosslinking immunoprecipitation with high-throughput sequencing (eCLIP).

last: Chen


title: Spatial and Temporal Mapping of Human Innate  Lymphoid Cells Reveals Elements of Tissue  Specificity

city: Cambridge

first: Christian

middle: Thomas

last: Covington

state: Massachusetts

address: 415 Main St.

department: Infectious Disease and Microbiome

institute: Broad Institute

summary: We provide a map of human ILC heterogeneity across multiple  anatomical sites. Tissue-specific distinctions    are particularly apparent for ILC1 populations, whose  distribution was markedly altered in obesity or aging.    Furthermore, the degree of ILC1 population hetero-  geneity differed substantially in lymphoid versus    mucosal sites. Together, these analyses comprise a  comprehensive characterization of the spatial and    temporal dynamics regulating the anatomical distri-  bution, subset heterogeneity, and functional poten-  tial of ILCs in non-diseased human tissues.

overall_design: We present a quantitative analysis of ILC distribution and  heterogeneity in lymphoid, mucosal, and metabolic tissues  obtained from a diverse cohort of 44 previously non-diseased  organ donors over a wide range of ages and body mass indexes  (BMIs).

first: Naomi

last: Yudanin

first: Isabel

last: Latorre


title: Mus musculus Gata2 +9.5 Ets C>T transition untreated and 10 days post 5-FU LSK cells

city: Madison

first: Emery

middle: H.

last: Bresnick

state: WI

address: 4009 WIMR 1111 Highland Ave

department: Cell and Regenerative Biology

institute: University of Wisconsin Madison

summary: The development and function of stem and progenitor cells that produce blood cells are vital in physiology. GATA2 mutations cause immunodeficiency, myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). GATA-2 physiological activities necessitate that it be strictly regulated and cell type-specific enhancers fulfill this role. The +9.5 intronic enhancer harbors multiple conserved cis-elements, and germline mutations of these cis-elements are pathogenic in humans. Since mechanisms underlying how GATA2 enhancer disease mutations impact hematopoiesis and pathology are unclear, we generated mouse models of the enhancer mutations. While a multi-motif mutant was embryonic lethal, a single-nucleotide Ets motif mutant was viable and steady-state hematopoiesis was normal. However, the Ets motif mutation abrogated stem/progenitor cell regeneration following stress. These results reveal a new mechanism in human genetics in which a disease mutation inactivates enhancer regenerative activity, while sparing developmental activity. Mutational sensitization to stress that instigates hematopoietic failure constitutes a paradigm for GATA-2-dependent pathogenesis.

overall_design: WT and Gata2 +9.5(Ets)-/- mice were injected with PBS or 250 mg/kg 5-fluorouracil. 10 days post injected, bone marrow was harvested and LSK cells sorted for sequencing. 16 samples were analyzed, using 3-5 replicates per condition.

first: Alexandra

last: Soukup

first: Ye

last: Zheng

first: Charu

last: Mehta

first: Jun

last: Wu

first: Peng

last: Liu

first: Miao

last: Cao

first: Inga

last: Hofmann

first: Yun

last: Zhou

first: Jing

first: Kirby

last: Johnson

first: Kyunghee

last: Choi

first: Sunduz

last: Keles


title: rDNA chromatin interactions in the MYC-driven Eμ-Myc transgenic mouse model of B-cell lymphoma [ChIP-seq UTF]

city: Badalona

first: Jeannine

last: Diesch

state: Barcelona

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

department: Research

institute: Josep Carreras Leukaemia Research Institute

summary: Analysis of Upstream Binding Transcription Factor (UBTF) binding patterns by ChIP-seq in mouse wildtype, premalignant and malignant Eμ-Myc cells.

overall_design: ChIP-seq using UBTF1/2 polyclonal antibody in mouse wildtype, premalignant and malignant primary preB Eμ-Myc cells

first: Gretchen

last: Poortinga


title: SHROOM2 gene knockdown effect on nasopharyngeal carcinoma cell

city: Guangzhou

first: Xue-Kang

last: Qi

address: Dongfeng East Road 651

department: Department of Experimental Research

institute: Sun Yat-sen University Cancer Center

summary:
Analysis of nasopharyngeal carcinoma cell line HONE1 following knockdown of SHROOM2 gene
We used microarrays to detail the global gene expression in tissues from HONE1 cells with or without SHROOM2 knockdown.

overall_design: NPC cell line HONE1 cells and HONE1 SHROOM2 gene knockdown cells were for RNA extraction and hybridization on Affymetrix microarrays.

