title: Expression profiling of SARS-CoV-2 infected patients by RNA-seq

city: Dhaka

first: Rasel

last: Ahmed

state: Dhaka

address: Manik Mia Avenue

country: Bangladesh

institute: Bangladesh Jute Research Institute

summary: We have collected nasal cell swab samples from SARS-CoV-2 infected confirmed COVID-19 patients. Both virus and host RNA were extracted and sequenced by RNA-seq. We mapped and assembled virus sequences and in this study transcriptional profile of host due to virus infection.

overall_design: Examining gene expression in Nasopharyngeal swab  cell using RNA-seq

first: M

last: Shahidul Islam

first: Md

last: Sabbir Hossain

first: AMAM

middle: Z

last: Siddiki

first: Goutam

last: Das


title: Transcriptome profile of leukocyte RNA from children with steroid sensitive and resistant nephrotic syndrome

status: Public on Feb 16 2021

city: Columbus

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

country: USA

institute: The Ohio State University

type: Expression profiling by high throughput sequencing

summary: Glucocorticoid resistance complicates the treatment of ~20% of children with nephrotic syndrome, yet the molecular basis for resistance remains unclear.  We generated the transcriptome profile by RNA sequencing of peripheral blood leukocytes from children obtained both at initial nephrotic syndrome presentation and after ~7 weeks of glucocorticoid therapy to identify genes or a gene panel able to differentiate steroid sensitive from steroid resistant nephrotic syndrome. RNA -seq analysis was followed by in-silico algorithm-based approaches and subsequent biochemical analyses on relevant candidate gene with important roles in podocyte and glomerular pathophysiology, using both patient samples and experimental models of nephrotic syndrome and podocyte injury.

overall_design: RNA sequencing to differentiate steroid sensitive from steroid resistant nephrotic syndrome from 28 patients, with 16 steroid sensitive and 12 steroid resistant

first: Shipra

last: Agrawal

first: William

middle: E

last: Smoyer

last: Webb

first: Audrey

middle: C

last: Papp

first: Wolfgang

last: Sadee

first: Richard

middle: F

last: Ransom


title: H3K27ac ChIP-seq for multiple myeloma cell lines, B-lymphoma cells and normal plasma cell

city: Singapore

first: Tze King

last: Tan

address: 14 Medical Drive

department: Cancer Science Institute

country: Singapore

institute: National University of Singapore

type: Genome binding/occupancy profiling by high throughput sequencing

summary: ChIP-seq analysis was performed in Multiple Myeloma cell lines to analyze acetylation of histone H3K27ac.

overall_design: Daudi, RAJI, H929, JJN3, KMS11, KMS12, KMS28BM, RPMI8226, U266 and NP (normal plasma cell) were crosslinked with formaldehyde for 10 min. DNA was enriched by chromatin-immunoprecipitation (ChIP) and analyzed by Illumina Hiseq 4000. A sample of whole cell extract (WCE) was sequenced and used as the background to determine enrichment. ChIP was performed using an antibody against histone H3 lysine 27 acetylation (H3K27Ac: Abcam, ab4729).

first: Yunlu

last: Jia

first: Tze

middle: K

first: Chng

middle: W

last: Joo


title: RNA-seq analysis after THZ1 treatment in JJN3 and H929

summary: RNA-seq analysis was performed in JJN3 and H929 to analyze gene expression changes after THZ1 treatment.

overall_design: JJN3 and H929 cells were treated with DMSO or THZ1 50 nM. Total RNA was harvested 24 hours after knockdown and RNA-seq analysis was performed.


title: A heterogeneous cellular response to ionizing radiation revealed by single cell transcriptome sequencing

city: Tianjin

first: Ping

last: Zhu

address: 288, Nanjing Road, Heping District

department: State Key Laboratory of Experimental Hematology

country: China

institute: Institute of Hematology and Blood Disease Hospital

summary: We report a heterogeneous cellular response to IR by single cell transcriptome sequencing utilizing the modified Smart-seq2 technology in cultured MDA-MB-231 cells. Single cell tSNE clustering analysis showed four distinctive clusters of cells. And in the absence of the ATM kinase, cells displayed much less transcriptional changes after IR. We also selected three detected IR-induced genes for functional validation to confirm their importance in radiosensitivity.

overall_design: Detection of transcriptional changes after IR in wild-type and ATM knock-down MDA-MB-231 cell lines.

first: Yan

last: Gao


title: Super-enhancer profiling combined with CDK7 inhibition-transcripts identifies novel oncogenes of multiple myeloma.

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

overall_design: Refer to individual Series


title: Mesocorticolimbic circuit mechanisms underlying the effects of ketamine on dopamine: a translational imaging study

city: London

first: Sanjay

middle: Padmakar

last: Khadayate

address: Du Cane Road

country: United Kingdom

institute: MRC London Institute of Medical Sciences

summary: Patients with schizophrenia show increased striatal dopamine synthesis capacity in imaging studies. However, the mechanism underlying this is unclear but may be due to N-methyl-D-aspartate receptor (NMDAR) hypofunction and parvalbumin (PV) neuronal dysfunction leading to disinhibition of mesostriatal dopamine neurons. Here, we test this in a translational mouse imaging study using a ketamine model. Mice were treated with sub-chronic ketamine (30mg/kg) or saline followed by in-vivo positron emission tomography of striatal dopamine synthesis capacity, analogous to measures used in patients. Locomotor activity was measured using the open field test. In-vivo cell-type-specific chemogenetic approaches and pharmacological interventions were used to manipulate neuronal excitability. Immunohistochemistry and RNA sequencing were used to investigate molecular mechanisms. Sub-chronic ketamine increased striatal dopamine synthesis capacity (Cohen’s d=2.5) and locomotor activity. These effects were countered by inhibition of midbrain dopamine neurons, and by activation of cortical and ventral subiculum PV interneurons. Sub-chronic ketamine reduced PV expression in these neurons. Pharmacological intervention with SEP-363856, a novel psychotropic agent with agonism at trace amine receptor 1 (TAAR1), significantly reduced the ketamine-induced increase in dopamine synthesis capacity. These results show that sub-chronic ketamine treatment in mice mimics the dopaminergic alterations in patients with psychosis, and suggest an underlying neurocircuit involving PV interneuron hypofunction in frontal cortex and hippocampus as well as activation of midbrain dopamine neurons. A novel TAAR1 agonist reversed the dopaminergic alterations suggesting a therapeutic mechanism for targeting presynaptic dopamine dysfunction in patients.

overall_design: Investigation of gene expression in the pre-limbic cortex in mice treated with sub-chronic ketamine or saline.

first: Michelle

last: Kokkinou

first: Eleanor

middle: J

last: Paul

first: Elaine

last: Irvine

first: Mark

middle: A

last: Ungless

first: Dominic

last: Withers

first: Oliver

middle: D

last: Howes


title: H3K27ac ChIP-seq for primary multiple myeloma patients’ samples (MM1-MM10)

summary: ChIP-seq analysis was performed in primary Multiple Myeloma patients’ samples to analyze acetylation of histone H3K27ac.

overall_design: Primary multiple myeloma patients’ samples (MM1-MM10) were crosslinked with formaldehyde for 10 min. DNA was enriched by chromatin-immunoprecipitation (ChIP) and analyzed by Illumina Hiseq 4000. A sample of whole cell extract (WCE) was sequenced and used as the background to determine enrichment. ChIP was performed using an antibody against histone H3 lysine 27 acetylation (H3K27Ac: Abcam, ab4729).


title: Expression data upon treatment of human mesothelioma mouse model with nucleolin-targeted nanoparticle (PEGASEMP)

city: Coimbra

first: João

middle: Nuno

last: Moreira

address: Faculty of Medicine, Polo 1, Rua Larga

country: Portugal

institute: Center for Neuroscience and Cell Biology

summary:
The goal of this study was to identify transcriptome alterations behind the antitumor effect of PEGASEMP, a liposomal formulation of doxorubicin targeted by the nucleolin-binding F3 peptide, and hence infer on the mechanism of action.
It was used microarray technology to assess the gene expression alterations upon treatment of a human biphasic mesothelioma orthotopic mouse model (aggressive disease subtype) with PEGASEMP.

overall_design: Tumor masses were collected from either PEGASEMP-treated or non-treated animals for RNA extraction and hybridization on Affymetrix arrays.

middle: N


title: Exceptional origin activation revealed by comparative analysis in two laboratory yeast strains

status: Public on Feb 15 2021

city: Syracuse

first: Wenyi

last: Feng

state: NY

address: 750 East Adams Street

department: Biochemistry and Molecular Biology

institute: SUNY Upstate Medical University

summary:
We mapped ssDNA formation in WT and rad53K227A cells in both A364a and W303 background.
We also performed whole genome sequencing of the A364a strain.

overall_design: Briefly, cell cultures were grown to an OD600 of 0.25~0.3 in YPD medium, followed by G1 arrest with 200 nM α-factor.  Pronase (0.02 mg/mL) was used to synchronously release cells into S phase in the presence of 200 mM hydroxyurea (HU).  G1 control and S phase samples were collected prior to cell cycle release and after 1 h treatment of HU, respectively.  Three-hundred ml of cells from each sample were collected and spheroplasted in agarose plugs for ssDNA labeling.  Differentially labeled G1 (Cy5-dUTP) and S phase (Cy3-dUTP) DNA were co-hybridized onto Agilent Yeast Whole Genome ChIP-to-chip 4 × 44K (G4493A) microarrays and the data were extracted by the Agilent Feature Extraction Software (v9.5.1).  The relative quantity of ssDNA at a given genomic locus was calculated as the ratio of the fluorescent signal from the S phase sample to that of the G1 control, followed by Loess-smoothing over a 6-kb window at a step size of 250 bp.

first: Jie

last: Peng


title: Developmental Transcriptome Profiling Uncovered Carbon Signaling Genes Associated with Almond fruit drop

city: Beijing

first: Yu

last: Wei

address: No.12 Zhongguancun South St.,Haidian District   Beijing  P.R.China

institute: Chinese academy of agricultural sciences

summary: Almond is one of the most featured nut crops owing to its high nutritional value. However, due to three different waves of flower and fruitlet drop, fruit drop is a major concern for growers. In this study, we carried out a time-course transcriptome analysis to investigate gene expression difference between normal and abnormal fruitlet development. By de novo assembly analysis, we identified 33,577 unigenes and provided their functional annotations. In total, we identified 8,676 differentially expressed genes and observed the most apparent difference between normal and abnormal fruits at 12 and 17 day after flowering. Their biological functions were enriched in carbon metabolism, carbon fixation in photosynthetic organisms and plant hormone signal transduction. RT-qPCR validated the expression pattern of 15 representative genes, including glycosyltransferase like family 2, MYB39, IAA13, gibberellin-regulated protein 11-like and POD44, which confirmed the reliability of our transcriptome data. This study provides an insight into the association between abnormal fruit development and carbohydrate signaling from the early developmental stages and could be served as useful information for understanding the regulatory mechanism related to almond fruit drop.

