title: Caenorhabditis elegans AF4/FMR2 family homolog affl-2 regulates heat shock induced gene expression

city: Emerald Hills

first: Sophie

middle: Jean

last: Walton

address: 346 Lakeview Way

department: Biology and Biological Engineering

institute: California Institute of Technology

summary: To mitigate the deleterious effects of temperature increases on cellular organization and proteotoxicity, organisms have developed mechanisms to respond to heat stress. In eukaryotes, HSF1 is the master regulator of the heat shock transcriptional response, but the heat shock response pathway is not yet fully understood. From a forward genetic screen for suppressors of heat shock induced gene expression in Caenorhabditis elegans, we found a new allele of hsf-1 that alters its DNA-binding domain, and we found three additional alleles of sup-45, a previously molecularly uncharacterized genetic locus. We identified sup-45 as one of the two hitherto unknown C. elegans orthologs of the human AF4/FMR2 family proteins, which are involved in regulation of transcriptional elongation rate.  We thus renamed sup-45 as affl-2 (AF4/FMR2-Like). Through RNA-seq, we demonstrated that affl-2 mutants are deficient in heat shock induced transcription. Additionally, affl-2 mutants have herniated intestines, while worms lacking its sole paralog (affl-1) appear wild type. AFFL-2 is a broadly expressed nuclear protein, and nuclear localization of AFFL-2 is necessary for its role in heat shock response. affl-2 and its paralog are not essential for proper HSF-1 expression and localization after heat shock, which suggests that affl-2 may function downstream or parallel of hsf-1. Our characterization of affl-2 provides insights into the regulation of heat shock induced gene expression to protect against heat stress.

overall_design: We measured the effect of the affl-2(sy975) mutation on heat shock induced transcriptional response.

first: Han

last: Wang

first: Porfirio

last: Quintero-Cadena

first: Alex

last: Bateman

middle: W

last: Sternberg


title: Dppa2/4 Counteract De Novo Methylation to Establish a Permissive Epigenome for Development

status: Public on May 27 2020

city: Monterotondo

first: Kristjan

middle: Holm

last: Gretarsson

state: Roma

address: Via Ercole Ramarini, 32

country: Italy

institute: EMBL Rome

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Mechanism of selective incorporation of lncRNA into a chromatin modifier

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Zentrum München

summary: The MLE DExH helicase and the roX lncRNAs are essential components of the chromatin modifying Dosage Compensation Complex (DCC) in Drosophila. To explore the mechanism of ribonucleoprotein complex assembly, we designed vitRIP, an unbiased, transcriptome-wide in vitro assay that reveals RNA binding specificity. We found that MLE has intrinsic specificity for U-rich sequences and tandem stem-loop structures. In vitro, the helicase binds and remodels many RNAs beyond its main target, roX2. Unwinding of roX2 by the helicase triggers their selective association with the DCC, via the MSL2 subunit. Whereas the core DCC alone does not show intrinsic RNA binding specificity, the presentation of remodeled roX2 by MLE induces a highly selective RNA binding surface in the unstructured C-terminus of MSL2. The exquisite selectivity of roX2 incorporation into the DCC thus originates from intimate cooperation between the helicase and the core DCC involving two distinct RNA selection principles and their mutual refinement.

overall_design: RNA-seq of in vitro and in vivo RIP experiments. IP and Input samples in at least 2 biological replicates per condition.

first: Marisa

last: Müller

first: Peter

middle: B

last: Becker


title: FSL0260 enhanced salinity stress response

city: Yokohama

first: motoaki

last: seki

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: CSRS

country: Japan

institute: RIKEN

summary: To identify salt-resistant related genes by FSL0260, expression profiles between plants treated with or without FSL0260 under salt stress were analyzed using the custom microarray (GPL19830).

overall_design: Wild-type plants (Arabidopsis thaliana ecotype Columbia) were grown on 1/2 MS 0.1 % Agar medium for four days. Then, the plants were administrated to FSL0260 for 24. Expression profiles were analyzed using the custom array (GPL19830).

first: Kaori

last: Sako

first: Akihiro

last: Matsui

first: Maho

last: Tanaka

first: Motoaki

last: Seki


title: Substrate reduction therapy using Genz-667161 reduces levels of pathogenic components in a mouse model of neuronopathic forms of Gaucher disease

status: Public on May 26 2020

city: Rehovot

first: Anthony

last: Futerman

address: Herzl

country: Israel

institute: Weizmann Institute of Science

summary: Most lysosomal storage diseases (LSDs) have a significant neurological component, including types 2 and 3 Gaucher disease (neuronal forms of Gaucher disease; nGD). No therapies are currently available for nGD since the recombinant enzymes used in the systemic form of Gaucher disease do not cross the blood-brain barrier. However, a number of promising approaches are currently being tested, including substrate reduction therapy (SRT), in which partial inhibition of the synthesis of the glycosphingolipids (GSLs) that accumulate in nGD lowers their accumulation. We now induce nGD in mice by injection with conduritol B-epoxide (CBE), an irreversible inhibitor of acid beta-glucosidase (GCase), the enzyme defective in nGD, with or without co-injection with GZ-667161, a prototype for SRT. Significant neuropathology, and a reduction in lifespan, was observed upon CBE injection, and this was largely reversed by co-injection with GZ-667161, along with a reduction in glucosylceramide and glucosylsphingosine levels. Analysis of gene expression by RNAseq revealed that GZ-667161 largely reversed the changes in genes and pathways that were differentially-expressed upon CBE injection, specifically pathways of GSL metabolism, lipoproteins and other lipid metabolic pathways, lipid droplets, astrocyte activation, neuronal function, and to some extent, neuroinflammation. Together, this demonstrates the efficacy of SRT to reverse the effects of substrate accumulation on pathological components and pathways in nGD brain.

overall_design: Brain homogenates from control mice (PBS), CBE injected mice and CBE+GZ-667161 injected mice

first: Shani

last: Blumenreich

first: Chen

last: Yaacobi

first: Ayelet

last: Vardi

first: Or

last: Barav

first: Einat

last: Vitner

first: Hyejung

last: Park

first: Bing

first: Seng

middle: H

last: Cheng

first: S

middle: P

last: Sardi


title: Evolution of Potato spindle tuber viroid quasi-species during the course of disease in tomato plants

city: Sherbrooke

first: Charith Raj

last: Adkar-Purushothama

state: Quebec

address: 3201 rue Jean-Mignault

department: Biochemistry

country: Canada

institute: Université de Sherbrooke

summary: In order to verify the production of viroid specific small RNAs (vd-sRNA) by viroids upon infecting plants, the tomato plants (Lycopersicum esculentum cv. Rutgers) were inoculated with Potato spindle tuber viroid (PSTVd) variants. After 21-days of post inoculation, total RNA was extracted and subjected for deep-sequencing using Illumina platform. Obtained data was analyzed for the presence of PSTVd specific small RNAs.

overall_design: Examination of viroid quasi-species at different stages of disease in tomato plants.

first: Charith

first: François

last: Bolduc

first: Pierrick

last: Bru

first: Jean-Pierre

last: Perreault


title: Type 3 innate lymphoid cells direct goblet cell differentiation via the LT-LTβR pathway during Listeria infection

city: Beijing

first: Mingzhao

last: Zhu

address: 15 Da Tun Rd, Chaoyang District

department: Key Laboratory of Infection and Immunity

country: China

institute: Institute of Biophysics, Chinese Academy of Sciences

summary: As a specialized subset of intestinal epithelial cells (IECs), goblet cells (GCs) play an important role during the antibacterial response via mucin production. However, the regulatory mechanisms involved in GC differentiation and function during infection, particularly the role of immune cell-IEC crosstalk, remain largely unknown. Here, using VillinΔLtbr conditional knockout mice, we demonstrate that LTβR, expressed on IECs, is required for GC hyperplasia and mucin 2 (MUC2) expression during Listeria infection for host defense but not homeostatic maintenance in the naïve state. Analysis of single gene-deficient mice revealed that the ligand lymphotoxin (LT) but not LIGHT and type 3 innate lymphoid cells (ILC3s) but not conventional T cells are required for MUC2-dependent Listeria control. Conditional deficiency of LT in ILC3s further confirmed the importance of LT signals derived from ILC3s. Lack of ILC3-derived LT or IEC-derived LTβR resulted in defective expression of genes related to GC differentiation but was not correlated with IEC proliferation and cell death, which were found to be normal by Ki-67 and Annexin V staining. In addition, the alternative NF-κB signaling pathway (involving RelB) in IECs was found to be required for the expression of GC differentiation-related genes and Muc2 and required for the anti-Listeria response. Therefore, our data together suggest a previously unrecognized ILC3-IEC interaction and LT-LTβR-RelB signaling axis governing GC differentiation and function during Listeria infection for host defense.

overall_design: Whole transcriptome sequencing (RNA-Seq) of ileum epithelial cells (IECs) in VillinΔLtbr (cKO) and control mice, in duplicate (for control) and triplicate (for cKO) samples, using Illumina NovaSeq system.

first: Qian

last: Chai

first: Yaya

last: Pian

first: Boyang

last: Ren


title: Transcriptomic effects of tributyltin (TBT) in zebrafish eleutheroembryos. A functional benchmark dose analysis.

city: Barcelona

first: Rubén

middle: Francisco

last: Martínez López

state: Cataluña

address: Carrer Jordi Girona, 18-26

department: Environmental Toxicology

country: Spain

institute: IDAEA-CSIC

summary:
Purpose: the goal of this project is to study the effects of the TBT (tributyltin) in the transcriptome profiling (RNA-seq) of exposed zebrafish larvae.
Methods: Total RNA was isolated from the samples using AllPrep DNA/RNA Mini Kit (Qiagen, CA, USA) as described by the manufacturer. Three high quality sample per condition were chosen to the mRNA enrichment using KAPA Stranded mRNA-Seq Kit Illumina® Platforms (Kapa Biosystems). Transcriptomic profiles were generated by deep sequencing using Illumina TruSeq SBS Kit v3-HS (pair-ended; 2x76bp) on a HiSeq2000 sequencing system. Image analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 1.13.48) and followed by generation of FASTQ sequence files by CASAVA.
Statistical analysis: RNA-seq reads were aligned to the D. rerio reference genome (GRCz10) using STAR version 2.5.1b . Genes annotated in GRCz10.84 were quantified using RSEM version 1.2.28 with default parameters. Differential expression analysis between all TBT conditions was performed with the DESeq2 (v.1.10.1) R package with the Likelihood ratio test option. ANOVA-PLS was performed on the normalized data using the lmdme package in R (v. 1.0.136, R Core Team).
Results: We generated on average 42 million paired-end reads for each sample and identified aproximatelly 24420  transcripts. 3238  differentially expressed genes (DEGs) were detected which could be divided in 2 clusters including 1703 and 1535 genes, respectively. Affected metabolic pathways were analyzed from the DEGs: DNA-binding, domain transcription factors, transcription, nucleus, regulation of cell proliferation, cell cycle and differentiation, NAD(P)-binding domain, carbon metabolism, transferases, nucleotide binding, catalytic activity, and specially steroid metabolism and biosynthesis, among others, were down or upregulated.
Conclusions: The dose-response setup allowed us to determine the most sensitive pathways affected by TBT, mostly related to the steroid biosynthesis, and general cell viability and development. Its covalent binding to RXR receptors seems to be the responsible for their specific disruption but also could be involved in its general toxicity along with an unspecific heavy metal poisoning. Transcriptomic general toxicity was related to a developmental delay which was in agreement with previous morphometric results. Other properties traditionally attributed to TBT as obesogenity only appeared at higher concentrations which were relative close to lethal levels. Other biological levels were also affected at concentrations relative closer to lethality than other endocrine disruptors, suggesting than its mode of action and/or lethality could differ from other EDCs. The present work contributes in the understanding of the environmental hazards associated to TBT.

