title: HSV-1 exploits host heterochromatin for egress [RNA-seq]

city: Seattle

first: Daphne

last: Avgousti

state: WA

address: 1100 Fairview Avenue North C1-201

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

summary: Herpes simplex virus replicates and forms progeny in the nucleus where it must overcome host chromatin to establish a successful infection. During lytic infection, newly formed viral capsids navigate through heterochromatin channels at the nuclear periphery to egress out of the nucleus. In uninfected cells, specific histone marks such as trimethylation on histone H3 lysine 27 (H3K27me3) and the histone variant macroH2A1 delineate heterochromatin regions, or repressed chromatin, that are predominantly located in the nuclear periphery. We examined these markers during HSV-1 lytic infection in primary cells and discovered a striking increase in the levels of macroH2A1 and H3K27me3. Here, we demonstrate that the loss of macroH2A1 results in significantly lower viral titers but does not impair viral transcription, protein production, or replication. By inhibiting the deposition of H3K27me3 by EZH2, we further show that reduction of H3K27me3 also leads to a significant decrease in viral titers. Through chromatin profiling via Cleavage Under Targets and tagmentation (CUT&Tag) of macroH2A1 and H3K27me3, we define the specific chromatin regions that change dynamically during HSV-1 lytic infection and show that regions with increased macroH2A1 and H3K27me3 correlate with decreased host transcription as measured by RNA-seq. Furthermore, we find by electron microscopy that loss of macroH2A1 results in reduced heterochromatin at the nuclear periphery and significantly more viral capsids trapped in the nuclear compartment. Using both high and low shedding clinical isolates of HSV-1, we similarly find that HSV-1 titers are significantly reduced in the absence of macroH2A1. Our work demonstrates that HSV-1 takes advantage of the dynamic nature of host heterochromatin formation during infection for efficient viral egress from the nuclear compartment.

overall_design: mRNA sequencing during lytic Herpes Simplex Virus-1 infection in human foreskin fibroblasts knocked out for histone variant macroH2A1 and wild-type human foreskin fibroblasts

first: Hannah

middle: C

last: Lewis

first: Laurel

last: Kelnhofer-Millevolte

first: Mia

middle: R

last: Brinkley

last: Arbach

first: Edward

last: Arnold

first: Srinivas

last: Ramachandran


title: MiRNA array analysis of VMRC-LCD cells following ASCL1 knockdown function.

status: Public on Jul 01 2023

city: Durham

first: Naoya

last: Miyashita

state: NORTH CAROLINA

address: 307 Research Drive Nanaline Duke Building Room 353

country: USA

institute: Duke university

summary:
To investigate the function of ASCL1 in ASCL1-positive lung adenocarcinoma, we established VMRC-LCD cell line in which the target gene has been knocked down by siRNA.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different cells.

overall_design: VMRC-LCD cells were trasfected with siRNAs for ASCL1, and RNA-sequencing was performed ugsing Illumina HiSeq. MiRNA array was performed using Affymetrix GeneChip® miRNA 4.0 Array. VMRC_LCD cells were tranfected with ASCL1 siRNA, and miRNA array was performed ugsing Illumina HiSeq.  derivatives (siASCL1_#1 and siASCL1_#2).

first: Takayoshi

last: Enokido

first: Akira

last: Saito


title: effect of bergapten gel on IMQ mice back skin

city: Shanghai

first: Shengjie

last: Zhu

state: Shanghai Municipality

address: 110 Ganhe Road Hongkou District

country: China

institute: Shanghai University of TCM

type: Expression profiling by high throughput sequencing

summary: We then performed gene expression profiling analysis using data obtained from RNA-seq of 9 skin tissues including 3 per group in vaseline-treated group, imq model group and bergapten-gel-treated imq model group.

overall_design: Comparative gene expression profiling analysis of RNA-seq data regulated by imq cream and bergapten gel

first: Sheng-jie

first: Teng

last: Chen

first: Yu-xia

last: Chu

first: Fu-lun

last: Li


title: Transcripotome analysis of platelet-rich plasma microneedles promoting hair regrowth in mice skin

city: Guangzhou

first: Yang

last: Sun

address: Nanfang Hospital

institute: Nanfang Hospital, Southern Medical University

summary: To fully interrogate mechanism of the platelet-rich plasma microneedles(PRP-MNs) in promoting hair regrowth in mice skin, we sought to perform a thorough and comprehensive transcripotome profiling of PRP-MNs,platelet-rich plasma(PRP) and microneedles(MNs) treatments of mice skin, with nective control(NC).

overall_design: Mice skin were harvested respectively from PRP-MNs,PRP,MNs and NC groups.

first: Zhiqi

last: Hu

first: Malcolm

last: Xing

first: Yong

last: Miao


title: Serine threonine kinase 24 (STK24) mediates immune evasion signals in tumors by regulating immuno-suppressive molecules

city: Shinanomachi,Shinjukuku

first: Shigeki

last: Ohta

state: Tokyo

country: Japan

institute: Keio University

summary: Effective anti-cancer immunity is achived by Cas9 mediated STK24 gene knockdowned CT26  cells (colorectal carcinoma cell ) transplatation mouse model.

overall_design: Total RNASeq reads covering mouse tumors derived from 4 different teratment protocols. A, CT26 +IgG, CT26 STK24 KO+IgG, C, CT26+PD-1 Antibody, D, T26 STK24 KO+PD-1 antibody.

first: S


title: Effect of depletion of NCOR2 on gene expression in neurofibromatosis type 1 - associated malignant peripheral nerve sheath tumours

city: Shang hai

first: Yuehua

state: State...

address: Manufacturing Bureau Road, Huangpu District, Shanghai

institute: The Ninth People's Hospital of Medical College of Shanghai Jiaotong University

summary: To investigate the function NCOR2 in the regulation of cell proliferation, we established T265 cell in which target gene has been knocked down by shRNA.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of control and knockdown of target gene group

last: LI

first: Yihui

last: Gu

first: Wei

last: Wang

first: Zhichao


title: Inter-organellar communication by a mitochondrial tRNA regulates nuclear metabolic transcription (RNA-Seq)

city: New York

first: Christopher

last: Rouya

address: 1230 York Avenue

institute: Rockefeller University

summary: To assess transcriptomic changes that occur upon mito-tRNA Asparagine inhibition, MDA-MB-231 cells were transfected with either a non-targeting control locked nucleic acid (LNA), two independent LNAs targeting mito-tRNA Asparagine, or an LNA against mito-tRNA Lysine.

overall_design: Transcriptomic, RNA-seq analysis in triplicate, comparing cells transfected with control, mito-tRNA Asparagine, or mito-tRNA Lysine LNAs

first: Sohail

middle: F

last: Tavazoie


title: HSV-1 exploits host heterochromatin for egress [CUT&Tag]

first: Daphne

last: Avgousti

type: Genome binding/occupancy profiling by high throughput sequencing

sample_organism:
Homo sapiens
Human alphaherpesvirus 1

platform_organism:
Homo sapiens
Human alphaherpesvirus 1

overall_design: Cleavage Under Targets and Tagmentation (CUT&Tag) for histone variant macroH2A1 and histone modification H3K27me3 during lytic Herpes Simplex Virus-1 infection in human foreskin fibroblasts both wild-type primary and tert-immortalized knocked out for macroH2A1.

first: Hannah

last: Lewis

first: Laurel

middle: E

last: Kelnhofer-Millevolte

first: Mia

last: Brinkley

last: Arbach

first: Edward

middle: A

last: Arnold

first: Srinivas

last: Ramachandran


title: Transcriptional effects of siRNA-mediated AhR knockdown on TLR7 activation of M-CSF-derived macrophages

city: Madrid

first: Angel

middle: L

last: Corbí

state: Madrid

address: Ramiro de Maeztu 9

department: Molecular Microbiology and Infection Biology

country: Spain

institute: Consejo Superior de Investigaciones Científicas

summary: Analysis of the role of AhR on the transcriptional signature of TLR7-activated human M-CSF-dependent monocyte-derived macrophages.   Methods: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes from three independent donors (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) at 37°C in a humidified atmosphere with 5% CO2 and 21% O2 for 5 days in the presence of 1000 U/ml M-CSF, with cytokine addition every two days. Then, monocyte-derived macrophages were transfected with AhR-specific siRNA or control siRNA, kept in culture for 48 hours, and then stimulated (or not) with the TLR7 ligand CL264 (1 microgram/ml). After 4 hours, cells were lysed and RNA isolated for transcriptional analysis.

overall_design: mRNA profiles of human M-CSF-derived macrophages activated with the TLR7 ligand CL264 after downregulation of AhR expession

first: Miriam

last: Simón Fuentes

first: Ángeles

last: Domínguez Soto

first: Miguel

last: Vega


title: Metabolic and molecular effects of intermittent fasting in humans: results from a randomized clinical trial

first: Ruteja

last: Barve

state: MO

address: 4515 McKinley Ave

department: Genetics

institute: Washington University

summary: This study describes the effects of intermittent fasting induced weight loss on metabolic and molecular pathways

overall_design: 6 month randomized controlled clinical trial. The study included an extension period, during which the Intervention group continued the intervention for an additional 6 months (for a total of 12 months) and the control group crossed-over to receive the delayed intervention. A total of 41 participants (20 Controls and 21 intervention) were tested at Baseline, and after 6 months of intervention.

first: Valeria

last: Tosti

first: R

first: Beatrice

last: Bertozzi

first: Nicola

last: Veronese

first: Francesco

last: Spelta

first: Edda

last: Cava

first: Mark

middle: P

last: Mattson

first: Laura

last: Piccio

first: Diana

middle: S

last: Early

first: Richard

middle: D

last: Head

first: Luigi

last: Fontana


title: GNL3/nucleostemin links DNA replication homeostasis and replication forks stability

city: Paris

first: Jean-Charles

last: Cadoret

address: 15 rue hélène Brion

country: France

institute: CNRS/ Université de Paris

summary: The regulation of replication forks stalling and replication origins firing must be tightly coordinated to prevents genomic instability. Here we show that GNL3/nucleostemin, a GTP-binding protein able to shuttle between the nucleolus and the nucleoplasm, limits replicative stress by limiting replication origins firing. GNL3 is in proximity of nascent DNA and its depletion reduces forks speed but increases forks density and replication origins firing. When subjected to exogenous replicative stress, cells impaired for GNL3 exhibits MRN-dependent resection and RPA phosphorylation.  Strikingly, inhibition of origin firing using CDC7 inhibitor decreased resection in absence of GNL3 but not in absence of BRCA1, suggesting that GNL3 does not protect nascent strand directly from resection. Consistent with this, overexpression of GNL3 leads to an increased resection in response to replicative stress and enhanced origin firing efficiency. These data indicate that the probability of origins firing is tightly regulated by GNL3 to limit replicative stress. Finally, we show that ORC2 and GNL3 interacts together in the nucleolus. We propose a model where GNL3 level is crucial to determine the correct amount of ORC2 on chromatin by sequestrating it in the nucleolus thanks to the capacity of GNL3 to shuttle between nucleoplasm and nucleolus.

overall_design: nascent-DNA from early S-phase versus nascent-DNA from late S-phase

first: Rana

last: Lebdy

first: Marine

last: Canut

first: Julie

last: Patouillard

first: Anne

last: Letessier

first: Jihane

last: Basbous

first: Benoit

last: Miotto

first: Angelos

last: Constantinou

first: Raghida

last: Abou-Merhi

first: Cyril

last: Ribeyre


title: Pimobendan attenuates pressure overload-induced myocardial hypertrophy by inhibiting the MAPKs pathway

city: Changchun

first: Yi

last: Gao

state: Jilin

address: 126th Xiantai Street, Changchun, Jilin, China.