overall_design: Gene expression profiling analysis in normal and abnormal fruitlets and identification of differentially expressed genes at different developmental stages were performed

first: Chunmiao

last: Guo

first: Bo

last: Yang

first: A

middle: Y

last: Mubarek

first: Ning

last: Li

first: Jun

last: Liu

first: Kang

last: Liao

first: Huan

last: Wang


title: Anterior-Posterior Rotation Transcriptome RNA-Sequencing Analysis of X. laevis

city: Williamsburg

first: Margaret

last: Saha

state: VA

address: 540 Landrum Drive

department: Biology

institute: College of William and Mary

summary: To analyze the limits of embryo robustness, several different types of surgeries were performed on the anterior-posterior neural axis of Xenopus laevis embryos. Our RNA-Seq data suggests a model in which aspects of early neural plasticity are associated with unique pathways and their associated genes. The transcriptome analysis reveals several combinations of pathways and genes that incorporate and heal foreign tissue, but also re-pattern the anterior-posterior axis. Maintaining plasticity in the transplants was correlated with expression of neuronal transcription factors, chromatin modifiers, Wnt signaling, calcium signaling, and pattern recognition molecules and pathways. In addition to identifying gene pathways involved in plasticity, the complexity and number of comparisons has necessitated a comparative gene approach and analysis of the RNA-Seq data. Several unique genes and pathways were discovered which support their important role in neural axis repatterning.

overall_design: RNA-Seq data of sequenced X.laevis embryos with varying surgeries and an accompanying sibling control

middle: S

first: LeAnn

last: Lo

first: Bryan

last: Weselman


title: RNA sequencing of posterior fossa ependymoma harboring 6q loss

city: Toronto

first: Vijay

last: Ramaswamy

state: ON

address: 555 University Avenue

country: Canada

institute: Hospital for Sick Children

summary: Two distinct groups of posterior fossa ependymoma, PF-EPN-A and PF-EPN-B have been identified in children and are often associated with widely distinct outcomes. We have identified an ultra-high-risk PF-EPN-A ependymoma with 6q loss. We performed RNA sequencing of posterior fossa ependymoma A (PF-EPN-A) tumor samples with chromosome 6q loss and balanced to understand the differences in 6q loss at the transcriptomic level

overall_design: Transcriptomic profiles of 10 ependymoma samples with chromosome 6q loss and balanced 6q status with 5 samples in each category


title: Association of RERG Expression to Female Survival Advantage in Malignant Pleural Mesothelioma

city: Boston

first: Assunta

last: De Rienzo

state: MA

address: 75 Francis Street

institute: Brigham and Women's Hospital


title: Association of RERG Expression to Female Survival Advantage in Malignant Pleural Mesothelioma II

summary: Sex differences in incidence, prognosis, and treatment response have been described for many cancers. In malignant pleural mesothelioma (MPM), a lethal disease associated with asbestos exposure, men outnumber women 4 to 1, but women consistently live longer than men following surgery-based therapy. This study investigated whether tumor expression of genes associated with estrogen signaling could potentially explain observed survival differences. Two microarray datasets of MPM tumors were analyzed to discover estrogen-related genes associated with survival. A validation cohort of MPM tumors was selected to balance the numbers of men and women and control for competing prognostic influences. The RAS like estrogen regulated growth inhibitor (RERG) gene was identified as the most differentially-expressed estrogen-related gene in these tumors and predicted prognosis in discovery datasets. In the sex-matched validation cohort, low RERG expression was significantly associated with increased risk of death among women.  No association between RERG expression and survival was found among men, and no relationship between estrogen receptor protein or gene expression and survival was found for either sex. Additional investigations are needed to elucidate the molecular mechanisms underlying this association and its sex specificity.

overall_design: This study investigated whether tumor expression of genes associated with estrogen signaling could potentially explain observed survival differences between men and women affected by malignant pleural mesothelioma.

first: Melissa

middle: H

last: Coleman

first: Beow

last: Yeap

first: David

middle: T

last: Severson

first: Benjamin

last: Wadowski

first: Corinne

last: Gustafson

first: Roderick

middle: V

last: Jensen

first: Lucian

middle: R

last: Chirieac

first: William

middle: G

last: Richards

first: Raphael

last: Bueno


title: Regulation of Tfh differentiation by PDK1

first: Shuyang

last: Yu

address: 2 Yuanmingyuan West Road

department: College of Biological Sciences

institute: China Agricultural University

summary: Follicular helper T (Tfh) cells, as important effector CD4+ T cells, are able to regulate antigen-specific B cell immunity in vivo. It is well characterized that transcription factors, cytokines, microRNA, epigenetic modifications exerts important roles in Tfh differentiation and function. Howerer, the regulatory mechanism of the major signaling pathways driving Tfh cell differentiation remains unclear. Multiple mice models were used by a series of experimental approaches to illustrate PDK1 signaling programs Tfh differentiation and function.

overall_design: WT and Pdk1-null Tfh cells (2 samples per group) were sorted at day 8 after LCMV Armstrong infection. Then the total RNAs were extracted and subjected to RNA sequencing.

first: S


title: Expression Data from Osteoblasts with a cell-type specific Piezo1-deficiency or treated with Yoda 1

city: Hamburg

first: Thorsten

last: Schinke

address: Martinistr. 52

department: Department of Osteology and Biomechanics

country: Germany

institute: University Medical Center Hamburg-Eppendorf

summary:
Piezo1 is a cellular mechanosensor that can be activated by the compound Yoda 1. Our aim was to evaluate the role of Piezo1 in skeletal metabolism. We investigated the effect of Yoda 1  or Runx2-Cre mediated Piezo1 deficiency on cultured primary murine calvarial osteoblasts.
We used microarray analysis to detail the global gene expression of osteoblasts in response to Piezo1-stimulation and deficiency

overall_design: 3 sample sets with 3 independent repetitions for each sample set were compared. 1st sample set: Piezo1-floxed, Runx2-Cre negative cells treated with DMSO; 2nd sample set:  Piezo1-floxed,Runx2-Cre negative cells treated with Yoda 1; 3rd sample set  Piezo1-floxed,Runx2-Cre positive cells treated with DMSO

first: Timur

last: Yorgan

first: Gretl

last: Hendrickx

first: Mona

last: Neven

first: Lana

last: Rosenthal


title: Expression Data from MC3T3-E1 cells subjected to laminar fluid flow (LFF)

summary:
Osteoblasts are responsive to shear stress. We investigated the effect of of laminar fluid flow (LFF) on osteoblast-like MC3T3-E1 cells at two timepoints.
We used microarray analysis to detail the global gene expression of MC3T3-E1 cells in response to 1 hour of laminar fluid flow directly and 4 hours after treatment.

overall_design: 4 samples generated from pools of 3 independent experiments each were analyzed. Effects of laminar fluid flow were assessed directly or 4 h after exposure compared to cells not subjected to laminar fluid flow.

first: Melanie

last: Haffner-Luntzer

first: Astrid

last: Lidert

first: Anita

last: Ignatius


title: Effect of Diesel Exhaust Particles in Normal Human Embryonic Lung Cell (WI-38) Line

status: Public on Feb 14 2021

city: Cheongju-si

first: Joong Won

last: Lee

state: Chungcheongbuk-do

address: 187, Osongsaengmyeong2-ro, Osong-eup, Heungdeok-gu

department: Division of Allergy and Respiratory Disease Research

country: South Korea

institute: Korea National Institute of Health

summary: We performed RNA sequencing to identify genes and pathways induced by Diesel exhaust particles exposure in WI-38 cells.

first: Joong

first: Hee


title: Transcriptomic profiling investigating altered cellular pathways upon QKI depletion in mouse eye lens tissue, mouse neural stem cell-derived lens progenitor-like cells (NLPCs), and human lens epithelial cell line (HLE-B3).

city: HOUSTON

first: Jian

last: Hu

state: TEXAS

address: 1881 East Road

department: Cancer Biology

institute: The University of Texas MD Anderson Cancer Center

summary: Significantly altered cellular pathways in the transcriptomic profiling upon QKI depletion potentially play an important role in protein homeostasis in eye lens cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Mouse eye lens tissues were isolated from the mice with tamoxifen-induced Qk deletion under the control of Nestin promoter and the control mice. NLPCs were differentiated from the neural stem cells isolated from Nestin-CreERT2; QkL/L, and 4OHT treatment induced the Qk deletion. HLE-B3 cells were obtained from ATCC (CRL-11421), and QKI KO was conducted using CRISPR-Cas9 system.

first: Seula

last: Shin

first: Yanjun

last: Wei

first: Yunfei

last: Wang

first: Yiwen

last: Chen


title: Mutations in Bcl9 and Pygo genes cause congenital heart defects by tissue-specific perturbation of Wnt/β-catenin signaling

city: Zurich

first: Claudio

last: Cantù

address: Winterthurerstrasse 190

department: IMLS

country: Switzerland

institute: University of Zurich


title: Mutations in Bcl9 and Pygo genes cause congenital heart defects by tissue-specific perturbation of Wnt/β-catenin signaling (RNA-seq data set)

summary: Gene expression profiling of Pygo2 mutant branchyal arches (BA) and developing heart tubes at 10.5 days post coitum

overall_design: isolation of branchyal arches and developing heart tubes from individual Pygo2 mutant mice and wild-type littermates (4 vs 4)

first: Dario

last: Zimmerli

first: Anastasia

last: Felker

first: Elena

last: Cabello

first: Konrad

last: Basler

first: Christian

last: Mosimann


title: Mutations in Bcl9 and Pygo genes cause congenital heart defects by tissue-specific perturbation of Wnt/β-catenin signaling (ChIP-seq data set)

summary: Genome-wide DNA binding profiles of the components of the Wnt signaling transcriptional complex, beta-catenin and Pygo2, in mouse developing branchyal arches (BA) and looping heart.

overall_design: Isolation of branchyal arches from 10.5 days post coitum mouse embryos (circa 250 embryos for 8 samples), to performa ChIP.


title: Long non-coding RNAs associated with metabolic traits in human white adipose tissue

city: Huddinge

first: hui

last: Gao

address: Novum

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

type: Non-coding RNA profiling by high throughput sequencing

summary: Long non-coding RNAs (lncRNAs) belong to a recently discovered class of molecules  proposed to regulate various cellular processes. Here, we systematically analyzed their  expression in human subcutaneous white adipose tissue (WAT) and found that a  limited set was differentially expressed in either obesity or the insulin resistance that  usually follows obesity. Two lncRNAs herein termed adipocyte-specific metabolic  related lncRNAs 1(ASMER-1) and ASMER-2 were enriched in adipocytes and  regulated by both obesity and insulin resistance. Knockdown of either ASMER-1or  ASMER-2 by antisense oligonucleotides using in vitro differentiated human adipocytes  altered lipolysis and adiponectin secretion, respectively. The observed effects could be  attributed to changes in the expression of genes controlling inflammation and lipid  metabolism. Our data demonstrate that lncRNAs are modulators of the metabolic and  endocrine functions in fat cells and also provide an emerging link between WAT and  common metabolic conditions.

overall_design: Human adipose tissues mRNA profiles of obese (13) and lean (15) subjects were generated by deep sequencing using Illumina 2000.

first: Hui

first: Ingrid

last: Dahlman

first: Peter

last: Arner


title: Next generation sequencing of transcript abundance during growth mycelia in the Magnaporthe oryzae [RNA-Seq III]

status: Public on Feb 13 2021

city: Hangzhou

first: Chuyu

last: Lin

state: Zhejiang

address: 866#, Yuhangtang Road

department: College of Agriculture and Biotechnology

institute: Zhejiang University

summary: We report that suppression of polycomb-mediated H3K27me3 epigenetically de-repressed the genome-wide expression of effectomes in the vegetative growth stage. Tthe chromatin regions of effectors were directly occupied with H3K27me3 modification in the vegetative growth stage. P55, the additional subunit of PRC2, could recruit Sin3 histone deacetylation complex to prompt H3K27me3 occupancy for stably maintaining transcriptional silencing of the target genes.

