title: Multiscale Analysis of Extracellular Matrix Remodeling in the Failing Heart

city: Brno

first: Ana

middle: Rubina

last: Perestrelo

address: Studentska

department: CTM

country: Czech Republic

institute: ICRC

summary:
Rationale: Cardiac extracellular matrix (ECM) comprises a dynamic molecular network providing structural support to heart tissue function. Understanding the impact of ECM remodeling on cardiac cells during heart failure (HF) is essential to prevent adverse ventricular remodeling and restore organ functionality in affected patients.
Objectives: We aimed to (i) identify consistent modifications to cardiac ECM structure and mechanics that contribute to HF and (ii) determine the underlying molecular mechanisms.
Methods and Results: We first performed decellularization of human and murine ECM (dECM) and then analyzed the pathological changes occurring in dECM during HF by atomic force (AFM), two-photon microscopy, high-resolution 3D image analysis and computational fluid dynamics (CFD) simulation. We then performed molecular and functional assays in patient-derived cardiac fibroblasts (CFs) based on YAP-TEAD mechanosensing activity and collagen contraction assays.
The analysis of HF dECM resulting from ischemic (IHD) or dilated cardiomyopathy (DCM), as well as from mouse infarcted tissue, identified a common pattern of modifications in their 3D topography. As compared to healthy heart, HF ECM exhibited aligned, flat and compact fiber bundles, with reduced elasticity and organizational complexity.
At the molecular level, RNA sequencing of HF CFs highlighted the overrepresentation of dysregulated genes involved in ECM organization, or being connected to TGFß1, Interleukin-1, TNF-alpha and BDNF signaling pathways. Functional tests performed on HF CFs pointed at mechanosensor YAP as a key player in ECM remodeling in the diseased heart via transcriptional activation of focal adhesion assembly.
Finally, in vitro experiments clarified pathological cardiac ECM prevents cell homing, thus providing further hints to identify a possible window of action for cell therapy in cardiac diseases.
Conclusions: Our multi-parametric approach has highlighted repercussions of ECM remodeling on cell homing, CF activation and focal adhesion protein expression via hyper-activated YAP signaling during HF.
Key words: Decellularization, extracellular matrix, dilated cardiomyopathy, ischemic heart disease, YAP, dilated cardiomyopathy, mechanobiology.

overall_design: RNA sequencing of DCM CFs from 2 patients (DCMA and DCMB) and 1 healthy CFs overexpressing YAP (YAP 8SA). 1 Healthy CFs were used as control or reference for differential gene expression analysis. The experiment was perfomed in triplicate.

middle: R

middle: C

last: Silva

first: Jorge

last: Oliver-De La Cruz

first: Fabiana

last: Martino

first: Vladimír

last: Horváth

first: Guido

last: Caluori

first: Ondřej

last: Polanský

last: Vinarský

last: Azzato

first: Giuseppe

last: de Marco

first: Víta

last: Žampachová

first: Petr

last: Skládal

first: Stefania

last: Pagliari

first: Alberto

last: Rainer

first: Perpétua

last: Pinto-do-Ó

first: Alessio

last: Caravella

first: Kamila

last: Koci

first: Diana

last: Nascimento

first: Giancarlo

last: Forte


title: Transcriptional response of Lotus japonicus roots to karrikin1 and rac-GR24

status: Public on Oct 26 2020

city: Freising

first: Caroline

last: Gutjahr

address: Emil Ramann Str. 4

department: TUM School of Life Sciences Weihenstephan

country: Germany

institute: Technical University of Munich

summary: Since roots showed different developmental responses to the two compounds, we asked whether this was also reflected in the transcriptome

overall_design: The 17 day old roots were incubated for 1h, 2h or 6h in 0.5x Hoagland solution containing solvent (control) or  1µM karrikin1 or 1µM rac-GR24

first: C

first: M

last: Griesmann

first: Y

last: Tang

last: Udvardi


title: Transcriptional programs of circuit assembly in the Drosophila visual system

city: Los Angeles

first: Yerbol

middle: Z.

last: Kurmangaliyev

state: CA

address: 675 Charles E. Young Drive South

country: USA

institute: University of California, Los Angeles

type: Expression profiling by high throughput sequencing

summary: Precise patterns of synaptic connections between neurons are encoded in their genetic programs. Here we used single-cell RNA sequencing to profile neuronal transcriptomes at multiple stages in the developing Drosophila visual system. We devised an efficient strategy for profiling neurons at multiple time points in a single pool, thereby minimizing batch effects and maximizing the reliability of time-course data.  A transcriptional atlas spanning multiple stages was generated including more than 150 distinct neuronal populations; of these 88 were followed through synaptogenesis. This analysis revealed a common (pan-neuronal) program unfolding in highly coordinated fashion in all neurons, including genes encoding proteins comprising the core synaptic machinery and membrane excitability. This program is overlaid by cell type-specific programs with diverse cell recognition molecules expressed in different combinations and at different times. We propose that a pan-neuronal program endows neurons with the competence to form synapses and cell type-specific programs control synaptic specificity.

overall_design: Single-cell transcriptional atlas of the developing Drosophila visual system. A transcriptional atlas covers 9 stages of pupal development (every 12 hours).

middle: Z

first: Lawrence

middle: S

last: Zipursky


title: Ascending colon-derived mucin-type O-glycans form key mucus layers encapsulating microbiota in the colon (RNA-seq)

status: Public on Oct 28 2020

first: David

last: Casero

address: 610 Charles Young Drive East

department: Pathology and Laboratory Medicine

institute: UCLA

summary: The colon contains a dense metabolically potent microbiota. The colonic O-glycan-rich mucus has been recognized as a key barrier to prevent microbial intrusion, but how this system forms and functions remains unclear. Here, we discovered that the colon mucus is mainly forged by microbiota-dependent secretion of O-glycosylated Muc2 by goblet cells in the ascending colon, where it seamlessly encapsulates the fecal materials including the microbiota. Deletion of O-glycans in the ascending colon impaired the segregating function of the mucous coating, leading to altered structure and metabolic output of the microbiota, and transcriptional homeostasis of the entire host mucosa. These findings represent a paradigm change of the prevailing model of the colon mucus system and provides new insights into host and microbiota symbiosis.

overall_design: RNA seq was performed on mouse colon tissue derived from the ascending and descending colon.  Global gene expression profiles were compared between 3 Groups of Healthy Control and O-glycan mutant littermates that were all colonized with the same microbiota

first: Kirk

last: Bergstrom

first: Xindi

last: Shan

first: Albert

last: Batushansky

first: Venu

last: Lagishetty

first: Jonathan

middle: P

last: Jacobs

first: Christopher

last: Hoover

first: J

middle: M

last: McDaniel

first: Samuel

last: McGee

first: Courtney

middle: W

last: Houchen

first: CV

last: Rao

first: Tim

last: Griffin

first: Justin

middle: L

last: Sonnenburg

first: Rodger

last: McEver

last: Braun

first: Lijun

last: Xia


title: Dysregulated erythroid gene expression after TET2 loss is partially corrected by 5-azacytidine in TF-1 cells [HMCP-Seq]

city: la jolla

first: Brian

last: Reilly

address: 3855 Health Sciences Drive

department: Moores Cancer Center

institute: UC San Diego

type: Methylation profiling by high throughput sequencing

summary: Using bisulfite padlock probes, mRNA sequencing, and hydroxymethylcytosine pull-down sequencing, we show that TET2 loss particularly influences DNA methylation (5mC) and hydroxymethylation (5hmC) patterns at erythroid gene enhancers and is associated with down-regulation of erythroid gene expression in the human erythroleukemia cell line TF-1. We show that 5-Aza disproportionately induces expression of these down regulated genes in TET2KO cells and that this effect may be related to 5mC changes at erythroid gene enhancers after 5-Aza exposure. This work highlights the role of 5mC and 5hmC changes at distal regulatory elements in regulating the expression of differentiation-associated gene signatures, and sheds light on how 5-Aza may be more effective in patients harboring TET2 mutations.

overall_design: We examine 5-hydroxymethylcytosine patterns of TF1 cell lines with 2 genetic conditions (TET2 KO vs WT; 2 biological replicates per genotype) at pre-treatment time point.

first: Rafael

last: Bejar


title: Cardiac fibroblast proliferation rates and collagen expression mature early in life and do not change with advancing age [Bisulfite-Seq]

city: Vienna

first: Anela

last: Tosevska

address: Waehringer Guertel 18-20

department: Division of Rheumatology

country: Austria

institute: Medical Univrsity of Vienna

summary: Cardiac fibrosis is a pathophysiologic hallmark of the aging heart. In the uninjured heart, cardiac fibroblasts exist in the quiescent state, but little is known about how proliferation rates and fibroblast transcriptional programs change throughout the lifespan of the organism from the immediate postnatal period to adult life and old age. Using EdU pulse labeling, we demonstrate that more than 50% of cardiac fibroblasts are actively proliferating in the first day of post-natal life. However, within 4 weeks of birth in the juvenile animal, only 10% of cardiac fibroblasts are proliferating. By early adulthood, the fraction of proliferating cardiac fibroblasts further decreases to approximately 2%, where it so remains throughout the rest of the organism’s life span. Examination of absolute cardiac fibroblast numbers demonstrated concordance with age related changes in fibroblast proliferation with no significant differences in absolute cardiac fibroblast numbers between animals 14 weeks and 1.5 years of age. We demonstrate that the maximal changes in cardiac fibroblast transcriptional programs and in particular collagen expression occur within the first weeks of life from the immediate postnatal to the juvenile period. We show that even though the aging heart exhibits an increase in the total amount of accumulated collagen, transcription of various collagens and ECM genes both in the heart and cardiac fibroblast is maximal in the newly born and juvenile animal and decreases with organismal aging. Examination of DNA methylation changes both in the heart and in cardiac fibroblasts did not demonstrate significant changes in differentially methylated regions between young and old mice. Our observations demonstrate that cardiac fibroblasts attain a stable proliferation rate and transcriptional program early in the life span of the organism and suggest a model of cardiac aging where phenotypic changes in the aging heart are not directly attributable to changes in proliferation rate or altered collagen expression in cardiac fibroblasts.

overall_design: Reduced representation bisulfite sequencing of DNA extracted from mouse hearts or PDGFR⍺ cardiac fibroblasts at 14 weeks of age and 1.5 years of age.

first: Rimao

last: Wu

first: Feiyang

last: Ma

first: Colin

last: Farrel

first: Matteo

last: Pellegrini

first: Arjun

last: Deb


title: Evaluation of the effects of low nanomolar bisphenol A-like compounds’ levels on early human embryonic development and lipid metabolism with human embryonic stem cell in vitro differentiation models

status: Public on Oct 27 2020

city: Beijing

first: Xiaoxing

last: Liang

address: 18 Shuangqing Road

country: China

institute: Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences,

summary: The widely used chemical bisphenol A (BPA) has been associated with several health effects. In recent years, many derivatives were developed to replace BPA without thorough toxicological evaluation. Here, we employed a human embryoid body (EB)-based in vitro global differentiation and hepatic specification models, followed by RNA-seq analyses, to comprehensively study the potential developmental toxicity of six BPA replacements (BPS, BPF, BPZ, BPB, BPE, and BPAF), as compared to BPA. We found that bisphenols may disrupt lineage commitment and lipid metabolism during early embryonic development. These effects mostly manifested via the dysregulation of HOX and APO family genes. Moreover, among the seven bisphenols analyzed, BPE, due to lower potential developmental toxicity, stood out as a relatively safe substitute of BPA in many applications, especially for infant/baby products.

