title: The changes of the nuclear landscape upon stimulation of neuronal cells are dependent on the histone deacetylase HDAC1

city: Warsaw

first: Bartosz

last: Wojtas

address: Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biology

summary: Spatial chromatin organization is crucial for transcriptional regulation and might therefore be particularly dynamic in neurons since these terminally differentiated cells dramatically change their transcriptome in response to external stimuli. Here, we show that stimulation of neurons causes condensation of large chromatin domains. We find that this phenomenon is not only induced in rat hippocampal neurons cultured in vitro, but is also present in vivo in amygdala neurons of rats subjected to fear conditioning, and hippocampal neurons of animals subjected to kainate evoked seizures or High-Frequency Stimulation (HFS). The activity-induced chromatin condensation is an active, very rapid, and reversible process, that is independent of transcription and precedes the expression of Immediate Early Genes (IEG). It is accompanied by the redistribution of posttranslational modifications of histones, and rearrangements in the spatial organization of chromosome territories. Moreover, it leads to the reorganization of nuclear speckles and active domains located in their proximity. Finally, we find that neurons depleted of the histone deacetylase HDAC1 fail to condense chromatin upon stimulation, a phenomenon that can be fully reversed by the introduction of human HDAC1. Taken together, our results suggest that the HDAC1-dependent chromatin reorganization might constitute an important level of fine-tuning of transcriptional regulation in stimulated neurons.

overall_design: Chemically-induced long-term potentiation of synaptic transmission (cLTP) was induced according to previously published protocol (Szepesi et al., 2013) by adding 50 μM forskolin (Sigma Aldrich), 50 nM rolipram (Sigma Aldrich), and 200 μM picrotoxin (Sigma Aldrich) to the medium on DIV13-15. As the chemicals were dissolved in DMSO, the same amount of the solvent was added to the medium of the control.

first: Adriana

last: Magalska


title: Depletion of demethylase KDM6 enhances early neuroectoderm commitment of human ESCs through inhibiting WNT activation

status: Public on Sep 29 2021

city: Wuhan

first: Wei

last: Jiang

address: Donghu Road 116, District Wuchang

department: Medical Research Institute

country: China

institute: Wuhan University

type: Expression profiling by high throughput sequencing

summary: Epigenetic modifications play a crucial role in learning, memory and neurogenesis, but the study of its role in early neuroectoderm commitment from pluripotent inner cell mass is relatively lack. Here we utilized the system of directed neuroectoderm differentiation from human embryonic stem cells and identified KDM6B, an enzyme responsible to erase H3K27me3, was the most upregulated enzyme of histone methylation during neuroectoderm differentiation by transcriptome analysis. We then constructed KDM6B-null embryonic stem cells and found strikingly, the cells with KDM6B knockout exhibited much higher neuroectoderm induction efficiency. Furthermore, we constructed a serial of embryonic stem cell lines knocking out the other H3K27 demethylase KDM6A, and depleting both KDM6A and KDM6B, respectively. These cell lines together confirmed KDM6 impeded early neuroectoderm commitment. By RNA-seq, we found a panel of WNT activation genes significantly downregulated while WNT inhibiting genes significantly upregulated upon depletion of KDM6. Functional rescue assayed that WNT agonist could abolish the differential neuroectoderm induction due to manipulating KDM6 demonstrated WNT was the major downstream of KDM6 during early neural induction. Taken together, our findings illustrated the important role of histone methylation modifier KDM6A and KDM6B in neuroectoderm differentiation and provided additional insights into the precise epigenetic regulation in different stage of neurogenesis.

overall_design: RNA-seq of KDM6 KO in neuroectoderm differentiation.

first: Yajing

last: Meng


title: DNA sequencing of Medicago truncatula from ChIP-seq experiments of Embryos at different developmental stages using the H3 pan Acethyl and the H3K27me3 antibodies

status: Public on Sep 27 2021

city: Angers

first: Jerome

last: Verdier

address: Rue Georges Morel

country: France

institute: INRAE / IRHS

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We analysed the presence of H3 pan-acethylation and H3K27me3 histone marks bound to DNA of Medicago (A17) at different stages of seed development from seeds produced at 20°C and 26°C.

overall_design: Regarding the H3 pan-acetyl marks, we performed ChIP-seq experiments on two replicates of at least 50 embryos of each stage/replicate (S1, S2) from seed produced at 20 and 26 degrees. Regarding the H3K27me3marks, we performed ChIP-seq experiments on one replicates of at least 50 embryos of each stage/replicate (S1, S2, S3 and S4) from seed produced at 20 and 26 degrees. The four selected stages correspond at before (S1) and after (S2) desiccation tolerance acquisition and before (S3) and after (S4) longevity acquisition in dissected seed embryo tissues of seeds produced at 20 and 26 degrees. Corresponding stages S1_20°C=17DAP, S2_20°C=26DAP, S3_20°C=36DAP, S4_20°C=44DAP, S1_26°C=14DAP, S2_26°C=17DAP, S3_26°C=22DAP, S4_26°C=28DAP (DAP=days after pollination)

first: Jaiana

last: Malabarba

first: Zhijuan

last: Chen

first: David

last: Windels


title: Melatonin Enhances Osteoblastogenesis from Senescent Mesenchymal Stem Cells via NSD2 Mediated Chromatin Remodeling [RNA-seq]

city: Tianjin

first: Liu

last: Zhiqiang

address: 22 Qxiangtai Rd

institute: Tianjin Medical University

summary: Functional crosstalk between histone modifications and chromatin remodeling has emerged as a key regulatory mode of transcriptional control during cell fate decisions, but the underlying mechanisms are not fully understood. Here we demonstrate that RUNX2 and BGLAP osteogenic genes coordinate histone H3 lysine 36 dimethylation (H3K36me2) and transcriptional elongation factor Pol II to regulate chromatin dynamic and gene transcription during osteogenesis. Mechanistically, melatonin favored osteogenic differentiation via the NSD2-mediated modification of H3K36me2 on the promoters of osteogenic driver genes in MSCs from the old donors.

overall_design: Examination MSCs from the old donors treated with melatonin and MSCs from different age groups

first: Ying

last: Xie

last: Han

first: Feng

last: Li

first: Lijuan

last: Wang


title: Melatonin Enhances Osteoblastogenesis from Senescent Mesenchymal Stem Cells via NSD2 Mediated Chromatin Remodeling [ChIP-seq]


title: Differential expression of Triggering Receptor Expressed on Myeloid Cells (Trem)-2 in tissue eosinophils

city: Bethesda

first: Philip

last: Murphy

state: MD

address: 10 CENTER DR RM 11N111

department: National Institute of Allergy and Infectious Diseases

country: USA

institute: National Institutes of Health

summary: No longer regarded as simply end-stage cytotoxic effectors, eosinophils are now recognized as complex cells with unique phenotypes that develop in response to the local microenvironment. In our previous study, we documented eosinophil infiltration in association with characteristic muscle damage in the dystrophin-deficient (mdx) mouse model of Duchenne muscular dystrophy. In this earlier study, we found that eosinophils did not promote formation of muscle lesions, as these persisted in eosinophil-deficient mdx.PHIL mice. To obtain additional insight into these findings, we performed RNA sequencing on eosinophils isolated from muscle tissue of mdx, IL5tg, and mdx.IL5tg mouse strains. We discovered profound up-regulation of classical eosinophil effector proteins (major basic protein-1, eosinophil peroxidase, and eosinophil-associated ribonucleases, or RNases) in eosinophils isolated from lesion-free muscle from IL5tg mice. By contrast, we observed significant upregulation of tissue remodeling genes, including proteases, extracellular matrix components, collagen, and skeletal muscle precursors, as well as the immunomodulatory receptor, TREM2, in eosinophils isolated from skeletal muscle tissue from the dystrophin-deficient mdx mouse strain. The anti-inflammatory properties of TREM2 have been described in the monocyte/macrophage lineage; however, there are no previous studies documenting TREM2 expression in eosinophils. Here we show that TREM2 is critical for full growth and differentiation of bone marrow-derived eosinophil cultures and for full expression of toll-like receptor 4. Immunoreactive TREM2 was also detected on human eosinophils at levels that correlated with donor body mass index. Taken together, our findings provide important insight into the immunomodulatory and remodeling capacity of mouse eosinophils and the flexibility of their gene expression profiles in vivo.

overall_design: 3 conditions (mdx, mdx+IL5, IL5), 3 biological replicates per condition

first: Albert

middle: C

last: Sek

first: Caroline

middle: M

last: Percopo

first: Arun

middle: K

last: Boddapati

first: Michelle

last: Ma

first: Wendy

middle: E

last: Geslewitz

first: Julia

middle: O

last: Krumholz

first: Justin

middle: B

last: Lack

first: Helene

middle: F

last: Rosenberg


title: Keap1 deletion-based Nrf2 activation accelerates mutant K-ras/p53-driven cholangiocarcinoma

city: Sendai

first: Shin

last: Hamada

state: Miyagi

address: 1-1 Seiryo-machi, Aobaku

department: Division of Gastroenterology

country: Japan

institute: Tohoku University Graduate School of Medicine

summary: Addition of liver-specific Keap1 deletion to mice harboring mutant K-ras and p53 accelerated cholangiocarcinoma formation, with hallmarks of Nrf2 activation.

overall_design: We introduced liver-specific mutant K-rasG12D and p53R172H expressions with (AKP::Keap1 mouse) or without (AKP mouse) Keap1 deletion.

first: Tatsuhide

last: Nabeshima

first: Keiko

last: Taguchi

first: Yu

last: Tanaka

first: Ryotaro

last: Matsumoto

first: Masayuki

last: Yamamoto

first: Atsushi

last: Masamune


title: Stabilization of Pol II protein, orchestration of transcription cycles, and maintenance of enhancer landscape by general transcription regulator SPT5 [PRO-seq]

city: Shanghai

first: Linna

last: Peng

address: Dong'an Road

institute: Fudan University

summary: Transcription machinery progression is governed by multitasking regulators including SPT5, an evolutionarily conserved factor implicated in virtually all transcriptional steps from enhancer activation to termination. Yet its mechanistic understanding in human cells remains incomplete. Here we utilize rapid degradation system and reveal crucial function of SPT5 in maintaining cellular and chromatin Pol II levels. Rapid SPT5 depletion causes a pronounced reduction of paused Pol II at promoters and enhancers, distinct from NELF degradation resulting in short-distance paused Pol II redistribution. Most of genes exhibit down- but not upregulation, accompanied by greatly impaired transcription activation and altered chromatin landscape at enhancers, and severe Pol II processivity defects at gene bodies. Phosphorylation of KOWx-4/5- linker potentiates pause release and is antagonized by Integrator-PP2A (INTAC) targeting SPT5 and Pol II. Our findings position SPT5 as an essential positive regulator of global transcription by controlling cellular Pol II levels, enhancer activation and landscape, paused Pol II stability, elongation processivity and termination in human.

overall_design: We performed PRO-seq, ATAC-seq, RNA-seq, ChIP-seq, or TT-seq to investigate the role of SPT5 in regulating transcription. In this study, samples for each condition were collected in biological duplicates. Cells were treated with dTAG13 for 3, 12,or 24 hours, the corresponding control cells were treated for the same duration with vehicle only (DMSO) at the same vol/vol dilution.