overall_design: Examination of 2 different mutants in Magnaporthe oryzae strain

first: Zeng

last: Tao


title: Lactobacillus Firm5 in vivo and in vitro RNA sequencing

city: Lausanne

first: Silvia

last: Brochet

state: Vaud

address: UNIL campus, Biophore building

department: Department of Fundamental Microbiology

institute: University of Lausanne

summary: We report the transcriptome of four strains of the Lactobacillus Firm5 phylotype obtained with  in vivo and  in vitro experiments under different nutrient conditions

sample_organism:
Lactobacillus apis
Lactobacillus kullabergensis
Lactobacillus helsingborgensis
Lactobacillus melliventris

overall_design: In vivo experiment: microbiota depleted bees were colonized with the four strains community and divided into a treatment without access to pollen and a treatment with access to pollen. In vitro experiment: Firm5 strains were cultures as a community as well as mono-cultures in presence or absence of pollen. We compare gene expression between treatments to understand the impact of diet and presence of other strains on gene expression.

first: Philipp

last: Engel


title: Next generation sequencing of transcript abundance during growth mycelia in the Magnaporthe oryzae [RNA-Seq II]

overall_design: Examination of 5 different mutants in Magnaporthe oryzae strain


title: Suppression of polycomb-mediated H3K27me3 epigenetically de-repressed the genome-wide expression of effectomes in the vegetative growth stage

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

overall_design: Refer to individual Series


title: Next generation sequencing of transcript abundance during growth mycelia in the Magnaporthe oryzae [RNA-Seq I]


title: K562 PRO-seq

city: Boulder

first: John

last: Rinn

state: CO

address: 3415 Colorado Ave

department: Biochemistry

institute: CU Boulder

summary: Nascent transcription measured by PRO-seq in untreated and DMSO treated conditions.

overall_design: To generate a profile of nascent transcription in K562 cells absent any perturbation, two PRO-seq experiments were performed.

first: Lai

last: Maria

first: Basken

last: Joel

first: Azofeifa

last: Joey

first: Smallegan

last: Michael


title: Hepcidin: a key regulator of inflammation

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

summary: Hepcidin is demonstrated to be the key iron regulatory hormone, produced by the liver. Here we show an unexpected role of hepcidin as a master initiator of the local and systemic inflammatory response. We demonstrated that Hepcidin is a key new essential component of the immune system and may be a promising target in many inflammatory diseases.

overall_design: We used microarrays to detail the global programme of gene expression of BMDM treat with hepcidin for 1 and 3 hours.

first: Jacques

last: Mathieu

first: Sara

last: Zumerle


title: Genome-wide mapping of H3K27me3 in two Magnaporthe oryzae strains


title: Infection of macrophages with functional Slc11a1 yields differences in global gene expression, regulation of metal ions, and infection outcomes

status: Public on Feb 12 2021

first: Lara

last: Janiszewski

state: Colorado

institute: University of Colorado Boulder

summary: Manipulation of zinc at the host-pathogen interface depends on both the identity of the pathogen and the nature of the host cell. In this study, we examine the response of bone marrow derived macrophages from 129S6/SvEvTac mice to infection by Salmonella Typhimurium.  Unlike Balb/c and C57BL/6 mice, 129S6/SvEvTac mice possess a functional Slc11a1 (Nramp-1), a phagosomal transporter of divalent cations.  We examine the changes in gene expression upon treatment with live or heat killed Salmonella at 2 Hrs and 18 Hrs post infection, and observed widespread changes in metal transport, metal-dependent, and metal homeostasis genes, suggesting significant remodeling of iron, copper, and zinc availability by host cells.

overall_design: Global RNA sequencing of mouse bone marrow derived macrophages treated with live or heat killed Salmonella Typhimurium and collected at 2 and 18 hours post exposure. Unexposed control macrophages were collected at 2 Hrs as well

first: Amy

last: Palmer


title: Genome-wide mapping of H3K4ac in two Magnaporthe oryzae strains


title: mRNA-seq of large airway basal cell, small airway basal cell and alveolar type2 cells from normal patients

first: avinash

last: waghray

address: 185 Cambridge Street, CPZN Room 4254A

department: Center for Regenerative Medicine

institute: Massachussets General Hospital

summary:
Angiotensin-converting enzyme 2 (ACE2) and accessory proteases (TMPRSS2 and CTSL) are needed for severe acute respiratory syndrome coronavirus 2 cellular entry, and their expression may shed light on viral tropism and impact across the body. We assess the cell-type-specific expression of ACE2, TMPRSS2 and CTSL across 107 single-cell RNA-sequencing studies from different tissues. ACE2, TMPRSS2 and CTSL are coexpressed in specific subsets of respiratory epithelial cells in the nasal passages, airways and alveoli, and in cells from other organs associated with coronavirus disease 2019 transmission or pathology. We performed a meta-analysis of 31 lung single-cell RNA-sequencing studies with 1,320,896 cells from 377  nasal, airway and lung parenchyma samples from 228 individuals. This revealed cell-type-specific associations of age, sex and smoking with expression levels of ACE2, TMPRSS2 and CTSL. Expression of entry factors increased with age and in males, including in airway secretory cells and alveolar type 2 cells. Expression programs shared by ACE2+TMPRSS2+ cells in nasal, lung and gut tissues included genes that may mediate viral entry, key immune functions and epithelial–macrophage cross-talk, such as genes involved in the interleukin-6, interleukin-1, tumor necrosis factor and complement pathways. Cell-type-specific expression patterns may contribute to the pathogenesis of coronavirus disease 2019, and our work highlights putative molecular pathways for therapeutic intervention.

Single-cell meta-analysis not included in this submission.

overall_design: Human lung tissue was received from New England Donor Services under the Massachusetts General Hospital approved institutional review board protocol. Tissue was used from three individual patients with no history of lung disease or smoking. Primary bronchus and a piece of right lung lobe were manually dissected out. Single cells were dissociated in HBSS media  (sigma, 55021C) containing collagenase (225 units/ml), dispase (2.5 units/ml), elastase (2 units/ml), pronase (1mg/ml), DNAse (1 unit/ml) and Y-27632 (5uM) inhibitor. Cell suspension was treated with ACK lysis buffer (thermofisher scientific A1049201) for 2 minutes on ice to remove red blood cells. Large airway basal cells were isolated from primary bronchus tissue while small airway basal cells and alveolar type 2 (AT2) cells were isolated from lung lobe tissue. Basal cells from both tissue suspensions were isolated using the anti-human CD271 MicroBeads kit (Miltenyl Biotech, 130-099-023) following manufacturers protocol. AT2 cells were isolated with Anti HT2-280 antibody (Terrace Biotech, TB-27AHT2-280) and anti-Mouse IgM MicroBeads kit (Miltenyl Biotech, 130-047-301) following manufacturers protocol. For mRNA-Seq sample preparation, the total RNA was isolated using Trizol reagent (Thermofischer Scientific, 15596026) following the manufacturer’s instructions. Quality and quantity of total RNA was assayed using Nanodrop and Agilent Bioanalyzer. Further, mRNA-seq libraries were prepared using the TrueSeq protocol from Illumina. For mRNA-Seq analysis, the raw fastq files were mapped to the human genome using STAR (Version 20201). The output files were processed through Cufflinks (Version 2.2.1.3)) and Cuffdiff (Version 2.2.1.6) to conduct differential gene expression analysis.

first: Avinash

last: Waghray

first: Brian

first: Jayaraj

last: Rajagopal


title: The role of mammalian DNA methyltransferases in the regulation of temporal order of DNA replication

city: Tsu

first: Shin-ichiro

last: Takebayashi

state: Mie

address: 2-174, Edobashi

department: Graduate School of Medicine

country: Japan

institute: Mie University

type:
Other
Expression profiling by array


title: CircETFA Upregulates CCL5 by Sponging miR-612 and Recruiting EIF4A3 to Promote Hepatocellular Carcinoma

city: Nanjing

first: Chen

last: Lu

address: Guangzhou Road

department: Department of General Surgery

institute: The First Affiliated Hospital of Nanjing Medical University

summary: In order to identify circRNAs involved in HCC tumorigenesis, we performed circular RNA microarray analysis on three pairs of total RNA from HCC patient plasma and healthy controls. A total of 5122 differentially expressed circRNAs were identified (FC ≥ 2 or FC ≤ -2, P-value ≤ 0.05) . Among them, 4162 circRNAs were significantly up-regulated, and 960 circRNAs were significantly down-regulated.

first: Weiwei

last: Tang


title: Evaluation of microRNA expression in sheep model for lung fibrosis

city: Melbourne

first: Udari

middle: Eshani

last: Perera

state: Victoria

address: Corner Flemington Road and Parkdrive, Parkville

country: Australia

institute: University of Melbourne

summary: There were similarities in the microRNA expression profiles in sheep model and idiopathic pulmonary fibrosis (IPF) suggest that bleomycin induced lung injuries share similar molecular mechanisms associated with the disease IPF

overall_design: Development of preclinical sheep model using bleomycin lung fibrosis that share hallmark features of IPF

middle: E

first: Habtamu

middle: B

last: Derseh

first: Sasika

last: Dewage

first: Andrew

last: Stent

first: Rukmali

last: Wijayarathna

first: Kenneth

last: Snibson


title: RNA-seq analysis reveals profound changes in transcript profiles between siCon and siH19 transfected aortic smooth muscle cells (AoSMC)

city: New Haven

first: Ying

last: Jiang

address: 310 Cedar Street

institute: Department of Obstetrics, Gynecology & Reproductive Sciences

summary: We used high throughput sequencing to analyze the gene expression profiling of human aortic smooth muscle cells (AoSMC). By comparing the gene expression profiling of AoSMC with or without H19 knockdown, 2940 genes were found at least 1.5-fold up-regulated in siH19 relative to siCon cells, meanwhile 2790 genes were found at least 1.5-fold down-regulated in siH19 over siCon cells.

overall_design: AoSMC cells were transfected with either control siRNA or siH19. 48h after transfection, total RNA was extracted for library preparation and RNA-seq analysis to compare gene expression profiles between siCon and siH19 cells.

last: Zhang

first: Gordon

last: Carmichael

first: Yingqun

last: Huang


title: Single-cell SLAM-seq profiling of normal and tumor organoids

status: Public on Feb 11 2021

city: Berlin

first: Nils

last: Blüthgen

address: Chariteplatz 1

department: Institute of Pathology

institute: Charite Universitätsmedizin Berlin

summary: Differentiation trajectories and cellular plasticity in CRC were assessed using single-cell SLAM seq on patient-derived organoids. Organoids were perturbed in MAPK and WNT signalling.

overall_design:
Patent-derived organoids derived from 6 CRC tumors and one normal colon were grown under different conditions (control/DMSO, different small molecule inhibitors, medium with EGF and WNT and with EGF), incubated with 4SU for 2h before harvesting, disagregated into single cell suspensions using TrypLE, and fixed with metanol. Samples were then incubated O/N with 10mM iodoacetamide for alkalyation. Samples were subsequently barcoded using BD sample TAG antibodies, and pooled (all perturbation of 2 organoids per library for inhibitor treatment, one perturbation of three organoids for growth condition), and subjected to droplet based scRNA-seq analysis (Chromium controller, 10x genomics)
----------------------------------------------------
Authors state "Unfortunately, we can currently not supply raw data files (sequencing) as these are patient sequences for which the current data access policies in our institution only allow submission of count data. "

first: Stefan

last: Peidli

first: Mareen

last: Lüthen

first: Anja

last: Sieber

first: Alexandra

last: Trinks

first: Markus

last: Morkel

first: Christine

last: Sers

first: Benedikt

last: Obermayer


title: Wilms' tumor lncRNA sequence in the blood

city: Chongqing

first: He

middle: xing

last: yue

address: 136, Zhongshan 2nd RD, Yuzhong District

institute: Children’s Hospital of Chongqing Medical University

summary: We performed microarray analysis and real-time quantitative PCR (RT-qPCR) to detect the expression levels of  lncRNA in blood collected from 2 WT patients. Goal was to determine the underlying mechanism by which lncRNA regulates WT progression.