department: Cardiovascular

institute: China-Japan Union Hospital of Jilin University

summary:
Background: Although myocardial hypertrophy is an essential component of heart’s response to many forms of stress, prolonger excessive hypertrophy contributes importantly to the pathogenesis of heart disease. The pimobendan is a drug that both inhibits phosphodiesterase 3 (PDE3) and acts as a calcium sensitizer, which has been used to treat heart failure. The effects of pimobendan on myocardial hypertrophy is controversial.
Objective: This study aims to evaluate the therapeutic effect of pimobendan on myocardial hypertrophy.
Methods: Mice were treated with low oral doses of pimobendan (1mg/kg/d) for 4 weeks after transaortic constriction. Heart structure and function was assessed using ultrasound, hemodynamic measurements and histology combined with biochemical assessments of myocardial hypertrophy. We also examined the effects of pimobendan (100 µM) on hypertrophy in cultured neonatal rat cardiomyocytes (NRCMs) induced by 50 µM phenylephrine (PE).
Results: The doses pimobendan used in our studies had no effect on baseline contractility. Nevertheless, pimobendan administration of mice subjected to TAC decreased heart weights (normalized to either tibia length or body weight) ventricular wall thickness, cardiomyocyte sizes, myocardial fibrosis and the levels of a number of key myocardial hypertrophy markers (WHICH ONES). In cultured neonatal cardiomyocytes, pimobendan attenuated the PE-induced hypertrophy. In both hypertrophy models pimobendan reduced the phosphorylation levels of several essential proteins in the MAPK pathway, PI3K-AKT pathway, and calcineurin signaling pathway.
Conclusion: Low pimobendan may attenuate myocardial hypertrophy. Although the underlying mechanisms remain to be elucidated, the MAPK pathway is likely to play a role.

overall_design: transcrptional analysis of pimobendan on pressure overload induced hypetrophy.

first: Peter

middle: H

last: Backx

first: Huan

last: Sun

first: Ping

last: Yang


title: RyR2 inhibitor attenuates cardiac hypertrophy by downregulating TNF-α/NF-κB/NLRP3 signaling pathway

summary:
Background: Cardiac Ryanodine receptors (RyR2) can regulate Ca2+ release in the excitation-contraction coupling, when activated, it releases a large amount of Ca2+ into the cytoplasm. Additionally, studies have shown that dantrolene (a RyR2 inhibitor) protects against heart failure and arrhythmias by inhibiting domain decompression, Ca2+ leakage and diastolic Ca2+ sparking. However, the role and mechanism of dantrolene in cardiac hypertrophy remain unclear.
Objective: In this study, we aimed to evaluate the therapeutic effects of dantrolene on pressure overload-induced cardiac hypertrophy in mice models by transverse aortic contraction (TAC) surgery and to explore its potential mechanism.
Methods: C57/B6 mice (age: 8 weeks) underwent TAC or sham surgical procedure and were administered oral dantrolene (30 mg/kg) or the solvent drug postoperatively. After 4 weeks of drug treatment, RNA sequencing of mice left ventricle was performed.qRT–PCR validation was performed using SYBR Green assays.
Results: We found that dantrolene significantly alleviated TAC-induced cardiac hypertrophy. According to RNA sequencing, 184 down-regulated genes were found after dantrolene treatment compared with TAC group, 8 of these were validated with qRT–PCR. According to the KEGG analysis, Creb3l3, IL18R1 and Ccl5 were down-regulated after dantrolene treatment, which were related to TNF-α pathway.
Conclusion: As a RyR2 inhibitor, dantrolene attenuates cardiac hypetrophy through downregulating the TNF-α/NF-κB/NLRP3 signaling pathway.

overall_design: transcrptional analysis of dantrolene on pressure overload induced hypetrophy.

first: Shuai

last: Li

first: Xueyan

last: Liu

first: Daoyuan

last: Si

first: Weiwei

last: chen

first: Fenghua

first: Kumaraswamy

last: Nanthakumar


title: RNA-sequencing of murine B16F10 melanoma cells with IFNg and FK866, a Nampt inhibitor

city: Salt Lake City

first: Ryan

last: O'Connell

state: UT

address: Emma Eccles Jones, Medical Research Building, 15 North Medical Drive East

department: Pathology, Microbiology & Immunology

institute: University of Utah

summary: NAMPT is expressed in all cells during normal cell homeostasis. However, melanoma cells have a higher energetic demand and increase NAMPT expression. Our data show that IFNg signaling upregulates NAMPT in both human and mouse melanoma cells leading to increased cell growth and expression kinetics. The purpose of this experiment was to identify how IFNg inducible Nampt alters cell kinetics and we did this by treating melanoma cells with the combination of IFNg and FK866.

overall_design: B16F10 murine melanoma cells were treated with IFNg (50ng/mL) and FK866 (50nM) for 6 hours and then processed for RNA-sequencing via 10x platform.

first: Cindy

last: Barba

middle: M


title: Comparative analyses of sperm DNA methylomes among three commercial pig breeds reveal vital hypomethylated regions associated with spermatogenesis and embryonic development

city: Beijing

first: Siqian

last: Chen

address: 2rd, Yuanmingyuan West Road

department: College of Animal Science and Technology

institute: China Agricultural University

type: Methylation profiling by high throughput sequencing

summary: This study is the first to report a genome-wide comparative DNA methylation map of adult pig sperm in three commercial pig breeds using WGBS technology. Our results showed that DNA methylation was more conserved in the three commercial pig breeds. Moreover, our results indicated that breed-specific HMRs are related to phenotypic changes and economically complex traits for each breed. The conserved HMRs between pig sperm and testis close to or located in the promoter regions of important genes are mainly involved in DNA repair and spermatogenesis.

overall_design: Investigate the sperm DNA methylomes using WGBS and analyze DNA methylation variation in three commercial pig breeds—Landrace, Duroc, and Yorkshire

first: Ying

last: Yu


title: RNA-Seq to probe transcription of patient-derived organotypic colorectal cancer.

city: Madison

first: Dustin

last: Deming

state: WI

address: 1111 Highland Ave., WIMR II, Rm. 6507

department: Hematology-Oncology

institute: University of Wisconsin

summary: Patient-derived cancer organoids (PCOs) provide a platform to model resistant to targeted therapies. Following culture maturation, PCOs were treated with stepwise dose escalation of EGFR inhibitors. Cultures were started at 20% physiologic Cmax panitumumab (46ug/ml) and assessed for growth (normalized change in diameter at 96 hours). If cultures surpassed ≥20% growth, stepwise dose escalation was repeated with interval increase of 20% Cmax. Time to resistant (TTR) was defined by duration of time from the initiation of dose escalation to persistent growth at 100% Cmax panitumumab. All samples were collected in triplicate biological replicates at baseline and after achieving resistance to EGFRi with persistent growth at 100% physiologic Cmax. RNA library was constructed using TruSeq Stranded total RNA with rRNA reduction (Illumina). Quality control was performed by Eukaryote Total RNA electrophoresis using NanoDropOne. The library included 2x150bp paired end reads with sequencing performed by NovaSeq 6000 using MiSeq NanoCell at University of Wisconsin Biotechnology Center.

overall_design: mRNA profiles of colorectal cancer (CRC) organoids that are resistant/non-resistant to EGFR inhibitor therapy.

first: Jeremy

last: Kratz

first: Sean

last: McIlwain

first: Irene

last: Ong


title: Tolerogenic dendritic cells protect against acute kidney injury

city: Westmead

first: Jennifer

address: 176 Hawkesbury Rd

country: Australia

institute: Westmead Institute for Medical Research

summary: We use tolDCs from syngeneic (C57BL6) and allogeneic (BALB/c) mice to show potent renoprotective abilities in a ischemia reperfusion AKI model. Dendritic cells were derived from mice bone marrow and cultured for 7 days with GM-CSF and IL-4. Tolerogenic DCs were cultured in the same DC media but with the addition of VitD3 and IL10. LPS was added on day 6 and cells harvested for use or analysis on day 7.

overall_design: C57BL6 mice bone marrow derived dendritic cells (BMDC) and VitD3/IL10 generated tolerogenic (tolDC) cells were sequenced with or without LPS stimulation (n = 3 per group)

first: Natasha

last: Rogers

first: Harry

last: Robertson


title: Glycan-Specific Natural Antibodies Mediate Blockade of Endogenous Retrovirus Emergence and Recognize a Broad-spectrum of Exogenous Viruses

city: New Haven

first: Yexin

state: CT

address: 300 Cedar St., The Anlyan Center

department: Department of Immunobiology

institute: Yale School of Medicine

summary: Endogenous retroviruses (ERV), comprising a substantial portion of the vertebrate genome, are remnants of ancient genetic invaders. ERV with near-intact coding potential reactivate in B cell-deficient mice. Here, we employed an antigen-baiting strategy to enrich B cells reactive to ERV surface antigens. We identified ERV-reactive B-1 cells expressing germline-encoded natural IgM antibodies in naïve mice, the level of which further increases upon innate immune sensor stimulation. B cell receptor repertoire profiling of ERV-reactive B-1 cells revealed increased usage of Igh VH gene that gives rise to glycan-specific antibodies targeting terminal N-acetylglucosamine moieties on ERV glycoproteins, which further engage the complement pathway to protect the host from ERV emergence. These same antibodies also recognize glycoproteins of other enveloped viruses, but not self-proteins. These results reveal an innate antiviral mechanism of germline-encoded antibodies with broad reactivity to enveloped viruses, whose absence leads to the emergence of infectious ERV.

overall_design: We developed a FACS based approach to enrich ERV specific B cells. PE labeled murine leukemia viruses (MLV) were used to probe ERV-reactive B cells and PE-Alexa Fluor 647 labeled virus-like particle (VLP) devoid of surface viral antigens were used to block non-specific interactions. ERV-reactive B-1 cells from the peritoneal cavities of naive C57BL/6 mice were sorted and the BCR repertoire was profiled by Chromium Single-cell Immune Profiling (10X Genomics). Total B-1 cells from the peritoneal cavities of naive C57BL/6 (age and gender matched) were sorted for the control repertoire prior to ERV-baited enrichment.

first: Rebecca

last: Treger

first: Juan

last: Hernandez-Bird

first: Akiko

last: Iwasaki


title: Transcriptome profiling between unfavorable and favorable Wilms Tumors and against human fetal kidney

city: West Hollywood

first: AGCT

last: Core

state: CA

address: 8687 Melrose Ave, PDC B230

department: BMS

institute: Cedars Sinai Medical Center

summary:
Purpose: The 10x Genomics Visium platform allows us to define the spatial topography of gene expression and provides detailed molecular maps that overcome limitations associated with sn/scRNA-seq and microscopy-based spatial transcriptomics methods. The goals of this study are to compare and identify unique transcriptome profiling (RNA-seq) signature between unfavorable and favorable Wilms Tumors and against human fetal kidney.
Methods: Human fetal kidney and Wilms tumor spatial topography of gene expression were generated using the 10X Visium platform
Results: Using an optimized data analysis workflow, we mapped the reads to the hg38 genome build and grouped the spots into 9 clusters based on gene expression profiles.
Conclusion: Our study represents the first implement of Visium technology in human fetal kidney and Wilms Tumor tissue, providing a number of important functional insights about the spatial and molecular definitions of cell populations across human fetal kidney and different subtypes of Wilms Tumor through analyzing gene expression within the intact spatial organization of the human samples.

