title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 0.05mGy/day gamma-rays for 400 days (Primary screening for 0.05mGyA familly).


title: Molecular mechanisms underlying zinc oxide nanoparticle induced insulin resistance in mice

status: Public on Aug 20 2022

city: Harbin

first: Hailong

last: Hu

address: No.2 of Yikuang Road, 2E-215

country: China

institute: Harbin Institute of Technology

type: Expression profiling by high throughput sequencing

summary: Zinc oxide nanoparticles (ZnO NPs) represent an important class of commercially applied materials. Recently, adverse effects of ZnO NPs were found in humans and animals following ingestion, although the effects on endocrine system disease remain unclear. In this study, ZnO NPs were orally administered to mice, and at doses of 25 mg/kg bw (body weight) ZnO NPs and above, plasma glucose increased significantly. The genome-wide effects of ZnO NPs were then investigated using RNA-sequencing technology. In the cluster analysis, the most significantly enriched Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways concerned membranes and their close association with endoplasmic reticulum (ER) stress and reactive oxygen species (ROS) generation. Biochemical and gene and protein expression analyses revealed that ZnO NPs activated a xenobiotic biodegradation response and increased the expression of cytochrome P450 (CYP) enzymes in mice livers, leading to ER stress. The ER stress increased ROS generation. The high levels of ROS activated the MAPK and NF-B pathways and induced an inflammation response, resulting in the phosphorylation of insulin receptor substrate 1. Thus, the insulin resistance that developed was the primary mechanism for the increase in the plasma glucose of mice treated orally with ZnO NPs.

overall_design: Examination of genome-wide expressions in Control, Week8 and Week 12 groups

first: Ning

last: Gu


title: Exploring the molecular mechanism and and related signaling pathways of annexin A2 in human retinal vascular endothelial cells

city: shanghai

first: zichang

last: zhao

address: 168 changhai road

department: Ophthalmology

institute: Changhai Hospital

summary: To investigate the role and mechanism of ANXA2 in retinal neovascularization, we used interfering and overexpressing lentivirus to intervene in HREC cells, respectively. Divided into interference group (negative control group and positive interference group), overexpression group (negative control group, overexpression positive control group). The mechanism of action of annexin A2 in human retinal vascular endothelium was explored by real-time PCR to quantify the expression of molecular genes in samples.

overall_design: We used interfering and overexpressing lentivirus to intervene in HREC cells for 72 hours and isolated samples for gene expression. Three independent experiments were performed for each sample.

first: Zi

middle: C

last: Zhao

first: Ting

last: Guo

first: Shi

middle: H


title: Effect of GSK591 on gene expression during decidualization of human endometrial stromal cells

city: Nanjing

first: Xinyu

last: Cai

address: No.321 Zhongshan Road

department: Reproductive Medicine Center

institute: Drum Tower Hospital，Nanjing University Medical School

summary: To investigate the role of PRMT5 in decidualization, RNA-seq and gene expression profiling analysis was applied in control hEnSCs, GSK591 treated hEnSCs, decidualized hEnSCs and GSK591 treated decidualized hEnSCs

overall_design: Comparative gene expression profiling analysis of RNA-seq data for human endometrial stromal cells with or without GSK591 treatment during decidualization


title: Single Cell Transcriptome Analysis of Regenerating RGCs Reveals Potent Glaucoma Neural Repair Genes [First_batch_sur_RGCs]

city: Palo Alto

first: Xue

last: Feng

state: CA

address: 1651 Page Mill road

country: USA

institute: Stanford

summary: Axon regeneration holds great promise for neural repair of CNS axonopathies, including glaucoma. Pten deletion in retinal ganglion cell (RGC) promotes potent optic nerve regeneration, but only a small population of Pten-null RGCs are actually regenerating RGCs (regRGCs); most surviving RGCs (surRGCs) remain non-regenerative. Here we developed a strategy to specifically label and purify regRGCs and surRGCs respectively from the same Pten deletion mice after optic nerve crush, in which they differ only in their regeneration capability. Smart-Seq2 single cell transcriptome analysis revealed novel regeneration-associated genes that significantly promote axon regeneration. The most potent of these, Anxa2, acts synergistically with its ligand tPA in Pten deletion-induced axon regeneration. Anxa2, its downstream effector ILK, and Mpp1 dramatically protect RGC somata and axons and preserves visual function in a clinically relevant model of glaucoma, demonstrating the exciting potential of this innovative strategy to identify novel effective neural repair candidates.