overall_design: Total RNA was extracted from blood samples from 2 WT and 2 healthy children using Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions, followed by purification using the NucleoSpin® RNA clean-up kit (MACHEREY-NAGEL, Germany).

first: Xingyue

last: He

first: Feng

last: Liu


title: Trait related and differential DNA Methylation in obese and normal weight Brazilian women.

city: Ribeirão Preto

first: Carla

middle: Barbosa

last: Nonino

state: São Paulo

address: Bandeirantes Avenue, 3900

department: Health Sciences Department

country: Brazil

institute: University of São Paulo

summary: Obesity has been linked to lifestyle and recently have been associated to DNA methylation changes that may cause alterations in the adipogenesis and lipid storage processes and contribute to the pathological state. We enrolled Obese (Ob) and Normal Weight (NW) women. We observed that DNA methylation patterns are different between normal weight and obese women. This can alter gene expression patterns affecting adipogenesis and lipid storage. This results confirms that an obesogenic lifestyle can promote epigenetic changes in the human DNA.

overall_design: Peripheral blood samples were collected to perform total leucocytes DNA extraction and bisulfite conversion in order to hybridize the samples on the Infinium Methylation Beadchip. Bioinformatics analysis were done using the Champ pipeline. A total of 32 women participated in the study, 15 obese (IMC=45.1± 5.4 kg/m2; Age=39.3±11.5 years old) and 17 normal weight (IMC=22.5±1.7 kg/m2; Age=39.1 ±13.4 years old).

first: Natalia

last: Noronha

first: Carolina

middle: F

last: Nicoletti

first: Marcela

last: Pinhel


title: Single-nuclei RNA sequencing of HVC and RA in zebra finches

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

summary: The evolution of the six-layered neocortex is often credited with an increased capacity for complex behaviors and cognition in humans and other mammals. However, birds, despite lacking a laminated neocortex, display complex and non-instinctual behaviors including vocal learning, tool use, and problem-solving1,2. The evolution of brain circuits and cell-types supporting advanced behavioral repertoires remains poorly understood. Here in songbirds, we use single-cell RNA-sequencing to characterize the molecular identities of cells in the song motor pathway, a pallial circuit with function and connectivity that has been likened to the mammalian neocortex1,2. We find that each song region contains different glutamatergic excitatory projection neurons but similar sets of GABAergic inhibitory interneurons, similar to patterns of neuronal diversity in mammals and reptiles3,4. Song motor pathway glutamatergic neurons have gene expression patterns similar to those described in neocortical projection neurons, but at the level of transcription factor expression, display stronger similarity to neurons in the ventral pallium. We observed multiple GABAergic neuron classes that are conserved across amniotes, yet the most abundant class strongly resembles a cell-class that in mammals is not found in the neocortex but is present in non-neocortical pallial regions3,4. Thus, although pallial song-control regions contain neurons with similar molecular profiles to neocortical neurons, these pallial areas have a regional identity distinct from neocortex, indicating that complex behaviors such as vocal learning have evolved through the use of different brain circuits under similar functional constraints.

overall_design: We carried out single-nuclei RNA-sequencing of zebra finch HVC and RA. Multiple individuals were pooled within each library.

first: Devin

middle: P

last: Merullo

first: Todd

last: Roberts


title: Autonomous TGFβ signaling induces phenotypic variation in human acute myeloid leukemia

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Heterogeneity of leukemia stem cells (LSCs) is involved in their collective chemoresistance. To eradicate LSCs, it is necessary to understand the mechanisms underlying their heterogeneity. Here, we aimed to identify signals responsible for variation in LSCs in human acute myeloid leukemia (AML). While healthy human hematopoietic stem/progenitor cells robustly expressed endothelial cell-selective adhesion molecule (ESAM), AML cells exhibited heterogeneous ESAM expression. Interestingly, ESAM- and ESAM+ AML cells were mutually interconvertible, and RNA sequencing revealed activation of TGFβ signaling in these cells. AML cells secreted TGFβ1, which autonomously activated TGFβ pathway and induced their phenotypic variation. Surprisingly, TGFβ signaling blockade inhibited the variation and proliferation of AML cells. Therefore, autonomous TGFβ signaling underlying LSC heterogeneity may be a promising therapeutic target.

overall_design: We conducted RNA sequencing on ESAM-Hi and ESAM-Neg KG1a fractions immediately after sorting.

first: Yasuhiro

last: Shingai


title: The Chromatin Remodeler Chromodomain Helicase DNA Binding Protein 2 Promotes Colorectal Cancer Progression

city: Durham

first: Ergang

last: Wang

state: NC

address: C215, LSRC

department: PCB

institute: Duke University

summary: Integrative analysis of colorectal cancer (CRC) whole genomes and matched transcriptomes revealed that somatic promoter mutations are associated with increased Chromodomain helicase DNA-binding protein 2 (CHD2) levels. In both primary and metastatic CRC patients, elevated CHD2 levels are associated with worse prognosis and overall survival. We find that CHD2 increases promoter-transcription start site-chromatin accessibility and transcriptional upregulation of multiple oncogenes. In vitro, elevated CHD2 promoted CRC cell proliferation, migration and growth. In orthotopic xenografts, CHD2 promoted higher tumor burden and abdominal metastases, most prominently to the liver. FTD/TPI is an FDA approved chemotherapy for advanced chemo-refractory CRC. In orthotopic CRC models, FTD/TPI was highly effective in reducing metastases and prolonging survival for CHD2 high expressing CRCs. Thus, high CHD2 expression may be a potential CRC chemopredictive biomarker for FTD/TPI. Overall, these results provide new insights into the role of non-coding mutations and CHD2 levels to promote CRC growth and metastasis.

overall_design: Examination of CHD2 high, basal and low expressing HT29 cells

first: Mavee

last: Witherspoon

first: Tawny

last: Cuykendall

first: Eric

middle: M

first: Maria

last: Revuelta

first: Olivier

last: Elemento

first: Xiling

last: Chen

first: Ekta

last: Khurana

first: Steven

last: Lipkin


title: Isolating and Cryo-Preserving Pig Skin Cells for Single Cell RNA Sequencing Study

city: Lincoln

first: Chi

last: Zhang

state: NE

address: 1901 Vine Street

institute: University of Nebraska - Lincoln

summary: The pig skin architecture and physiology are similar to these of humans. Thus, the pig model is valuable for studying skin biology and testing therapeutics for skin diseases. The single-cell RNA sequencing technology allows quantitatively analyzing cell types, cell states, signaling, and receptor-ligand interactome at single-cell resolution and at high throughput. scRNA-Seq has been used to study mouse and human skins. To maximize the use of pig skin as a model system to study skin biology, we described a robust method for isolating and cryo-preserving pig single cells for scRNA-Seq. We showed that pig skin could be efficiently dissociated into single cells with high cell viability using the Miltenyi Human Whole Skin Dissociation kit and the Miltenyi gentleMACS Dissociator. In addition,  we showed that the subsequent single cells could be cryopreserved using DMSO without causing additional cell death, cell aggregation, or changes in gene expression profiles. Using the developed protocol, we were able to identify all the major skin cell types. The protocol and results from this study will be very valuable for the skin research scientific community.

overall_design: Examination of fresh and frozen single-cell samples of pig skin

first: Marc

last: Libault

first: Yuguo

last: Lei


title: MEIS-WNT5A axis regulates development of 4th ventricle choroid plexus

city: Shanghai

first: Feizhen

last: Wu

state: Shanghai

address: Zhangheng Road 825, Pudong

department: Intelligent Medicine Institute

institute: Fudan Univ, Shanghai, China

summary: MEIS1 binding is enriched in proximal Wnt5a promoter.

overall_design: Examination of potential Meis1 binding to Wnt5a in mouse E18.5 4th ventricle choroid plexus (4VChP).

first: Benoit

last: Laurent

middle: K

last: Lehtinen


title: Whole-transcriptome analysis of spleens from WT and myeloid ferritin H-deficient animals upon Salmonella infection

city: Innsbruck

first: Piotr

last: Tymoszuk

state: Tirol

address: Anichstrasse 35

department: University Clinic of Internal Medicine VI

country: Austria

institute: Medical University of Innsbruck

summary: Iron is an essential nutrient for humans as well as for pathogens. Hence, its correct distribution at the systemic and cellular level is mandatory for mounting an effective innate immune defense. Here we delved into the role of macrophage-expressed iron storing protein ferritin H (FTH) in immune response against the model intracellular pathogen Salmonella Typhimurium. Mice lacking FTH in the myeloid lineage (LysM-Cre+/+ Fthfl/fl) displayed impaired iron storage capacities in tissue leukocyte compartment, increased levels of labile iron in macrophages and an accelerated macrophage-mediated iron turnover. Without iron supplementation, wildtype (WT) and LysM-Cre+/+ Fthfl/fl animals showed comparable susceptibility to Salmonella infection. Interestingly, iron supplementation rapidly elicited symptoms of cytokine storm and drastically shortened survival of LysM-Cre+/+ Fthfl/fl mice. Mechanistically, we traced this phenotype back to labile iron-mediated hyperactivity of the inflammasome in FTH-deficient macrophages, culminating in excessive IL-1β secretion and secondary triggering of NF-kappaB-dependent inflammatory circuits. Accordingly, bacterial burden and cytokine levels in iron-loaded LysM-Cre+/+ Fthfl/fl mice could be effectively kept at bay by pharmacological inflammasome and IL-1β blockade. These findings point towards a previously unrecognized role of ferritin as an inhibitor of iron-dependent inflammasome activity in macrophages and a checkpoint of systemic innate response.

overall_design: 8-week old male WT (LysM-Cre-/- Fthfl/fl) and myeloid FthKO (LysM-Cre+/+ Fthfl/fl) animals were intravenously administered PBS or iron (2 mg elementary Fe, iron isomaltoside) and infected with 500 CFU Salmonella Typhimurium 3 days later. Spleen samples were isolated 12 hours post infection

first: David

last: Haschka


title: The underlying pathway involved in inter-subspecific hybrid male sterility in rice

city: Nanning

first: Jianwei

last: Shan

address: Daxue road

department: college of life science and technology

institute: Guangxi University

summary: Asian cultivated rice (Oryza sativa L.) consists of two major subspecies, indica and japonica. Inter-subspecific hybrids between indica and japonica, usually accompanying hybrid sterility, exhibit much more vigorous heterosis than intra-subspecific hybrids. f5 locus, also called S24 or Sb, confers significant effects on hybrid male sterility and segregation distortion. BC14F2 plants with f5-i/i, f5-j/j and f5-i/j genotype respectively, were used to dissect the underlying pathway of f5-caused hybrid male sterility via comparative transcriptome analysis. 350, 421, and 480 differentially expressed genes (DEGs) were identified from f5-i/j vs. f5-j/j, f5-j/j vs. f5-i/i, and f5-i/j vs. f5-i/i respectively. 145 DEGs demonstrated simultaneously differential expression in both f5-i/j vs. f5-j/j and f5-i/j vs. f5-i/i. Enrichment analysis with MapMan and AgriGO indicated that protein and DNA metabolism, and cell control related processes were enriched in the 145 DEGs. Stress and cell control related processes were enriched in the DEGs of f5-i/j vs. f5-j/j and f5-i/j vs. f5-i/i, whereas, these two processes were not enriched in the DEGs of f5-j/j vs. f5-i/i. Biotic and abiotic stress resistance genes were suppressed, which may result in pollen cell more sensitive to various stresses. The down regulation of ascorbate peroxidase (APX) may break the dynamic homeostasis of ROS (reactive oxygen species) and cause oxidative stress, which can damage cellular components. The expression of most of the heat shock protein (HSP) genes, which can protect proteins and cells from been destroyed, were also decreased. Based on these results, a model was proposed to summarize the underlying process for f5-caused rice hybrid male sterility. These results provide significant clues to further dissecting the molecular mechanism of f5-caused intersubspecific reproductive barrier.