overall_design: Three total samples, one healthy fetal kidney and two Wilms tumor samples

first: Laura

last: Perin


title: RNA-sequence facilitates analysis of mesenchymal stem cells treating with concanavalin A mice

city: Hangzhou

first: Fen

last: Zhang

address: Qingchun Road

institute: Zhejiang University

summary:
Purpose: The goals of this study are to find the mechanisms of mesenchymal stem cells (MSC) ameliorating concanavalin A (Con A) induced inflammatory mice
Methods: Liver tissues were harvested at 6h, 12h after Con A injected with/without MSC (n = 3 per group) for  transcriptome profiling.
Results: Filter the raw data obtained fromDNBSEQ-G400, and compare the filtered clean reads to the reference sequence. Quantitative analysis of known genes and new genes, differential expression analysis based on gene expression in different sample groups, GO function analysis, Pathway function analysis, cluster analysis, and protein interaction for the selected differentially expressed genes Network, transcription factor coding ability prediction and other in-depth mining analysis.
Conclusions: Our study discoveres  following processes were significantly affected: apoptosis, MAPK signaling pathway and cytokine-cytokine receptor interaction.

overall_design: Total hepatocyte RNA was extracted for RNA-seq of 6h, 12h after Con A injected with/without MSC (n = 3 per group)

first: Lanlan

last: Xiao

first: Ya

last: Yang

first: Lanjuan

last: Li


title: Genome-wide maps of chromatin state in cultured male germline stem cells [scATAC-seq]

city: Hong Kong

first: Jinyue

last: Liao

address: Room 38016, 1/F Lui Che Woo Clinical Sciences Building

department: Department of Chemical Pathology

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: We report the application of single-cell ATAC-seq to reconstruct the epigenetic program and identify key transcription factors and cis-regulatory elements associated with the epithelial and mesenchymal heterogeneity and G9a inhibition in cultured male germline stem cells (GSCs). First, we identified epithelial-like and mesenchymal-like clusters in the sample. Pseudotime trajectory also indicated that GSCs could undergo EMT-like process with unique regulators in different stages. Lastly, we showed that G9a inhibition could suppress the EMT-like process in GSCs.

overall_design: Chromatin accessibility profiles of untreated GSCs, UNC0638-treated GSCs and GSCs undergoing EMT-like process.


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [17A, 17B, 18A]

status: Public on Jul 02 2023

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

summary: Illustrating the cellular architecture of the mammalian brain is critical to understanding its diverse functions and complex animal behaviors. With support from NIMH and NINDS as part of the BRAIN Initiative Cell Census Network (BICCN), the Center for Epigenomics of the Mouse Brain Atlas (CEMBA) applied single nucleus methylation sequencing in 117 brain funtional regions across the whole adult male P56 C57BL/6J mouse brain. In each major brain regions, we identified distinct cell clusters and formed them in a hierarchical taxonomy. These clusters include known primary brain cell types and possible sub-types. We use these data to identify the epigenomic characteristics and to define specific regulatory elements for each cell cluster. We integrate the single cell methylome with single cell gene expression and chromatin accessibility profiles from the same brain region to further identify potential enhancers and their corresponding genes for several neuronal cell types. By brain region spacial comparisons, we found spatial specificity among excitatory neuronal clusters within the same cortical layer. We identify brain-region-specific transcription factors that may regulate cortical region development of excitatory neurons. These data define the landscape of cell type and spatial heterogeneity in the mouse brain and the underlining regulatory epigenomic basis.

overall_design: Apply snmC-seq2 to 117 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (17A_210810, 17A_210812, 17B_210422, 17B_210429, 18A_201217).

first: Hanqing

last: Liu

first: Anna

last: Bartlett

first: Jacinta

last: Lucero

first: Julia

middle: K

last: Osteen

first: Jordan

last: Altshul

first: Mia

last: Kenworthy

first: Rosa

middle: G

last: Castanon

last: Nery

first: Peter

last: Berube

first: Huaming

last: Chen

first: Michael

last: Nunn

first: Jesse

last: Dixon

first: M

last: Behrens


title: Transcriptome analysis of knockdown NUP210 in Huh7 hepatocyte-derived carcinoma cell line

city: seoul

first: Jueng Soo

last: You

address: 120 Neungdong-ro

country: South Korea

institute: Konkuk University

summary: This study delineated the downstream activity of NUP210 and evaluated the genome-wide expression change

overall_design: Global change of expression in control and NUP210 knodkdown liver cancer cell line (Huh7)

first: Jueng

first: Seong

last: Hong

first: Keun

last: Son


title: Comparative study on berry development of two grape cultivars by transcriptomic analyses [Victoria]

city: WuHan

first: Guosong

last: Jiang

state: Hubei Province

address: Jiefang Road, No. 1277

department: Department of Urology

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: Grape berry development is a highly coordinated, intricate and complex process with many morphological, biochemical and physiological changes occurring during the ripening process. Equally, ripening is an organoleptic characteristic linked to fruit development. The fruits Seedless (FS) and Victoria (VT) grape varieties exhibit many morphological and phytochemical differences, but genetic mechanisms underlying them remain poorly explored. Herein, we comparatively analysed the phenotypic and transcriptomic patterns of Victoria (VT) and Flame Seedless (FS) grape varieties during berry development. We studied the physiological analysis and transcriptomic profiles sequencing were performed at four berry developmental stages time-points (40, 50, 60 and 80 DPA). Notably, the VT variety berry size was comparatively larger to the FS variety. At maturity, 80DPA, the FS soluble solids were 61.8% higher than VT. Further, a total of 4889 and 2802 DEG’s were identified from VT and FS 40 DPA to 80 DPA development stages, respectively. 1386 DEGs were common in the two varieties. GO analysis identified Cysteine biosynthetic process, response to red light, chlorophyll binding, polysaccharide biosynthetic process and chloroplast thylakoid membrane as some of the dominant terms under the biological processes, molecular function and cellular component categories.

overall_design: Transcriptome analysis for berry development of two grape cultivars,in triplicate, using Illumina  HiSeq X-ten.

first: Haixia

last: Zhong


title: Comparative study on berry development of two grape cultivars by transcriptomic analyses

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

overall_design: Refer to individual Series


title: Comparative study on berry development of two grape cultivars by transcriptomic analyses [Flame Seedless]

summary: Grape berry development is a highly coordinated, intricate and complex process with many morphological, biochemical and physiological changes occurring during the ripening process. Equally, ripening is an organoleptic characteristic linked to fruit development. The fruits Seedless (FS) and Victoria (VT) grape varieties exhibit many morphological and phytochemical differences, but genetic mechanisms underlying them remain poorly explored. Herein, we comparatively analysed the phenotypic and transcriptomic patterns of Victoria (VT) and Flame Seedless (FS) grape varieties during berry development. We studied the physiological analysis and transcriptomic profiles sequencing were performed at four berry developmental stages time-points (40, 50, 60 and 80 DPA). Notably, the VT variety berry size was comparatively larger to the FS variety. At maturity, 80DPA, the FS soluble solids were 61.8% higher than VT. Further, a total of 4889 and 2802 DEG’s were identified from VT and FS 40 DPA to 80 DPA development stages, respectively. 1386 DEGs were common in the two varieties. GO analysis identified cysteine biosynthetic process, response to red light, chlorophyll binding, polysaccharide biosynthetic process and chloroplast thylakoid membrane as some of the dominant terms under the biological processes, molecular function and cellular component categories.


title: The different role of YKL-40 in glioblastoma is a function of MGMT promoter methylation status

first: Wei

last: Zhang

address: No. 168 Litang Road, Changping District

institute: Department of Neurosurgery, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University

summary: To explore what could distinguish the difference in the function of YKL-40 in GSCs, we performed RNA-Seq to identify the molecular subclasses of each GSC

overall_design: RNA profiles of GSC cultures from glioblastoma specimens


title: Palbociclib interferes with origin firing in a pRb independent manner

first: Jean-Charles

last: Cadoret

type: Genome variation profiling by genome tiling array

summary: Over the last decade, CDK4/6 inhibitors (palbociclib, ribociclib and abemaciclib) have emerged as promising anticancer drugs. Numerous studies have demonstrated that CDK4/6 inhibitors efficiently block the pRb-E2F pathway and induce cell cycle arrest in pRb-proficient cells. Based on these studies, the inhibitors have been approved by the FDA for treatment of advanced hormonal receptor (HR) positive breast cancers in combination with hormonal therapy. However, some evidence has recently shown unexpected effects of the inhibitors, promoting needs to understand more about the mechanism of inhibitors beyond pRb. Our study demonstrates here for the first time how palbociclib impairs the origin firing in the DNA replication process in pRb-deficient cell lines. Strikingly, despite the absence of pRb, cells treated with palbociclib synthesize less DNA without any induced cell cycle arrest. Furthermore, palbociclib treatment disturbs the temporal program of DNA replication and reduces the density of replication forks. Cells treated with palbociclib show a defect in the loading of proteins of the Pre-initiation complex (Pre-IC) on chromatin, indicating a reduced initiation of DNA replication. Our findings highlight hidden effects of palbociclib on the dynamics of DNA replication and on its cytotoxic consequences on cell viability in the absence of pRb. This study provides a potential therapeutic application of palbociclib to target genomic instability towards pRb deficient patient

first: Su-Jung

last: Kim

first: Stéphane

last: Koudrioukoff

first: Chrystelle

last: Jean-Charles Cadoret


title: Multi-level characterization of a glioblastoma cell line panel

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

country: Germany

institute: LMU University Hospital

type: Methylation profiling by genome tiling array


title: Optogenetic control of Wnt signaling models cell-intrinsic embryogenic patterning using 2D human pluripotent stem cell culture

city: Berkeley

first: Nicole

middle: Anne

last: Repina

address: Stanley Hall

department: Bioengineering

institute: UC Berkeley

summary:
Purpose: To establish a molecular fingerprint for optoWnt-induced differentiation, we measured global transcriptional changes using bulk-population RNA-seq of optoWnt and WT hESCs after 48 hrs of light stimulation. Illuminated WT cells served as a phototoxicity control, and unilluminated optoWnt cells controlled for potential CRISPR/Cas9 knock-in effects, cell perturbation due to optoWnt expression, and dark-state Wnt pathway activation. We also measured feedback between optoWnt/WT populations during co-culture (1:1) by FACS sorting for each population after 48 hrs of growth.