overall_design: Examination of 18 samples in total. There are 14 treated samples: seven bisphenols-treatment samples (BPAF, BPA, BPB, BPE, BPF, BPS and BPZ in 100 nM) and each treatment has two replicates. There are 2 controls which are 0.01% DMSO. Treated samples and controls are day21 samples. There are 2 day0 samples which are human embryonic stem cells (H1 hESCs).

first: Renjun

last: Yang

first: Nuoya

last: Yin

first: Francesco

last: Faiola


title: Temporal evolution of single-cell transcriptomes of Drosophila olfactory projection neurons

status: Public on Nov 11 2020

city: Stanford

first: Qijing

last: Xie

state: California

address: Bass Biology Building, Room 334

department: Department of Biology

institute: Howard Hughes Medical Institute

summary: Neurons undergo substantial morphological and functional changes during development to form precise synaptic connections and acquire specific physiological features. What are the underlying transcriptomic bases? Here, we obtained the single-cell transcriptomes of Drosophila olfactory projection neurons (PNs) at four developmental stages. We decoded the identity of 21 transcriptomic clusters corresponding to 20 PN types and developed methods to match transcriptomic clusters representing the same PN type across development. We discovered that PN transcriptomes reflect unique biological processes unfolding at each stage—neurite growth and pruning during metamorphosis at an early pupal stage; peaked transcriptomic diversity during olfactory circuit assembly at mid-pupal stages; and neuronal signaling in adults. At early developmental stages, PN types with adjacent birth order share similar transcriptomes. Together, our work reveals principles of cellular diversity during brain development and provides a resource for future studies of neural development in PNs and other neuronal types.

overall_design: Single-cell RNA-seq of Drosophila olfactory projection neurons during development and in adult stage


title: Dysregulated erythroid gene expression after TET2 loss is partially corrected by 5-azacytidine in TF-1 cells [Bisulfite-seq]

overall_design: We examine DNA methylation profiles (BSPP, bisulfite sequencing) of TF1 cell lines with 2 genetic conditions (TET2 KO vs WT; 2 biological replicates per genotype) at three separate time points (pre-treatment,  72hrs and 264hrs after first treatment) in relation to treatment with 5-azacytidine or DMSO (vehicle)


title: Gene expression profile of Cxcl12-DsRed+ stromal cells from E15.5, P5, and P10 livers.

city: New York

first: Yeojin

last: Lee

state: NY

address: 650 WEST 168TH STREET, BB 1108

institute: Columbia University Medical Center

summary: The study is designed to identify transcriptional differences of CD45-Ter119-Cxcl12-DsRed+ stromal cells at different develomental stages. 50,000 CD45-Ter119-Cxcl12-DsRed+ stromal cells from freshly prepared livers of E15.5, P5 and P10 Cxcl12DsRed/+ mice were sorted into Trizol by flow cytometry. Total RNA was isolated and amplified with the WT-Ovation Pico RNA Amplification system (Nugen) as the manufacturer’s instructions. Sense strand complementary DNA was generated using the WT-Ovation Exon Module (Nugen). Then, cDNA was fragmented and labelled using FL-Ovation DNA Biotin Module V2 (Nugen). The labelled cDNA was hybridized to Affymetrix Mouse Gene ST 1.0 chips following the manufacturer's instructions.

overall_design: Three independent replicates for each conditions.

first: Lei

last: Ding


title: Chromatin-associated RNA of HSV-1 infected primary human fibroblasts including infection with vhs mutants

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

institute: Ludwig-Maximilians-Universität München

summary: Primary human foreskin fibroblasts (HFF) were infected with wild-type herpes simplex virus 1 (HSV-1) strain 17 or its vhs null mutant, or with BAC-derived viruses expressing either a wild-type or catalytically inactive vhs with the D195N mutation at a multiplicity of infection (MOI) of 10. Chromatin-associated RNA was prepared and subjected to RNA-seq.

overall_design: HFF were infected with HSV-1 strain 17, its vhs-null mutant, BAC-derived strain 17 (WT-BAC), or BAC-derived strain 17 with the vhsD195N mutation (WT-BAC VhsD195N) for 8h (or mock). Chromatin-associated RNA was prepared combining the following two protocols (PMID: 19656867, RNA 2009; and PMID: 23449254, Nature Protocols 2013) as described in Hennig et al., PLoS Pathogens 2018 (https://doi.org/10.1371/journal.ppat.1006954). Two independent biological replicates were analysed.

first: Adam

last: Whisnant

first: Lara

last: Djakovic

first: Andrzej

middle: J

last: Rutkowski

first: Marie-Sophie

last: Friedl

first: Michael

last: Kluge

first: Somesh

last: Sai

first: Ramon

last: Oliveira Vidal

first: Thomas

last: Hennig

first: Sascha

last: Sauer

first: Florian

last: Erhard

first: Lars

last: Dölken


title: H3K4me3 ChIPmentation on HSV-1 infected primary human fibroblasts

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Primary human fetal foreskin fibroblasts (HFFFs) were infected with wild-type simplex virus 1 (HSV-1) strain 17 at a multiplicity of infection (MOI) of 10. ChIPmentation libraries were prepared starting with 500,000 cells per condition following the protocol described by Christian Schmidl et al, Nature Methods 2015

overall_design: HFFF were infected with HSV-1 strain 17 for 8h (or mock). ChIPmentation samples were prepared at the indicated times of infection. Two independent biological replicates were analysed.


title: Total and newly transcribed (4sU-RNA) RNA of primary human fibroblasts infected with the vhs-null mutant of HSV-1

summary: Primary human foreskin fibroblasts (HFF) were infected with vhs-null mutant of HSV-1 strain 17 at a multiplicity of infection (MOI) of 10. Newly transcribed RNA was labelled by adding 500µM 4-thiouridine (4sU) to the cell culture media for 1h. Total cellular RNA was isolated using Trizol. Newly transcribed RNA was purified following the protocol described in Raedle et al. JoVE 2013.

overall_design: Primary human foreskin fibroblasts (HFF) were infected with the vhs-null mutant of HSV-1 strain 17 at a multiplicity of infection (MOI) of 10. Newly transcribed RNA was labelled by adding 500µM 4-thiouridine (4sU) to the cell culture media for 1h. Total cellular RNA was isolated using Trizol. Newly transcribed RNA was purified following the protocol described in Raedle et al. JoVE 2013 and Rutkowski et al. 2015.


title: Subcellular RNA fractions of HSV-1 infected primary human fibroblasts including infection with delta-Vhs mutant

summary: Primary human foreskin fibroblasts (HFF) were infected with wild-type simplex virus 1 (HSV-1) strain 17 or its vhs null mutant at a multiplicity of infection (MOI) of 10. Subcellular RNA fractions including total RNA, cytoplasmic RNA, nucleoplasmic RNA and chromatin-associated RNA were prepared and subjected to RNA-seq.

overall_design: HFF were infected with HSV-1 strain 17 or its vhs-null mutant for 8h (or mock). Subcellular RNA fractions were prepared combining the following two protocols (PMID: 19656867, RNA 2009; and PMID: 23449254, Nature Protocols 2013) as described in Hennig et al., PLoS Pathogens 2018 (https://doi.org/10.1371/journal.ppat.1006954). Two independent biological replicates were analysed. Data for HFF infected with wild-type HSV-1 strain 17 for 8h (or mock) can  be found under accession GSE100576.

first: Marco

last: Michalski

first: Bhaskar

last: Jha

first: Marisa

last: Baptista

first: Anne

last: L'Hernault


title: Histone acetylation targeting to transcribed chromatin through RNAPII

city: Vancouver

first: Benjamin

last: Martin

state: BC

address: 2350 Health Sciences Mall

department: Biochemistry

country: Canada

institute: UBC

summary: Histone acetylation is a ubiquitous hallmark of transcriptional activity, but whether the link is of a causal or consequential nature is still a matter of debate. In this study we resolve this question. Using both immunoblot analysis and chromatin immunoprecipitation-sequencing (ChIP-seq) in S. cerevisiae, we show that the majority of histone acetylation is dependent on transcription. Loss of histone H4 acetylation upon transcription inhibition is partially explained by depletion of histone acetyltransferases (HATs) from gene bodies, implicating transcription in HAT targeting. Despite this, HAT occupancy alone poorly predicts histone acetylation, suggesting that HAT activity is regulated at a step post-recruitment. Collectively, these data show that the majority of histone acetylation is a consequence of RNAPII promoting both the recruitment and activity of histone acetyltransferases.

overall_design: ChIP-seq for histone acetylation and Epl1

first: LeAnn

last: Howe


title: Secretory mucin 5AC promotes neoplastic progression by augmenting KLF4-mediated pancreatic cancer cell stemness

status: Public on Oct 25 2020

city: Omaha

first: Pranita

last: Atri

state: NE

address: S 42nd and Emile St

institute: UNIVERSITY OF NEBRASKA MEDICAL CENTER

summary: Pancreatic cancer (PC) is the third deadliest malignancy with a dismal five-year survival rate. The KrasG12D initiator mutation, present in 95% of the PC patients, leads to the development of pancreatic intraepithelial neoplasia (PanIN). The PanIN lesions, the most common precursor lesion of PC, exhibit de novo expression of mucins, which significantly contributes to PC pathobiology. The poor clinical outcome of PC warrants the identification of molecular player(s) that facilitate the progression of Kras-driven precursor lesions to invasive ductal carcinoma. Gel-forming mucin 5AC (MUC5AC) is one of the top differentially expressed genes in PC as compared to the normal pancreas. The expression of MUC5AC appears de-novo at PanIN-1A stage and elevates in tumor tissues, while remaining absent in the normal pancreas. To delineate the mechanistic contribution of Muc5ac in PC pathology, we genetically depleted Muc5ac in an autochthonous murine model (KrasG12D; Pdx-1cre, KC), which mirrors the early stages of PC. The onset of neoplastic growth and the progression of low-grade to high-grade PanIN lesions were significantly delayed in Muc5ac knockout (KrasG12D; Muc5ac-/-; Pdx-1cre, KCM) animals.  We utilized high-throughput RNA seq. analysis to investigate the downstream molecular targets of Muc5ac-associated PC progression.  Our study demonstrated that knockout of Muc5ac led to a significant decline in the genes associated with cancer stem cell (CSC) maintenance and epithelial-to-mesenchymal transition (EMT). The contribution of MUC5AC in CSC maintenance was validated via in vitro experiments, and tumor formation frequency using limiting dilution assay upon subcutaneous administration.

overall_design: Pancreatic tissue from KC (KrasG12D; Pdx-1cre) and KCM (KrasG12D; Pdx-1cre; Muc5ac-/-)

first: Koelina

last: Ganguly

first: Sushil

last: Kumar

first: Surinder

last: Batra


title: RNA-seq of CD4 CD8 lineage differentiation in the mouse thymus

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

summary: We used flow cytometry to sort phenotypically defined thymocyte populations and profiled gene expression by paired end RNA-sequencing.

overall_design: We used CD4, CD8, CD69 and TCRbeta cell surface markers to sort phenotypically defined thymocyte populations by flow cytometry from the thymi of 6 weeks old mice on a mixed C57BL/6 and 129 background. Populations include CD69neg pre-selection DP thymocytes, CD4 and CD8 SP thymocytes, and a series of selection intermediates (CD69pos DP, TCRhigh DP and CD4pos CD8low). We profiled gene expression by paired end RNA-sequencing.

