title: Targeted reprogramming of H3K27me3 resets epigenetic memory in plant paternal chromatin [mature pollen]

city: Tübingen

first: Michael

last: Borg

address: Max Planck Ring 5

department: Algal Development & Evolution

institute: Max Planck Insititue for Biology

summary: Epigenetic marks are reprogrammed in the gametes to reset genomic potential in the next generation. In most animal species, paternal chromatin is extensively reprogrammed through the global erasure of DNA methylation and the exchange of histones with protamine. Precisely how the paternal epigenome is reprogrammed in flowering plants remains unclear since sperm chromatin is not demethylated and histones are retained. Here, we show that the sperm-specific histone, H3.10, is immune to lysine 27 methylation and that its deposition in sperm contributes to the global and specific resetting of the epigenetic mark H3K27me3 by uncoupling its inheritance during DNA replication. The loss of H3K27me3 facilitates transcription of genes essential for spermatogenesis and pre-configures sperm with a chromatin state that forecasts gene expression in the next generation, revealing a global wave of epigenetic resetting that coordinates with early plant life. Thus, in contrast to the indiscriminate removal of epigenetic marks in animal sperm, plants have evolved a specific mechanism to simultaneously differentiate male gametes and reprogram the paternal epigenome.

overall_design: Gene expression profiling of WT, htr10, elf6;ref6;jmj13 and elf6;ref6;jmj13;htr10 mutant pollen.


title: Targeted reprogramming of H3K27me3 resets epigenetic memory in plant paternal chromatin [sperm - third party reanalysis]

status: Public on Mar 17 2020

country: Germany

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Epigenetic marks are reprogrammed in the gametes to reset genomic potential in the next generation. In mammals, paternal chromatin is extensively reprogrammed through the global erasure of DNA methylation and the exchange of histones with protamines1,2. Precisely how the paternal epigenome is reprogrammed in flowering plants remains unclear since DNA is not demethylated in sperm and histones are retained3,4. Here, we describe a multi-layered mechanism by which H3K27me3 is globally lost from histone-based sperm chromatin in Arabidopsis. This mechanism involves silencing of H3K27me3 ‘writers’, the activity of H3K27me3 ‘erasers’ and deposition of a sperm-specific histone, H3.105, which we show is immune to lysine 27 methylation. The loss of H3K27me3 facilitates transcription of genes essential for spermatogenesis and pre-configures sperm with a chromatin state that forecasts gene expression in the next generation. Thus, plants have evolved a specific mechanism to simultaneously differentiate male gametes and reprogram the paternal epigenome.

relation:
SubSeries of: GSE120669
Reanalysis of: GSM2700477
Reanalysis of: GSM2700478
Reanalysis of: GSM2700483
Reanalysis of: GSM2700484

sample_organism:
Arabidopsis thaliana
Homo sapiens

overall_design: Genome-wide maps of H3K27me1 and H3K27me3 in Arabidopsis htr10 mutant sperm chromatin


title: Functional and molecular heterogeneity of D2R neurons along dorsal ventral axis in the striatum

status: Public on Mar 16 2020

city: Montpellier

first: Emmanuel

last: Valjent

address: 141, rue de la cardonille

department: Neurobiology

country: France

institute: INSERM

type: Expression profiling by high throughput sequencing

summary: Action control is a key brain function determining the survival of animals in their environment. In mammals, neurons expressing dopamine D2 receptors (D2R) in the dorsal striatum (DS) and the nucleus accumbens (Acb) jointly but differentially contribute to the fine regulation of movement. However, their region-specific molecular features are presently unknown. By combining RNAseq of striatal D2R neurons and histological analyses, we identified hundreds of novel region-specific molecular markers, which may serve as tools to target selective subpopulations. As a proof of concept, we characterized the molecular identity of a subcircuit defined by Wfs1 neurons and evaluated multiple behavioral tasks after its temporally-controlled deletion of D2R. Consequently, conditional D2R knockout mice displayed a significant reduction in digging behavior and an exacerbated hyperlocomotor response to amphetamine. Thus, targeted molecular analyses reveal an unforeseen heterogeneity in D2R-expressing striatal neuronal populations, underlying specific D2R’s functional features in the control of specific motor behaviors.

overall_design: D2R-Cre mice were crossed with Ribotag-LoxP/LoxP mice to generate D2R-Cre/+:Ribotag-LoxP/+ mice that express the hemagglutinin (HA) epitope fused to the ribosomal protein rpl22 selectively in D2R-expressing cells. Cell type-specific tagged ribosomes from the dorsal striatum and nucleus accumbens were immunoprecipitated using anti-HA antibodies and their bound mRNAs -as well as the input fractions that contain the RNAs from all the cell types- were deeply sequenced in triplicate using Illumina HiSeq4000. In parallel, Wfs1-CreERT2 mice were crossed with Ribotag-LoxP/LoxP mice to generate Wfs1-Cre/+:Ribotag-LoxP/+ mice that express the HA epitope fused to the ribosomal protein rpl22 selectively in Wfs1-expressing cells. Cell type-specific tagged ribosomes from the nucleus accumbens were immunoprecipitated using anti-HA antibodies and their bound mRNAs -as well as the input fraction- were deeply sequenced in triplicate using Illumina HiSeq4000.

first: Emma

last: Puighermanal

first: Marta

last: Gut

first: Anna

last: Esteve


title: Targeted reprogramming of H3K27me3 resets epigenetic memory in plant paternal chromatin

overall_design: Genome-wide maps of H3K4me3, H3K27ac, H3K27me1, H3K27me3 and H3.10 deposition in Arabidopsis sperm chromatin


title: Effect of the noncoding RNA produced by ZIKA virus (ZIKV) on expression of Aedes aegypti genes

status: Public on Mar 24 2020

city: St Lucia

first: Andrii

last: Slonchak

state: QLD

address: Bldg 76 Cooper Rd

department: School of Chemistry and Molecular Biosciences

country: Australia

institute: The University Of Queensland

summary: We report that ZIKV noncoding RNA (sfRNA) affect expression of mosquito genes upon ZIKV infection. We constructed sfRNA-deficient ZIKV mutant (xrRNA2') and conducted transcriptome-wide gene expression profiling of mosquitos infected with WT and xrRNA2' viruses. We found that sfRNA inhibits apoptosis in the infected tissues of Ae. aegypti by altering expression of mosquito genes that control cell death and survival.

overall_design: Aedes aegypti mosquitos were injected intrathoracically with 200 nL of wild type ZIKV Uganda MR766 or xrRNA2’ mutant viruses respectively at 5x104 FFU/ml. At 10 days after inoculation mosquitos were euthanised by carbon dioxide exposure, combined into pools of 10 mosquitos in each and subjected to total RNA isolation using TRIreagent (Sigma). Three biological replicates representing three pools of mosquitos were used for library preparation and sequencing on Illumina HiSeq4000 instrument. Libraries were barcoded and 3 of them were loaded into the same lane. To minimize lane-to-lane variations, each library was loaded into 3 different lanes.

first: Francisco

middle: J

last: Torres

first: Sonja

last: Hall-Mendelin


title: O-linked β-N-acetylglucosamine transferase plays an essential role in heart development through regulating angiopoietin-1

status: Public on Mar 14 2020

city: La Jolla

first: Yongxin

last: Mu

state: CA

address: 9500 Gilman Drive

department: medicine

country: USA

institute: University of California SD

summary: Using RNA sequencing we compared the transcriptome change between control and OGT knockout heart samples

overall_design: Four control or OGT knockout hearts at embryonic day 11.5 were subjected to sequencing

first: Ju

last: Chen


title: Enhanced Reduced Representation Bisulfite Sequencing of BPH and control samples

status: Public on Mar 18 2020

city: New York

first: Deli

last: Liu

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

type: Methylation profiling by high throughput sequencing

summary: We investigated the epigenetic landscape of benign prostatic hyperplasia (BPH) by defining the DNA methylation profile of 18 BPH samples and 5 controls from normal transitional zone.  We identified 92,046 hypermethylated CpG and 10,117 hypomethylated CpG across different genomic regions in BPH, and hypermethylation was the dominant signal across all genomic regions, even when controlling for bias of CpG-rich loci.  We defined a methylation signature for BPH that included 696 differentially methylated CpGs in promoter regions.

overall_design: For reduced representation bisulfite sequencing genomic DNA was isolated from control and BPH samples. One replicate was done for each sample.

first: Christopher

last: Barbieri


title: HyperTRIBE uncovers MSI2 increased RNA binding activity and differential regulation in leukemic stem cells [Molm13_ADA_RRM_controls]

status: Public on Mar 11 2020

first: Diu

middle: Thi Thanh

last: Nguyen

address: 417 East 68th street

institute: Memorial Sloan Kettering Cancer Center

summary: Understanding RBPs’ molecular functions as well as their cell-type specific activity requires identification of RBPs’ direct mRNA targets. However, efforts to identify RNA targets of RNA binding proteins in stem cells have been hindered by limited cell numbers. Here we adapt the HyperTRIBE method using an RBP fused to a Drosophila RNA editing enzyme (ADAR) to allow for global mapping of mRNA targets of the RBP MSI2 in rare mammalian adult stem cells. We first tested to see if this method is applicable in mammalian systems. We overexpressed MSI2 fusion with the catalytic domain of the Hyperactive ADAR mutant (MSI2-ADA) or with the dead catalytic mutant (MSI2-DCD) in MOLM-13 human leukemia cells. As ADAR converts A to I (G), the fusion leaves a "finger-print" where MSI2 binds. MSI2-DCD and empty vector controls were used to normalize the background editing.

overall_design: MOLM-13 cells overexpressing ADA only, RRM(del)MSI2-ADA or RRM(mut)MSI2-ADA fusions for 48 hours were harvested for RNA-seq to look for A-G editing events.

middle: T

first: Yuheng

last: Lu

first: Zi-Ning

last: Choo

first: Karen

middle: L

last: Chu

middle: R

last: Chin

first: Alexandra

last: Schurer

first: Ersilia

last: Barin

first: Xuejing

last: Yang

first: Christina

last: Leslie

middle: G

last: Kharas


title: Copy number analysis of BPH (Benign Prostatic Hyperplasia)

summary: BPH samples harbored minimal copy number alterations, and the fraction of altered genome was far lower than primary prostate cancer and other neoplastic diseases.

overall_design: *T_GenomeWideSNP_6.CEL represents BPH samples, and *B_GenomeWideSNP_6.CEL represents match control samples (blood).


title: SMaRT lncRNA controls translation of a G-quadruplex containing mRNA antagonizing the DHX36 helicase

city: Rome

first: Julie

last: Martone

address: P.le Aldo Moro 5

country: Italy

institute: "Sapienza" University

summary: Guanine-quadruplexes (G4) present in RNA and DNA exert a number of different functions in the nucleus and in the cytoplasm. However, the molecular mechanisms of G4-mediated regulation are still poorly understood.  We describe a regulatory circuitry operating in the early phases of muscle differentiation in which a long non coding RNA (SMaRT) base pairs with a G4-containing mRNA (Mlx-g) and represses its translation in an antagonistic way with the RNA helicase DHX36.  MLX-g is required to allow the nuclear translocation of the MLX-a and b dimerization partners and to control proper myogenesis. We show that by controlling MLX-g, lnc-SMaRT is able to regulate the overall quantity of nuclear MLX proteins and their transcriptional output.  Therefore, the circuitry composed by lnc-SMaRT, Mlx-g and Dhx36 not only plays an important role in the control of myogenesis but unravels a molecular mechanism where G4 structures and G4 unwinding activities are controlled in vivo.