overall_design: Whole embryo (5 dpf; wild type zebrafish) mRNA profiles of 4 groups (control, 3.0, 30 and 100 nM of TBT) were generated by deep sequencing, in triplicate, using Illumina TruSeq SBS Kit v3-HS (pair-ended) on a HiSeq2000 sequencing system.

last: Martínez

first: Anna

last: Esteve-Codina

first: Carlos

last: Barata

first: Romà

last: Tauler

first: Laia

last: Navarro-Martín

first: Benjamin

last: Piña


title: Transcriptomic profile of circulating memory CD8 T cells can differentiate between latent tuberculosis individuals and healthy controls

city: La Jolla

first: Bjoern

last: Peters

state: California

address: 9420 Athena Cir

country: USA

institute: La Jolla Institute for Immunology

summary: Tuberculosis (TB) is responsible for the majority of mortality and morbidity associated with infectious diseases worldwide. The characterization of exact molecular components of immune response associated with protection against TB may help design more effective therapeutic interventions. In this study, we aimed to characterize the immune signature of memory T cells associated with latent infection with Mycobacterium tuberculosis. Transcriptomic profiling using RNA sequencing was performed on memory CD8 T cells isolated from individuals with latent tuberculosis, as well as from tuberculosis negative healthy controls. Overall, we found specific gene signatures in each cell subset that could successfully discriminate between individuals with latent tuberculosis and healthy controls.

overall_design: RNA-sequencing of sorted memory CD8 T cells from cryopreserved PBMC of 20 subjects with latent tuberculosis infection and 20 tuberculosis negative healthy controls

first: Julie

last: Burel

first: Cecilia

last: Lindenstam

first: Gregory

last: Seumois

first: Zheng

last: Fu

first: Jason

last: Greenbaum

first: Alessandro

last: Sette

first: Pandurangan

last: Vijayanand


title: Light-Activatable TET-Dioxygenases Reveal Dynamics of 5-Methylcytosine Oxidation and Transcriptome Reorganization

status: Public on May 25 2020

city: Dortmund

first: Daniel

last: Summerer

state: NRW

address: Otto-Hahn-Str. 4a

department: Chemistry and Chemical Biology

institute: TU Dortmund University

summary: We report activation of TETs in mammalian cells by incorporation of genetically encoded 4,5-dimethoxy-2-nitrobenzyl-L-serine as transient active site block, and its subsequent deprotection with light. Our approach allows time-resolved monitoring of target gene activation and transcriptome reorganization. This sets a basis for dissecting the order and kinetics of chromatin-associated events triggered by TET catalysis, ranging from DNA demethylation to chromatin and transcription regulation.

overall_design: mRNA sequencing prior to deprotection, 4h, and 8h after activation of hTET2.

first: Shubhendu

last: Palei

middle: C

last: Buchmuller


title: Prediabetes Induced by a Single Autoimmune B cell Clone

city: Freiburg

first: Manching

last: Ku

address: Mathildenstrasse 1

department: Hematology and Oncology

institute: Medical Center - University of Freiburg


title: Gene expression profiling of blood of Ebola virus disease survivors and Healthy donors by Next Generation Sequencing

city: Créteil

first: cecile

last: lefebvre

address: 51 Avenue du Marechal De Lattre de Tassigny

country: France

institute: INSERM U955_VRI

summary: Clinical follow-up of Ebola virus disease (EVD) survivors revealed a persistence of clinical symptoms and higher risk of mortality. Long-term analyses of the immune and inflammatory profiles of EVD survivors are currently lacking. Here, we evaluate gene expression profiles in 26 Guinean Ebola virus disease survivors (EBOV_S) and 33 Healthy donnors (HD). We show a persistent increase of several biomarkers of inflammation, immune activation and gut tissue damage in EBOV_S compared to healthy donors living in the same area. Gene expression profiling in blood revealed a significant enrichment in genes associated with antiviral responses in EBOV_S.

overall_design: Analysis of whole-blood gene expression profiles of 26 Ebola virus disease survivors and 33 Healthy donnors

first: Aurélie

last: Wiedemann

first: Hakim

last: Hocini

first: Cécile

last: Lefebvre

first: Christine

last: Lacabaratz

first: Yves

last: Lévy

first: Miriam

last: Krueger

first: Melany

last: Durand

first: Rodolphe

last: Thiébaut


title: Functional characterization of a PROTAC directed against BRAFV600E

city: Toronto

first: Jeff

last: Wrana

state: Ontario

address: 600 University Avenue

institute: Lunenfeld-Tanenbaum Research Institute

summary: The RAF family kinases function in the RAS-ERK pathway to transmit signals from activated RAS to the downstream kinases MEK and ERK. This pathway regulates cell proliferation, differentiation, and survival enabling mutations in RAS and RAF to act as potent drivers of human cancers. Drugs targeting the prevalent oncogenic mutant BRAFV600E have shown great efficacy in the clinic but long-term effectiveness is limited by resistance mechanisms that often exploit the dimerization-dependent process by which RAF kinases are activated. Here, we investigated a proteolysis targeting chimera (PROTAC) approach to BRAF inhibition. The most effective PROTAC termed P4B displayed superior specificity and inhibitory properties relative to non-PROTAC controls in BRAFV600E cell lines. In addition, P4B displayed utility in two cell lines harboring alternate BRAF mutations that impart resistance to conventional BRAF inhibitors. This work provides a rationale for optimizing the drug-like properties of P4B to enable proof of concept studies in vivo.

overall_design: Each of 6 treatments in triplicate, with solvent DMSO as the control sample

first: Ganna

last: Posternak

first: XiaoJing

last: Tang

first: Pierre

last: Maisonneuve

first: Ting

last: Jin

first: Hugo

last: Lavoie

first: Salima

last: Daou

first: Stephen

last: Orlicky

first: Theo

last: Goullet De Rugy

first: Lauren

last: Caldwell

first: Kin

last: Chan

first: Ahmed

last: Aman

first: Michael

last: Prakesch

first: Gennady

last: Poda

first: Pavel

last: Mader

first: Cassandra

last: Wong

first: Stefan

last: Maier

first: Julia

last: Kitaygorodsky

first: Brett

last: Larsen

first: Karen

last: Colwill

first: Zhe

last: Yin

first: Derek

middle: F

last: Ceccarelli

first: Robert

middle: A

last: Batey

first: Mikko

last: Taipale

first: Igor

last: Kurinov

first: David

last: Uehling

last: Durocher

first: Anne-Claude

last: Gingras

first: Rima

last: Al-Awar

first: Marc

last: Therrien

first: Frank

last: Sicheri


title: Molecular plant responses to combined abiotic stresses put a spotlight on unknown and abundant genes

city: Düsseldorf

first: Andreas

middle: PM

last: Weber

address: Universitätsstr. 1

department: Institute for Plant Biochemistry

institute: Heinrich-Heine-University

summary: Environmental stresses such as drought, heat and salinity limit plant development and agricultural productivity. While individual stresses have been studied extensively, much less is known about the molecular interaction of responses to multiple stresses. To address this problem, we investigated molecular responses of Arabidopsis thaliana to single, double, and triple combinations of salt, osmotic, and heat stresses. A metabolite profiling analysis indicated the production of specific compatible solutes depending on the nature of the stress applied. We found that in combination with other stresses, heat has a dominant effect on global gene expression and metabolites level patterns. Treatments that include heat stress lead to strongly reduced transcription of genes coding for abundant photosynthetic proteins and proteins regulating the cell life cycle, while genes involved in protein degradation are upregulated. Under combined stress conditions, the plants shifted their metabolism to a survival state characterized by low productivity. Our work provides molecular evidence for the dangers for plant productivity and future world food security posed by heat waves resulting from global warming. We highlight candidate genes, many of which are functionally uncharacterized, for engineering plant abiotic stress tolerance.

overall_design: Arabidopsis seedlings (n = 3) were treated with single stress treatments (S, salt; M, mannitol; H, heat) or stress combinations (SM; SH; MH; SMH) and compared to non-stressed control plants.

first: Nasser

last: Sewelam

first: Dominik

last: Brilhaus

first: Andrea

last: Bräutigam

first: Saleh

last: Alseekh

first: Alisdair

middle: R

last: Fernie

first: Veronica

middle: G

last: Maurino


title: Calcium signaling as a possible mechanism behind increased locomotor response in zebrafish larvae exposed to a human relevant persistent organic pollutant mixture or PFOS

city: Utrecht

first: Jorke

last: Kamstra

state: Non United States Or Canada

address: PO Box 80177

department: Faculty of Veterinary Medicine

country: Netherlands

institute: Utrecht University

summary: Persistent organic pollutants (POPs) are widespread in the environment and bioaccumulate in organisms. Previously we observed hyperactivity of zebrafish larvae exposed to a mixture of POPs based on average blood levels from the Scandinavian population and identified perfluorooctanesulfonic acid (PFOS) as the driving agent for the behavioral changes. We exposed zebrafish larvae from 6 to 96 h post fertilization to the same mixture of POPs in two concentrations or a single PFOS exposure (0.3 and 2.06mg/L) and performed behavioral tests and transcriptomics analysis. Results confirmed previous observations that exposure to POPs and PFOS causes hyperactivity and higher anxiety levels. Transcriptomic analysis showed upregulation of transcripts related to muscle contraction. Muscle contraction is highly regulated by the availability of calcium in the sarcoplasmic reticulum. Ingenuity pathway analysis showed that one of the affected pathways in larvae exposed to the POPs mixture and PFOS was calcium signalling via the activation of the ryanodine receptors. We also found effect on lipid metabolism in those larvae exposed to the lower concentration of PFOS. By using omics technology, we observed that the altered behavioral pattern in exposed zebrafish larvae might be controlled directly by mechanisms affecting muscle function rather than from mechanisms connected to neurotoxicity.

overall_design: The POPs mixture used in this study was based on average levels of chemicals found in blood of the Scandinavian population. The low concentration of POP (POP10) reflected levels x 10 higher of what is found in human blood and the high concentration (POP70) reflected levels x 70. PFOS10 and PFOS70 single exposure were based on the levels of PFOS in the POPs mixture. Zebrafish larvae were exposed from 6 hpf until 96 hpf to either POP10, POP70, PFOS10 or PFOS70 in 4 replicates. We also included a control condition of zebrafish larvae exposed only to the solvent (0.1% DMSO) in 4 replicates. Each sample contained 10 zebrafish larvae.

first: Thomas

last: Fraser

first: Vidar

last: Berg

first: Erik

last: Ropstad

first: Maria

last: Christou


title: Prokaryotic Single-Cell RNA Sequencing by In Situ Combinatorial Indexing

city: New York

first: Sydney

last: Blattman

state: NY

address: 1150 St. Nicholas Ave

institute: Columbia University

summary: We present Prokaryotic Expression-profiling by Tagging RNA In Situ and sequencing (PETRI-seq), a high-throughput prokaryotic scRNA-seq pipeline. We demonstrated that PETRI-seq effectively barcoded single bacterial cells in a species-mixing experiment with E. coli (MG1655) and S. aureus (USA300). Within the S. aureus population, we found rare prophage induction in 0.04% of cells. We further demonstrated that PETRI-seq was able to distinguish between E. coli growth phases based on mRNA expression patterns by combining stationary E. coli with exponential E. coli in multiple experiments.