first: Lin

last: Feng

last: Yuan


title: Loss of a proteostatic checkpoint in intestinal stem cells contributes to age-related epithelial dysfunction

city: South San Francisco

first: Imilce

last: Rodriguez-Fernandez

state: CA

address: 103 DNA WAY, BUILDING 12, OFFICE 12-232-13

department: Immunology Discovery

institute: Genentech, Inc

summary:
Abstract: Protein homeostasis (proteostasis) is critical for cell function, and its decline is  proposed as a hallmark of aging. Somatic stem cells (SCs) have a unique ability to maintain their proteostatic capacity, yet mechanisms to achieve this remain incompletely understood. Here, we describe and characterize a ‘proteostatic checkpoint’ in Drosophila intestinal SCs (ISCs). Following a breakdown of proteostasis, ISCs coordinate cell cycle arrest with protein aggregate clearance by Atg8-mediated activation of the Nrf2-like transcription factor cap-n-collar C (CncC), which induces the cell cycle inhibitor Dacapo and proteolytic genes. The capacity to engage this checkpoint is lost in ISCs from aging flies, and we show that it can be restored by treating flies with an Nrf2 activator, or by over-expression of CncC or Atg8a. This limits age-related intestinal barrier dysfunction and can result in lifespan extension. Our findings identify a new mechanism by which somatic SCs preserve proteostasis, and highlight potential intervention strategies to maintain regenerative homeostasis.
Purpose of Study: To explore the transcriptional program downstream of CncC in Drosophila ISCs in more detail, we performed RNAseq analysis on FACS-purified wild-type or CncC-deficient escargot-positive cells (ISCs/EBs) in which the proteostatic checkpoint was engaged through the expression of HttQ138 or through the knockdown of rpn3.
Results: While knockdown of rpn3 resulted in a more pronounced and broader transcriptional response than the expression of HttQ138, 93 of the 200 genes that were induced by HttQ138 expression (using a cut-off of 3-fold induction and a minimum expression of 10 FPKM) were also induced by knockdown of rpn3, illustrating a broad overlap of transcriptional changes elicited by the two conditions. Induction of 167 of those 200 genes was dependent on CncC. GO analysis of either the 93 genes induced in both stress conditions, or of the 167 CncC-dependent genes revealed a significant enrichment of genes encoding proteins involved in proteolysis and protein metabolism.

overall_design:
Methods: Intact guts from adult female flies (total of 6 different genotypes, ~ 100 guts per sample) were dissected in cold PBS supplemented with 1% bovine serum albumin and 2% fetal bovine serum. Tissues (~ 100 guts per sample) were trypsinized twice using 0.5% Trypsin EDTA (Gibco Cat.No.15400054) for 30 min on rocker at RT each time, and at each step all cells in suspension were collected. All recovered cells were pooled and washed in cold PBS supplemented with 1% bovine serum albumin and 2% fetal bovine serum. Cells in suspension were passed through the fine mesh of a cell-strainer cap of a 5 ml polystyrene-round bottom tube (Cat. No.Falcon 352235) and then all GFP-positive cells (GFP was driven by escargot promoter expressed in ISCs and EBs) were sorted using FACS. Total RNA was isolated from sorted cells using Trizol reagent, and used as template to generate RNA-seq libraries for Illumina MiSeq sequencing (150bp paired-end reads were obtained). Reads were mapped to the Drosophila genome (release 5.75) using a standard Tuxedo suite pipeline, and FPKM (Fragments Per Kilobase per Million reads) values were recorded for each gene. Analysis of the data was done in Excel, and Gene Ontology analysis was performed using tools at Flymine.org.
Grant info used for the project:

Heinrich Jasper
NIH R01s AG047497 and GM117412

http://grantome.com/grant/NIH/R01-AG047497-04

http://grantome.com/grant/NIH/R01-GM117412-03

first: Yanyan

first: Heinrich

last: Jasper


title: Next Generation Sequencing Facilitated Differential Transcriptome Study of melanoma cells transduced with Notch 1 Intracellular Domain (NICD)

city: MADISON

first: Vijayasaradhi

last: Setaluri

address: 1300 University Avenue

department: Dermatology

institute: University of Wisconsin-Madison

summary: Transcriptome profiling (mRNA-seq) of melanoma cells overexpressing NICD

overall_design: mRNA profiles are generated for melanoma cells transduced with NICD or empty vector control in duplicates using Illumina’s HiSeq 2500 platform

first: Ranjan

last: Perera


title: Transcriptomic analysis of KDM4B-mediated genes in AGS cells

city: Hsinchu city

first: Meng-Chen

last: Wu

address: 101, Section 2 Kuang Fu Road

department: Institute of Molecular and Cellular Biology

institute: National Tsing Hua University

summary: KDM4B, an important epigenetic regulator of cell proliferation, metastasis and genome stability, is often overexpressed in gastric cancer. Notably, elevated expression of KDM4B is associated with a poor clinical outcome. A global transcriptomic analysis between KDM4B control and KDM4B-knockdown AGS cells without or with Helicobacter pylori challenge reveals differentially expressed genes involved in response to virus, multi-organism process, and response to stimulus, suggesting KDM4B as an inducible epigenetic factor under H. pylori challenge.