overall_design: High-throughput sequencing of total RNA from C2C12 cells  treated with si-Scr and si-SMaRT collected after two days from switch to differentiation medium ; High-throughput sequencing of total RNA from lnc-SMaRT pull-down experiments performed using specific and aspecific (LacZ) biotynilated antisense probes.

first: Irene

last: Bozzoni

first: Davide

last: Mariani

first: Sama

last: Shamloo

first: Tiziana

last: Santini

first: Alessio

last: Colantoni

first: Adriano

last: Setti

first: Francesca

last: Capparelli

first: Alessandro

last: Paiardini

first: Dacia

last: Dimartino

first: Mariangela

last: Morlando


title: Single-cell RNA-seq with spike-in cells enables accurate quantification of cell-specific drug effects in pancreatic islets [10X]

status: Public on Mar 19 2020

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

summary: Single-cell RNA-seq (scRNA-seq) is emerging as a powerful tool to dissect cell-specific effects of drug treatment in complex tissues. This application requires high levels of precision, robustness, and quantitative accuracy beyond those achievable with current methods for qualitative single cell characterization. Here, we establish the use of standardized reference cells as spike-in controls for accurate and robust dissection of single-cell drug responses. We find that contamination by cell-free RNA can constitute up to 20% of reads in human primary tissue samples, and show that the ensuing biases can effectively be removed by a novel bioinformatics method. Applying this method to both human and mouse pancreatic islets treated ex vivo, we obtain an accurate and quantitative assessment of cell-specific drug effects on the transcriptome. We observe that FOXO inhibition induces dedifferentiation of both alpha and beta cells, while artemether treatment upregulates insulin and other beta cell marker genes in a subset of alpha cells. In beta cells, dedifferentiation and insulin repression upon artemether treatment occurs predominantly in mouse but not in human samples. This new method for quantitative, error-correcting, scRNA-seq data normalization using spike-in reference cells allows to clarify the complexities of the cell-specific effects of pharmacological perturbations with single-cell resolution and high quantitative accuracy.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single-cell RNA sequencing using 10 X of pancreatic islets from 3 human donors and 3 mice. Islets were treated ex-vivo with drugs that alter islet cell identity for 72 hrs. Methanol-fixed cells were spiked-in with the islet cells to bioinformatically detect and remove contaminating cell-free RNA. Upon data cleanup and an algorithm to assign cell types, we could study cell-specific drug effects on the transcriptome.

first: Brenda

middle: M

last: Sanchez

first: Nikolaus

last: Fortelny

first: Matthias

last: Farlik

first: Andhira

last: Vieira

first: Patrick

last: Collombat

first: Stefan

last: Kubicek


title: Identification of the causative mutation (using Whole Genome Sequencing) in Arabidopsis EMS mutants showing subcellular trafficking defects

city: Brno

first: Vivek

middle: Kumar

last: Raxwal

address: building A26, Kamenice 753/5

department: Plant Molecular Biology

country: Czech Republic

institute: Central European Institute of Technology

type: Genome variation profiling by high throughput sequencing

summary: Goal of the study was to identify mutants resistant to auxin inhibition of endocytosis.

overall_design: M2 generation of 5-day-old EMS-mutagenized PIN1:PIN1-GFP seedlings (progenies of 1, 920 M1) were  co-treated with 10 μM NAA and 25 μM BFA for 1 hour and screened under the fluorescent microscope for individuals with PIN1- GFP signal accumulated in BFA bodies, therefore insensitive to auxin effect on endocytosis. In M3 generation, the candidates were confirmed, obtained alleles were back crossed to the parental line 3 times and the homozygous lines were selected showing clear cellular phenotype.  For next generation sequencing, genomic DNA of 3 homozygous backcrossed individuals and the parental PIN1:PIN1-GFP plant were submitted to Vienna Biocenter Core Facility for whole-genome sequencing. Interactive tool, artMAP (Javorka et al., 2019) was used to map EMS induced mutations.

first: Vendula

last: Pukyšová

first: Adrià

last: Sans Sánchez

first: Marta

last: Zwiewka

middle: K

first: Tomasz

last: Nodzyński


title: Transcriptional comparison of in vitro and in vivo generated human dendritic cells

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

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 differentiation approach using cord blood CD34+ hematopoietic stem and progenitor cells (HSPCs) co-cultured with bone marrow-derived murine mesenchymal cell line (MS5) engineered to express human FLT3L, SCF and CXCL12 (MS5_FS12). We also show that the engraftment of engineered mesenchymal stromal cells (MS5_FS12) together with CD34+ HSPCs creates an in vivo synthetic niche in the dermis of immunodeficient mice driving the differentiation of cDCs and CD123+AXL+CD327+ pre/AS-DCs. This approach provides a unique platform recapitulating the full spectrum of cDC subsets enabling their functional characterization in vivo.

overall_design: RNA-seq study comparing human dendritic cell subsets differentiated in vitro and in vivo from cord blood-derived CD34+ HSPCs. Hematopoietic progenitors were either co-cultured in vitro or co-injected in NSG mice with bone marrow-derived murine mesenchymal cell line (MS5) engineered to co-express human FLT3L, SCF and CXCL12 (MS5_FS12).

first: Pierre

last: Guermonprez

first: Giorgio

last: Anselmi

first: Yoann

last: Missolo-Koussou


title: Tet2-mediated clonal hematopoiesis in nonconditioned mice accelerates age-associated cardiac dysfunction

status: Public on Mar 12 2020

city: Charlottesville

first: Anupreet

last: Kour

state: Virginia

address: 415 Lane road

department: CVRC

institute: University of Virginia

summary: Clonal hematopoiesis of indeterminate potential is prevalent in elderly individuals and associated with increased risks of all-cause mortality and cardiovascular disease. However, mouse models to study the dynamics of clonal hematopoiesis and its consequences on the cardiovascular system under homeostatic conditions are lacking. We used a model of clonal hematopoiesis using adoptive transfer of unfractionated ten-eleven translocation 2-mutant (Tet2-mutant) bone marrow cells into nonirradiated mice. Consistent with age-related clonal hematopoiesis observed in humans, these mice displayed a progressive expansion of Tet2-deficient cells in multiple hematopoietic stem and progenitor cell fractions and blood cell lineages. The expansion of the Tet2-mutant fraction was also observed in bone marrow-derived CCR+ myeloid cell populations within the heart, but there was a negligible impact on the yolk sac-derived CCR2- cardiac resident macrophage population. Transcriptome profiling revealed an enhanced inflammatory signature in the donor-derived macrophages isolated from the heart. Mice receiving Tet2-deficient bone marrow cells spontaneously developed age-related cardiac dysfunction characterized by greater hypertrophy and fibrosis. Altogether, we show that Tet2- mediated hematopoiesis contributes to cardiac dysfunction in a nonconditioned setting that faithfully models the human clonal hematopoiesis in unperturbed bone marrow. Our data support clinical findings that clonal hematopoiesis per se may contribute to diminished health span.

overall_design: There are a total of 6 samples analyzed. Both Tet2+/+ and Tet2-/- samples have three replications. This is paired end RNA seq data. After running Trimgalore (version 0.6.4) on raw data files the output files were aligned to reference mouse transcriptome using Kallisto (version 0.44.0).

first: Ying

last: Wang

first: Soichi

last: Sano

first: Yoshimitsu

last: Yura

first: Zhonghe

last: Ke

first: Miho

first: Kosei

last: Oshima

first: Hayato

last: Ogawa

first: Keita

last: Horitani

first: Kyung-Duk

last: Min

first: Emiri

last: Miura-Yura

first: Megan

middle: A

last: Evans

first: Maria

last: Zuriaga

first: Karen

last: Hirschi

first: Jose

last: Fuster

first: Eric

last: Pietras

first: Kenneth

last: Walsh


title: Context specificity of the EMT transcriptional response

city: Ottawa

first: David

last: Cook

state: ON

address: 501 Smyth Rd

department: Cancer Therapeutics Program

country: Canada

institute: Ottawa Hospital Research Institute

summary: Epithelial-mesenchymal plasticity contributes to a variety of biological processes, including tumour progression. A variety of epithelial-mesenchymal transition (EMT) responses have been reported and no common, EMT-defining gene expression program has been identified. Here, we have performed a comparative analysis of the EMT response, leveraging highly multiplexed single-cell RNA sequencing (scRNA-seq) to measure expression profiles of 103,999 cells from 960 samples, comprising 12 EMT time course experiments and independent kinase inhibitor screens for each.

overall_design: Single-cell RNA-seq profiles of 12 EMT time course experiments spanning multiple cell lines and EMT inducers, and independent kinase inhibitor screens for each.

middle: P

first: Barbara

middle: C

last: Vanderhyden


title: HyperTRIBE uncovers MSI2 increased RNA binding activity and differential regulation in leukemic stem cells

first: Diu

last: Nguyen

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

overall_design: Refer to individual Series


title: Genome wide anaylsis of rats exposed to endocrine disruptors.

city: Houston

first: Cheryl

last: Walker

state: TX

address: 1 Baylor Plaza

department: Center for Precision Environmental Health

institute: Baylor College of Medicine


title: Genome wide anaylsis of histone modifications in rats exposed to endocrine disruptors. [ChIP-Seq]

summary: Our early life environment has a profound influence on developing organs and tissues that impacts metabolic function, and determines health and disease susceptibility across the life-course. We show an adverse early-life exposure that causes metabolic dysfunction in adulthood reprograms active and repressive histone marks in the developing liver to accelerate acquisition of an adult epigenomic signature at specific genes and chromatin states. This epigenomic reprogramming persists long after the initial exposure, but remarkably, can remain transcriptionally- and metabolically-silent until later-life exposure to a Western-style (high fat-fructose-cholesterol) diet. These findings reveal the importance of epigenome:environment interactions across the life-course, which early in life accelerate epigenomic aging and reprogram the epigenome, and later in adulthood, can unlock metabolically restriced epigenetic reprogramming to drive metabolic dysfunction.

overall_design: Examination of 4 different histone modifications in liver samples from neonatal (PND5) and adult (D70) rats exposed orally to vehicle or bisphenol A on post-natal days 1, 3, and 5.

first: Coarfa

last: Cristian


title: Genome wide anaylsis of transcriptome modifications in rats exposed to endocrine disruptors. [RNA-Seq]

overall_design: Examination of transcriptomics via RNA-Seq in liver samples from  adult (D70) rats on normal chow and adult (D240) rats on Western style diet exposed orally to vehicle or bisphenol A on post-natal days 1, 3, and 5.


title: Targeted reprogramming of H3K27me3 resets epigenetic memory in plant paternal chromatin [sperm]

first: Michael

last: Borg

overall_design: Genome-wide maps of H3K27me1 and H3K27me3 in Arabidopsis htr10 mutant sperm chromatin


title: HyperTRIBE uncovers MSI2 increased RNA binding activity and differential regulation in leukemic stem cells [LSK cells]

summary: Understanding RBPs’ molecular functions as well as their cell-type specific activity requires identification of RBPs’ direct mRNA targets. However, efforts to identify RNA targets of RNA binding proteins in stem cells have been hindered by limited cell numbers. Here we adapted the HyperTRIBE method using an RBP fused to a Drosophila RNA editing enzyme (ADAR) to allow for global mapping of mRNA targets of the RBP MSI2 in rare mammalian adult stem cells. We applied this method to identify MSI2 RNA binding targets in subcompartments of mouse HSPCs including long-term HSCs (LT-HSCs), short-term HSCs (ST-HSCs), multipotent progenitors MPP2 and MPP4. MSI2 fusion with the catalytic domain of the Hyperactive ADAR mutant (MSI2-ADA) or with the dead catalytic mutant (MSI2-DCD) were overexpressed in sorted LSK cells, which were transplanted into mice. After 7 weeks, mouse HSPCs were sorted into 4 populations for RNA-seq. As ADAR converts A to I (G), the fusion leaves a "finger-print" where MSI2 binds. MSI2-DCD and empty vector controls were used to normalize the background editing. We were able to identify MSI2 RNA binding targets in hematopoietic stem and progenitor cells for the first time. Furthermore, we show differential RNA binding activity (by target transcripts and editing frequency) of MSI2 in different subcompartments of HSPCs.