Methods: Bulk RNA-seq of hESCs using Illumina TruSeq Stranded mRNA Library Prep Kit and sequenced on HiSeq 4000

Results: Principal component analysis (PCA) showed clustering of biological triplicates for each condition and strong transcriptional changes upon optoWnt stimulation that account for 95% gene variance among samples. Dark and illuminated monoculture WT cells clustered together, and differential analysis of monocultures showed minimal gene expression differences, demonstrating minimal phototoxicity effects after 48 hrs of continuous 0.8 µW/mm-2 blue light stimulation. In contrast, optoWnt stimulation induced a broad transcriptional effect, with ~5,500 differentially expressed genes between the dark and illuminated conditions. Direct B-catenin target genes, such as CDX1, DKK1, T, and TBX3, are among the most differentially expressed genes, all with a log fold change (LFC) of ~ 9 – 13. Lastly, WT cells grown in illuminated co-culture with optoWnt cells showed differential gene expression and upregulation of TGF-B target genes when compared with WT cells grown in monoculture or in dark co-cultures, indicating signaling feedback between the optoWnt and WT populations.

overall_design: Bulk RNA sequencing of WT and optoWnt hESCs in triplicate. Cells were cultured in monoculture or in optoWnt/WT co-cultures (1:1) and were FACS sorted for OptoWnt (mCherry+) and WT (GFP+) cells.

first: David

middle: V

last: Schaffer


title: Nicotinamide mononucleotide supplementation reverses the declining quality of maternally aged oocytes

city: Nanjing

first: Miao

last: Yilong

address: Tongwei Road

institute: Nanjing Agricultural University

summary: Advanced maternal age, defined as 35 years or older, is associated with a decline in  both ovarian reserve and oocyte quality, which leads to the female infertility, pregnancy  loss, fetal anomalies, stillbirth, and obstetric complications. At present, the effective  approaches to counteract the maternal age-related decay of oocyte quality are still not  fully determined. Here, we report that in vivo supplementation of nicotinamide  mononucleotide (NMN) efficaciously ameliorates the quality of oocytes from naturally  aged mice by recovering nicotinamide adenine dinucleotide (NAD + ) levels in  oocytes. NMN supplementation increases the number of antral follicles, ovulated  oocytes and matured oocytes from aged mice. Specifically, NMN supplementation  maintains the normal spindle/chromosome structure and dynamics of cortical granule  component ovastacin to ensure the meiotic competency and fertilization ability of aged  oocytes. Moreover, single cell transcriptome analysis shows that the beneficial effect of  NMN on the aged oocytes is mediated by the restoration of the mitochondrial function,  thereby reducing the accumulated ROS to suppress the occurrence of apoptosis. To  sum up, our data reveal that supplementation of NMN is a feasible approach to prevent  oocyte quality from advanced maternal age-related deterioration, contributing to  improve the reproductive outcome of aged women and the assisted reproductive  technology.

overall_design: Transcriptomic analysis of matured oocytes was carried out using a protocol for single cell RNA-Seq. The constructed library was sequenced with Illumina platform.

first: Bo

last: Xiong

first: YiL

last: Miao


title: Genomic copy number number characterisation of glioblastoma (GBM) cell lines.

summary: Early passages (< 10) of frequently used GBM cell lines A172, LN18, LN229, T98G, U87-MG, U138-MG and U251-MG were characterised for genomic copy number by array CGH.

overall_design: Genomic DNA from cell lines was hybridised against a pooled reference DNA (Promega).


title: Gene expression analysis of glioblastoma (GBM) cell lines.

summary: Early passages (< 10) of frequently used GBM cell lines A172, LN18, LN229, T98G, U87-MG, U138-MG and U251-MG were characterised for gene expression microarray analysis.

overall_design: Total RNA from cell lines was used for gene expression microarray analysis.


title: DNA methylation characterisation of glioblastoma (GBM) cell lines.

summary: Early passages (< 10) of frequently used GBM cell lines A172, LN18, LN229, T98G, U87-MG, U138-MG and U251-MG were characterised for global DNA methylation patterns.

overall_design: Genomic DNA from cell lines was hybridised on Illumina EPIC DNA methylation arrays.


title: Analysis of circRNAs expression in melanocytes and melanoma cells

status: Public on Jun 30 2023

city: Chang Sha

first: Qi

last: Wang

state: Other (Non U.S.)

address: Tongzipo Road

institute: The Third Xiangya Hospital of Central South University

summary: Malignant melanoma (MM) is a highly malignant tumor with poor prognosis. However, the molecular mechanism of melanoma invasion and metastasis remains unclear. In the present study, we performed the profiling of circRNA expression in normal melanocytes and melanoma cells with different invasive abilities using circRNA microarray analysis.

overall_design: To screen the potential circRNAs that affect melanoma invasion and metastasis. A circRNA microarray was performed to profile circRNA expression in the low-metastatic melanoma WM35 cell line and in the high-metastatic melanoma WM451 cell line in comparison to control human melanocytes.

first: Ke

last: Cao

first: Jianda

last: Zhou


title: Gene expression array of irradiated and/or lithium exposed iPSC-derived human neural progenitor cells

city: Solna Stockholm

first: Christina

last: Neofytou

address: Tomtebodavägen 16, 32B

department: Neuroscience

country: Sweden

institute: Karolinska Institutet

summary:
RNA isolation was performed using the RNeasy Mini Kit (Qiagen), per manufacturer instructions. For differential gene expression analysis, the Affymetrix Whole Transcript Assay with the Clariom S cartridge for human samples (n=2, BEA core facility, Sweden) was used.
Cells were irradiated in an CIX2 Xstrahl X-Ray Irradiator with Aluminum filter at a focus-to-skin distance (FSD) of 40 cm and with an energy of 195kV, 10 mA, for and absorbed dose of 4 GY. To allow for assessment of irradiation damage, cells remained in the incubator for 1 hour. Pre-warmed DMEM/F-12 was mixed with the appropriate amount of LiCl powder (Sigma-Aldrich, Cat# L9650-100G), passed through a 0.22 μm filter, and supplemented with 1% Penicillin-Streptomycin, 1% N2, 0.1% B27, 0.1% EGF, and 0.1% FGF2 to produce 3mM Lithium Chloride (LiCl) hNSPC medium.

overall_design: 4 experimental groups were included (control, +/- LiCl, +/- IR, combination treatment) in 2 biological replicates.

first: Alexandra

last: Backlund

first: Klas

last: Blomgren

first: Ola

last: Hermanson


title: Gene Expression in Dunaliella tertiolecta +/- Iron

first: Sean

middle: D.

last: Gallaher

state: California

address: 176 Stanley Hall, room 408

department: California Institute for Quantitative Biosciences

summary: Dunaliella tertiolecta is an extremophilic, green alga from the Chlorophyte lineage. It is found in coastal marine environments around the world. D. tertiolecta can tolerate extremes of heat, light, pH, and salinity. D. tertiolecta is under development for the production biofuels and other bioproducts because it can produce large quantities of neutral lipids, and it can be grown in open raceway ponds using only the inputs of seawater and sunlight. This isolate of D. tertiolecta (UTEX LB 999) was found in Oslofjord, Norway in 1938. This accession includes an RNA-Seq analysis of D. tertiolecta cultures grown in iron-replete (1.5 µM) or iron-deficient (0 µM) media.

overall_design: Precultures of Dunaliella tertiolecta (UTEX LB 999) were inoculated at 4x10^5 cells/mL into triplicate flasks containing media with 1.5 µM or 0 µM added iron and 2 M NaCl. Cultures were grown on shaking platforms (140 rpm) at 24°C under constant light (100 µE m^-2 sec^-1). After two days of growth, total RNA was collected, poly(A)-selected, and subjected to 50 nt single-end sequencing on the Illumina HiSeq platform. Sequenced data was aligned to the genome assembly included with this accession by RNA STAR. Expression was quantified in terms of Fragments per kb of transcript per million reads mapped (FPKMs) by cuffdiff.

first: Lital

last: Davidi

first: Sabeeha

last: Merchant


title: Chromatin remodeling events associated with gARID are essential for gametocyte development in Plasmodium [ChIP-seq]

city: tsu

first: masao

last: yuda

state: mie

address: edobashi 2-174

institute: mie university

summary: To investigate the genome-wide binding sites of gARID in gametocytes of Plasmodium berghei, the chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) analyses were performed. Parasites expressing GFP-fused gARID were harvested after treating the infected mice with sulfadiazine and subjected to ChIP-seq experiments using anti-GFP antibody. Binding sites of gARID were determined from the sequence data.

overall_design: Mice were infected with transgenic parasites and treated with sulfadiazine in their drinking water. Chromatins associated with GFP-tagged gARID were IPed with anti-GFP antibody, and DNA fragments purified from the IPed chromoatins were sequenced by the Next Generation Sequencing. Using non-IPed samples as a control (INPUT), binding sites of gARID were determined from the sequence data.

first: Tsubasa

last: Nishi

first: Izumi

last: Kaneko

first: Shiroh

last: Iwanaga

first: Masao

last: Yuda


title: The homing of exogenous hair follicle mesenchymal stem cells into hair follicle niches

city: Guangzhou

first: Kaitao

last: Li

state: Guangdong Province

address: 1838 North Guangzhou AV

institute: Nanfang Hospital of Southern Medical University

summary: In our study, we found that low-passage dermal papilla cells (DPCs) and dermal sheath cells (DSCs)  has higher homing rate than that of high-passage DPCs and DSCs. To uncover the molecular mechanisms underlying the difference of homing rate between low-passage DPCs/DSCs and high-passage DPCs/DSCs, we perform transcriptome analysis of mRNA expression profiles of low-passage and high-passage DPCs and DSCs.

overall_design: The mRNA expression profiles of low-passage and high-passage DPCs and DSCs were detected.

first: Fang

last: Liu

first: Ye

last: He

first: Zhiqi

last: Hu

first: Yong


title: DNA methylation array of irradiated and/or lithium exposed iPSC-derived human neural progenitor cells

first: Christina

summary:
DNA isolation was performed following the DNeasy Blood and Tissue Kit (Qiagen).
Cells were irradiated in an CIX2 Xstrahl X-Ray Irradiator with Aluminum filter at a focus-to-skin distance (FSD) of 40 cm and with an energy of 195kV, 10 mA, for and absorbed dose of 4 GY. To allow for assessment of irradiation damage, cells remained in the incubator for 1 hour. Pre-warmed DMEM/F-12 was mixed with the appropriate amount of LiCl powder (Sigma-Aldrich, Cat# L9650-100G), passed through a 0.22 μm filter, and supplemented with 1% Penicillin-Streptomycin, 1% N2, 0.1% B27, 0.1% EGF, and 0.1% FGF2 to produce 3mM Lithium Chloride (LiCl) hNSPC medium.


title: Gene expression and chromatin accessibility profiles of cultured male germline stem cells [RNA-seq and ATAC-seq]

first: Jinyue

last: Liao

summary: We report the application of RNA-seq to profile the transcriptome associated with Oct4-GFP intensity, feeder v.s. feeder-free culture, epithelial and mesenchymal heterogeneity  and G9a inhibition in cultured male germline stem cells (GSCs). First, we confirmed that the self-renewal gene expression levels of feeder culture and feeder-free culture were comparable to each other. Next, we investigatied the transcriptional differences among GSCs with different Oct4-GFP intensity. Then, we explored the transcriptonal differences between epithelial-like and mesenchymal-like GSCs, demonstrating GSCs could undergo an EMT-like process. Lastly, we showed that G9a inhibition could suppress the EMT-like process in GSCs.

overall_design: Transcriptomes of GSCs in feeder culture GSCs in feeder-free culture, UNC0638-treated GSCs, epithelial-like GSCs and mesenchymal-like GSCs.