overall_design: KDM4B control and knockdown cell lines were established in AGS cells based on the lentivirus system: pLKO (control) and shKDM4B (shRNA-specific RNA) lines. Global expression analysis was performed in AGS cells (pLKO vs. KDM4B-knockdown) uninfected or infected by H. pylori at an moi of 50 for 6 h. Microarray analysis was conducted by the National Health Research Institutes, using Affymetrix GeneChip Human Gene 2.0 ST Array (Affymetrix, Santa Clara, California, USA).

first: M

first: Y

last: Li

first: W

last: Wang


title: Gene expression profiles in double transgenic (DT, Pum2;rtTA3) and control (CTR, Pum2 and wild-type) spleens [RNA-seq]

first: Joshua

last: Mendell

first: Florian

last: Kopp

first: Beibei

last: Chen

first: He

last: Zhang

first: Sungyul

last: Lee

first: Yang

last: Xie


title: The Forkhead Box F1 Transcription Factor Inhibits Collagen Deposition and Accumulation of Myofibroblasts During Liver Fibrosis

city: Cincinnati

first: Hannah

middle: M

last: Flood

state: OH

address: 3333 Burnet Ave

department: Department of Pediatrics

institute: CCHMC

summary: Hepatic fibrosis is the common end stage to a variety of chronic liver injuries and is characterized by an excessive deposition of extracellular matrix (ECM), which disrupts the liver architecture and impairs liver function. The fibrous lesions are produced by myofibroblasts, which differentiate from hepatic stellate cells (HSC). The myofibroblasts transcriptional networks remain poorly characterized. Previous studies have shown that the Forkhead box F1 (FOXF1) transcription factor is expressed in HSCs and stimulates their activation during acute liver injury; however, the role of FOXF1 in the progression of hepatic fibrosis is unknown. In the present study, we generated αSMACreER;Foxf1fl/fl mice to conditionally inactivate Foxf1 in myofibroblasts during carbon tetrachloride-mediated liver fibrosis. Foxf1 deletion increased collagen depositions and disrupted liver architecture. Timp2 expression was significantly increased in Foxf1-deficient mice while MMP9 activity was reduced. RNA sequencing of purified liver myofibroblasts demonstrated that FOXF1 inhibits expression of pro-fibrotic genes, Col1α2, Col5α2, and Mmp2 in fibrotic livers and binds to active repressors located in promotors and introns of these genes. Overexpression of FOXF1 inhibits Col1a2, Col5a2, and MMP2 in primary murine HSCs in vitro. Altogether, FOXF1 prevents aberrant ECM depositions during hepatic fibrosis by repressing pro-fibrotic gene transcription in myofibroblasts and HSCs.

overall_design: RNAseq on isolated hepatic stromal cells from Foxf1 fl/fl and αSMACreER;Foxf1 fl/fl mice after 5 weeks of carbon tetrachloride-induced liver injury.

first: Nupur

last: Dasgupta

first: Vladimir

last: Kalinichenko


title: Single-cell analysis of human kidney organoids

city: Ann Arbor

first: Rajasree

last: Menon

state: Michigan

address: 4544E, MSRB2, Catherine Street, University of Michigan

department: Department of Computational  Medicine and Bioinformatics

institute: University of Michigan

summary: We have used single-cell transcriptomics to characterize gene expression in different cell populations, and to study individual cell dynamics and lineage trajectories in organoid cell differentiation

overall_design: We have used DropSeq to perform single cell sequencing of 8 organoid samples that were harvested between 19-21 days.

first: Jennifer

last: Harder

first: Edgar

last: Otto

first: Matthias

last: Kretzler


title: RNA-seq profile of expanded human ST2-transduced Tregs cultured with IL-2 and TCR in the presence or absence of IL-33

status: Public on Feb 04 2019

city: Vancouver

first: Megan

middle: K

last: Levings

address: 950 West 28th Ave

country: Canada

institute: University of British Columbia

summary: Because of the extensive data in mice supporting the concept that ST2+ Tregs might have desirable therapeutic properties, including tissue repair function, high suppressive capacity, and enhanced stability, we engineered human blood Tregs to constitutively express ST2 (IL-33R). Here we used RNA sequencing to explore the effects of short-term culture with IL-33 on human ST2-transduced Tregs.

overall_design: Human naive Tregs flow-sorted from 4 independent donors were lentivirally transduced with ST2, expanded for 13 days, then stimulated with IL-2 and TCR (16 h) or IL-2, TCR, and IL-33 (16 h).