overall_design: MSI2-ADA, MSI2-DCD fusion or MIG (empty vector) were overexpressed in LSK cells sorted from normal C57/BJ6 mice for 48hrs and then transplanted into lethally irradiated C57/B6J mice. After 7 weeks, engraftment was confirmed and bone marrow cells were sorted into LT-HSCs, ST-HSCs, MPP2 and MPP4 for RNA-seq to look for A-G editing events.

first: Yuheng

last: Lu

first: Zi-Ning

last: Choo

last: Chu

first: Christopher

last: Chin

first: Alexandra

last: Schurer

first: Ersilia

last: Barin

first: Saroj

last: Gourkanti

first: Christina

last: Leslie

last: Kharas


title: Pre-analytical factors affecting the establishment of a single tube assay for multi-parameter liquid biopsy detection in melanoma patients

status: Public on Mar 10 2020

city: Hamburg

first: Harriet

last: Wikman

address: Martinistrasse 52

department: Department of Tumor Biology

institute: University Medical Center Hamburg-Eppendorf

type: Non-coding RNA profiling by high throughput sequencing

summary: NGS liquid biopsy sequencing of miRNAs in total plasma and EV-associated miRNAs

overall_design: Comparison of miRNA profiles between EDTA and Streck tubes

first: Svenja

last: Schneegans

first: Melanie

last: Hussong

first: Jonathan

last: Shaffer


title: Transcriptomic analysis of pip5k1 pip5k2 mutant and wild type plants before or after inoculation with powdery mildew Erysiphe cichoracearum

city: Wuhan

first: Qiang

last: Li

state: Saskatchewan

address: #1 Shizishan Street

country: China

institute: Huazhong Agricultural University

summary: To explore the transcriptional regulations in pip5k1 pip5k2 mutant and wild type plants before or after inoculation with powdery mildew Erysiphe cichoracearum

overall_design: Total RNA were extracted from wild type and pip5k1 pip5k2 mutant leaves before or after inoculation with Erysiphe cichoracearum at 2, 5 and 7 dpi. 3 biological replicates per time point for each line.

first: Yangdou

last: Wei

first: Li

last: Qin


title: HyperTRIBE uncovers MSI2 increased RNA binding activity and differential regulation in leukemic stem cells [MOLM-13]

first: Diu

last: Nguyen

overall_design: MOLM-13 cells overexpressing MSI2-ADA, MSI2-DCD fusion or MIG (empty vector) for 48 hours were harvested for RNA-seq to look for A-G editing events.

first: Karen


title: Bioenergetic control of synaptic plasticity by astrocytes during acute stress

status: Public on Mar 13 2020

city: Los Angeles

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

summary: Aldh1l1CreERT2-RiboTag mice were used to purify and sequence astrocyte actively translated mRNAs from acute stress mouse models (20 minute forced swim) and non stressed controls.

overall_design: Four weeks after tamoxifen injection, somatosensory cortex was homogenized and RNA was purified from (i) cleared lysate as the input and control, and (ii) astrocyte-specific ribosome-associated RNA precipitated via a hemagglutinin (HA) tag. Stress mouse astrocyte transcriptomes were compared to non stressed.

first: Ciaran

last: Murphy-Royal

first: Andrew

last: Boyce

first: Blanca

last: Diaz-Castro

first: Baljit

middle: S

last: Khakh

first: Roger

last: Thompsom

first: Jaideep

last: Bains

first: Grant

last: Gordon


title: Redundant and specific roles of cohesin STAG subunits in chromatin looping and transcription control (Hi-C)

status: Public on Mar 06 2020

city: Göttingen

first: Argyris

last: Papantonis

address: Robert-Koch-Straße 40

department: Institut für Pathologie

institute: Universitätsmedizin Göttingen

summary: Cohesin is a ring-shaped multiprotein complex that is crucial for 3D genome organization and transcriptional regulation during differentiation and development. It also confers sister chromatid cohesion and facilitates DNA damage repair. Besides its core subunits SMC3, SMC1A and RAD21, cohesin contains in somatic cells one of two orthologous STAG subunits, SA1 or SA2. How these variable subunits affect the function of the cohesin complex is still unclear. SA1- and SA2-cohesin were initially proposed to organize cohesion at telomeres and centromeres, respectively. Here, we uncover redundant and specific roles of SA1 and SA2 in gene regulation and chromatin looping using HCT116 cells with an auxin-inducible degron (AID) tag fused to either SA1 or SA2. Following rapid depletion of either subunit, we perform high resolution Hi-C, RNA-sequencing and sequential ChIP studies to show that SA1 and SA2 do not co-occupy individual binding sites and have distinct ways how they affect looping and gene expression. These findings are supported at the single cell level by single-molecule localizations via dSTORM super-resolution imaging. Since somatic and congenital mutations of the SA subunits are associated with cancer (SA2) and intellectual disability syndromes with congenital abnormalities (SA1 and SA2), we verified SA1-/SA2-dependencies using human neural stem cells, hence highlighting their importance for understanding particular disease contexts.

overall_design: HiC experiments on HCT116 cells with an auxin-inducible degron (AID) tag fused to either the SA1 or SA2 cohesin complex subunit.

first: Valentina

last: Casa

first: Macarena

last: Gines

first: Anne

last: Zirkel

first: Eduardo

last: Gusmao

first: Kerstin

last: Wendt


title: Redundant and specific roles of cohesin STAG subunits in chromatin looping and transcription control (RNA-Seq)

overall_design: RNA-seq experiments on HCT116 cells with an auxin-inducible degron (AID) tag fused to either the SA1 or SA2 cohesin complex subunit.

first: Natasa

last: Josipovic

first: Wilfred

middle: F

last: van Ijcken

first: Edwin

last: Oole


title: Redundant and specific roles of cohesin STAG subunits in chromatin looping and transcriptional control


title: Impact of splicing factors (ESRP1 and KHDRBS3) on prostate cancer biology

status: Public on Mar 04 2020

city: Changsha

first: Dingxiao

last: Zhang

state: Hunan

address: Yuelushan

department: School of BioMedical Sciences

institute: Hunan University

summary: Dysregulation of mRNA alternative splicing (AS) has been implicated in development and progression of hematological malignancies. How the global AS dysregulation contributes to the development and progression of solid tumors remains generally unclear. Recently, we show that many splicing factors (such as ESRP1 and KHDRBS3) are overexpressed in human primary prostate cancer (PCa) versus normal tissues. To further determine the biological impact of splicing factors on PCa aggressiveness, we treated AR- PC3 cells with siRNAs against either ESRP1 or KHDRBS3 and both. RNA-seq analysis was done in triplicates of rRNA-depleted total RNAs isolated from PC3 cells 48-72hr after siRNA infection. rMATS and DEseq2 were used to reveal the effect of knocking down ESRP1 and/or KHDRBS3 individually or in combination on mRNA splicing landscape and gene expression change.

overall_design: Quantification of changes in RNA splicing and gene expression in prostate cancer cells treated with siRNAs to knockdown either ESRP1 or KHDRBS3 individually and in combination.

first: Qiang

last: Hu

first: Dean

last: Tang


title: Gamma aminobutyric acid increases erythropoietin overexpression of hypoxia inducible factors in rats

city: seoul

first: keuntae

last: Park

address: 5FL, D-dong, Beopwon-ro 9 gil, Songpa-gu

country: South Korea

institute: Milaebioresource

summary:
Erythropoietin (EPO) is the primary regulator of erythropoiesis in the mammalian fetus and the adult through interaction with erythropoietin receptor (EPOR). Deficiency of EPO induces anemia that is a major cause of death in patients with chronic kidney disease. Thus, development of safe treatment for anemia is an urgent issue.
In this study, we investigated the effect of γ-aminobutyric acid (GABA) on serum EPO level and erythropoiesis, and its mechanism was elucidated in rat. GABA significantly (P < 0.05) increased EPO level in serum and expression levels of EPO and EPOR in a dose dependent manner. GABA increased the expression levels of HIF-1 and HIF-2 in a dose dependent manner compared with the negative control; while GABA did not affect the expression of prolyl-hydroxylase domain protein-2α (PHD-2α) gene, an oxygen sensor. GABA supplementation alters energy production pathway resulted in hypoxic condition, which increases EPO level in rat through overexpression of HIF-1 and HIF-2. This study shows a new physiological role of GABA in EPO production and thus GABA could contribute to the prevention of anemia by using alone or in combination with other anemia treating drugs.

overall_design: Sprague-Dawley rats (5 weeks old, male) were purchased from Koatech (Pyungtaek, Korea). Animals were acclimated for 1 week under 12 h light and 12 h dark conditions in a room with constant temperature (20 ± 2 °C) and humidity (50 ± 5%) and a Standard diet (Harlan Diet 2018S, Harlan Laboratories, Madison, WI, USA), and drinking water were provided freely. All experimental procedures were approved by the Korea University Institutional Animal Care and Use Committee (Approval No.: KUIACUC-2016-148) and animals were maintained in accordance with the Guide for the Care and Use of Laboratory Animals (NIH Publication No. 85-23, 1996). After a week of adaptation, the rats were randomly divided into two groups (n = 3 per group), and the groups treated with 200 ppm γ-aminobutyric acid (GABA) (Sigma-Aldrich, St. Louis, Mo, USA) were designated G200. GABA was supplied via water containing 200 ppm.

first: Keun

first: Jong

last: Han

first: Seong

last: Kim

first: Young

middle: H

last: Lim


title: HyperTRIBE uncovers MSI2 increased RNA binding activity and differential regulation in leukemic stem cells [LSC and LSK]

first: Diu

last: Nguyen

summary: Understanding RBPs’ molecular functions as well as their cell-type specific activity requires identification of RBPs’ direct mRNA targets. However, efforts to identify RNA targets of RNA binding proteins in stem cells have been hindered by limited cell numbers. Here we adapted the HyperTRIBE method using an RBP fused to a Drosophila RNA editing enzyme (ADAR) to allow for global mapping of mRNA targets of the RBP MSI2 in rare mammalian adult stem cells. We applied this method to identify MSI2 RNA binding targets in mouse HSPCs (Lin- Sca1+ Kit+ or LSK cells) and mouse leukemic stem cells (LSCs). MSI2 fusion with the catalytic domain of the Hyperactive ADAR mutant (MSI2-ADA) or with the dead catalytic mutant (MSI2-DCD) were overexpressed for 48 hours in LSKs and LSCs, followed by RNA-seq. As ADAR converts A to I (G), the fusion leaves a "finger-print" where MSI2 binds. MSI2-DCD and empty vector controls were used to normalize the background editing. We show that despite comparable expression of the MSI2-ADA fusion protein and endogenous MSI2 in LSCs vs LSKs, MSI2 RNA binding activity (number of targets and editing frequency) in LSCs is significantly higher than that in LSKs. This elevated RNA binding activity is independent of abundancy of the target transcripts.