first: Shibin

last: Hu

first: Zhenning

last: Wang

first: Aixia

last: Song

first: Fei

middle: X

last: Chen


title: Controlling tissue patterning by translational regulation of signaling transcripts through the core translation factor eIF3c

status: Public on Sep 30 2021

city: Stanford

first: Gun Woo

last: Byeon

state: CA

address: 279 Campus Dr., Beckman Center B309

institute: Stanford University

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

overall_design: Refer to individual Series


title: Melatonin Enhances Osteoblastogenesis from Senescent Mesenchymal Stem Cells via NSD2 Mediated Chromatin Remodeling.

first: Liu

last: Zhiqiang


title: Transcriptome analysis of genes that regulated by lnc-CXCL2-4-1

status: Public on Sep 26 2021

city: Beijing

first: Shuo

last: Liu

address: 5 Dong Dan San Tiao

department: Department of Immunology

institute: Chinese Academy of Medical Sciences

summary: To demonstrate the regulating function of lnc-CXCL2-4-1 in lung epithelial cells after viral infection, we performed transcriptome sequencing of wild-type and lnc-CXCL2-4-1-silenced A549 cells after influenza A virus (IAV) infection, and then analyzed differentially expressed genes.

overall_design: Transcriptome analysis of negative ctrl siRNA or lnc-CXCL2-4-1 siRNA-transfected A549 cells after IAV infection for 12 h.

first: Jiaqi

first: Xue

last: Yang

first: Xuetao

last: Cao


title: Differential gene regulation in DAPT-treated Hydra reveals candidate direct Notch signalling targets

city: Planegg-Martinsried

first: Jasmin

last: Moneer

state: Munich

address: Grosshadernerstrasse

department: Biologie II

country: Germany

institute: LMU

summary: In Hydra, Notch inhibition causes defects in head patterning and prevents differentiation of proliferating nematocyte progenitor cells into mature nematocytes. To understand the molecular mechanisms by which the Notch pathway regulates these processes, we performed RNA-seq and identified genes that are differentially regulated in response to 48 h of treating the animals with the Notch inhibitor DAPT. To identify candidate direct regulators of Notch signalling, we profiled gene expression changes that occur during subsequent restoration of Notch activity and performed promoter analyses to identify RBPJ transcription factor-binding sites in the regulatory regions of Notch-responsive genes. Interrogating the available single-cell sequencing data set revealed the gene expression patterns of Notch-regulated Hydra genes. Through these analyses, a comprehensive picture of the molecular pathways regulated by Notch signalling in head patterning and in interstitial cell differentiation in Hydra emerged. As prime candidates for direct Notch target genes, in addition to Hydra (Hy)Hes, we suggest Sp5 and HyAlx. They rapidly recovered their expression levels after DAPT removal and possess Notch-responsive RBPJ transcription factorbinding sites in their regulatory regions

overall_design: We aimed to identify the transcriptional target genes of Notch signalling by comparing DAPT-treated animals to control ones at three different time points. Six biological repeats were used.

first: Angelika

last: Boettger


title: lnc-Cxcl2 suppressed Cxcl2 expression in mouse lung epithelial cells

summary: In this study,  we performed RNA-seq in GFP-VSV infected  mouse lung epithelial cell lines (MLE-12 cells) and found that the expression of a non-coding RNA was increased upon VSV infection in Cxcl2 locus, which we termed it as lnc-Cxcl2. We further detected the function of lnc-Cxcl2 by performing transcriptome analysis in lnc-Cxcl2-deficient MLE-12 cells with and without VSV infection, and found that lnc-Cxcl2 suppressed Cxcl2 expression in MLE-12 cells with and without VSV infection.

overall_design: RNA-seq was performed in non-infected and GFP-VSV infected-MLE-12 cells (each had two replicates), transcriptome analysis was performed in wild-type and lnc-Cxcl2-deficient MLE-12 cells with and without VSV infection for 12h.

first: Minghong

last: Jiang


title: Loss of cadherin-11 in atherosclerosis immune response: altered macrophage migration and T cell activation

city: Nashville

first: Lance

last: Riley

state: TN

address: 9445 MRB4, 2213 Garland Ave

department: Biomedical Engineering

institute: Vanderbilt University

summary: The objective of this study was to understand the impact of losing cadherin-11 (CDH11) on the immune response in atherosclerosis. CDH11 has previously been demonstrated to be associated with a number of fibrotic diseases, but its exact role in inflammation remains relatively unknown. In vivo models of atherosclerosis demonstrated altered immune cell profiles with CDH11-deficiency, including decreased circulating myeloid cell populations. In vitro studies of CDH11-deficient macrophages revealed increased expression of genes associated with migration, despite a functional decrease in migration, possibly due to compensatory mechanisms. RNAseq analysis also showed increased expression of MHC class II molecule genes in CDH11-/- macrophages, indicating that loss of CDH11 in macrophages could alter T cell populations through increased activation of CD4+ helper T cells. These results together indicate that CDH11 can alter the immune response, in part by impairing macrophage migration and by affecting T cell activation.

overall_design: Macrophages were collected from the bone marrow of 3 WT controls and 4 CDH11-/- experimental animals. Macrophages were differented in L929 conditioned media for 7 days in vitro prior to total RNA collection.

first: Camryn

middle: L

last: Johnson

middle: A

first: Matthew

last: Bersi

first: MacRae

last: Linton

first: W

middle: D

last: Merryman


title: Differentially polarized human monocyte-derived macrophages (M0, M1, M2/IL10, M2/IL4, TAM-like)

status: Public on Sep 25 2021

city: Saarbruecken

first: Jessica

last: Hoppstaedter

address: Campus C2 3

department: Pharmacy

institute: Saarland University

summary: In order to assess whether differences in the transcriptomic profile of human tumor-associated macrophages vs. alveolar macrophages from adjacent non-tumor-tissue (GSE162669) were caused by factors secreted by tumor cells, primary human monocyte-derived macrophages (MDMs) were polarized towards a TAM-like phenotype by cultivating them in tumor cell-conditioned medium. A genome-wide comparison by bulk RNA-Seq confirmed a high similarity of ex vivo TAMs and in vitro polarized TAM-like macrophages. Other polarization schemes (M1: LPS/IFN-gamma, M2: IL10 or IL4) did not lead to similar transcriptomic changes. For details, see Hoppstädter et al., 2021 (doi:10.1016/j.ebiom.2021.103578).

overall_design:
After differentiation, MDMs were polarized for another 24 hours. To this end, MDM medium was supplemented with 20 ng/ml IFNγ and 100 ng/ml LPS for M1 polarization; either 20 ng/ml IL4  or IL10 for M2 polarization; or left without further supplementation for M0 macrophages. TAM-like macrophages were generated by cultivation in A549 tumor cell-conditioned medium (TCM) supplemented with 20 ng/ml M-CSF.
MDM Samples from one female (donor 1) and two male donors (donor 2 and 3) were used for RNA sequencing.

last: Hoppstädter

first: Anna

last: Dembek

first: Charlotte

last: Dahlem

first: Gilles

last: Gasparoni

first: Jörn

last: Walter

first: Martin

last: Simon

first: Marcel

middle: H

last: Schulz

first: Alexandra

last: Kiemer


title: Human tumor-associated macrophages from lung adenocarcinoma vs. alveolar macrophages from adjacent non-tumor tissue

summary: Human tumor-associated macrophages (TAMs) were isolated from lung adenocarcinoma tissues and compared with alveolar macrophages (AMs) obtained from adjacent non-tumor tissues. For details, see Hoppstädter et al., 2021 (doi:10.1016/j.ebiom.2021.103578).

overall_design: Next-generation sequencing of human alveolar macrophages and tumor-associated macrophages. Cells were obtained from three donors and analyzed in triplicate.

first: Hanno

last: Huwer


title: The transcriptomes of PC3 cells with or without POH1 interference

first: Wandong

last: Yu

state: China

address: No. 801, Heqing Road, Minhang District, Shanghai

institute: The Fifth People’s Hospital of Shanghai, Fudan University

summary: Total RNA was obtained from PC3 cells with or without POH1 interference to perform a High-throughput sequencing

overall_design: The prostate cancer cell line PC3 transfected with either the control or POH1 siRNAs. The gene transcript expression profiles were generated by deep sequencing.

first: Guowei

last: Shi


title: Next Generation Sequencing Facilitates Quantitative Analysis of Dura macrophage Transcriptomes post adoptive T cell reconstitution of RAG-1 deficient mice I

city: Mainz

first: Nir

last: Yogev

address: Langenbeck Str.1

institute: University Medical Center of the Johannes Gutenberg University of Mainz

summary: The goal of this study was to compare transcriptional changes evoked by T cells cross talk with meningeal macrophages. Furthermore, the role of specific T cell subsets or selected cytokine deficiency were used to evaluate their role in regulating such transcriptional changes

overall_design: Dural macrophage mRNA profiles post T cell reconstitution of RAG-1 deficient mice were generated by deep sequencing, in replicate, using Illumina HiSeq

first: Dev

middle: S

last: Sams

first: Federico

last: Marini

first: Andrea

last: Cugurra

first: Matthias

last: Klein


title: Identification of Jmjd2a KO regulated genes in the mouse hearts

city: Dalals

first: zhi-ping

last: liu

state: TX

address: 6000 Harry Hines Blvd

department: internal medicine

institute: ut southwestern

summary:
Cardiac hypertrophy and failure are accompanied by a reprogramming of gene expression that involves transcription factors and chromatin remodeling enzymes. Little is known about the role of histone methylation and demethylation in this process. To understand the role of JMJD2A, a trimethyl demethylase for histone 3 lysine 9 and 36, in cardiac hypertrophy, we generated heart specific JMJD2A deletion (JMJD2A hKO) and overexpression (JMJD2A-Tg) mouse lines. JMJD2A hKO and JMJD2A-Tg mice are viable and have no overt baseline phenotype. However, they have altered responses to cardiac stresses.
While inactivation of JMJD2A in hKO mice resulted in an attenuated hypertrophic response to transverse aortic constriction (TAC)-induced pressure overload compared to that of control littermates, JMJD2A-Tg mice have exacerbated cardiac hypertrophy after TAC.

overall_design: Jmj2a KO

first: Zhi-Ping

last: Liu

first: Qing-Jun

last: Zhang


title: Next Generation Sequencing Facilitates Quantitative Analysis of Dura macrophage Transcriptomes post adoptive T cell reconstitution of RAG-1 deficient mice


title: Transcriptome analysis of the mandibles from FcgRIIB-deficient mouse model of lupus

city: Bangkok

first: Nithidol

last: Sakunrangsit

address: Rama IV

country: Thailand

institute: Chulalongkorn University

summary: To identify the extensive complexity of transcriptome in Fc gamma receptor IIB knockout (FcgRIIB−/−) mandibles. We performed gene expression profiling of mandibular bone from wild-type (WT) and FcgRIIB−/− mice at 6 months of age. Our study reports the first transcriptomic analysis in mandibles of FcgRIIB-deficient mice using RNA-sequencing (RNA-seq). The data were validated by qPCR analysis. qPCR analysis revealed similar results compared to RNA-seq data. This finding disclosed the relevant differentially expressed genes (DEGs) and clarify the mechanism underlying the pathogenesis of osteopenia. We provide novel candidate genes and enriched pathways that contribute to mandibular bone loss in FcgRIIB−/− mice during lupus development. Sufu and Serpina12 were identified as candidate molecular targets regulating osteoclastogenesis and osteogenesis, respectively.