overall_design: RGCs mRNA profiles of Pten knock out mice

first: Pei

last: Zhuang


title: Single Cell Transcriptome Analysis of Regenerating RGCs Reveals Potent Glaucoma Neural Repair Genes [Second_batch_sur_RGCs]


title: Single Cell Transcriptome Analysis of Regenerating RGCs Reveals Potent Glaucoma Neural Repair Genes [Second_batch_reg_RGCs]


title: Transcriptomic profiling and analyses of murine prostate orthografts

city: Glasgow

first: Rachana

middle: Ravindra

last: Patel

state: Outside the United States or Canada

address: Bearsden, Switchback Road

department: Prostate Cancer

country: United Kingdom

institute: Cancer Research UK Beatson Institute

summary: RNA was extracted from the frozen prostate tumours or tissues of P1 prostate tumours (n=3), CP1 prostate tumours (n=3) and CP2 prostate tumours (n=4). RNA quality of RNA extracted was evaluated by RNA integrity number (RIN>7.3), calculated using an Agilent 2100 Bioanalyzer (Agilent Technologies) with the Agilent RNA 6000 Nano Kit.

overall_design: For orthograft experiments, approximately 5 million murine prostate cancer cells (P1, CP1 and CP2) were injected in one of the anterior prostate lobes of male CD-1 Nude mice. Prostate orthograft tumours were used for RNA extraction and RNA seq.

first: Peter

last: Repiscak


title: Leucine-induced Regulatory LARS B cells Contribute to Colorectal Cancer Immunoevasion

status: Public on Aug 19 2022

city: Shanghai

first: hua

middle: rong

last: Liu

state: Shanghai

address: 130 Dong'an Road, Xuhui District

department: Institutes of Biomedical Sciences

institute: Fudan University

summary: Immunoregulatory B cells impede anti-tumor immunity through unknown features and mechanisms. In this study, by single-cell sequencing, clusters and features of CRC-infiltrating B cells were analyzed.

overall_design: Mouse CRC model was constructed by treatment with azoxymethane (AOM) plus dextran sodium sulfate (DSS). Subsequently, CD45+cells in colon tissues with low/high-grade (T1/T3) intraepithelial neoplasia and the healthy control tissues were purified by FACS for single cell sequencing.

first: Zhiqiang

last: Wang

first: Yifan

last: Li

first: Ronhua

first: Yiwei

last: Chu


title: Transcriptomic profiling and analyses of murine primary prostate tumours and metastases

summary: RNA was extracted from the frozen localised prostate tumour (primary prostate tumours), proximal (epididymal fat) and distal (lung) metastases from Ctnnb1pc(ex3)Δ/+ Ptenpc+/- (n=3 matched; ~9-10 months)

overall_design: RNA from matched localised prostate tumours and metastases (proximal and distal) used for RNAseq


title: Transcriptomic profiling and analyses of murine prostate tumours

summary: RNA sequencing was performed on wildtype prostate tissues and tumours from mice with prostate-specific deletion of Pten (Ptenpc-/-) and oncogenic activation of ß-catenin (Ctnnb1pcex3(Δ)/+ Ptenpc-/+ , Ctnnb1pcex3(Δ)/+, Mock and ADT treated Ctnnb1Nkx3-1CreERT2(ex3)Δ/+ Pten Nkx3-1CreERT2(ex3)Δ+/-).

overall_design: RNA was extracted from prostate tissues and tumours and sequenced by BGI

first: Hing

last: Leung


title: Chromatin Immunoprecipitation (ChIP) sequencing to explore Androgen Receptor (AR) binding in activated ß-catenin (Ctnnb1) driven murine prostate tumours relative to wildtype prostate tissue.