first: Jiangyi

last: Yang


title: HRP2-MINA complex reprograms t(4;14) multiple myeloma epigenome to dictate chemosensitivity to proteasome inhibitors

city: Tianjin

first: Liu

last: Zhiqiang

address: 22 Qxiangtai Rd

institute: Tianjin Medical University

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


title: MITF WT and K243-mutant binding and expression [ChIP-Seq]

city: Oxford

first: Colin

last: Goding

address: ORCRB

institute: LICR, University of Oxford

summary: MITF is the master regulator of the melanocyte lineage and a melanoma lineage oncogene. It controls a wide range of target genes fulfilling many distinct functions, but relatively little is known about how its DNA-binding is regulated to select the correct target genes. The datasets presented here were used investigate the effects of MAPK signaling-induced MITF-acetylation on MITF activity in melanoma cells through ChIP-Seq of wild-type and acetyl-mutant MITF.

overall_design: 8 samples corresponding to WT and mutant MITF ChIP-Seq profiles in 501mel cells. Anti-HA ChIP-Seq in 501mel cells expressing empty vector was used as a control.

first: Robert

last: Siddaway


title: Analysis of 3D human airway epithelial cultures by single-cell RNA-seq

city: New York

first: Joseph

middle: C

last: Devlin

state: NY

address: 430 East 29th Street

department: Microbiology

institute: New York University Langone Health

summary: We report the application of single-cell-based sequencing technology for high-throughput profiling of cell types and and transcriptional state of cells in the complex tissue of the human airway epithelium. Our model system is that of polarized human airway epithelial cultures, differentiated from hTert-immortalized basal-like precursor cells.

overall_design: Examination of single-cell transcriptomics in pseudostratified human airway epithelial cultures

first: Dittmann

last: Meike

first: Koralov

last: Sergei

first: Ruggles

last: Kelly


title: IGF1R controls mechanosignaling in myofibroblasts required for pulmonary alveologenesis.

city: Cincinnati

first: John

middle: M.

last: Snowball

state: OH

address: 3333 Burnet Ave

department: Pulmonary Research

institute: Cincinnati Childrens Hospital

summary: Igf1r signaling is required in fibroblasts to drive the formation of new alveoli, and those activities is depend upon its regulation on mechanical property of myofibroblasts via an Akt/Yap mechanism.

overall_design: RNA-Seq analysis of FACS sorted Rosa-EGFP cells from P6 lungs after Igf1r was deleted at P0 by Gli1creER.

first: Hua

last: He

first: Jeff

last: Whitsett


title: Next Generation Sequencing Facilitates Quantitative Analysis of MSMEG_0179 overexpressed, MSMEG_0180 overexpressed and wild-type transcriptomes in Mycobacterium smegmatis strains

city: Wuhan

first: Jialing

last: Hu

address: 1 street of Shizi Shan

department: College of Life Science and Technology

institute: Huazhong Agricultural University

summary: Compare the gene expression difference between MSMEG_0179 overexpressed strain, MSMEG_0180 overexpressed strain and wild-type strain by RNA sequencing in Mycobacterium smegmatis. The goal of this study is detecting the regulation of transcriptional factors MSMEG_0179 and MSMEG_0180 on target genes expression.

overall_design: Three samples in triplicate are analyzed. The control sample is the wild-type strains in Mycobacterium smegmatis.

first: Zhengguo


title: HRP2-MINA complex reprograms t(4;14) multiple myeloma epigenome to dictate chemosensitivity to proteasome inhibitors [ChIP-Seq]

summary: Changes in these genes are probably a consequence of aging, and the real regulators governing BMSC senescence and osteogenesis are still unclear.In the current study, we report that nucleosome assembly-related protein NAP1L2 serves as an important regulator of both the senescence and osteogenic differentiation of BMSCs through inhibition of NF-κB signaling and recruitment of SIRT1 to deacetylate the H3K14ac level on promoters of osteogenic genes. Thus, targeting NAP1L2 using an aging antagonist such as NMN would benefit aging-related disease.

overall_design: Examination of histone modification in non-target control and knockdown HRP2 LP-1 cells and HRP2 modification in LP-1 cells

first: JingJing

last: Wang

first: Lin

last: Dang

first: Xu

last: Zhu


title: HRP2-MINA complex reprograms t(4;14) multiple myeloma epigenome to dictate chemosensitivity to proteasome inhibitors [RNA-Seq]

summary: Depletion of HRP2 induced remarkable resistance to PIs induced apoptosis of MM cells in vitro and in vivo, and suppressed expression of HRP2 was observed in bortezomib-resistant (BR) MM cells. Notably, HRP2 altered chemosensitivity more obviously in MM cells with t(4;14) translocation, and much remarkable resistant to PIs than other reagents. Moreover, HRP2 abolition of HRP2 augmented H3K27me3 modification, consequentially intensifying transcriptome alteration prone to cell survival and restriction of endoplasmic reticulum (ER) stress. Mechanistically, HRP2 recognized H3K36me2 and recruited the histone demethylases MYC-induced nuclear antigen (MINA) to degrade H3K27me3, released suppression on genes responsible for drug resistance, such as ATF3 and NR4A1. Thus, an EZH2 inhibitor, tazemetostat, synergistically sensitized anti-MM effect of bortezomib both in vitro and in vivo. Collectively, our study provides novel knowledge to understand the origination of chemoresistance in MM patients with t(4;14), and rationale for managing MM patients according to different genomic backgrounds.

overall_design: Non-target control and knockdown HRP2 knockdown LP-1 cells were divided into the following two groups : NC, HRP2 KD. And cells were harvested for gene expression profiling. Two replicates were performed.


title: Comparative Chromatin Dynamics and Expression Profiles of Neural Progenitor and Definitive Endoderm Lineage Differentiation in Two Mammalian Species

city: Irvine

first: Seyed

middle: Ali

last: Mortazavi

state: CA

address: 2300E Biological Sciences 3 519 Ring Rd

department: Developmental and Cellular Biology

institute: University of California, Irvine

summary: One of the fundamental questions in developmental biology is how lineage specification is regulated and what regulatory transcription factors and signaling molecules are required.  Lineage specification and differentiation are driven, at least in part, by chromatin remodeling causing changes in the accessibility of transcription factor binding sites.  Changes in expression of required transcription factors are also important in the regulation of differentiation.  To better understand which transcription factors drive differentiation and how these transcription factors differ between different species and differentiation lineages we differentiated ESCs into two different lineages, definitive endoderm and neural progenitors, and performed pooled RNA-seq and ATAC-seq in two different species, human and rat.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: Time-course of ESC differentiation into two distinct lineages, definitive endoderm and neural progenitor cells, in human and rat.

first: Christina

middle: W

last: Thai

first: Shan

last: Jiang

first: S

middle: A


title: A study of differential circRNA and lncRNA expressions in COVID-19-infected peripheral blood

city: yiwu

first: yingping

last: wu

address: shangcheng road N1

institute: Department of Clinical Laboratory, Fourth Affiliated Hospital of Zhejiang University School of Medicine

summary:
we found a total of 570 circRNA that have difference, among which 155 are up-regulated and 415 are down-regulated; and 898 lncRNA that have difference, in which 414 are up-regulated and 484 are down-regulated; and 476 mRNA that have difference, in which 98 are up-regulated and 378 are down-regulated.
In this work, we sequenced circRNA, lncRNA and mRNA from recurrent COVID-19 patients and healthy people, and compared the differences.

overall_design: In this study, total RNA was extracted from the whole blood of three recurrent COVID-19 patients and three healthy people for further microarray analysis.

first: Yingping

last: Wu

first: Tiejun

last: Zhao

first: Riqiang

last: Deng


title: A novel KRAB zinc finger gene has changed the balance of HES1 autoregulation during primate evolution

status: Public on Feb 10 2021

city: Santa Cruz

first: Ali

middle: S

last: Shariati

address: 1156 High St

department: Biomolecular Engineering

institute: University of California Santa Cruz

summary: KRAB zinc finger (KZNF) proteins are a class of transcriptional repressors important for epigenetic silencing of specific genomic regions. About 170 primate-specific KZNFs are present in the human genome. While KZNFs are primarily associated with repressing retrotransposon-derived DNA, evidence is emerging that they can be co-opted for other gene regulatory processes. We focused on the 19p12 locus, which shows copy-number variations associated with neurodevelopmental disorders, implying it is required for human brain development. The two genes in this locus, ZNF675 and ZNF681, arose via duplication in primates. Genetic deletion of ZNF675 caused developmental defects in cortical organoids and our data suggest that the observed neurodevelopmental phenotype is mediated by ZNF675 binding to the promoter of the neurodevelopmental gene HES1. We show that ZNF675 interferes with HES1 auto-inhibition, a process essential for maintenance of neural progenitors. As a striking example of how some KZNFs have integrated into pre-existing gene expression networks, these findings suggest the emergence of ZNF675 has caused a change in balance of HES1 autoregulation. The association of ZNF675 CNV with human developmental disorders suggests that this new balance has become essential for normal human brain development.

overall_design: Transcriptomics comparison of wild-type and ZNF675-KO H9 human embryonic stem cells differentiated to cortical organoids, isolated at day 28 of differentiation.

first: Gerrald

last: Lodewijk

first: Matthijs

last: de Geus

first: Rita

middle: L

last: Guimarães

first: Frank

last: Jacobs


title: Ribosomes act as cryosensors in plants

city: Cambridge

first: Philip

last: Wigge

address: 47 Bateman street

department: Sainsbury Laboratory

institute: Cambridge University

summary: Cold temperatures are a threat to temperate plants, and Arabidopsis thaliana has acquired an adaptive gene expression network controlled by CBF transcription factors. The CBFs are sufficient to enable plants to survive otherwise lethal subzero temperatures. Constitutive CBF expression causes delayed flowering and stunted growth, and plants have evolved the ability to restrict CBF expression to occur only in the cold. This allows plants to anticipate likely freezing events and selectively deploy cold tolerance. The mechanism by which cold stress is sensed is however unknown. Here we show that protein translation rates in plants are proportional to temperature, and reduced translation rates trigger a rise in intracellular free calcium that activates the CAMTA transcription factors, and these directly activate cold-induced gene expression.

overall_design: Single samples were taken at each time point. RNA-Seqs and ChIP-Seqs were performed for different genotypes at different temperature and objective time.