overall_design: MSI2-ADA, MSI2-DCD fusion or MIG (empty vector) for 48 hours were overexpressed in LSK cells sorted from normal C57/BJ6 mice and LSCs sorted from quaternary MLL-AF9 Actin-DsRed mice. Cells were harvested for RNA-seq to look for A-G editing events.

first: Yuheng

last: Lu

first: Zi-Ning

last: Choo

first: Karen

last: Chu

first: Christopher

last: Chin

first: Alexandra

last: Schurer

first: Ersilia

last: Barin

first: Saroj

last: Gourkanti

first: Christina

last: Leslie

first: Michael

last: Kharas


title: Time course regulatory analysis based on paired expression and chromatin accessibility data

city: Stanford

first: Zhana

last: Duren

address: 318 Campus Drive

institute: Stanford university

summary: We propose a tool named TimeReg to do Time Course Regulatory Analysis from paired gene expression and chromatin accessibility data.

overall_design: To generate RNA-seq and ATAC-seq data on the retinoic acid-induced mESC differenation at Day 0, Day 2, Day 4, Day 10 and Day 20.

first: Xi

last: Chen

first: Yong

last: Wang

first: Wing

last: Wong


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

first: Kristine

last: Vaivode

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).

overall_design: Blood cDC1 and cDC2 were isolated from healthy donor buffy coats. In vitro generated cDC1, cDC2 CD206- and cDC2 CD206+ cells were collected at day 14. All cell types were analysed in triplicates with up to 100 cells per sample.

first: Guermonprez

last: Pierre

first: Anselmi

last: Giorgio

first: Vaivode

last: Kristine


title: A method for the generation of human stem cell-derived alpha cells

city: Rochester

first: Caden

middle: Dale

last: Duffy

state: Minnesota

address: 11-20 Stabile 150 3rd St SW

department: Biomedical Engineering and Physiology

institute: Mayo Clinic

summary: The generation of pancreatic cell types from renewable cell sources holds promise for cell replacement therapies for diabetes. Although most effort has focused on generating pancreatic beta cells, there is considerable evidence that glucagon secreting alpha cells are critically involved in disease progression and proper glucose control. Here we report on the generation of stem cell-derived human pancreatic alpha (SC-alpha) cells from pluripotent stem cells via a transient pre-alpha cell intermediate. These pre-alpha cells exhibit a transcriptional profile similar to mature alpha cells and although they produce proinsulin protein, they do not secrete significant amounts of processed insulin. The resulting SC-alpha cells do not express insulin, share an ultrastructure similar to cadaveric alpha cells, express and secrete glucagon in response to glucose and some glucagon secretagogues, and elevate blood glucose upon transplantation in mice.

overall_design: Single cell mRNA sequencing data generated from stem cell-derived alpha cells and precursor (2 samples total, no replicates)

middle: D

first: Quinn

last: Peterson


title: Redundant and specific roles of cohesin STAG subunits in chromatin looping and transcription control (ChiP-Seq 2)

first: Argyris

last: Papantonis

summary: Cohesin is a ring-shaped multiprotein complex that is crucial for 3D genome organization and transcriptional regulation during differentiation and development. It also confers sister chromatid cohesion and facilitates DNA damage repair. Besides its core subunits SMC3, SMC1A and RAD21, cohesin contains in somatic cells one of two orthologous STAG subunits, STAG1 or STAG2. How these variable subunits affect the function of the cohesin complex is still unclear. STAG1- and STAG2-cohesin were initially proposed to organize cohesion at telomeres and centromeres, respectively. Here, we uncover redundant and specific roles of STAG1 and STAG2 in gene regulation and chromatin looping using HCT116 cells with an auxin-inducible degron (AID) tag fused to either STAG1 or STAG2. Following rapid depletion of either subunit, we perform high resolution Hi-C, RNA-sequencing and sequential ChIP studies to show that STAG1 and STAG2 do not co-occupy individual binding sites and have distinct ways how they affect looping and gene expression. These findings are supported at the single cell level by single-molecule localizations via dSTORM super-resolution imaging. Since somatic and congenital mutations of the STAG subunits are associated with cancer (STAG2) and intellectual disability syndromes with congenital abnormalities (STAG1 and STAG2), we verified STAG1-/STAG2-dependencies using human neural stem cells, hence highlighting their importance for understanding particular disease contexts.

overall_design: ChIP-seq experiments on HCT116 cells with an auxin-inducible degron (AID) tag fused to STAG1.

first: Valentina

last: Casa

first: Macarena

last: Moronta Gines

first: Eduardo

last: Gusmao

first: Kerstin

last: Wendt


title: A mammalian Wnt5a–Ror2–Vangl2 axis controls the cytoskeleton and confers cellular properties required for alveologenesis

status: Public on Mar 03 2020

city: San Francisco

first: Pao-Tien

last: Chuang

address: 555 Mission Bay Blvd. South

institute: University of California, San Francisco

summary: Alveolar formation increases the surface area for gas-exchange and is key to the physiological function of the lung. Alveolar epithelial cells, myofibroblasts and endothelial cells undergo coordinated morphogenesis to generate epithelial folds (secondary septa) within the saccules to form alveoli. A mechanistic understanding of alveologenesis remains incomplete. We found that the planar cell polarity (PCP) pathway is required in both alveolar epithelial cells and myofibroblasts for alveologenesis. Our studies uncovered a Wnt5a–Ror2–Vangl2 cascade that endows cellular properties and thus novel mechanisms of alveologenesis. This includes PDGF secretion from alveolar type I and type II cells, cell shape changes of type I cells and migration of myofibroblasts. All these cellular properties are conferred by changes in the cytoskeleton and represent a new facet of PCP function. These results extend our current model of PCP signaling from polarizing a field of epithelial cells to conferring new properties at subcellular levels to regulate collective cell behavior.

overall_design: Build the signal pathway axis of Ror2 - Vangl2 in lung alveolar development

first: Kuan

last: Zhang

first: Erica

last: Yao


title: Chromatin architecture in hexaploid wheat is hierarchically organized around genome territories and transcription factories (Wheat Hi-ChIP)

status: Public on Mar 02 2020

city: Paris

first: Lorenzo

last: Concia

email: colore@gmail.com, concia@bio.ens.psl.eu

address: 46 Rue d'Ulm

department: Institut de Biologie

institute: École Normale Supérieure

summary: Polyploidization events are known to trigger extensive epigenetic and transcriptional alteration of the duplicated or merged genomes, accompanied by small- and large-scale conformational changes. The genome of modern hexaploid wheat (Triticum aestivum L.; 2n = 6x = 42) is the product of two rounds of interspecific hybridization between three closely related diploid species, resulting in the presence of distinct but highly syntenic sub-genomes (AA, BB and DD). We examined the large-scale chromatin architecture of the nucleus of wheat using Hi-C, a genome-wide chromatin conformation capture (3C) method and GISH, (genomic in situ hybridization). We found evidence that physical interactions occur with significantly higher frequency within sub genomes (A with A, B with B or D with D) than between sub genomes (A with B or D, etc. ...), defining sub-nuclear “genomic territories”. In addition, we observed a polarized distribution of facultative and constitutive heterochromatin that suggests a functional compartmentalization within the nucleus. On a local scale, we found that genes tend to interact mainly with other genes over long-distance “loops” that are especially established between genes presenting similar expression levels and bearing the same histone marks. Moreover, gene pairs in spatial proximity show similar changes in expression levels between shoots and roots. Consistently, we found that physical contact between genes is mediated by RNA polymerase II (RNAPII). Immunofluorescence assays with anti RNAP2 antibodies revealed the presence of “transcription factories” in which multiple interacting genes are co-transcribed. This indicates that local-scale topology is an important factor for transcriptional regulation as it determines the micro-compartimentalization of active genes within the nucleus.Our results provide a framework for understanding the physical organization of wheat genome and highlight the interplay between chromosome conformation and gene expression in wheat.

overall_design: 2 HiChIP libraries were sequenced

first: Moussa

last: Benhamed

first: David

last: Latrasse


title: Chromatin architecture in hexaploid wheat is hierarchically organized around genome territories and transcription factories (Wheat_Hi-C)

overall_design: 2 Hi-C-seq library were sequenced


title: Chromatin architecture in hexaploid wheat is hierarchically organized around genome territories and transcription factories (Rapeseed_Hi-C)


title: Chromatin architecture in hexaploid wheat is hierarchically organized around genome territories and transcription factories (Wheat_ATAC)

overall_design: 1 ATAC-seq library was sequenced


title: Chromatin architecture in hexaploid wheat is hierarchically organized around genome territories and transcription factories (Wheat_ChIP)

overall_design: 1 ChIP-seq library was sequenced


title: Epithelial planar bipolarity emerges from Notch-  mediated asymmetric inhibition of Emx2

status: Public on Mar 05 2020

city: Neuherberg

first: Hernán

last: López-Schier

address: Ingolstaedter Landstr. 1

department: Research Unit Sensory Biology and Organogenesis

institute: Helmholtz Zentrum München

summary: This dataset consists of single-cell RNA-seq (mcSCRBseq) data of neuromast hair cells from wild type and Emx2 mutant zebrafish larvae. Posterior lateral-line neuromast hair cells were isolated by fluorescence activated cell sorting (FACS) from the dissociated trunks of wild type and Emx2-mutant Tg[myo6b:actb1-EGFP] transgenic zebrafish larvae expressing the green fluorescent protein EGFP in hair cells and unipotent hair-cell progenitors (UHCPs).

overall_design: mcSCRB-seq experiment of hair cells from wild type and Emx2-mutant larvae.

first: Eva

last: Kozak

first: Subarna

last: Palit

first: Jerónimo

last: Miranda-Rodríguez

first: Aleksandar

last: Janjic

first: Anika

last: Böttcher

first: Heiko

last: Lickert

first: Wolfgang

last: Enard

first: Fabian

last: Theis


title: Redundant and specific roles of cohesin STAG subunits in chromatin looping and transcription control (ChIP-Seq)

first: Argyris

last: Papantonis

overall_design: ChIP-seq experiments on HCT116 cells with an auxin-inducible degron (AID) tag fused to either the SA1 or SA2 cohesin complex subunit.

first: Valentina

last: Casa

first: Macarena

last: Gines

first: Wilfred

last: van Ijcken

first: Edwin

last: Oole


title: Gonadotropin surge-induced expression of progesterone receptor serves the ovary as a trigger of ovulation and a terminator of ovulatory inflammation

status: Public on Mar 07 2020

city: Urbana

first: CheMyong

middle: Jay

last: Ko

state: Illinois

address: 2001 S. Lincoln Ave.

department: Comparative Biosciences

institute: University of Illinois at Urbana Champaign

summary: Ovulation is triggered by the gonadotropin surge that induces the expression of two key genes, progesterone receptor (Pgr) and prostaglandin-endoperoxide synthase 2 (Ptgs2) in the granulosa cells of preovulatory follicles.  Their gene products PGR and PTGS2 activate two separate pathways that are both essential for successful ovulation. Here we show that the PGR plays an additional essential role; attenuate ovulatory inflammation by diminishing the gonadotropin surge-induced Ptgs2 expression. PGR indirectly terminates Ptgs2 expression and PGE2 synthesis in granulosa cells by inhibiting the NF-κB, a transcription factor required for Ptgs2 expression. When the expression of PGR was ablated in the granulosa cells, the ovary undergoes hyperinflammatory condition manifested by excessive PGE2 synthesis, immune cell infiltration, oxidative damage, and neoplastic transformation of ovarian cells. Despite the ovary undergoes ovulations dozens or hundreds of times in one’s lifetime, the repetitive ovulatory inflammations do not leave significant tissue damage in the ovary. The PGR-driven termination of PTGS2 expression may protect ovary from the ovulatory inflammation.