first: A

last: Lam


title: Single-cell transcription profiling in KS1 patient iPSCs and NPCs

city: Baltimore

first: Jonathan

middle: Joseph

last: Augustin

state: MD

address: 733 N. Broadway Rm#332

institute: Johns Hopkins Medical Institute

summary: We conducted single-cell RNA-seq (scRNA-seq) in human-derived induced pluripotent stem cells (iPSCs) and neural progenitor cells (NPCs) generated from Kabuki syndrome 1 (KS1) patients and healthy controls

overall_design: scRNA-seq of iPSCs and differentiating NPCs induced by synergistic inhibition of GSK3, TGF-B, and Notch

first: Giovanni

last: Carosso

first: Loyal

last: Goff

first: Briana

last: Winer


title: Retinoic acid receptor alpha represses a Th9 transcriptional and epigenomic program to reduce allergic pathology

city: Bethesda

first: Hong-wei

last: Sun

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

summary: T helper (Th) differentiation is regulated by diverse inputs including the Vitamin A metabolite retinoic acid (RA). RA acts through its receptor RAR to repress transcription of inflammatory cytokines, but it is also essential for Th-mediated immunity, pointing to complex effects of RA in Th specification and the outcome of the immune response. We examined the impact of RA on the genome-wide transcriptional response during differentiation of CD4+ T cells to multiple Th subsets.  RA effects were subset-selective, and quantitatively greatest in Th9 cells.  RA globally antagonized Th9-promoting transcription factors (TFs) and inhibited Th9 differentiation.  RA directly targeted the extended Il9 locus and broadly modified the Th9 epigenome through RARa. RA-RARaactivity limited Th9-associated pulmonary inflammation in mice, and allergic inflammation in humans was associated with reduced expression of RA target genes. Thus, repression of the Th9 program is a major function of RA-RARa signaling in Th differentiation, arguing for a role for RA in IL-9 related diseases.

overall_design: Integrated analysis of epigenome and transcriptome data from Th subsets treated with vehicle control or retinoic acid, and of in vivo Th subsets from papain-sensitized mice

first: D

middle: S

last: Schwartz

first: F

last: Meylan

first: H

middle: Y

last: Shih

first: Y

last: Mikami

last: Petermann

middle: W

first: C

last: Yao

first: K

last: Jiang

last: Davis

last: Kanno

first: J

last: O'Shea


title: C. elegans total RNA profiles of worms treated with RNAi for different Integrator complex

city: Logrono

first: María

last: de Toro

state: La Rioja

address: C/Piqueras 98

department: Genomics & Bioinformatics Core Facility

institute: Centro de Investigación Biomédica de La Rioja

summary: C. elegans totalRNA profiles of worms treated with RNAi for different Integrator complex genes or L4440 (Control). Worms were grown at 15ºC and samples were taken six days after silencing

overall_design: C. elegans totalRNA profiles of worms treated with RNAi for different Integrator complex genes or L4440 (Control). Three replicates per sample. Deep sequencing in Illumina HiSeq1500.


title: Variation in placenta-specific genomic imprinting is associated with intrauterine growth restriction.

city: L'Hospitalet de Llobregat, Barcelona

first: Jose Ramon

last: Hernandez

address: Av. Gran Via de l'Hospitalet 199-203

department: Cancer Epigenetics and Biology Program (PEBC)

institute: Institut d'Investigació Biomèdica de Bellvitge (IDIBELL)

type: Methylation profiling by genome tiling array

summary: The placenta has a critical role in fetal growth, with many key functions regulated by genomic imprinting. With the recent description of polymorphic placenta-specific imprinting, the molecular mechanisms leading to this curious epigenetic phenomenon are unknown, as is their involvement in pregnancies complications. Profiling ubiquitous and placenta-specific imprinted differentially methylated regions (DMRs) exposed isolated aberrant methylation at ubiquitous DMRs as well as abundant hypomethylation at placenta-specific DMRs. Analysis of underlying chromatin at polymorphic placenta-specific imprinted DMRs revealed biallelic enrichment of histone H3K4 methylation, a modification normally mutually exclusive with DNA methylation. Furthermore, characterisation of expression in intrauterine growth restricted samples (IUGRs) uncovered coordinated deregulation of the GPR1AS1-ZDBF2-ADAM23 locus. Our results emphasize that methylation is less stable at placenta-specific imprints compared to their ubiquitous counterparts and that further work is required to determine if these differences are the IUGR cause or reflect unique adaption of the placenta epigenome to developmental stresses.

overall_design: Bisulphite converted DNA from 13 IUGR human placenta samples together with 9 control (no-IUGR) ones were hybridised to the Illumina HumanMethylation450 BeadChip v1.2

first: Jose

middle: R

first: David

last: Monk


title: Non-lytic clearance of influenza B virus from infected cells [RNA-seq]

