title: Signal requirement for cortical potential of transplantable human neuroepithelial stem cells [array]

status: Public on Feb 04 2022

city: Quebec City

first: Samer

last: Hussein

state: Quebec

address: 9 rue Mcmahon

department: Departement of medecine

institute: CHU de Québec - Université Laval

summary:
The cerebral cortex develops from dorsal forebrain neuroepithelial progenitor cells. Initial expansion of the progenitor cell pool is followed by the generation of neurons of all the cortical layers and later, astrocytes and oligodendrocytes. However, the regulatory pathways that control the expansion and maintenance of the neuroepithelial progenitor cell pool are currently unknown. Here we define six basic pathway components that regulate proliferation of cortically specified human neuroepithelial stem cells (cNESCs) in vitro without the loss of developmental potential. We show that activation of FGF and inhibition of BMP and ACTIVIN A signalling are required for long-term cNESC proliferation. We also demonstrate that cNESCs preserve dorsal telencephalon-specific potential when GSK3, AKT and nuclear CATENIN-b1 activity are low. Remarkably, regulation of these six pathway components supports the clonal expansion of cNESCs. Moreover, cNESCs differentiate to lower and upper layer cortical neurons both in vitro and in vivo. Identifying the mechanisms that drive the self-renewal and fate of cNESCs decision of neuroepithelial stem cells is key to developing new stem cell-based therapeutic approaches to treat neurological conditions.
In this study, we performed Oxford Nanopore technologies long-read RNA-sequencing (lrRNA-seq) of human cNESCs and of the human embryonic stem cells used to generate them. Two hESC cell lines were differentiated to cNESCs, which were then maintained in either six factors (6F : BMPRi, TGFBRi, GSK3i, FGF, TANKYRASEi, AKTi) or 4 factors (6F-2F : BMPRi, TGFBRi, GSK3i, FGF). All samples (hESCs, cNESCs in 6 factors, cNESCs in 4 factors) are submitted to lrRNA-seq as duplicates.

overall_design: Balasz,V,Varga

first: Gabriel

last: Khelifi

first: Andras

last: Nagy


title: Transcriptomic analysis of undifferentiated human embryonic stem cells (hESCs) and day-25 differentiated cortical neuronal progenitor cells from 5 isogenic hESC lines with low and high levels of alpha-synuclein expression

city: Edinburgh

first: Tilo

last: Kunath

address: 5 LIttle France Drive

department: Centre for Regenerative Medicine

country: United Kingdom

institute: University of Edinburgh

type: Expression profiling by high throughput sequencing

summary:
Purpose: To compare the cortical neuroonal differentiation capacity of clonal isogenic hESC lines with different levels of alpha-synuclein (aSyn) expression.
Methods 1: Shef4 hESCs was used as a parental line to create an allelic series of clonal transgenic hESC lines expressing a human SNCA (encoding aSyn) contruct. Clonal transgenic lines with high (S8, S37) and low (S9, S34) aSyn expression were established and characterized.
Methods 2: hESCs were cultured on Laminin-521 (BioLamina) in StemMACS iPS-Brew XF self-renewal media (Miltenyi) prior to lifting for isolation of total RNA.
Methods 3: Cortical neuronal progenitor cells were differentiated from hESCs on Laminin-111 coated (Biolamina) 24-well plates at an initial plating density of 80,000 cells/cm2. Differentiation commenced in neural induction media (NIM) consisting of 50% DMEM/F12 (ThermoFisher Scientific), 50% Neurobasal Media (ThermoFisher Scientific), B27 supplement with Retinoic Acid (ThermoFisher Scientific), N2 supplement (ThermoFisher Scientific) and 2 mM L-Glutamine (ThermoFisher Scientific), 10μM SB431542 (Tocris) and 100 nM LDN-193189 (Miltenyl Biotec). From day 4 onwards, the base media was changed to 50% NIM, 25% DMEM/F12 and 25% Neurobasal Media. SB431542 (10 μM) and LDN-193189 (100 nM) were present for the first 12 days of differentiation. Cells were lifted and re-plated at day 12 and day 17 with Collagenase Type IV (Life Technologies). At day 25, differentiated cells were lifted for total RNA isolation.

overall_design: Total RNA was isolated from self-renewing hESCs with low aSyn (Shef4, S9, S34) and high aSyn (S8, S37) expression, and from the same cell lines at Day 25 of cortical neuronal differentiation using the dual-Smad inhibition protocol

first: Ammar

last: Natalwala

first: Ranya

last: Behbehani


title: Real-time quantitative PCR analysis of insulin-producing cells differentiation from canine adipose-derved mesenchymal stem cells

status: Public on Feb 05 2022

city: Pathumwan

first: QUYNH

middle: Dang

last: LE

state: Bangkok

address: Phayathai

country: Thailand

institute: FALCUTY OF VETERIANARY, CHULALONGKORN UNIVERSITY

summary: We established a useful protocol for generating insulin -producing cells (IPCs) from canine adipose mesenchymal stem cells (cAD-MSCs). IPCs were induced from cAD-MSCs with the three-stepwise protocol. For the first stage , cAD-MSCs was induced to definitive endoderm (DE) with the cooperation of Chir99021 and Activin A for 3 days. For the second stage, pancreatic endocrine (PE) progenitor was induced from DE after treatment with taurine, retinoic acid, FGF2 EGF, TGFβ inhibitor, dorsomorphin, nicotinamide, and DAPT for the next 5 days. In the last stage, the combination of taurine, nicotinamide, Glp-1, forskolin, PI3K inhibitor, and TGFβ inhibitor was used to yield efficiently functional IPCs from PE precursors for 5 days. To indentify differences in the expression pattern of genes related to pancreatic beta cell development, we performed real time quantitative polymerase chain reaction (RT-qPCR).

overall_design: qPCR gene expression profiling of differentiation cells at every stage of induction (day 3, day 5, and day 13) compared to undifferentiated cells.

first: R

last: Watchareewan

first: D

middle: L

last: Quynh


title: Next Generation Sequencing of sorted central memory CD4 T cells (TCM) from young and elderly severe SARS-CoV-2 patients

status: Public on Feb 01 2022

city: Modena

first: Andrea

last: Cossarizza

state: Modena

address: Via Campi 287

country: Italy

institute: University of Modena and Reggio Emilia

summary: Purpose: The goal of this study is to compare the transcriptome profiling (RNA-seq) of central memory CD4 T cells among young and elderly samples from healthy donors and SARS-CoV-2 subjects.

overall_design: We enrolled 3 young (CUN) and 3 elderly (COV) Sars-CoV-2 patients with a median age of 46 ± 6.6 and 72.3 ± 3.2 years and were matched with 3 young (HUN) and 3 elderly (HOV) healthy donors with a median age of 50.7 ± 4.9 and 75 ± 6.4 years. All samples were sequenced at the depth of 40*106 reads using fragments length of 100 base pair (bp)

first: Domenico

last: Lo Tartaro


title: Signal requirement for cortical potential of transplantable human neuroepithelial stem cells

country: Canada

summary: The cerebral cortex develops from dorsal forebrain neuroepithelial progenitor cells. Initial expansion of the progenitor cell pool is followed by the generation of neurons of all the cortical layers and later, astrocytes and oligodendrocytes. However, the regulatory pathways that control the expansion and maintenance of the neuroepithelial progenitor cell pool are currently unknown. Here we define six basic pathway components that regulate proliferation of cortically specified human neuroepithelial stem cells (cNESCs) in vitro without the loss of developmental potential. We show that activation of FGF and inhibition of BMP and ACTIVIN A signalling are required for long-term cNESC proliferation. We also demonstrate that cNESCs preserve dorsal telencephalon-specific potential when GSK3, AKT and nuclear CATENIN-b1 activity are low. Remarkably, regulation of these six pathway components supports the clonal expansion of cNESCs. Moreover, cNESCs differentiate to lower and upper layer cortical neurons both in vitro and in vivo. Identifying the mechanisms that drive the self-renewal and fate of cNESCs decision of neuroepithelial stem cells is key to developing new stem cell-based therapeutic approaches to treat neurological conditions.

overall_design: In this study, we performed Oxford Nanopore technologies long-read RNA-sequencing (lrRNA-seq) of human cNESCs and of the human embryonic stem cells used to generate them. Two hESC cell lines were differentiated to cNESCs, which were then maintained in either six factors (6F : BMPRi, TGFBRi, GSK3i, FGF, TANKYRASEi, AKTi) or 4 factors (6F-2F : BMPRi, TGFBRi, GSK3i, FGF). All samples (hESCs, cNESCs in 6 factors, cNESCs in 4 factors) are submitted to lrRNA-seq as duplicates.

first: Balasz

middle: V

last: Varga

middle: M


title: Influence of gallic acid on gene expression in Blastobotrys raffinosifermentans LS3

status: Public on Feb 03 2022

city: Seeland

first: Anja

last: Hartmann

state: Saxony-Anhalt

address: Corrensstraße 3

department: PZB

country: Germany

institute: IPK Gatersleben

summary: Gene expression profiling of Blastobotrys raffinosifermentans LS3 cells based on 6.025 annotated chromosomal Blastobotrys raffinosifermentans LS3 sequences and 36 putative mitochondrial gene oligos was performed following exposure to gallic acid. Microarray data were successfully used to identify expression changes of main candidate genes involved in tannic acid degradation, protocatechuic acid degradation, β-oxidation, the glyoxylate cycle, the methyl citrate cycle and the catabolism of the branched-chain amino acids valine, leucine and isoleucine.

overall_design: In the study presented here, gene expression profiling was performed using a microarray produced by Agilent Technologies in 8 x 60 k format. The microarray was based on 6,025 annotated chromosomal sequences and 36 putative mitochondrial gene oligos, resulting in a total of 56,312 Blastobotrys raffinosifermentans LS3 specific oligos. Blastobotrys raffinosifermentans LS3 cells were cultivated overnight in YMM-glucose-NaNO3 and shifted to YMM-NaNO3 containing a mixture of either 0.5 % gallic acid plus 1 % glucose or 1 % glucose only. After 15 min, 30 min, 2 h and 5 h of cultivation at 30 °C and 180 rpm, cells were harvested, total RNA was isolated, samples were labelled, and the microarray was hybridized according to the Agilent Technologies “One-Color Microarray-Based Gene Expression Analysis (v6.5)” instructions. R package limma was used for microarray data analysis. Background of raw expression data was corrected by “normexp” and normalized between arrays using “quantile”.

first: Falko

last: Matthes

first: Sebastian

last: Worch

first: Anna

last: Meier

first: Gotthard

last: Kunze


title: Liver-derived cell lines from cavefish Astyanax mexicanus as an in vitro model for studying metabolic adaptation

status: Public on Feb 02 2022

city: Kansas City

first: Huzaifa

last: Hassan

state: MO

country: USA

institute: Stowers Institute for Medical Research

summary: Cell lines have become an integral resource and tool for conducting biological experiments ever since the Hela cell line was first developed (1). They not only allow detailed investigation of molecular pathways but are faster and more cost-effective than most in vivo approaches. The last decade saw many emerging model systems strengthening basic science research. However, lack of genetic and molecular tools in these newer systems pose many obstacles. Astyanax mexicanus is proving to be an interesting new model system for understanding metabolic adaptation. To further enhance the utility of this system, we developed liver-derived cell lines from both surface-dwelling and cave-dwelling morphotypes. In this study, we provide detailed methodology of the derivation process along with a comprehensive biochemical and molecular characterization of the cell lines, which reflects key metabolic traits of cavefish adaptation. We anticipate these cell lines to become a useful resource for the Astyanax community as well as researchers investigating fish biology, comparative physiology, and metabolism.