overall_design: Wild type (Pgr flox/flox) and Esr2-driven Pgr conditional knockout (Esr2 iCre/wt Pgr flox/flox) mice were injected with PMSG at the age of 25 days after birth. On day 27, mice were injected with hCG to induce the superovulation. At 6h after hCG injection, 8 ovaries were collected from 4-different mice in each group and single-cell mRNA libraries were generated by Single-Cell 3’ Chromium kit version 3 from 10X Genomics.

first: Chan

middle: J

last: Park

first: Po-Ching

last: Lin

first: Sherry

last: Zhou

first: Radwa

last: Barakat

first: Shah

last: Bashir

first: Jeong

last: Choi

first: Joseph

last: Cacioppo

first: Oliver

last: Oakley

first: Diane

last: Duffy

first: John

last: Lydon


title: The Dopamine Receptor Antagonist TFP Prevents Phenotype Conversion and Improves Survival in Mouse Models of Glioblastoma

first: Frank

last: Pajonk

address: 10833 Le Conte Ave

institute: UC Los Angeles

summary: Glioblastoma is the deadliest adult brain cancer and all patients ultimately succumb to the disease. Radiation therapy (RT) provides survival benefit of 6 months over surgery alone but these results have not improved in decades. We report that radiation induces a glioma-initiating cell phenotype and identified trifluoperazine (TFP) as a compound that interferes with this phenotype conversion. TFP caused loss of radiation-induced Nanog mRNA expression, activation of GSK3 with consecutive post-translational reduction in p-Akt, Sox2 and -catenin protein levels. TFP did not alter the intrinsic radiation sensitivity of glioma-initiating cells (GICs). Continuous treatment with TFP and a single dose of radiation reduced the number of GICs in vivo and prolonged survival in syngeneic and patient-derived orthotopic xenograft (PDOX) mouse models of glioblastoma. Our findings suggest that combination of a dopamine receptor antagonist with radiation enhances the efficacy of RT in glioblastoma by preventing radiation-induced phenotype conversion of radiosensitive non-GICs into treatment resistant, induced GICs.

overall_design: Cells were irradiated with 0 or 4 Gy and treated with solvent or Trifluoperazine at 10µM


title: Th1/Th2 cross-regulation controls early Leishmania infection in the skin by modulating the size of the permissive monocytic host cell reservoir

status: Public on Mar 01 2020

city: Calgary

first: Nathan

last: Peters

state: AB

address: 3330 Hospital Dr NW

department: Microbiology, Immunology and Infectious Diseases

institute: University of Calgary

summary: The impact of T helper (Th) 1 versus Th2 immunity on intracellular infections is attributed to classical versus alternative activation of macrophages leading to resistance or susceptibility. However, observations in multiple infectious settings demonstrate deficiencies in mediators of Th1/Th2 immunity have paradoxical or no impact. We report that prior to influencing activation, Th1/Th2 immunity first controls the size of the permissive host cell reservoir. During early Leishmania infection of the skin, IFN-γ- or STAT6-mediated changes in phagocyte activation were counteracted by changes in IFN-γ-mediated recruitment of permissive CCR2+ monocytes. Monocytes were required for early parasite expansion and acquired an alternatively activated phenotype despite the Th1 dermal environment required for their recruitment. Surprisingly, STAT6 did not enhance intracellular parasite proliferation, but rather modulated the size and permissiveness of the monocytic host cell reservoir via regulation of IFN-γ and IL-10. These observations expand our understanding of the Th1/Th2 paradigm during infection.

overall_design: C57BL/6 mice were infected with 10^4 Leishmania amazonensis-RFP parasites into the skin. After 2 wks non-infected (RFP-) and infected (RFP+) monocytes were sorted out for genetic expression analysis.n=3 for each control (non-infected monocytes) and experimental group (infected monocytes). The impact of the infection on monocytes were analysed for 254 genes (248 inflammation-related mouse genes + 6 internal reference controls. We performed the multiplex gene expression analysis using the nCounter® Mouse Inflammation v2 Panel from NanoString.

first: Matheus

middle: B

last: Carneiro

first: Matthew

last: Workentine


title: Chromatin architecture in hexaploid wheat is hierarchically organized around genome territories and transcription factories

first: Lorenzo

last: Concia

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

sample_organism:
Brassica napus
Triticum aestivum

platform_organism:
Brassica napus
Triticum aestivum

overall_design: Refer to individual Series


title: Innate immunity in the C. elegans intestine is programmed by a neuronal regulator of AWC olfactory neuron development

city: Worcester

first: Read

last: Pukkila-Worley

state: MA

address: 364 Plantation Street

department: Medicine

institute: University of Massachusetts Medical School

summary: Olfactory neurons allow animals to discriminate nutritious food sources from potential pathogens. From a forward genetic screen, we uncovered a surprising requirement for the olfactory neuron gene olrn-1 in the regulation of intestinal epithelial immunity in Caenorhabditis elegans. During nematode development, olrn-1 is required to program the expression of odorant receptors in the AWC olfactory neuron pair. Here, we show that olrn-1 also functions in AWC neurons in the cell non-autonomous suppression of the canonical p38 MAPK PMK-1 immune pathway in the intestine. Low activity of OLRN-1, which activates the p38 MAPK signaling cassette in AWC neurons during larval development, also de-represses the p38 MAPK PMK-1 pathway in the intestine to promote immune effector transcription, increased clearance of an intestinal pathogen and resistance to bacterial infection. These data reveal an unexpected connection between olfactory receptor development and innate immunity, and show that anti-pathogen defenses in the intestine are developmentally programmed.

overall_design: Transcriptional profiles of C. elegans from wild-type and olrn-1 loss of function animals

first: Kyle

last: Foster

first: Hilary

last: Cheesman

first: Pengpeng

last: Liu

first: Nicholas

last: Peterson

first: Sarah

last: Anderson


title: AR regulated transcriptome in prostate cancer cells

first: Dingxiao

last: Zhang

summary: It has been well established that the transcription factor androgen receptor (AR) is obligatory for prostate cancer (PCa) development and progression, but the precise role of the AR in these processes is still unclear. To dissect the role of AR in shaping the transcriptome of prostate cancer cells, RNA-seq data were obtained from AR-positive LNCaP cells treated with various regimens to manipulate endogenous AR signaling. LNCaP cells were cultured in normal medium containing fetal bovine serum (FBS) to represent an androgen-dependent (AD) growth state. To mimic the clinical androgen-deprivation-therapy (ADT) settings, cells were grown for 4 days in conditions of either depletion of androgen (i.e., medium containing charcoal:dextran stripped fetal bovine serum (CDSS)) or the presence of AR antagonist Enzalutamide (MDV3100, 10 μM) to represent androgen-independent (AI) growth states. Aside from the pharmaceutical modulations, we also utilized siRNA to knockdown AR. To examine the direct effects of AR signaling on gene transcription and splicing, cells were primed with CDSS for 3 days followed by treatment of 10nM dihydrotestosterone (DHT) for 8-9 hrs. Deep sequencing of rRNA-depleted total RNAs was performed in biological duplicates on abovementioned LNCaP cultures.

overall_design: Quantification of RNA expression in prostate LNCaP cancer cells treated with various regimens to manipulate endogenous AR signaling.

first: Qiang

last: Hu

first: Dean

last: Tang


title: ATAC-seq comparing CD8CD38low vs CD8CD38high T cells from healthy donors and SLE

city: Boston

first: Eri

last: Katsuyama

state: Massachusetts

address: 330 Brookline Avenue, CLS 937

department: Rheumatology

institute: Harvard Medical School, Division of Rheumatology Beth Israel Deaconess Medical Center

overall_design: biological duplicate from each group

first: Abel

last: Suarez Fueyo

first: Joon

last: Yoon

first: Ho

last: Shannan

first: George

last: Tsokos


title: Influence of glycine betaine on the transcriptional profile of the Bacillus subtilis SigB regulon

city: Greifswald

first: Ulrike

last: Mäder

address: F.-L.-Jahn-Str. 15A

department: Functional Genomics

institute: University Medicine Greifswald

summary:
To investigate whether salt-stress dependent activation of SigB is mitigated when cells are pre-loaded with the compatible solute glycine betaine, we analyzed salt induction of the SigB regulon in the presence of the precursor choline at a genome-wide level.
The median expression value of SigB-regulated genes was 1.7-fold higher in cells that received choline immediately before salt stress compared to cells where choline was added 60 minutes prior to the salt stress.

platform_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design:
Cells were grown under vigorous agitation at 37 °C in Spizizen minimal medium. To induce hyperosmotic stress, osmolarity was increased by addition of NaCl to a final molarity of 0.4 M. Choline (1 mM) was added immediately, 15, 30 or 60 minutes before NaCl shock, respectively.
Samples were taken 10 min after salt addition. Microarray hybridizations were performed with RNA from two biological replicates. The individual samples were labeled with Cy3.

first: Hermann

last: Rath

first: Uwe

last: Völker


title: Therapeutic targeting of splicing in aggressive prostate cancer

summary: Androgen deprivation therapy (ADT) is the main therapeutic regimen for patients with advanced prostate cancer (PCa). However, most treated patients invariably develop the castration-resistant disease (i.e., CRPC). Mechanisms underlying CRPC development and maintenance remain poorly understood. Recent studies have established splicing dysregulation as a new molecular hallmark of cancer. However, the functional and clinical relevance of such misregulation have not been systematically explored in PCa. Experimentally, we show that splicing modulator, E7107, can significantly inhibits CRPC cell growth both in vitro and in vivo. To determine the mechanistic origins of therapeutic effect of E7107 in vitro, we treated AR+ LNCaP and AR- PC3 cells with DMSO or E7107 at 10nM for 6 h, followed by deep RNA-seq analysis of rRNA-depleted total RNAs isolated from biological triplicates. Furthermore, to evaluate the activity of E7107 against CRPC in vivo, we utilized Enzalutamide-resistant LAPC9-AI (androgen-independent) and PC3 models. RNA-seq experiments we performed on tumors exactly 4 h after the fifth injection of E7107 (5mg/kg/day, 5-days injection considered as 1-dose treatment). Five tumors were included for each group (vehicle or E7107) for deep RNA-seq.

overall_design: Quantification of changes in RNA splicing and expression in prostate cancer cells and xenograft tumors treated with E7107 to manipulate endogenous spliceosome activity.


title: Targeting CD36-PPARβ signaling-mediated metabolic adaptation in intratumoral Tregs primes tumors for PD-1 blockade

city: Epalinges

first: Ping-Chih

last: Ho

state: Vaud

address: Ch. des Boveresses 155

department: Department of Fundamental Oncology

country: Switzerland

institute: University of Lausanne

summary: Though high frequency of Tregs in tumor obstructs anti-tumor immune responses, systemic depletion of Tregs caused severe autoimmune disease in mice model. Therefore, specifically targeting intratumoral Tregs is direly needed to fight against tumor. Our study provides a novel approach to target intratumoral Tregs to enhance anti-tumor immunotherapy.