city: Durham

first: Nicholas

last: Heaton

state: NC

address: 213 Research Drive, 426 CARL Building

department: Molecular Genetics and Microbiology

institute: Duke University School of Medicine

summary: Influenza B virus (IBV) is an acute respiratory pathogen that induces phenotypic alterations to the lung epithelium, such as the denudation of the respiratory cilium, during and after IBV infection.  It has been assumed that these epithelial changes are non-adaptive, and simply the result of cellular death following lytic virus infection. However, previous reports have shown that not all infected cells are killed after viral infection; some cells can completely clear viral RNA and protein and persist in the host long-term.  In this study, we utilized a novel recombinant virus in combination with a Cre recombinase-responsive transgenic mouse model to demonstrate that IBV infection leads to the formation of a population of survivor ciliated cells in the proximal airways of infected mice. We then performed transcriptional profiling on infected and surviving ciliated cell populations to determine how surviving viral infection affected these cells. To specifically profile ciliated cells, we digested mouse lungs and sorted cells based on their expression of CD24 with tdTomato as a marker of infection.  We sorted cell populations from the lungs of animals mock infected with PBS (Mock), during active infection (2 DPI), and matched ciliated cell populations at 14 days post-infection that had either experienced direct viral infection (14 DPI Survivor Cell) or those that had never been infected (14 DPI). The resulting data indicate that after surviving infection and clearing the virus, survivor ciliated cells undergo significant transcriptional reprogramming.

overall_design: Analysis of RNA from lung ciliated cells  at various timepoints after influenza virus infection, 4 samples collected in duplicate on 2 lanes for a total of 16 samples.

first: Rebekah

middle: E

last: Dumm


title: RNA-Seq of Circulating Tumor Cells in Stage II-III Breast Cancer

city: Los Angeles

first: Julie

last: Lang

address: 1510 San Pablo Street, Suite 412

department: Deparment of Surgery

institute: University of Southern California

summary:
BACKGROUND: We characterized the whole transcriptome of circulating tumor cells (CTCs) in Stage II-III breast cancer to evaluate correlations with primary tumor biology.
METHODS: CTCs were isolated from peripheral blood (PB) via immunomagnetic enrichment followed by fluorescence-activated cell sorting (IE-FACS). CTCs, PB and fresh tumors were profiled with RNA Seq. Formalin-fixed, paraffin-embedded (FFPE) tumors were subjected to RNA Seq and NanoString PAM50 assays with Risk of Recurrence (ROR) scores.
RESULTS: CTCs were detected in 29/33 (88%) of patients. We selected 21 cases to attempt RNA Seq (median number of CTCs=9). 16 CTC samples yielded results that passed quality control metrics. These samples had a median of 4,311,255 uniquely mapped reads, less than PB or tumors.
Intrinsic subtype predicted by comparing estrogen receptor (ER), progesterone receptor (PR) and HER2 versus PAM50 for FFPE tumors was 85% concordant. However, CTC RNA Seq subtype assessed by the PAM50 classification genes was highly discordant both with the subtype predicted by ER/PR/HER2 as well as by tumor PAM50. Two patients died of metastatic disease - both had high ROR scores and high CTC counts.
We identified significant genes, canonical pathways, upstream regulators and molecular interaction networks comparing CTCs by various clinical factors. We identified a 75-gene signature with highest expression in CTCs and tumors taken together that was prognostic in The Cancer Genome Atlas and METABRIC datasets.
CONCLUSION: It is feasible to use RNA Seq of CTCs in non-metastatic patients to discover novel tumor biology characteristics.

overall_design: 6 peripheral blood samples from healthy individuals (negative controls) were compared to circulating tumor cells from n=16 patients, with comparison to the primary tumors available for n=12 of these patients

first: Daniel

last: Campo


title: Molecular Characterization of a Partial Masculinization in Embryonic Ovaries Grafted into Male Nude Mice

city: Tokyo

first: Kento

last: Miura

address: Yayoi 1-1-1, Bunkyo-ku

department: Veterinary Anatomy

country: Japan

institute: The University of Tokyo

summary:
The fetal ovarian grafts under the kidney capsule of adult male mice undergo a partial sex-reversal showing ectopic SOX9-positive Sertoli cell-like cells around 15-20 days post-transplantation. However, the molecular bases of such masculinization of fetal ovaries in the paternal environment were unclear.
We examined the temporal changes of the gene expression profiles of the grafted fetal ovaries during the partial masculinizing process in the male nude mice.

overall_design: The ovarian transplants initiated at the E13.0 (approximately 10 grafts used per each sample) were recovered at days 4, 7, 10, 15, and 20 post-transplantation from the host kidneys and  analyzed by comparing with E13.0 ovaries before transplantation (at day 0 post-transplantation). Two biological replicates were analyzed about transplants at days 0, 10, and 20 post transplantation.

first: Yoshiakira

last: Kanai


title: RNA-seq data for tumor tissues from mice fed with normal diet (ND) or high cholesterol diet (HCD) [Hep1-6]

status: Public on Feb 03 2019

city: shanghai

first: Fu

last: jing

address: No.225 Changhai road

department: Liver Centre of SMMU

institute: Eastern Hepatobiliary Surgery Hospital

summary: To address how serum cholesterol affected tumor progression, C57BL/6J mice were placed on either normal diet or high cholesterol diet for 4 weeks, and then Hep1-6 cells were subcutaneously injected into the right flanks of mice. We performed transcriptome sequencing analysis (RNA-seq) on tumor tissues from ND and HCD groups.