overall_design: Mandibular transcriptional profiles of 6-month-old WT controls and FcgRIIB−/− male mice

first: Jatuphol

last: Pholtaisong

first: Pinidphon

last: Prombutara

first: Sutada

last: Lotinun


title: Next Generation Sequencing Facilitates Quantitative Analysis of Dura macrophage Transcriptomes post adoptive T cell reconstitution of RAG-1 deficient mice II


title: miRNA changes after overexpression of LINC01126 in HepG2 cells

city: Pingyi City

first: Yixiu

last: Chen

address: No.7 Jinhua Road, Pingyi Economic Development Zone, Shandong Province, 273300, P.R. China

institute: Neurosurgery, Pingyi people's Hospital

summary: To identify putative miRNA targets for LINC01126, we overexpressed LINC01126 in HepG2 cells and carried out a microarray analysis. A total of 66 miRNAs present in the array demonstrated 1.5-fold upregulation or downregulation of expression upon LINC01126 transfection.

overall_design: HepG2 cells were transfected with ad-LINC01126 or ad-NC for 48 h. The RNA was collected and further applied for microarray analysis.

first: Xianli

first: Lili

last: Zhao


title: Removal of levofloxacin by an oleaginous microalgae Chromochloris zofingiensis under photoautotrophic and heterotrophic conditions

city: Guanghzou

first: Juan

last: Peng

address: No 164, Xingang west road,Haizhu district

department: Marine sciences

institute: Sun Yat-sen University

summary:
Purpose: The goals of this study are to investigate the global gene expression of  Chromochloris zofingiensis when treated with LEV by  transcriptome profiling (RNA-seq) analysis.
Methods:  Chromochloris zofingiensis mRNA profiles of 15-day cultivition Control (Y0) and Treatment (Y10) were generated by deep sequencing, in triplicate, using Illumina NovaSeq platform. The paired-end clean reads  that passed quality filters were  aligned to reference genome using TopHat v2.0.12 and HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. Differential expression analysis of two conditions was performed using the DEGSeq R package (1.20.0)
Results:The results showed that LEV could be bioaccumulated in algal cells and the reactions of demethylation, oxidation, hydroxylation, decarboxylation, dehalogenation and ring cleavage involved in the metabolic pathways play a major role in biodegradation of LEV by heterotrophic C. zofingiensis.
Conclusions: . Collectively, this research shows that the heterotrophic C. zofingiensis can be identified as a promising candidate for LEV removal in wastewater remediation.

first: Yongyi

last: He


title: γH2AX-associated RNA in mouse spermatocytes

city: Hangzhou

first: Xiaochun

last: Yu

state: Zhejiang

address: 18 Shilongshan Street

institute: Westlake University

summary: In the testis of the mice, most spermatogonia are in pachytene stage. We have harvested spermatogonia from 3-week-old mice. As γH2AX is the marker of the XY body, we performed RNA-seq following RNA-ChIP using anti-γH2AX antibody in germ cells to report the γH2AX associated RNA in mouse spermatocytes, while IgG as the negative control. Process of RNA-ChIP for germ cells was as the ChIP protocol with some modifications.

overall_design: Examination of γH2AX associated RNA in mouse spermatocytes

first: Xiaochen

last: Gai

first: Qilin

last: Li

first: Di

last: Xin


title: Epigenome analysis of adipose/connective tissue from thyroid-associated ophthalmopathy

first: Lian-Qun

last: Wu

address: 83 Fenyang Road

type: Methylation profiling by genome tiling array

summary: Using Illumina Infinium MethylationEPIC  850K  BeadChip, the genome-wide DNA methylation difference between adipose/connective tissue from TAO patients and normal subjects were compared

overall_design: Bisulphite converted DNA from the 8 samples were hybridised to the Infinium MethylationEPIC BeadChip microarray


title: Mitochondria-originating novel coding gene sORF2146 controls flowering

status: Public on Sep 24 2021

city: Iizuka-shi

first: Tomoyuki

last: Takeda

state: Fukuoka

address: 680-4 Kawazu

department: Bioscience and Bioinformatics

institute: Kyushu Institute of Technology

summary: It has been reported that a number of small coding genes (30–100 amino acids) tend to be lineage-specifically emerged in evolution but such de-novo genes tend to be missed in genomes. Plant mitochondrial genomes might be fostering sources of de-novo genes because of a high rearrangement rate. However, the functional role of de-novo genes derived from mitochondria is unclear. Here, in the best model species of plants (Arabidopsis thaliana), we showed that Arabidopsis-specifically emerged de-novo genes derived from mitochondrial genome contributed to phenotypic variation in a species. We previously identified 49 candidates of small coding genes inducing abnormal morphological changes on overexpression in the nuclear genome. Among them, we focused on a candidate (sORF2146) potentially encoding 66 amino acids in large-scale intergenic genomic transferring region from mitochondrial genome. Comparative genome analysis showed that sORF2146 had been appeared in Arabidopsis lineage. Mitochondrial sORF2146 is fixed among A. thaliana ecotypes but nucleus sORF2146 is not fixed in A. thaliana ecotypes. After showing evidence that nucleus sORF2146 was transcribed and translated as a coding gene, we performed transcriptome analysis in transgenic plant overexpressing sORF2146. Genes associated with flowering transition are highly regulated in the transgenic plant. We then examined phenotypic effects of overexpression and knockdown transgenic plant. Overexpression and knockdown transgenic plant induce late and early flowering, respectively. Taken together, we conclude that a nucleus de-novo gene derived from mitochondria contributes to the variation of floral timing in Arabidopsis population.

overall_design: To address the physiological role of sORF2146, we compared gene expression between transgenic plants overexpressing sORF2146 (sORF2146ox) and those of transgenic plants inserting only vector as negative control (control) with three biological replicates.

first: Kousuke

last: Hanada


title: Intestinal Tuft-2 cells exert antimicrobial immunity via sensing bacterial metabolite N-undecanoylglycine by vomeronasal receptor Vmn2r26

first: Zhen

last: Xiong

address: 15 Datun Road, Beijing 100101, China

department: Institute of Biophysics

institute: Chinese Academy of Sciences

summary:
Tuft cells as a type of intestinal epithelial cells exist in epithelial barriers that play a critical role in immunity against parasite infection. It remains elusive about whether Tuft cells participate in bacterial eradication. Here we identify Sh2d6 as a signature marker for CD45+ Tuft-2 cells. Tuft-2 cells are derived from Lgr5+ intestinal stem cells but not bone marrow cells. Depletion of Tuft-2 cells is susceptible to bacterial infection. Tuft-2 cells quickly expand over bacterial infection and sense bacterial metabolite N-undecanoylglycine through vomeronasal receptor Vmn2r26. Mechanistically, Vmn2r26 engagement with N-undecanoylglycine activates GPCR-PLCγ2-Ca2+ signal axis, which initiates prostaglandin D2 (PGD2) production. PGD2 enhances mucus secretion of Goblet cells and induces antibacterial immunity. Moreover, Vmn2r26 signaling also promotes SpiB expression, which is responsible for Tuft-2 cell development and expansion over bacterial challenge. Our findings reveal a novel function of Tuft-2 cells in immunity against bacterial infection through Vmn2r26-mediated recognition of bacterial metabolites.
We used microarrays to detail the gene expression of Tuft-2 cells compared with non Tuft-2 epithelial cells under Shigella infection.

overall_design: 3×10^5 Sh2d6+ Tuft cells (EGFP+EpCAM+Siglec-F+), 3×105 Sh2d6− Tuft cells (EGFP−EpCAM+Siglec-F+) and non-Tuft epithelial cells (EpCAM+Siglec-F−) from Sh2d6EGFP mice were sorted by flow cytometer and cells were digested with TRIzol reagent (Invitrogen). RNA quality was monitored using NanoDrop ND-1000. RNA integrity was tested by agarose gel electrophoresis. RNA samples were then assayed with Affymetrix Mouse Transcriptome Array 1.0 (Beijing Cnkingbio Biotechnology).

first: Xiaoxiao

last: Zhu


title: m6A MeRIP-seq of skeletal muscle during innervation and denervation

city: Shenzhen

first: Yuantong

last: Liu

address: 1017 Dongmen Bei Road

department: Spine Surgery

institute: The Second Clinical Medical College, Jinan University

type: Methylation profiling by high throughput sequencing

summary: To assess the m6A methylome during denervation-induced muscle atrophy, the methylated RNA immunoprecipitation sequencing (MeRIP-seq) was performed.

overall_design: Altered m6A-tagged transcript profiles in mouse gastrocnemius (GAS) muscles were measured at 14 days after denervation. Contralateral GAS muscle served as innervation control.


title: 4DNESCX7WHJ1 - sci-RNA-seq on mESCs differentiated to embryoid body

city: Boston

last: DCIC

state: MA

address: 10 Shattuck St

institute: 4D Nucleome - Data Coordination and Integration Center

summary:
Mammalian development is associated with extensive changes in gene expression, chromatin accessibility, and nuclear structure. Here, we follow such changes associated with mouse embryonic stem cell differentiation and X inactivation by integrating, for the first time, allele-specific data obtained by high-throughput single-cell RNA-seq, ATAC-seq, and Hi-C. In differentiated cells, contact decay profiles, which clearly distinguish the active and inactive X chromosomes, reveal loss of the inactive X-specific structure at mitosis followed by a rapid reappearance, suggesting a bookkeeping mechanism. In differentiating embryonic stem cells, changes in contact decay profiles are detected in parallel on both the X chromosomes and autosomes, suggesting profound simultaneous reorganization. The onset of the inactive X-specific structure in single cells is notably delayed relative to that of gene silencing, consistent with the idea that chromatin compaction is a late event of X inactivation. Novel computational approaches to effectively align single-cell gene expression, chromatin accessibility, and 3D chromosome structure reveal that long-range structural changes to chromosomes appear as discrete events, unlike progressive changes in gene expression and chromatin accessibility.