sample_organism:
Escherichia coli
Staphylococcus aureus

platform_organism:
Escherichia coli
Staphylococcus aureus

overall_design: Eight libraries were prepared by PETRI-seq, including species-mixed libraries of E. coli and S. aureus and/or E. coli cells in distinct growth stages (stationary, exponential). PETRI-seq libraries are detailed in Supplementary Table 4. Ten bulk libraries were prepared, including nine E. coli libraries and one S. aureus library.

first: Wenyan

last: Jiang

first: Panos

last: Oikonomou

first: Saeed

last: Tavazoie


title: Gene architecture and sequence composition underpin selective dependency of long RNAs on components of the nuclear export pathway

first: Igor

last: Ulitsky

address: Hertzl St.

summary: The nuclear export pathway transports long RNAs produced in the nucleus to the cytoplasm. The core components of this pathway are thought to be required for export of virtually all polyadenylated RNAs. Here, we depleted different proteins that act in nuclear export in human cells, and quantified the transcriptome-wide consequences on RNA localization. Different genes exhibited substantially variable sensitivities, with depletion of NXF1 and TREX components causing some transcripts to become strongly retained in the nucleus while others were not affected. Specifically, NXF1 is preferentially required for export of single- or few-exon transcripts with long exons or high A/U-content, whereas depletion of TREX complex components preferentially affects spliced and G/C-rich transcripts. Using massively parallel reporter assays we identified short sequence elements that render transcripts dependent on NXF1 for their export, and identified synergistic effects of splicing and NXF1. These results revise the current model of how nuclear export shapes the distribution of RNA within human cells.

overall_design: In order to obtain further evidence that the observed effects are a direct consequence of NXF1 depletion, we used SLAM-seq (Herzog et al. 2017), which included labeling of newly synthesized RNA using 4-thiouridine followed by iodoacetamide treatment of extracted RNA and sequencing. We labeled RNA for 4 hours just 16 hours after transfection of siRNAs targeting NXF1, which was sufficient for partial depletion of the NXF1 protein. In order to identify sequences that may promote NXF1-dependent export of intronless RNAs, we used a massively parallel RNA assay (Lubelsky and Ulitsky 2018; Shukla et al. 2018). We designed short oligos tiled across the sequences of NORAD, ATXN7L3B, MEX3C, and eight additional single-exon, cytoplasmic, and NXF1-sensitive human genes, including six PCGs and two lncRNAs. As a control, we also included the JPX lncRNA and a fragment of the MLXIPL gene, which we studied previously (Lubelsky and Ulitsky 2018). Most of the transcripts were tiled with 140 nt sequences with offsets of 20 nt (10 nt for NORAD and 25 nt for JPX). Overall, 2,545 sequences (collectively called CytoLib) were cloned into the 3'UTR of an intronless variant of the ?-globin gene (??1,2), which is relatively inefficiently exported, and was previously used as a model sequence for study of elements affecting nuclear export (Akef, Lee, and Palazzo 2015; Brown and Steitz 2016). In order to test the potential importance of RBM15 binding and m6A in nuclear export, we knocked down RBM15 alongside its paralog RBM15B, and WTAP, a core member of the m6A writer complex, and examined localization of CytoLib tiles.

first: Binymain

last: Zuckerman

first: Maya

last: Ron


title: Transcriptional and functional analysis of CD1c+ human dendritic cells identifies a CD163+ subset priming CD8+CD103+ T cells

status: Public on May 23 2020

city: London

first: Kristine

last: Vaivode

address: CIBCI, First Floor, New Hunt's House, Great Maze Pond

department: Centre for Inflammation Biology and Cancer Immunology

country: United Kingdom

institute: King's College London


title: Single-cell RNA-sequencing of mesenteric artery and aorta of 16-18 week old Wistar Kyoto rats or Spontaneously hypertensive rats

first: Wenduo

last: Gu

address: James Black Centre, 125 Coldharbour Lane

summary: We reported the cellular heterogeneity in the mesenteric artery and aortic artery

overall_design: This entry contains 10X Single-cell RNA-seq data of vascular cells from the mesenteric artery and aortic artery of 16-18 week old WKY or SHR rats

first: Jun

last: Cheng

first: Ting

last: Lan

first: Xu

last: Qingbo


title: Expression data from progeroid smooth muscle cells

city: Coimbra

first: Lino

last: Ferreira

state: Azinhaga de Santa Comba,

address: Pólo das Ciências da Saúde,Unidade Central

country: Portugal

institute: Faculty of Medicine

summary:
Hutchinson-Gilford Progeria syndrome (HGPS or Progeria) is a rare and fatal genetic condition, characterized by premature aging symptoms in children and it affects approximately 1 in 4-8 million newborns. Individuals with HGPS appear to show aging-related phenotypes at a much faster rate than normal, leaving young children with the appearance and health conditions of an aged individual. This syndrome causes changes in various organs and systems such as the skin, skeleton, hair, body fat and cardiovascular system. One of the hallmarks of the disease is the loss of SMCs in the medial layer of large arteries with replacement by collagen and extracellular matrix, and in many cases calcification.
We used microarrays to detail the global programme of gene expression underlying smooth muscle cell loss and identified distinct classes of up- and down-regulated genes during this process.

overall_design: The analyses were performed on progeria smooth muscle cells derived from progeria iPSCs and healthy (N) smooth muscle cells derived from iPSCs at static conditions or cultured for 4 days in arterial flow conditions. In both cases total RNA from cells was extracted and gene expression was evaluated by a whole human genome microarray Human Gene 2.1 ST Array Strip from Affymetrix.


title: Prediabetes Induced by a Single Autoimmune B cell Clone [ATAC-seq]

first: Manching

last: Ku

summary: SCNT-derived B cell model displays spontaneous germinal center reaction, infiltration of pancreas (in RAG1-/- background) and impaired glucose tolerance.

overall_design: To better understand the role of B cells in autoimmune diabetes, we used somatic cell nuclear transfer (SCNT) to develop a novel model from a physiological pancreas-infiltrating B cell on pure non-obese diabetic (NOD) background. Contrary to previous transgenic autoimmune B cell models, the SCNT-derived B cell model (referred to as B1411) displayed neither a developmental block nor anergy. Instead, B1411 underwent spontaneous germinal center reaction, and on RAG1-deficient background B1411 was capable of infiltrating the pancreas, and of undergoing class-switch recombination. RNA-Seq analysis identified 93 differentially expressed genes in B1411, among which were Irf7, Usp18, Mda5 that had been linked to a potential viral etiology of autoimmune diabetes, as well as various members of the oligoadenylate synthase (OAS) family. Strikingly, when challenged with glucose B1411-Rag1-/- mice displayed impaired glucose tolerance.

first: Eugene

last: Ke

first: Oktay

last: Kirak


title: Various modes of HP1a interactions with the euchromatic chromosome arms in Drosophila ovarian somatic cells

city: Stockholm

first: Artem

last: Ilin

address: Svante Arrhenius väg 20C

department: MBW

country: Sweden

institute: Stockholm University

summary: Heterochromatin protein 1a (HP1a) is a well-known component of pericentromeric and telomeric heterochromatin in Drosophila. However, its role and the mechanisms of its binding in the chromosome arms (ChAs) remain largely unclear. Here, we identified HP1a-interacting domains in the somatic cells of Drosophila ovaries using a DamIDseq approach and compared them with insertion sites of transposable elements (TEs) revealed by genome sequencing. Although HP1a domains cover only 13% of ChAs, they non-randomly associate with 42% of TE insertions. Furthermore, HP1a propagates from TE insertions at distances up to 10-kb. These data confirm the role of TEs in formation of HP1a islands in ChAs. However, only 18% of HP1a domains have adjacent TEs, indicating the existence of other mechanisms of HP1a domain formation besides spreading from TEs. In particular, many TE-independent HP1a domains correspond to the regions attached to the nuclear pore complexes (NPCs), or contain active gene promoters. Surprisingly, HP1a occupancy on the promoters of these genes does not lead to their repression. However, the steady-state transcript level of many genes located outside of HP1a domains was altered upon HP1a knockdown in the somatic cells of ovaries, thus pointing to the strong indirect effect of HP1a depletion. Collectively, our results support an existence of at least three different mechanisms of HP1a domain emergence in ChAs: spreading from TE insertions, interaction with the chromatin located near NPCs and targeting to the promoters of moderately expressed genes.

overall_design: Amplified PCR fragments from DamID procedure were sequenced on Illumina HiSeq 2500, cDNA libraries were sequenced on Illumina HiSeq 1500.

last: Ilyin


title: IDLV capture for gRNA off-target analysis

city: EVRY

first: Mario

last: Amendola

address: 1 rue de l'internationale

department: research and development

institute: genethon

summary: Vector capturing  was used for experimental identification of potential off-target sites of 2 gRNA targeting alpha globin genes

overall_design: K562 cells were transduced with an Integrase-defective lentiviral vector expressing GFP and subsequently nucleofected with 30 pmol of Cas9:gRNA complex to induce double-strand breaks. Two weeks later GFP positive cells were sorted and integration sites were identified in this population using LM-PCR

first: Giulia

last: Pavani

first: Guillaume

last: Corre


title: Expression of RUNX1-ETO Rapidly Alters the Chromatin Landscape and Growth of Early Human Myeloid Precursor Cells (RNA-Seq)

city: Birmingham

first: Peter

last: Keane

address: Vincent Drive

department: Institute for Cancer and Genomic Sciences

institute: University of Birmingham

summary: Acute myeloid leukemia is a hematopoietic malignancy caused by recurrent mutations in genes encoding transcriptional, epigenetic and/or signaling regulators. The t(8;21) translocation generates the aberrant transcription factor RUNX1-ETO, whose expression can be detected in utero but is insufficient to cause overt disease. Although patients harboring cells with the t(8;21) translocation have acquired additional mutations and show extensive epigenetic reprogramming, the effects directly and solely attributable to RUNX1-ETO expression are unclear. To address this question, we used a human embryonic stem cell differentiation system capable of forming definitive human myeloid progenitor cells to express RUNX1-ETO in an inducible fashion. Induction of RUNX1-ETO causes extensive chromatin reprogramming by interfering with RUNX1 binding, blocks differentiation and arrests cellular growth, whereby growth arrest is reversible following RUNX1-ETO removal. Single cell gene expression analyses show that RUNX1-ETO induction alters the differentiation of a defined sub-population of progenitors, indicating that oncoprotein-mediated transcriptional reprogramming is highly target cell-specific.

overall_design: RNA-Seq of human embryonic stem cells that have undergone hematopoietic differentiation. These cells contain a doxycycline-inducible RUNX1-ETO construct. Cells were treated with 0, 3, 5 or 10 ng/ml of dox prior to sequencing. All experiments were conducted in triplicate.

first: Monica

last: Nafria

first: Elizabeth

last: Ng

first: Edouard

last: Stanley

first: Andrew

last: Elefanty

first: Constanze

last: Bonifer


title: Peri-pubertal High-Fat Diet Promotes c-Myc Stabilization in Mammary Gland Epithelium

status: Public on May 24 2020

city: Kanazawa

first: Shin-ichi

last: Horike

state: Ishikawa

address: 13-1 Takaramachi

department: Research Center for Experimental Modeling of Human Disease

institute: Kanazawa University

summary: Dietary fat consumption during rapid mammary gland developing period such as peri-pubertal maturation or pregnancy increases the risk for breast cancer. However, the molecular mechanism underlying this observation is not well elucidated. To provide mechanistic insight, we examined gene expression profile in mouse mammary epithelial cells (MMECs) exposed to high-fat diet (HFD) or control diet (CD). Trp53-/- female mice were treated with experimental diets for 5 weeks during the peri-puberty period (3 to 8 weeks of age). This treatment induced insignificant difference in body weight between mice exposed to HFD and CD. Gene Set Enrichment Analysis (GSEA) predicted elevated expression of c-Myc target genes when exposed to HFD. Consistently, we detected marked elevation of c-Myc protein and prolongation of its half-life in MMECs exposed to HFD suggesting that HFD increased its stability. Additionally, we observed increased phosphorylation at c-MycS62 with concomitant increase in ERK phosphorylation. HFD rendered Trp53-/- MMECs more colonogenic and spherogenic, which was antagonized by a c-Myc inhibitor. Oleic acid the main fatty acid constituent of the HFD and TAK-875 an agonist for G protein-coupled receptor 40 (a receptor for oleic acid) as well enhanced c-Myc stabilization and MMECs proliferation. Collectively, these data suggest that HFD exerts its effect on MMECs through the stabilization of an oncoprotein, deciphering a novel mechanism whereby dietary fat promotes mammary carcinogenesis.