first: Ya

last: Guo

first: Matthias

last: Merkenschlager

first: Husayn

middle: A

last: Pallikonda

first: Yi-Fang

last: Wang

first: Mohammad

last: Karimi


title: Environmental signals rather than layered ontogeny imprint the function of type 2 conventional dendritic cells in young and adult mice

status: Public on Nov 06 2020

city: Planegg-Martinsried

first: Nikolaos

last: Papaioannou

address: Großhaderner Straße 9

institute: Biomedical Center

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

overall_design: Refer to individual Series


title: Molecular atlas of fetal and adult human liver sinusoidal endothelial cells: a F8 secreting cell [methylation III]

city: Bonn

first: Muhammad Ahmer

last: Jamil

state: NRW

address: Sigmund-Freud Str. 25

department: Institute of experimental haematology and transfusion medicine

institute: University Clinic Bonn

summary: In-silico analysis to identify molecular signature of liver sinusoidal endothelial cells in comparison to other endohtelial cells

overall_design: Commercial endothelial cells were ordered from ScienCell research laboratories via Provitro GmbH. All molecular materials were isolated at passage one as stated by manufacturing certificate.

first: Muhammad

first: Osman

last: El-Maarri


title: RNA sequencing analysis of SF-539-shControl and SF-539-shFKBP9 cells

city: Dalian

first: Huizhe

last: Xu

address: lvshun south road no.9

institute: Dalian Medical University

summary: We performed RNA-seq to determine the impact of FKBP9 depletion on global gene expression profile. The results show knock down of FKBP9 activated ER stress or UPR signaling related genes.

overall_design: mRNA profiles of SF-539-shControl and SF-539-shFKBP9 cells were generated by deep sequencing using Illumina Hiseq

first: Songshu

last: Meng


title: Identification of required host factors for SARS-CoV-2 infection in human cells [RNA-seq]

status: Public on Oct 24 2020

city: New York City

first: Zharko

last: Daniloski

state: New York

address: 1 Washington square village, 2P

department: Biology

institute: New York University

summary: RNA-seq was performed to determine gene expression (RNA) levels and SARS-CoV-2 viral reads in A549-ACE2 cells treated with DMSO or Amlodipine.

overall_design: ACE2-A549s cells were treated with either DMSO or amlodipine (Millipore Sigma, Cat #A5605) resuspended in DMSO one hour before infection. Amlodipine was used at a concentration of 10uM. A549-ACE2 cells were infected at MOI of 0.1 with SARS-CoV-2 for 24 hours before harvest. RNA-seq libraries were built from 1ug of RNA per sample using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions. Sequencing libraries were sequenced using an Illumina NextSeq 500 platform and fastq files were generated using bcl2fastq (Illumina). Reads were aligned to hg19 using STAR aligner via the RNA-Seq Alignment application (Basespace, Illumina). Alignments to the SARS-CoV-2 genome (GenBank: MN985325.1) were determined using bowtie (Robinson et al., 2010).

first: Tristan

middle: X

last: Jordan

first: Daisy

last: Hoagland

first: Ben

last: tenOever

first: Neville

middle: E

last: Sanjana


title: Dysregulated erythroid gene expression after TET2 loss is partially corrected by 5-azacytidine in TF-1 cells

first: Brian

last: Reilly


title: Identification of required host factors for SARS-CoV-2 infection in human cells [ECCITE-seq]

summary: To better understand host-virus genetic dependencies and find potential therapeutic targets for COVID-19, we performed a genome-scale CRISPR loss-of-function screen to identify host factors required for SARS-CoV-2 viral infection of human alveolar epithelial cells. Top-ranked genes cluster into distinct pathways, including the vacuolar ATPase proton pump, Retromer, and Commander complexes. We validate these gene targets using several orthogonal methods such as CRISPR knock-out, RNA interference knock-down, and small-molecule inhibitors. Using single-cell RNA- sequencing, we identify shared transcriptional changes in cholesterol biosynthesis upon loss of top-ranked genes. In addition, given the key role of the ACE2 receptor in the early stages of viral entry, we show that loss of RAB7A reduces viral entry by sequestering the ACE2 receptor inside cells. Overall, this work provides a genome- scale, quantitative resource of the impact of the loss of each host gene on fitness/response to viral infection.

overall_design:
Identification of systemic changes upon SARS-CoV-2 entry hit gene perturbation using ECCITE-seq.
ECCITE-seq (Expanded CRISPR-compatible Cellular Indexing of Transcriptomes and Epitopes by sequencing)

first: Hans-Hermann

last: Wessels


title: MEF2C hypofunction in neuronal and neuroimmune populations produces MEF2C haploinsufficiency syndrome behaviors in mice

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

summary: Microdeletions of the MEF2C gene are linked to a syndromic form of autism termed MEF2C haploinsufficiency syndrome (MCHS). Here, we show that MCHS-associated missense mutations cluster in the conserved DNA binding domain and disrupt MEF2C DNA binding. DNA binding-deficient global Mef2c heterozygous mice (Mef2c-Het) display numerous MCHS-like behaviors, including autism-related behaviors, as well as deficits in cortical excitatory synaptic transmission. We find that hundreds of genes are dysregulated in Mef2c-Het cortex, including significant enrichments of autism risk and excitatory neuron genes. In addition, we observe an enrichment of upregulated microglial genes, but not due to neuroinflammation in the Mef2c-Het cortex. Importantly, conditional Mef2c heterozygosity in forebrain excitatory neurons reproduces a subset of the Mef2c-Het phenotypes, while conditional Mef2c heterozygosity in microglia reproduces social deficits and repetitive behavior. Together our findings suggest that MEF2C regulates typical brain development and function through multiple cell types, including excitatory neuronal and neuroimmune populations.

overall_design: We compared gene expression profiles  between control and Mef2c heterozygous mice. We analyzed genome-wide expression levels from cortical tissue from 4 Mef2c heterozygous mice compared with 4 control mice. Gene expression was balanced for technical and biological covaraites.

first: Stefano

last: Berto

first: Adam

middle: K

last: Harrington

first: Catherine

last: Bridges

first: Christopher

last: Cowan


title: The confined environment in microfluidic reveals a hidden role of self-organizing extracellular-matrix in hepatic commitment and organoid formation of hiPSCs

city: Bologna

first: Camilla

last: Luni

address: Via Terracini 28

department: DICAM

country: Italy

institute: University of Bologna

summary: The specification of cell identity during human liver development is strictly controlled by extrinsic signals that restrict and define distinct cell fates. However, it is still not clear how cells, when exposed to exogenous signals, activate secretory cascades involving morphogens, growth factors and cytokines, extracellular matrix (ECM) deposition and remodeling, which are extremely relevant especially in 3D self-organizing system such as hepatic organoids. Here, we investigated how the proteins secreted by human pluripotent stem cells (hPSCs) in response to developmental exogenous signals affect the progression from endoderm to the hepatic lineage, including their competence to generate nascent hepatic organoids. By using a microfluidics-based approach coupled with SILAC-MS-based quantitative proteomic analysis we found high abundancy of ECM-associated proteins. Hepatocyte-like cells derived in microfluidics, where accumulation of cell-secreted proteins is enhanced up to 7-fold, showed organized deposition of COL1, FN, LAM and COL4, consistent with observations in human fetal liver at 8-15pcw. Further differentiation leads to a more mature hepatic transcriptomic signature and 1.5-fold higher ammonia detoxification capacity compared to conventional culture conditions. Hepatic committed cells in an early stage either derived in microfluidics and exposed to exogenous ECM stimuli show a significant higher potential for hepatic organoids formation. Nascent organoids can be rapidly expanded for several passages and further differentiated into functional hepatocytes. These results proved an additional control over the efficiency of hepatic organoid formation and differentiation for downstream applications.

overall_design: Comparison of mature hepatocyte cells derived in microfluidics and conventional culture system from hiPSCs. Pluripotent cells were used as undifferentiated control.

first: Federica

last: Michielin

first: Giovanni

middle: G

last: Giobbe

first: Qianjiang

last: Hu

first: Ida

last: Maroni

first: Michael

last: Orford

first: Anna

last: Manfredi

first: Lucio

last: Di Filippo

first: Davide

last: Cacchiarelli

first: Paolo

last: De Coppi

first: Simon

last: Eaton

first: Nicola

last: Elvassore


title: Comparison of lncRNA and mRNA expression levels in peri-implantitis and periodontitis

city: Guangzhou

first: Yudong

last: Liu

state: Guangdong

address: No. 56, Lingyuan west road

department: Department of Implantology

institute: Sun Yat-sen University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary:
Objectives:
The aim of this study was to identify the long noncoding RNAs (lncRNAs) and mRNAs that influence the different manifestations of peri-implantitis and periodontitis (I vs. P).
Materials and methods:
Gingival tissues from 6 peri-implantitis patients, 6 periodontitis patients, and 6 healthy individuals were analysed using lncRNAs and mRNAs gene expression microarrays. A lncRNAs subgroup analysis, a lncRNAs cluster graph, gene ontology (GO), and a pathway analysis of mRNAs were performed to analyse the data extracted from microarrays. To verify the results of the microarray studies, quantitative real-time polymerase chain reaction (qRT-PCR) was used to assess some differentially expressed lncRNAs and mRNAs.
Results:
In the gene expression microarray studies, 1,079 differentially expressed lncRNAs and 1,003 differentially expressed mRNAs were identified when comparing I vs. P. The lncRNAs subgroup analysis showed that there were 9 significantly up-regulated antisense lncRNAs and 18 significantly down-regulated antisense lncRNAs when comparing I vs. P. GO analysis on mRNAs revealed that the cyclooxygenase pathway is the most prominent signal among the up-regulated transcripts (3 genes) and that hemidesmosome assembly represents the most significant biological process among the down-regulated transcripts (4 genes) when comparing I vs. P. The expression levels of antisense lncRNA GACAT2 and mRNA MTCL1, antisense lncRNA MSC-AS1 with its sense mRNA MSC and TRPA1 were verified by RT-qPCR.
Conclusions:
Results indicated that peri-implantitis and periodontitis exhibit significantly different lncRNAs and mRNAs expression profiles. Additionally, specific lncRNAs may take part in the pathogenesis mechanisms of peri-implantitis and periodontitis through influencing their nearby mRNAs.

overall_design: Six cases of peri-implantitis tissue samples, six cases of periodontitis tissue samples and six cases of healthy periodontal tissue samples were included.

first: Zhipeng

last: Li

first: Zetao

last: Chen

first: Quan

first: Zhuofan

first: Baoxin

last: Huang


title: Circulating serum microRNAs as potential diagnostic biomarkers of post-traumatic stress disorder: A pilot study

city: Maastricht

first: Julian

last: Krauskopf

address: Universiteitssingel 50

country: Netherlands

institute: Maastricht University

type: Non-coding RNA profiling by high throughput sequencing

summary: In this pilot study, we analyzed serum microRNA profiles of subjects with post-traumatic stress disorders in order to determine their potential to be used as diagnostic biomarkers. We discovered that serum microRNAs could potentially serve as diagnostic biomarkers of PTSD, both individually or grouped within a cluster of co-expressed miRNAs.