overall_design: 3 replicates each for 2 cell lines - SFL and CFL

first: Jaya

last: Krishnan

first: Yan

last: Wang

first: Olga

last: Kenzior

first: Luke

last: Olsen

first: Dai

last: Tsuchiya

first: Yongfu

first: Chongbei

last: Zhao

first: Nicolas

last: Rohner


title: Expression data from OSM-overexpressing and control MDA-MB-231 triple negative breast cancer cells

city: San Sebastian

first: Andrea

last: Abaurrea

state: Gipuzkoa

address: Paseo Doctor Begiristain, s/n, 20014 San Sebastián

department: Oncology

country: Spain

institute: Biodonostia HRI

summary:
The cytokine Oncostatin M (OSM) promotes cancer progression by acting as central node for multicellular interactions between cancer cells and surrounding stromal cells. OSM is mainly secreted by myeloid cells and the oncostatin M receptor (OSMR) is expressed by cancer cells and cancer associated fibroblasts (CAFs), among others.
To understand the effect of OSM in triple negative breast cancer cells, a small and well-annotated Clariom S gene microarray was performed in OSM-overexpressing (MDA-MB-231-hOSM) and control (MDA-MB-231-hC) MDA-MB-231 cells.

overall_design: MDA-MB-231 breast cancer cells were stably transfected with pUNO1-empty vector (MDA-MB-231-hC) and pUNO1-hOSM vector (MDA-MB-231-hOSM) and selected by adding blasticidin to the culture medium. MDA-MB-231-hC and MDA-MB-231-hOSM cells were cultured in parallel under blasticidin selection and RNA was extracted from three non-consecutive cell passages. RNA quality evaluation and microarray chips processing were performed at the Genomics Facility of the Biodonostia Health Research Institute.

first: Maria

last: Caffarel

first: Angela

last: Araujo

first: Peio

last: Azcoaga


title: Global leaf and root transcriptome reprogramming in response to cadmium reveals tolerance mechanisms in Arundo donax L.

city: Catania

first: Angela Roberta

last: Lo Piero

state: CT

address: Via S. Sofia 98

institute: University of Catania

summary: The expected increase of sustainable energy demand has shifted the attention towards bioenergy crops. Due to their know tolerance against abiotic stress and relatively low supply request, they have been proposed as election crops to be cultivated in marginal lands without disturbing the part of lands employed for agricultural purposes. Arundo donax L. is a promising bioenergy crop whose behaviour under water and salt stress has been recently studied at transcriptomic levels. As the anthropogenic activities produced in the last years a worrying increase of cadmium contamination worldwide, the aim of our work was to decipher the global transcriptomic response of A. donax leaf and root in the perspective of its cultivation in contaminated soil. In our study, RNA-seq libraries yielded a total of 416 million clean reads and 10.4 Gb per sample. De novo assembly of clean reads resulted in 378,521 transcripts and 126,668 unigenes with N50 length of 1812 bp and 1555 bp, respectively. Differential gene expression analysis revealed 5,303 deregulated transcripts (3,206 up- and 2,097 down regulated) specifically observed in the Cd-treated roots compared to Cd-treated leaves. Among them, we identified genes related to “Protein biosynthesis”, “Phytohormone action”, “Nutrient uptake”, “Cell wall organisation”, “Polyamine metabolism”, “Reactive oxygen species metabolism” and “Ion membrane transport”. Globally, our results indicate that ethylene biosynthesis and the downstream signal cascade are strongly induced by cadmium stress. In accordance to ethylene role in the interaction with the ROS generation and scavenging machinery, the transcription of several genes (NADPH oxidase 1, superoxide dismutase, ascorbate peroxidase, different glutathione S-transferases and catalase) devoted to cope the oxidative stress is strongly activated. Several small signal peptides belonging to ROTUNDIFOLIA,  CLAVATA3, and C-TERMINALLY ENCODED PEPTIDE 1 (CEP) are also among the up-regulated genes in Cd-treated roots functioning as messenger molecules from root to shoot in order to communicate the stressful status to the upper part of the plants. Finally, the main finding of our work is that genes involved in cell wall remodelling and lignification are decisively up-regulated in giant reed roots this being a mechanism of cadmium avoidance adopted by giant cane and strongly supporting its cultivation in cadmium contaminated soils in a perspective to save agricultural soil for food and feed crops.

overall_design: Examination of Arundo donax response to cadmium treatment. The experimental was conducted using G10 ecotype of Arundo donax. Three control plants were transplanted in pots with simple soil and they were irrigated with water containing 5.777g/L of ammonium nitrate three times per week. Soil contamination of three trated plants was obtained by adding 4 ppm (4 mg/kg) of cadmium nitrate to the soil and they were irrigated with tap water trhee times per week. Leaves and roots were sampled from both control and treated plants.

first: Danilo

middle: F

last: Santoro

first: Angelo

last: Sicilia

first: Giorgio

last: Testa

first: Salvatore

last: Cosentino

middle: R


title: Influence of protocatechuic acid on gene expression in Blastobotrys raffinosifermentans LS3

first: Anja

last: Hartmann

summary: Gene expression profiling of Blastobotrys raffinosifermentans LS3 cells based on 6.025 annotated chromosomal Blastobotrys raffinosifermentans LS3 sequences and 36 putative mitochondrial gene oligos was performed following exposure to protocatechuic acid. Microarray data were successfully used to identify expression changes of main candidate genes involved in tannic acid degradation, protocatechuic acid degradation, β-oxidation, the glyoxylate cycle, the methyl citrate cycle and the catabolism of the branched-chain amino acids valine, leucine and isoleucine.

overall_design: In the study presented here, gene expression profiling was performed using a microarray produced by Agilent Technologies in 8 x 60 k format. The microarray was based on 6,025 annotated chromosomal sequences and 36 putative mitochondrial gene oligos, resulting in a total of 56,312 Blastobotrys raffinosifermentans LS3 specific oligos. Blastobotrys raffinosifermentans LS3 cells were cultivated overnight in YMM-glucose-NaNO3 and shifted to YMM-NaNO3 containing a mixture of either 0.5 % protocatechuic acid plus 1 % glucose or 1 % glucose only. After 15 min, 30 min, 2 h and 5 h of cultivation at 30 °C and 180 rpm, cells were harvested, total RNA was isolated, samples were labelled, and the microarray was hybridized according to the Agilent Technologies “One-Color Microarray-Based Gene Expression Analysis (v6.5)” instructions. R package limma was used for microarray data analysis. Background of raw expression data was corrected by “normexp” and normalized between arrays using “quantile”.

first: Falko

last: Matthes

first: Sebastian

last: Worch

first: Anna

last: Meier

first: Gotthard

last: Kunze


title: Transcriptional regulation and chromatin architecture maintenance are decoupled functions at the Sox2 locus.

city: Illkirch

first: Tom

last: Sexton

address: 1 rue Laurent Fries

country: France

institute: IGBMC (Institute of Genetics and Molecular and Cellular Biology)

summary: How distal regulatory elements regulate gene transcription and chromatin topology is not clearly defined, yet these processes are intimately linked to cell lineage specification during development. Through allele-specific genome editing and chromatin interaction analysis of the Sox2 locus in mouse embryonic stem cells, we found a striking decoupling of transcriptional control and chromatin architecture. We trace nearly all Sox2 transcriptional activation to a small number of key transcription factor binding sites, whose deletion has no effect on promoter-enhancer interaction frequencies or topological domain organization. Local chromatin architecture maintenance, including at the topologically associating domain (TAD) boundary downstream of the Sox2 enhancer, is conversely widely distributed over multiple transcription factor bound regions and maintained in a CTCF independent manner. Furthermore, disruption of promoter-enhancer interactions via induced ectopic chromatin loop formation has no effect on Sox2 expression. These findings indicate many transcription factors are involved in modulating chromatin architecture independently from CTCF.

sample_organism: Mus musculus musculus x Mus musculus castaneus

overall_design: Allele-specific 4C-seq interrogation of the mouse Sox2 locus in ESCs with different deletions of regulatory regions. Overall: 4 baits; 14 different genotypes; 1-4 replicates

first: Natalia

last: Sikorska


title: The Xia-Gibbs Syndrome protein Gibbin regulates mesodermal DNA methylation to pattern epithelial development (RNA-Seq)

status: Public on Feb 13 2022

city: Stanford

first: Anthony

last: Oro

state: CA

address: 269 Campus Drvie

department: Dermatology

institute: Stanford University

summary: The goal of these RNA-seq experiments was to determine changes in gene expression caused by loss of Gibbin (AHDC1) or GATA3 at various time points following addition of RA/BMP4.

overall_design: All samples were performed in biological duplicate.

first: Annie

last: Collier

first: Sadhana

last: Gaddam


title: Expression data from cancer associated fibroblasts (CAFs) treated with OSM

first: Andrea

last: Abaurrea

summary:
The cytokine Oncostatin M (OSM) promotes cancer progression by acting as central node for multicellular interactions between cancer cells and surrounding stromal cells. OSM is mainly secreted by myeloid cells and the oncostatin M receptor (OSMR) is expressed by cancer cells and cancer associated fibroblasts (CAFs), among others.
To understand the effect of OSM in CAFs, a small and well-annotated Clariom S gene microarray was performed in CAF-173 cells cultured in 3D spheroids and treated with OSM or vehicle (PBS).

overall_design: CAF-173 cells are inmortalised fibroblasts isolated from a human triple negative breast cancer tumour. CAF-173 cells were seeded in 3D spheroids and treated with 30 ng/ml OSM (or PBS) for 4 days before total RNA extraction in three independent experiments. RNA quality evaluation and microarray chips processing were performed at the Genomics Facility of the Biodonostia Health Research Institute.

first: Maria

last: Caffarel

first: Angela

last: Araujo


title: Human iPSC-derived cerebral organoids reveal progenitor pathology in EML1-linked cortical malformation

status: Public on Jan 31 2022

city: Mannheim

first: Philipp

last: Koch

state: Deutschland

institute: Hector Institute for Translational Brain Research

summary: We report the single-cell RNA sequencing of day 33±2 human iPSC derived cerebral organoids harboring a CRIPSR/CAS9 mediated, heterozygous knock-out of the gene EML1 or the respective isogenic control organoids. By microdissection of several ventricular zones per organoid from 3 different batches followed by dissociation into single cells we obtained transcriptomic data of several thousand cells and we were able to identify different cell populations including RG cells (RG1), RG cells transitioning to bRG cells (RG to bRG), RG cells transitioning to neurons (RG2), intermediate progenitors and young neurons based on known marker genes (Nowakowski et al., 2017; Fan et al., 2020; Velasco et al., 2019; Pollen et al., 2015; Liu et al., 2017). When comparing the cell type composition between EML1-heKO and isogenic control-derived organoids we found a clear decrease of RG1 cells and a striking increase in the abundance of RG to bRG cells in the EML1-heKO condition, while only minor variations in the other cell clusters were observed. We further investigated molecular characteristics of the EML1-heKO derived RG to bRG cluster compared to control. Here we found a set of differentially expressed genes in the EML1-heKO compared to control. When further investigating these genes, we identified a clear upregulation of ECM and bRG markers  Our data suggest that the RG to bRG cell cluster in the EML1-heKO is composed of a rather perturbed progenitor population not found as such in control organoids and most likely not reflecting a cell population present during normal human brain development.