overall_design: Comparison between mouse mammary glands isolated from 8-week-old female Trp-53 knockout mice that had been fed with HFD (high-fat diet) or CD (control diet) for five weeks. There are three biological replicates for each condition.

first: Nilakshi

last: Kulathunga

first: Susumu

last: Kohno

first: Paing

last: Linn

first: Yuuki

last: Nishimoto

first: Hayato

last: Muranaka

first: Chiaki

last: Takahashi


title: Genome-wide RNA-expression analysis after p53 activation in hepatocellular carcinoma

city: chengdu

first: yin

last: zhang

address: Jinniu District

institute: southwest jiaotong university

summary: In order to characterize the differentially expressed mRNAs after the p53 activation ,RNA-seq were used after the overexpression of p53 in HepG2 cells.

overall_design: Four samples of HepG2 cells were subjected to RNA-seq in two biological replicates.The HepG2 cells were treated with 1µg/ml doxorubicin for 24 hours to induce the expression of p53. The experimental group(dox-treated HepG2：HepG2_24h_rep1 and HepG2_24h_rep2) and control group(untreated HepG2: HepG2_0h_rep1 and HepG2_0h_rep2) were subjected to RNA-seq to identify the p53-regulated mRNAs.

first: Zhi

middle: Y

last: Guo

first: Ya

middle: L

last: Yang

first: Wen

last: Liu


title: microRNA profiling of RBC transcriptome during ex vivo storage

city: Durham

first: Jen-Tsan

last: Chi

state: NC

address: 101 Science Drive, DUMC 3382

department: Molecular Genetics and Microbiology

institute: Duke University

summary: Mature human red blood cells (RBCs) are terminally differentiated anuclear cells. While initially thought to lack any nucleic acids, human RBCs are found to contain abundant and diverse species of RNA transcripts with functional relevance. Given the absence of novel transcription, RBCs may provide an interesting cellular context to study RNA metabolism over time. One clinically relevant context is the ex vivo storage of RBCs in blood banks for use in blood transfusion. Some studies have indicated that the transfusion of “old” or aged stored RBCs may be associated with adverse outcomes due to various storage changes termed “storage lesions”. However, other studies do not support these effects, and much remains unknown about the relevant changes associated with RBC storage. Here, we employed the NanoString nCounter assay for global miRNA profiling to comprehensively define the miRNA turnover during ex vivo RBC storage. This profiling demonstrates that the abundance of most RBC miRNAs did not change significantly during the 42 days of refrigerated storage, indicating extremely long decay half-lives. Unexpectedly, miR-720, a cleavage product of tRNAThr, increased dramatically in the first two weeks and persisted during storage. Furthermore, we present evidence for a role of angiogenin in tRNA cleavage to generate miR-720 during RBC storage. The dramatic increase in miR-720 may serve as a new characteristic for storage lesion and may be used to monitor transfused RBCs in clinical patients and athletes performing blood doping.

overall_design: RBC were processed as in the rountine blood bank practice, the RBC RNA were then purifed and interrogated by Nanostring microRNA v2

first: Wen-Hsuan

first: Jennifer

last: Doss

first: Katelyn

last: Walzer

first: Shannon

middle: M

last: McNulty

first: John

last: Roback


title: Transcriptional and functional analysis of CD1c+ human dendritic cells identifies a CD163+ subset priming CD8+CD103+ T cells [Breast_iLN]

first: Kristine

last: Vaivode

summary: Dendritic cells (DC) are antigen presenting cells controlling T cell activation. In human, the diversity, ontogeny and functional capabilities of DC subsets are not fully understood. Here, we identified circulating CD88-CD1c+CD163+ DC (termed as DC3) as an immediate precursor of inflammatory CD88-CD14+CD1c+CD163+FcεRI+ DC. DC3 develop via a specific pathway activated by GM-CSF, independent from the cDC-restricted (CDP) and monocyte-restricted (cMoP) progenitors. As classical DC, but unlike monocytes, DC3 drove the activation of naïve T cells. In vitro, DC3 displayed a distinctive ability to prime CD8+ T cells expressing a tissue-homing signature and the epithelial homing alpha-E integrin (CD103) through transforming growth factor-b (TGF-β) signaling. In vivo, DC3 infiltrated luminal breast cancer primary tumors and DC3 infiltration correlated positively with CD8+CD103+CD69+ tissue-resident memory T cells. Altogether, these findings define DC3 as a lineage of inflammatory DC endowed with a strong potential to regulate tumor immunity.

overall_design: Tumor-draining lymph nodes (tdLN) and primary tumors were collected and processed within few hours after the primary surgery. CD11c+HLADR+CD14-CD1a-CD206-CD1c+,  CD11c+HLADR+CD1a-CD1c-CD14+ and CD11c+HLADR+CD1a-CD1c+CD14+ cells were sorted in triplicates with up to 1000 cells per sample.

first: Pierre

last: Bourdely

first: Giorgio

last: Anselmi

first: Rodrigo

middle: N

last: Ramos

first: Yoann

last: Missolo-Kousou

first: Sofia

last: Hidalgo

first: Jimena

last: Tosselo

first: Nicolas

last: Nunez

first: Wilfrid

last: Richer

first: Anne

last: Vincent-Salomon

first: Alka

last: Saxena

first: Kristie

last: Wood

first: Alvaro

last: Lladser

first: Eliane

last: Piaggio

first: Julie

last: Helft

last: Guermonprez


title: Expression of RUNX1-ETO Rapidly Alters the Chromatin Landscape and Growth of Early Human Myeloid Precursor Cells (ATAC-Seq)

first: Peter

last: Keane

overall_design: ATAC-Seq of human embryonic stem cells that have undergone hematopoietic differentiation. These cells contain a doxycycline-inducible RUNX1-ETO construct. Cells were treated with 0, 3, 5 or 10 ng/ml of dox prior to sequencing.

first: Monica

last: Nafria

first: Elizabeth

last: Ng

first: Edouard

last: Stanley

first: Andrew

last: Elefanty

first: Constanze

last: Bonifer


title: Transcriptome analysis of Drosophila whole larval lymph glands

city: Montréal

first: Marc

last: Therrien

state: Québec

address: 2950, Chemin de Polytechnique

institute: Institute for Research in Immunology and Cancer

summary: The balance between hematopoietic progenitors and differentiated hemocytes is finely tuned during development. In the larval hematopoietic organ of Drosophila, called the lymph gland, the receptor tyrosine kinase Pvr signals from differentiated cells to maintain a pool of undifferentiated progenitors. However, little is known about the processes that support Pvr function. The small GTPase Ral is involved in the regulation of several membrane trafficking events. Drosophila has a single Ral protein, Rala, which has been implicated in the development of various tissues. Here, we investigated the involvement of Rala in the larval fly hematopoietic system. We discovered that the loss of Rala activity phenocopies Pvr loss of function by promoting hemocyte progenitor differentiation. Moreover, using epistasis analysis, we found that the guanine exchange factor RalGPS lies upstream of Rala in this event, whereas the exocyst and Rab11 are acting downstream. Strikingly, the loss of Rala activity leads to a considerable accumulation of Pvr at the plasma membrane, hence suggesting a trafficking defect and reduced Pvr function. Consistent with this hypothesis, Rala loss of function phenotype in the lymph gland is fully suppressed by constitutive STAT activity, which normally mediates Pvr function in the lymph gland. Together, our findings unravel a novel RalGPS-Rala-exocyst-Rab11 axis for the maintenance of lymph gland homeostasis through Pvr.

overall_design: RNA-seq libraries were prepared from 200 ng of RNA extracted from third instar larval lymph glands (wild-type tissues, six biological replicates).

first: Caroline

last: Baril

first: Gwenaëlle

last: Gavory


title: Expression of RUNX1-ETO Rapidly Alters the Chromatin Landscape and Growth of Early Human Myeloid Precursor Cells (ChIP-Seq)

overall_design: ChIP-Seq of human embryonic stem cells that have undergone hematopoietic differentiation. These cells contain a doxycycline-inducible RUNX1-ETO construct. Cells were treated with 0 or 5 ng/ml of dox prior to sequencing.


title: Expression of RUNX1-ETO Rapidly Alters the Chromatin Landscape and Growth of Early Human Myeloid Precursor Cells (scRNA-Seq)

overall_design: Chromium 10x genomics - single cell RNA-seq of embryonic stem cells that have undergone hematopoietic differentiation. These cells contain a doxycycline-inducible RUNX1-ETO construct. Cells were treated with 0 of 5 ng/ml of Dox prior to sequencing.


title: Prediabetes Induced by a Single Autoimmune B cell Clone [RNA-seq]

first: Manching

last: Ku

address: Mathildenstrasse 1

first: Eugene

last: Ke

first: Oktay

last: Kirak


title: Forkhead box Q1-regulated transcriptome in human breast cancer cells

city: Pittsburgh

first: Shivendra

middle: V

last: Singh

state: PA

address: 5117 Centre Avenue UPMC HCC Research Pavilion Suite 2.32A

department: Pharmacology and Chemical Biology

institute: University of Pittsburgh

summary: RNA-seq was performed to identify novel mechanistic targets of FoxQ1 in human breast cancer cells using empty vector-transfected control (EV) and FoxQ1 overexpressing SUM159 cells. We found that interleukin-1α and interleukin-8 are direct transcriptional targets of FoxQ1.

overall_design: Examination of altered genes expression in empty vector-transfected control (EV) and FoxQ1 overexpressing SUM159 cells (n=3 for each)


title: Expression of RUNX1-ETO Rapidly Alters the Chromatin Landscape and Growth of Early Human Myeloid Precursor Cells

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

overall_design: Refer to individual Series


title: Single-cell omics reveal human blood mononuclear CD14+ and/or CD1c+ cell heterogeneity

first: Kristine

last: Vaivode

summary: Dendritic cells (DC) are antigen presenting cells controlling T cell activation. In human, the diversity, ontogeny and functional capabilities of DC subsets are not fully understood. Here, we identified circulating CD88-CD1c+CD163+ DC (termed as DC3) as an immediate precursor of inflammatory CD88-CD14+CD1c+CD163+FcεRI+ DC. DC3 develop via a specific pathway, independent from the cDC-restricted (CDP) and monocyte-restricted (cMoP) progenitors, and are activated by GM-CSF. As classical DC, but unlike monocytes, DC3 drove the activation of naïve T cells. In vitro, DC3 displayed a distinctive ability to prime CD8+ T cells expressing a tissue-homing signature and the epithelial homing alpha-E integrin (CD103) through transforming growth factor-b (TGF-β) signaling. In vivo, DC3 infiltrated luminal breast cancer primary tumors and DC3 infiltration correlated positively with CD8+CD103+CD69+ tissue-resident memory T cells. Altogether, these findings define DC3 as a lineage of inflammatory DC endowed with a strong potential to regulate tumor immunity.