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We report genomic binding of AR in murine prostate tumours with oncogenic activation of ß-catenin and heterozygous loss of tumour suprresor,Pten using AR specific ChIP-sequencing

overall_design: AR ChIP followed by sequencing was carried out in 3 independent age-matched wildtype prostate tissues and prostate tumours obtained from Ctnnb1pcex3(Δ)/+Ptenpc-/+ mice at 9 months of age. Input from each sample was also sequenced.

first: Elspeth

last: Brzezinska


title: Single Cell Transcriptome Analysis of Regenerating RGCs Reveals Potent Glaucoma Neural Repair Genes [First_batch_reg_RGCs]


title: Microarray expression profiles  of mRNAs, lncRNAs, and circRNAs in human colorectal cancer

status: Public on Aug 18 2022

city: xinxiang

first: Fei

last: Tu

address: 601 Jin Sui Road

institute: xinxiang medical university

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

summary: Colorectal cancer (CRC) is recognized as the third most common cancer worldwide, and it is one of the leading causes of cancer-related death. However, the current therapeutic regimens were not always effective. Here, the expression profiles of mRNAs, lncRNAs and circRNAs in four pairs of HCT116 and FHC cells were detected by microarray technology

overall_design: We performed microarray analysis in HCT116 and FHC cells using Agilent Human ceRNA Microarray 2019

first: Mengfan

first: Lun

last: Hai

first: Luyao

first: Tiesuo

first: Zhiwei

first: Qingzhi


title: Gene expression data from primary human hepatocytes treated with idelalisib for 24 h

city: Chapel Hill

first: Merrie

last: Mosedale

state: North Carolina

address: 301 Pharmacy Lane, Kerr Hall CB#7569

department: Division of Pharmacotherapy and Experimental Therapeutics

institute: UNC Eshelman School of Pharmacy

summary:
Idelalisib is a phosphatidylinositol 3-delta kinase inhibitor that has shown good efficacy in treating some hematologic malignancies. Rare, but potentially serious liver toxicity was associated with idelalisib use in clinical trials. The objective of this study was to evaluate the idelalisib-induced activation of stress response pathways in human hepatocytes to inform mechanisms of liver injury observed in the clinic
Primary human hepatocytes from three donors were sandwich cultured and assayed for global gene expression across 5 concentrations of idelalisib after a 24 h exposure. The most significantly enriched pathway among genes upregulated in response to idelalisib was “Endoplasmic Reticulum Stress”. These data suggest that oxidative stress is a dominant mechanism contributing to liver injury associated with idelalisib.

overall_design: 24 samples were analyzed representing N=1 per donor and treatment


title: Effect of oscillating shear stress on gene expression of endothelial progenitor cells

city: Weifang

first: lan

middle: lan

last: li

state: shandong

address: Weifang Medical University, Weifang, Shandong, 261053, China

institute: weifang medical university

summary: To investigate the function of oscillating shear stress in the regulation of endothelial progenitor cell (EPCs) differentiation, we used EPCs derived from the umbilical cord blood loaded with OSS for 12h. OSS (±3.5 dynes/cm2, 1 Hz frequency) was loaded using a Flexcell flow STR-4000 parallel plate flow chamber system.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different cells after EPCs loaded with OSS for 12h compared with the static EPCs as the control.

first: Min

last: Cheng

first: Hong


title: Fusobacterium nucleatum Induces PD-L1 Expression by Tumor-Associated Macrophages and Inhibits Anti-Tumor Immunity in Colorectal Cancer.