### Competing Interest Statement

The authors have declared no competing interest.

overall_design:
lab: Christine Disteche, UW
award: 1U54DK107979-01
accession: 4DNESCX7WHJ1
submitted_by: Giancarlo Bonora
dataset_label: sci-RNA-seq on mESCs differentiated to embryoid body
contributing_labs: William Noble, UW, Zhijun Duan, UW, Jay Ashok Shendure, UW
experiment_type: sci-RNA-seq
url: https://data.4dnucleome.org/experiment-sets/4DNESCX7WHJ1/
number_of_experiments: 10

experiment: 4DNEXAY3ALVE; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEX2VTS1YZ; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXXCVEEE2; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXCWGVH6G; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEX7A9NPK2; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXPGR1CVZ; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXYO7LG9X; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXT7D5EOI; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXA8OVCDB; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXNPCRAKI; replicate_number: Biorep 1, Techrep 1

Series supplementary files:
***************
genome_assembly: GRCm38
description: A tarball containing processed sci-RNA-seq data.
file name: 4DNFISJGP9HU.tar
file_format: tar
***************
file_type: readme
description: A text file describing the contents and processing steps for the sci-RNA-seq processed data in 4DNFISJGP9HU.
file name: 4DNFIMO8WA45.txt
file_format: txt
***************
file_type: directory tree
description: A text file with a directory tree for the sci-RNA-seq processed data in 4DNFISJGP9HU.
file name: 4DNFIWL392QV.txt
file_format: txt


title: Gene expression data from trastuzumab-hypersensitive clones

city: Salamanca

first: Laura

last: Díaz-Gil

state: SALAMANCA

address: Campus Miguel Unamuno s/n

country: Spain

institute: Instituto de Biología Molecular y Celular del Cáncer

summary: Genes involved in trastuzumab response were identified using transcriptomic data from cells hypersensitive to trastuzumab derived from BT474.

overall_design: RNA from trastuzumab-hypersensitive clone (BTSH) was isolated and cRNA was hybridized to HuGene 2.0 ST microarrays. Raw.CEL files were normalized using Expression Console 1.4 and differential gene expression analysis was performed with Transcription Analysis Console 4.0 and transcriptomic data previously published (GSE119397). Three biological replicates were analyzed.

first: L

first: A

last: Pandiella


title: RNA expression and m5c modification in NSUN2 kncok down CaSki cell

first: Lingfang

last: Wang

state: Zhejiang Province

address: 866 Yuhangtang Road

department: Department of Obstetrics and  Gynecology

institute: Zhejiang University

summary: 5-methylcytosine (m5C) modification ubiquitously occurs on mammalian mRNAs and plays important roles in multiple biological processes. Currently, the role of m5C in cancer initiation and progression is gaining more and more research attention, but the detailed mechanism remains unclear. As an m5C methyltransferase with unique mRNA catalytic activity, NSUN2 was found to be highly expressed in multiple cancers including gastric, bladder, gallbladder, and breast cancers, suggesting NSUN2 might exert oncogenic properties through affecting m5C levels in cancer cells. Therefore, to understand the potential roles of RNA m5C modification in tumorigenesis of cervical cancer, we established NSUN2 stable knockdown CaSki cell, and perform RNA-seq and RNA-BisSeq to figure out the possible pathway involved in cervical cancer development.

overall_design: NSUN2 stable knockdown CaSki cell was established by lentivirus infection. RNA of wildtype cells and NSUN2 stable knockdown CaSki cells were extracted for RNA-seq and RNA bisulfite sequencing measurement.

first: Jian

last: Zhang

first: Yingfeng

last: Su

first: Chih-Hung

last: Hsu


title: 4DNESOUYRIO9 - sci-ATAC-seq on mESCs differentiated to embryoid body

overall_design:
lab: Christine Disteche, UW
award: 1U54DK107979-01
accession: 4DNESOUYRIO9
submitted_by: Giancarlo Bonora
dataset_label: sci-ATAC-seq on mESCs differentiated to embryoid body
contributing_labs: William Noble, UW, Zhijun Duan, UW, Jay Ashok Shendure, UW
experiment_type: sci-ATAC-seq
url: https://data.4dnucleome.org/experiment-sets/4DNESOUYRIO9/
number_of_experiments: 9

experiment: 4DNEXUTXVJNS; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXOSQFCTM; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXXXQ7SNN; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXMJVA3ZW; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXP788IVD; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXOLF62PK; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXOKNIX5B; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXX4XDGPO; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEX55NM5L3; replicate_number: Biorep 1, Techrep 1

Series supplementary files:
***************
genome_assembly: GRCm38
description: A tarball containing processed sci-ATAC-seq data.
file name: 4DNFI3GQKK43.tar
file_format: tar
***************
file_type: readme
description: A text file describing the contents and processing steps for the sci-ATAC-seq processed data in 4DNFI3GQKK43.
file name: 4DNFIEIH3BBX.txt
file_format: txt
***************
file_type: directory tree
description: A text file with a directory tree for the sci-ATAC-seq processed data in 4DNFI3GQKK43.
file name: 4DNFIB8E2QM9.txt
file_format: txt


title: Hippocampal transcriptome analysis following environmental enrichment in a mouse model of fetal alcohol spectrum disorder

city: London

first: Shiva

last: Singh

state: ON

address: 1151 Richmond Street

department: Biology

country: Canada

institute: Western University

summary: Maternal alcohol consumption during pregnancy results in a spectrum of lifelong behavioral and cognitive deficits collectively known as Fetal Alcohol Spectrum Disorders (FASD). FASD is a major health burden in most societies, there is no cure, and the molecular mechanism involved in its development is poorly understood. Human neurodevelopment is a continuum that extends over two decades after birth, with the potential to influence outcomes both prenatally and postnatally. Here, we experimentally investigate if positive postnatal environment enrichment ameliorates behavioral deficits caused by ethanol exposure. Furthermore, we assessed if this modulation is associated with alterations in hippocampal gene expression. To accomplish this, we used a binge model of ethanol exposure followed by environmental enrichment in C57BL/6 mice to generate four groups of animals: (1) control mice raised in standard conditions, (2) mice raised in enriched environments, (3) ethanol-exposed mice raised in standard conditions, and (4) ethanol-exposed mice raised in enriched environments. The environmental enrichment includes larger home cages with more individuals for social interaction, regular exposure to novel items, and access to running wheels. Ethanol exposure results in anxiety-like behavior (light-dark box) as well as learning and memory deficits (Barnes maze) that are at least partially ameliorated by enrichment. Environmental enrichment also improves performance for individuals not exposed to ethanol. Ethanol exposure induces changes in adult hippocampal gene expression (RNA-Seq). Some of the changes in adult hippocampal gene expression following ethanol exposure are reversed by environmental enrichment. The results offer a potential mechanism of behavioral deficits caused by ethanol exposure, including the potential for amelioration after an FASD diagnosis.

overall_design: Hippocampal RNA profiles of adult mice that had been prenatally exposed to alcohol and/or postnatal environmental enrichment as well as non-exposed controls were generated by sequencing, using Illumina HiSeq.

first: Bonnie

last: Alberry

first: Aniruddho

last: Chokroborty Hoque


title: MiRNAome of dry cows transitioned from forage to 65% grain diet

city: Vienna

first: Cátia

last: Pacífico

state: Vienna

address: Veterinaerplatz 1

country: Austria

institute: University of Veterinary Medicine Vienna

type: Non-coding RNA profiling by high throughput sequencing

summary: This study aimed to explore the changes in miRNAome in the rumen epithelium during diet transition from forage to high-grain and the modulation through supplementation with phytogenic feed additives (PHY).

overall_design: Rumen biopsies were collected from 9 ruminally-canulated non-lactating Holstein cows fed a 100% baseline forage diet (FD) and then transitioned to high-grain (HG; 65% concentrate) feeding. Cows were randomly allocated into two groups, 5 control (CON) and 4 supplemented with PHY.

first: Catia

last: Pacifico

first: Susanne

last: Kreuzer-Redmer


title: Bulk RNA-seq profiling of murine endothelial cells in response to pulmonary hypertension

city: Edinburgh

first: Julie

last: Rodor

address: 47 Little France Crescent

department: Centre for Cardiovascular Science

country: United Kingdom

institute: UNIVERSITY OF EDINBURGH

summary: Endothelial cell dysfunction plays a critical role in the development and pathogenesis of pulmonary arterial hypertension (PAH). We aimed to characterize the endothelial cell transcriptomic changes in PAH. We carried out bulk RNA sequencing of lung endothelial cells isolated from an endothelial cell lineage tracing mouse model in control and SU5416/Hypoxia-induced PAH conditions.

overall_design: To study ECs in murine lungs, we used a Cdh5-CreERT2-TdTomato mouse line, in which the EC-specific (Cdh5) expression of TdTomato is inducible with tamoxifen. After a two week wash out period, we exposed the mice to chronic hypoxia for three weeks in combination with weekly subcutaneous injections of SU5416 to induce PAH while Control mice were kept in normoxic condition. RNA extraction and bulk RNA-seq were carried out on 5 Control (b-Cont1-5) and 4 PAH (b-PAH1-4) mice.

first: Shiau-Haln

last: Chen

first: Jessica

last: PScanlon

first: Ana-Mishel

last: Spiroski

first: João

middle: P

last: Monteiro

first: Axelle

last: Caudrillier

first: Alena

last: Shmakova

first: Andrew

last: Baker


title: BET Inhibition Enhances TNF Mediated Anti-Tumor Immunity [RNA-Seq]

city: South San Francisco

first: Simon

middle: J

last: Hogg

state: California

address: 1000 Gateway Boulevard

department: Oncology Discovery Research

institute: AbbVie

summary: Targeting chromatin binding proteins and modifying enzymes can concomitantly affect tumor cell proliferation and survival, as well as enhance anti-tumor immunity and augment cancer immunotherapies. By screening a small molecule library of epigenetics-based therapeutics, BET bromodomain inhibitors (BETi) were identified as agents that sensitize tumor cells to the anti-tumor activity of CD8+ T-cells. BETi modulated tumor cells to be sensitized to the cytotoxic effects of the pro-inflammatory cytokine TNF. By preventing the recruitment of BRD4 to p65-bound cis-regulatory elements, BETi suppressed the induction of inflammatory gene expression, including the key NF-B target genes BIRC2 (cIAP1) and BIRC3 (cIAP2). Disruption of pro-survival NF-B signaling by BETi led to unrestrained TNF-mediated activation of the extrinsic apoptotic cascade and tumor cell death. Administration of BETi in combination with T-cell bispecific (TCB) antibodies increased bystander killing of tumor cells and enhanced tumor growth inhibition in vivo in a TNF-dependent manner. This novel epigenetic mechanism of immunomodulation may guide future use of BETi as adjuvants for immune oncology agents.

overall_design: RNA-sequencing of E0771 and MC38 cells treated with TNF alone or in combination with clinical BET Bromodomain inhibitor RG6146.


title: BET Inhibition Enhances TNF Mediated Anti-Tumor Immunity [ChIP-Seq, ATAC-Seq]

overall_design: ChIP-sequencing of MC38 cells treated with TNF alone or in combination with clinical BET Bromodomain inhibitor RG6146.


title: Transcriptome analysis of dry cows transitioned from forage to 65% grain diet

summary: This study aimed to explore the changes in global gene expression in the epithelial transcriptome during diet transition from forage to high-grain and the modulation through supplementation with phytogenic feed additives (PHY).


title: Rat transcriptomic profiling of liver sinusoidal endothelial cells during chronic liver disease reveals stage-specific secretory signature

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

institute: CIBEREHD

summary: RNAseq was applied to define the transcriptome of primary LSECs from rats with acute liver injury, mild liver fibrosis and advanced chronic liver disease (CLD) (due to CCl4 or thioacetamide administration). Results showed different transcriptomic profile during progression of CLD, and a large number of significant de-regulated genes (1412) were shared in cirrhotic CCl4- and TAA-LSECs (fold-change>1.5 and p-vale<0.05)compared with their respective healthy-LSECs.

overall_design: RNA-seq transcriptomic profiles were derived from liver sinusoidal endothelial cells (LSECs) isolated during chronic liver disease (CLD). Wistar Han rats underwent inhalation exposure to carbon tetrachloride (CCl4) for 2 weeks (n=5), 6 weeks (n=5) or 12-14 weeks (n=6). Healthy LSECs were isolated of Wistar Han animals (n=6). Additionally, RNA-seq was performed from LSECs isolated of healthy Sprague-Dawley rats (n=5) and of TAA-cirrhotic rats (n=5).

first: A

last: Fernandez-Iglesias

first: J

last: Gracia-Sancho


title: Local chromatin context dictates the genetic determinants of the heterochromatin spreading reaction.