overall_design: Single cell RNAseq (scRNAseq) of human peripheral blood dendritic cells and monocytes. 3 healthy donors were equally pooled.

first: Pierre

last: Bourdely

first: Giorgio

last: Anselmi

first: Rodrigo

last: Ramos

first: Yoann

last: Missolo-Kousou

first: Sofia

last: Hidalgo

first: Jimena

last: Tosselo

first: Nicolas

last: Nunez

first: Wilfrid

last: Richer

first: Anne

last: Vincent-Salomon

first: Alka

last: Saxena

first: Kristie

last: Wood

last: Lladser


title: Transcriptional comparison of in vitro generated human dendritic cells and peripheral blood circulating dendritic cells

summary: Classical dendritic cells (cDCs) are rare sentinel cells specialized in the regulation of adaptive immunity. Modelling cDC development is both crucial to study cDCs and harness their potential in immunotherapy. Here we present a novel in vitro cDC differentiation protocol using cord blood CD34+ hematopoietic stem and progenitor cells (HSPCs) co-cultured with bone marrow-derived murine mesenchymal cell line (MS5) engineered to co-express human FLT3L, SCF and CXCL12 (MS5_FS12) or MS5 engineered to express human GM-CSF (MS5_GM).

overall_design: In vitro generated CD1c+CD14+, CD14+CD16+, CD1c-CD14+, Clec9A+CD141+ and CD1c+CD206+ cells were collected at day 14. All cell types were analyzed in triplicates with up to 100 cells per sample.

first: Alvaro

first: Eliane

last: Piaggio

first: Julie

last: Helft

last: Guermonprez


title: Single-cell omics reveal human GM-CSF-dependent mononuclear phagocyte subsets in humanized mice

overall_design: 3 independent immunodeficient NSG mice were injected intravenously with B16 producing human GM-CSF. Lung metastasis bearing mice were engrafted with 3 independent human PBMCs. Human CD45+ cells were isolated from metastatic mouse lungs. Sorted cells from each mouse were pooled together and CD1c+ and CD14+ cells were mixed at 80:20 ratio.


title: Transcriptome of CD4+ T cells from mice conditionally lacking YAP1 versus WT in different synthetic micromechanical environments

city: Los Angeles

first: Manish

middle: J

last: Butte

state: CA

address: 10833 Le Conte Ave, MDCC Building Room 12-430

institute: UCLA

summary: Upon immunogenic challenge, lymph nodes become mechanically stiff as immune cells activate and proliferate within their encapsulated environments, and with resolution, they reestablish a soft, baseline state. Here we show that sensing these mechanical changes in the microenvironment require the mechanosensor YAP. YAP is induced upon activation and suppresses metabolic reprogramming of effector T cells. Unlike in other cell types where YAP promotes proliferation, YAP in T cells suppresses proliferation in a stiffness-dependent manner by directly restricting the translocation of NFAT1 into the nucleus. YAP slows T-cell responses in systemic viral infections and retards effector T cells in autoimmune diabetes. Our work reveals a paradigm whereby tissue mechanics fine-tune adaptive immune responses in health and disease.

overall_design: T-cell mRNA profiles of adult YAP fl/fl CD4-Cre-negative (WT) and YAP1 fl/fl CD4-Cre-positive  (YAPcKO) mice

first: Kevn

last: Meng


title: Genome-wide analysis of gene expression in EBV(+) GC cell lines [RNA-seq]

city: Chiba

first: Masaki

last: Fukuyo

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

department: Department of Molecular Oncology

institute: Chiba University

summary: We analysed gene expression in EBV(+) GC cell lines to elucidate their contribution to tumorigenesis by performing RNA-seq. Besides, we performed RNA-seq in normal gastric epithelial cells before and after EBV infection to elucidate expression changes after EBV infection.

overall_design: Examination of gene expression in three EBV(+) gastric cancer cells and normal gastric epithelial cells before and after EBV infection.

first: Atsushi

last: Okabe

last: Kaneda


title: Transcriptome profiling of organoids from the human and murine gastrointestinal tract

city: Wuerzburg

first: Ozge

last: Kayisoglu

address: Josef-Schneider-Str. 2/D15

institute: Research Center for Infectious Diseases (ZINF)

summary: The epithelial layer of the gastrointestinal tract is the body’s first line of defense against gut pathogens. However, our current understanding of the innate immune response of the epithelial layer is limited. For this study, we used gastrointestinal organoids which have the advantage of being primary, non-transformed epithelium that retains organ-specific characteristics in culture, and also that they lack any confounding immune cells. We systematically profiled the transcriptomes of gastrointestinal epithelial cells using a newly generated biobank of human and murine GI organoids grown from tissue-resident stem cells, providing an atlas of gene expression along the GI tract of both species. RNA sequencing of all lines confirmed the preservation of tissue identity, and in addition revealed extensive organization of innate immune signaling components along the cephalocaudal axis, endowing a specific innate immune profile to each segment.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We generated a biobank of 18 human, 18 adult murine organoid lines, comprised of 3 lines each for the individual gastrointestinal segments of corpus, pylorus, duodenum, jejunum, ileum and colon. Additionally, organoids were generated from E16 embryonic mice and 2 organoid lines generated from embryonic stomach and 3 lines generated from proximal intestine.

first: O

first: F

last: Weiss

first: C

last: Niklas

first: N

last: Wallaschek

first: I

last: Pierotti

first: M

last: Pompaiah

middle: T

last: Germer

first: A

last: Wiegering

first: B

last: Bartfeld


title: Functional transcriptomics reveal distinct combat strategies between lineages of wood-degrading fungi with redundant wood decay mechanisms

status: Public on May 22 2020

city: saint paul

first: Jonathan

last: Schilling

state: minnesota

address: 2004 folwell ave

institute: University of Minnesota

summary: Wood-degrading fungi vary in their strategies for deconstructing wood, and their competitive successes shape the rate and fate of  carbon released from wood, Earth’s largest pool of aboveground terrestrial carbon. In this study, one-on-one interspecific  interactions between two model brown rot (carbohydrate-selective) fungi, Gloeophyllum trabeum and Rhodonia (Postia) placenta,  were studied on wood wafers where a clearly resolved interaction zone (IZ) could be generated, reproducibly. Comparative  RNAseq and proteomics between the IZ and non-interacting hyphae of each species identified combative strategies for each fungus.  Glycoside hydrolases were a relatively smaller portion of the interaction secretome compared to non-interacting hyphae. The  interaction zone showed higher pectinase specific activity than all other sampling locations, and higher laminarinase specific  activity (branched β‐glucan proxy) was seen in the IZ secretome relative to equivalent hyphae in single‐species cultures. Our  efforts also identified two distinct competitive strategies in these two fungi with a shared nutritional mode (brown rot) but  polyphyletic ancestral lineages. Gloeophyllum trabeum (Gloeophyllum clade) employed secondary metabolite (SM) synthesis in  response to a competitor, as shown by the upregulation of several SM-synthesizing genes in the interaction. R. placenta (Antrodia  clade) instead upregulated a larger variety of uncharacterized oxidoreductases in interacting hyphae, suggesting that an  oxidative burst may be a response to competitors in this fungus. Both species produced several hypothetical proteins exclusively  in the interaction zone, leaving abundant unknowns on the battlefield. This work supports the existence of multiple interaction  strategies among brown rot fungi and highlights the functional diversity among wood decay fungi.

sample_organism:
Rhodonia placenta
Gloeophyllum trabeum

platform_organism:
Rhodonia placenta
Gloeophyllum trabeum

overall_design: We sequenced mRNA from two brown rot fungi to compare the gene regulations as they combat. Two species were used to colonize a wood wafer from two ends towards middle. Then, 3 wood sections on wood wafer were sampled for RNA extraction, representing two sections colonized by two individual species, respectively, and the interactive zoom where they are combating. Two bioreplicates were included.

first: Gerald

last: Presley

first: Jiwei

last: Zhang

middle: S


title: Genome-wide analysis of histone modification alteration in EBV(+) GC cell lines (ChIP-Seq).

summary: We analysed epigenetic status in EBV(+) GC cell lines to elucidate their contribution to tumorigenesis by performing ChIP-seq on H3K4me3, H3K4me1, H3K27ac, H3K27me3 and H3K9me3.

overall_design: Examination of 5 different histone modifications in EBV(+) gastric cancer cells.


title: Transcriptome analysis of wild type, sbp1 and scd6 deletion Saccharomyces cerevisiae strains upon RNA granule inducing sodium azide stress

city: Bangalore

first: Purusharth

middle: I

last: Rajyaguru

state: Karnataka

address: Lab No FE-16, Dept. of Biochemistry, IISc

country: India

institute: Indian Institute of Science

summary: We report here transcriptome wide changes in S. cerevisiae in response to sodium azide treatment. The observed changes are consistent with those observed in response to oxidative stress such as H2O2. We also identify transcripts that are specifically affected by Scd6 and/or Sbp1. Some of these mRNAs could be direct targets of Scd6/Sbp1.

overall_design: With an aim to identify transcriptome wide changes in wild type, Δscd6 and Δsbp1 cell of S. cerevisiae in response to sodium azide stress, RNA seq experiments were carried out for normally growing cells and sodium azide treated cells. Two replicates were used for each sample. Validation of RNA seq results using Real time quantitative PCR (RT-qPCR) indicated that the results obtained by RNA sequencing were reproducible and the extent of changes were comparable.

first: Mani

last: Garg


title: Whole Transcriptome Changes in Arabidopsis Seedlings After 1 h of NAE 18:3 Treatment

city: Denton

first: Ashley

middle: Elisabeth

last: Cannon

state: TX

address: 1155 Union Circle #305220

department: Biological Sciences

institute: The University of North Texas

summary:
Purpose: The purpose of this experiment was to identify the gene expression changes in Arabidopsis thaliana seedlings induced by 1 h of 100 µM NAE 18:3 treatment.
Methods: mRNA profiles of 4-day-old Arabidopsis thaliana seedling were generated by deep sequencing, in triplicate, using Illumina HiSeq. The sequence reads that passed quality filters were analyzed at the transcript level using TopHat followed by Cufflinks. qRT–PCR validation was performed using SYBR Green assays

overall_design: mRNA profiles of 4-day old Arabidopsis seedlings treated with DMSO or 100 µM NAE 18:3 for 1 h were generated by deep sequencing, in triplicate, using Illumina HiSeq.

first: Chengshi

last: Yan

first: Bibi

last: Khan

first: Elison

last: Blacaflor

first: Rajeev

middle: K

last: Azad

middle: E

first: Kent

middle: D

last: Chapman


title: Genome-wide analysis of histone modification alteration in EBV(+) GC cell lines (4C-Seq).

first: Masaki

last: Fukuyo

first: Atsushi

last: Okabe

last: Kaneda


title: Epigenetic Targeting of Mcl-1 is Synthetically Lethal with Bcl-xL/Bcl-2 Inhibition in Model Systems of Glioblastoma

city: New York

first: Markus

last: Siegelin

state: New York

department: Pathology and Cell Biology

institute: Columbia University

summary: Glioblastomas harbor a super-enhancer at the MCL1 locus, which translates to increased MCL1 levels as compared to normal brain tissue. While suppression of Mcl-1 alone did not yield in significant apoptosis induction, combined inhibition of Bcl-xL/Bcl-2 along with Mcl-1 led to strong cell killing and reduction of tumor growth in patient-derived xenograft models in vivo.