overall_design: Three tumor tissues from ND group (ND-1,ND-2,ND-3) and three tumor tissues from HCD group (HCD-1,HCD-2,HCD-3) were analyzed.

first: Wenhao

last: Qin

first: Zhishi

last: Yang

first: Jing

last: Fu

first: Hongyang

last: Wang


title: Genotype and methylome study of celiac disease and control individuals

city: Leioa

last: Bilbao

state: Outside the US or Canada

address: Bº Sarriena

department: Genetics, Physical Anthropology and Animal Physiology

institute: University of the Basque Country (UPV/EHU)

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

overall_design: Refer to individual Series


title: Modelling G2019S-LRRK2 sporadic Parkinson’s disease in 3D midbrain organoids

status: Public on Feb 02 2019

city: Jung-gu

first: BYOUNGGOOK

last: CHO

state: Seoul

address: 30, Pildong-ro 1-gil

country: South Korea

institute: Dongguk Univ

summary: Recent advances in generating 3 dimensional (3D) organoid systems from stem cells offer new possibilities for disease modeling. In this study, we generate isogenic 3D midbrain organoids with or without a Parkinson’s disease-associated LRRK2 G2019S mutation. LRRK2-G2019S midbrain organoids derived from LRRK2 targeted human iPSCs in vitro have LRRK2-associated sporadic Parkinson's disease phenotypes. Midbrain-like 3D organoids expressing LRRK2-G2019S showed dynamic changes in globle gene expression.

overall_design: Affymetrix GeneChip Human Gene 1.0 ST Array was performed according to the manufacturer's protocol. Changes in the gene expression profile of 2D control, 2D LRRK2-G2019S, 3D midbrain organoids and LRRK2-G2019S 3D oragnoids

first: Hong

last: Kim

first: Hyeok

middle: J

last: Park


title: PTex - Purification of Cross-linked RNA-Protein Complexes by Phenol-Toluol Extraction

city: Berlin

first: Benedikt

last: Beckmann

address: Philippstrasse 13

department: IRI Life Sciences

institute: Humboldt University

summary: PTex is a protocol to purify UV-cross-linked ribonucleoproteins (RNPs) in an unbiased and sequence-independent fashion. Total RNA from HEK293 cells was analysed by RNASeq from whole cell lysates as well as after purification of RNPs.

overall_design: Human HEK293 cells were in vivo UV-cross-linked with light at 254 nm wavelength and subjected to the PTex procedure (a modified phenol extraction) which will enrich for cross-linked RNA-protein hybrids and deplet non-cross-linked RNA and proteins. RNA from HEK293 cells was prepared (input total RNA control) as well as RNA purified in complexes (PTex samples). 3 different UV-cross-linking intensities were used (resulting in 4 conditions: no cross-link (noCL), 0.015 J/cm2 (0015), 0.15 J/cm2 (015) and 1.5 J/cm2 (15)).

first: Erika

middle: C

last: Urdaneta


title: Epigenomic analysis of sperm cells from patients with psoriatic arthritis, psoriasis without arthritis, and healthy controls

city: Toronto

first: Dafna

middle: D

last: Gladman

state: Ontario

address: 60 Leonard Ave

department: Rheumatology Research

institute: Toronto Western Research Institute

summary: Genome-wide DNA methylation profiling of motile spermatozoa from 23 patients with psoriasis without arthritis, 13 psoriatic arthritis, and 18 unaffected controls using the Infinium HumanMethylation 450k v1 platform.

overall_design: Bisulfite converted DNA from the 54 samples were hybridized to the Illumina Infinium HumanMethylation 450k v1 BeadChip.

first: Remy

middle: A

last: Pollock


title: Contrasting in vitro and in vivo methanol oxidation activities of lanthanide-dependent alcohol dehydrogenases XoxF1 and ExaF from Methylobacterium extorquens AM1

status: Public on Feb 01 2019

city: East Lansing

first: Nathan

last: Good

state: MI

address: 567 Wilson Rd

department: Microbiology and Molecular Genetics

institute: Michigan State University

summary: We report gene expression profiles for cultures grown in minimal salts medium with 125 mM methanol with and without addition of 2 uM lanthanum chloride

overall_design: Examination of 2 culture conditions for 1 strain

first: Riley

last: Moore

first: Carly

last: Suriano

first: Norma

last: Martinez-Gomez


title: Gene expression profiles of BxPC-3, MiaPaCa-2 and PANC-1 cell lines treated with DMSO and THZ1 respectively

city: Shanghai

first: Ningning

last: Niu

address: 160 Pu Jian Road, Shanghai

department: Clinical Stem Cell Research Center

institute: Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital

summary: By screening an epigenetic-related compound library, we identified THZ1, a covalent inhibitor of CDK7, as a promising candidate. Multiple long-established and patient-derived PDAC cell lines (PDC) were used to validate the efficacy of THZ1 in vitro. In addition, patient-derived xenograft (PDX) models and animal models of PDAC were utilized for examining THZ1 efficacy in vivo. Furthermore, RNA-Seq and H3K27Ac-based Super-Enhancers (SEs) analyses were performed to reveal the molecular mechanism of THZ1 treatment. Lastly, PDAC cell lines with primary or acquired resistance to THZ1 were investigated to explore the potential mechanism of THZ1 susceptibility.