overall_design: Acquisition and examination of single cell RNA sequencing data of day 33±2 human iPSC derived cerebral organoids harboring a CRIPSR/CAS9 mediated, heterozygous knock-out of the gene EML1 or the respective isogenic control organoids.

first: Julia

last: Ladewig

first: Ammar

last: Jabali

first: Anne

last: Hoffrichter


title: Light-activated molecular machines are new mode-of-action, fast-acting broad-spectrum antibacterials that target the membrane

status: Public on Jan 27 2022

city: Houston

first: Ana

last: Santos

state: Texas

address: 6500 Main St, APT 892

institute: BioScience Research Collaborative

summary: Light-activated molecular machines (MNM) are synthetic molecular structures that, following light activation, undergo successive unidirectional rotation that results in a drilling-like rapid motion that can thrust the motor through biological membranes.Visible light (405 nm) activated MM were investigated for their antibacterial potential and their mechanism of action was investigated by RNAseq.

overall_design: E. coli BW25113 was treated with 1% DMSO (CT) or 0.5x MIC of MNM and then irradiated with 405 nm light. RNA was isolated using the RNeasy Mini Kit (Qiagen, Valencia, CA). RNA-Seq libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Plus rRNA Depletion Kit and sequenced on the Illumina NovaSeq6000 platform (Illumina, San Diego, CA). An average of 70 million reads was obtained for each sample.

first: Dongdong

last: Liu

middle: K

last: Reed

first: Aaron

last: Wyderka

first: Alexis

last: van Venrooy

first: John

middle: T

last: Li

first: Victor

middle: D

first: Mikita

last: Misiura

first: Olga

last: Samoylova

first: Jacob

last: Beckham

first: Ciceron

last: Ayala-Orozco

first: Anatoly

middle: B

last: Kolomeisky

first: Lawrence

last: Alemany

first: Antonio

last: Oliver

first: George

middle: P

last: Tegos

first: James

last: Tour


title: Expression data from CRS with nasal polyps (CRSwNP) and normal control

city: Tampa

first: Seong

middle: H

last: Cho

state: FL

address: 3802 Spectrum Blvd Suite 303

department: Internal Medicine

institute: University of South Florida

summary:
Chronic rhinosinusitis (CRS) is a prevalent chronic rhinologic disease, characterized by persistent symptomatic inflammation of the nasal mucosa and paranasal sinuses. Sinonasal tissues were obtained during sinus surgeries performed at Northwestern University. For the microarray, NP tissues and uncinate tissues from normal healthy controls were divided into elderly (≥65 years old, each n=3-4), or non-elderly (18-49 years old, each n=3-4) according to age. This study protocol was approved by the independent ethics committees or institutional review boards (IRB) at Northwestern University. Total RNA was isolated from NP tissues and control uncinate tissues. RNA concentration was calculated, and the highest quality RNA used for microarray. The quality of total RNA was evaluated by Bioanalyzer (Agilent Technologies, Santa Clara, CA). The samples were at a concentration ≥125ng/μl and a A260/A280 ratio that was ≥1.80 and a RIN value that was ≥7.0 were considered acceptable. The highest quality RNA was used to generate labeled cRNA and hybridized to Affymetrix Human Gene 2.1ST array following the manufacturer’s protocol (Affymetrix Inc., Santa Clara, CA). Chip processing and image capturing were performed using Affymetrix AGCC software.
We investigated age- and disease-related differential gene expression in chronic rhinosinusitis with nasal polyps.

overall_design: Microarrays using NP and uncinate tissues from health controls (elderly, age ≥65 vs. non-elderly, age 18-49) were performed, and gene expression profiles were evaluated using Affymetrix Human Gene 2.1ST array.

first: Ara

last: Jo


title: Dietary emulsifier consumption alters gene expression in the amygdala and paraventricular nucleus of the hypothalamus in mice

city: Atlanta

first: Kim

last: Huhman

state: Georgia

department: Neuroscience Institute

institute: Georgia State University

summary:
Purpose: The goal of the current study was to test whether emulsifier consumption is associated with changes in gene expression in the amygdala and PVN
Methods: Adult male C57BL/6J mice received drinking water containing either 1% sodium carboxymethylcellulose (CMC), 1% polysorbate-80 (P80) or water without emulsifier for 12 weeks. PVN and amygdala gene expression was generated by RNA-Seq using an Illumina NextSeq 500. FastQ quality filter was used to filter low quality sequences and Tophat, Bowtie, Cufflinks, and Cuffdiff were used for RNA-Seq analysis.  qRT–PCR validation was performed using 6 differential genes of interest.
Results: A total of 243 genes were differentially expressed in the amygdala and PVN of emulsifier-treated mice compared to controls. There was minimal overlap of differentially expressed genes in CMC- and P80-treated animals, suggesting that each emulsifier acts via distinct molecular mechanisms to produce an anxiety-like phenotype. Furthermore, gene ontology and pathway analysis revealed that various stress, metabolic, and immune terms and pathways were altered in emulsifier conditions. RNA-seq data was validated with qRT–PCR data (R2= 0.8815).
Conclusions: These findings are the first to demonstrate that emulsifier consumption changes gene expression in brain regions that are critical for stress responding, providing possible molecular mechanisms that may underly the observed anxiety-like phenotype

overall_design: Amygdala and PVN gene expression in adult male mice that consumed emulsifiers for 12 weeks

first: Amanda

last: Arnold

first: Benoit

last: Chassaing


title: mRNA expression profile in the Laiwu black goat kid liver

status: Public on Jan 28 2022

city: Tai’an

first: Chao

last: Tianle

state: Shandong

address: Daizong street, no. 61, 6/5000 Shandong Agricultural University

country: China

institute: 6/5000 Shandong Agricultural University

summary: Laiwu black goat kid liver mRNA expression profile were sequenced with novaSeq 6000. The liver tissues were procured at 5-time points from the Laiwu black goats of 1 day, 2 weeks, 4 weeks, 8 weeks, and 12 weeks of age, respectively with 5 goats per time point, for a total of 25 goats.

overall_design: The goat kid liver mRNA  profiles  of 1 day, 2 weeks, 4 weeks, 8 weeks, and 12 weeks of age

first: Xiaodong

last: Zhao

first: Tianle

last: Chao

first: Jianmin

last: Wang


title: MAT2A and methionine dependency are indispensible for H3K27M mutant gliomas.

city: Memphis

first: Stephen

middle: C

last: Mack

state: Tennessee

address: 262 Danny Thomas Place

institute: St. Jude Children’s Research Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Gliomas bearing driver mutations of histone 3 lysine 27 (H3K27M) are incurable brain tumors. H3K27M mutant tumors display unique epigenomes with global loss of the chromatin repressive H3K27 trimethylation mark. Here, we generated a syngeneic H3K27M mouse model to study the dependence upon amino acid (AA) metabolism by performing an AA drop out screen. H3K27M mutant cells, but not histone wildtype cells, were highly dependent on the amino acid, methionine. Interrogating the methionine cycle dependency through an siRNA screen identified the enzyme Methionine Adenosyltransferase 2A (MAT2A), which catalyzes production of S-adenosylmethionine (SAM), a methyl donor. Sensitivity to MAT2A loss in H3K27M mutant cells was not mediated through the canonical mechanism of MTAP deletion; instead, H3K27M mutant cells have lower MAT2A protein levels, which is mediated by Adenosylmethionine Decarboxylase 1 (AMD1) production of decarboxylated SAM (dcSAM). MAT2A loss induces global depletion of H3K36me3, a potent chromatin mark of transcriptional elongation, as evaluated by quantitative chromatin immunoprecipitation with reference exogenous genome sequencing (ChIP-Rx-Seq) in multiple DIPG lines. Tandem H3K36me3 ChIP-Rx-seq and RNA-seq identified several oncogenic and developmental transcriptional programs associated with MAT2A loss. Moreover, inducible knockdown of MAT2A or methionine-restricted diets (MR) extended survival in both syngeneic and patient-derived xenograft models (PDXs) in vivo. Collectively, our results provide novel connections between AA metabolism and the epigenome in H3K27M gliomas, suggesting that MAT2A, a central regulator of methionine metabolism, presents exploitable therapeutic vulnerabilities in H3K27M gliomas.

overall_design: ChIP-Rx

first: Sameer

last: Agnihotri


title: Effect of Oncostatin M (OSM) in breast cancer cells and cancer associated fibroblasts

first: Andrea

last: Abaurrea

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

overall_design: Refer to individual Series


title: Heat shock-mediated global gene downregulation is achieved by premature transcription termination [4SU_mRNA-seq]

status: Public on Jan 24 2022

city: London

first: Richard

middle: James

last: Mitter

state: LONDON

address: 1 Midland Road

department: Bioinformatics & Biostatistics

institute: The Francis Crick Institute

summary: The Heat Shock response (HSR) is a highly conserved transcriptional program induced by the exposure to a variety of environmental stressors. Following an insult, a small subset of genes, known as the Heat Shock genes, are rapidly induced by the Heat Shock Factors (HSFs) to maintain protein homeostasis and ensure cell survival. In parallel, a large portion of the genome becomes repressed. HS associated global gene repression is still largely poorly understood. In this study, we demonstrate that transcription downregulation during Heat shock is mainly achieved by premature transcription termination through the regulation of U1snRNA and the disruption of U1-telescripting.

overall_design: Newly-made mRNAs synthesized during HS were selected by labelling the RNA with 4SU and selecting the polyA(+) fraction of the labelled RNA.

first: Simona

last: Cugusi

first: Gavin

last: Kelly

first: Jesper

middle: Q

last: Svejstrup


title: Heat shock-mediated global gene downregulation is achieved by premature transcription termination [FP_TTchem-seq]

overall_design: Determining the transcription elongation rate during HS using FP-TTchem-seq. New transcription elongation is prevented by addition of Flavopiridol. The receding wave of already transcribing RNA polymerase is measured at different time points by labelling nascent RNA with 4SU and used to estimate elongation speed.


title: Heat Shock induces premature transcript termination and reconfigures the human transcriptome

summary: The Heat Shock response (HSR) is a highly conserved transcriptional program induced by the exposure to a variety of environmental stressors. Following an insult, a small subset of genes, known as the Heat Shock genes, are rapidly induced by the Heat Shock Factors (HSFs) to maintain protein homeostasis and ensure cell survival. In parallel, a large portion of the genome becomes repressed. HS associated global gene repression is still largely poorly understood. In this study, we demonstrate that transcription downregulation during Heat shock is mainly achieved by premature transcription termination through the disruption of telescripting.

overall_design: Generating a snapshot of transcriptional activity at different times of HS exposure by pulse-labelling nascent RNA with 4SU.


title: Heat shock-mediated global gene downregulation is achieved by premature transcription termination [DRB_TTchem-seq]

overall_design: Determining the transcription elongation rate during HS using DRB-TTchem-seq. Transcription is synchronized at the pausing site with DRB. After release, the transcription wave front is measured at different time points by labelling nascent RNA with 4SU and used to estimate elongation speed.


title: Transcriptomic analysis of Bacteroides thetaiotaomicron inositol lipid knockout strains

status: Public on Jan 21 2022

city: Tuebingen

first: Stacey

last: Heaver

address: Max-Planck-Ring 5

department: Microbiome Science

institute: Max Planck Institute for Biology Tuebingen

summary: We report next generation sequencing RNA-seq data of human gut commensal Bacteroides thetaiotaomicron strains deficient in inositol lipid synthesis, including dBT_1522 (phosphoinositol dihydroceramide synthase knockout) and its wild-type background strain, and iSPTdBT_1526 (myo-inositol-phosphate synthase) knockout with its background strain ("iSPT," inducible serine palmitoyltransferase).