overall_design: Compared Mcl1 level between U87 cells treated with DMSO or THZ1

first: Trang

last: Nguyen


title: Methylome signature of bronchoalveolar cells from Multiple Sclerosis patients in relation to smoking

first: Mikael

last: Ringh

state: Choose state (US & Canada)

address: Medical Epigenetics, CMM L8:00, Karolinska University Hospital Solna

institute: Karolinska Institutet

summary:
Background  Despite compelling evidence that cigarette smoking impacts the risk of developing Multiple Sclerosis  (MS), little is known about smoking-associated changes in the primary exposed cells in the lung of  patients. We aimed to examine molecular changes occurring in pulmonary immune cells from MS  patients in relation to smoking and in comparison to healthy controls (HC).  Methods  We profiled genome-wide DNA methylation (5mC) and hydroxymethylation (5hmC) in bronchoalveolar  lavage (BAL) cells collected from female MS patients (9 smokers, 8 non-smokers) and healthy  volunteers (10 smokers, 12 non-smokers), using Illumina Infinium EPIC arrays on conventional (BS) and  oxidative (oxBS) bisulfite DNA. We profiled gene expression using RNA-sequencing in non-smoker MS  patients and controls.  Findings  The most prominent changes were found in relation to smoking, with 1376 BS-differentially  methylated positions (DMPs), 131 5mC-DMPs and 4 5hmC-DMP (adjusted P < 0.05) differing between  MS smokers and non-smokers. Approximately 30% of the affected genes overlapped with smoking-associated changes in HC, leading to a strong common smoking signature in both MS and HC after gene  ontology analysis. Smoking in MS patients resulted in additional discrete changes related to neuronal  processes. To further explore MS-specific signature, we performed RNA sequencing in BAL cells from  non-smoker MS patients and controls. Overall, methylome and transcriptome analyses in non-smokers  suggest that BAL cells from MS patients display very subtle but concordant changes associated to genes  connected to reduced transcriptional/translational processes and enhanced cellular adhesion and  migration, further corroborating findings from animal studies.  Interpretation  Our study provides new insights into the impact of smoking on lung inflammation in the  immunopathogenesis of MS.
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overall_design: 39 bronchoalveolar lavage samples (mainly alveolar macrophages) from healthy (H) individuals and multiple sclerosis (MS) patients; smokers (S) and nonsmokers (NS). Includes both BS-treated and oxBS-treated samples for 5mC and 5hmC interrogation.

first: Lara

last: Kular


title: Resistance to PD1 blockade in the absence of metalloprotease-mediated LAG3 shedding

first: Anthony

middle: Richard

last: Cillo

address: The Assembly, Room 4070C Bay 10, 5051 Centre Ave

department: Immunology

summary: Mechanisms of resistance to cancer immunotherapy remain poorly understood. Lymphocyte Activation Gene-3 (LAG3) signaling is regulated by A Disintegrin And Metalloprotease-10 (ADAM10) and ADAM17-mediated cell surface shedding. We developed and utilized mutant mice expressing a metalloprotease-resistance version of LAG3 that can be selectively expressed in T cell subsets. We sorted live T cells from tumors of mice bearing MC38 tumors following 3  treatments with either anti-PD1 or IgG control, and performed single-cell RNAseq using 10X 3' v2 reagents.

overall_design: Investigation of transcription profiles of T cells from tumors of wild-type or mutant M38 bearing mice folllowing treatment with anti-PD1 or isotype

first: Lawrence

middle: P

last: Andrews

first: Dario

middle: A

last: Vignali


title: ALKBH1 deficiency leads to loss of homeostasis in human diploid somatic cells

city: Beijing

first: jiang

middle: xiao

last: yu

address: 15 Datun Road Chaoyang District

institute: institute of zoology, CAS

summary: DNA N6-methyladenosine (6mA) in eukaryotic genomes has recently been observed in diverse species. 6mA has been reported to associate with multiple physiological processes including embryonic development and tumorigenesis, and ALKBH1 is a primary 6mA demethylase in mouse and human cells. To research the roles of 6mA and its putative regulators such as putative ALKBH1 in the homeostatic maintenance of human stem cells and their differentiated derivatives, We generated ALKBH1-deficient human embryonic stem cells (hESCs) via CRISPR/Cas9-mediated non-homologous end joining (NHEJ). We next differentiated ALKBH1+/+ and ALKBH1-/- hESCs into human mesenchymal stem cells (hMSCs) and vascular smooth muscle cells (hVSMCs). Early-onset growth arrest of ALKBH1-/- hMSCs was observed, and increased apoptosis and enhanced migration ability were observed in ALKBH1-/- hVSMCs. However, liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) analysis revealed no change in 6mA levels between ALKBH1+/+ and ALKBH1-/- hESCs, between ALKBH1+/+ and ALKBH1-/- hMSCs, and between ALKBH1+/+ and ALKBH1-/- hVSMCs, respectively. These data demonstrate that depletion of ALKBH1 exerts minimal impact on 6mA levels in hESCs and their differentiated derivatives and that ALKBH1 regulates the homeostasis of hMSCs and hVSMCs possibly in a DNA 6mA-independent manner.

overall_design: RNA/WGS sequencing of ALKBH1+/+ and  ALKBH1-/-  hMSCs.

first: Guanghui

last: Liu


title: RNA-seq of AKP organoids over different stages of differentiation

city: Sabadell

first: Antoni

last: Berenguer-LLergo

state: Barcelona

address: Parc del Taulí, 1

department: A8G2 Group - Rheumatology Service

institute: Parc Taulí Research and Innovation Institute (I3PT)

summary: Transcriptomic profiling of mouse tumoroids at early (2 days of Apc restoration) versus late stage differentiation (7 days of Apc restoration)

overall_design: AKP organoids were cultured under control condions (Apc OFF) or were induced to differentiate during two days (2 days Apc restoration) or seven days (7 days Apc restoration). Cells from the three different conditions were collected and RNA was extracted for sequencing.

first: J

last: Stanisavljevic

first: E

last: Batlle


title: The microRNA miR-22 represses T helper 17 cell pathogenicity by targeting PTEN-regulated pathways

city: Shenzhen

first: Zhijun

last: Han

state: Guangdong

address: No 1088,xueyuan Rd., Nanshan District

institute: Southern University of Science and Technology

summary: Multiple sclerosis is a chronic autoimmune disease driven by pathogenic Th17 cells. Here, we dissected the role of miR-22 in pathogenic Th17 cells by autoantigen-specific disease models. We first showed that miR-22 was upregulated in peripheral lymphoid organs and spinal cords of mice developed autoimmune encephalomyelitis. Although miR-22 was upregulated in multiple helper T cell subsets, it was dispensable for T helper cell differentiation in vitro. While miR-22-/- mice exhibited milder symptoms of disease in an active EAE model, adoptive transfer of miR-22-/- 2D2 Th17 cells into naive recipient mice promoted higher disease incidence and severity compared to mice transferred with control 2D2 Th17 cells. Global transcriptional analysis of miR-22-deficient pathogenic Th17 cells revealed upregulated genes in phosphatase and tensin homologue (PTEN)-mediated pathways, and Pten was further identified as one of its potential targets. Therefore, we identified that Th17 cell intrinsic-miR-22 could protect mice from autoimmunity by targeting PTEN-regulated pathways.

overall_design: RNA-seq for Mir-22 wild-type and knock-out in Th17 (23) cells with 3 replicates.

first: Li

last: Wang

first: Rong

last: Qiu

first: Zhaoyang

last: Zhang

first: Chao

last: Yao

first: Guojun

last: Hou

first: Dai

last: Dai

first: Wenfei

last: Jin

first: Yuanjia

last: Tang

first: Xiang

last: Yu

last: Shen


title: A cancer stem cell hierarchy based on differential ribosomal RNA and protein synthesis capacities [POLR1A]

summary: Ribosomal RNA (rRNA) transcription and protein synthesis are heterogeneously regulated in colorectal tumors and are gradually shut down during cell differentiation. Cancer stem cell hierarchy and tumor growth is defined by a tumor cell population that displays elevated rRNA and protein synthesis.

overall_design: Tumor cells expressing different levels of POLR1A were isolated from subcutaneous patient derived xenografts

first: Clara

last: Morral

first: Eduard


title: A cancer stem cell hierarchy based on differential ribosomal RNA and protein synthesis capacities [EPHB2]

overall_design: Tumor cells expressing different levels of EPHB2 were isolated from fresh surgically resected CRC samples


title: Sulfoxidation modification of NON-RIPENING (NOR) transcription factor is involved in the regulation of fruit ripening in tomato

city: Guangzhou

first: Jiang

last: Guoxiang

address: No.723,Xingke Road

institute: South China Botanical Garden, Chinese Academy of Sciences

summary:
Transcription factors (TFs) are important regulators of plant growth and development and responses to stresses. TFs themselves are also susceptible to multiple post-translational modifications (PTMs). Relatively, redox-mediated PTM of TFs in plants is not well elucidated. Here, we found that NON-RIPENING (NOR), a master TF regulating tomato fruit ripening, is a target of SlMsrE4 or SlMsrB2, the methionine sulfoxide reductase A and B in tomato, respectively. Methionine oxidation in NOR, i.e. sulfoxidation, or mimicking sulfoxidation by mutating Met138 to glutamine, leads to the decreased DNA-binding capacity and transcriptional regulatory activity in vitro. On the other hand, SlMsrE4 and SlMsrB2 can partially repair oxidized-NOR and restore its DNA-binding capacity. Genetic transformation of the nor mutant with NOR genomic DNA almost completely rescues the ripening phenotype. However, transformation of nor with NOR-M138Q, the mimicked methionine sulfoxidation, inhibits the restore of fruit ripening phenotype, and this is associated with the decreased DNA-binding and transcriptional activation of numerous ripening-related genes. Taken together, these findings uncover a novel mechanism by which Msr-mediated redox modification of NOR regulates the expression of ripening-related genes, thereby influencing tomato fruit ripening. To our knowledge, this is the first report that redox modification of TF regulates fruit ripening.
nor is a NOR mutant, the phenotype is obstructed by maturity; NOR-12 is a rotational NOR in NOR mutant, the phenotype is a mature inhibition phenotype that basically restores nor mutant; Nor-18 is a rotation of NOR-M138Q in nor mutant, phenotype with the effect of restoring maturity, but the recovery efficiency is lower than the swing NOR.

overall_design: Tomato fruits of nor, NOR-12 and NOR-M138Q-18 lines at 55 dpa  were generated by deep sequencing, in triplicate, using  Illumina HiSeqTM 2000 .

first: G

last: Jiang

last: Zeng

first: Z

last: Li

last: He

first: H

last: Yan

first: Y

first: X

last: Duan


title: Auxin treatment of grapevine (Vitis vinifera L.) berries delays ripening onset by inhibiting cell expansion

city: Verona

first: Silvia

last: Dal Santo

address: Strada Le Grazie, 15

department: Department of Biotechnology

institute: University of Verona

summary: Auxin treatment of grape (Vitis vinifera L.) berries delays ripening by inducing changes in gene expression and cell wall metabolism and could combat some deleterious climate change effects. Auxins are inhibitors of grape berry ripening and their application may be useful to delay harvest to counter effects of climate change. However, little is known about how this delay occurs. The expression of 1892 genes was significantly changed compared to the control during a 48 h time-course where the auxin 1-naphthaleneacetic acid (NAA) was applied to pre-veraison grape berries. Principal component analysis showed that the control and auxin-treated samples were most different at 3 h post-treatment when approximately three times more genes were induced than repressed by NAA. There was considerable cross-talk between hormone pathways, particularly between those of auxin and ethylene. Decreased expression of genes encoding putative cell wall catabolic enzymes (including those involved with pectin) and increased expression of putative cellulose synthases indicated that auxins may preserve cell wall structure. This was confirmed by immunochemical labelling of berry sections using antibodies that detect homogalacturonan (LM19) and methyl-esterified homogalacturonan (LM20) and by labelling with the CMB3a cellulose-binding module. Comparison of the auxin-induced changes in gene expression with the pattern of these genes during berry ripening showed that the effect on transcription is a mix of changes that may specifically alter the progress of berry development in a targeted manner and others that could be considered as non-specific changes. Several lines of evidence suggest that cell wall changes and associated berry softening are the first steps in ripening and that delaying cell expansion can delay ripening providing a possible mechanism for the observed auxin effects.