overall_design: Briefly, BxPC-3, MiaPaCa-2 and PANC-1 cell lines were treated with DMSO or THZ1(100nM) for 6hr were collected in biological triplicates.Each sample has 3 repeats. Each sample has 3 repeats.

last: Xue

first: Yujie

last: Tang


title: A fast PAR-CLIP variant using phenolic extractions

summary: We performed PAR-CLIP in three variants using ELAVL1 (HuR) as example.

overall_design: HuR-interacting transcripts were identified by three methods: 1. Classical PAR-CLIP as described by Hafner et al. (2010); 2. a variant using on-bead ligation of adapters as described in Benhalevy et al. (2017), and 3. a variant in which all gel or membrane excision steps were replaced by phenolic extraction to remove non-cross-linked RNA (pCLIP).

first: Hans-Hermann

last: Wessels


title: Reactivation of Human Herpesvirus 6 (HHV-6) in Diverticulitis

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

summary:
Background: Diverticular disease is a significant healthcare burden in the United States. Younger diverticulitis patients are at increased risk for recurrence. How the molecular pathophysiology differs from those that develop disease at an older age is not understood. We aimed to profile the colonic transcriptome from younger versus older diverticulitis patients to identify differential biological pathways contributing to disease.

Methods: We performed RNA-seq on full-thickness sigmoid colon tissue obtained at the time of surgery on diverticulitis patients (n=26) diagnosed at a younger age (<42 years old) or at an older age (>65 years old). Viral reads were identified from the RNA-seq dataset and associated with clinical metadata and the host transcriptome. HHV-6 positivity was evaluated in diverticulitis patients by PCR and immunofluorescence. Patient sera was profiled for HHV-6 using qPCR and ELISA to detect anti-HHV-6 antibodies.

Results: Using RNA-seq, diverticulitis patients were profiled for differential expression associated with age of diagnosis. A subset of younger diverticulitis patients (diverticulitis colonic transcriptome-viral signature (DCT-VS)) demonstrated increased expression of anti-viral response genes. We identified viral transcripts in the RNA-seq dataset and found HHV-6 transcripts negatively correlated with DCT-VS. Younger patients more frequently displayed evidence of HHV-6 infection through DNA analysis and immunofluorescence of colonic tissue. During acute disease, HHV-6 DNA was detected in the serum but was absent during disease quiescence.

Conclusions: Patients diagnosed with diverticulitis at a younger age demonstrate reactivation of HHV-6 in the sigmoid colon that remains persistent. Future studies to assess the role of pathogenicity and the use of anti-virals for acute uncomplicated diverticulitis should be considered.

overall_design: Examination of full-thickness sigmoid colon tissue from 26 diverticulitis patients, including 13 diagnosed at an younger age (<42 years old) and 13 diagnosed at an older age (>65 years old)

first: Kathleen

last: Schieffer

first: Bryan

middle: P

last: Kline

first: Stephen

last: Matthews

first: Leonard

last: Harris

first: Sue

last: Deiling

first: Justin

last: Wright

first: Vasily

last: Tokarev

first: Regina

last: Lamendella

first: Walter

last: Koltun

first: Gregory

last: Yochum


title: C. elegans on pathogenic Pseudomonas aeruginosa

city: Cambridge

first: Dennis

last: Kim

state: MA

address: 31 Ames Street

institute: MIT


title: Transcriptional profiling of C. elegans on pathogenic Pseudomonas aeruginosa

summary: RNA-seq of Wild Type (N2), pmk-1 or atf-7 mutant animals exposed to either non-pathogenic E. coli OP50 or pathogenic P. aeruginosa PA14

overall_design: mRNA profiles were generated using 3 replicates (>1,000 animals each) of each condition were prepared and sequenced, except for atf-7(qd22qd130) on PA14 which had only 2 replicates. Sequenced on Illumina NextSeq 500

first: Marissa

last: Fletcher

first: Vincent

last: Butty

middle: H


title: Binding profile of the bZIP transcription factor, ATF-7, in C. elegans on pathogenic Pseudomonas aeruginosa

summary: ChIP-seq of ATF-7::GFP from Wild Type or pmk-1 mutant animals exposed to either non-pathogenic E. coli OP50 or pathogenic P. aeruginosa PA14

overall_design: ChIP profiles were generated using 3 replicates (>15,000 animals each) of each condition were prepared and sequenced, except for WT on PA14 which had only 2 replicates. Sequenced on Illumina HiSeq2000

first: Erik

last: Tillman


title: Drosophila melanogaster female late third instar larval gonads single-cell RNA-Seq (scRNA-Seq) profiling

middle: Matthew

last: Fear

address: 50 South Drive

department: LCDB

institute: NIDDK, NIH

summary: The larval ovary is made up of multiple cell types including germ cells and somatic cells. The diversity of cell types and transcriptional regulation is not fully understood. To get single cell resolution of larval ovary regulation, we generated single-cell RNA expression profiles (scRNA-Seq) from late third instar larval ovaries of a reference Drosophila melanogaster genotype w[1118].