overall_design: Next generation sequencing of small RNAs from serum samples of 24 (PTSD, control or resilient) subjects

first: Clara

last: Snijders

first: Ehsan

last: Pishva

first: Lars

last: Eijssen

first: Barbie

last: Machiels

first: Jos

last: Kleinjans

first: Gunter

last: Kenis

first: Daniel

last: van den Hove

first: MyeongOk

last: Kim

first: Marco

last: Boks

first: Christiaan

middle: H

last: Vinkers

first: Eric

last: Vermetten

first: Elbert

last: Geuze

first: Bart

last: Rutten

first: Laurence

last: de Nijs


title: Long first exons and epigenetic marks distinguish conserved pachytene piRNA clusters from other mammalian genes

city: Worcester

first: Tianxiong

last: Yu

state: MA

address: 364 Plantation St

institute: Umass Med

summary: In the male germ cells of eutherian animals, 26–30-nt-long PIWI-interacting RNAs (piRNAs) emerge when spermatocytes enter the pachytene phase of meiosis. These pachytene piRNAs derive from ~100 discrete autosomal loci resemble canonical protein-coding genes and long non-coding RNA-producing genes—they are transcribed by RNA polymerase II, bearing 5´ caps and 3´ poly(A) tails, and their transcripts often contain introns that are removed before nuclear export and processing into piRNAs. However, it is unclear which genic and epigenetic features distinguish pachytene piRNA genes from other types of genes and dictate their germline-specific expression. We report that an unusually long first exon (≥ 10 kb) or a long gene absent of introns altogether is highly correlated with both the germline-specific production of piRNA precursor transcripts from mouse pachytene piRNA loci. We also found that these precursor transcripts are enriched in the binding by THOC1 (also known as HPR1) and THOC2, subunits of the THO complex critical for transcription elongation and nuclear export of mRNAs. Our integrative analysis of transcriptome, piRNA, and epigenome datasets across multiple species reveals that a long first exon is an evolutionarily conserved feature of pachytene piRNA loci. We further found that a highly methylated promoter, often containing a low or intermediate level of CG dinucleotides, correlates with germline expression and somatic silencing of pachytene piRNA loci.

sample_organism:
Macaca mulatta
Mus musculus

platform_organism:
Macaca mulatta
Mus musculus

overall_design: RIPseq for adult mouse testis and ChIPseq for adult rhesus testis

first: Kaili

last: Fan

first: Gen

last: Zhang

first: Deniz

last: Ozata

first: Philip

middle: D

last: Zamore

first: Zhiping

last: Weng


title: Dysregulated erythroid gene expression after TET2 loss is partially corrected by 5-azacytidine in TF-1 cells [RNA-seq]

city: la jolla

first: Brian

last: Reilly

address: 3855 Health Sciences Drive

institute: UC San Diego

summary: Using bisulfite padlock probes, mRNA sequencing, and hydroxymethylcytosine pull-down sequencing, we show that TET2 loss particularly influences DNA methylation (5mC) and hydroxymethylation (5hmC) patterns at erythroid gene enhancers and is associated with down-regulation of erythroid gene expression in the human erythroleukemia cell line TF-1. We show that 5-Aza disproportionately induces expression of these down regulated genes in TET2KO cells and that this effect may be related to 5mC changes at erythroid gene enhancers after 5-Aza exposure. This work highlights the role of 5mC and 5hmC changes at distal regulatory elements in regulating the expression of differentiation-associated gene signatures, and sheds light on how 5-Aza may be more effective in patients harboring TET2 mutations.

overall_design: We examine gene expression (bulk mRNAseq) of TF1 cell lines with 2 genetic conditions (TET2 KO vs WT; 2 biological replicates per genotype) at three separate time points (pre-treatment,  72hrs and 264hrs after first treatment) in relation to treatment with 5-azacytidine or DMSO (vehicle). Note: Sample 9 (F4_KO_T72_DMSO_BATCH1) did not pass sequencing QC and was removed prior to downstream analyses.

first: Rafael

last: Bejar


title: Ignition of supporting cell activation for hair cell regeneration in the avian auditory epithelium: an explant culture model

status: Public on Oct 23 2020

city: Kyoto

first: Takayuki

last: Nakagawa

state: Kyoto

address: 54 Kawahara-cho, Shogoin, Sakyo-ku

department: Department of Otolaryngology Head and Neck Surgery

country: Japan

institute: Kyoto University Hospital

summary: Sensorineural hearing loss is included in the most common disabilities, and often caused by loss of sensory hair cells in the cochlea. Hair cell regeneration has long been a main target for developing novel therapeutics for sensorineural hearing loss. In the mammalian cochlea, hair cell regeneration occurs in very limited situations, while auditory epithelia of non-mammalians retain the capacity for hair cell regeneration. In the avian basilar papilla, an auditory sensory epithelium, supporting cells, which are sources for regenerated hair cells, are usually quiescent, while hair cell loss induces both direct transdifferentiation of supporting cells and mitotic division of supporting cells. In the present study, we aimed to establish an explant culture model for hair cell regeneration in chick basilar papillae, and validated usefulness of our model to investigate the initial phase of hair cell regeneration. Histological assessments demonstrated that hair cell regeneration via direct transdifferentiation of supporting cells occurred in our model. Labeling assay using 5-ethynyl-2'-deoxyuridine (EdU) revealed the occurrence of mitotic division of supporting cells in the specific location in basilar papillae, while no EdU labeling was identified in newly generated HCs. RNA sequencing indicated alterations in known signaling pathways associated with hair cell regeneration, which is consistent with previous findings. In addition, unbiased analyses of RNA sequencing data indicated novel genes and signaling pathways that could be related to the ignition of supporting cell activation in chick basilar papillae. These results indicate the advantages of our model using explant cultures of chick basilar papillae for exploring molecular mechanisms for hair cell regeneration. Further studies such as single-cell RNA sequencing will allow us to capture the spatiotemporal information by using our explant culture model.

overall_design: mRNA profiles in explant cultures of chick basilar papillae during the initial phase of hair cell regeneration after damage by streptomycin

first: Mami

last: Matsunaga

first: Tomoko

last: Kita

first: Ryosuke

last: Yamamoto


title: Single-cell RNA sequencing of mouse olfactory sensory neurons

city: Plainsboro

first: Patrick

last: Pfister

state: New Jersey

address: 250 Plainsboro Road

department: Corporate R&D

institute: Firmenich Inc.

summary: The goal of this study was to identify those odorant receptors conferring a response to indole or related odorants (2-methylindole, 3-methylindole, 6-methylindole, 2-methoxynaphthalene, and Lilyflore®) in olfactory sensory neurons (OSNs). Odorants were sequentially delivered to dissociated OSNs, and six OSNs with three different response profiles were isolated for transcriptome analysis. OSN1 and OSN2 responded to indole, 2-methylindole, 3-methylindole, and 6-methylindole; OSN3 and OSN4 responded to Indole and 2-methoxynaphthalene; OSN5 and OSN6 responded to indole, 3-methylindole, 6-methylindole, and  2-methoxynaphthalene. RNA transcripts encoding Olfr740 (OSN1, OSN2), Olfr741 (OSN3, OSN4), and Olfr743 (OSN5, OSN6) were retrieved, with high level expression of a single OR transcript in each OSN. The expression of mature OSN markers OMP, Golf, Adcy3, Cnga2 and Rtp1 was also confirmed.

overall_design: Individual olfactory sensory neuron mRNA profiles of 6 week old wild type (C57BL/6) mice were generated by single-cell RNA-Seq via the Cel-Seq2 method and sequenced on the Illumina NovaSeq 6000.

first: Benjamin

last: Smith

first: Barry

last: Evans

first: Jessica

last: Brann

first: Daniel

last: Raps

first: Rodrigo

last: Pacifico

first: Matthew

last: Rogers


title: scRNA-seq of mouse thymocyte CD4 CD8 lineage choice and differentiation

first: LMS

last: Bioinformatics Core

summary: CD4 and CD8 identify helper and cytotoxic T cell lineages, and serve as co-receptors for MHC-restricted TCR recognition. Despite decades of investigation, questions remain about how TCR specificity and co-receptor gene expression are matched during T cell repertoire selection. Here we address the order and logic of CD4/CD8 lineage choice and differentiation by scRNA-seq. Maturation, activation, and lineage specification emerged as principle components, in this order. Co-receptor gene expression uncovered waves of Cd4+Cd8a+, Cd4+Cd8a- and Cd4-Cd8a+ selection intermediates and revealed gene expression programs associated with each pattern, including TCR- and cytokine signaling genes, lineage markers and transcription factors. While in the unperturbed thymus early Cd4+Cd8a+ selection intermediates were followed first by CD4-like Cd4+Cd8a- and later by CD8-like Cd4-Cd8a+ selection intermediates, the order of co-receptor gene expression was not inherently fixed. These data provide a benchmark for models of CD4/CD8 lineage choice, and a rich resource for interrogating T cell differentiation.

overall_design: Thymocyte cell suspensions from two wild type C57BL/6 thymi and one MHC class II-deficient thymus (Madsen et al., Proc Natl Acad Sci U S A. 1999; 96: 10338-43) were stained with antibodies to CD4, CD8a, TCRb and CD69-. Single cells representing thymocytes before, during and after lineage choice and differentiation (CD4+ CD8+ Cd69, CD4+ CD8+ Cd69+, CD4+ CD8+ TCRbhi , CD4+ CD8low, CD4+ CD8 -, and CD4- CD8+ TCRbhi) were sorted by flow cytometry into 96 well plates containing lysis buffer for construction of RNA-seq libraries.

first: Mohammad

last: Karimi

first: Husayn

last: Pallikonda

first: Holger

last: Heyn

first: Matthias

last: Merkenschlager


title: Microarray from both control and activated Hematopoietic stem cells

city: BRONX

first: Shuxian

last: Dong

address: 1300 morris park ave., Chanin 504

institute: albert einstein college of medicine

summary:
Activation of mostly quiescent hematopoietic stem cells (HSC) is a prerequisite for life-long blood production. This process requires major molecular adaptations to meet the regulatory and metabolic requirements for cell division. The mechanisms governing cellular reprograming upon stem cell activation and their subsequent return to quiescence are still not fully characterized. Here, we describe a central role for a selective type of autophagy (CMA) in sustaining adult HSC function both through to stem cell protein quality control and to timely stimulation of linoleic fatty acid metabolism upon HSC activation. We identify that reduced CMA in old HSC contributes to the loss of stem cell activity during aging and show that genetic or chemical activation of CMA can restore old HSC function. Together, our findings provide mechanistic insights into a new role for CMA in sustaining long-term HSC quality control, appropriate energetics and overall hematopoietic stem cell function.  Our work supports that CMA may be a promising therapeutic target to enhance hematopoietic stem cell function in conditions such as aging or stem cell transplantation.
We used microarrays to identify the most affected genes and pathways by CMA deficiency in both basal and activated conditions.

overall_design: Mice were injected with a single dose of 5FU to activate HSCs, mice were sacrificed and bone marrow were taken and sorted with hematopoietic stem and progenitor cell markers at day0 and day8 after the injection.

first: Ana Maria

last: Cuervo


title: Tetrachloroethene respiration in Sulfurospirillum species is regulated by a two-component system as unraveled by comparative genomics, transcriptomics, and regulator binding studies

city: Würzburg

first: Thorsten

last: Bischler

address: Josef-Schneider-Straße 2 / D15

department: Core Unit SysMed

institute: University of Wuerzburg

summary: Sulfurospirillum multivorans is one of the few bacteria, which can anaerobically respire organohalides such as tetrachloroethene. The regulation of this organohalide respiration is in most parts unknown. Sulfurospirillum multivorans was shown to downregulate the expression of organohalide respiration-specific genes slowly when no substrate is present, over the time of approximately 100 generations. To unravel the molecular details of this peculiar regulation and the involved factors, we sequenced the primary transcriptome of the organism.