overall_design: Whole cell RNA-seq profiles of Bacteroides thetaiotaomicron grown 15 hours in minimal medium at 37 deg C.

first: Ruth

middle: E

last: Ley


title: Heat shock-mediated global gene downregulation is achieved by premature transcription termination


title: MicroRNA expression profile of Chicken cecum in different stages during Histomonas meleagridis infection

city: Yangzhou

first: 金俊

middle: 许金俊

last: 许

address: Floor 29, campus of Wenhui Road

institute: College of Veterinary Medicine, Yangzhou University

type: Non-coding RNA profiling by high throughput sequencing

summary:
Background: Histomonas meleagridis is an anaerobic, intercellular parasite that infects the Galliformes such as turkeys and chickens. In recent years, the reemergence of Histomoniasis has caused serious economic losses as drugs to treat the disease have been banned. At present, studies on H. meleagridis mainly focus on virulence, gene expression analysis, and the innate immunity of the host. However, there are no studies on differential expression of miRNAs (DEMs) in host immune and inflammatory response induced by H. meleagridis infection in chickens. In this study, the expression profile of cecum miRNA at 10 and 15 days post-infection (DPI) with Chinese JSYZ-F strain H. meleagridis was studied by high-throughput sequencing.
Results: Compared with the control group, 94 and 127 DEMs were found in the cecum of infected chickens at 10 DPI (CE vs CC) and 15 DPI (CEH vs CCH), respectively, of which 60 DEMs were shared at two-time points. Gene Ontology (GO) enrichment analysis of the target genes of DEMs showed that 881 and 1027 GO terms were significantly enriched at 10 and 15 DPI. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of the target genes of DEMs showed that only 5 and 3 pathways were significantly enriched at 10 and 15 DPI, respectively. The integrated analysis of miRNA–gene network revealed that the DEMs played important roles in the host immune and inflammatory responses to H. meleagridis infection by dynamically regulating the expression of immune and inflammation-related cytokines.
Conclusion: Our results not only suggested that host miRNA expression was dynamically altered by H. meleagridis and host, but also revealed that more miRNAs and genes were involved in the later stage of the disease. In addition, host and H. meleagridis regulated the expression of immune and inflammation-related cytokines to respond to H. meleagridis infection. Our results will contribute to future research on miRNA-target interaction during H. meleagridis infection in chickens and provide new ideas for H. meleagridis control.

overall_design: cecum miRNA profiles of 10 and 15 days old infect/control chicken

first: Yu-Ming

last: Zhang

first: Jin-jun

last: Xu


title: Comparison of gene expression between parental adrenocortical carcinoma cells and a subpopulation overexpressing Ptch1

status: Public on Jan 19 2022

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: Chemotherapy resistance supposes a  challenge  for  cancer  treatment.  Multidrug efflux pumps are able to  extrude  chemotherapeutic  agents increasing  their  resistance  to  the  treatment.  Ptch1 is overexpressed in many  metastatic  cancers,  where it  acts  as  a  multidrug  efflux  pump. Indeed, Ptch1 strongly contributes to the drug efflux in H295R, a human adrenal carcinoma cell line.  This efflux is  coupled  to the proton  motive force, restricting Ptch1 drug efflux to acidify environments like cancers. Even though Ptch1 is overexpressed in H295R cells, only 1% of these cells present Ptch1 at the cell surface (Ptch1 positive  or PTC subpopulation ).  We showed that these Ptch1 positive cells had  an  increased chemotherapy resistance, migration and clonogenicity compared to the parental cell lines. The RNA seq analysis performed on H295R Ptch1 positive cells and parental H295R cells show an increase of the expression of genes involved in the Hedgehog signaling such as Ptch1, of genes involved in EMT and drug resistance, and of genes involved in stem cell maintenance suggesting that these cells could be cancer stem cells.

overall_design: Comparison between parental H295R cells (WT) and a subpopulation overexpressing Ptch1 (PTC) (3 replicates)

first: Isabelle

last: Mus-Veteau


title: The Induced Expression of BPV E4  Gene in Equine Adult Dermal Fibroblast Cells As A Potential Model of Skin Neoplasia

city: Krakow

first: Tomasz

last: Szmatoła

state: Małopolskie

address: Mickiewicza 21

department: OMEI

country: Poland

institute: University of Agriculture in Krakow

summary:
Purpose: RNA-sequencing (RNA-seq) was used to identify the changes in gene expression profile in horse skin fibroblast cell line expressing one of the BPV genes encoding transforming proteins (BPV-E4 and BPV-E4^E1). The whole transcriptome sequencing allows us to establish the influence of BPV gene transfection on host cells and indicates which virus genes can be responsible for the neoplastic process. It is the first study concerning a cell model of horse skin transfected with BPV genes. Such a model could contribute to a more accurate understanding of changes inside cells during viral infection.
Methods: The equine fibroblast cell lines were transfected using the nucleofection method with BPV-E4 and BPV-E4^E1 constructs. RNA was isolated from cell lines directly from culture dishes with PureLink™ RNA mini kit. The quality and quantity of obtained libraries (the TruSeq RNA Kit v2 kit (Illumina, San Diego, CA, USA) ) were assessed using Qubit 2.0 (Qubit™ dsDNA BR AssayKit, Invitrogen, Waltham, MA, USA ) and TapeStation 2200 (D100 screencaps, Agilent). Next, the cDNA libraries were sequenced on NextSeq 500 Illumina platform (Illumina, San Diego, CA, USA) and NextSeq 500/550 High Output KIT v 2.5 (75 cycles) according to protocol. The qPCR validation was used to confirm RNA-seq data. Then, the quality of raw reads was checked with FastQC software followed by removal of adapters and reads of low quality (under phred quality of 20) and reads under length of 36 (Flexbar software). Next, the filtered reads were mapped to EquCab3 genome with STAR software and reads were counted to specific gene thresholds provided in Ensembl gtf file version 100 by htseq-count software. Differential expresion extimation was followed with the use of Deseq2 software.
Results: The transcriptome profiling allowed us to perform a comparison of the whole expression profile between the control and both BPV-E4 and BPV-E4^E1 groups. According to the comparison of control and BPV-E4 groups, the 1640 DEGs were identified, of which 624 were up-regulated and 1016 down-regulated in the BPV-E4 group. The highest number of DEGs – 3328 were detected from the control and BPV-E4^E1 comparison. Among them, 1626 genes were up-regulated and 1602 down-regulated in the BPV-E4^E1 group compared to control samples. The most overrepresented Gene  Ontology  Term between control and BPV-E4 groups were negative regulation of cell proliferation – 34 DEGs (FDR<0.002); positive regulation of cell migration – 24 DEGs (FDR<0.0001); cell adhesion and cell migration; 21 DEGs in both GO terms (FDR<0.003 and 0.0005; respectively). The enrichment analysis performed for differentially expressed genes between control and BPV-E4^E1 samples showed the focal adhesion GO terms were overrepresented by 99 DEGs of which 65 were up-regulated and 34 down-regulated (FDR<0.0001). For cells transfected BPV-E4 and BPV-E4^E1 constructs, the most significant were pathways: of the cell cycle, cytoskeleton, and ECM-matrix remodelling; regulation of actin cytoskeleton;  focal adhesion and ECM-receptor interaction. The Pathways in cancer were identified uniquely for cells transfected by BPV-E4 construct, while only for BPV-E4^E1 cells the FoxO, Rap1, and TNF-signaling path-ways and Proteoglycans in cancer.
Conclusions: The results obtained showed that both transfection types significantly affected cells transcriptome towards cancer transformation. Nevertheless, cells transfected with BPV-E4^E1 genes seem to be closer to the molecular modification that occurred in vivo in equine sarcoids. The present study showed how equine fibroblast cells could be modified, at the molecular level, in the presence of BPV E4 gene. These findings broaden the knowledge  about the possible interaction of BPV viruses on host cells.

overall_design: The whole transcriptome sequencing of equine fibroblast cel line transfected with BPV-E4 and BPV-E4^E1 gene was performed for 10 samples using NextSeq 550 High Output KIT v2.5 (Illumina) into 75 single-end cycles.

first: Przemysław

last: Podstawski

first: Marcin

last: Samiec

first: Maria

last: Skrzyszowska

first: Ewelina

last: Semik-Gurgul

first: Katarzyna

last: Ropka-Molik


title: Characterization of sequence determinants of enhancer function using natural genetic variation [ChIP-seq]

status: Public on Jan 17 2022

city: Los Angeles

first: Marty

middle: G

last: Yang

address: 615 Charles E Young Dr S

department: Biological Chemistry

institute: University of California, Los Angeles

summary: Sequence variation in enhancers, a class of cis-regulatory elements that control cell type-specific gene transcription, contributes significantly to phenotypic variation within human populations. Enhancers are short DNA sequences (∼200 bp) composed of multiple binding sites (4-10 bp) for transcription factors (TFs). The transcriptional regulatory activity of an enhancer is encoded by the type, number, and distribution of TF binding sites that it contains. However, the sequence determinants of TF binding to enhancers and the relationship between TF binding and enhancer activity are complex, and thus it remains difficult to predict the effect of any given sequence variant on enhancer function. Here, we generate allele-specific maps of TF binding and enhancer activity in fibroblasts from a panel of F1-hybrid mice that have a high frequency of sequence variants. We identified thousands of enhancers that exhibit differences in TF binding and/or activity between alleles and use these data to define features of sequence variants that are most likely to impact enhancer function. Our data demonstrate a critical role for AP-1 TFs at many fibroblast enhancers, reveal a hierarchical relationship between AP-1 and TEAD TF binding at enhancers, and delineate the nature of sequence variants that contribute to AP-1 TF binding. These data represent one of the most comprehensive assessments to date of the impact of sequence variation on enhancer function in chromatin, with implications for identifying functional cis-regulatory variation in human populations.

overall_design: Genome-wide maps of H3K27ac, H3K4me1/2, H3K4me3, AP-1, CTCF, TEAD, chromatin accessibility, chromatin-associated RNA-seq in starved and serum-stimulated primary mouse embryonic fibroblasts from F1-hybrid mice.

first: Emi

last: Ling

first: Michael

last: Greenberg

first: Thomas

last: Vierbuchen


title: Heat shock-mediated global gene downregulation is achieved by premature transcription termination [TTchem-seq]

first: Richard

last: Mitter

first: Simona

last: Cugusi

first: Gavin

last: Kelly

first: Jesper

last: Svejstrup


title: Characterization of sequence determinants of enhancer function using natural genetic variation


title: RNA-seq in wildtype and TFAP2A knockout non-neural ectoderm

first: Anthony

last: Oro

summary: The objective of this study is to determine the effects TFAP2A loss in non-neural ectoderm

first: Jillian

last: Pattison

first: Sadhana

last: Gaddam


title: Next Generation Sequencing Analysis of Mice Glioma Exomes

status: Public on Jan 11 2022

city: Zhejiang

first: Chong

last: Liu

address: NO.866 of Yuhang Tong Road

institute: Medical College of Zhejiang University

type: Genome variation profiling by high throughput sequencing

summary: Six samples from two Glioma_CKO mice (one normal brain tissue, two tumor tissues per mouse) were performed Whole Exome Sequencing

overall_design: Six tissues were generated by deep sequencing, using Illumina.