city: San Francisco

first: Bassem

last: Al-Sady

address: 513 Parnassus Ave HSW1501

institute: UCSF

summary: Heterochromatin spreading, the expansion of gene-silencing structures from DNA-encoded nucleation sites, occurs in distinct settings. Spreading re-establishes gene-poor constitutive heterochromatin every cell cycle, but also invades gene-rich euchromatin de novo to steer cell fate decisions. How chromatin context, i.e. euchromatic, heterochromatic, or different nucleator types, influences the determinants of this process remains poorly understood. Previously, we documented distinct behaviors of heterochromatin spreading in different contexts using a single-cell heterochromatin spreading sensor (Greenstein et al. 2018). In this work, building on this sensor system, we now genetically identify the factors that positively or negatively alter the propensity of a nucleation site to spread heterochromatin. We find that different chromatin contexts are dependent on unique sets of genes for the regulation of heterochromatin spreading. Further, we find that spreading in constitutive heterochromatin requires Clr6 histone deacetylase complexes containing the Fkh2 transcription factor, while the Clr3 deacetylase is globally required for silencing. Fkh2 acts by recruiting Clr6 to nucleation-distal chromatin sites. Our results segregate the pathways that control lateral heterochromatin spreading from those that instruct DNA-directed assembly in nucleation.

overall_design: ChIP-Seq was performed for H3K9me2 in 5 genotypes. Both ChIP and Control/Input samples are included.


title: Role of BHLHE40 in shaping macrophage inflammatory response

city: Cleveland

first: Ernest

middle: R

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

summary: BHLHE40 is a member of basic helix-loop-helix family transcription factors and highly conserved across mammalian species. Structurally, BHLHE40 consists of an N-terminal basic DNA binding domain, a helix-loop-helix dimerization domain, and a protein interacting orange domain. BHLHE40 is known to regulate a wide variety of essential cellular processes, including cell cycle, cellular proliferation, programmed cell death, cellular development and differentiation, and circadian rhythm. Here we isolated thioglycollate-elicited peritoneal macrophages (PMs) from 3 mice per group (Lyz2cre and Lyz2cre:BHLHE40Fl/Fl).  These cells were stimulated with 100ng/ml LPS for 4 hours. Total RNA was isolated and subjected to RNAseq analyses.

first: Ganapati

last: Mahabeleshwar

first: E


title: ATAD2 maintains the equilibrium between nucleosome assembly and disassembly

city: La Tronche

first: Sophie

last: Rousseaux

address: Bd de la Chantourne

department: IAB

institute: INSERM-UGA

summary: To avoid toxic histone overload, histone deposition and removal must be finely tuned. Following a series of functional studies in human, mouse and S. pombe, we show here that the AAA ATPase ATAD2 is a conserved mediator of histone removal and a regulator of histone deposition. In Atad2 knockout (KO) spermatogenic cells, the late-stage genome-wide eviction of histones and their replacement by protamines are significantly delayed. In S. pombe, deletion of abo1 leads to a dramatic decrease in cell growth, with the appearance of suppressor clones recovering normal growth. Identification of the corresponding suppressor mutations revealed that the causes of cell toxicity are mainly the deregulated activity of the histone chaperone HIRA and histone overload. We also show that, in Atad2 KO mouse ES cells, HIRA and FACT are trapped on nucleosomes at transcription start sites of active genes, resulting in histone overload and abnormal histone deposition on nucleosome-free regions. Overall, these data shed new light on a need for energy-consuming auxiliary factors, such as ATAD2, to maintain a balanced and dynamic histone chaperone basal activity and to avoid a deleterious histone overload.

overall_design: ChIP-seq experiments with HIRA and SSRP1 antibodies in wild type (WT) and ATAD2 KO (KO) embryonic stem (ES) cells

first: Florent

last: Chuffart

first: Tao

last: Wang

last: Barral

first: Denis

last: Puthier

first: Lisa

last: Bargier

first: Saadi

last: Khochbin


title: Transcriptomic profiling of liver sinusoidal endothelial cells during chronic liver disease reveals stage-specific secretory signature

summary: In this study RNAseq was used for studying the transcriptome profile of primary liver sinusoidal endothelial cells (LSECs) isolated from non-lesioned non-tumorous liver tissues (considered as healthy) and from cirrhotic liver explants (ethanol etiology). Results showed different transcriptomic profile between two populations of LSECs with 1374 significant deregulated genes (fold-change>1.5 and p-vale<0.05) in cirrhotic-LSECs compared with healthy-LSECs.

overall_design: RNA-seq transcriptomic profiles were derived from Liver sinusoidal endothelial cell from four cirrhotic patients and five healthy subjects

last: Gracia


title: Single cell RNA-seq profiling of murine endothelial cells in response to pulmonary hypertension

first: Julie

last: Rodor

summary: (1) Rationale: Endothelial cell dysfunction plays a critical role in the development and pathogenesis of pulmonary arterial hypertension (PAH). (2) Objectives: We aimed to characterise the endothelial cell dynamics in PAH at a single cell resolution. (3) Methods: We carried out single-cell RNA sequencing of lung endothelial cells isolated from an endothelial cell lineage tracing mouse model in control and SU5416/Hypoxia-induced PAH conditions. (4) Measurements and Main Results: Endothelial cell populations corresponding to the different lung vessel types could be identified in both control and PAH mice. Differential gene expression analysis revealed novel global and vessel-type specific responses in endothelial cells due to PAH. Global changes included the up-regulation of the major histocompatibility complex class II pathway, supporting a role for endothelial cells in the inflammatory response in PAH. We also identified a PAH response specific to the second capillary EC population, with the up-regulation of genes involved in cell localization and angiogenesis. Comparison with human genetics and transcriptomics data revealed the regulation of four genes with variants associated to PAH and five genes up-regulated in endothelial cells in both human and mouse scRNA-seq. Among them, Aqp1 and Adam15 genes represent promising new candidates to target endothelial dysfunction. Finally, we identified zonation-dependent changes across the arteriovenous axis in PAH using an in-silico cell ordering approach and showed the up-regulation of the Serine/threonine-protein kinase Sgk1 at the junction between the macro- and micro-vasculature. (5) Conclusions: This study uncovers the murine endothelial cell transcriptomics changes in PAH at a high resolution, revealing novel candidates relevant to PAH.

overall_design: (1) Experiment1: To study ECs in murine lungs, we used a Cdh5-CreERT2-TdTomato mouse line, in which the EC-specific (Cdh5) expression of TdTomato is inducible with tamoxifen. After a two week wash out period, TdTomato-positive cells were obtained from the lung of two mice using flow cytometry and analysed using 10X Genomics scRNA-seq (ContA/ContB). (2) Experiment2: To examine EC changes due to pulmonary arterial hypertension (PAH), we used the SuHx model, exposing the Cdh5-CreERT2-TdTomato mice to chronic hypoxia for three weeks in combination with weekly subcutaneous injections of SU5416. ScRNA-seq was carried out for three SuHx mice (PAH1, PAH2, PAH3) and one control mouse that was maintained in normoxia (Cont1).

first: Jessica

last: Scanlon

first: Ana-Mishel

last: Spiroski

first: João

last: Monteiro

first: Axelle

last: Caudrillier

first: Katherine

last: Stewart

last: Shmakova

first: Ross

last: Dobie

first: Beth

last: Henderson

first: Shiau-Haln

last: Chen

first: Neil


title: Ionizing Radiation-induced Acute Damage in the Salivary Gland

status: Public on Sep 23 2021

city: xiamen

first: Qingxiang

last: Gao

address: Xiang'an south way

institute: Xiamen University

summary: Ionizing radiation (IR) – induced salivary gland damage is a common adverse effect in radiotherapy for patients with head and neck cancers. Currently, there is no effective treatment for the resulting salivary gland hypofunction and xerostomia (dry mouth). Here we profiled the acute gene expression change in the mouse submandibular salivary gland, and defined its damage response patterns at the transcriptome level.

overall_design: Mouse submandibular salivary gland was irradiated at 5Gy, and samples were collected as control (T0), and 6h, 24h post irradiation. Total RNAs were extracted for RNA sequencing analysis.

first: Zhicao

last: Yue


title: Impact of ADA2 on human macrophages

first: Zhenghui

middle: G

last: Jiang

address: 3 Blackfan Cir, CLS605

department: Gastroeneterology

institute: Beth Israel Deaconess Medical Center

summary: This study aims to understand the impact of adenosine deaminase 2 (ADA2) on human monocyte-derived macrophages

overall_design: Human CD14/CD16 positive monocytes were isolated from PBMC and differentiated into macrophages in vitro. The cells were then either treated with ADA2 (100 nM) or PBS control.

first: Shilpa

last: Tiwari-Heckler

first: Z


title: Mesenchymal cell type-specific roles of KLF4 in lung fibrosis

city: New Haven

first: Rolando

last: Garcia-Milian

state: CT

address: 333 Cedar St

department: CWML

institute: Yale University

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

overall_design: Refer to individual Series


title: Transcriptomic analysis of cardiomyocyte upon OSKM induction

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: We generated i4F (Heart) mice which has cardiac-specific and doxycycline (DOX) controllable OSKM expression system. Using next generation sequencing (NGS), we analyzed the whole transcriptomic profiles in isolated adult cardiomyocytes from i4F (Heart) mice, which were under different DOX-treatments. We found the i4F (Heart) mice upon 6 days and 12 days DOX their cardiomycytes had remarkable change of transcriptome to be like neonatal and embryonic cardiomyocytes, which exhibited dedifferentiation, significant change in metabolism, and cell-cycle reactivation. While cardiomyocytes showed molecular re-differentiation when DOX withdrawn after 6 days treatment.

overall_design: Total RNA of isolated cardiomocytes were extracted from 12-16 weeks old i4F (Heart) mice. Those mice had different DOX treatments, DOX- (no DOX), DOX6 (6 days of DOX), DOX12 (12 days of DOX), DOX6Water6 (6 days DOX and no DOX for additional 6 days). Two biological replicates were profiled for each cell type.

first: Yanpu

first: Johnny

last: Kim

first: Thomas

last: Braun


title: Single-cell profiling of human bone marrow progenitors reveals mechanisms of failing erythropoiesis in Diamond-Blackfan anemia

first: Deena

last: Iskander

address: Du Cane Road

institute: Imperial College

summary: Ribosome dysfunction underlies the pathogenesis of many cancers and heritable ribosomopathies. Here we investigate how mutations in either ribosomal protein large (RPL) or ribosomal protein small (RPS) subunit genes selectively affect erythroid progenitor development and clinical phenotypes in Diamond-Blackfan anemia (DBA), a rare ribosomopathy with limited therapeutic options. Using single-cell assays of patient-derived bone marrow, we delineated two distinct cellular trajectories segregating with ribosomal protein genotypes: almost complete loss of erythroid specification were observed in RPS-DBA. In contrast, we observed relative preservation of qualitatively abnormal erythroid progenitors and precursors in RPL-DBA. Although both DBA genotypes exhibited a pro-inflammatory bone marrow milieu, RPS-DBA was characterized by erythroid differentiation arrest, whereas RPL-DBA was characterized by preserved GATA1 expression and activity. Compensatory stress erythropoiesis in RPL-DBA exhibited disordered differentiation underpinned by an altered glucocorticoid molecular signature, including reduced ZFP36L2 expression, leading to milder anemia and improved corticosteroid response. This integrative analysis approach identified distinct pathways of erythroid failure and defined genotype-phenotype correlations in DBA. These findings may help facilitate therapeutic target discovery.