overall_design: Sulfurospirillum multivorans was grown anaerobically with pyruvate as energy and C-source and either tetrachloroethene or fumarate as electron acceptor; RNA was isolated from four samples each for transcriptional start site analysis – two for a library treated with and two for a library treated without terminator 5′-phosphate-dependent exonuclease.

first: Tobias

last: Goris

first: Jens

last: Esken

first: Gabriele

last: Diekert

first: Konrad

last: Förstner

first: Cynthia

last: Sharma


title: 4EHP and GIGYF1/2 induce translation-coupled messenger RNA decay

city: Schlieren

first: Ramona

last: Weber

address: Wagistrasse 12

department: Institute for Regenerative Medicine

country: Switzerland

institute: University of Zurich

summary: Although canonical mRNA degradation is generally recognized to be translation dependent, our understanding of the molecular events that coordinate ribosome movement with the decay machinery is still limited. Here, we show that the 4EHP–GIGYF1/2 complex triggers co-translational mRNA decay as a result of altered ribosome activity during elongation. Human cells lacking 4EHP and GIGYF1 and 2 proteins accumulate transcripts known to be degraded in a translation dependent manner or with prominent ribosome pausing. These include mRNAs encoding secretory and membrane-bound proteins or specific tubulin isotypes, among others. 4EHP–GIGYF1/2 fails to reduce target mRNA levels in the absence of ribosome stalling or upon disruption of its interaction with the cap structure, DDX6 and a GYF domain-associated protein. Our studies reveal how a repressor complex linked to neurological disorders minimizes the protein output of a subset of mRNAs.

overall_design: Three cell types with two biological replicates analysed using RNA-Seq and Ribo-Seq

first: Cátia

last: Igreja


title: Differential gene expression profiles by septin 2 suppression and TNF-a treatment in human microvascular endothelial cells

city: St. Louis

first: Joanna

last: Kim

state: MO

address: 660 S Euclid Ave

institute: Washington University

summary: Arrangements of juntional proteins of endothelial monolayers were altered by both septin 2 KD and TNF-a treatment. Therefore, differential gene expression profiles by septin 2 KD comapred to control and TNF-a treatment compared to untreat were analyzed using RNA-seq.

overall_design: HDMVECs were suppressed with septin 2 and RNA-seq was performed. HDMVECs were treated with TNF-a overnight and RNA-seq was perfomed.

first: John

last: Cooper


title: Transcriptome of T cell subsets

city: Naples

first: Mario

last: Galgani

address: via S. Pansini, 5

institute: IEOS Istituto per l'endocrinologia e l'oncologia sperimentale

summary: Whole transcriptome of TR3-56, NK, CD3+CD56- and CD8+ cell subsets

overall_design: Flow sorted TR3-56, NK, CD3+CD56- and CD8+ were analyzed for mRNA trancripts

first: Giuseppina

last: Ruggiero


title: A comprehensive library of human transcription factors for cell fate engineering (scRNA-Seq)

status: Public on Oct 22 2020

city: Boston

first: Alex

last: Ng

address: 77 Avenue Louis Pasteur Rm 233

department: Genetics

institute: Harvard Medical School

summary: Human pluripotent stem cell (hPSC)-derived cells offer an unprecedented opportunity to model diverse human tissue functions. However, the field lacks a generalized approach to rapidly and efficiently generate individual cell types of interest and to incorporate them into complex but defined tissues. To systematically explore the transcription factor (TF)-mediated hPSC programming landscape, we constructed the Human TFome: a comprehensive human TF library containing 1,564 TF (1,732 splice-isoforms). We discovered 241 previously unreported factors that individually converted hPSCs into diverse lineages with up to 99% efficiency in four days without alteration of external factors. Among these, we programmed neurons, fibroblasts, oligodendrocytes and endothelial cells that have molecular, transcriptomic and functional similarity to primary cells. Splice-isoform-specificity doubled endothelial conversion efficiency into in vivo-functional cells. Our cell-autonomous approach enabled parallel and orthogonal hPSCs programming into multiple cell types simultaneously without altering any microenvironmental cues. We generated in vivo-engraftable induced oligodendrocytes that expedited myelination within synthetically accelerated cerebral organoids.

overall_design: This dataset contains single cell RNA-seq for two cell types programmed using TFs discovered by screening the Human TFome library. Two hiPSC lines were engineered to express a TF, and programmed into vascular endothelial cells using ETV2 or into oligodendrocytes using SOX9 by TF induction. Differentiated cells and control cells were collected and analyzed by single cell RNA-seq.

first: Parastoo

last: Khoshakhlagh

first: Giovanni

last: Pasquini

first: Volker

last: Busskamp

first: George

last: Church


title: A comprehensive library of human transcription factors for cell fate engineering (Lentiviral Screen PGP1)

overall_design: This dataset contains the PGP1 hiPSC portion of the paper. This paper describes three hiPSC lines that were transduced with lentiviruses containing the Human TFome. TFs were induced for four days and cells sorted for TRA-1-60 signal. PCR using universal primers amplified TFs from genomic DNA, and PCR products were sequenced.

first: Anka

last: Swiersy

first: Jesus

middle: R

last: Arias


title: A comprehensive library of human transcription factors for cell fate engineering (Bulk RNA-Seq)

overall_design: This dataset contains bulk RNA-seq for four cell types programmed using TFs discovered by screening the Human TFome library. Four hiPSC lines were engineered to express a TF, and programmed into neurons using ATOH1, into fibroblasts using NKX3-1, into vascular endothelial cells using ETV2 or into oligodendrocytes using SOX9 by TF induction. Differentiated cells and control cells were collected and analyzed by RNA-seq.


title: Detecting Tumor Antigen-Specific T Cells via Interaction-Dependent Fucosyl-Biotinylation

city: San Diego

first: Peng

last: Wu

address: 10550 North Torrey Pines Road

department: Molecular Medicine

institute: Scripps Research

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

overall_design: Refer to individual Series


title: Peripheral inflammation is associated with remote global gene expression changes in the brain

city: Glasgow

first: Jonathan

last: Cavanagh

address: 120 University Place

department: Immunology

institute: University of Glasgow

summary:
Microarray analysis of whole brain RNA collected 48 hr after LPS (4mg/kg i.p.) injection
We induced systemic inflammation by injecting mice with LPS. We then performed global gene expression profiling of whole brain RNA and looked for genes that may be involved in behavioural changes.

overall_design: Male C57BL6 mice were injected (i.p.) with 4mg/kg LPS (Escherichia coli serotype 055:B5) or PBS (n=3/group). Mice were euthanised 48 hours after injection and GeneChip Mouse Gene 1.0 ST Arrays (Affymetrix) were used for transcriptional analysis of whole brain RNA.

first: Carolyn

last: Thomson

first: Alison

last: McColl

first: Gerard

last: Graham


title: Increased IL-6 Trans-Signaling in the Airways After an Allergen Challenge

city: Madison

first: Yury

last: Bochkov

state: WI

address: 600 Highland Ave, K4/945 CSC

department: Pediatrics

institute: University Of Wisconsin-Madison

summary: The pro-inflammatory cytokine IL-6 is elevated in both blood and airways in asthma. IL-6 signaling is regulated by its receptor composed of two proteins, IL-6R and GP130, that are found in both membrane and soluble forms. The interaction of IL-6 with soluble IL-6R (sIL-6R) can trigger IL-6 trans-signaling in cells such as epithelial cells and fibroblasts, which express GP130, but do not produce sufficient IL-6R. We aimed to analyze IL-6 trans-signaling in the airways after an allergen challenge and to examine the potential source of sIL-6R and sGP130. In addition to protein analysis of bronchoalveolar lavages by ELISA and flow cytometry, we performed next-generation RNA sequencing (RNA-seq) to study the expression of the IL-6R subunits by eosinophils activated by IL-3 in vitro. RNA-seq and proteomic analyses confirmed that eosinophils do not produce GP130 but produce both IL-6R and ADAM10, a metalloproteinase that cleaves membrane IL-6R into sIL-6R.

overall_design: Gene expression profiles of blood eosinophils from three subjects with allergy and mild asthma that were cultured in RPMI and 10% serum with or without IL-3 (2 ng/ml) for 4 h and 20 h.

first: Stephane

last: Esnault


title: Gene expression analysis of pancreatic cancer tissues in mice

city: Los Angeles

first: Kinji

last: Asahina

address: 1333 San Pablo Street

department: Pathology

institute: University of Southern California

summary: To examine effects of environmental risk factors on pancreatic cancer development, we fed control Pdx1-Cre (WT) and Pdx1-Cre; Kras-flox (Kras) mice with a Western alcohol diet containing high-cholesterol and high-saturated fat diet and 3.5% alcohol for 5 months. To enhance alcohol-induced pancreatic injury, we added a low dose of lipopolysaccharide (LPS, 1 μg/ml) to the diet. Mice were also given 7 hourly injections of cerulein (50 μg/kg) 4 times from the 1st to 4th month. To mimic tobacco smoking, we injected tobacco-derived carcinogen 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK, 100 mg/kg) 4 times from the 1st to 4th month. Pancreas tissues were collected from Pdx1-Cre (n=3, normal) and Pdx1-Cre; Kras-flox (n=6, all) mice. Kras-flox (Kras) mice were also fed a regular chow (n=3, control) or 3.5% alcohol diet (N=3, alcohol) for 5 months. RNA-seq analysis revealed induction of cancer-associated genes by these risk factors in the pancreatic cancer tissues.

overall_design: Examination of RNA expression in 2 different pancreas tissues.


title: ZNF143 mediates CTCF-bound promoter-enhancer loops required for murine hematopoietic stem and progenitor cell function

city: Singapore

first: Qi-Ling

last: Zhou

address: 14 Medical Drive

department: Cancer Science Institute

country: Singapore

institute: National University of Sigapore

summary: CCCTC binding factor (CTCF) is an important factor in the maintenance of chromatin chromatin interactions, yet the mechanism regulating its binding to chromatin is unknown. We demonstrate that zinc finger protein 143 (ZNF143) is a key regulator for CTCF bound promoter enhancer loops. In the murine genome, a large percentage of CTCF and ZNF143 DNA binding motifs are distributed 37 bp apart in the convergent orientation. Furthermore, deletion of ZNF143 leads to loss of CTCF binding on promoter and enhancer regions associated with gene expression changes. CTCF bound promoter enhancer loops are also disrupted after excision of ZNF143. ZNF143 CTCF bound promoter enhancer loops regulate gene expression patterns essential for maintenance of murine hematopoietic stem and progenitor cell integrity. Our data suggest a common feature of gene regulation that ZNF143 is a critical factor for CTCF bound promoter enhancer loops.

overall_design: investigate 2 histone mark, 2 transcription factors, RNA expression and HiC interactions in two different cell types

first: Qiling

first: Miao

last: Yu

first: Roberto

last: Tirado Magallanes

first: Bing

last: Li

first: Lingshi

last: Kong

first: Mingrui

last: Guo

first: Zi

last: Tan

first: Sanghoon

last: Lee

first: Touati

last: Benoukraf

first: Melissa

last: Fullwood

first: Motomi

last: Osato

last: Ren

first: Daniel

last: Tenen


title: A comprehensive library of human transcription factors for cell fate engineering

first: Alex

last: Ng


title: Gene expression data from human myeloid dendritic cells stimulated with peanut protein and other allergens

status: Public on Oct 21 2020

first: Wayne

middle: G.