first: Pengxiang

last: Chen


title: Hepatic Interferon Regulatory Factor 3 Fuels Gluconeogenesis via PP2A-mediated Inactivation of AMP Kinase

city: Boston

first: NORC

last: Boston

state: MA

address: 3 Blackfan Circle, CLS0733

institute: Beth Israel Deaconess Medical Center

summary: We report the IRF3 transcriptome and cistrome in primary mouse hepatocytes.

overall_design: RNA-seq and IRF3 CUT&RUN was performed in primary mouse hepatocytes expressing constitutively active IRF3 (IRF3-2D) and control mCherry.

first: Suraj

middle: J

last: Patel

first: Evan

last: Rosen


title: Next Generation Sequencing Analysis of Mice Glioma Cells co-cultured with OB Neurons

summary: Glioma cells which were co-cultured with OB neurons and stimulated by 20ng/ml IGF-1 compared to those without IGF-1 stimulation.

overall_design:
mRNA profiles of glioma cells co-cultured with OB neurons after IGF-1 stimulation
Glioma cells were collected from the tumor mouse model with mixed background including CD-1 and C57BL/6. OB Neurons were collected from C57BL/6 mice.

first: Rui

last: Jing


title: The profile of microRNA expression and potential role in the regulation of drug-resistant genes in cisplatin and paclitaxel resistant ovarian cancer cell lines

status: Public on Jan 03 2022

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embriology

institute: Poznan University of Medical Science

summary: Ovarian cancer is the most lethal gynecological malignancy. The high mortality results from late diag-nosis and the development of drug resistance. Drug resistance results from changes in the expression of different drug-resistance genes that may be regulated miRNA. The main aim of our study was to detect changes in miRNA expression levels in two cisplatin (CIS) and two paclitaxel (PAC) - resistant vari-ants of the A2780 drug-sensitive ovarian cancer cell line — by miRNA microarray

overall_design: The human ovarian carcinoma A2780 cell line was purchased from ATCC. A2780 sublines that were resistant to CIS [A2780CR1, A2780CR2 (A2780 cisplatin resistant)], and PAC [A2780PR1 and A2780PR2 (A2780 paclitaxel resistant)] were obtained by exposing A2780 cells to the relevant drugs at gradually increasing concentrations. The final con-centrations used to select the resistant cells were 1000 ng/ml of CIS for both A2780CR1 and A2780CR2 cell lines, 300 ng/ml of PAC for A2780PR1 cell line and 1100 ng/ml of PAC for A2780PR2 cell line

first: Dominika

last: Kaźmierczak

last: Ruciński

first: Radosław

last: Januchowski


title: The Granulosa Cell Response to Luteinizing Hormone is Partly Mediated by YAP1-Dependent Induction of Amphiregulin

status: Public on Jan 01 2022

city: Saint-Hyacinthe

first: Philippe

last: Godin

state: Québec

address: 3200 Sicotte

institute: Université de Montréal

summary:
The LH surge is a pivotal event that triggers multiple key ovarian processes including oocyte maturation, cumulus expansion, follicular wall rupture and luteinization of mural granulosa and theca cells. Recently, LH-dependent activation of the Hippo signaling pathway has been shown to be required for the differentiation of granulosa cells into luteal cells. This study aimed to better characterize the role of the Hippo pathway in the LH response in murine granulosa cells.
In order to highlight specific roles of Hippo in murine GC physiology, we conducted a microarray analysis to identify genes differentially expressed in cultured granulosa cells with knocked-down expression of YAP1/TAZ (the two co-regulators of Hippo signaling).

overall_design:
We used a microarray to identify up- and down-regulated genes after 18h of YAP1 and Taz knockdown in culture GCs isolated from eCG-primed mice
Granulosa cells from Yap1^flox/flox;Taz^floz/flox mice superstimulated with 5IU of equine chorionic gonadotropin (eCG) for 44h were isolated and placed in culture. They were then treated with an adenovirus expressing either eGFP (Ad-eGFP, control) or expressing the Cyclic recombinase (Ad-cre, to knockdown YAP1/TAZ expression). Granulosa cells were harvested after 18h for microarray analyses. N=3 for each condition, 6 samples in total

first: Derek

last: Boerboom


title: Mechanical Strain Induces Transcriptomic Reprogramming of Saphenous Vein Progenitors

status: Public on Jan 10 2022

city: Milano

first: Gaia

last: Spinetti

address: Via Fantoli 16/15

institute: IRCCS MultiMedica

summary:
Purpose: Intimal hyperplasia is the leading cause of graft failure in aortocoronary bypass grafts performed using human saphenous vein (SV). The long-term consequences of the altered pulsatile stress on the cells that populate the vein wall remain elusive, in particular onto saphenous vein progenitors (SVPs), adult cell phenotype of the human adventitia that upholds differentiation capacity. In the present study, we performed global transcriptomic profiling of SVPs that underwent in vitro uniaxial cyclic strain, a type of mechanical stimulation that we recently found to be involved in the pathology of the SV.
Methods: To investigate the effect of mechanical strain on cultured cells, SVPs were subjected to cyclic strain using the FlexCell Tension Plus FX-5000T system. Cells were subjected to uniaxial cyclic deformation protocol (0-10% deformation, 1 Hz frequency), for 24 and 72 hours, while static controls were provided by seeding an equal amount of cells, under the same atmospheric conditions, but without mechanical stimulation. For RNA-Seq analysis, total RNA was extracted from 5 different donors of SVPs using TRIzol, treated with DNase I, and quantified by using NanoDrop-1000 spectrophotometer before integrity assessment with Agilent 2100 Bioanalyzer (RNA Integrity Number values >8).
Results: Results showed a consistent stretch-dependent gene regulation in cyclically strained SVPs vs. controls, especially at 72hrs. We also observed a robust mechanically related overexpression of Adhesion Molecule with Ig Like Domain 2 (AMIGO2), a cell surface type I transmembrane protein involved in cell adhesion. The overexpression of AMIGO2 in stretched SVPs was associated with the activation of the transforming growth factor β pathway and modulation of cell signalling, cell-cell, and cell-matrix interactions.
Conclusions: These results show that mechanical stress promotes SVPs' molecular phenotypic switching and increases their responsiveness to extracellular environment alterations, thus prompting the targeting of new molecular effectors to improve the outcome of bypass graft procedure.

overall_design: mRNA profiles of human saphenous vein progenitors that underwent in vitro uniaxial cyclic strain for 24 and 72 hours

first: Davide

last: Maselli

first: Gloria

last: Garoffolo

first: Giada

middle: A

last: Cassanmagnago

first: Rosa

last: Vono

first: Paolo

last: Madeddu

first: Maurizio

last: Pesce


title: Differential Expression of Super-enhancer-associated Long Non-coding RNAs in Uterine Leiomyomas

city: torrance

first: Omid

last: Khorram

address: 1124  w carson st

institute: The lundquist Institute at UCLA medical center

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

summary: Arraystar SE-lncRNAs Arrays was used to systematically profile the differentially expressed SE-lncRNAs along with corresponding SE-regulated protein coding genes from eight leiomyomas and paired myometrium. The analysis indicated 7680 SE-lncRNAs were expressed, of which 721 SE-lncRNAs were increased, while 247 SE-lncRNAs were decreased by 1.5-fold or greater in leiomyoma. Thirteen novel SE-lncRNAs and their corresponding protein coding genes were selected, and their expression was confirmed in eighty-one paired leiomyoma tissues by quantitative real-time PCR. The thirteen pairs of SE-lncRNAs and their corresponding protein coding genes included RP11-353N14.2/CBX4, SOCS2-AS1/SOCS2, RP1-170O19.14/HOXA11, CASC15/PRL, EGFLAM-AS1/EGFLAM, RP11-225H22/NEURL1, RP5-1086K13.1/CD58, AC092839.3/SPTBN1, RP11-69I8.3/CTGF, TM4SF1-AS1/TM4SF1, RP11-373D23/FOSL2, RP11-399K21.11/COMTD1 and CTB-113P19.1/SPARC. Collectively, our results indicate that the differential expression of SE in fibroids is another mechanism contributing to dysregulation of protein coding genes in fibroids.

overall_design: Identify the expression profile of SE-lncRNAs along with corresponding SE-regulated protein coding genes in leiomyomas and paired myometrium using Arraystar SE-lncRNAs Arrays

first: Tsai-Der

last: Chuang


title: Dual role of histone variant H3.3B in spermatogenesis: positive regulation of piRNA transcription and implication in X-chromosome inactivation

city: ILLKIRCH-GRAFFENSTADEN

first: Christophe

last: Papin

address: 1 rue Laurent Fries

institute: IGBMC - CNRS UMR 7104 - Inserm U 964

summary: The histone variant H3.3 is encoded by two distinct genes, H3f3a and H3f3b, exhibiting identical amino-acid sequence. H3.3 is required for spermatogenesis, but the molecular mechanism of its spermatogenic function remains obscure. Here, we have studied the role of each one of H3.3A and H3.3B proteins in spermatogenesis. We have generated transgenic conditional knock-out/knock-in (cKO/KI) epitope-tagged FLAG-FLAG-HA-H3.3B and FLAG-FLAG-HA-H3.3A mouse lines. We show that H3.3B, but not H3.3A, is required for spermatogenesis and male fertility. Analysis of the molecular mechanism unveils that the absence of H3.3B led to alterations in the meiotic/post-meiotic transition. Genome-wide RNA-seq reveals that the depletion of H3.3B in meiotic cells is associated with increased expression of the whole sex X and Y chromosomes as well as of both RLTR10B and RLTR10B2 retrotransposons. In contrast, the absence of H3.3B resulted in down-regulation of the expression of piRNA clusters. ChIP-seq experiments uncover that RLTR10B and RLTR10B2 retrotransposons, the whole sex chromosomes and the piRNA clusters are markedly enriched of H3.3. Taken together, our data dissect the molecular mechanism of H3.3B functions during spermatogenesis and demonstrate that H3.3B, depending on its chromatin localization, is involved in either up-regulation or down-regulation of expression of defined large chromatin regions.

overall_design: In this work we have carried out an in depth study on the role of the histone variant H3.3 in spermatogenesis. The use of transgenic H3.3A and H3.3B conditional knock-out/knock-in (cKO/KI) mouse lines combined with a large number of genome-wide approaches has allowed to demonstrate that H3.3B, but not H3.3A, is a key factor in the spermatogenetic process.

first: Emeline

last: Fontaine

first: Guillaume

last: Martinez

first: Stephanie

last: Le Gras

first: Roland

last: Abi Nahed

first: Patrick

last: Héry

first: Thierry

last: Buchou

first: Khalid

last: Ouararhni

first: Bertrand

last: Favier

last: Gautier

first: Jamal S M

last: Sabir

first: Matthieu

last: Gerard

first: Jan

last: Bednar

last: Arnoult

first: Stefan

last: Dimitrov

first: Ali

last: Hamiche


title: Histone deacetylase 4 reverses cellular senescence via DDIT4 in dermal fibroblasts

status: Public on Dec 31 2021

city: Daegu

first: Ji Hwan

last: Park

state: Gyeongbuk

address: 333, Techno jungang-daero, Hyeonpung-eup, Dalseong-gun

department: Newbiology

country: South Korea

institute: DGIST

summary: Histone deacetylases (HDACs) are known to be a class of enzymes that remove acetyl groups from lysine chains on histones or other proteins, and play a crucial role in epigenetic regulation and aging process. Previous studies have identified that HDAC4 is down-regulated in aged and UV-irradiated skin in vivo. Therefore, HDAC4 may be an important role in skin aging process. However, the role of HDAC4 in skin aging is rarely known. In this study, we conducted the integrative transcriptome analysis of overexpression and knockdown of HDAC4, and UV- or H2O2-induced senescence in human dermal fibroblast and identified candidate genes which are regulated by HDAC4. Among these genes, DNA damage-inducible transcript 4 (DDIT4) was significantly regulated by HDAC4. We demonstrated that DDIT4 expression was downregulated during senescence and HDAC4 overexpression prevented senescence-induced decrease of DDIT4. In addition, overexpression of DDIT4 reduced SASP and aged-related genes that could promote aging, suggesting that DDIT4 may prevent senescence. Collectively, our results have shown that HDAC4 may play an important role in preventing skin aging by inducing DDIT4 expression.