overall_design: From a vineyard in the Adelaide Hills (Hahndorf, South Australia, -35.018223, 138.838220) 40 bunches at the pre-veraison stage were harvested from ten vines (Vitis vinifera L. cv. Shiraz).  Fruit was harvested on 21 Dec 2009, 35 days before veraison. Bunches were harvested between 09:00 and 10:00 and rapidly transported to the lab for use. Randomly picked berries from the sampled bunches were sterilized in 0.1% (v/v) Chemwet 1000 (Nufarm, Laverton, VIC, Australia) containing half a Milton antibacterial tablet L-1 (Milton Australia, Laverton North, Victoria) for 10 min and washed three times with sterile nanopure water. A thin transverse slice of each berry was cut off from the brush area to facilitate compound absorption. Twenty berries were then placed on each petri dish containing 25 mL of Gamborg media, 0.025% (w/v) casein hydrosylate, 0.8% (w/v) agar, pH 5.7-5.8 alone (‘Control’) or also containing 0.5uM NAA (Gibo BRL Life Technologies, Grand Island, NJ, ‘NAA-treated’). Each plate constituted a replicate and three replicates per treatment per time point were used. Berries were placed on the plates with the cut surface facing the agar, the plates were sealed with Parafilm and kept in the dark at room temperature. Berries were harvested at 3, 6, 12, 24, 48h after placement on the media, wiped to remove agar, deseeded and frozen in liquid nitrogen.

first: Matthew

middle: R

last: Tucker

first: Hwei-Ting

last: Tan

first: Crista

last: Burbidge

first: Marianna

last: Fasoli

first: Christine

last: Böttcher

first: Paul

last: Boss

first: Mario

last: Pezzotti

first: Christopher

last: Davies


title: Targeted RNA Sequencing of a panel of ovarian cancer cell lines

status: Public on May 21 2020

city: Newcastle upon Tyne

first: Sweta

last: Sharma Saha

address: Framlington Place

department: Translational and Clinical Research Institute

institute: Newcastle University

summary: Assess the baseline expression of the genes in the Oncology Biomarker Panel across the panel of ovarian and cervical cancer cell lines. This data will then be compared to the sensitivity of the cell lines to DDR inhibitors. The expression data will be correlated with the sensitivity of the cell lines to see whether determinants of sensitivity described  in the literature translate. A hierarchy of genes will be determined. It is expected that the cells that are more sensitive to DDR inhibitors will have decreased expression of the genes known to be determinants of sensitivity.

overall_design: mRNA profile of 2,567 genes in the HTG EdgeSeq Oncology Biomarker Panel

first: Alice

last: Bradbury

first: Yvette

last: Drew

first: Nicola

last: Curtin

last: Saha


title: HIF-1a and HIF-2a differently regulate tumour development, metabolism and inflammation of clear cell renal cell carcinoma in mice

city: Freiburg

first: Patrick

last: Metzger

address: Breisacher Str. 153

department: Institute for Medical Bioinformatics and Systems Medicine

institute: University Hospital Freiburg

summary: Mutational inactivation of VHL is the earliest genetic event in the majority of clear cell renal cell carcinomas (ccRCC), leading to accumulation of the HIF-1alpha and HIF-2a transcription factors. While correlative studies of human ccRCC and functional studies using human ccRCC cell lines have implicated HIF-1a as an inhibitor and HIF-2a as a promoter of aggressive tumour behaviours, their roles in tumour onset have not been functionally addressed. Using an autochthonous ccRCC model, we show genetically that Hif1a is essential for tumour formation whereas Hif2a deletion has only minor effects on tumour initiation and growth. Both HIF-1a and HIF-2a are required for the clear cell phenotype. Transcriptomic and proteomic analyses revealed that HIF-1alpha regulates glycolysis while HIF-2a regulates genes associated with lipoprotein metabolism, ribosome biogenesis and E2F and MYC transcriptional activities. HIF-2a-deficient tumours were characterised by increased antigen presentation, interferon signalling and CD8+ T cell infiltration and activation. Single copy loss of HIF1A or high levels of HIF2A mRNA expression correlated with altered immune microenvironment in human ccRCC. These studies reveal an oncogenic role of HIF-1alpha in ccRCC initiation and suggest that alterations in the balance of HIF-1alpha and HIF-2a activities can affect different aspects of ccRCC biology and disease aggressiveness.

overall_design:
Examination of mRNA of renal or tumor biopsies

Genotype definitions:
VpR: silencing of the genes Vhl, Trp53 and Rb1
VpRH1: silencing of the genes Vhl, Trp53, Rb1 and HIF1A
VpRH: silencing of the genes Vhl, Trp53, Rb1 and HIF2A

first: Rouven

last: Höfflin

first: Sabine

last: Harlander

last: Schäfer

first: Fengshen

last: Kuo

first: Désirée

last: Schönenberger

first: Mojca

last: Adlesic

first: Asin

last: Peighambari

first: Philipp

last: Seidel

first: Chia-yi

last: Chen

first: Miguel

last: Consenza-Contreras

first: Andreas

last: Jud

first: Bernd

last: Lahrmann

first: Niels

last: Grabe

first: Danijela

last: Heide

first: Franziska

last: Uhl

first: Timothy

last: Chan

first: Justus

last: Duyster

first: Robert

last: Zeiser

first: Christoph

last: Schell

first: Mathias

last: Heikenwalder

first: Oliver

last: Schilling

first: Abraham

last: Hakimi

first: Melanie

last: Boerries

first: Ian

last: Frew


title: Genome-wide DNA methylation analysis in cfDNA from pancreatic cancer patients

city: Nagoya

first: Keiko

last: Shinjo

state: Aichi

address: 65 Tsurumai, Showa-ku

department: Cancer Biology

institute: Nagoya Univ. Graduate School of Medicine

summary:
Heterogeneity in DNA methylation status may exist between primary tumors and cfDNA. We compared the genome-wide DNA methylation status between FNA sample of pancreatic tumor and cfDNA samples from the same patients. MBD-sequencing (seq) was performed in paired samples of FNA and cfDNA from two patients.
The majority of DNA methylation peaks overlapped in FNA and cfDNA samples (82.6% and 82.9% in patients #1 and #73, respectively). DNA methylation levels of each gene in FNA and cfDNA samples were highly correlated with each other (r=0.98 and 0.97 in samples 1 and 73, respectively)

overall_design: DNA methylation status was analyzed by MBD-seq in cfDNA from pancreatic cancer patients and corresponding tumor and cfDNA from normal patients.

first: Yutaka

last: Kondo


title: RNA-binding Protein ZFP36L2 Downregulates Helios Expression and Suppresses the Function of Regulatory T Cells

first: Sohei

last: Makita

state: Chiba

address: 1-8-1 inohana chuo-ku

institute: Chiba university

summary: The zinc finger protein 36-like 2, ZFP36L2, is a member of a small family of RNA-binding proteins composed by ZFP36 (also known as tristetraprolin, TTP), ZFP36L1 and ZFP36L2 in humans, with corresponding murine orthologs. These proteins bind to adenine uridine-rich element (ARE) in the 3’untranslated region of target messenger RNA and stimulate target degradation. ZFP36 functions as an anti-inflammatory modulator in murine models of inflammatory diseases by down-regulating the production of inflammatory cytokines such as tumor necrosis factor-alpha. However, how ZFP36L1 and ZFP36L2 alter the function of CD4+ T cells is not completely understood. We addressed this issue by searching for the target genes of ZFP36L2 by comprehensive transcriptome analysis. We observed that ZFP36L2 is highly expressed in naïve CD4+ T cells; however, when CD4+ T cells are stimulated with T cell receptors, ZFP36L2 expression is rapidly reduced in both humans and mice. Among CD4+ T cell populations, the expression levels of ZFP36L2 in regulatory T cells (Tregs) were lower than those in naïve or effector CD4+ T cells. RNA-sequence analysis revealed that the forced expression of ZFP36L2 decreased Ikzf2 (encoding Helios) expression in Foxp3+ Tregs and inhibited the ability of induced Tregs (iTregs). ZFP36L2 destabilized the 3’untranslated region of Ikzf2 mRNA, which contains AU-rich elements. These results indicate that ZFP36L2 reduces the expression of Ikzf2 and suppresses iTreg function, suggesting that the inhibition of ZFP36L2 in iTregs could be a therapeutic strategy for autoimmune diseases.

overall_design: Changes in mRNA expression levels by ZFP36L2 overexpression in T cells

first: Takatori

last: Hiroaki

first: Arifumi

last: Iwata

first: Hiroshi

last: Nakajima


title: Opposing functions of BRD4 isoforms in breast cancer

city: Dallas

first: Cheng-Ming

last: Chiang

state: Texas

address: 5323 Harry Hines Blvd. ND2.210H

department: Simmons Comprehensive Cancer Center

institute: UT Southwestern Medical Center

summary: Bromodomain-containing protein 4 (BRD4) is a cancer therapeutic target in many ongoing clinical trials disrupting primarily BRD4-regulated transcription programs. A critical role of BRD4 in cancer development has been reported and attributed mainly to the abundant long isoform (BRD4-L). Here we show, by isoform-specific knockdown and endogenous protein detection along with transgene expression, the less abundant BRD4 short isoform (BRD4-S) is oncogenic while BRD4-L is tumor-suppressive in breast cancer cell proliferation and migration as well as mammary tumor formation and metastasis. Through integrated RNA-seq transcriptome and genome-wide ChIP-seq and CUT&RUN association profiling, we identify Engrailed-1 (EN1) homeobox transcription factor as a key BRD4-S coregulator particularly in triple-negative breast cancer. BRD4-S and EN1 co-modulate the extracellular matrix (ECM)-associated matrisome network, including type II cystatin gene cluster, mucin 5 and cathepsin loci, via enhancer regulation of cancer-associated genes and pathways. Our work highlights the importance of targeted therapy for the oncogenic but not tumor-suppressive activity of BRD4.

overall_design: Whole-genome expression profiling by RNA-seq with BRD4 pan or isoform-specific siRNA knockdown in MCF-7 and MDA-MB-231 cells and genome-wide binding profilling of BRD4 isoforms and EN1 by ChiP-seq and CUT&RUN in MDA-MB-231 and also in its derived line (named 3f:S) ecopotically expressing three FLAG-tagged BRD4-S with or without JQ1 treatment

first: Shwu-Yuan

last: Wu

first: Ji-Eun

last: Lee

first: Kai

last: Ge


title: A cancer stem cell hierarchy based on differential ribosomal RNA and protein synthesis capacities

first: Antoni

last: Berenguer-LLergo

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

overall_design: Refer to individual Series


title: Topoisomerase 3b is essential for neuronal activity-dependent transcription, neurogenesis, and synaptic and behavioral neuroplasticity

city: Baltimore

first: Weidong

last: Wang

state: Maryland

address: 251 Bayview Blvd

institute: National Institute on Aging/NIH

summary: Topoisomerase 3b (Top3b) is the only dual-activity topoisomerase in animals that can change topology for both DNA and RNA, and facilitate transcription on DNA and translation on mRNAs. Top3b mutation has been linked to schizophrenia, autism, epilepsy, and cognitive impairment. However, whether and how Top3b mutations are causal to these disorders remain unclear. Here we show that Top3b knockout mice exhibit behavioral phenotypes related to psychiatric disorders and cognitive impairment, including increased anxiety and fear, abnormal social interactions, impaired context discrimination, and defective spatial learning and memory. In addition, these mice display deficits in adult hippocampal neurogenesis and synaptic plasticity. Notably, the brains of the mutant mice exhibit impaired global neuronal activity-dependent transcription in response to fear conditioning stress, and the affected genes include many that are critical for neuronal functions and mental health. Our data suggest that Top3b is essential for normal brain function in multiple domains, and defective neuronal activity-dependent transcription may be a mechanism by which Top3b deletion causes cognitive impairment and psychiatric disorders.