first: Hoi

last: Suen

first: Tin-Lap

last: Lee


title: Transcriptome Analysis of PLC/PRF/5 cells Infected with Adenovirus Overexpression SCL27A5

city: chongqing

first: tang

last: ni

address: yixueyuan Road NO.1

institute: Chongqing Medical University

summary: Purpose:To understand the change in cellular metabolism and function for the overxepression of SCL27A5 in hepatoma cells. Methods:Total RNAs of AdSLC27A5- or AdGFP-infected PLC/PRF/5 cells were extracted using TRIzol (Invitrogen), following the manufacturer’s instructions. RNA-seq and bioinformatic data analysis were performed by Shanghai Novel Bio Ltd. Briefly, strand-specific RNA-seq libraries were prepared using the Total RNA-seq (H/M/R) Library Prep Kit (Vazyme Biotech, Nanjing, China) and were sequenced on a HiSeq X Ten sequencing platform. Raw reads in FASTQ format were subjected to quality control using FastQC. RNA-seq reads were aligned to the reference genome using Bowtie. Uniquely mapped reads were used for further analysis. Gene expression levels are expressed as RPKM (reads per kilobase per million reads) and differences in gene expression were calculated with rSeq. Results:There were 17 genes differentially expressed in AdSLC27A5-infected PLC/PRF/5 cells compare to the GFP control group (fold change >1.5 or < 0.667; FDR < 0.05).

overall_design: mRNA profiles of AdGFP1- or AdSLC27A5-infected  PLC/PRF/5 cells were generated by deep sequencing in triplicate, using Illumina HiSeq X Ten sequencing platform.

first: Ni

last: Tang

first: Ailong

last: Huang

first: Kai

last: Wang

first: Qingzhu

last: Gao

first: Guiji

last: Zhang

first: Yaqiu

last: Zheng

first: Yi

last: Yang


title: Gene Expression in Dunaliella salina Bardawil +/- Iron

first: Sean

last: Gallaher

summary: Dunaliella salina Bardawil (also known as Dunaliella bardawil) is an extremophilic, unicellular green alga from the Chlorophyte lineage. D. salina is found in hypersaline environments where it can tolerate extremes of heat, light, pH, and up to saturating concentrations of salt. The D. salina Bardawil isolate (UTEX LB 2538) was found in a salt pond near the Bardawil Lagoon on the Sinai peninsula in 1976. This isolate of D. salina is the richest natural source of beta-carotene, a highly valuable commercial product. This accession includes an RNA-Seq analysis of D. salina Bardawil cultures grown in iron-replete (1.5 µM) or iron-deficient (0 µM) media.

overall_design: Precultures of Dunaliella salina Bardawil (UTEX LB 2538) were inoculated at 4x10^5 cells/mL into triplicate flasks containing media with 1.5 µM or 0 µM added iron and 1 M NaCl. Cultures were grown on shaking platforms (140 rpm) at 24°C under constant light (50 µE m^-2 sec^-1). After three days of growth, total RNA was collected, poly(A)-selected, and subjected to single-end 50 nt sequencing on the Illumina HiSeq platform. Sequenced data was aligned to the genome assembly included with this accession by RNA STAR. Expression was quantified in terms of Fragments per kb of transcript per million reads mapped (FPKMs) by cuffdiff.

first: Lital

last: Davidi

first: Sabeeha

last: Merchant


title: Analysis of reversibility of transcriptome responses to abiotic stress conditions in Arabidopsis thaliana

status: Public on Jun 28 2023

city: Cerdanyola del Vallès

first: ANTONI

last: GARCIA-MOLINA

state: Barcelona

address: Campus UAB - CRAG Building

department: Plant Development and Signal Transduction

institute: Centre for Research in Agrigenomics

summary: Plants acclimate to environmental fluctuations by transitory reconfigurations the homeostatic network. Primary studies suggested that transcriptome responses to deal with fluctuations in light intensity and temperature tend to reversibility after stress removal in the model plant Arabidopsis thaliana. To gain more insight into this pattern in the context of acclimation, RNA-Seq analysis were conducted in Arabidopsis thaliana after different abiotic stress treatments consisting in high light (HL), high humidity, drought, heat, cold and combinations among factors or after recovery periods. Our transcriptome study is in line of a general pattern wherby transcriptome changes in response to adverse environments are prone to return to the basal state during the de-acclimation phase.

overall_design: In this study, the dynamics of acclimation responses in Arabidopsis thaliana at transcriptional level has been conducted by comparing transcriptome profiles of plants exposed to wide range of  abiotic stress factors applied individually or simultaneously  to those of plants after a period of recovery.

first: Antoni

last: Garcia-Molina


title: Single-cell transcriptome profiling reveals macrophage and dendritic cell heterogeneity across six zebrafish organs

status: Public on Jun 27 2023

city: HK

first: Zilong

last: WEN

address: Academic Bld., HKUST, Clearwater Bay, Kowloon

department: Division of Life Science

institute: Hong Kong University of Science and Technology

summary: Tissue-resident macrophages (TRMs) and dendritic cells (DCs) are highly diverse and play essential roles in immunity, tissue regeneration, and homeostasis maintenance. To systematically assess the heterogeneity of TRM and DC in adult zebrafish, we performed droplet-based scRNA-seq on mpeg1.1+ cells sorted from six different organs (epidermis, gill, intestine, liver, heart, and brain) of 6-month-old Tg(mpeg1.1:DsRedx) fish, a widely used myeloid cell reporter line. We identified two macrophage subpopulations with pro-inflammatory and pro-remodeling signatures, respectively, as well as one conventional dendritic cell population with prominent antigen presentation capacity and plasmacytoid dendritic cells featuring anti-viral properties.  Our study provides a comprehensive landscape of TRMs and DCs in zebrafish and offers valuable tools for future in-depth investigations of these cell types.

overall_design: scRNA-seq (10X genomics 3’ V3.1) of FACS-sorted mpeg1.1+ cells isolated from six different organs (epidermis, gill, intestine, liver, heart, and brain) of 6-month-old Tg(mpeg1.1:DsRedx) fish

first: Qiuxia

last: Zhou

first: Changlong

last: Zhao

first: Zhiyong

first: Rui

last: Qu

first: Yunbo

last: Li

last: Wen


title: Transcription factor EGR2 controls homing and pathogenicity of TH17 cells in the central nervous system.

city: Bethesda

first: Behdad (Ben)

last: Afzali Khoshkbijari

state: MD

address: 10 Center Drive, 10/8D03

department: Kidney Diseases Branch

institute: National Institutes of Diabetes, Digestive, and Kidney Diseases

summary: CD4+ T helper 17 (TH17) cells protect barrier tissues but also trigger autoimmunity. The mechanisms behind these opposing processes remain unclear. Here, we found that the transcription factor EGR2 controlled the transcriptional program of pathogenic TH17 cells in the central nervous system (CNS) but not that of protective TH17 cells at barrier sites. EGR2 was significantly elevated in myelin-reactive CD4+ T cells from patients with multiple sclerosis and mice with autoimmune neuroinflammation. The EGR2 transcriptional program was intricately woven within the TH17 cell transcriptional regulatory network and showed high interconnectivity with core TH17 cell-specific transcription factors. Mechanistically, EGR2 enhanced TH17 cell differentiation and myeloid cell recruitment to the CNS by upregulating pathogenesis-associated genes and myelomonocytic chemokines. T cell-specific deletion of Egr2 attenuated neuroinflammation without compromising the host’s ability to control infections. Our study shows that EGR2 regulates tissue-specific and disease-specific functions in pathogenic TH17 cells in the CNS.

overall_design: Genome-wide binding analysis of EGR2 in nuclei from in vitro polarized mouse 2D2 WT or Egr2ΔT TH17 cells via CUT&Tag.

first: Yuanyuan

first: Yan

first: Daniel

last: Chauss

first: Alejandro

last: Villarino

first: Verena

last: Link

first: Hiroyuki

last: Nagashima

first: Camille

last: Spinner

first: Vishal

middle: N

last: Koparde

first: Nicolas

last: Bouladoux

first: Michael

last: Abers

first: Timothy

middle: J

last: Break

first: Laura

middle: B

last: Chopp

first: Jung-Hyun

last: Park

first: Jinfang

last: Zhu

first: David

last: Wiest

first: Warren

last: Leonard

first: Michail

last: Lionakis

first: John

last: O’Shea

first: Behdad

last: Afzali

first: Yasmine

last: Belkaid

first: Vanja

last: Lazarevic


title: Single genomic enhancers drive experience-dependent GABAergic plasticity to maintain sensory processing in the adult cortex (RNA-Seq)

city: Rehovot

first: Ivo

last: Spiegel

address: 234 Herzl St

country: Israel

institute: Weizmann Institute of Science

summary: Experience-dependent plasticity of synapses modulates information processing in neural circuits and is essential for cognitive functions. The genome, via non-coding enhancers, was proposed to control information processing and circuit plasticity by regulating experience-induced transcription of genes that modulate specific sets of synapses. To test this idea, we analyze here the cellular and circuit functions of the genomic mechanisms that control the experience-induced transcription of Igf1 (insulin-like growth factor 1) in vasoactive intestinal peptide (VIP) interneurons (INs) in the visual cortex of adult mice. We find that two sensory-induced enhancers selectively and cooperatively drive the activity-induced transcription of Igf1 to thereby promote GABAergic inputs onto VIP INs and to homeostatically control the ratio between excitation and inhibition (E/I ratio)—in turn, this restricts neural activity in VIP INs and principal excitatory neurons and maintains spatial frequency tuning. Thus, enhancer-mediated activity-induced transcription maintains sensory processing in the adult cortex via homeostatic modulation of E/I ratio.

overall_design: RNA-Seq of dark-housed or light stimulated VIP INs nuclei after removal of one or both of the Igf1 enhancers

first: Ori

last: Roethler

first: Eran

last: Zohar

first: Katayun

last: Cohen-Kashi Malina

first: Lidor

last: Bitan

first: Harrison

last: Wren Gabel


title: Time-series transcriptome analysis of peripheral blood mononuclear cells obtained from individuals who received the SARS-CoV-2 mRNA vaccine

city: Kawasaki-City

first: Yoshiyuki

last: Watanabe

state: Kanagawa

address: 3-13-1 Nakajima, Kawasaki-ku

department: Dept. of Internal Medicine

institute: Kawasaki Rinko General Hospital

summary: Messenger ribonucleic acid (mRNA) vaccination against coronavirus disease 2019 (COVID-19) is an effective prevention strategy, despite a limited understanding of the molecular mechanisms underlying the host immune system and individual heterogeneity of the variable effects of mRNA vaccination. We assessed the time-series changes in the comprehensive gene expression profiles of 200 vaccinated healthcare workers by performing bulk transcriptome and bioinformatics analyses, including dimensionality reduction utilizing the uniform manifold approximation and projection (UMAP) technique. For these analyses, blood samples, including peripheral blood mononuclear cells (PBMCs), were collected from 214 vaccine recipients before vaccination (T1) and on Days 22 (T2, after second dose), 90, 180 (T3, before a booster dose), and 360 (T4, after a booster dose) after receiving the first dose of BNT162b2 vaccine (UMIN000043851). UMAP successfully visualized the main cluster of gene expression at each time point in PBMC samples (T1–T4). Through differentially expressed gene (DEG) analysis, we identified genes that showed fluctuating expression levels and gradual increases in expression levels from T1 to T4, as well as genes with increased expression levels at T4 alone. We also succeeded in dividing these cases into five types based on the changes in gene expression levels. High-throughput and temporal bulk RNA-based transcriptome analysis is a useful approach for inclusive, diverse, and cost-effective large-scale clinical studies.

overall_design:
Time-course gene expression profiling analysis of RNA-seq data for COVID-19 vaccinated samples.
Raw data not provided due to patient privacy concerns.

first: Hiroyuki

last: Yamamoto

first: Hiroki

last: Danno

first: Masakazu

last: Fukuda


title: Gene expression profile at single cell level of peripheral blood mononuclear cells (PBMCs) from 17 healthy donor

status: Public on Jun 29 2023

city: Beijing

first: Jiawe

last: Chen

state: Beijing

address: Peking university

institute: Peking university

summary: Quantifying aging rate is important for evaluating age-associated decline and mortality. Here we generate a similar dataset for a reference 17-sample aging cohort to compute a single cell level aging clock. The cell type annotations are available in https://doi.org/10.6084/m9.figshare.23789844.v1.

overall_design:
All volunteers were evaluated as generally healthy at the time of blood collection based on evaluation of their medical history and assessment of their vital signs. In our present study, 17 healthy volunteers were enrolled in the single-cell RNA sequencing.