last: Shreffler

address: 149 13th Street

institute: Massachusetts General Hospital

summary:
Peanut protein is a remarkably potent food allergen in susceptible individuals. The frequency of peanut allergy is approximately 1% in the US population. Peanut allergy often presents with severe symptoms, and it is seldom outgrown.
We sought to understand how peanut protein activates human dendritic cells, which are crucial in promoting the activation and differentiation of pathogenic peanut-specific Th2 cells that drive allergic responses.

overall_design: Human myeloid dendritic cells (mDC) isolated from buffy coats of non-identified blood bank donors were stimulated for 8h or 24h with peanut protein extract (PN) or with various other food and inhalant allergens, as well as with the positive controls lipopolysaccharide (LPS) and cholera toxin (CT). The other allergens were the purified peanut proteins Ara h 1 and Ara h 2, soybean protein extract (SB), cow's milk protein (CM), birch pollen extract (BP), cockroach allergen extract (CR), and cat dander extract (CD). For each variable, mDC-derived RNA was pooled from either 4 donors (pilot experiment) or 7 donors (main experiment) and analyzed using one gene chip.

first: Bert

last: Ruiter


title: Spontaneous Cell Fusions as a Mechanism of Parasexual Recombination in Tumor Cell Populations. [2]

city: TAMPA

first: Daria

last: Miroshnychenko

state: FL

address: 12902 USF Magnolia Drive

department: Cancer Physiology

institute: Moffitt Cancer Center

summary: Initiation and progression of cancers reflect the underlying process of somatic evolution, which follows a Darwinian logic, i.e., diversification of heritable phenotypes provides a substrate for natural selection, resulting in the outgrowth of the most fit subpopulations.  Although somatic evolution can tap into multiple sources of diversification, it is assumed to lack access to (para)sexual recombination – a key diversification mechanism throughout all strata of life. Based on observations of spontaneous fusions involving cancer cells, reported genetic instability of polypoid cells, and precedence of fusion-mediated parasexual recombination in fungi, we asked whether cell fusions could serve as a source of parasexual recombination in cancer cell populations. Using differentially labelled tumor cells, we found evidence of low-frequency, spontaneous cell fusions between carcinoma cells in multiple cell line models of breast cancer both in vitro and in vivo. While some hybrids remained polyploid, many displayed partial ploidy reduction, generating diverse progeny with heterogeneous inheritance of parental alleles, indicative of partial recombination. Hybrid cells also displayed elevated levels of phenotypic plasticity, which may further amplify the impact of cell fusions on the diversification of phenotypic traits. Using mathematical modeling, we demonstrated that the observed rates of spontaneous somatic cell fusions may enable populations of tumor cells to amplify clonal heterogeneity, thus facilitating the exploration of larger areas of the adaptive landscape, relative to strictly asexual populations, which may substantially accelerate a tumor’s ability to adapt to new selective pressures.

overall_design: Illumina CytoNP arrays were performed according to the manufacturer's protocol. DNA was extracted from frosen cell pellet using Quiagen DNAeasy kit. 12 samples were analysed: 8 subclones of hybrid between SUM159 and MDA231 cell lines, 2 bulk samples from passage 3 ans passage 8 of hybrid SUM159-MDA231 cells. Parental cell lines: MDA231, SUM159. Cell were grown in correcponding media before collecting the samples, no treatment was applied.


title: Spontaneous Cell Fusions as a Mechanism of Parasexual Recombination in Tumor Cell Populations. [1]


title: Spontaneous Cell Fusions as a Mechanism of Parasexual Recombination in Tumor Cell Populations


title: An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease (RNA-seq) [RNA-seq]

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: We report the bulk RNA-seq in human hippocampus subject to normal aging and Alzheimer's disease.

overall_design: RNA-seq in postmortal lateral temporal lobe of Alzheimer's disease affected brains (AD), control Old (Old) and control Young (Young).

first: Raffaella

last: Nativio

first: Berger

last: Shelley


title: RNAseq Transcriptomic Analysis of Polysaccharide A (PSA)-responding CD4+ T cells in Mice

city: Cleveland

first: Brian

last: Cobb

state: OH

address: 10900 Euclid Avenue, WRB 5132

institute: Case Western Reserve University School of Medicine

summary: Polysaccharide A (PSA), a capsular carbohydrate from the commensal gut bacteria Bacteroides fragilis, has been shown to possess both potent T cell-dependent pro- and anti-inflammatory properties. PSA is able to induce abscess and adhesion formation in sepsis models, but can also inhibit asthma, inflammatory bowel disease (IBD) and experimental autoimmune encephalomyelitis (EAE) through MHCII-dependent activation of CD4+ T cells. Yet, despite decades of study, the ability of PSA to balance both these pro- and anti-inflammatory responses remains poorly understood. Here we utilized an unbiased systems immunology approach consisting of RNAseq transcriptomics, high-throughput flow cytometry and Luminex analysis to characterize the full impact of PSA-mediated stimulation of CD4+ T cells. We found that exposure to PSA resulted in the upregulation and secretion of IFNγ, TNFα, IL-6 and CXCL10, consistent with an interferon responsive gene (IRG) signature. Importantly, PSA stimulation also led to expression of immune checkpoint markers Lag3, Tim3 and especially PD1, which were also enriched and sustained in the gut associated lymphoid tissue of PSA-exposed mice. Taken together, PSA responding cells display an unusual mixture of pro-inflammatory cytokines and anti-inflammatory surface receptors, consistent with the ability to both cause and inhibit inflammatory disease.

overall_design: Splenic CD4+ T cells were stimulated with splenic antigen presenting cells (MHCII+) and 50 ug/ml purified Polysaccharide A (PSA) derived from the commensal bacterium Bacteroides fragilis for either zero or 7 days. CD4+ T cells were isolated after activation using magnetic beads and used as a source of mRNA for deep sequencing. There are three replicates in each group (zero stimulation, 7 days stimulation).

first: Carlos

last: Alvarez

first: Mark

middle: B

last: Jones

first: John

last: Hambor


title: Single cell analysis reveals distinct immune landscapes in transplant and primary sarcomas that determine response or resistance to immunotherapy: Bulk Tumor RNA Sequencing for Rag2-/- and Rag2+/- primary p53/MCA tumors

city: Durham

first: David

last: Kirsch

state: NC

address: PO Box 96100

institute: Duke University

summary: Abstract: Immunotherapy fails to cure most cancer patients. Preclinical studies indicate that radiotherapy synergizes with immunotherapy, promoting radiation-induced antitumor immunity. Most preclinical immunotherapy studies utilize transplant tumor models, which overestimate patient responses. Here, we show that transplant sarcomas are cured by PD-1 blockade and radiotherapy, but identical treatment fails in autochthonous sarcomas, which demonstrate immunoediting, decreased neoantigen expression, and tumor-specific immune tolerance. We characterize tumor-infiltrating immune cells from transplant and primary tumors, revealing striking differences in their immune landscapes. Although radiotherapy remodels myeloid cells in both models, only transplant tumors are enriched for activated CD8+ T cells. The immune microenvironment of primary murine sarcomas resembles most human sarcomas, while transplant sarcomas resemble the most inflamed human sarcomas. These results identify distinct microenvironments in murine sarcomas that coevolve with the immune system and suggest that patients with a sarcoma immune phenotype similar to transplant tumors may benefit most from PD-1 blockade and radiotherapy.

overall_design: Methods: Primary p53/MCA sarcomas were generated in Rag2-/- and Rag2+/- mice after harvested when they reached 70-150 mm3.  Samples were processed for bulk RNA-seq

first: Amy

last: Wisdom

first: Yvonne

last: Mowery

first: Dadong

last: Zhang

first: Xiaodi

last: Qin

first: Kouros

last: Owzar


title: Single cell analysis reveals distinct immune landscapes in transplant and primary sarcomas that determine response or resistance to immunotherapy

summary: Abstract: Despite impressive responses in some patients, immunotherapy fails to cure most cancer patients. Preclinical studies indicate that radiotherapy synergizes with immunotherapy, promoting radiation-induced antitumor immunity. Nearly all preclinical immunotherapy studies utilize transplant tumor models, but cure rates of transplant tumors treated with immunotherapy overestimate patient responses. Here, we show that transplant sarcomas are cured by PD-1 blockade and radiotherapy, but identical treatment fails in autochthonous sarcomas, which demonstrate tumor-specific immune tolerance. We characterize tumor-infiltrating immune cells from transplant and primary tumors and reveal striking differences in their immune landscapes. Although radiotherapy remodels myeloid cells in primary and transplant sarcomas, only transplant tumors are enriched for activated CD8+ T cells associated with tumor clearance. By CIBERSORTx, the immune microenvironment of primary sarcomas in mice transcriptionally resembles most human sarcomas, while transplant sarcomas model the most inflamed sarcomas in patients. These results identify distinct microenvironments in murine sarcomas that coevolve with the immune system and suggest that patients whose sarcomas have an immune phenotype similar to transplant tumors may benefit most from PD-1 blockade and radiotherapy.

overall_design: Methods: Primary and allograft sarcomas were harvested 3 days after treatment with either 0 or 20 Gy radiation and anti-PD-1 or isotype control treatment.


title: Metabolic stress induced by continuous stimulation under hypoxia rapidly drives T cell exhaustion

city: Pittsburgh

first: Amanda

middle: Catherine

last: Poholek

state: Pennsylvania

address: 4401 Penn Ave., Rangos Research Center 8129

institute: University of Pittsburgh

summary: Expression profiling of in vitro generated CD8 T cells and CD8 TIL isolated ex vivo.

overall_design: RNAseq of in vitro generated CD8 T cells and CD8 TIL isolated ex vivo

first: Nicole

last: Scharping

first: Dayana

last: Rivadeneira

first: Ashley

middle: V

last: Menk

first: Natalie

last: Rittenhouse

first: Paolo

last: Vignali

first: Ronal

last: Peralta

first: Kristin

last: DePeaux

first: B

last: Ford

middle: C

first: Greg

last: Delgoffe

first: B. Rhodes

first: Yiyang

last: Wang

first: Yupeng


title: Hydroxychloroquine inhibits trained immunity

city: Hinxton

first: Rik

last: Lindeboom

address: Wellcome Trust Genome Campus

department: Cellular Genetics

institute: Wellcome Sanger Institute

summary: We demonstrate that hydroxychloroquine inhibits trained immunity at the functional and epigenetic level and is accompanied by reduced expression of interferon-stimulated genes. Trained immunity comprises a functional adaptation induced by epigenetic reprogramming which facilitates the anti-viral innate immune response.

overall_design: We performed ChIP sequencing and RNA sequencing on trained monocytes that are treated with HCQ, and RNA-seq on monocytes from COVID-19 patients that were treated with HCQ.

first: Nils

last: Rother

first: Raphaël

last: Duivenvoorden


title: A comprehensive library of human transcription factors for cell fate engineering (Lentiviral Screen ATCC)

first: Alex

last: Ng

overall_design: This dataset contains the ATCC-DYS0100 hiPSC portion of the paper. This paper describes three hiPSC lines that were transduced with lentiviruses containing the Human TFome. TFs were induced for four days and cells sorted for TRA-1-60 signal. PCR using universal primers amplified TFs from genomic DNA, and PCR products were sequenced.

middle: M

first: Parastoo

last: Khoshakhlagh

first: Anka

last: Swiersy

first: Jesus

last: Arias

first: Volker

last: Busskamp

first: George

last: Church


title: RNA sequencing reveals the transcriptomic profile of human neuroblastoma SK-N-BE(2) cell line after MCM6 interfered by small interfering RNA

status: Public on Oct 20 2020

city: Shanghai

first: Yaoyao

last: Gu

state: State...