overall_design: ChIP-seq and total RNA-seq of wildtype and Top3b KO mice in normal (non-fear) condition and fear condition to assay activity dependent transcription.

first: Yuyoung

last: Joo

first: Yutong

last: Xue

first: Yue

first: Ross

last: McDevitt

first: Nirnath

last: Sah

first: Simone

last: Bossi

first: Shuaikun

last: Su

first: SeungKyu

first: Aoji

last: Xie

first: Wei

last: Peng

first: Yongqing

last: Zhang

first: Yi

last: Ding

first: WaiLim

last: Ku

first: Soumita

last: Ghosh

first: Kenneth

last: Fishbein

first: Weiping

last: Shen

first: Richard

last: Spencer

first: Kevin

last: Becker

first: Keji

last: Zhao

first: Mark

last: Mattson

first: Henriette

last: van Praag

first: Alexei

last: Sharov


title: The delivery of alpha1-antitrypsin therapy through transdermal route: is this worse to explore?

city: Hannover

first: Stephan

last: Immenschuh

state: Deutschland

address: Carl-Neuberg-Str. 1

department: Institute for Transfusion Medicine and Transplant Engineering

institute: Hannover Medical School

summary: Human α1-antitrypsin (AAT) is an abundant acute phase glycoprotein performing anti-protease, anti-apoptotic and immunomodulatory functions. Purified human plasma AAT used as a specific therapy for patients with lung emphysema and panniculitis due to inherited AAT deficiency, and it is beneficial in treating of other disorders. This therapy administered intravenously although other routes of administration are tested. Herein, we examined the transdermal application of native or recombinant AAT by using epiCS®, the 3D human epidermis equivalent reconstructed from human primary epidermal keratinocytes. Topically applied AAT protein (50µl, prepared in Hank`s balance solution, HBSS) freely diffused across epidermis layers in a concentration and time-dependent manner. We concluded that within 18 hours topically added 0.2 mg AAT well penetrates the stratum corneum and can be detected inside the cytosol of keratinocytes. Importantly, treatments with AAT did not induce obvious morphological changes in keratinocyte layers. Next, we supplemented culture medium with 100µg/ml of combined bacterial lipopolysaccharide (LPS) and peptidoglycan (PNG) mixture and incubated epiCS for 18h with or without the topical application of 0.2 mg AAT. Under these conditions, LPS/PNG triggered a strongly activation of epidermis model. Even though AAT exhibited a limited capacity to neutralize the effect of LPS/PNG, it lowered expression of IL-18 and IL-8, and preserved levels of filaggrin, an important protein for maintaining the epidermal barrier integrity. Our results suggest that the transdermal route for delivering AAT is worth exploration. If successful, this approach may offer easy-to-use therapy with AAT.

overall_design: In this study, we used the 3D human epiCS reconstructed from the normal human primary epidermal keratinocytes, which resemble human epidermis containing a basement membrane, proliferating keratinocytes and a stratum corneum with an intact barrier function. Our aim was to study a free diffusion of AAT across epidermis.   epiCS were treated with various concentrations of AAT added topically or into the culture medium (basolaterally) for different time points up to 48 h. The control epiCS we treated by adding the same volume of Hank`s balance salt solution (HBSS cat nr. 14025092, ThermoFisher Scientific, Germany) as for the AAT treatments. Additionally, epiCS were cultured for 18 h in the medium containing 100µg/ml of combined bacterial lipopolysaccharide (LPS, Sigma-Aldrich, Darmstadt, Germany) and peptidoglycan (PGN, stock solution prepared in 0.1 mg/ml in sterile water and few seconds sonicated; Sigma-Aldrich) mixture with and without topical application of 0.2 mg of native or recombinant AAT. At the end of experiment, we collected culture supernatants and cells for further studies.

first: Srinu

last: Tumpara

first: Beatriz

last: Delgado

first: Bin

last: Liu

first: David

last: DeLuca

first: Elena

last: Korenbaum

first: Danny

last: Jonigk

first: Frank

last: Jugert

first: Florian

last: Wurm

first: Maria

first: Tobias

last: Welte

first: Sabina

last: Janciauskiene


title: Gene expression profiling of TNBC and OVCA cell lines in response to Azacitidine and Talazoparib

status: Public on May 20 2020

first: Michael

middle: Jonathan

last: Topper

state: MD

address: 1650 Orleans St., Suite 530

department: Oncology

institute: Johns Hopkins University

summary: Triple negative breast cancer and ovarian cancer cell lines were treated with Azacitidine, Talazoparib, or combination for a period of 10 days to assess global transcriptional response. The focus of these transcriptional studies were on the assessment of DNA repair and immune pathway alteration by the therapeutics under study with the aim of defining novel inducers of BRCAness.

overall_design: Therapeutic induced gene expression changes were assayed in human cell lines after 10 days of continuous in vitro exposure to Azacitidine, Talazoparib, or combination treatment.


title: Arsenic is more potent than cadmium or manganese in disrupting the INS-1 beta cell microRNA landscape

city: Ithica

first: Praveen

last: Sethupathy

state: NY

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

type: Non-coding RNA profiling by high throughput sequencing

summary: Diabetes is a metabolic disorder characterized by fasting hyperglycemia and impaired glucose tolerance. Laboratory and population studies have shown that inorganic arsenic (iAs) can impair these pathways. Other metals including cadmium (Cd) and manganese (Mn) have also been linked to diabetes phenotypes. MicroRNAs, short non-coding RNAs that regulate gene expression, have emerged as potential drivers of metabolic dysfunction. MicroRNAs responsive to metal exposures in vitro have also been reported in independent studies to regulate insulin secretion in vivo. We hypothesize that microRNA dysregulation may associate with and possibly contribute to insulin secretion impairment upon exposure to iAs, Cd, or Mn. We exposed insulin secreting rat insulinoma cells to non-cytotoxic concentrations of iAs (1 µM), Cd (5 µM), and Mn (25 µM) for 24 h followed by small RNA sequencing to identify dysregulated microRNAs. RNA sequencing was then performed to further investigate changes in gene expression caused by iAs exposure. While all three metals significantly inhibited glucose-stimulated insulin secretion, high-throughput sequencing revealed distinct microRNA profiles specific to each exposure. One of the most significantly upregulated microRNAs post-iAs treatment is miR-146a (~ + 2-fold), which is known to be activated by nuclear factor κB (NF-κB) signaling. Accordingly, we found by RNA-seq analysis that genes upregulated by iAs exposure are enriched in the NF-κB signaling pathway and genes down-regulated by iAs exposure are enriched in miR-146a binding sites and are involved in regulating beta cell function. Notably, iAs exposure caused a significant decrease in the expression of Camk2a, a calcium-dependent protein kinase that regulates insulin secretion, has been implicated in type 2 diabetes, and is a likely target of miR-146a. Further studies are needed to elucidate potential interactions among NF-kB, miR-146a, and Camk2a in the context of iAs exposure.

overall_design: Exposure of rat insulinoma cells to iAs, Cd, or Mn followed by small RNA sequencing (iAs, Cd, & Mn) or RNA sequencing (iAs)

first: Rowan

last: Beck

first: Matt

last: Kanke


title: Developmentally programmed tankyrase activity upregulates β-catenin and licenses progression of embryonic genome activation

city: Research Triangle Park

first: Carmen

last: Williams

state: NC

address: 111 TW Alexander Dr.

department: Reproductive & Developmental Biology Laboratory

institute: NIH/NIEHS

summary: Embryonic genome activation (EGA) is orchestrated by an intrinsic developmental program initiated during oocyte maturation with translation of stored maternal mRNAs. Here we show that tankyrase, a poly(ADP-ribosyl) polymerase that regulates β-catenin levels, undergoes programmed translation during oocyte maturation and serves an essential role in mouse EGA. Newly translated TNKS triggers proteasomal degradation of axin, reducing targeted destruction of β-catenin and promoting β-catenin-mediated transcription of target genes, including Myc. MYC mediates ribosomal RNA transcription in 2-cell embryos, supporting global protein synthesis. Suppression of tankyrase activity using knockdown or chemical inhibition causes loss of nuclear β-catenin and global reductions in transcription and histone H3 acetylation. Chromatin and transcriptional profiling indicate that development arrests prior to the mid-2-cell stage, mediated in part by reductions in β-catenin and MYC. These findings indicate that post-transcriptional regulation of tankyrase serves as a ligand-independent developmental mechanism for post-translational β-catenin activation and is required to complete EGA.

overall_design:
Examination of open chromatin regions and transcription in 2-cell embryos following inhibition of tankyrase activity relative to controls.

Grant ID: 1ZIAES102985
Funding source: The Intramural Research Program of the NIH, National Institutes of Environmental Health Sciences
Title: Environmental influence on gametes and embryos
Recipient: Carmen J. Williams

first: Andrés

last: Gambini

first: Paula

last: Stein

first: Virginia

last: Savy

first: Edward

last: Grow

first: Brian

last: Papas

first: Yingpei

last: Zhang

first: Anna

middle: C

last: Kenan

first: Elizabeth

last: Padilla-Banks

first: Bradley

last: Cairns


title: Hedgehog-regulated genes in the chick coelomic epithelium

city: Haifa

first: Thomas

last: Schultheiss

address: Efron 1

department: Faculty of Medicine

institute: Technion-Israel Institute of Technology

summary: In the experimental group, the coelomic cavity of HHStage 12-13 chick embryos was electroporated  with  a plasmid expressing PatchedDLoop2 (a dominant negative hedgehog pathway inhibitor) and GFP.  In the control group, a plasmid expressing GFP alone was  electroporated.  After 14 hours, embryos were dissociated into single cells, FACS sorted, and processed for RNAseq.

overall_design: 5 experimental and 4 controls were analyzed. These were all separate biological replicates.

first: Alaa

last: Arraf

first: Ronit

last: Yelin

first: Inbar

last: Reshef

first: Jenny

last: Schneider

first: Fanny

last: Vladimirov

middle: M


title: YY1 ChIP-seq on Patient Dirived Xenograft (PDX) material from one T-cell acute lymphoblastic leukemia (T-ALL) patient.

city: Shanghai

first: Yu

last: Liu

address: 1678 Dongfang Road, Pudong District

department: Pediatric Translational Medicine Institute

institute: Shanghai Children's Medical Center

summary: ChIP-seq experiment was carried out to characterize YY1 binding in one T-ALL PDX sample.

overall_design: YY1 ChIP-seq.

first: Shuhong

last: Shen

first: Jinghui


title: SMARCA4 Rescue Profiling

city: SEATTLE

first: John

last: Stamatoyannopoulos

state: WA

address: 2211 Elliott Avenue, 6th Floor

department: Genome Sciences

institute: Altius Institute / University of Washington