>>>Submitter states that raw data are not publicly available due to patient privacy concerns.<<<

first: Hongming

last: Zhu

first: Jiawei

first: Lei

last: Gao

first: Kangping

last: Liu

first: Jieru

last: Zhou

first: Liangliang

last: Ma

first: Zhongmin

first: Jing-Dong

last: Han


title: Single genomic enhancers drive experience-dependent GABAergic plasticity to maintain sensory processing in the adult cortex (ChIP-Seq)

first: Ivo

last: Spiegel

summary: Experience-dependent plasticity of synapses modulates information processing in neural circuits and is essential for cognitive functions. The genome, via non-coding enhancers, was proposed to control information processing and circuit plasticity by regulating experience-induced transcription of genes that modulate specific sets of synapses. To test this idea, here we analyze the cellular and circuit functions of the genomic mechanisms that control the experience-induced transcription of Igf1 (Insulin-like growth factor 1) in VIP interneurons (INs) in the adult visual cortex. We find that two sensory-induced enhancers selectively and cooperatively drive the activity-induced transcription of Igf1 to thereby promote GABAergic inputs onto VIP INs and to homeostatically control the ratio between excitation and inhibition (E/I-ratio), and that this restricts neural activity in VIP INs and principal excitatory neurons and maintains spatial frequency tuning. Thus, enhancer-mediated activity-induced transcription maintains sensory processing in the adult cortex via homeostatic modulation of E/I-ratio.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone 3 lysine 27 acetylation (H3K27Ac) in primary neuronal cortical cultures before and after 2hr stimulation with KCl

first: Ori

first: Eran

middle: W

last: Gabel


title: An auto-suppression mechanism for Tet dioxygenase protects the mouse genome from oxidative demethylation

status: Public on Jun 26 2023

city: shanghai

first: Zhenyu

last: Shao

state: --- Select a state ---

address: Yueyang Road 320

department: Center for Excellence in Molecular Cell Science

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary: Dynamic DNA methylation and demethylation regulate gene expression during development. While DNA methyltransferases (DNMTs) establish and maintain cytosine methylation patterns, Ten-eleven translocation (Tet) dioxygenases catalyze sequential oxidation of 5-methylcytosine (5mC) to promote demethylation. Target-specific 5mC oxidation requires precise regulation of the Tet enzymatic activity. However, the mechanism underlying their activity control remains largely unexplored. Here we show a large low-complexity domain (LCD), present within the catalytic domain of Tet3, functions to repress the dioxygenase activity. Recombinant LCD-deleted Tet3 exhibits enhanced activity to convert 5mC into oxidized species. Deletion of the Tet3 LCD in mouse oocytes renders 5mC oxidation indiscriminately across the genome, leading to most prominently the derepression of ERVK retrotransposons and upregulation of adjacent genes. The extensive 5mC oxidation is associated with impairments in oocyte development. These findings suggest an intrinsic auto-regulatory mechanism of Tet3 dioxygenase operating to ensure a tight regulation of its enzymatic activity to achieve spatiotemporal specificity of methylome reprogramming during oocyte development.

overall_design: Genome binding/occupancy profiling by high throughput sequencing for H3K9me3 in WT, Tet3 LCD KO, and Dnmt3a, Tet3 LCD DKO GV oocytes

first: Zhen-Yu

first: Xiao-Jie

last: Zhang

first: Ya-Rui

last: Du


title: Maternal TDP-43 interacts with RNA Pol II and regulates zygotic genome activation

status: Public on Jun 23 2023

first: Fengling

address: 30 Shuangqing Rd.

institute: Tsinghua University

summary: Zygotic genome activation (ZGA) is essential for early embryonic development. However, the regulation of ZGA remains elusive in mammals. Here we report that a maternal factor TDP-43, a nuclear transactive response DNA-binding protein, regulates ZGA through RNA Pol II and is essential for mouse early embryogenesis. Maternal TDP-43 translocates from the cytoplasm into the nucleus at the early two-cell stage when minor to major ZGA transition occurs. Genetic deletion of maternal TDP-43 results in mouse early embryos arrested at late two-cell stage and female infertile. TDP-43 co-occupies with RNA Pol II as large foci in the nucleus and also at the promoters of ZGA genes at the late two-cell stage. Biochemical evidence indicates that TDP-43 binds Polr2a and Cyclin T1. Depletion of maternal TDP-43 caused the loss of Pol II foci and reduced Pol II binding on chromatin at major ZGA genes, accompanied by defective ZGA. Collectively, our results suggest that maternal TDP-43 is critical for mouse early embryonic development, in part through facilitating the correct RNA Pol II configuration and zygotic genome activation.

overall_design: RNA-seq experiments were performed in WT and TDP-43 knockout mouse oocytes, one-cell and two-cell embryos.Stacc-seq experiments were applied to WT FGO and embryos with the antibodies against  Pol II or TDP43 and to  TDP-43 knockout two-cell embryos with the Pol II antibody.

first: Xiaoqing

last: Nie

first: Qianhua

last: Xu

first: Feng

last: Li


title: Single genomic enhancers drive experience-dependent GABAergic plasticity to maintain sensory processing in the adult cortex

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


title: Cysteine-Rich Intestinal Protein 1 is a Novel Surface Marker for Myometrial Stem/Progenitor Cells [SingleCell_RNAseq]

status: Public on Jun 22 2023

city: Grand Rapids

first: Emmanuel

last: Paul

state: Michigan

address: 400 Monroe Ave NW

institute: MSU

summary: To find new stem/progenitor myometrium human cell surface marker

overall_design: Combining bulk-RNA-seq and single cell RNA-seq from 5 human myometrial samples

first: Tyler

last: Carpenter

first: Sarah

last: Fitch

first: Rachael

last: Sheridan

first: Kin

last: Lau

first: Ripla

last: Arora

first: Jose

last: Teixeira


title: Cysteine-Rich Intestinal Protein 1 is a Novel Surface Marker for Myometrial Stem/Progenitor Cells [SidePopulation_RNAseq]


title: Cysteine-Rich Intestinal Protein 1 is a Novel Surface Marker for Myometrial Stem/Progenitor Cells

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

overall_design: Refer to individual Series


title: Cysteine-Rich Intestinal Protein 1 is a Novel Surface Marker for Myometrial Stem/Progenitor Cells [SUSD2_RNAseq]


title: Inhibition of AXL Receptor Tyrosine Kinase Enhances Brown Adipose Tissue Functionality in mice.

city: Schwerzenbach

first: Adhideb

last: Ghosh

address: Schorenstrasse 16

department: Health Sciences and Technology

country: Switzerland

institute: ETH Zurich


title: Inhibition of AXL Receptor Tyrosine Kinase Enhances Brown Adipose Tissue Functionality in mice [HiSeq]

summary: To identify transcriptomic differences in interscapular brown adipose tissue depots from HFD-challenged wild-type (WT) vs. Axl KO (whole-body Axl Receptor knockout) mice

overall_design: WT or Axl KO mice were placed on a HFD challenge at 6-8 weeks of age for a total of 24 weeks. At the end of the study, iBAT depots were dissected.

first: Vissarion

last: Efthymiou

first: Umesh

last: Ghoshdastider

first: Lianggong

last: Ding

first: Christian

last: Wolfrum


title: WAPL functions as a rheostat of Protocadherin isoform diversity that controls neural wiring

city: SAN FRANCISCO

first: Lea

last: Kiefer

address: 1651 4th Street, Weill Neurosci RM 471A

institute: UCSF

summary: Neural-type specific expression of clustered Protocadherin (Pcdh) proteins is essential for the establishment of connectivity patterns during brain development. In mammals, deterministic expression of the same Pcdh isoform promotes minimal overlap of tiled projections of serotonergic neuron axons throughout the brain, while stochastic expression of Pcdh genes allows for convergence of tightly packed overlapping olfactory sensory neuron axons into targeted structures. How can the same gene locus generate opposite transcriptional programs that orchestrate distinct spatial arrangements of axonal patterns? Here, we reveal that cell-type specific Pcdh expression and axonal behavior rest on the activity of cohesin and its unloader WAPL. While cohesin erases genomic-distance biases in Pcdh choice, WAPL functions as a rheostat of cohesin processivity that determines Pcdh isoform diversity.

overall_design: Examination of RNA and genome folding within the clustered Protocadherin locus in olfactory sensory neurons, the olfactory epithilium, and the Raphe from mice carrying genetic mutations.

first: Daniele

last: Canzio


title: Systemwide effects of ER-intracellular membrane contact site disturbance in primary endothelial cells

city: Helsinki

first: Juuso

last: Taskinen

address: Tukholmankatu 8

country: Finland

institute: Minerva Foundation Institue for Medical Research

summary: We investigate how the double knock down of VAPA and VAPB affected the macromolecule profile of human umbilical vein endothelial cells by transcriptomic and lipidomic profiling

overall_design: Comparative gene expression profiling analysis of RNA-seq data for VAPA & VAPB shRNA treated cells or non-targeting shRNA treated cells

first: Vesa

last: Olkkonen

first: Hanna

last: Ruhanen

first: Reijo

last: Käkelä

first: Silke

last: Matyisk


title: DNA Methylation Signatures Differentiate Meningiomas from Normal Dura

city: Los Angeles

first: Michelle

middle: Ariana

last: Wedemeyer

address: 1200 N State St, Suite 3300

department: Neurosurgery

institute: University of Southern California


title: DNA Methylation Signatures Differentiate Meningiomas from Normal Dura [OmniSNP]

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: Meningiomas are the most common primary brain tumor.  Though typically benign with a low mutational burden, histopathologic analysis has poor predictive value for malignant behavior and there are no proven chemotherapies.  Although DNA methylation patterns distinguish subgroups of meningiomas and have higher predictive value for tumor behavior than histologic classification, little is known about differences in DNA methylation between meningiomas and surrounding normal dura tissue.  Using multimodal studies of meningioma/dura pairs, we identified 4 distinct DNA methylation patterns.  Diffuse DNA hypomethylation of malignant meningiomas readily facilitated their identification from lower grade tumors by unsupervised clustering.  All clusters and 12/12 meningioma-dura pairs exhibited hypomethylation of the gene promoters of a module associated with the craniofacial patterning transcription factor FOXC1 and its upstream lncRNA FOXCUT.  Furthermore, we identified an epigenetic continuum of increasing hypermethylation of polycomb repressive complex target promoters with increased histopathologic grade suggesting progressive epigenetic dysregulation is associated with increasing tumor aggressiveness.  These findings are a starting point for future investigations of the role of epigenetic dysregulation of FOXC1 and cranial patterning genes in early stages of meningioma formation as well as studies of the utility of polycomb inhibitors for treatment of aggressive meningiomas.