overall_design: Examination of HDAC4 role in UV- or H2O2-induced senescence

first: Yuri

last: Lee

first: Daehee

last: Hwang

first: Dong

first: Jin

last: Chung


title: Interstitial mesenchymal cells in skeletal muscle

city: Seoul

first: Ji Hoon

last: Kim

address: Kwanakro 1

institute: Seoul national University, Seoul, Korea

summary: Skeletal muscle tissues are comprised of muscle fibers, muscle stem cells (MuSCs), immune cells, endothelial cells, motor/sensory nerves with Schwann cells, and interstitial mesenchymal cells. Each cell population plays a unique role in muscle physiology and homeostasis. The mesenchymal progenitors in the skeletal muscle have been identified as a subpopulation that reside between muscle fibers, whose role is to coordinate muscle regeneration in a finely tuned manner by supporting the expansion and differentiation of MuSCs. These cells have been referred to as fibro/adipogenic progenitor cells (FAPs), termed according to their differentiation potentials in specific in vitro culture conditions and known to cause fibrous tissue and fatty degeneration under pathological environments and result in compromised muscle function. To gain insight into how Bap1 plays a role in skeletal muscle homeostasis, we performed RNA sequencing analysis using freshly isolated Sca1 positive cells from 1.5-week-old WT or cKO hindlimb muscles

overall_design: Gene expression profiling of mesenchymal cells from WT and Prx1-Cre;Bap1f/f conditional knock out MuSCs.

first: Ji-Hoon

first: Young-Yun

last: Kong


title: Genetic screens discover proteases as synthetic lethal partners of PI3K inhibition in breast cancer cells

city: Freiburg

first: Maria

middle: Elena

last: Hess

address: Breisacherstr. 153

department: Institute for Medical Bioinformatics and Systemsmedicine

institute: Universitaetsklinikum Freiburg

summary: The RNA-Seq analysed the changes in protease gene expression upon short-term PI3K inhibition in three breast cancer cell lines.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: MCF7, MDA-MB-231 and PyB6-313 breast cancer cells were seeded, 16 h later RNA was isolated (T0; Medium control). Remaining plates were treated with the PI3K inhibitor BKM (NVP-BKM-120 [Buparlisib], CT-BKM120; Chemitek) at EC50 (200 nM [MCF7], 1300 nM [MDA-MB-231], 1500 nM [PyB6-313]), or the same dilution of DMSO (solvent control). After 3 h of treatment, RNA was isolated. Conditions were prepared in triplicates.

first: Lena

last: Hölzen

first: Claudia

last: Schönichen

first: Thomas

last: Reinheckel

first: Melanie

last: Boerries


first: Christophe

last: Papin

summary: The histone variant H3.3 is encoded by two distinct genes, H3f3a and H3f3b, exhibiting identical amino-acid sequence. H3.3 is required for spermatogenesis, but the molecular mechanism of its spermatogenic function remains obscure. Here, we have studied the role of each one of H3.3A and H3.3B proteins in spermatogenesis. We have generated transgenic conditional knock-out/knock-in (cKO/KI) epitope-tagged FLAG-FLAG-HA-H3.3B and FLAG-FLAG-HA-H3.3A mouse lines. We show that H3.3B, but not H3.3A, is required for spermatogenesis and male fertility. Analysis of the molecular mechanism unveils that the absence of H3.3B led to alterations in the meiotic/post-meiotic transition. Genome-wide RNA-seq reveals that the depletion of H3.3B in meiotic cells is associated with increased expression of the whole sex X and Y chromosomes as well as of both RLTR10B and RLTR10B2 retrotransposons. In contrast, the absence of H3.3B resulted in down-regulation of the expression of piRNA clusters. ChIP-seq experiments uncover that RLTR10B and RLTR10B2 retrotransposons, the whole sex chromosomes and the piRNA clusters are markedly enriched of H3.3. Taken together, our data dissect the molecular mechanism of H3.3B functions during spermatogenesis and demonstrate that H3.3B, depending on its chromatin localization, is involved in either up-regulation or down-regulation of expression of defined large chromatin regions


title: Small Noncoding RNAome Changes during Human Bone Marrow Mesenchymal Stem Cells Senescence

status: Public on Dec 27 2021

city: Shanghai

first: Chuandong

last: Wang

address: NO.1665 Kongjiang Road

institute: Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: The proliferation capability and functionality of BMSCs are known to decline with aging, which severely impairing the extensive applications of BMSCs-based therapies. In this study, replicative senescence model of hBMSCs was established and the expression changes of small noncoding RNAs during senescence was detected by small RNA high-throughput sequencing analysis and qPCR.

overall_design: We subcultured hBMSCs and collected P1 and P10 hBMSCs respectively.The small RNA sequence detected expression of small RNA in P1 and P10 hBMSCs

first: Fei

last: Xiao

first: Xiaodong

last: Chen

first: Jianping

last: Peng


title: Desmosterol suppresses inflammasome activation and protects against atherosclerosis

city: New Haven

first: Xinbo

last: Zhang

state: Connecticut

address: Rm320, 10 Amistad St

department: Comparative Medicine

institute: Yale University

summary: Cholesterol biosynthetic intermediates such as lanosterol and desmosterol are emergent immune regulators of macrophages in response to inflammatory stimuli or lipid overloading, respectively. However, the participation of these sterols in regulating macrophage functions in the physiological context of atherosclerosis, an inflammatory disease driven by the accumulation of cholesterol-laden macrophages in the artery wall, has remained elusive. Here we report that desmosterol, the most abundant cholesterol biosynthetic intermediate in human coronary artery lesions, plays an essential role during atherogenesis, serving as a key molecule integrating cholesterol homeostasis and immune responses in macrophages. Depletion of desmosterol in myeloid cells by overexpression of 3β-hydroxysterol Δ24-reductase (DHCR24), the enzyme that catalyzes conversion of desmosterol to cholesterol, promotes the progression of atherosclerosis. Single cell transcriptomics in isolated CD45+CD11b+ cells from atherosclerotic plaques demonstrate that depletion of desmosterol increases interferon (IFN) responses and attenuates the expression of anti-inflammatory macrophage markers. Lipidomic and transcriptomic analysis of in vivo macrophage foam cells demonstrate that desmosterol is a major endogenous liver X receptor (LXR) ligand involved in LXR/RXR activation and thus, macrophage foam cell formation. Decreased desmosterol accumulation in mitochondria promotes macrophage mito-ROS production and NLRP3-dependent inflammasome activation. Deficiency of NLRP3 or ASC rescues the increased inflammasome activity and atherogenesis observed in desmosterol-depleted macrophages. Altogether, these findings underscore the critical function of desmosterol in the atherosclerotic plaque to dampen inflammation, by integrating with macrophage cholesterol metabolism and inflammatory activation, and protecting from disease progression.

overall_design: scRNA-seq of CD45+CD11B+ cells from atherosclerotic plaques of WT or Dhcr24TG mice injected with PCSK9 adeno-associated virus (AAV8-Pcsk9) and fed on a western diet (WD) for 16 weeks

first: Carlos

last: Fernández-Hernando


title: Single cell RNA-seq analysis of Etv2 induced MEFs reprogramming.

status: Public on Jan 12 2022

city: Minneapolis

first: Daniel

last: Garry

state: MN

address: 2231 6th Street SE, 4th Floor

department: Lillehei Heart Institute

institute: University of Minnesota

summary: The vasculature is an essential organ for the delivery of blood and oxygen to all tissues of the body and thus relevant to the treatment of ischemic diseases, injury-induced regeneration, and solid tumor growth. Therefore, the definition of pioneer factors and regulatory pathways that govern the specification and differentiation of endothelial progenitors will serve as a platform for targeted therapies to promote cardiovascular regeneration and treatment of solid organ tumors. Previously, we demonstrated that ETV2 was an essential transcription factor for the development of cardiac, endothelial and hematopoietic lineages.  Here, we report that ETV2 functions as a novel pioneer factor that relaxes closed chromatin and regulates endothelial development. By comparing engineered embryonic stem cell differentiation and reprogramming models with single cell RNA-seq, ATAC-seq and ChIP-seq techniques, we demonstrated that ETV2 was able to bind nucleosomal DNA and function as a pioneer factor independent of the cellular context. We determined that ETV2 executes a pioneering role by recruiting BRG1 to remodel chromatin around endothelial genes and help maintain an open configuration.  ETV2 chromatin binding also resulted in increased H3K27ac deposition.  Collectively, these results will serve as a platform for the development of therapeutic initiatives directed towards cardiovascular and oncological diseases.

overall_design: Single cell RNA sequencing (scRNA seq) was performed on iHA-Etv2 MEF reprogrammed cells with and without Brg1 shRNA knockdown using the previously described protocol9. Briefly, single cells from reprogrammed D1, D2, D7 and D7-Flk1+ sorted iHA-Etv2 MEFs were barcoded using the 10x Chromium Single Cell platform, and cDNA libraries were prepared according to the manufacturer’s protocol (Single Cell 30v3, 10x Genomics, USA) . Final libraries were analyzed on an Agilent Bioanalyzer High Sensitivity DNA chip for qualitative control purposes. cDNA libraries were then sequenced on a NovaSeq S4 Illumina platform (2x150 bp) aiming for 50,000 reads per cell.  Lentiviral particles to knockdown Brg1 were obtained using three unique 21-mer shRNA for Brg1 (pLKO.1 -TRC shRNA library). We generated these lentiviral particles using standard protocols and tested each one of them by infecting NIH 3T3 MEFs12. The most efficient lentivirus shRNA construct was used in our studies to knockdown Brg1 in iHA-Etv2 MEFs. Cultured iHA-Etv2 MEFs were infected with lentiviruses using the Lentiblast Premium reagent (OZBiosciences) as per the manufacturer′s instruction. After 72 hrs of infection, doxycycline was added to cells in order to reprogram them. iHA-Etv2 MEFs were harvested for analysis 24 hrs and 7 days following the addition of doxycycline.

first: Wuming

last: Gong

first: Nikita

last: Dsouza


first: Emeline

last: Fontaine

first: Guillaume

last: Martinez

first: Stéphanie

last: Le Gras

first: Roland

last: Abi Nahed

first: Patrick

last: Héry

first: Thierry

last: Buchou

first: Khalid

last: Ouararhni

first: Bertrand

last: Favier

last: Gautier

first: Jamal S M

last: Sabir

first: Matthieu

last: Gerard

first: Jan

last: Bednar

last: Arnoult

first: Stefan

last: Dimitrov

first: Ali

last: Hamiche


title: The second polar body contributes to the fate asymmetry in the mouse embryo

city: Beijing

first: Hongbin

last: Jin

state: Beijing

address: Haidian District

institute: Tsinghua University

summary: The second polar body (PB2) of mouse embryo may contains some crutial factors that control fate asymmetry. This study is aimed at discovering differentially expressed genes in PB2 compared with zygote.