address: No. 1665 Kongjiang Road

institute: Xinhua Hospital

summary: Minichromosome maintenance complex component 6 (MCM6), as an important replication permission factor, is involved in the pathogenesis of various tumors. we studied the expression of MCM6 in neuroblastoma and its influence on tumor characteristics and prognosis, and we found MCM6 has significant effect on tumor growth promotion. To investigate the underlying mechanism that MCM6 in neuroblastoma, we compared the transcriptomes of siRNA interfered MCM6 and negative control neuroblastoma cells.

overall_design: 6 samples of human neuroblastoma cells were divided into two groups: MCM6 interference group and control group, with 3 replicates in each group.

first: Xiaoxiao

last: Hu

first: Xiaowei

last: Liu

first: Cheng

last: Cheng

first: Kai

last: Chen

first: Yeming

last: Wu

first: Zhixiang


title: The oncogenomic function of androgen receptor in esophageal squamous cell carcinoma is directed by GATA3

first: Zhong

address: 905 S. LaSalle Street

summary: Esophageal squamous cell carcinoma (ESCC) is the sixth leading cause of cancer death worldwide. Emerging evidence suggests that the androgen receptor (AR) is involved in ESCC tumorigenesis. However, how AR exerts its genomic functions in ESCC remains unknown. Here, by defining AR cistromes and analyzing androgen-regulated transcriptomes, we find that AR downregulates the majority of its target genes in ESCC cells. We further find that the pioneer factor GATA3 governs AR-repressed transcription by recruiting SMRT/HDAC3 co-repressors to target gene loci. Importantly, genetic inhibition of GATA3 or pharmacological inhibition of AR/HDAC3 relieves AR-mediated gene repression, leading to ESCC cell growth inhibition in vitro and in vivo. Our findings reveal molecular mechanisms underlying the oncogenomic function of AR in ESCC and identify the GATA3-directed AR transcriptional repression program as a therapeutic target for ESCC.

overall_design: AR cistrome and mRNA profiles of ESCC cells treated with vehicle or R1881 were generated by deep sequencing using Illumina HiSeq4000

first: Furong

last: Huang

first: Qianben


title: MicroRNA effects on breast cancer cell migration

city: Oklahoma City

first: Julio

middle: Cesar

last: Morales

state: OK

department: Department of Neurosurgery

institute: University of Oklahoma Health Science Center

summary: Screening of miRNA mimics resulted in differential motility capacity.  To discover novel miRNA motility regulators, gene expression of breast cancer cells transfected with miRNA mimics were compared.

overall_design: Total RNA isolated from cell lines treated with different miRNAs  to modulate motility

first: Gray

middle: W

last: Pearson


title: 10X genomics single cell sequencing of sheep testis

city: Nanjing

first: Hua

last: Yang

state: 请选择

address: Weigang No.1

institute: Nnanjing Agricultural University

summary: A 1.5-year-old healthy male Hu sheep was selected and castrated for testis collection, then single cell suspension was obtained using enzymatic digestion method for single cell sequencing. And the cell types of sheep testis and marker genes of each cell type were identified based on the RNA sequencing.

overall_design: mRNA profile of one Hu sheep testis sample was generated by single cell sequencing

first: Yanli

last: Zhang

first: Feng

last: Wang


title: A holistic systems approach to characterize the impact of pre- and post-natal oxycodone exposure on neurodevelopment and behavior

city: OMAHA

first: Sowmya

last: Yelamanchili

state: Nebraska

address: 984455 Nebraska Medical Center

department: Anesthesiology

institute: UNIVERSITY OF NEBRASKA MEDICAL CENTER

summary: RNA-sequencing of total RNA isolated from P14 PFC tissues of animals exposed to oxycodone or saline revealed alterations in the expression of key genes associated with synaptic transmission, neurodevelopment, mood disorders, and addiction in the treatment groups.

overall_design: Total RNA from prefrontal cortex (PFC) tissue was isolated from the randomly selected pups (n = 6) from each treatment group at P14 using the Direct-Zol RNA kit (Zymo Research, CA, USA) based on the manufacturer’s protocol. Samples were sent to UNMC’s Next Generztion Sequencing (NGS) core. RNAseq libraries were generated beginning with 1 ug of total RNA from each sample using the TruSeq V2 RNA sequencing library kit from Illumina following recommended procedures (Illumina Inc., San Diego, CA). Resultant libraries were assessed for size of insert by analysis of an aliquot of each library on a BioAnalyzer instrument (Agilent Technologies, Santa Clara, CA). Each library contained a unique indexing identifier barcode allowing the individual libraries to be multiplexed together for efficient sequencing.  Multiplexed libraries (18 samples per pool) were sequenced on a single flow cell of the NextSeq550 DNA Analyzer (Illumina) to generate a total of approximately 28 million 75 bp single reads for each sample.

first: Katherine

last: Odegaard

first: Jagadesan

last: Sankarasubramanian

first: Yelamanchili

last: SV


title: Tetraspanin CD151 protects against pulmonary fibrosis by maintaining epithelial integrity

city: Suita-city

first: Yoshito

last: Takeda

state: Osaka

address: Yamada-oka, 2-2

department: Department of Respiratory Medicine and Clinical Immunology

institute: Osaka University Graduate School of Medicine

summary:
Comparison of gene expressions between the lungs of CD9KO and CD151KO mice
A microarray study identified an enrichment of genes involved in connective tissue disorders in the lungs of CD151 KO mice, but not in CD9 KO mice.

overall_design: wild-type: n=4, CD151KO: n=5, CD9KO: n=5

first: Kazuyuki

last: Tsujino


title: Transcriptome analysis of enzalutamide-sensitive and -resistant C4-2B cells

city: Spokane

first: Boyang

state: Washington

address: 412 E. Spokane Falls Blvd

institute: Washington State University

summary: The overall goal of this study was to identify genes differentially expressed in enzalutamide-sensitive (C4-2B Con) and enzalutamide-resistant (C4-2B ENZR) C4-2B cells.

overall_design: Two samples were analyzed by RNA-Seq analysis: C4-2B Con and  C4-2B ENZR.


title: Calcineurin Controls Proximodistal Blastema Polarity in Zebrafish Fin Regeneration

city: 赣州

first: yunlong

last: meng

state: 江西

address: 江西省赣州市

institute: 赣南师范大学

summary: Planarian flatworms regenerate their heads and tails from anterior or posterior wounds and this blastema regeneration polarity is controlled by Wnt/β-catenin signaling. It is well known that a regeneration blastema of appendages of vertebrates such as fish and amphibians grows distally. However, it remains unclear whether a regeneration blastema in vertebrate appendages can grow proximally. Here, we show that a regeneration blastema in zebrafish fins can grow proximally along the proximodistal axis by calcineurin inhibition. We used fin excavation in adult zebrafish to observe the unidirectional regeneration, from the anterior cut edge (ACE) to the posterior cut edge (PCE) of the cavity and this unidirectional regeneration polarity occurs as the PCE fails to build blastemas. Furthermore, we found that calcineurin activities in the ACE were greater than in the PCE. Calcineurin inhibition induced the PCE blastemas, and calcineurin hyperactivation suppressed fin regeneration. Collectively, these findings identify calcineurin as a molecular switch to specify the PCE blastema of the proximodistal axis and regeneration polarity in zebrafish fin.

overall_design: Zebrafish Fin mRNA profiles of the anterior cut edge (ACE) and the posterior cut edge (PCE) at 24, 48, and 72 hpa (hours post amputation)

first: Zigang

last: Cao

first: Yunlong

last: Meng

first: Fanghua

last: Gong

first: Chaopeng

last: Xu

first: Fasheng

first: Mengjie

last: Fang

first: Lufang

last: Zou

first: Xinjun

last: Liao

first: Xinjuan

first: Lingfei

last: Luo

first: Xiaokun

last: Li

first: Huiqiang

last: Lu


title: Non-Canonical Targets of HIF1a Impair Oligodendrocyte Progenitor Cell Function [ATAC-seq]

first: Paul

last: Tesar

state: Ohio

address: 10900 Euclid Ave.

department: Genetics & Genome Sciences

institute: Case Western Reserve University

summary: Mammalian cells respond to insufficient oxygen through transcriptional regulators called hypoxia-inducible factors (HIFs). Although transiently protective, prolonged HIF activity drives distinct pathological responses in different tissues. Using a model of chronic HIF1a accumulation in pluripotent-stem-cell-derived oligodendrocyte progenitors (OPCs), we demonstrate that HIF1a activates non-canonical targets to impair generation of oligodendrocytes from OPCs. HIF1a activated a unique set of genes in OPCs through interaction with the OPC-specific transcription factor OLIG2. Non-canonical targets, including Ascl2 and Dlx3, were sufficient to block differentiation through suppression of the oligodendrocyte regulator Sox10. Chemical screening revealed that inhibition of MEK/ERK signaling overcame the HIF1a-mediated block in oligodendrocyte generation by restoring Sox10 expression without affecting canonical HIF1a activity. MEK/ERK inhibition also drove oligodendrocyte formation in hypoxic regions of human oligocortical spheroids. This work defines mechanisms by which HIF1a impairs oligodendrocyte formation and establishes that cell-type-specific HIF1a targets perturb cell function in response to low oxygen.

overall_design: This subseries consists of biological replicates (A and B) of Omni ATAC-seq experiments in wild-type untransduced OPCs.

first: Kevin

last: Allan


title: miRNA repertoires of ex-vivo bronchial, nasal, and polyps cells cultured from healthy and CF donors

city: Montpellier

first: Magali

last: Taulan-Cadars

address: 641 avenue du Doyen Gaston Giraud

country: France

institute: EA7402 Laboratoire de génétique de maladies rares

summary: Cystic fibrosis (CF), a genetic disorder, is characterized by chronic lung disease. Small non-coding RNAs are key regulators of gene expression and participate in various processes, which are dysregulated in CF; however, they remain poorly studied. Here, we determined the complete microRNAs (miRNAs) expression pattern in three CF ex-vivo models.   The miRNA profiles of air-liquid interface cultures of airway epithelia (bronchi, nasal cells, and nasal polyps) samples from patients with CF and non-CF controls were obtained by deep sequencing. Compared with non-CF controls, several miRNAs were deregulated in CF samples, for instance miR-181a-5p and the miR-449 family were upregulated. Moreover, mature miRNAs often showed variations (i.e., isomiRs) relative to their reference sequence, such as miR-101, suggesting that miRNAs consist of heterogeneous repertoires of multiple isoforms with different effects on gene expression. Analysis of miR-181a-5p and miR-101-3p roles indicated that they regulate the expression of WISP1, a key component of cell proliferation/migration programs. We showed that miR-101 and miR-181a-5p participated in aberrant recapitulation of wound healing programs by controlling WISP1 mRNA and protein level.  Our miRNA expression data bring new insights into CF physiopathology and define new potential therapeutic targets in CF

overall_design: miRNA expression profile of NCF and CF cells from Nasal, Polyps and Bronchial cells

first: Jessica

last: Varilh


title: Non-Canonical Targets of HIF1a Impair Oligodendrocyte Progenitor Cell Function

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

overall_design: Refer to individual Series


title: Non-Canonical Targets of HIF1a Impair Oligodendrocyte Progenitor Cell Function [ChIP-Seq]

overall_design: This subseries consists of biological replicates (A and B) of ChIP-seq experiments in VHL knockout and control OPCs for HIF1a, HIF1b, H3K27Ac, and Olig2 and biological replicates (A and B) of HA ChIP-seq in HA-Ascl2 overexpression and control OPCs. Inputs used to analyze ChIP-seq for each antigen are also provided.