overall_design: The goals of this study are to use NGS to perform transcriptome profiling (RNA-seq) to find the changes of the global gene expression programs among Tregs from different tissues including spleen, lymph node, and tumor. Comparison is also done between Tregs isolated from WT (FoxP3-YFPCre+/+) tumor and KO (CD36floxed FoxP3-YFPCre+/-). Total RNA was extracted and submitted to RNA-seq

first: Haiping

last: Wang


title: Klf6 protects β-cells against insulin resistance-induced dedifferentiation

city: Lausanne

first: Ana

last: Rodriguez Sanchez-Archidona

address: Genopode building - Quartier Sorge

department: CIG

summary: In the pathogenesis of type 2 diabetes development of insulin resistance triggers an increase in pancreatic β-cell insulin secretion capacity and β-cell number. Failure of this compensatory mechanism is caused by a dedifferentiation of β-cells, which leads to insufficient insulin secretion and diabetic hyperglycemia. The β-cell factors that normally protect against dedifferentiation remain poorly defined. Here, through a systems biology approach, we identify the transcription factor Klf6 as a regulator of β-cell adaptation to metabolic stress. We show that inactivation of Klf6 in mouse β-cells blunts their proliferation induced by the insulin resistance of pregnancy, high-fat high-sucrose feeding, and insulin receptor antagonism. Transcriptomic analysis showed that Klf6 controls the expression of β-cell proliferation genes and, in the presence of insulin resistance, it prevents the down-expression of genes controlling mature β-cell identity and the induction of disallowed genes that impair insulin secretion; its expression also limits the transdifferentiation of β-cells into alpha cells. Our study identifies a new transcription factor that protects β-cells against dedifferentiation and which may be targeted to prevent diabetes development.

overall_design:
Islet transcriptomic analysis, searching for genes differentially expressed between Ctrl and βKlf6KO mouse islets in saline or S961 treated mice. 12 mice were treated with saline (6 Ctrl and 6 βKlf6KO mice), and 16 with S961 (8 Ctrl and 8 βKlf6KO mice)
Ins1Cre/+ mice were crossed with Klf6flox/flox mice to generate Klf6flox/flox;Ins1Cre/+ mice (βKlf6KO) and Klf6flox/flox;Ins1+/+mice l (CTL).

first: Christopher

last: Dumayne

first: David

last: Tarussio

first: Alexandre

last: Picard

first: Davide

last: Basco

first: Xavier

last: Berney

first: Mark

last: Ibberson

first: Bernard

last: Thorens


title: Genome-wide changes in active RNAPII occupancy in the presence of mutated TFIIS (TFIISmut)

city: Illkirch-Graffenstaden

first: Jules

last: Deforges

address: Boulevard Gonthier d'Andernach

institute: Transgene SA

summary: The expresion of dominant negative version of Arabidopsis TFIIS (TFIISmut) in plants lacking funtional TFIIS leads to severe growth defects. The genome-wide analysis of changes in active RNAPII occupancy upon TFIISmut expression was determined using ChIP-seq in order to better understand the biological importance of TFIIS. 10DAS seedlings of transgenic lines carring inducible GFP-TFIIS or GFP-TFIISmut transgenes were studied by ChIP-seq following plants exposure to 24h b-estradiol or EtOH (mock) induction.

overall_design: Chromatin DNA immunoprecipitation was performed to determine active RNAPII occupancy using antbodies directed agains S2P-RNAPII or S5P-RNAPII. RNAPII occupancy was studied in 10-day old transgenic plants with inducible expression of GFP-TFIIS or GFP-TFIISmut fusion proteins and analysed comparatively with uninduced plants.

first: Wojciech

last: Antosz

first: Yves

last: Poirier

first: Klaus

last: Grasser


title: Ribosome profiling of Streptomyces griseus NBRC13350 and Streptomyces venezuelae ATCC15439

city: Daejeon

first: Soonkyu

last: Hwang

address: 291 Daehakro, Yuseong-gu

department: Biological Sciences

institute: KAIST

summary: We performed ribosome profiling which is the deep-sequencing of mRNA fragments protected by translating ribosome for two Streptomyces species through different growth phases to provide the translatome data

sample_organism:
Streptomyces griseus
Streptomyces venezuelae

overall_design: Ribosome profiling data of Streptomyces griseus NBRC13350 and Streptomyces venezuelae ATCC15439 at four different growth phases in duplicates using Illumina HiSeq

first: Namil

last: Lee

first: Yongjae

first: Woori

last: Kim

first: Suhyung

last: Cho

first: Bernhard

middle: O

last: Palsson

first: Byung-Kwan


title: Assessment of the Mode of Action Underlying the Effects of GenX in Mouse Liver and Implications for Assessing Human Health Risks

city: Austin

first: Grace

last: Chappell

address: 9390 Research Blvd, Bldg 2, Ste. #100

department: Health Sciences

institute: ToxStrategies, Inc.

summary: To investigate the potential role of peroxisome proliferator activated receptor–alpha (PPARa) activation in mice, RNA sequencing was conducted on paraffin-embedded liver sections from a  90-day toxicity study of GenX conducted in mice. the TempO-Seq platform was utilized for RNA sequencing data collection. Differentially expressed genes were identified for each treatment group, and gene set enrichment analysis was conducted using gene sets that represent biological processes and known canonical pathways. Significant enrichment of peroxisome signaling was evident in males and females exposed to 0.5 and 5 mg/kg GenX, with no enrichment at 0.1 mg/kg. PPAR signaling and fatty acid metabolism were among the most significantly enriched gene sets, and two gene sets specific to the PPARa subtype were also significantly enriched.

overall_design: Examination of whole transcriptome expression by targeted sequencing in liver tissue from male and female mice treated with varying concentrations of ammonium 2,3,3,3-tetrafluro-2-(heptafluoropropoxy)-propanoate (CASRN 62037-80-3, "GenX").

first: Chad

last: Thompson


title: Chromatin architecture in hexaploid wheat is hierarchically organized around genome territories and transcription factories (Wheat_RNAseq)

first: Lorenzo

last: Concia

overall_design: 3 RNA-seq libraries were sequenced

first: Moussa

last: Benhamed

first: David

last: Latrasse


title: Gene Expression Following Transaortic Constriction in Cardiomyocyte Specific Insulin Receptor Substrate Knockout Mice

city: Iowa City

first: Renata

last: Pereira

state: Iowa

address: 169 Newton Rd

department: Internal Medicine

institute: University of Iowa

summary: mRNA expression profiles from alpha-MHC-Cre X IRS1-flox, alpha-MHC-Cre X IRS2-flox, or IRS2-flox mouse hearts 3 days after transaortic constriction surgery or sham surgery

overall_design: Mice were subjected to transaortic constriction and sacrificed 3 days after surgery, mRNA extracted from the apex, and libraries prepared for high throughput sequencing

first: E

last: Abel

first: Eric

middle: T

last: Weatherford


title: Responses to DNA vaccine against H5 virus in White Leghorn SPF and Rosa 1 chickens

city: Warsaw

first: Barbara

last: Kalenik

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics Polish Academy of Sciences


title: Transcription profiles of oocytes during maturation and embryos during preimplantation development in vivo in the goat

city: Gainesville

first: Zongliang

last: Jiang

state: FL

address: 2033 Mowry Rd

department: Animal Sciences

institute: University of Florida

summary: Preimplantation embryonic development is a dynamic, complex and precise regulated process to govern embryonic development and maintain embryo viability. The complete dynamics transcriptional activities during preimplantation development in the important domestic species goat is not available. Here, we performed RNA sequencing to establish a comprehensive transcriptional profiling of goat in vivo matured oocytes and preimplantation embryos. We found that the embryonic genome activation (EGA) in goat occurs at 16-cell stages, not previously defined at 8-cell stage, and showed much later EGA process compared to all other mammalian species. A total of 6,482 genes were identified to be significantly differentially expressed across all consecutive developmental stage comparisons and the important signaling pathways involved in each development transition were revealed. Additionally, we identified genes that appear to be transcribed only in a specific stage of development. Using weighted gene co-expression network analysis, we found 9 stage-specific modules of co-expressed genes that can be used to represent the corresponding stage of development. Furthermore, we identified conserved key members (or hub genes) of the goat expressed gene networks. Their vast association with other embryonic genes suggests that they may have important regulatory roles in embryo development. Our cross-mammalian species transcriptomic comparisons demarcated both conserved and goat specific features of preimplantation development.

overall_design: RNA-Seq profiles from in vivo matured oocytes and in vivo developed embryos from the 2-cell to the blastocyst stages generated by RNA sequencing

first: Yusheng

last: Li

first: Yunhai

last: Zhang


title: The effect of apolipoprotein E on asthmatic bronchial brushing cell gene signature

city: Bethesda

first: Mehdi

last: Pirooznia

state: MD

address: 12 SOUTH DR

institute: National Institutes of Health

summary: Human asthmatic bronchial brushing cells stimulated with apolipoprotein E demonstrate increased expression of mRNA transcripts encoding multiple pro-inflammatory genes

overall_design: Asthmatic research volunteers (n=8) provided informed consent to participate in the National Heart, Lung, and Blood Institute (NHLBI) research protocol 99-H-0076. Research participants underwent flexible bronchoscopy and cytologic brushings were performed. Bronchial brushing cells from each participant were divided into two batches and treated with apolipoprotein E (500 nM) or media as control.

first: Or

last: Kalchiem-Dekel

first: Stewart

last: Levine


title: Evaluation of cisplatin-induced injury in human kidney organoids

status: Public on Feb 29 2020

city: Auckland

first: Veronika

last: Sander

address: 85 Park Road

department: Molecular Medicine and Pathology

country: New Zealand

institute: University of Auckland

summary: Acute kidney injury (AKI) remains a major global healthcare problem and there is a need to develop human-based models to study AKI in vitro. Towards this goal, we have characterized induced pluripotent stem cell-derived human kidney organoids and their response to cisplatin, a chemotherapeutic drug that induces AKI and preferentially damages the proximal tubule. We found that a single treatment with 50 µM cisplatin induces HAVCR1 and CXCL8 expression, DNA damage (γH2AX) and cell death in the organoids in a dose-dependent manner but greatly impairs organoid viability. DNA damage was not specific to the proximal tubule but also affected the distal tubule and interstitial cell populations. This lack of specificity correlated with low expression of the proximal tubule-specific SLC22A2/OCT2 transporter for cisplatin. To improve viability, we developed a repeated low-dose regimen of 4x 5 µM cisplatin over 7 days and found this causing less toxicity while still inducing a robust AKI response that included secretion of known AKI biomarkers and inflammatory cytokines. This work validates the use of human kidney organoids to model aspects of AKI, with the potential to identify new AKI biomarkers and develop better therapies.

overall_design: Examination of control and cisplatin-treated kidney organoids

first: Jenny

middle: L

last: Digby

first: Thitinee

last: Vanichapol

first: Aneta

last: Przepiorski

first: Alan

last: Davidson


title: Loss of MBNL1 induces RNA mis-processing in the thymus and peripheral blood.

city: Las Vegas

first: Łukasz

middle: J.

last: Sznajder

state: Nevada

address: 4505 S. Maryland Pkwy.

department: Chemistry and Biochemistry

institute: University of Nevada-Las Vegas (UNLV)

summary: The thymus is a primary lymphoid organ that plays an essential role in T lymphocyte maturation and selection during development of one arm of the mammalian adaptive immune response. Although transcriptional mechanisms have been well documented in thymocyte development, co-/post-transcriptional modifications are also important but have received less attention. Here, we demonstrate that the RNA alternative splicing factor MBNL1, which is sequestered in nuclear RNA foci by C(C)UG short tandem repeat expansions in myotonic dystrophy (DM), is essential for normal thymus development and function. Mbnl1 129S1 knockout mice develop postnatal thymic hyperplasia with thymocyte accumulation. Transcriptome analysis indicates numerous gene expression and RNA mis-splicing events, including transcription factors from the TCF/LEF (T-cell factor/lymphoid enhancer factor) family. CNBP, the gene affected in DM type 2 (DM2), is coordinately expressed with MBNL1 in the developing thymus and DM2 CCTG expansions induce similar transcriptome alterations in DM2 blood, which thus serve as disease-specific biomarkers.