first: David

last: Guillaume-Schöpfer

first: Katja

last: Jaeger

first: Feng

last: Geng


title: Functional genomics identify distinct and overlapping genes mediating resistance to different classes of heterobifunctional degraders of oncoproteins

city: Boston

first: Ricardo

last: de Matos Simoes

state: MA

address: 450 Brookline AVE

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Heterobifunctional proteolysis-targeting chimeric compounds leverage the activity of E3 ligases to induce degradation of target oncoproteins and exhibit potent preclinical antitumor activity. To dissect the mechanisms regulating tumor cell sensitivity to different classes of pharmacological "degraders" of oncoproteins, we performed genome-scale CRISPR/Cas9-based gene-editing studies. We observed that myeloma cell resistance to "degraders" of different targets (BET bromodomain proteins, CDK9) and operating through CRBN (degronimids) or VHL is primarily mediated by prevention of, rather than adaptation to, breakdown of the target oncoprotein; involves loss-of-function for the cognate E3 ligase or interactors/regulators of the respective cullin-RING ligase (CRL) complex. The substantial gene-level differences for CRBN- vs. VHL-based degraders explains mechanistically the lack of cross-resistance for degraders targeting the same protein via different E3 ligase/CRLs.

overall_design: dBET6 (100nM or 500nM) or JQ1 (500nM) treatment to MM1S cells

first: Ryosuke

last: Shirasaki

first: Geoffrey

last: Matthews

first: Constantine

last: Mitsiades


title: Identification of the iron-limitation stimulon in Staphylococcus lugdunensis

city: Caen

first: Francois

last: Gravey

state: Normandy

address: Esplanade de la paix

institute: Normandy Université

summary: Using RNAseq approach, we performed global a transcriptomic analysis of cells incubated in absence and in presence of iron chelator in Staphylocuccus lugdunensis. 175 genes were identified as members of the iron-limitation stimulon (127 up- and 48 down-regulated).

overall_design: Comparison of gene expression between Staphylocuccus lugdunensis strains with or without 2,2′-dipyridyl (DIP)

first: Marion

last: Aubourg

first: François

first: Anne

last: Dhalluin

first: Jean-Christophe

last: Giard


title: Differential mRNA expression upon microRNA-125a overexpression in murine hematopoietic cells

city: Groningen

first: Leonid

last: Bystrykh

state: Groningen

address: A. Deusinglaan 1

department: European Research Institute for the Biology of Ageing - ERIBA

country: Netherlands

institute: University Medical Center Groningen

summary: We report differential gene expression in hematopoietic cells (lineage-Sca+) upon overexpression and transplantation of murine hematopoietic stem cells.

overall_design: MicroRNA-125a was overexpressed in murine hematopoietic stem cells (LSK/SLAM) and transplanted into lethally irradiated reciepients. Twelve weeks after transplantation, 2000 (lineage-Sca+) bone marrow cells were directly sorted into lysis buffer and snap frozen immediately before moving to library prep.

first: Daniëlle

middle: G

last: Luinenburg

first: Arthur

last: Svendsen


title: Characterization of chromatin accessibility in Oct4 expressing cells in cranial and trunk regions of 4 and 6 somite stage embryos

city: Palo Alto

first: Antoine

last: Zalc

address: 265 Campus Drive

institute: Stanford University

summary: We report chromatin acessibility of trunk and cranial Oct4+ cells in mouse embryos at 4 and 6 somites

overall_design: Oct4-GFP+ cells were sorted using flow cytometry from Oct4-GFP/+ embryos dissected at 4 and 6 somites stages

first: Rahul

last: Sinha

first: Gunsagar

last: Gulati

first: Daniel

middle: J

last: Wesche

first: Patrycja

last: Daszczuk

first: Tomek

last: Swigut

first: Irving

last: Weissman

first: Joanna

last: Wysocka


title: The FOS/AP-1 regulates the expression of selective genes involved in ovulation and luteinization in human granulosa cells

city: LEXINGTON

first: Yohan

last: Choi

state: KY

address: 800 Rose St, UKMC MS341

institute: University of Kentucky

summary: FOS, a subunit of the activator protein-1 (AP-1) transcription factor, has been implicated in various cellular changes. In the human ovary, the expression of FOS and its heterodimeric binding partners JUN, JUNB, and JUND increases in periovulatory follicles. However, the specific role of the FOS/AP-1 remains elusive. The present study determined the regulatory mechanisms driving the expression of FOS and its partners and functions of the FOS/AP-1 using primary human granulosa/lutein cells (hGLC). hCG induced a biphasic increase in the expression of FOS, peaking at 1-3h and 12h. The levels of JUN proteins were also increased by hCG, with varying expression patterns. Co-immunoprecipitation analyses revealed that FOS is present as heterodimers with all JUN proteins. hCG immediately activated PKA and p42/44MAPK signaling pathways, and inhibitors for these pathways abolished hCG-induced increases in the levels of FOS, JUN, and JUNB. To identify the genes regulated by FOS, high throughput RNA sequencing was performed using hGLC treated with hCG ± T-5224 (FOS inhibitor). Sequencing data analysis revealed that FOS inhibition affects the expression of numerous genes, including a cluster of genes involved in the periovulatory process such as matrix remodeling, prostaglandin synthesis, glycolysis/gluconeogenesis, and cholesterol biosynthesis. qPCR analysis verified hCG-induced, T-5224-regulated expression of a selection of these genes. Consistently, T-5224 attenuated hCG-induced increases in metabolic activities and cholesterol levels. This study unveiled potential downstream target genes of and a role for the FOS/AP-1 in granulosa cell metabolic changes and cholesterol biosynthesis in human periovulatory follicles.

overall_design: Cultured human granulosa-lutein cells treated with hCG and hCG+T-5224 were used to perform RNA-seq analysis.

first: Hayce

last: Jeon

first: James

last: Akin

first: Thomas

middle: E

last: Curry

first: Misung

last: Jo


title: Unbiased characterization of transcriptional heterogeneity of murine cranial neural crest cells

summary: We report murine cranial neural crest cells are heterogenous and identified a population of cells re-expressing canonical pluripotency factors

overall_design: Single-cell RNA sequencing of single cell sorted cells by flow cytometry directly into lysis buffer. Labelled cells were obtain from Wnt1::Cre; Rosa26TdTomato embryos dissected at 4, 6, 8 and 10 somites stages


title: Reactivation of the pluripotency program precedes formation of the cranial neural crest

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

overall_design: Refer to individual Series


title: Dual role of the unfolded protein response in the therapeutic effect of AZD1775 on TP53 mutant high grade serous ovarian cancer

first: Rouou

last: Xiao

state: hubei province

address: Donghu road

institute: Zhongnan hospital

summary: we demonstrate that the WEE1 inhibitor AZD1775 triggers endoplasmic reticulum (ER) stress and activates the PERK and IRE1α branches of the unfolded protein response (UPR) in TP53 mutant HGSOC cells. Upon AZD1775 treatment, PERK facilitates apoptotic signaling in these cells via activating CHOP, whereas IRE1α-induced spliced XBP1 (XBP1s) confers survival in response to WEE1 inhibition. Our data uncover an important dual role of UPR in TP53 mutant HGSOC cells in response to AZD1775, where additional inhibition of IRE1α-XBP1s signaling may offer synergistic efficacy.

overall_design: OVCAR8 cells were treated with DMSO or AZD1775 and the  mRNA expression levels were detected by RNA-seq.

first: Rourou

first: Lixin

last: You

first: Sheng

last: Xia

first: Chaoyang

last: Sun

first: Gang

last: Chen


title: Effect of PAK5 gene on miRNA expression in MDA-MB-231 cells

city: Shenyang

first: Yang

last: Li

state: Liaoning

address: No. 77, Puhe Road, Shenyang North New Area

department: Department of Cell Biology, Key Laboratory of Cell Biology, National Health Commission of the PRC, and Key Laboratory of Medical Cell Biology, Ministry of Education of the PRC

institute: China Medical University

summary: P21-activated kinase 5 (PAK5) plays an important role in tumors. Yet,  the connection of PAK5 with miRNA biogenesis is so far unclear.In this work, we studied the change in microRNA profiles of breast cancer MDA-MB-231 cells as a result of overexpression of PAK5 protein.

overall_design: Total RNA was prepared from MDA-MB-231 cells with overexpression of Flag-PAK5 gene as well as from control MDA-MB-231(Flag vector) cells.

first: Yao

last: Xing

first: Feng


title: CytoScan HD array for multiple myeloma samples

city: Little rock

first: CAN

last: LI

state: AR

address: 4301 W MARKHAM ST

institute: University of Arkansas for Medical Sciences

summary: Affymetrix CytoScan HD array for newly diagnosed multiple myeloma patients.

overall_design: We performed and analyzed CytoScan HD arrays from CD138-selected bone marrow aspirate samples of multiple myeloma patients.

first: Fenghuang

last: Zhan


title: Cancer growth and metastasis gene pathways are regulated by Methyl-CpG Binding Domain Protein 2 (Mbd2) in liver cancer and are altered by the ubiquitous methyl donor S-adenosyl methionine (SAM)

city: BeiJing

first: Wang

last: Yan

address: 16# LinCui Road

institute: Institute of Psychology

type: Methylation profiling by high throughput sequencing

summary: Perpose:We examined here whether SAM, which alters DNA methylation dynamics, interferes with the activity of Methyl-CpG Binding Domain Protein 2(Mbd2). Methods: mRNA of MBD2 knocked down of Skhep1 and HepG2 cells were generated by deep sequencing using Illumina GAIIx. DNA enriched by our designed microarray of MBD2 knocked down Skhep1 and HepG2  cells were also generated by deep sequencing using Illumina GAIIx. ChIP (Chromatin immunoprecipitation) was performed using ChIP-IT Express Kit with MBD2 antibody of SAM treated Skhep1, HepG2 and NorHep cells. concluds: SAM treatment results in reduction and redistribution of Mbd2 binding across genomic features in liver cancer cells, which is different from the response in untransformed liver cells. There is significant overlap between genes whose Mbd2 binding, DNA methylation and transcription are altered by Mbd2 depletion or SAM treatment. These data suggest that Mbd2 has a cancer specific footprint in binding, DNA methylation and transcription in liver cancer cells that is altered by SAM treatment. SAM selective impact on liver cancer cells is partially mediated by altering cancer specific Mbd2 binding. These data provide a molecular rationale for using either SAM or other Mbd2 modulators for treating/preventing liver cancer.

first: Yan

last: Wang

first: Moshe

last: Zsyf


title: Expression data (mRNA) from GD-9.5 (E9.5), Folr1+/+ (Folr1 WT) and Folr-/- (Folr1 KO) mouse embryos

city: LOUISVILLE

first: Partha

last: Mukhopadhyay

address: 501 S PRESTON ST

department: Division of Craniofacial Development & Anomalies

institute: University of Louisville

summary: Folic acid is a nutrient essential for embryonic development. Folate deficiency can cause embryolethality or neural tube defects and orofacial anomalies. Folate receptor 1 (Folr1), is a folate binding protein that facilitates the cellular uptake of dietary folate. Animal studies highlighted critical roles of folate in embryogenesis including orofacial development. Orofacial clefts were observed in the offspring of experimental animals on folic acid-deficient diets. Mice lacking Folr1 (the gene encoding folate receptor 1) also demonstrated a variety of orofacial defects. In order to investigate potential roles of Folr1 during embryogenesis and to identify various genes functionally associated with this receptor, total RNA preparations from gestation day (GD)-9.5, Folr1+/+ and Folr1-/- mouse embryos were used to hybridize messenger RNA arrays, to identify genes expressed in wild type (Folr1+/+) and knockout (Folr1-/-) embryos.