overall_design: Directional paired-end bulk RNAseq of CD34-Lin-CD71+GYPA+ erythroblasts FACS-isolated from human bone marrow from healthy controls (n=3) and patients with Diamond- Blackfan anemia (n=3 transfusion-dependent; n=1 transfusion independent and n=1 steroid-dependent)

first: Anastasios

last: Karadimitris


title: The ATP-hydrolyzing ectoenzyme E-NTPD8 attenuates colonic inflammation through regulation of P2X4 receptor-dependent metabolism in myeloid cells [F1347]

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Extracellular adenosine triphosphate (ATP) released by mucosal immune cells and by microbiota in the intestinal lumen elicits diverse immune responses that mediate the intestinal homeostasis via P2 purinergic receptors, while overactivation of the ATP signaling leads to disruption of mucosal immune system linked to pathogenesis of intestinal inflammation. In the small intestine, hydrolysis of luminal ATP by E-NTPD7 in epithelial cells is essential for control of the number of Th17 cells. However, the molecular mechanism underlying regulation of microbiota-derived ATP in the colon is poorly understood. Here, we show that E-NTPD8 is highly expressed in large intestinal epithelial cells and hydrolyzes microbiota-derived luminal ATP. Compared to wild-type mice, Entpd8-/- mice develop more severe DSS-induced colitis. In this context, either depletion of neutrophils and monocytes by injecting with anti-Gr-1 antibody or introduction of P2rx4 deficiency into hematopoietic cells ameliorates colitis in Entpd8-/- mice. Increased level of luminal ATP in the colon of Entpd8-/- mice promotes glycolysis in neutrophils and monocytes through P2X4 receptor-dependent Ca2+ influx, which links to prolonged survival and elevated ROS production in these cells. Together, these results indicate that E-NTPD8 limits intestinal inflammation by controlling metabolic alteration toward glycolysis via P2X4 receptor in myeloid cells.

overall_design: We analyzed colonic myeloid cells with RNA-seq analysis.

first: Hisako

last: Kayama


title: The ATP-hydrolyzing ectoenzyme E-NTPD8 attenuates colonic inflammation through regulation of P2X4 receptor-dependent metabolism in myeloid cells [F1413]

overall_design: We analyzed Gr-1+ CD11b+ cells with RNA-seq analysis.


title: The ATP-hydrolyzing ectoenzyme E-NTPD8 attenuates colonic inflammation through regulation of P2X4 receptor-dependent metabolism in myeloid cells


title: Single cell RNA sequencing to identify the PDGFR-β expressing lung cells

summary:
Purpose:Single cell RNA sequencing to identify PDGFR-beta expressing cells in the normal adult lung
Methods: Adult Pdgfrb-CreERT2, ROSA26R(Zs/+) mice were induced with tamoxifen (1mg/day for 5 days) and rested for 5 days. Lungs were then harvested and prepared to obtain single cell suspension. Live Zs+ and Zs- cells were isolated by FACS and hash-tagged. Cells were then pooled together in PBS with 0.04% bovine serum albumin and subjected to library preparation and DropSeq. scRNA-seq data was processed with Cell Ranger v 3.1.0. Reads were aligned to a modified version of the mouse transcriptome mm10, including the sequence for the gene ZsGreen1. The top cell barcodes selected by Cell Ranger were utilized for downstream analysis.
Results: In lung mesenchymal cells, populations of fibroblasts and pericytes express Pdgfr-beta.

overall_design:
Lung PDGFR-beta+ cells (Zs+ cells isolated from tamoxifen-induced Pdgfrb-CreERT2, ROSA26R(Zs/+)mice) and PDGFR-beta- cells (Zs- cells) were isolated by FACS and subjected to 10X Genomics single cell 3’ RNA-seq libraries construction and sequencing.
Both PDGFR-beta+ and PDGFR-beta- were included in this sample. Pdgfrb-beta status was identified based on the expression of Zs transcript (and Pdgfrb transcript) in the data.

first: Rachana

last: Chandran

first: Daniel

last: Greif


title: Transcriptional profiling of HIV-negative participants before and after vaccination with an DNA/rAd5 vaccine.

city: Chicago

first: Slim

last: Fourati

state: Illinois

address: 300 E Superior St

department: Medicine

institute: Northwestern University

summary: A safe and effective vaccine for the prevention of human immunodeficiency virus type 1 (HIV-1) infection is a global priority. Tthe efficacy of a DNA prime–recombinant adenovirus type 5 boost (DNA/rAd5) vaccine regimen was testd in persons at increased risk for HIV-1 infection in the United States. The DNA/rAd5 vaccine regimen did not reduce either the rate of HIV-1 acquisition or the viral-load set point in the population studied. System biology analysis, including RNA-sequencing, was used to identify markers of risk of HIV-1 acquisition.

overall_design: Peripheral blood mononuclear cells were collected before and after vaccination with the DNA/rAd5 vaccine in  47 HIV-negative participants. B cells and Monocytes were flow-sorted from the peripheral blood mononuclear cells. RNA was extracted from 5000 cells and sequenced to determine their transcriptomic profiles. In total, the dataset comprises of 221 samples.

first: Jianfei

last: Hu

middle: C

last: Douek

first: Krystelle

last: Nganou-Makamdop


title: Altered mRNA expression of cultured dorsal root ganglia neurons at different times of rat

city: Nantong

first: Lili

last: Zhao

address: 19 Qixiu

institute: Nantong university

summary: To explored  the altered genes during the axon regeneration of rat dorsal root ganglia neurons, we utilized Gene Expression Array to find out the altered expression of genes in cultured DRG neurons at different times. When we digest the cells from rat DRGs with enzymes, we only get the cell bodies of neurons without axons. During the axons re-growth after the neurons planted, it must be amount of genes expression will changed. However, we still not fully understand which genes will changed and the function of these genes. In addition, this cell model could mimic the regeration of sciatic nerve after injure in vivo, which is still a challenge  in clinical.

overall_design: At 0h, 1.5h, 3h, 6h, 12h, 18h, 24h, 30h, 36h after neurons planted, the total RNA was isolated from these cells for Gene Expression Array. Three independent experiments were performed at each time point.

first: Zhao

last: lili

first: Zhou

last: songlin


title: U2AF1 is a haplo-essential gene required for hematopoietic cancer cell survival in mice

city: St Louis

first: Matthew

last: Walter

state: MISSOURI

address: 660 South Euclid Avenue

department: Oncology

institute: Washington University School of Medicine

summary: Somatic mutations in the spliceosome gene U2AF1 are common in patients with myelodysplastic syndromes. U2AF1 mutations that code for the most common amino acid substitutions are always heterozygous, and the retained wild-type allele is expressed, suggesting that mutant hematopoietic cells may require the residual wild-type allele to be viable and cause disease. We show that hematopoiesis and RNA splicing in U2af1 heterozygous knock-out mice was similar to control mice, but that deletion of the wild-type allele in U2AF1 (S34F) heterozygous mutant expressing hematopoietic cells (i.e., hemizygous mutant) was lethal. These results confirm that U2AF1 mutant hematopoietic cells are dependent on the expression of wild-type U2AF1 for survival in vivo and that U2AF1 is a haplo-essential cancer gene. Mutant U2AF1 (S34F) expressing cells were also more sensitive to reduced, but not absent, expression of wild-type U2AF1 than non-mutant cells. Furthermore, mice transplanted with leukemia cells expressing mutant U2AF1 had significantly reduced tumor burden and improved survival after the wild-type U2af1 allele was deleted compared to when it was not deleted. These results suggest that selectively targeting the wild-type U2AF1 allele in heterozygous mutant cells could induce cancer cell death and be a therapeutic strategy for patients harboring U2AF1 mutations.

overall_design: Mouse E14.5 fetal liver cells or adult bone marrow were harvested and RNA was then isolated from sorted hematopoietic progenitor cells (Lin- cKit+ Sca1-) using the NucleoSpin RNA Plus XS kit (Macherey-Nagel), per manufacturer’s instructions. The RNA-sequencing libraries were prepared using KAPA RNA Hyper Prep Kit with RiboErase, per manufacturer’s protocol. After amplification, ~300 bp fragments were sequenced on Illumina NovaSeq 6000, generating 2 x 150bp paired-end reads. The reads were then mapped using HISAT2 (version 2.1.0) against the GRCm38 version of the mouse genome from Ensembl consortium. Differentially expressed genes were identified using DESeq2, and splicing event classification was performed using rMATS (version 4.1.0). For Fetal liver samples due to experimental limitations few samples have potential confounding batch effects that may impact differential gene expression. Therefore, we focused using samples within each batch for splicing analysis only.

first: Brian

last: Wadugu

first: Sridhar

last: Nonavinkere Srivatsan

first: Amanda

last: Heard


title: Transcriptomic profiling of human peripheral blood samples collected three days or two weeks after the primary RV144 ALVAC/gp120 vaccine series

city: Silver Spring

first: Rasmi

last: Thomas

state: MD

address: 503 Robert Grant Avenue

department: MHRP

institute: Walter Reed Army Institute of Research

summary: We previously showed in NHP studies that a protective gene signature that was enriched in uninfected monkeys after Ad26/gp140 vaccination also associated with higher magnitude of ADCP (Ehrenberg et al., 2019). In the RV144 human trial a number of immunological parameters were previously measured as part of the immune-correlates analysis, but not ADCP. The RV306 immunogenicity trial that employed a similar prime boost RV144 vaccine regimen with additional late boosts provided us with a unique opportunity to test if the gene signature was associated with ADCP (Pitisuttithum et al., 2020). We generated transcriptome-wide gene expression data from peripheral blood two weeks after the RV144 vaccine regimen (prior to the additional boosts) and assessed for enrichment of the gene signature with the magnitude of ADCP measured at the same timepoint in 24 participants. The gene signature with 118 enriched genes was significantly associated with higher magnitude of ADCP (NES=3.0, P<0.001). Using the same geneset, 93 genes were found to be enriched in a subset of overlapping participants (N=21), where samples were collected 3 days after the RV144 immunizations (NES=2.5, P<0.001).

overall_design: The RV306 vaccine trial was conducted in Thailand and all participants received the primary RV144 ALVAC/gp120 vaccine series, with additional late boosts assigned to specific groups (Pitisuttithum et al., 2020). Bulk RNA-seq was performed in 24 participants two weeks after the RV144 vaccine regimen (week 26). Additionally, RNA-seq was also performed 3 days after the same primary endpoint in a subset of the participants (N =21).

first: Shida

last: Shangguan

first: Aviva

last: Geretz


title: Vemurafenib acts as molecular switch in Langerhans Cell Histiocytosis

first: Sebastian

last: Eder

address: Zimmermannplatz 10

institute: Children's Cancer Research Institute

summary: Langerhans cell histiocytosis (LCH) is a neoplasm marked by the accumulation of CD1a+CD207+ cells. It is most commonly driven by a somatic activating mutation in the BRAF kinase (BRAFV600E). Multisystem disease with risk-organ involvement requires intensive chemotherapy, making BRAF-inhibitors an attractive option. Here, we present a comprehensive analysis of the course of an LCH patient treated with the combination of vemurafenib with salvage chemotherapy who achieved complete clinical and molecular remission. We conclusively show that there is no relationship between blood-BRAF levels and clinical presentation during treatment with vemurafenib, but that vemurafenib leads to a fast, efficient, but reversible inhibition of clinical manifestations of high-risk LCH such as cytopenia, fever, and hypoproteinemia. In line, serum levels of inflammatory cytokines exactly mirror vemurafenib administration. Genotyping for the BRAFV600E mutation shows its presence in multiple hematopoietic cell types, including NK cells and granulocytes. Single-cell transcriptome analysis of peripheral blood and bone marrow cells at time of diagnosis and during treatment indicate that RAF-inhibition abrogates the expression of inflammatory cytokines previously implicated in LCH. Together, our data suggest that while the CD1a+CD207+ histiocytes are the hallmark of LCH, other BRAF-mutated cells themselves contribute significantly to morbidity in patients with multisystem LCH.