overall_design: 19 meningiomas (11 WHO grade I, 6 WHO grade II, 4 WHO grade III) underwent genotyping with a HumanOmni-Express v12.

first: Gabriel

last: Zada

first: Suhn

last: Rhie

middle: A

first: Ivo

last: Muskins

first: Joseph

last: Wiemels

first: Daniel

last: Weisenberg

first: Kai

last: Wang

first: Debraj

last: Mukerjee

first: Ben

last: Strickland


title: Thymic epithelial cell potency and fate in early organogenesis assessed by single cell transcriptional and functional analysis [Smart-Seq2]

status: Public on Jun 21 2023

city: Edinburgh

first: Catherine

middle: Clare

last: Blackburn

address: IRR North, 5 Little France Drive

department: School of Biological Sciences

country: United Kingdom

institute: University of Edinburgh

summary: During development, cortical (c) and medullary (m) thymic epithelial cells (TEC) arise from the third pharyngeal pouch endoderm.  Current models suggest that within the thymic primordium most TEC exist in a bipotent/common thymic epithelial progenitor cell (TEPC) state able to generate both cTEC and mTEC, at least until embryonic day 12.5 (E12.5) in the mouse.  This view, however, is challenged by recent transcriptomics and genetic evidence.  We therefore set out to investigate the fate and potency of TEC in the early thymus.  Here using single cell (sc) RNAseq we identify a candidate mTEC progenitor population at E12.5, consistent with recent reports.  Via lineage-tracing we demonstrate this population is mTEC fate-restricted, validating our bioinformatics prediction.  Using potency analyses we also establish that most E11.5 and E12.5 progenitor TEC are cTEC-fated.  Finally, we show that overnight culture causes most if not all E12.5 cTEC-fated TEPC to acquire functional bipotency and provide a likely molecular mechanism for this changed differentiation potential.  Collectively, our data overturn the widely held view that a common TEPC predominates in the E12.5 thymus, showing instead that sublineage-primed progenitors are present from the earliest stages of thymus organogenesis but that these early fetal TEPC exhibit cell-fate plasticity in response to extrinsic factors.  Our data provide a significant advance in understanding of fetal thymic epithelial development and thus have implications for thymus-related clinical research, in particular research focussed on generating TEC from pluripotent stem cells.

overall_design: scRNAseq SmartSeq2 profiling of individual EPCAM+PLET1+ cells from E10.5 or E12.5 primordia

first: An

last: Chengrui

first: Alison

last: Farley

first: Sam

last: Palmer

first: Dong

last: Liu

first: Anastasia

middle: I

last: Kousa

first: Paul

last: Rouse

first: Viktoria

last: Major

first: Joanna

last: Sweetman

first: Jan

last: Morys

first: Andrea

last: Corsinotti

first: Jennifer

last: Nichols

last: Ure

first: Renee

last: McLay

first: Luke

last: Boulter

first: Jon

last: Chapman

first: Simon

middle: R

last: Tomlinson

first: C

middle: C


title: Ethanol induced transcriptional and translational changes in Aldh1l1-EGFP/Rpl10a cortical astrocyte cultures

city: Portland

first: Marina

last: Guizzetti

state: OR

address: 3710 SW US Veterans Hospital Rd

department: Behavioral Neuroscience

institute: Oregon Health & Science University; Portland VA Research Service

summary: The role astrocytes play in brain development and function has come under increased focus as the diversity of roles they are involved in has become apparent. We have previously shown ethanol exposed astrocytes alter neuronal neurite outgrowth in an in vitro co-culture system and that ethanol alters the astrocyte produced extracellular matrix (ECM) in vitro, with similar alterations in vivo. Here we utilize the translating ribosome affinity purification (TRAP) procedure in Aldh1l1-EGFP/Rpl10a transgenic mouse primary cortical astrocyte cultures to transcriptionally and translationally profile the astrocyte response to ethanol. We found large differences in the total RNA pool in comparison to the translating RNA pool while the ethanol response within each pool showed a large degree of overlap. Comparisons to published datasets indicate the in vitro model used here are most similar to PD1-PD7 in vivo cortical astrocytes and the ethanol regulated genes showed significant overlap with models of chronic ethanol exposure in astrocytes and a model of third-trimester ethanol exposure in the hippocampus and cerebellum. These findings will further our understanding of the effects of ethanol on astrocyte gene expression and protein translation and how these changes alter brain development.

overall_design: Primary cortical astrocyte cultures from Aldh1l1-EGFP/Rpl10a mice, treated with 50 mM ethanol or control. Translating RNA Affinity Purification (TRAP) was run on the in vitro astrocytes to collect total RNA (input) and TRAP RNA.

first: Joel

last: Hashimoto

first: Xiaolu

last: Zhang


title: Single Cell Transcriptomic Analysis of Clinical-used MSCs Derived From Adipose Tissue, Bone Marrow, Placenta Membrane and Umbilical Cord

status: Public on Jun 19 2023

city: TianJin

first: Yuchen

last: Gao

address: 288 Nanjin Road, Tianjin

institute: Institute of Hematology &Blood Disease Hospital,Chinese Academy of Medical Sciences

summary: Here, we use single cell transcriptomics to characterize a dynamic senescence process of in vitro expanded MSC products from adipose tissue (AD), bone marrow (BM), placenta membrane (PM) and umbilical cord (UC). We found that cultured MSCs underwent progressive cell aging. As compared to perinatal MSCs (derived from PM and UC), adult MSCs (derived from AD and BM)  showed higher degree of senescence and impaired immunosuppressive function. Moreover, we identified the transcriptional network regulating the intra-population functional diversity, which provides us guidance to drive reprogramming of determined MSCs lineage with specific cellular functions for a particular therapeutic intent.

overall_design: We performed droplet-based scRNA-seq of over 40,000 cells to construct a molecular landscape and dissecting the heterogeneity of MSCs from perinatal and adult human tissues.

first: Ying

last: Chi

first: Jun

last: Wei

first: Lei


title: Single-cell RNA sequencing reveals peripheral blood mononuclear immune cell landscape associated with operational tolerance in a kidney transplant recipient

status: Public on Jun 20 2023

city: Baltimore

first: Amol

middle: Carl

last: Shetty

state: Maryland

address: 670 W. Baltimore Street, Floor 3

department: Institute for Genome Sciences

institute: University of Maryland Baltimore


title: A comprehensive DNA methylation atlas for noncancer human tissue types

status: Public on Jun 15 2023

first: Shuo

last: Li

address: 630 Charles E Young Dr S

institute: UCLA

summary: Deciphering the tissue origin of cfDNA can reveal abnormal cell death because of diseases, which has great clinical potential in disease detection and monitoring. Here we present one of the largest comprehensive and high-resolution methylation atlas based on Reduced Representative Bisulfite Sequencing (RRBS) data of 521 noncancer tissue samples spanning 29 major types of human tissues. We systematically identified fragment-level tissue-specific methylation patterns and extensively alidated the methylation signature atlas in independent methylation datasets, orthogonal epigenomic markers, and transcription regulatory elements. Based on the rich tissue methylation atlas, we develop the first supervised tissue deconvolution approach, a deep-learning-powered model, cfSort, for sensitive and accurate tissue deconvolution in cfDNA.

overall_design:
The RRBS libraries of the genomic DNA from the 521 tissue samples were constructed following the standard RRBS protocol. 100-200 ng of intact genomic DNA in the volume of 21.5ul was used as input material. Restriction digestion was done with 2.5ul 10xCutSmart buffer and 1ul MspI (NEB) for 18h at 37 oC and 20min at 65 oC. 0.5ul 10xCutSmart buffer, 0.3ul dACGTP mixture (100mM dATP, 10mM dCTP, 10mM dGTP), 1ul Klenow (exo-, 5U/ul, NEB) and 2.6ul RT-PCR water, 0.6ul 50mM DTT (ThermoFisher) was added to the mixture for end repair and A-overhang addition with the program 30 oC for 20min, 37 oC for 1h and 75 oC for 20min. Adapter ligation was then performed with 1ul 10xThermoFisher HC T4 ligase buffer, 0.4ul 100mM ATP (ThermoFisher), 0.2ul 50mM DTT, 1ul ThermoFisher HC T4 DNA ligase (30 Weiss Unit/ul), 30ng home-made duplex UMI adapter with all the cytosines methylated (protocol adopted from Kennedy et al.) at 16 oC for 20h and 65 oC for 20min. Bisulfite conversion of the adapter-ligated product was carried out with QIAGEN EpiTect plus DNA bisulfite kit following their protocol for two rounds of conversion. The converted product was purified with Qiagen MinElute spin column and eluted with 20ul RT-PCR water. PCR amplification was done using the NEBNext Multiplex Oligos for Illumina (2.5ul of universal and index primer each) and 25ul KAPA HiFi HotStart Uracil+ ReadyMix (Roche) with the following cycling conditions: 98 oC for 45s, 9 cycles of 98 oC for 15s, 60 oC for 30s and 72 oC for 30s, followed by a final extension at 72 oC for 5min. The PCR product was purified with 1x AmpureXP beads and eluted with 30ul EB buffer. DNA concentration was measured by Qubit 1xdsDNA HS assay. 5% TBE-UREA PAGE and bioanalyzer assay was performed as quality control on each library before sequencing.
***Submitter declares that the raw data have been deposited in EGA (EGAS00001007213) due to patient privacy concerns***

first: Weihua

last: Zeng

first: Qiao

last: Liu

first: Wenyuan

first: Mary

middle: L

last: Stackpole

first: Yonggang

last: Zhou

first: Arjan

last: Gower

first: Kostyantyn

last: Krysan

first: Preeti

last: Ahuja

first: David

last: Lu

first: Steven

middle: S

last: Raman

first: William

last: Hsu

first: Denise

last: Aberle

first: Clara

middle: E

last: Magyar

first: Samuel

last: French

first: Steven-Huy

last: Han

first: Edward

last: Garon

first: Vatche

last: Agopian

first: Wing

middle: H

last: Wong

middle: M

last: Dubinett

first: Xianghong


title: Transgene directed induction of a human embryo model from pluripotent stem cells

status: Public on Jun 14 2023

city: Seattle

first: Nobuhiko

last: Hamazaki

state: Washington

address: Foege Building S-210 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

summary: The human embryo undergoes morphogenetic transformations following implantation into the uterus and yet our knowledge of this crucial stage is limited by the inability to observe the embryo in vivo. Here, we establish a stem cell-derived human post-implantation embryo model comprised of embryonic and extraembryonic tissues. Overexpression of the transcription factors GATA6 and SOX17 or GATA3 and AP2g in hESCs allowed us to generate hypoblast-like and trophoblast-like cells, respectively. We established conditions to combine these extraembryonic-like cells with wildtype embryonic stem cells and promote their self-organization into structures that mimic aspects of the post-implantation human embryo. These aggregates contain an inner pluripotent epiblast-like domain surrounded by both hypoblast- and trophoblast-like tissues. We show that this human embryo stem cell model robustly generates several cell types, including amnion-, extraembryonic mesenchyme- and primordial germ cell-like cells. Using perturbation experiments, we demonstrated that these populations arise in response to BMP signaling. This model also allowed us to identify an inhibitory role for SOX17 in the specification of anterior hypoblast-like cells. Modulation of the subpopulations in the hypoblast-like compartment demonstrated that these extraembryonic-like cells impact epiblast-like domain differentiation, highlighting functional tissue-tissue crosstalk. In conclusion, this modular, tractable model of the human embryo that includes both embryonic- and extraembryonic-like cells has the potential to probe key questions of human post-implantation development.