overall_design: We used total RNA preparations from gestation day (GD)-9.5 Folr1+/+ (wild type) mouse embryos (3x biological replicates/samples) and Folr1-/- (knockout) mouse embryos (2x biological replicates/samples) to perform global gene (mRNA) expression profiling analyses. For messenger RNA profiling we used Affymetrix GeneChip® Mouse Genome 430A arrays. One of the objectives of this study is to identify and compare the expression of constitutively and differentially expressed genes between Folr1+/+ (Wild type) and Folr1-/- (knockout) mouse embryos.

first: Ratnam

last: Seelan

first: Robert

last: Greene

first: M

last: Pisano


title: Therapy of Established Tumors with Rationally Designed Multiple Agents Targeting Diverse Immune-Tumor Interactions: Engage, Expand, Enable

city: bethesda

first: james

middle: w

last: hodge

state: md

address: 10/8b13, 9000 rockville pike

department: LTIB

institute: NCI

summary: Immunotherapy of immunologically cold solid tumors may require multiple agents to (a) engage immune effector cells, (b) expand effector populations and activities, and (c) enable immune response in the tumor microenvironment (TME). To target these distinct phenomena, we strategically chose five clinical-stage immuno-oncology agents, namely, (a) a tumor antigen-targeting adenovirus-based vaccine (Ad-CEA) and an IL-15 superagonist (N-803) to activate tumor specific T cells, (b) OX40 and GITR agonists to expand and enhance the activated effector populations, and (c) an IDO inhibitor (IDOi) to enable effector cell activity in the TME. Flow cytometry, TCR sequencing, and RNAseq analyses showed that in the CEA-transgenic murine colon carcinoma (MC38-CEA) tumor model, Ad-CEA + N-803 combination therapy resulted in immune-mediated anti-tumor effects and promoted the expression of costimulatory molecules on immune subsets, OX40 and GITR, and the inhibitory molecule IDO. Treatment with Ad-CEA + N-803 + OX40 + GITR + IDOi, termed the pentatherapy regimen, resulted in the greatest inhibition of tumor growth and protection from tumor rechallenge without toxicity. Monotherapy with any of the agents had little to no anti-tumor activity, while combining two, three, or four agents had minimal anti-tumor effects. Immune analyses demonstrated that the pentatherapy combination induced CD4+ and CD8+ T cell activity in the periphery and tumor and anti-tumor activity associated with decreased Treg immunosuppression in the TME. The pentatherapy combination also inhibited tumor growth and metastatic formation in 4T1 and LL2-CEA murine tumor models.  Significance: This study provides the rationale for the combination of multi-modal immunotherapy agents to engage, enhance, and enable adaptive anti-tumor immunity.

overall_design: CEA-Transgenic mice were implanted with CEA expressing MC38-CEA tumors. Mice were treated with nothing (none)_, Ad-CEA vaccine, IL-15 superagonsit N803, OX40 mab, GITR mab, IDO inhibotor (epacadostat), pr the combination (vaccine, N803, OX40, 41BB, IDO inhibotor) aka pentatherapy.,Tumor were harvested in Day 28 post tumor transplant.

first: James

last: Hodge


title: Immune synapse instructs epigenomic and transcriptomic functional reprogramming in dendritic cells

city: Madrid

first: Enrique

last: Vazquez de Luis

state: Madrid

address: Melchor Fernandez Almagro, 3

country: Spain

institute: CNIC

summary: Understanding the fate of dendritic cells (DCs) after productive immune synapses (postsynaptic DCs) with T cells during antigen presentation has been largely neglected in favor of deciphering the nuances of T-cell activation and memory generation. Here, we describe that postsynaptic DC switch their transcriptomic signature, correlating with epigenomic changes including DNA accessibility and histone methylation. We focus on the chemokine receptor Ccr7 as a proof of concept gene that is increased in postsynaptic DCs. Consistent with our epigenomic observations, post-synaptic DCs migrate more efficiently towards CCL19 in vitro and display enhanced homing to draining lymph nodes in vivo. This work describes a new DC population whose transcriptomics, epigenomics and migratory capacity change in response to their cognate contact with T cells.

overall_design: We performed RNA and ATAC sequencing using CD11c+ MHCIIhigh dendritic cells incubated with LPS and pulsed (psDCs) or not (nsDCs) with the peptide OVA323-339 and then cocultured with CD4+ OT-II T cells for 24h.

first: Ana

last: Alcaraz-Serna

first: Eugenio

last: Bustos-Morán

first: Irene

last: Fernández-Delgado

first: Diego

last: Calzada-Fraile

first: Daniel

last: Torralba

first: Ester

last: Marina-Zárate

first: Erika

last: Lorenzo-Vivas

last: Vázquez

first: Juliana

last: Barreto de Alburquerque

first: Nora

last: Ruef

first: Manuel

last: Gómez

first: Fátima

last: Sánchez-Cabo

last: Dopazo

first: Jen

middle: V

last: Stein

first: Almudena

last: Ramiro

first: Francisco

last: Sánchez-Madrid


title: MAPS integrates regulation of actin-targeting effector SteC into the virulence control network of Salmonella small RNA PinT

city: Würzburg

first: Tom

last: Gräfenhan

address: Josef-Schneider-Str. 2, Bau D15

department: Core Unit SysMed

institute: University of Wuerzburg

summary: In this study we take an integrative approach to capturing targets of the Hfq- associated sRNA PinT, a known post-transcriptional timer of the two major virulence programs of Salmonella enterica, using MS2 affinity purification and RNA- sequencing (MAPS).

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design: MS2 affinity purification and RNA- sequencing (MAPS) to identify PinT ligands in bacteria under in-vitro conditions mimicking specific stages of the infection cycle, and in bacteria growing inside macrophages.

first: Sara

last: Santos

first: Thorsten

last: Bischler

first: Alexander

last: Westermann

first: Jörg

last: Vogel


title: Expression data from APC min/+ mice treated with Lon protease

city: Lund

first: Ines

last: Ambite

address: Klinikgatan 28

department: Laboratory Medicine

institute: Lund University

summary: MYC has been named the quintessential oncogene and is deregulated in the majority of human cancers. Still, finding c-MYC inhibitors for therapeutic use has been problematic and MYC itself has long been viewed as “undruggable”. Here we present a novel strategy for achieving c-MYC inhibition, involving specific bacterial effector molecules. We made the surprising observation that uropathogenic E. coli activate c-MYC degradation and attenuate MYC expression in host cells and tissues. We further identified effector molecules responsible for this effect. The bacterial Lon protease is shown to rapidly degrade c-MYC and therapeutic efficacy is demonstrated in bladder and colon cancer models. Long-term protection, defined by delayed tumor progression, increased survival and low toxicity further supports the therapeutic potential of Lon. These results suggest that bacteria have evolved strategies to control c-MYC tissue levels in the host, which can be exploited to target c-MYC therapeutically in different cancers.

overall_design: C57BL/6J-APCmin/J mice develop spontaneous intestinal adenoma formation, mice were used at either the age of 11 weeks, or 20 weeks. The mice were treated twice daily for 14 days using oral gavage (200 µl) of E. coli 536 WT supernatants (10 µg/kg) or using recombinant Lon Protease (250 µg/ml). At sacrifice, intestines were aseptically harvested for mRNA extraction and analysis. For long-term follow-up experiments, mice were treated per-orally, twice daily for 14 days with Lon protease (250 µg/ml) or received PBS (Sham). Surviving animals were sacrified at week 25. Isolated RNA was subjected to Affymetrix whole genome transcriptomic analysis. For toxicity testing in C57BL/6J WT mice (8 weeks old) were exposed to recombinant Lon protease (rLon) per-orally twice daily for 14 days. Controls received PBS.

first: Murphy

last: Wan

first: Hien

last: Tran

first: Catharina

last: Svanborg


title: Title:  Leaf transcriptomics  of Catalan A. thaliana demes under alkaline and carbonated stress at 3h and 48 hours.

city: Cerdanyola del Vallès

first: Laura

last: Pérez-Martín

state: Barcelona

address: Cerdanyola del Vallès

department: Biologia animal biologia vegetal i ecologia

institute: Universitat Autònoma de Barcelona

summary:
Purpose: High carbonate and bicarbonate concentrations of calcareous soils with high pH can affect crop  performance due to different constraints. The goal of this study is to perform a comparative transcriptomic analysis using demes moderate-tolerance and sensitive under alkaline stress ( high pH 8.3 and  10 mM NaHCO3)
Methods: Transcriptomic analysis was performed on two naturally selected Arabidopsis thaliana demes. Carbon soil tolerant A1(c+) and the sensitive T6(c-). Plants 15 day-old were exposed for 3 or 48 h to either pH stress alone (pH 5.9 vs pH 8.3 adjusted by BTP and MES buffers) or to alkaline stress (pH 8.3) caused by 10 mM of
Results Shoot transcriptome analysis revealed that bicarbonate quickly (3 h) induced Fe-deficiency related genes in T6(c-) leaves, while in A1 (c+) main initial changes were found in receptor-like proteins (RPL), jasmonate (JA) and salicylate (SA) pathways, methionine-derived glucosinolate (GS), Sulphur starvation, starch degradation, and cell cycle.
Conclusions:  Our results suggest that leaves of carbonate tolerant plants do not sense iron deficiency as fast as sensitive ones.  This is in line with the ability to translocate more iron to aerial parts, producing a higher biomass and maintaining silique production. In leaves of A1(c+) plants, the activation of other genes related to apoplastic stress perception, signal transduction, GS, sulphur acquisition, and cell cycle regu-lation precedes the induction of iron homeostasis mechanisms yielding an efficient response to bicarbonate stress

overall_design: Plant mRNA profile from 15-day old plant subjected in 3 hours and 48 under treatment. 3 technical replicate from 2 biological replicate.

first: Silvia

last: Busoms

first: Roser

last: Tolrà

first: Charlotte

last: Poschenreider


title: Giardia lamblia WB: 5'5npac control vs pPMBF1

city: Taipei

first: Chin-Hung

last: Sun

address: Department of Parasitology, College of Medicine, National Taiwan University

department: Department of Parasitology

country: Taiwan

summary:
Transcriptional profiling of Giardia lamblia WB comparing control 5'5npac cells with pPMBF1 cells.
Multiprotein bridging factor 1 (MBF1) gene family proteins are involved in cell growth and differentiation in various organisms. We asked whether Giardia MBF1-like protein can induce various endogenous genes. We used epitope-tagged system to overexpress Giardia MBF1 by constructing and transfecting pPMBF1, a plasmid for expressing MBF1, to trophozoites. The control cell line is 5'5npac cell line, which expressed only the puromycin selection marker. To understand the effect of MBF1 overexpression on transcription profiles, we performed microarray analysis for pPMBF1 and 5'5npac cell lines.

overall_design: Two-condition experiment 5'5npac cells with pPMBF1 cells.


title: Expression data profile of A498 cells infected with E. coli 536 or PAI I delation mutant

overall_design: A498 kidney epithelial cells were infected with 10^5 CFU/ml of E. coli 536 or E. coli 536 PAI I deletion mutant for 4 hours. Cells with culture medium with PBS were used as a control. Isolated RNA was subjected to Affymetrix whole genome transcriptome analysis.