overall_design:
Single-cell RNA sequencing of peripheral blood and bone marrow cells at time of diagnosis and during RAF-inhibition

>>>Submitter states that raw data are unavailable due to patient privacy concerns<<<

first: Raphaela

last: Schwentner

first: Philipp

last: Ben Soussia

first: Giulio

last: Abagnale

first: Florian

last: Halbritter

first: Milen

last: Minkov

first: Andishe

last: Attarbaschi

first: Caroline

last: Hutter


title: Cellular fractionation reveals transcriptome responses of human fibroblasts (MRC5_VA cells and CS1AN cells) to UV-C irradiation

status: Public on Sep 22 2021

city: Guangzhou

first: Yuming

last: Wang

state: Guangdong

address: Room 512, Anatomy Building

department: School of Basic Medical Science

institute: Guangzhou medical university

summary: Cells activate a multifaceted DNA damage response to remove transcription-blocking DNA lesions, The genome-wide reduction of RNA synthesis and the paradoxical continuous loading of RNAP II at initiation sites is still poorly understood. Uncovering how dramatic changes to the transcriptional program contribute to TC-NER (transcription-coupled nucleotide excision repair) comprises one of the most fascinating frontiers in DNA repair research. Here we examined UV-induced gene regulation in human fibroblasts by performing RNA-seq with fractionated chromatin-associated and cytoplasmic transcripts. This approach allowed us to separate the synthesis of nascent transcripts from the accumulation of mature RNAs. In addition to documenting the subcellular locations of coding transcripts, our results also provide a high-resolution view of the transcription activities of noncoding RNAs in response to cellular stress. At the same time, the data showed that vast majority of chromatin-enriched DNA damage response transcripts are cis-acting. Distinct from coding genes that transcripts with shorter length are prefered to be recovered first, repression of lncRNA transcription after UV exposure is inactivated first on noncoding transcripts with longer length. This work provides an updated framework for cellular RNA organization in response to stress and may prove useful in understanding how cells respond to transcription-blocking DNA damage.

overall_design: MRC5_VA cells and CSB-deficient CS1AN cells were either left untreated as control or treated with 10 J/m2 of UV-C irradiation, followed by recovery for 30 minutes, 3 or 24 hours. Cellular fractionation was performed to isolate total RNA from cytoplasm and chromatin extracts.

first: Jiena

last: Liu

first: Zhenzhen

last: Wu

first: Jin

last: He


title: Transcriptome analysis of Pará rubber tree (Hevea brasiliensis) seedlings under ethylene stimulation

city: Tsukuba

first: Nobutaka

last: Mitsuda

state: Ibaraki

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

institute: National Institute of Advanced Industrial Science and Technology

summary: Nutural rubber (NR) production, latex is harvested by periodical tapping of the trunk bark. Ethylene enhances and prolongs latex flow and latex regeneration. Ethephon, which is an ethylene-releasing compound, applied to the trunk before tapping usually results in a 1.5- to 2-fold increase in latex yield. We investigated gene expression in response to ethephon treatment using Pará rubber tree seedlings as a model system. After ethephon treatment, 3,270 genes showed significant differences in expression compared with the mock treatment. Genes associated with carotenoids, flavonoids, and abscisic acid biosynthesis were significantly upregulated by ethephon treatment, which might contribute to an increase in latex flow. Genes associated with secondary cell wall formation were downregulated, which might be because of the reduced sugar supply. Given that sucrose is an important molecule for NR production, a trade-off may arise between NR production and cell wall formation for plant growth and for wound healing at the tapping panel.

overall_design: Ethrel-induced genes in Para rubber tree are monitored for 48 hours after induction in time-course manner.

first: Yoshimi

last: Nakano

first: Kohei

last: Ide

first: Teppei

last: Mori

first: Farida

last: Rosana Mira

first: Syofi

last: Rosmalawati

first: Norie

last: Watanabe

first: Kaoru

last: Suzuki


title: Expression profile of microenvironment of morphological structures in breast cancer

city: Tomsk

first: Sofia

middle: Yuryevna

last: Zolotaryova

address: pereulok Kooperativny, 5

country: Russia

institute: Cancer Research Institute Tomsk NRMS

summary: The aim of this work is to compare the expression profiles of the microenvironment of various morphological structures of luminal breast cancer obtained by laser microdissection. For this, sections of primary breast carcinoma were stained according to the RNA-preserving protocol, fragments of the stroma around alveolar, trabecular, solid structures and single tumor cells were isolated using a laser capture microdissection, and then RNA-sequencing was performed using Illumina NextSeq500. Our study presents the first analysis of DEGs and activated signaling pathways of the microenvironment of various morphological structures of breast cancer.

overall_design: Gene expression profiles in cells located in the closest microenvironment to the morphological structures of breast cancer

first: Liubov

last: Tashireva

first: Tatiana

last: Gerashchenko

middle: Y

last: Zolotareva

first: Evgeny

middle: V

last: Denisov

first: Vladimir

middle: M

last: Perelmuter


title: ChIP-seq facilitates the quantitative analysis of Rvb proteins' enrichment on the genome during stress

city: La Jolla

first: Brian

middle: Matthew

last: Zid

address: 9500 Gilman Drive

department: Chemistry and Biochemistry

institute: University of California San Diego

summary: The goals of this study are to quantitatively analyze the enrichment of Rvb1/Rvb2 on the yeast genome during glucose starvation. The ChIP-seq files were generated from 2 biological replicates of Rvb1’s immunoprecipitation (IP), Rvb2-IP, and Pgk1-IP in 10-min glucose starved yeast cells, respectively, using NextSeq 500 SR 75. The sequence reads that passed quality filters were analyzed by calculation of the read counts on 2 regions: -500 bp to TSS and TSS to +500 bp. Using an optimized data analysis workflow, we found Rvb1/Rvb2’s enrichment peaks and that they are significantly more enriched on the Class II alternative glucose metabolism promoters than Class I heat shock promoters.

overall_design: Rvb1-IP, Rvb2-IP and Pgk1-IP in 10-min glucose starved cells

first: Yang

last: Chen


title: Single-cell deconvolution of colon organoids exposed to carcinogens reveals novel insights into the early molecular events defining the role of smoking in colorectal cancer

city: Charlottesville

first: Matthew

last: Devall

state: Virginia

address: 1335 Lee Street

institute: University of Virginia

summary: Here, we used bulk RNA-seq data derived from healthy colon organoids (un)exposed to carcinogen. Through the use of external single cell RNA-seq data, we estimate changes in cell composition. We extend this analysis by controlling for cell composition and performing WGCNA to identify modules of co-expression differentially affected by carcinogen treatment in colon organoids.

overall_design: Analysis of the effects of carcinogen treatment on gene expression in colon organoids

first: Casey

last: Graham

first: Devall

last: Matthew


title: LncRNA HOXA-AS2 regulates microglial polarization via recuitment of PRC2 and epigenetic modification of PGC-1α expression

city: Shanghai

first: Yi

last: Zhang

address: Ruijin er road

institute: Ruijin hospital

summary: We profiled the expressioon of lncRNAs in the peripheral blood mononuclear cells (PBMCs) of PD patients and healthy controls. the enrichment of lncRNAs from PBMCs using Arraystar Human lncRNAs chip (Arraystar).

overall_design: The experiment is divided into two groups: healthy controls and PD patients. PBMCs were collected and lncRNAs chips were then performed by Arraystar Human lncRNAs chip (Arraystar).

first: Xiaodong

last: Yang

first: Qin

last: Xiao


title: Small noncoding RNA Expression Following Respiratory Syncytial Virus or Measles Virus Infection of Neuronal Cells

city: Athens

first: Ralph

last: Tripp

state: GA

address: 113B, Animal Health Research Center

department: Department of Infectious Diseases

institute: University of Georgia

summary: In this dataset, we identify microRNAs and other ncRNAs in neuronal (SHSY5Y) cells following a 12h or 24h infection with Respiratory Syncytial Virus (RSV) or Measles virus (MeV) relative to mock treated neuronal cells

overall_design: Neuronal cells (SHSY5Y) were infected with RSV A2 / MeV Dublin-3267 strain for 12h or 24h in triplicate. Total RNA was isolated from mock-treated or infected cells, fractionated into small RNA   and sequenced on an Illumina MiSeq

first: Abhijeet

last: Bakre

first: Catherine

last: Duffy

first: Sara

last: Cosby


title: Altered miRNA expression of cultured dorsal root ganglia neurons at different times of rat

first: Lili

last: Zhao

summary: To explored  the function of miRNAs during the axon regeneration of rat dorsal root ganglia neurons, we utilized miRCURYTM LNA Array (v.18.0) to find out the altered expression of miRNAs in cultured DRG neurons at different times. When we digest the cells from rat DRGs with enzymes, we only get the cell bodies without axons. During the axons re-growth after the neurons planted, it must be amount of gene and miRNAs will changed. However, we still not fully understand which miRNAs and mRNA will changed and the function of these miRNAs and mRNAs. In addition, this cell model could mimic the regeration of sciatic nerve after injure in vivo, which is still a challenge  in clinical.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: At 0h, 1.5h, 3h, 6h, 12h, 18h, 24h, 30h, 36h after neurons planted, the total RNA was isolated from these cells for miRNA and mRNA array respectively. Three independent experiments were performed at each time point.

first: Zhao

last: lili

first: Zhou

last: songlin


title: A Runx1-enhancer element eR1 identified lineage restricted mammary luminal stem cells

city: Singapore

first: Yoshiaki

last: Ito

state: Select...

address: 14 Medical Drive #12-01

country: Singapore

institute: National University of Singapore

summary: Mammary gland homeostasis is maintained by adult tissue stem-progenitor cells residing within the luminal and basal epithelia. Dysregulation of mammary stem cells is a key mechanism for cancer development. However, stem cell characterization is challenging because reporter models using cell-specific promoters do not fully recapitulate the mammary stem cell populations. We previously found that a 270-basepair Runx1 enhancer element, named eR1, marked stem cells in the blood and stomach. Here, we identified eR1 activity in a rare subpopulation of the ERα-negative luminal epithelium in mouse mammary glands. Lineage-tracing using an eR1-CreERT2 mouse model revealed that eR1+ luminal cells generated the entire luminal lineage and milk-secreting alveoli – eR1 therefore specifically marks lineage-restricted luminal stem cells. eR1-targeted-conditional knockout of Runx1 led to the expansion of luminal epithelial cells, accompanied by elevated ERα expression. Our findings demonstrate a definitive role for Runx1 in the regulation of the eR1-positive luminal stem cell proliferation during mammary homeostasis. Our findings identify a mechanistic link for Runx1 in stem cell proliferation and its dysregulation in breast cancer. Runx1 inactivation is therefore likely to be an early hit in the cell-of-origin of ERα+ luminal type breast cancer.

overall_design: Examinination of RNA expression profiles in CD24high/CD29low luminal epithelial cells and  CD24low/CD29high basal epithelial cells from mammary gland of wild type mice.