overall_design: PB2 and Zygote of 1-cell mouse embryos were sperated after removing zona pellucida. Then mRNA profile of collected PB2 and zygote were analysed.

first: Yang

last: Han

first: Huasong

last: Wang

first: J

middle: X

last: Li

first: Weimin

last: Shen

first: Lin

last: Zhang

first: Luxi

last: Chen

first: Shunji

last: Jia

first: Ping

last: Yuan

first: Hui

first: Anming

last: Meng


title: Next Generation Sequencing Analysis of Transcriptomes of Mice OBs with Left Naris Occlusion

first: Chong

last: Liu

summary: Three wild type mice with left naris occlusion were dissected for OBs. Total six OBs were used for searching the genes decreased after left naris occlusion.

overall_design: Six OB tissue were generated by deep sequencing, using Illumina.

first: Pengxiang


title: Effects of ACTH-induced long-term hypercortisolemia on the transcriptome of canine visceral adipose tissue

city: Zurich

first: Hubert

last: Rehrauer

address: Winterthurerstr. 190

department: FGCZ

country: Switzerland

institute: ETH Zurich / University of Zurich

summary: Cushing’s syndrome is one of the most common endocrinopathies in adult dogs. It is a consequence of chronic hypercortisolemia (HC), that may present a pathological or iatrogenic origin. Among other alterations, Cushing’s syndrome involves the differential modulation of lipid metabolism, i.e., while enhanced lipolysis is observed in subcutaneous adipose tissue, an increased accumulation is observed in visceral adipose tissue (VAT). VAT acts in a variety of mechanisms besides energy storage, playing an important role as an endocrine organ. Strikingly, the effects of HC in VAT were never investigated in the dog. Thus, in the present project the transcriptome of visceral adipose tissue (VAT) of dogs sampled before and after long-term HC was investigated. HC was induced by subcutaneously implanted ACTH-releasing pumps and canine VAT was collected before and after treatment, followed by deep RNA sequencing (RNA-Seq) analysis. A total of 1190 differentially expressed genes (DEG) were found in response to ACTH treatment (P and FDR < 0.01). Genes upregulated post-ACTH were mostly associated with translation; in contrast, terms enriched in downregulated DEGs were related to cell adhesion and migration, intracellular signaling, immune response, extracellular matrix and angiogenesis. Transcript counts of HSD11B2, enzyme responsible for the conversion of active cortisol into cortisone, and of the glucocorticoid receptor, were decreased after ACTH treatment, while HSD11B1, activator of cortisol, were increased. Furthermore, treatment further appeared to modulate insulin signaling, hormonal sensitivity, cell proliferation, extracellular matrix organization, lipolysis, vasculogenesis and immune signaling. These results allowed the identification of factors that might play an important role in HC-related expansion of VAT, e.g., TIMP4, FGF1, CCR2, CXCR4 and HSD11B1/2. Similarities in the effects of chronic hypercortisolemia on VAT of dogs and humans were further highlighted.

overall_design: Hypercortisolemia (HC) was induced in five adult Beagle dogs by the permanent administration of tetracosactide, a synthetic ACTH hormone, which stimulates endogenous cortisol secretion, using osmotic pumps for 25 weeks. The pumps were implanted subcutaneously in the dorsolateral region of the neck and replaced every 4 weeks. Tetracosactide dosage started at 1.3-1.95 μg/kg/day, increasing to a final dosage of 6-10 μg/kg/day. After 25 weeks of treatment, HC was confirmed with a positive ACTH stimulation and a low-dose dexamethasone suppression test. Visceral adipose tissue was collected by laparotomy prior to treatment (Pre-ACTH samples) and after the 25 weeks of tetracosactide administration (Post-ACTH samples). RNA-seq was then performed with Next Generation Sequencing methodology and the effects of prolonged HC were evaluated by pairwise comparison between Pre-ACTH and Post-ACTH groups.

first: Miguel

last: Tavares Pereira

first: Mariusz

last: Kowalewski

first: Felicitas

last: Boretti

first: Nadja

middle: S

last: Sieber-Ruckstuhl


title: Single-cell transcriptome reveals insights into the development and function of the zebrafish ovary

status: Public on Dec 19 2021

city: Davis

first: Yulong

address: 3105 Life Science

department: Molecular and Cellular Biology

institute: University of California, Davis

summary: Zebrafish are an established research organism that has made many contributions to our understanding of vertebrate tissue and organ development, yet there are still significant gaps in our understanding of the genes that regulate gonad development, sex, and reproduction. Unlike the development of many organs, such as the brain and heart that form during the first few days of development, zebrafish gonads do not begin to form until the larval stage ( ≥5 dpf). Thus, forward genetic screens have identified very few genes required for gonad development. In addition, bulk RNA sequencing studies which identify genes expressed in the gonads do not have the resolution necessary to define minor cell populations that may play significant roles in development and function of these organs. To overcome these limitations, we have used single-cell RNA sequencing to determine the transcriptomes of cells isolated from juvenile zebrafish ovaries. This resulted in the profiles of 10,658 germ cells and 14,431 somatic cells. Our germ cell data represents all developmental stages from germline stem cells to early meiotic oocytes. Our somatic cell data represents all known somatic cell types, including follicle cells, theca cells and interstitial stromal cells. Further analysis revealed an unexpected number of cell subpopulations within these broadly defined cell types. To further define their functional significance, we determined the location of these cell subpopulations within the ovary. Finally, for select examples, we used gene knockout experiments to determine the role of newly identified genes. Our results reveal novel insights into ovarian development and function and the sequencing information will provide a valuable resource for future studies.

overall_design: Single-cell RNA sequencing of 40 day post-fertilization zebrafish ovaries

first: Michelle

last: Kossack

first: Matthew

last: McFaul

first: Stefan

last: Siebert

first: Celina

last: Juliano

first: Bruce

middle: W

last: Draper


title: Disrupting Mechanotransduction Decreases Fibrosis and Contracture in Porcine Split Thickness Skin Grafting

status: Public on Dec 16 2021

city: Tucson

first: Kellen

state: AZ

address: 1501 N Campbell Ave

department: Surgery

institute: University of Arizona

summary: We quantify the effects of FAK inhibition on porcine cells at the cellular and transcriptomic level using single-cell RNA-sequencing. We characterize fibrotic porcine dermal cells and compare them to regenerative cells and also unwounded tissue.

overall_design: scRNA-seq was performed on porcine cells collected from multiple pigs subjected to full thickness wounds with split thickness skin grafting (STSG). STSG treated with FAK inhibitor and unwounded skin cells were collected as well.

first: Dominic

last: Henn

first: Michael

last: Januszyk

first: Geoffrey

last: Gurtner


title: Single cell trajectory modeling identifies a primitive trophoblast state defined by BCAM enrichment

status: Public on Dec 14 2021

city: Vancouver

first: Alexander

last: Beristain

state: BC

address: 950 West 28th Ave

department: Obstetrics & Gynecology

institute: The University of British Columbia

summary: The establishment and function of the human placenta is dependent on specialized cells called trophoblasts. Unfortunately, little is known about the cellular and molecular processes controlling human trophoblast stem cell maintenance and differentiation into mature trophoblast sub-populations/cell states. To address this, we here report transcriptomic data from n=7 first trimester human placental tissues, n=3 regenerative human trophoblast stem cell (hTSC) derived trophoblast organoids, and n=3 EVT-differentiated hTSC derived organoid cultures at single-cell resolution. This study sought to identify the molecular programs and cell states important in trophoblast progenitor establishment, renewal, and differentiation. Placental tissues were collected following elective termination at the British Columbia Women’s Hospital CARE clinic. hTSC cultures were established as described and sequenced on either day 0 of culture (for regenerative organoid colonies), or day 7 of culture (for EVT-differentiated organoid colonies).

overall_design: Placental tissues: First trimester placental tissues were collected from consenting women at two gestational age timepoints: early first trimester (n=4, 6-7 weeks’ gestational age) or late first trimester (n=3, 11-12 weeks’ gestational age). Live cells were purified for mRNA sequencing using the 10X Genomics chromium single cell 3’ reagent v2 chemistry kit. Human trophoblast stem cell derived organoids: Trophoblast organoids were established from 3 hTSC cell lines using a modified version of previously described protocols and differentiated into EVT by removal of WNT signaling components. Live cells were purified for mRNA sequencing from n=3 regenerative cultures on culture day 0 and from n=3 EVT-differentiated cultures on culture day 7 using the 10X Genomics chromium single cell 3’ reagent v3 chemistry kit.

last: Shannon

first: Jennet

last: Baltayeva

first: Barbara

last: Castellana

first: Jasmin

last: Wächter

first: Samantha

last: Yoon

first: Jenna

last: Treissman

first: Hoa

last: Le


title: Transcriptome data of wt, Rbx1- or Ube2m- deficient Treg cells from mice

status: Public on Dec 28 2021

city: Hangzhou

first: Di

last: Wu

state: Zhejiang

address: No. 268, Kaixuan Road

institute: Zhejiang University

summary:
Cullin-RING Ligases (CRLs), upon activation by neddylation, play the key roles in regulating many biological processes. However, how CRL-neddylation regulates the function of Treg cells remains elusive. Here we show that mice with Treg-specific deletion of Rbx1, a RING component of CRLs required for its activity, developed an early-onset fetal inflammatory disorders and death at day ~25 after birth with disrupted homeostasis and impaired suppressive functions of Treg cells. Specifically, Rbx1 is essential for maintenance of the effector subpopulations in Treg cells, and regulates several inflammatory pathways. Similar phenotypes were seen in mice with deletion of Ube2m, a neddylation E2, in Treg cells, but with much lesser severity. Interestingly, Treg-specific deletion of Rbx2/Sag or Ube2f, the family member of Rbx1 or Ube2m, respectively, had no obvious phenotype. Thus, the Ube2m-Rbx1 axis is required for the maintenance of homeostasis and functions of Treg cells; and Rbx1 has Ube2m-independent roles in the fitness of Treg cells, suggesting a layer of complexity in neddylation activation of CRLs.
We use the tranpritome dara to show the mechanism of the function of Rbx1 and Ube2m in Treg cells, also research the relationship of Rbx1 and Ube2m in Treg cells.

overall_design: CD4+YFP+ Treg cells were isolated from the peripheral lymph nodes and spleens of mice (8-12 weeks old) with indicated genotypes. To generate enough materials, the pooled tissues from 2-3 mice (Foxp3cre/wt), 8-11 (Foxp3cre/wt;Rbx1fl/fl) or 3-4 (Foxp3cre/wt;Ube2mfl/fl) were used. Each type of contains three biological replications.