overall_design: single cell 10x multiome (RNA+ATAC) sequencing on transgene-directed human embryo models.

first: Bailey

last: Weatherbee

first: Carlos

last: Gantner

first: Riza

last: Daza

first: Lisa

middle: K

last: Iwamoto Stohl

first: Jay

last: Shendure

first: Magdalena

last: Zernicka-Goetz


title: Single genomic enhancers drive experience-dependent GABAergic plasticity to maintain sensory processing in the adult cortex (RNA-Seq II)

first: Ivo

last: Spiegel

summary: Experience-dependent plasticity of synapses modulates information processing in neural circuits and is essential for cognitive functions. Genomic enhancers are thought to modulate specific sets of synapses by regulating experience-induced transcription to thereby promote neural circuit plasticity. However, this idea remains untested. Thus, here we analyze the cellular and circuit functions of the genomic mechanisms that control the experience-induced transcription of Igf1 (Insulin-like growth factor 1) in disinhibitory VIP interneurons in the adult visual cortex. We find that two sensory-induced enhancers selectively and cooperatively drive sensory-induced Igf1 transcription and that these enhancers homeostatically control the ratio between excitation and inhibition (E/I-ratio) and neural activity in VIP interneurons to thereby restrict visual acuity. Thus, single experience-regulated enhancers are essential for maintaining sensory processing. Since cortical plasticity scales with neural activity in VIP interneurons, this also suggests that experience-induced transcription restricts plasticity in adult neural circuits to preserve the brain’s functional integrity.

overall_design: Assessing the impact of residual neuronal activity in the visual cortex during dark-housing. Cortex was silenced with a viral vector expressing the Kir2.1 channel in all neurons.

first: Ori

last: Roethler

first: Eran

last: Zohar

first: Katayun

last: Cohen-Kashi Malina

first: Lidor

last: Bitan

first: Harrison

last: Wren Gabel


title: Single-cell sequencing reveals cancer cell heterogeneity in a murine breast cancer lymph node metastasis model

city: Boston

first: Pin-Ji

last: Lei

state: Massachusetts

address: 100 Blossom Street

department: Department of Radiation Oncology

institute: Massachusetts General Hospital

summary: Using a mouse model of breast cancer that develops spontaneous lymph node metastasis, we performed high-resolution single-cell RNA sequencing (scRNA-Seq) of the primary tumor and TDLN to measure how cancer cells adapt to the dynamic lymph node microenvironment. To understand the dynamic change of lymph node microenvironment after cancer cell invasion, we also compared the gene-expression alteration between naive lymph node and TDLN at single-cell level.

overall_design: 4T1 cells were implanted into the left-side (supine position) fourth mammary fat pad of adult (6-10 weeks) female Balb/c mice. The primary tumors were collected at day 14 or when tumor size reached 250 mm3. After resection, we sutured the wound and allowed these mice to grow spontaneous lymph node metastases. The primary tumors were cut into 1-2 mm pieces and dissociated into single cells. To decrease bias from individual mice, we collected primary tumors from 4 mice and pooled them together for single-cell library preparation. On day 28, we sacrificed the mice and collected the inguinal lymph nodes (n = 4) to create the sample for the TDLN datasets. All analyzed lymph nodes were dissociated into single cells with digestion buffer (200 ug/ml collagenase I, 800 ug/mL Dispase, 100ug / ml DNase I). All samples used ACK buffer (Thermo Fisher) to lyse red blood cells and had the cell concentration and viability tested using a Nadia instrument (Dolomite Bio). The loading quantity of viable cells for 10x Genomics platform was estimated to capture around 5000 cells.

first: Ethel

last: Pereira

first: Semir

last: Beyaz

first: Timothy

middle: P

last: Padera


title: 2-hydroxypropyl-beta-cyclodextrin treatment induces modest immune activation in healthy rhesus macaques

status: Public on Jun 12 2023

first: Jason

last: Brenchley

address: 4 Center Drive

institute: NIAID


title: 2-hydroxypropyl-beta-cyclodextrin treatment induces modest immune activation in healthy rhesus macaques [RNA-seq]

summary: Experimental SIV infection of Asian macaques is an excellent model for HIV disease progression and therapeutic development. Recent coformulations of nucleoside analogs and an integrase inhibitor have been used for parenteral antiretroviral (ARV) administration in SIV-infected macaques, successfully resulting in undetectable plasma SIV RNA. In a cohort of SIVmac239-infected macaques, we recently observed that administration of co-formulated ARVs resulted in an unexpected increase in plasma levels of soluble CD14 (sCD14), associated with stimulation of myeloid cells. We hypothesized that the coformulation solubilizing agentKleptoseTM(2-hydroxypropyl-beta-cyclodextrin; HPβCD) may induce inflammation with myeloid cell activation and the release of sCD14. Herein, we stimulated peripheral blood mononuclear cells (PBMCs) from healthy macaques with HPβCD from different commercial sources and evaluated inflammatory cytokine productionin vitro.Treatment of PBMCs resulted in increased sCD14 release and myeloid cell IL-1bproduction - with stimulation varyingsignificantlyby HPβCD source - and destabilized lymphocyte CCR5 surface expression.We further treated healthy macaques withKleptosealone.In vivo, we observed modestly increased myeloid cell activation in response to Kleptose treatment without significant perturbation of the immunological transcriptome or epigenome.Our resultsdemonstrate a need for vehicle-only controls and highlight immunological perturbations that can occur when using HPβCD in pharmaceutical co-formulations.

overall_design: Samples were obtained before or after treating animals with 2-hydroxypropyl-beta-cyclodextrin at 15% (w/w) Kleptose(TM) HBP parenteral grade (Roquette #346111109D) subcutaneously at 1 ml/kg/day for up to 120 days.

first: Alexandra

last: Ortiz

first: Andrew

last: Rahmberg

first: Tovah

last: Markowitz


title: Global Epigenome and Transcriptome Maps of Human Trophoblast Cell Lineage Development

city: Kansas City

first: Boryana

last: Koseva

state: MO

address: 2420 Pershing Road

department: CMRI

institute: Children's Mercy Hospital


title: Effects of  Erlotinib treatment on GSCs (RNA-seq)

status: Public on Jun 10 2023

city: Wuhan

first: Wei

last: Wang

state: Hubei

address: 13 Hangkong Road

institute: Huazhong University of Science and Technology Tongji Medical College

summary: We investigated the transcriptional regulation by EGFR signaling in GSCs

overall_design: GSC456 cells treated with DMSO or Erlotinib were subjected to RNA-seq

last: Huang


title: A history of repeated alcohol intoxication promotes cognitive impairment and gene expression signatures of disease progression in the 3xTg mouse model of Alzheimer’s disease

status: Public on Jun 09 2023

city: Bologna

first: Chiara

last: Cabrelle

address: Via Irnerio, 49

country: Italy

institute: University of Bologna

summary: The impact of alcohol abuse on AD is poorly understood. Here we show that the onset of neurocognitive impairment in a mouse model of AD is hastened by repeated alcohol intoxication through exposure to alcohol vapor and we provide a comprehensive gene expression dataset of the prefrontal cortex by single nucleus RNA sequencing of 113,242 cells. Several genes previously associated with AD in humans by GWAS were differentially regulated in specific neuronal populations. Gene expression patterns of AD mice with a history of alcohol intoxication were more similar to the gene expression signatures of older AD mice with more advanced disease and cognitive impairment than to those of younger AD mice with prodromic disease, suggesting that alcohol promotes transcriptional changes consistent with AD progression. Our gene expression dataset at the single cell level provides a unique resource for investigations of the molecular bases of the detrimental role of excessive alcohol intake in AD.

overall_design: Single nucleus RNA-Seq of the prefrontal cortex of 16 male 3xTg-AD and WT mice with and without histories of repeated alcohol intoxication through exposure to alcohol vapor (n=4).

first: Pietro

last: Sanna

first: Federico

last: Giorgi

first: Vez

last: Repunte-Canonigo

first: Daniele

last: Mercatelli


title: Inhibition of AXL Receptor Tyrosine Kinase Enhances Brown Adipose Tissue Functionality in mice [NovaSeq]

first: Adhideb

last: Ghosh

summary: To identify transcriptomic differences in interscapular brown adipose tissue depots from HFD-challenged wild-type (Axl-floxed Cre-) vs. iFAXLKO (Axl-floxed Cre+) mice

overall_design: WT (floxed-Axl Cre-) vs. iFAXLKO under HFD challenge

first: Vissarion

last: Efthymiou

first: Lianggong

last: Ding

first: Christian

last: Wolfrum


title: ASH1L methyltransferase deposits H3K4me3 and FACT for damage verification in nucleotide excision repair [ChIP-Seq]

status: Public on Jun 08 2023

city: Zurich

first: Michelle

last: Yancoskie

address: Winterthurerstr. 260

department: Vetsuisse Faculty

institute: Institute of Veterinary Pharmacology and Toxicology, University of Zurich

summary: To recognize DNA damage, nucleotide excision repair (NER) deploys a multipart mechanism by which the XPC sensor detects helical distortions followed by engagement of TFIIH for lesion verification. Accessory players ensure that this factor handover takes place on chromatin where DNA is wrapped around histones. We show that the histone methyltransferase ASH1L, once activated by MRG15, accelerates global-genome NER activity. Upon UV irradiation, ASH1L deposits H3K4me3 marks all over the genome (except in gene promoters), thus priming chromatin for relocations of XPC from native to damaged DNA. ASH1L further recruits the histone chaperone FACT to UV lesions. In the absence of ASH1L, MRG15 or FACT, XPC persists on damaged DNA without being able to deliver lesions to the TFIIH verifier. We conclude that ASH1L implements repair hotspots whose H3K4me3 and FACT occupancy confers an active promoter-like code and organization of histones that make DNA damage verifiable by the NER machinery.

overall_design: Chromatin immunoprecipitation sequencing (ChIP-seq) for XPC protein and for histone mark H3K4me3 in wildtype U2OS cells and in U2OS cells in which ASH1L or (as a control for WT and ALKO cells instead of an input control) XPC has been deleted. Wildtype, ASH1L knockout, and XPC knockout cells were either not exposed to UV or assayed 1 or 3 hours post UV.

first: Corina

last: Maritz

middle: N

first: Sarah

last: Diethelm

first: Reihaneh

last: Khaleghi

first: Sonja

last: Brülisauer

first: Natalia

last: Ferreira

first: Yang

last: Jiang

first: Shana

middle: J

last: Sturla

first: Hanspeter

last: Naegeli


title: ASH1L-MRG15 methyltransferase deposits H3K4me3 and FACT for damage verification in nucleotide excision repair

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

overall_design: Refer to individual Series


title: ASH1L methyltransferase deposits H3K4me3 and FACT for damage verification in nucleotide excision repair [ATAC-Seq]

overall_design: Assay for transposase-accessible chromatin using sequencing (ATAC-seq) was performed in wild type and ASH1L knockout U2OS cells either untreated (not exposed to UV) or 3 hours after UV treatment.