first: Junichi

last: Matsuo

first: Naing

middle: N

last: Mon

first: Daisuke

last: Douchi

first: Akihiro

last: Yamamura

first: Madhura

last: Kulkarni

first: Dede

last: Heng

first: Sabirah

first: Napat

last: Nuttonmanit

first: Ying

last: Li

first: Henry

first: May

last: Lee

first: Wai

last: Tam

first: Motomi

last: Osato

first: Linda

last: Chuang


title: EVs MSC miRNA-seq

city: Valencia

first: Imelda

last: Ontoria-Oviedo

address: Avda Fernando Abril Martorell 106

department: Regeneration and Heart transplantation Unit

institute: Instituto de Investigación Sanitaria La Fe

summary: The goal of this project was to analyze the EVs cargoes. EVs were isolated from dental pulp mesenchymal stem cells.

overall_design: EVs were isolated by serial ultracentrifugation method from dental pulp mesenchymal stem cells. Two samples were used for miRNA-seq

first: Pilar

last: Sepúlveda

first: Rafael

last: Sánchez-Sánchez

first: Marta

last: Gómez-Ferrer

first: Akaitz

last: Dorronsoro


title: Comparative transcriptome analysis of different root types of a salinity sensitive rice cultivar under salinity stress

city: Nagoya

first: Joyce

last: Cartagena

address: Furo-cho, Chikusa-ku

institute: Nagoya University

summary: Changes in the gene expression during exposure to salinity stress were compared among nodal roots, S-type lateral roots, and L-type lateral roots.

overall_design: Using RNA sequencing, key genes involved in lateral root development under salinity stress conditions were identified.


title: Silencing branched-chain ketoacid dehydrogenase kinase exacerbates doxorubicin induced cytotoxicity in triple-negative breast cancer cells

city: Saint John

first: Thomas

last: Pulinilkunnil

state: New Brunswick

address: 100 Tucker park road

department: Biochemistry and Molecular Biology

institute: Dalhousie University

summary: TO BE FILLED IN WITH ABSTRACT

overall_design: MDA-MB-231 cells were transfected with either of two siRNA’s targeting BCKDK (n=3 for each siRNA) or a non-targeting control (n=4) and cultured for 48 h before cells were harvested and RNA extracted using the Qiagen RNeasy mini kit according to the manufacturer’s instructions.

first: Dipsikha

last: Biswas

first: Logan

last: Slade

first: Luke

last: Duffley

first: Neil

last: Mueller

first: Khoi

middle: T

last: Dao

first: Angella

last: Mercer

first: Yassine

last: El Hiani

first: Petra

last: Kienesberger


title: CircGLIS3 promotes high-grade glioma invasion via modulating Ezrin phosphorylation

first: Yan

last: Li

address: Industrial Road No.253, Guangzhou, Guangdong, 510282, China

department: Department of Neurosurgery

institute: Zhujiang Hospital

summary: High-grade glioma is highly aggressive and malignant, resistant to combined therapies and easy to relapse. A better understanding of circRNA biological function in high-grade glioma might contribute to the therapeutic efficacy. Here, a circRNA merely up-regulated in high-grade glioma, circGLIS3 (hsa_circ_0002874, originating from exon 2 of GLIS3), was validated by microarray and qRT-PCR. Functional experiments uncovered that up-regulation of circGLIS3 promoted glioma cell migration and invasion, and showed aggressive characteristics in tumor-bearing mice. Fluorescence in situ hybridization, RNA pull-down, RNA immunoprecipitation and immunohistochemical staining showed that circGLIS3 could promoted Ezrin T567 phosphorylation. Further investigation showed that circGLIS3 could be excreted by glioma through exosomes and induced endothelial cells angiogenesis. This study indicates that circGLIS3 is up-regulated in high-grade glioma and contributes to the invasion and angiogenesis of glioma via promoting Ezrin T567 phosphorylation.

overall_design: mRNA profiles of cell line U251 after transfected with sh-circGLIS3 or sh-NC lentivirus

first: Yiquan

last: Ke

first: Jiansheng

last: Chen


title: Screening and identification of differentially expressed microRNAs in diffuse large B-cell lymphoma based on microRNA microarray

city: Urumqi

first: Xinxia

state: Xinjiang

address: The First Affiliated Hospital of Xinjiang Medical University

department: Department of Pathology

summary: to screen and identify differentially expressed microRNAs (miRNAs) between diffuse large B-cell lymphoma (DLBCL) and control (lymph node reactive hyperplasia, LRH) groups, investigate whether miRNAs associated with DLBCL and could serve as potential therapeutic targets.

overall_design: Five DLBCL experimental samples and 5 control samples were obtained from fresh tissues. The exclusion criteria were expressed as follows: patients with other lymphoid diseases and patients undergoing chemical treatment. Firstly, fresh samples were analyzed using microRNA microarray to identify differentially expressed miRNAs. Next, three databases (Targetscan, microRNAorg, PITA) were used to intersection predict the potential target gene of the 204 differential miRNAs and performed Venn diagram of the results. Then, target genes of differential miRNAs were performed by Gene ontology (GO) and Kyoto Encyclopedia of Gene and Genome (KEGG) pathway analysis. Finally, to validate the microRNA microarray data, we performed Real-time reverse transcription PCR (qRT-PCR) for eight differentially expressed miRNAs (miR-193a-3p, miR-19a-3p, miR-19b-3p, miR-370-3p, miR-1275, miR-490-5p, miR-630 and miR-665) using DLBCL and LRH fresh samples.

first: Hai-Xia

last: Gao


title: Altered miRNA and mRNA expression of cultured dorsal root ganglia neurons at different times of rat

first: Lili

last: Zhao

address: 19 Qixiu

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

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

overall_design: Refer to individual Series


title: RNA-sequencing reveals a gene expression signature in skeletal muscle of a mouse model of age-associated post-operative functional decline

city: Greenville

first: Weihua

last: Huang

state: North Carolina

address: 600 Moye Blvd, Brody 7S-24

department: Pathology

institute: East Carolina University

summary: This study aimed to characterize the effects of laparotomy on post-operative physical function and skeletal muscle gene expression in C57BL/6N mice at 3, 20 and 24 months of age to investigate late-life vulnerability and resiliency to acute surgical stress. Pre- and post-operative physical functioning were assessed by forelimb grip strength and motor coordination on the accelerating rotarod. RNA sequencing of soleus muscles collected on post-operative day 5 (POD 5) showed that laparotomy induced age-associated differential gene expression and canonical pathway activation with the greatest effects in the youngest mice. The 24-month-old mice were stratified into low functioning (LF) and high functioning (HF) groups based on their baseline motor performance on the accelerating rotarod. RNA-sequencing showed 224 and 228 differentially expressed genes (DEGs) for HF and LF, respectively, compared to their respective controls. Only 21 DEGs were observed in both groups. We conclude that pre-operative performance on the accelerating rotarod correlates with differences in skeletal muscle gene expression, which may contribute to the differences in functional outcomes post-operatively in HF and LF mice. These findings demonstrate a mouse model of laparotomy which recapitulated some features of post-operative skeletal muscle decline in older adults following surgery, and identified age-associated, laparotomy-induced molecular signatures in skeletal muscles.

overall_design: 24 soleus muscle samples from C57BL/6N male mice were analyzed by RNA-sequencing. Muscles were collected from the laparotomy groups and age matched control groups 5 days post laparotomy surgery. 6 samples (3 replicates for control and 3 replicates for laparotomy) were analyzed per age group for the 3-month-old and 20-month-old groups. Two groups of 24-month-old mice were analyzed. They were designated as 24-month-old low functioning (LF) and 24-month-old high functioning (HF) groups based on the animal’s performance on the accelerating rotarod. Both 24-month-old groups contained 6 samples, 3 replicates for control and 3 replicates for laparotomy. For all groups the expression levels for the laparotomy group was compared to control group.

first: Fred

last: Ko

first: Samantha

middle: L

last: Asche-Godin


title: Pulmonary infection induces scarred lipidome influencing response to unrelated challenge

city: Hamilton

first: Craig

last: Martens

state: MT

address: 903 S. 4th St

department: DIR

institute: NIAID

summary: Resolution of infection results in development of trained innate immunity which is typically beneficial for the host in defense against unrelated secondary infection. Epigenetic changes underlie the establishment of trained innate immunity therefore host metabolism and this response are intimately linked. However, little is known regarding the influence of lipids on the development and function of trained immunity. Utilizing two models of pulmonary bacterial infection combined with multi-omic approaches, we identified persistent, pathogen-specific changes to the lung lipidome that correlated with differences in the trained immune response. Further, we establish the specific cellular populations in the lung that contribute to this altered lipidome. Together these results expand our understanding of the pulmonary trained innate immune response and the contributions of host lipids in informing that response.

overall_design: Mice were inoculated intranasally with 1X10e5 CFU of Bordetella pertussis D420, 150 CFU of f. tularensis subspecies holarctica Live Vaccine Stratin (LVS), or PBS only. Whole lungs were harvested and digested into single cell suspensions for analysis using the 10X Genomics V.2 3' sequencing kit.

first: Lydia

last: Roberts

first: Benjamin

last: Schwarz

first: Emily

last: Speranza

first: Ian

last: Leighton

first: Tara

last: Wehrly

first: Sonja

last: Best

first: Catharine

last: Bosio


title: KDELR2 promotes breast cancer proliferation via HDAC3-mediated cell cycle progression

city: Hefei

first: haoran

last: wei

state: Anhui

address: University of Science & Technology of China, 443 Huangshan Road, Hefei, Anhui

institute: ustc

summary: Epigenetics is critical for cell fate decision and contributes greatly to cancer initiation and development. However, the underlying mechanisms are still largely elusive, thus impeding the effective targeting of histone deacetylases (HDACs) for clinical cancer therapy. Here, We used RNA-seq to study potential targets of HDAC inhibitors for breast cancer therapy. And we performed RNA-seq assays in the MDA-MB-231 cell line treated separately with three HDAC inhibitors TSA, TDPA, FK228.

overall_design: MDA-MB-231 cells were treated separately with three HDAC inhibitors TSA, TDPA, FK228 for 48 hours. Total RNA was extracted using TRIzol Reagent (Invitrogen-Life Technologies, Waltham, Massachusetts, USA) following the manufacturer’s instructions. The following sequencing work using these RNA samples were performed on the BGISeq500 platform (BGI-Shenzhen, Shenzhen, Guangdong, China) by BGI-Shenzhen (Shenzhen, Guangdong, China).

first: Haoran

last: Wei


title: Transcriptome Analysis of treated cells in Philadelphia Chromosome-Like Acute Lymphoblastic Leukemia

city: Philadelphia

first: Ruitao

last: Zhang

state: PA

address: 2930 Chestnut St. Apt. 1709-B

department: Pediatrics

institute: Children's Hospital of Philadelphia

summary: To elucidate the transcriptomic effects of targeted therapy on Ph-like ALL cells, we performed RNA sequencing of the three Ph-like cell lines treated with venetoclax, TKI, or both drugs in combination for 72 hours. This allowed us to analyze differentially expressed genes and global transcriptomic shifts after inhibitor therapy in several Ph-like ALL models.

overall_design: Differential gene expression comparing vehicle, single agent, or combined venetoclax and tyrosine kinase inhibitor treatment in Ph-like ALL cell lines

first: Yang-Yang

last: Ding

first: Kai

last: Tan