first: Andrew

last: Morton


title: Gene expression profiles of Dclk1+ and Dclk1- PDAC cells

city: Kyoto

first: Takahisa

last: Maruno

state: Kyoto

address: 54 Syogoin-Kawahara-cho, Sakyo-ku

department: Gastroenterology and hepatology

institute: Kyoto university

summary: Doublecortin-like kinase 1 (Dclk1) is known as a cancer stem cell marker of pancreatic ductal adenocarcinoma (PDAC). But the functional evidence to define the stem cell activity of these cells within tumors has not been explored. We compared the gene expression profiles of Dclk1-positive and -negative PDACs cells.

overall_design: To determine the molecular characteristics of Dclk1+ PDAC cells, we performed microarray analysis on FACS-sorted Dclk1+ and Dclk1- PDAC cells obtained from Dclk1CreERT2-IRES-EGFP/+; Pdx1-Flp; KrasFSF-G12D/+; Trp53frt/frt (DKPF) mice.

first: Hiroshi

last: Seno


title: Non-Canonical Targets of HIF1a Impair Oligodendrocyte Progenitor Cell Function [RNA-Seq]

overall_design: This subseries consists of two different RNAseq experiments. The first is analyzing VHL knockout and control OPCs. The second is analyzing VHL knockout and control OPCs treated with either DMSO (D) or AZD8330 (AZ) for 14 hours.


title: Single cell gene expression of melanocyte specific Braf mutant mouse skin

city: Irvine

first: Arthur

last: Lander

state: CA

address: 2300 Biological Science

institute: University of California Irvine

summary: Mutational activation of the BRAF proto-oncogene in melanocytes reliably produces benign nevi (pigmented “moles”), yet the same change is the most common driver mutation in melanoma. One of the abiding mysteries of carcinogenesis is why oncogene activation doesn’t always lead to cancer.  The reason nevi stop growing, and do not progress to melanoma, is widely attributed to a cell-autonomous process of “oncogene-induced senescence”. Senescence is usually accompanied by distinctive gene expression and various gene expression “signatures” have been developed to help investigators identify senescent cells and distinguish them from cells that have become growth arrested by other processes. Using a mouse model of Braf-driven nevus formation, we analyzed single-cell gene expression and found no evidence that nevus cells are senescent, either compared with other skin cells, or other melanocytes.

overall_design: Single Cell suspensions were obtained from BrafWT, Tyr::CreER or BrafV600E, Tyr::CreER mice at either P30 (n = 2 of each genotype) or P50 (n = 3 of each genotype). RNA was isolated using 10X Genomics technologies. Under the sample titles, "WT" represents cells obtained from wild type skin, and "MT" represents cells from mice in which the Braf oncogene was activated in the melanocytic lineage.

first: Rolando

last: Ruiz-Vega

first: Anand

last: Ganesan

first: Lander


title: Cell-type specific epigenetic regulome in Systemic Sclerosis skin

city: Stanford

first: Kun

last: Qu

address: 269 Campus Dr. CCSR 2150

department: Dermatology

institute: Stanford University

summary: Skin systemic sclerosis (Scleroderma, SSc) is an autoimmune disease while its epigenetic regulatory mechanism is not known.  We surveyed the genome-wide active regulatory elements in fresh human skin cells, using Assay of Transposase Accessible Chromatin with sequencing (ATAC-seq) in longitudinal skin from healthy volunteers and affected and unaffected skin from patients with SSc. We created robust pipelines that enable accurate single molecule counting and allelic discrimination from clinical material in vivo without clonal expansion.  We generated high-resolution epigenetic regulomes of 9 cell types in normal and SSc skins, and identified 106044 cell type specific accessible sites. Motif analysis of these peaks predicted known and novel transcription factors regulating each cell type. For each cell type, we discovered thousands of accessible sites are differential in normal versus unaffected and affected skin from patients with SSc. We predicted novel transcription factors regulating SSc in a cell type specific manner, and predicted the relative contributions of each cell type in driving skin SSc. ATAC-seq also revealed novel elements that escape X chromosome inactivation, which coordinately impact genes with immune function.

overall_design: In this study, we developed a systematic approach to characterize chromatin dynamics in normal and patients with systemic sclerosis. We examined chromatin structure using ATAC-seq in normal human skin and affected and unaffected skin cells from patients with SSc. We generate and analyze 114 high-resolution personal regulomes of a multiple cell type, CD4+ and CD8+ T cell, pericyte, dendritic, langerhan, endotheliocyte, macrophage, fibroblast and keratinocyte, and comprised over 4.5 billion measurements. Samples were accumulated from 11 normal donors and 8 SSc patients. We develop methods to integrate diverse sources of genomic and epigenomic information to address the regulatory pattern in divergent cells in human skin in vivo. Healthy human donors provided 5 mm punch skin sample and each sample was digested to single cell suspension. Patients’ samples were obtained from clinically affected skin of the arm and clinically unaffected skin of the back of patients with SSc. From each skin biopsy, we isolated CD4+ and CD8+ T cells, fibroblasts, melanocytes, macrophages, endothelial and dendritic cells using flow cytometry. For each cell type we then performed ATAC-seq to map the location and accessibility of regulatory elements genome-wide from 50,000 cells.

first: Qian

last: Liu

first: Michelle

last: Longmire

first: Lisa

last: Zaba

first: Rui

last: Giresi

first: Youn

last: Kim

first: Howard

middle: Y

last: Chang


title: BAZ2A safeguards genome architecture of ground-state pluripotent stem cells

city: Zurich

first: Raffaella

last: Santoro

address: Winterthurerstrasse 190

department: Dep. of Molecular Mechanisms  of Disease

institute: University of Zurich

summary: Chromosomes have an intrinsic tendency to segregate into compartments, forming long-distance contacts between loci of similar chromatin states. How genome compartmentalization is regulated remains elusive. Here, comparison of mouse ground-state embryonic stem cells (ESCs) characterized by open and active chromatin, and advanced serum ESCs with a more closed and repressed genome, reveals distinct regulation of their genome organization due to differential dependency on BAZ2A/TIP5, a component of the chromatin remodeling complex NoRC. On ESC chromatin, BAZ2A interacts with SNF2H, DNA topoisomerase 2A (TOP2A) and cohesin. BAZ2A associates with chromatin subdomains within the active A compartment, which intersect through long-range contacts. We found that ground-state chromatin selectively requires BAZ2A to limit the invasion of active domains into repressive compartments. BAZ2A depletion increases chromatin accessibility at B compartments. Furthermore, BAZ2A regulates H3K27me3 genome occupancy in a TOP2A-dependent manner. Finally, ground-state ESCs require BAZ2A for growth, differentiation, and correct expression of developmental genes. Our results uncover the propensity of open chromatin domains to invade repressive domains, which is counteracted by chromatin remodeling to establish genome partitioning and preserve cell identity.

overall_design: RNAseq, ChIPseq, ATACseq and HiC in mouse ESCs

first: Damian

last: Dalcher

first: Jennifer

last: Tan

first: Cristiana

last: Bersaglieri

first: Rodrigo

last: Peña-Hernández

first: Eva

last: Vollenweider

first: Stefan

last: Zeyen

first: Marc

last: Schmid

first: Valerio

last: Bianchi

last: Butz

first: Marcin

last: Roganowicz

first: Rostyslav

last: Kuzyakiv

first: Tuncay

last: Baubec

first: Ana

last: Marques


title: Modifying macrophages at the periphery has the capacity to change microglial reactivity and increase ALS survival

status: Public on Oct 19 2020

city: Paris

first: Severine

last: Boillee

address: Pitie-Salpetriere Hospital, 47 bd de l'Hopital, Batiment ICM

department: Institut du Cerveau - ICM

institute: Paris Brain Institute, Inserm U1127, CNRS, Sorbonne University

summary: Microglia and peripheral macrophages, combined, have been implicated in the motor neuron disease Amyotrophic Lateral Sclerosis (ALS), but without discriminating their respective roles. We now show that macrophages along peripheral motor neuron axons of ALS mice and patients react to neurodegeneration. In ALS mice, peripheral myeloid cell infiltration into the spinal cord was limited and disease duration dependent. Targeted gene modulation of the reactive oxygen species pathway in peripheral myeloid cells of ALS mice, using cell replacement, reduced both peripheral macrophage and microglial activation, delayed symptoms and increased ALS mouse survival. Transcriptomics revealed that sciatic nerve macrophages and microglia reacted very different to neurodegeneration, with abrupt temporal changes in macrophages and progressive, unidirectional activation in microglia. Modifying peripheral macrophages suppressed proinflammatory microglial responses, with a strong shift towards neuronal support. Thus, modifying macrophages at the periphery has the capacity to influence disease progression and is of therapeutic value for ALS.

overall_design:
GENERAL: The project has 2 parts: PART 1 (NON_GRAFTED) are non-grafted mutant hSOD1-G93A ALS mice (for a total of 51 RNAseq samples; all females), from which both spinal cord microglial cells (MG) (33 samples) and sciatic nerve peripheral macrophages (MP) (18 samples) were isolated for RNAseq analysis; PART 2 (GRAFTED) are mutant hSOD1-G93A ALS mice (for a total of 23 RNAseq samples; all females) that were grafted with bone-marrow (BM) at onset from either (1) mutant hSOD1-G93A ALS mice (as baseline disease control) (12 samples), or (2) wildtype hSOD1 mice (as experimental disease modifying condition) (11 samples). Like for Part 1, from these mice both spinal cord microglial cells (MG) (12 samples) and sciatic nerve peripheral macrophages (MP) (11 samples) were isolated for RNAseq analysis.
DETAILED: both spinal cord microglial cells (MG) and sciatic nerve peripheral macrophages (MP), were isolated by anti-CD11b magnetic microbead-coupled antibody (MACS). For PART 1 (NON_GRAFTED): MG and MP were isolated at 4 disease stages from (non-grafted) mutant SOD1-G93A ALS mice. Disease stages were: pre-symptomatic, onset (weight peak), early symptomatic (10% weight loss) and end stage (see "Samples" for precise ages). For each diseae stage, 3-5 replicates (n=3-5) were done (1 mouse per sample/replica). For MG, one spinal cord/sample was used, for MP, two sciatic nerves/mouse/sample were used (see Publication for more details). As controls, both non-transgenic C57BL6/J mice (n=4) and wildtype hSOD1 transgenic mice (n=4) were used (at 2 ages corresponding to onset and end stage). For PART 2 (GRAFTED): MG and MP were isolated at 2 disease stages from (grafted) mutant SOD1-G93A ALS mice. Disease stages were: early symptomatic and end stage (see "Samples" for precise ages). For each diseae stage, 3 replicates (n=3) were done (1 mouse per sample/replica). For MG, one spinal cord/sample was used, for MP, two sciatic nerves/mouse/sample were used (see Publication for more details).

first: Aude

last: Chiot

first: Sakina

last: Zaïdi

first: Charlène

last: Iltis

first: Matthieu

last: Ribon

first: Félix

last: Berriat

first: Lorenzo

last: Schiaffino

first: Ariane

last: Jolly

first: Pierre

last: de la Grange

first: Michel

last: Mallat

first: Delphine

last: Bohl

first: Stéphanie

last: Millecamps

first: Danielle

last: Seilhean

first: Christian

middle: S

last: Lobsiger

first: Séverine

last: Boillée