first: Caterina

last: Cafaro


title: Expression data from mice bladder with MB49-induced cancer treated with Lon protease

overall_design: Bladder cancer was induced in C57BL/6J female mice by intravesical instillation of MB49 cells. The treatment group received Lon protease (250 µg/ml) or E. coli 536 or PAI I536 bacterial supernatant (approximately 1 hour) by intravesical instillation on days 3, 5, 7, 9 and 11. Sham treated mice received PBS and healthy mice bladders were used as control. Bladder samples were collected after 12 days or 27 days (follow-up). Isolated RNA was subjected to Affymetrix whole genome transcriptomic analysis. For long-term experiments, mice were treated for 12 days with Lon protease (250 µg/ml) followed by twice weekly until day 35. For toxicity testing in C57BL/6J healthy female mice, recombiant Lon protein (250 µg/ml) was instilled intravesically on days 3, 5, 7, 9 and 11 and bladders were collected for RNA isolation after 12 days. Controls received PBS. Isolated RNA was subjected to Affymetrix whole genome transcriptomic analysis.


title: Bacterial effect on gene expression


title: Ubiquitin-dependent transfer of PAF1c from MYC onto RNA Polymerase controls double-strand break repair at active promoters [ChIP-seq BI8626]

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

summary:
MYC family proteins are oncogenic transcription factors that can globally affect the function of RNA Polymerase II (RNAPII). The ability of MYC proteins to promote transcription elongation depends on their ubiquitination, but the underlying mechanism and its biological relevance are unknown. Here we show that MYC and the Polymerase II associated factor, PAF1c, interact directly and their function is mutually dependent, since the specific binding of MYC to active promoters depends on PAF1c and, conversely, PAF1c is required for MYC-dependent pause release.
Upon binding, PAF1c is rapidly transferred from MYC onto RNAPII and this transfer is driven by the HUWE1 ubiquitin ligase. Both MYC and HUWE1 globally control histone H2B ubiquitylation, which promotes transcriptional elongation and alters chromatin structure for double-strand break repair. Consistently, MYC suppresses the accumulation of double-strand breaks at promoters in response to topoisomerase II inhibition.
While depletion of PAF1c has only minor effects on MYC-dependent gene expression, MYC induces rampant transcription-dependent DNA damage in PAF1c-depleted cells. We propose that the HUWE1-dependent transfer of PAF1c from MYC onto RNAPII is critical for absorbing the topological stress accompanied with deregulated and oncogenic transcription.

overall_design: U2OS cells expressing doxycycline-inducible MYC. Treated with/without doxycycline for 24 hrs and with or without BI8626 for 4 hrs

first: Theresa

last: Endres

first: Daniel

last: Solvie


title: Temporally Distinct Myeloid Cell Reponses Mediate Damage and Repair After Cerebrovascular Injury.

city: Bethesda

first: Kory

middle: R

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

country: USA

institute: NINDS/NIH

summary: Cerebrovascular injuries can cause severe edema and inflammation that adversely affect human health. Here, we observed recanalization after successful endovascular thrombectomy for acute large vessel occlusion was associated with cerebral edema and poor clinical outcomes in patients who experienced hemorrhagic transformation. To understand this process, we developed a cerebrovascular injury model using transcranial ultrasound that enabled spatiotemporal evaluation of resident and peripheral myeloid cells. We discovered that injurious and reparative responses diverged based on time and cellular origin. Resident microglia initially stabilized damaged vessels in a purinergic receptor-dependent manner, which was followed by influx of myelomonocytic cells that caused severe edema. Prolonged blockade of myeloid cell recruitment with anti-adhesion molecule therapy prevented severe edema but also promoted neuronal destruction and fibrosis by interfering with vascular repair later orchestrated by pro-inflammatory monocytes and pro-angiogenic repair-associated microglia (RAM). These data demonstrate how temporally distinct myeloid cell responses can contain, exacerbate, and ultimately repair a cerebrovascular injury.

overall_design: Bulk RNA-Seq profiling of twelve different B6 mice (4 uninjured, 4 injured, 4 injured with αLFA1/VLA4).

first: Panagiotis

last: Mastorakos

first: Nicole

last: Mihelson

first: Marie

last: Luby

first: Scott

last: Burks

first: Amie

last: Hsia

first: Jaclyn

last: Witko

first: Joseph

last: Frank

first: Lawrence

last: Latour

first: Dorian

middle: B

last: McGavern


title: Ubiquitylation of MYC couples transcription elongation with double-strand break repair at active promoters [CHIP-seq_MYC-ER]

overall_design:
U2OS cells which stably express a MYC-ER system. Cells were either treated with ETOH OR 4-OHT (200 nM) for 10 min or 30 min
Input samples for ChIPseq_MYCER rep1: For each of the conditions '0min' (= ethanol treatment only), '10min', '30min',  two separate 'input' chromatin samples were prepared, designated as 'rep1A'and 'rep1B'.  All six resulting fastq files were subsequently merged. This merged input file was mapped to hg19 and randomly subsampled to different read numbers, resulting in the bedgraph files ChIPseq_MYCER_INPUT_CTR9_rep1.bedgraph, ChIPseq_MYCER_INPUT_MYC_rep1.bedgrap, ChIPseq_MYCER_INPUT_pS2_rep1.bedgraph, to be used as controls for the CTR9, MYC, and pS2 ChIPseq samples, respectively.


title: Ubiquitin-dependent transfer of PAF1c from MYC onto RNA Polymerase controls double-strand break repair at active promoters (BLISS II)

overall_design: U2OS cells expressing doxycycline-inducible MYC, shRNA targeting CTR9 or control and K562 cells carrying endogenously AID-tagged MYC. Treated with/without doxycycline for 24 hrs, with or without Etoposide for 3 hrs and with or without IAA for 3.5h


title: HDAC8i/NAMPTi combination on the transcriptomes of leukemia initiating cells of AML patients

city: Columbus

first: Pu

last: Zhang

address: 1258 Bunkerhill Blvd, AptB

institute: Ohio State University

summary: 300 cell RNA-seq on FACS-sorted leukemia initiating cells (CD34+CD38-) from AML patients treated ex vivo with AR-42, KPT-9274 and AR-42/KPT-9274 combination

overall_design: Bone marrow cells from 5 patients were treated with vehicle, single agents or drug combination ex vivo for short time period (12 hours). Treated LICs were analyzed for transcriptional differences and DNA repair mechanisms were highlighted.

first: P

first: R

last: Lapalombella

last: Yan


title: Expression data of peripheral blood cells from mice after trauma/hemorrhage

city: Ulm

first: Markus

last: Huber-Lang

address: Helmholtzstrasse 8/1

department: Institute of Clinical and Experimental Trauma-Immunology

institute: University Hospital Ulm

summary:
The immune response following trauma represents a major driving force of organ dysfunction and poor outcome. Therefore, we investigated the influence of an additional hemorrhagic shock (HS) on the early posttraumatic immune dysbalance in the whole population of blood leukocytes.
After additional HS in PT mice, gene expression of pathways related to the innate immunity, such as IL-6 production, neutrophil chemotaxis, cell adhesion, and toll-like receptor signaling was up-regulated, whereas pathways of the adaptive immune system, such as B- and T-cell activation as well as the MHC class II protein complex were down-regulated.

overall_design: A well-established murine polytrauma (PT) model with or without an additional pressure-controlled HS (mean arterial pressure of 30 mmHg (±5 mmHg) for 60 mins, afterwards fluid resuscitation with balanced electrolyte solution four times the volume of blood drawn) was used. C57BL/6 mice were randomized into a control, PT and PT+HS group with three animals in each group. Four hours after trauma, corresponding to three hours after induction of hemorrhage, RNA was isolated from all peripheral blood leukocytes and a microarray analysis was performed. Enrichment analysis was conducted on selected genes strongly modulated by the HS.

first: Lisa

last: Debler

first: Annette

last: Palmer

first: Sonja

last: Braumüller

first: Bettina

last: Klohs

first: Tom

last: Mollnes

first: Karlheinz

last: Holzmann

first: Rebecca

last: Halbgebauer


title: Blood-brain barrier alterations in human brain tumors revealed by genome-wide transcriptomic profiling

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

institute: SIB Swiss Institute of Bioinformatics

summary: Brain tumors, either primary or secondary, have limited therapeutic options despite advances in understanding tumor driving gene mutations and heterogeneity within tumor cells. The cellular and molecular composition of brain tumor stroma, an important modifier of tumor growth, has been less investigated and understood. Especially, studies focusing on brain tumor blood vessels are rare, yet, the brain endothelium and the blood-brain barrier (BBB) are the major obstacle for efficient drug delivery. In this study we have employed the RNA sequencing approach to get insights into transcriptional alterations of endothelial cells isolated from primary and secondary brain tumors. We used an immunoprecipitation approach to enrich for endothelial cells of normal brain, glioblastoma (GBM) and adenocarcinoma brain metastasis (BM). Analysis of the endothelial transcriptome showed that both the GBM and the BM vasculature showed deregulation of genes implicated in cell proliferation, angiogenesis, deposition of extracellular matrix (ECM), and deregulation of genes defining the BBB dysfunction module. We describe alterations in the BBB genes in the GBM and BM vasculature and identify proteins that could be exploited for developing drug delivery platforms into primary and secondary brain tumors. In addition, we identify deregulated expression of genes defining vessel-associated fibroblasts in the GBM tissue, highlighting that the cellular composition of the brain tumor stroma deserves further investigation.

overall_design: Transcriptomic analysis of endothelial cells isolated from primary and secondary brain tumors.

first: Johanna

last: Schaffenrath

first: Elisabeth

last: Rushing

first: Mauro

last: Delorenzi

first: Flavio

last: Vasella

first: Luca

last: Regli

first: Marian

last: Neidert

first: Annika

last: Keller


title: MOLECULAR PROFILING OF DECOMPENSATED CIRRHOSIS BY A NOVEL microRNA SIGNATURE

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

institute: CIBEREHD

summary:
Objectives
Non-invasive staging of decompensated cirrhosis is an unmeet clinical need. The aims of this study were to characterize and validate a novel miRNA signature to stage decompensated cirrhosis and predict the portal pressure and cardiac dysfunction response to non-selective beta-blockers (NSBB).
Design
Serum samples from patients with decompensated cirrhosis (n=36) and healthy controls (n=36) were tested for a novel signature of five miRNAs (miR-452-5p, miR-429, miR-885-5p, miR-181b-5p, and miR-122-5p) identified in the secretome of primary human hepatocytes, and three miRNAs (miR-192-5p, miR-34a-5p and miR-29a-5p) previously discovered as biomarkers of chronic liver disease. All patients had ascites, that was refractory in 18 (50%), and were placed on NSBB for variceal bleeding prophylaxis. In all patients, serum miRNAs, hepatic venous pressure gradient (HVPG), and echocardiogram study was performed before and 1 month after NSBB.
Results
Cirrhotic patients had lower serum levels of miR-429, miR-885-5p, miR-181b-5p, miR-122-5p, miR-192-5p and miR-29a-5p (p<0.05). miR-452-5p and miR-429 expression were lower in NSBB responders  (p=0.006). miR-181b-5p expression was greater in refractory- than in diuretic sensitive ascites (p=0.008) and correlated with serum creatinine. miR-452-5p and miR-885-5p were inversely correlated with baseline systemic vascular resistance (ρ=-0.46 p=0.007; and ρ=-0.41 p=0.01 respectively), and with diminished systolic contractility in patients with refractory ascites after NSBB (ρ=-0.55 p=0.02; and ρ=-0.55 p=0.02, respectively).
Conclusion
Analysis of a miRNA signature in serum distinguishes patients with decompensated cirrhosis who show more severe systemic circulatory dysfunction and compromised systolic function after beta-blockade, and those more likely to benefit from NSBB.

overall_design: Exosomes from three samples with decompesated cirrhosis and three healthy samples

first: J

last: Gracia-Sancho

last: Falcón

first: A

last: Albillos

first: R

last: Bañares