first: Yi

last: Sun


title: The genetic basis of structural colour variation in mimetic Heliconius butterflies

status: Public on Dec 10 2021

city: Sheffield

first: Nicola

last: Nadeau

address: Western Bank

department: Ecology and Evolutionary Biology

institute: The University of Sheffield

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

sample_organism:
Heliconius melpomene rosina
Heliconius melpomene cythera
Heliconius erato cyrbia
Heliconius erato demophoon

overall_design: Refer to individual Series


title: Cohesin-mediated loop anchors confine the location of human replication origins

status: Public on Dec 05 2021

city: Tallahassee

first: David

middle: M

last: Gilbert

address: 319 Stadium Drive

department: Department of Biological Science

institute: Florida State University

summary: DNA replication occurs through an intricately regulated series of molecular events and is fundamental for genome stability. It is currently unknown how the location of replication origins is determined in the human genome. Here, we dissect the role for topologically associating domains (TADs), subTADs, and loops in the positioning of replication initiation zones (IZs). We stratify TADs/subTADs by the presence of corner-dots indicative of loops and the orientation of CTCF motifs. We find that high-efficiency, early replicating IZs localize to boundaries between adjacent corner-dot TADs anchored by high-density arrays of divergently and convergently-oriented CTCF motifs. By contrast, low-efficiency IZs localize to weak boundaries devoid of CTCF and corner-dots. Upon ablation of cohesin-mediated loop extrusion in G1, high-efficiency IZs become diffuse and de-localized specifically at boundaries with complex CTCF motif orientation. Moreover, G1 knock-down of the cohesin unloading factor WAPL results in gained long-range loops and narrowed localization of IZs at the same boundaries. Finally, targeted deletion or insertion of specific boundaries causes local replication timing shifts consistent with loss and gain of IZs, respectively. Our data support a model in which cohesin-mediated loop extrusion and stalling at a subset of genetically-encoded TAD/subTAD boundaries is an essential determinant of the precise location of replication initiation in human S phase.

overall_design: Repli-Seq on HAP1 cells with contact domain boundaries inserted via a transposon based approach (cell line generated in PMID: 32868908)

first: Peiyao

last: Zhao

first: Jennifer

last: Phillips-Cremins


title: 10X genomics single cell sequencing of sheep testis

status: Public on Dec 30 2021

city: Lanzhou

first: Yao

middle: jing

last: Yue

address: NO.335 Jiangouyan, Qilihe District Lanzhou 730050, Gansu, P. R. C

department: Lanzhou Institute of Husbandry and Pharmaceutical Sciences,

institute: Chinese Academy of Agricultural Sciences

summary: Sheep testes undergo a dramatic rate of development with structural changes during sexual maturity, including the proliferation and maturation of somatic niche cells and the initiation of spermatogenesis. To explore this complex process, 12,843 testicular cells from three sexual maturity (3 month-old) rams were sequenced using 10x Genomic platform single-cell sequencing (scRNA-seq).Nine testicular somatic cell types and five male germ cell types were observed.The study revealed significant changes in germline stem cells during sexual maturation. Candidate factors and pathways for the regulation of germ and somatic cell development were identified that represent the scientific basis for the development of a livestock stem cell breeding program.

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

first: Bohui

last: Yang

first: Yaojing


title: LGR5 is a conserved marker of hair follicle stem cells across species

status: Public on Dec 04 2021

city: Raleigh

first: Jorge

last: Piedrahita

state: North Carolina

address: 1060 William Moore Drive, BPC Suite 200

institute: North Carolina State University

summary: Using a transgenic pig expressing H2B-GFP under the control of the endogenous LGR5 promoter, we used fluorescence activated cell sorting to isolate LGR5-high and LGR5-negative epidermal cells to generate mRNA profiles of the hair follicle stem cell population, n=2 pigs. Bulk RNAseq samples were prepared from porcine cells, at least 500ng of RNA was extracted from sorted LGR5-GFP-high or LGR5-GFP-negative populations. RNAseq was performed externally by GENEWIZ; library preparation with poly(A) selection was performed followed by paired end 150bp sequencing on Illumina HiSeq.

overall_design: Comparison of LGR5+ vs LGR5- cell populations isolated from FACS sorted porcine epidermal cells.

first: Kathryn

last: Polkoff


title: Identification of transcriptional regulatory networks that function in early response to cold stress in Vitis amurensis

status: Public on Dec 08 2021

first: Huayang

last: Li

address: Haidian strict, Xiang Mountain South Road, Xiang Mountain South Village 20#

department: Institute of Botany

institute: University of Chinese Academy of Sciences

summary: We report the RNAseq technologies for high-throughput profiling of accessible chromatin regions and differentially expressed genes after cold treatment in Vitis amurensis, respectively. By combining the RNAseq results, we built putative transcriptional regulatory networks involving in cold responses in grape, and found some new transcription factors that may participate in cold responses in grape.

overall_design: Examination of accessible chromatin regions and gene expression profiles of in votro V. amurensis plants under control and cold stress conditions

first: Chong

last: Ren

first: Zhenchang

last: Liang

last: Wang


title: The genetic basis of structural colour variation in mimetic Heliconius butterflies [erato]

summary: We use RNAseq data to perform differential gene expression to identify genes controlling structural colouration in two co-mimetic species of Heliconius butterfly - Heliconius erato and Heliconius melpomene. We use comparisons between iridescent and non-iridescent subspecies of Helcionius erato (H. e. cyrbia and H. e. demophoon, respectively) and Helcionius melpomene (H. m. cythera and H. m. rosina, respectively) at two separate developmental stages, 50% and 70% of development. In addition, in the iridescent subspecies of both H. erato and H. melpomene, we compared the iridescent wing regions (forewing and hindwing combined) to the non-iridescent androconial wing region using differential gene expression.

sample_organism:
Heliconius erato cyrbia
Heliconius erato demophoon

overall_design: Differential gene expression between iridescent and non-iridescent sub-species (and wing regions) of Heliconius melpomene and Heliconius erato at 50% and 70% pupal wing development.

first: Victoria

last: Lloyd


title: Critical contribution of 3’ non-seed base pairing to the in vivo function of the evolutionarily conserved let-7a microRNA [miRNA-seq]

status: Public on Dec 06 2021

city: Worcester

first: Ye

last: Duan

state: MASSACHUSETTS

address: 373 Plantation Street, Biotech Two, Suite 306

department: Program of Molecular Medicine

institute: Umass Medical School

summary: Small RNA sequencing of all the let-7a single-nucleotide mutants to confirm the expression of the mutant miRNAs.We found that the abundance of the mutated let-7a miRNA in each mutant was similar to that of the native let-7a in WT, with a variance (<10%) that we judge not sufficient to cause lf phenotypes by reduced expression (Fig. 3B). Note that the strains with mutations at g11-g16 also contained a WT let-7 allele on a genetic balancer umnIs25(mnDp1), hence both WT and mutant let-7a were expressed.

overall_design: small RNA seq of let-7a 3' non-seed single nucleotide mutants.

first: Isana

last: Veksler-Lublinsky

first: Victor

last: Ambros


title: LNCap cell chromatin accessibility regulator of pioneer factor GATA2 binding model

status: Public on Dec 09 2021

city: San Antonio

first: Tianbao

state: Texas

address: 7703 Floyd Curl

department: Molecular Medicine

institute: University of Texas Health Science Center at San Anotnio

summary: Purpose: The dynamic chromatin accessibility was regulated by pioneer factors. The goals of this study are revealing the mechanism of GATA2 and SOX9 required for the change of nucleosome states. Methods: LNCaP cells between passage number 30-35 were used for assay. cell nucleus was extracted, digested by Tn5 transposase and ChIP was performed, the ChIP products were further used to generate library with illumina ChIP-seq kit. Hi-seq 3000 was used for sequencing and the data was analyzed by MACS2 for peaks. Results: GATA2 is associated with condensed nucleosome states and SOX9 is recruit for unwrapped the nucleosomes. Conclusions: Our study represents the first detailed nucleosome footprint of LNCap cells and mechanism underlining GATA2 and nucleosome reorganization in whole genomic DNA.

overall_design: LNCaP cells was used as cell model, ATAC-seq and ChIP-seq were applied for chromatin accessiblity, GATA2 and SOX9 binding compariing in vehicle and DHT conditions.

first: Zhong

last: Chen

last: Jin


title: Constitutive expression of Progesterone Receptor B in the uterine epithelium prevents implantation by inhibiting estrogen regulation of LIF signaling [RNAseq-PRAoe_PRBoe_oil_P4]

status: Public on Dec 02 2021

city: RTP

first: Franco

last: Demayo

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

summary: RNA-seq analysis of uterine luminal epithelium at D4.5 indicates that epithelial PGRA and PGRB shares conseved pathways. Constitutive epithelial PGRA and PGRB disrupts the embryo implantation both through the suppressed FOXO1 signaling by excluding FOXO1 from the nuclear at the uterine epithelium. There are three layers of regulation. Firstly, PGRA and PGRB diminishes Lif transcription in uterine glands by blocking ESR1 binding at the Lif promoter at D3.5 which is critical for the FOXO1 nuclear expression at D4.5 through LIF/pSTAT3/FOXO1. Secondly, PGRA and PGRB directly suppres Foxo1 transcription at the uterine epithelium probably through direct binding at Foxo1 promoter. Thirdly, PGRA and PGRB promotes the Sgk1 transcription, the kinases that phosphorylate FOXO1 to translocate it into cytoplasma for degradation.

overall_design: PgrcrePgrALsL/+ and PgrcrePgrBLsL/+ mice were ovariectomized for 2 weeks. And the whole uterus were collected for RNA-Seq after 6h oil or progesterone treatment.

first: Rong

first: Tianyuan

first: Lecong

last: Zhou

first: San-Pin

last: Wu

first: Francesco

last: DeMayo


title: Plasmacytoid dendritic cell precursors give rise to conventional dendritic cells via a Siglec-H+ Zbtb46+ Ly6D+ intermediary stage

status: Public on Dec 01 2021

city: Planegg

first: Anne

middle: Barbara

last: Krug

state: Bavaria

address: Großhaderner Str. 9

department: Institute for Immunology

institute: LMU Munich

summary: Plasmacytoid and conventional dendritic cells (pDC, and cDC) are generated from distinct lymphoid and myeloid progenitor cells in murine bone marrow. Despite the early separation of pDC and cDC lineages, CD11c+ MHCII-/lo Siglec-H+ CCR9lo pDC-like precursor cells are able to differentiate into both pDC and cDC. Single-cell transcriptomics and high-dimensional flow cytometry combined with cell fate analysis revealed the heterogeneity and commitment of subsets in this compartment. While Ly6D– cells within this fraction were cDC-committed and B220hi Ly6Dhi Zbtb46– cells were immediate precursors of pDCs, B220lo Ly6Dhi Zbtb46– cells still had the potential to generate cDCs in addition to pDCs. Transition to cDCs occurred via an intermediary stage marked by coexpression of Siglec-H, Ly6D and Zbtb46. Type I IFN stimulation limited cDC and promoted pDC output from these precursors, demonstrating their plasticity in response to inflammation. Thus, flexibility to divert to cDCs is retained in the pDC lineage at later differentiation stages.

overall_design: mRNA profiles of pre-cDC, CCR9lo-B220lo, CCR9lo-B220hi and pDCs from healthy, wild type murine bone marrow

first: Andrea

last: Musumeci

first: Konstantin

last: Lutz

first: Christopher

last: Sie

first: Ezgi

last: Dursun

first: Elena

last: Winheim

first: Johannes

last: Bagnoli

first: Christoph

last: Ziegenhein

first: Volker

last: Bergen

first: Malte

middle: D

last: Lucken

first: Robert

last: Oostendorp

first: Tobias

last: Straub

first: Fabian

last: Theis

first: Wolfgang

last: Enard

first: Thomas

last: Korn

middle: B


title: The role of epithelial Progesterone Receptor Isoforms in embryo implantation  [RNAseq-ePRAoe_ePRBoe_LE]

first: Franco

last: Demayo

overall_design: The uterine luminal epithelium were collected from Wnt7acre, Wnt7acrePgrALsL/+, and Wnt7acrePgrBLsL/+ mice at pregnancy day 4 by laser capture for RNA-seq analysis

first: Rong

last: Li

first: Tianyuan

last: Wang

first: Lecong

last: Zhou

first: San-Pin

last: Wu