overall_design: RNA-Seq was performed on Mbnl1 knockout and wild type mouse thymi as well as human DM2, DM1, C9-ALS/FTD, sporadic ALS, and unaffected control PBMCs and/or whole blood.

first: Marina

middle: M

last: Scotti

first: Jihae

last: Shin

first: Katarzyna

last: Taylor

first: Franjo

last: Ivankovic

first: Curtis

last: Nutter

first: Faaiq

middle: N

last: Aslam

first: S

last: Subramony

first: Laura

last: Ranum

first: Maurice

last: Swanson


title: Genome-wide profiling of age-dependent changes in gene expression between L4 larvae and Day 6 adult Caenorhabditis elegans

city: Villanova

first: Matthew

last: Youngman

state: PA

address: 800 E. Lancaster Ave., Mendel Hall Rm. 118

department: Biology

institute: Villanova University

summary:
Purpose: The objective of this study was to identify genes whose expression changes significantly between the L4 larval stage (Day 0 of adulthood) and the sixth day of adulthood (Day 6) in C. elegans.
Methods: Wild type N2 animals were synchronized by sodium hypochlorite treatment and dropped as L1 larvae to NGM RNAi plates containing 2mM IPTG, 100 mg/mL carbenicillin and seeded with E. coli strain HT115 harboring the L4440 plasmid (vector only control for feeding-based RNAi experiments). Animals were maintained on these plates at 20˚C until the L4 larval stage when half of the cohort was harvested for total RNA (brief description to follow). The other half of the cohort was transferred to new NGM RNAi plates containing 2mM IPTG, 100 mg/mL carbenicillin, 25ug/mL FUDR and seeded with E. coli strain HT115 harboring the L4440 plasmid. C. elegans were maintained on these plates at 20˚C until they reached the sixth day of adulthood when they were harvested for total RNA. To isolate RNA, worms were washed off of plates in M9 buffer, pelletted by centrifugation and resuspended in Trizol. Following a phenol/chloroform extraction, total RNA was precipitated in isopropanol, washed in 70% ethanol, and resuspended in RNase-free H2O. Total RNA was treated with DNase and reisolated using Qiagen RNeasy columns. RNA was isolated from two independent cohorts of L4 animals and three independent cohorts of Day 6 adults. rRNA was depleted from total RNA using Ribo-Zero and libraries were prepared by strand-specific cDNA synthesis for Illumina HiSeq sequencing. Following quality control steps to check for ribosomal depletion, contamination, and leftover adapter sequences, sequences were trimmed and alinged to the C. elegans genome using TopHat2. Alignments were then run with featureCounts then normalized using edgeR's calcNormFactors then transformmed using limma's voom. Changes in gene expression were identified by performing a differential expression analysis using DESeq2 on the Igenbio ERGO platform (Igenbio, Inc., Chicago, Il).
Results: Results from DESeq2 were filtered for statistically significant changes in expression by accepting only those changes with a q-value of less than 0.05. As compared to expression at the L4 larval stage, at Day 6 of adulthood we found there to be 1441 genes that were upregulated by more than 5-fold and 2660 genes were downregulated by more than 5-fold.
Conclusions: Aging is commensurate with significant and substantial changes in gene expression in C. elegans. By the time adults enter the post-reproductive phase of their life, we found that approximately 4000 genes are differentially expressed as compared to their expression levels in L4 larvae. While some of these changes in expression may drive the aging process, others may protect animals from age-associated damage.

overall_design: Transcriptomic analysis of age-related changes in gene expression were identified by isolating RNA from L4 and Day 6 adult wild type N2 Caenorhabditis elegans. After rRNA depletion, RNA was sequenced on the Illumina HiSeq platform and changes in expression identified by DESeq2 analysis.

first: Daniel

middle: R

last: McHugh


title: β2-adrenergic agonists rescue lysosome acidification and function in PSEN1 deficiency by reversing defective ER to lysosome delivery of ClC-7

city: Orangeburg

first: Sandipkumar

last: Darji

state: NY

address: 140 Old Orangeburg Rd, Bldg 39

department: Center for Dementia Research

institute: Nathan Kline Institute for Psychiatric Research

summary: Lysosomal dysfunction is considered pathogenic in Alzheimer Disease (AD). Loss of Presenilin-1(PSEN1) function causing early onset AD impedes acidification via defective vATPase V0a1 subunit delivery to lysosomes. We report that isoproterenol and related β2-adrenergic agonists re-acidify lysosomes in PSEN1 KO cells and fibroblasts from PSEN1 familial AD(FAD) patients, restores lysosomal calcium homeostasis and proteolysis, and reverses impaired autophagy flux. We identify a novel rescue mechanism involving PKA-mediated facilitated delivery of ClC-7 to lysosomes, which stimulates chloride influx and reverses markedly lowered Cl- content of PSEN1 KO lysosomes. Notably, PSEN1 loss-of-function impedes ER-to-lysosome delivery of ClC-7, thus accounting for lysosomal Cl- deficits that compound pH deficits due to deficient vATPase function. Transcriptomics of PSEN1-deficient cells reveal strongly down-regulated ER-to-lysosome transport pathways and reversibility by isoproterenol. Our findings uncover a broadened PSEN1 role in lysosomal ion homeostasis and novel pH modulation of lysosomes through β-adrenergic regulation of ClC-7, which can be therapeutically modulated.

overall_design: mRNA-seq profiling of PSEN1 KO and WT murine blastocysts (BD) cells with and without Isoproterenol (ISO) treatment; 3 biological replicates from each group.

first: Ju-Hyun

last: Lee

first: Devin

last: Wolfe

first: Mary-Kate

last: McBrayer

last: Colacurcio

first: Asok

last: Kumar

first: Philip

last: Stavrides

first: Panaiyur

last: Mohan

first: Ralph

middle: A

last: Nixon


title: Genome wide DNA methylation profiling of normal saliva from females and males

city: London

first: Andrew

middle: E

last: Teschendorff

address: 72 Huntley Street

department: UCL Cancer Institute/Institute for Women's Health

institute: University College London

type: Methylation profiling by genome tiling array

summary: The Illumina Infinium EPIC/850k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpGs in a total of 168 samples, 24 from females and 144 from males

overall_design: Bisulphite converted DNA from the 168 samples were hybridised to the Illumina Infinium EPIC Human Methylation Beadchip

first: Amy

last: Webster

first: Laurence

last: Lovat


title: Responses to DNA vaccine against H5 virus in spleens of Rosa 1 chickens

first: Barbara

last: Kalenik

summary: Laying hens Rosa 1 were immunized with two doses of DNA vaccine, based on the hemagglutinin (HA) DNA from H5N1 virus, in comparison to the control group, which was administered an empty vector (pCI).  Additional groups of Rosa 1 hens were treated with one dose of above described vaccine or empty vector. Gene expression changes in the spleens of chickens were investigated at 7 day post last vaccination dose.

overall_design: Rosa 1 laying hens maintained at an experimental poultry house in standard bedding conditions, were divided into four groups. Animals from ‘Rosa[2x]’  group were vaccinated twice with DNA vaccine, based on the hemagglutinin (HA) DNA from H5N1 virus, at 7 and 21 day post hatch (dph). Group ‘Rosa[1x]’ was immunized once at 7 dph with above mentioned vaccine. Chicken from groups:  ‘Rosa_k [2x]’ and ‘Rosa_k [1x]’ were controls to ‘Rosa[2x]’ and ‘Rosa[1x]’ groups, respectively. Four biological replicates from 'Rosa[1x]’ group and three biological replicates from the remaining groups were selected for final analysis. Totally thirteen samples of RNA were analysed. Obtained data were contrasted with our previously reported results - the transcriptomic profiles of broilers vaccinated twice with DNA vaccine vs. treated with empty vector - series accession number GSE102972 and with White Leghorn SPF chickens immunized as broilers.

first: Anna

last: Gora-Sochacka

last: Stachyra

first: Monika

last: Olszewska-Tomczyk

first: Róża

last: Sawicka

last: Fogtman

first: Krzysztof

last: Śmietanka

first: Agnieszka

last: Sirko


title: Loss of H3K27me3 imprinting in the Sfmbt2 miRNA cluster causes enlargement of cloned mouse placentas

city: Tsukuba

first: Kimiko

last: Inoue

state: Ibaraki

address: 3-1-1 Koyadai

department: Bioresource Engineering Division

country: Japan

institute: BRC, RIKEN

summary: Abnormal placentation in cloned animals remains an unsolved problem. We demonstrated the involvement of micro RNAs (miRNAs) in the abnormal enlargement (hyperplasia) of placentas in cloned mice. Using a comparative transcriptome analysis of cloned placentas, we noted the consistent upregulation of clustered miRNAs within Sfmbt2, a paternally expressed imprinted gene. This region was biallelically activated by loss of imprinting (LOI) in cloned placentas. Deletion of the maternal allele of the whole miRNA cluster resulted in the correction of their expression levels and upregulation of their putative target genes with antitumor or apoptotic functions. Consequently, the placental size was reduced to the normal level and histology was ameliorated. In contrast, correcting the expression of the LOI genes (Sfmbt2, Gab1, and Scl38a4) in cloned placentas had no impact on placental size. Thus, we identified that LOI of clustered miRNAs within Sfmbt2 in cloned placentas was the major cause of abnormal placental enlargement.

overall_design: Mouse total RNAs were collected from in vitro fertilized and somatic cell nuclear transferred placentas with three genotypes and two embryonic days and sequenced.

first: Atuso

last: Ogura


title: Gene expression signatures between lean and diabetes resistant B6 mice and obese and diabetes susceptible NZO mice. [ liver]

city: Nuthetal

first: Pascal

last: Gottmann

address: Arthur-Scheunert-Allee 114-116

institute: Deutsches Institut für Ernährungsforschung

summary: Whole genome microarray expression was measured in liver tissue of 6 week old mice to detect changes in gene expression related to early onset of diabetes and obesity.

overall_design: Male NZO and B6 mice were kept on a high fat diet (HFD) until week 6. Than samples of liver were aliquoted for RNA extraction

first: Nicole

last: Hallahan

first: Anne

last: Kamitz

first: Annette

last: Schürmann


title: PIF7 DNA binding in response to long days with daily oscillating temperatures in Arabidopsis thaliana

city: Cambridge

first: Philip

last: Wigge

address: 47 Bateman street

department: Sainsbury Laboratory

institute: Cambridge University

summary: This study aimed to characterise the genome-wide PIF7-mediated responses of Arabidopsis thaliana seedlings to long photoperiods with a warm 27°C midday in comparison to long photoperiods at constant 17°C. Transcriptomic responses were observed in Col-0 wild-type and pif7-1 loss-of-function mutants investigate the potential contribution of the transcription factor PIF7 to the warm temperature response under the described conditions. In parallel, ChIP-seq of a PIF7-MYC-expressing line under the same conditions was employed to investigate global DNA binding changes of PIF7 in response to a change in temperature.

overall_design: Single experiments at different growth conditions. Sample 186CS12 has been included for its superior efficiency while 192C series shows better differential binding.