overall_design: We generated scRNA-Seq profiles of late third instar larval ovaries in biological triplicate pools using the 10X Chromium System (10X Genomics, Pleasanton, CA) and sequenced (Read1=26 bp, Read2=98 bp and Readi7=8 bp) on a HiSeq 2500 (Illumina, San Diego, CA).

first: Sharvani

last: Mahadevaraju

first: Brian

last: Oliver


title: Expression data from pancreatic islets of prolactin receptor null pregnant mice

city: Calgary

first: Carol

last: Huang

state: Alberta

address: 3330 Hospital Drive NW

institute: University of Calgary

summary:
Pancreatic islets adapt to the increase in insulin demand during pregnancy by up-regulating beta cell proliferation, insulin synthesis, and lowering the threshold of glucose-stimulated insulin secretion.
In vitro studies suggest that pregnancy hormones, such as placental lactogens and prolactin, both act through the prolactin receptor, are required for these adaptation. Furhtermore, we found that transgenic mice with heterogenous prolactin receptor null mutation are glucose intolerant, with a lower beta-cell mass and lower insulin levels. The goal here is to discover novel targets of prolactin receptor signaling in pancreatic beta cells during pregnancy.

overall_design: Islets were isolated from wild type and heterozygous prolactin receptor knockout mice on day 15 of pregnancy. Islets from each mouse were analyzed separately. After isolation, islets were lysed using the RLT lysis buffer (Qiagen, Valencia, USA) and stored at -80C for RNA extraction.

first: Xiuling

last: Wang


title: Genome-wide identification of miRNAs associated with alcoholism endophenotypes - Full LXS recombinant inbred panel

city: Aurora

first: Laura

last: Saba

state: CO

address: 12850 E. Montview Blvd

department: Skaggs School of Pharmacy and Pharmaceutical Sciences

summary: We conducted a high-throughput sequencing study to measure whole brain miRNA expression levels in alcohol naïve animals in the LXS panel of recombinant inbred (RI) mouse strains. We then combined the sequencing data with genotype data, microarray gene expression data, and data on alcohol-related behavioral phenotypes such as 'Drinking in the dark', 'Sleep time', and 'Low dose activation' from the same RI panel.

overall_design: This dataset includes small RNA NGS sequencing data from 59  strains from the Inbred Long Sleep (ILS) and Inbred Short Sleep (ISS) Recombinant inbred  mouse whole brain RNA samples. 175 mice (2-3 from each strain) were untreated (naive). The naive samples were provided by Boris Tabakoff, University of Colorado Anschutz Medical Campus. All expression data generation and analysis were conducted by the Kechris Group,  University of Colorado Anschutz Medical Campus.

first: Katerina

last: Kechris

first: Boris

last: Tabakoff


title: Thymidylate synthase maintains the de-differentiated state of triple negative breast cancers

city: PHILADELPHIA

first: Irfan

last: Asangani

address: 421 Curie Bld.

department: Cancer Biology

institute: University of Pennsylvania

summary: Cancer cells frequently boost nucleotide metabolism (NM) to support their increased proliferation, but the consequences of elevated NM on tumor de-differentiation are mostly unexplored. Here, we identified a role for thymidylate synthase (TS), a NM enzyme and established drug target, in cancer cell de-differentiation and investigated its clinical significance in breast cancer (BC). In vitro, TS knockdown increased the population of CD24+ differentiated cells, and attenuated migration and sphere-formation. RNA-seq profiling indicated a repression of epithelial-to-mesenchymal transition (EMT) signature genes upon TS knockdown, and TS-deficient cells showed an increased ability to invade and metastasize in vivo, consistent with the occurrence of a partial EMT phenotype. Mechanistically, TS enzymatic activity was found essential for the maintenance of the EMT/stem-like state by fueling a dihydropyrimidine dehydrogenase – dependent pyrimidine catabolism. In patient tissues, TS levels were found significantly higher in poorly differentiated and in triple negative BC, and strongly correlated with worse prognosis. The present study provides the rationale to study in-depth the role of NM at the crossroads of proliferation and differentiation, and depicts new avenues for the design of novel drug combinations for the treatment of BC

overall_design: Gene expression analysis by RNAseq in Triple Negative Breast Cancer Cell Line MDA-MB-231 with knock down of Thymidylate Synthase and scrambled pLKO control.

first: Paolo

last: Ceppi

first: Paradesi

last: Naidu Gollavilli

first: Ram

last: Natesan