first: Katja

last: Jaeger

first: Martin

last: Balcerowicz

first: Feng

last: Geng


title: Total RNA Sequencing in microglia isolated from N-AS treated APP/PS1 mice

city: Daegu

first: Hee Kyung

last: Jin

address: 80 Daehakro, Buk-gu

institute: Kyungpook National University

summary: To examine the regulation of microglia by N-AS-triggered SPMs, we analyzed the gene expression patterns of microglia derived from WT, APP/PS1, and N-AS-injected APP/PS1 mice using RNAseq. These results indicated that N-AS-triggered SPMs activated an anti-inflammatory, positive immune response, and enhanced the phagocytic abilities of microglia in N-AS-treated APP/PS1 mice, leading to resolution of neuroinflammation and upregulation of phagocytic microglia in this AD animal model.

overall_design: We analyzed the gene expression patterns of microglia derived from WT, APP/PS1, and N-AS-injected APP/PS1 mice using RNAseq

first: Jae-sung

last: Bae

first: Hee

middle: K


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

overall_design: Refer to individual Series


overall_design: Mouse total RNAs were collected from in vitro fertilized and somatic cell nuclear transferred placentas at E11.5 and their miRNAs were hybridized with Agilent microarray.

first: Atsuo


title: Gene expression profiling in Bmi1 knockout innate B-1a cells

city: Kalamazoo

first: Momoko

last: Yoshimoto

state: MI

address: 300 Portage St.

department: Investigative Medicine

institute: WMU Homer Stryker MD School of Medicine

summary: In order to identify the key genes for self-renwal abiity of innate immune B-1a cells, we have gene expression analysis using Aglinant Whole Mouse gGenome Oligo Microarrays performed by  Miltenyi Biottec. We isolated peritoneal B-1a cells from wild type mice and Bmi1 kockout (KO) mice that lost self-renewal ability of B-1a cells, and submitted purified RNA from each samples to Miltenyi.

overall_design: The peritoneal B-1a cells were isolated from wild type mice and Bmi1 KO mice. Total 7 samples from Bmi1KO and 7 samples from WT mice from 2 sets of expeiments were submitted to the Whole genome micro array analysis.

first: Yan

last: Liu

first: Yunlong

first: Michihiro

last: Kobayashi


title: Responses to DNA vaccine against H5 virus in White Leghorn SPF chickens.

first: Barbara

last: Kalenik

summary: White Leghorn SPF chickens were immunized with two doses of DNA vaccine, based on the hemagglutinin (HA) DNA from H5N1 virus, in comparison to the control group, which was administered an empty vector (pCI). Gene expression changes in the spleens of chickens were investigated at 7 day post booster dose.

overall_design: White Leghorn SPF chickens from 'WL[2x]' group were housed in a biosafety level 3 containment and vaccinated twice with DNA vaccine, based on the hemagglutinin (HA) DNA from H5N1 virus, at 7 and 21 day post hatch (dph). Control chicken (group ‘WL_k[2x]’) were treated as animals from 'WL[2x]' group, however they received vaccine formulation with an empty vector. Two and three biological replicates from 'WL[2x]’ and ‘WL_k[2x]’ groups, respectively, were selected for final analysis. Totally five samples of RNA were analysed. Obtained data were contrasted with our previously reported results - the transcriptomic profiles of broilers and Rosa 1 laying hen, vaccinated twice with DNA vaccine vs. treated with empty vector .

first: Anna

last: Gora-Sochacka

last: Stachyra

first: Monika

last: Olszewska-Tomczyk

first: Róża

last: Sawicka

last: Fogtman

first: Krzysztof

last: Śmietanka

first: Agnieszka


title: C19orf66 is an interferon-induced inhibitor of HCV replication restricting formation of the viral replication organelle

status: Public on Feb 28 2020

city: Bochum

first: Daniel

last: Todt

address: Universitätsstr. 150

department: Molecular & Medical Virology

institute: Ruhr University Bochum

summary: Hepatitis C virus (HCV) infection constitutes a global health problem with 71 million people currently chronically infected. Recent studies have reported that C19orf66 is expressed as an interferon (IFN)-stimulated gene; however, the intrinsic regulation of this gene within the liver as well as its antiviral effects against HCV remains elusive. In this study, we observed an upregulation of C19orf66 in vivo and ex vivo in response to HCV infection and to IFN therapy. Expression of C19orf66 restricted HCV infection, whereas CRIPSPR/Cas9 mediated knockout of C19orf66 attenuated IFN-mediated suppression of HCV replication. Co-immunoprecipitation followed by mass spectrometry identified a stress granule dominated interactome of C19orf66. Mechanistic studies revealed that C19orf66 expression impairs HCV-induced elevation of PI(4)P and alters the morphology of the viral replication organelle, designated membranous web, thus suppressing viral RNA replication. Collectively, our data suggest that C19orf66 contributes to the innate immune response against HCV in the liver.

overall_design: Huh-7.5 cells stably expressing empty vector or 3xFLAG-C19orf66 were subjected to RNA-seq.

first: Volker

last: Kinast

last: Plociennikowska

last: Anggakusuma

first: Thilo

last: Bracht

first: Richard

middle: P

last: Brown

first: Tujana

last: Boldanova

first: Yudi

last: Zhang

first: Yannick

last: Brueggemann

first: Martina

last: Friesland

first: Michael

last: Engelmann

first: Gabrielle

last: Vieyres

first: Ruth

last: Broering

first: Florian

last: Vondran

first: Markus

last: Heim

last: Sitek

first: Ralf

last: Bartenschlager

first: Thomas

last: Pietschmann

first: Eike

last: Steinmann


title: Region-specific DNA-binding properties of NFIA in the adult mouse brain

city: Houston

first: Brittney

last: Lozzi

state: TX

address: 1 Baylor Plaza

department: Cell & Gene Therapy

institute: Baylor College of Medicine

summary: The goal of this study is to profile NFIA DNA-binding properties in the adult mouse brain. We performed chromatin immunoprecipitation of NFIA in the hippocampus and olfactory bulb of wildtype mice, and samples were subjected to sequencing. We find that NFIA preferentially binds DNA in the hippocampus but not in the olfactory bulb as evidenced by the distinct lack of NFIA binding peaks in the olfactory bulb. Mass spectrometry results suggested that NFIA has a significantly higher binding affinity for NFIB in the olfactory bulb, potentially blocking NFIA’s ability to bind DNA. Virally induced siRNAs against NFIB or scramble were injected into the olfactory bulb of adult wildtype mice to knock down NFIB. We performed chromatin immunoprecipitation of NFIA in the olfactory bulb injected with siRNA-NFIB or siRNA-scramble. Subsequent sequencing revealed an increase of NFIA binding in the olfactory bulb upon the depletion of NFIB as compared to the siRNA-scramble and wildtype controls.

overall_design: Equal starting concentrations of NFIA chromatin immunoprecipitated DNA from the hippocampus, olfactory bulb, siRNA-NFIB olfactory bulb, and siRNA-scramble olfactory bulb was used for ChIP-sequencing.

first: Anna

middle: Y

last: Huang

first: Debosmita

last: Sardar

first: Benjamin

last: Deneen


title: The effect of mismatches and wobble base pairs in the upper stem of pri-miRNAs on DROSHA cleavage using small RNA sequencing

city: Hong Kong

first: Duc

middle: Trung

last: Nguyen

address: Clear Water Bay

department: Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

summary: The experiments were conducted to check whether mismatches and wobble base pairs in the upper stem of pri-miRNAs affects the DROSHA cleavage and thereby miRNA biogenesis.

overall_design: HCT116 cells were transfected with pCDNA3 empty, pCDNA3 wild-type or mutant pri-miRNA plasmids. Small RNA sequencing libraries of the transfected HCT116 cells were generated using the TruSeq Small RNA Library Prep kit.

first: Tuan

last: Anh Nguyen

first: Trung

last: Duc Nguyen

first: Shaohua

last: Li


title: De novo methylaton of the unmethylated K. phaffii genome by human DNA methyltransferases (DNMTs) [BiSulfite-seq]

city: Urbana

first: Jun

middle: S

last: Song

email: songj@illinois.edu, jssong137@gmail.com

state: IL

address: 1110 West Green Street, MC 704

institute: University of Illinois, Urbana-Champaign

summary: We engineered combinatorial knock-in of human DNMTs in Komagataella phaffii, a yeast species lacking endogenous DNA methylation, to characterize methylation preferences and functional consequences of individual de-novo DNMTs as well as their combinations.  Methylation preferences were determined through whole-genome bisulfite sequencing (WGBS) experiments. Effects of knock-in on gene expression were determined by RNA-seq. Measurements of genome-wide methylation produced by distinct de-novo DNMTs permitted determination of methylation preferences and aversions specific to individual DNMTs. Combining methylation and gene expression data provided insight about cellular response to the stress of DNA methylation and about the association between gene methylation patterns and changes in transcriptional output.

overall_design: Whole-genome bisulfite sequencing (WGBS) for 13 experimental conditions. Five of these conditions were single gene knock-ins of DNMT1A, DNMT3A1, DNMT3A2, DNMT3B1,or DNMT3L. Three conditions were double knock-ins of DNMT1A and DNMT3L, DNMT3A1 and DNMT3L, or DNMT3A2 and DNMTL. For each of these conditions as well as for the control condition, WGBS was performed on DNA extracted from K. phaffii cells 5 days after generating and validating knock-in strains. The remaining conditions composed a time-course experiment for the double knock-in of DNMT3B1 and DNMT3L in which WGBS was performed on DNA extracted 1, 2, 3, and 4 days after generating and validating knock-in strains. All experiments were performed as biological duplicates. Sequencing data from each replicate was analyzed separately, and final methylation rates of CpG context cytosines were determined from the sum of methylated and unmethylated observations across replicates corresponding the same condition.

first: Pablo

last: Perez-Pinera


title: De novo methylaton of the unmethylated K. phaffii genome by human DNA methyltransferases (DNMTs)


title: High-throughput in vitro DROSHA processing on human pri-miRNA variants

summary: The in vitro high-throughput human pri-miRNA processing assays were conducted to check whether mismatches and wobble base pairs in the upper stem of pri-miRNAs affects the DROSHA cleavage.

overall_design: 151,248 variants generated from three human pri-miRNAs (pri-mir-106a, pri-mir-342 and pri-mir-514a-1) were processed by mutant DROSHA. The original substrates and cleaved products were cloned and sequenced.


title: High-throughput in vitro DROSHA processing on artificial variants

summary: MicroRNAs (miRNAs) are small RNAs that regulate gene expression. miRNAs are produced from primary miRNAs (pri-miRNAs), the cleavage of which is catalyzed by the Microprocessor complex. Microprocessor therefore plays a key role in determining the efficiency and precision of miRNA production, and thus the function of the final miRNA product. In this study, we utilized high-throughput sequencing-integrated enzymology with purified Microprocessor proteins and randomized pri-miRNA sequences to investigate the catalytic mechanism of Microprocessor. We identified multiple mismatches and wobble base pairs in the upper stem of pri-miRNAs, which determine the efficiency and accuracy of pri-miRNA processing. The existence of these RNA elements helps to explain the alternative cleavage mechanism of Microprocessor, which occurs for some human pri-miRNAs. We also showed that these RNA elements are targets of RNA-editing or single nucleotide polymorphisms (SNPs) for regulating miRNA biogenesis. These findings considerably improve our understanding of pri-miRNA processing mechanisms, and provide a foundation for interpreting differential miRNA expression by several mechanisms, such as RNA modifications and SNPs.

overall_design: 9 samples

middle: D