first: Kong

address: 270 Dong 'an Road

institute: fudan university shanghai cancer center

summary: Fusobacterium nucleatum (Fn) infection has been linked to the initiation and development of colorectal cancer (CRC). However, the underlying mechanisms remains unexplored.   Tissues from Fn-infected mice were first collected for single-cell RNA sequencing. we investigated the correlation between Fn infection and accumulations of tumor associated macrophages (TAMs) in tissues from human CRC or AOM/DSS treated mice. The impact of Fn on biological function of TAMs were interrogated. We deciphered the mechanisms for interaction between Fn and TAMs in CRC. We explored the impact of Fn infection on immune-checkpoint blockade (ICB) treatment in a multicohort study.The analysis of single-cell RNA sequencing revealed an enrichment of TAMs in Fn positive tissues. A significant correlation between Fn DNA level and TAMs was observed. Functionally, Fn could recruit TAMs in CRC tissues and promote their biological functions by enhancing PD-L1 expression and thus suppressing CD8+ T cells. Mechanistically, Fn infection led to increased secreted IL-6 via TLR4/MyD88/NF-κB pathways, and the activated IL-6/STAT3 pathway enhanced PD-L1 expression in TAMs. By using several mice models, we found IL-6 inhibition, loss of MyD88 or anti-PD-L1 treatment could significantly inhibit tumorigenesis. Clinically, Fn positive patients tended to be more sensitive to ICB treatment, with a better prognosis than Fn-negative patients.

overall_design: We constructed a mouse CRC model with AOM/DSS intervention. After Fusobacterium nucleatum (Fn) or PBS (control) intervention, we extracted colorectal tumor tissues in both group for single cell sequencing (n = 3 in control(PBS) group and n = 3 in Fn group)

first: Yz

last: Yang

first: Yl

last: Ma


title: RNA-Seq of normal and infarcted DBA/2J and C57Bl6/N adult female hearts.

city: INDIANAPOLIS

first: Loren

middle: J.

last: Field

state: Indiana

address: 1044 West Walnut, R4-376

department: Medicine

institute: Indiana University

summary: We have observed that DBA/2J and C57Bl6/N mice exhibit different responses to permanent coronary artery ligation, with mice in a C57 background having about a 14-fold increase in cardiomyocyte S-phase activity as compared to DBA mice.  We mapped the responsible gene to the distal arm of Chromosome 3 in the C57 background.  We then RNA-Seq analyses on hearts from normal and infarcted DBA and C57 mice, with the hope of identifying candidate genes within the region of interest on the distal arm of Chromosome 3 which are differentially expressed. These genes identified Tnni3k as a potential candidate contributing to the elevated S-phase phenotype.

overall_design: Adult female mice (3 moths old) were subjected to permanent coronary artery ligation and harvested 2 weeks later.  Control animals were untreated.  Hearts were harvested, and the intraventricular septum and right ventricles were dissected and used to generate RNA for RNA-Seq analyses. 8 DBA/2J mice (4 with ligation and 4 control) and 8 C57Bl6/N mice (4 with ligation and 4 control) were analyzed.

first: Sean

last: Reuter

first: Hongyu

last: Gao

first: Ed

last: Simpson

first: Nick

last: Green


title: Dose-Dependent Hepacivirus Infection Reveals Linkage between Infectious Dose and Immune Response

city: Bochum

first: Daniel

last: Todt

address: Universitätsstr. 150

department: Molecular & Medical Virology

country: Germany

institute: Ruhr University Bochum

summary: More than 70 million people worldwide are still infected with the hepatitis C virus 30 years after its discovery, underscoring the need for a vaccine. To develop an effective prophylactic vaccine, detailed knowledge of the correlates of protection and an immunocompetent surrogate model are needed. In this study, we describe the minimum dose required for robust equine hepacivirus (EqHV) infection in equids and examined how this relates to duration of infection, seroconversion, and transcriptomic responses. To investigate mechanisms of hepaciviral persistence, immune response, and immune- mediated pathology, we inoculated eight EqHV naive horses with doses ranging from 1 to 2 to 1.3 106 RNA copies per inoculation. We characterized infection kinetics, pathology, and transcriptomic responses via new generation sequencing. The minimal infec- tious dose of EqHV in horses was estimated at 13 RNA copies, whereas 6 to 7 copies were insufficient to cause infection. Peak viremia did not correlate with infectious dose, while seroconversion and duration of infection appeared to be affected. Notably, sero- conversion was undetectable in the low-dose infections within the surveillance period (40 to 50 days). In addition, transcriptomic analysis revealed a nearly dose dependent effect, with greater immune activation and inflammatory response observed in high-dose infections than in low-dose infections. Interestingly, inoculation with 6 to 7 copies of RNA that did not result in productive infection was associated with a strong immune response, similar to that observed in the high-dose infections. IMPORTANCE We demonstrated that the EqHV dose of infection plays an important role for inducing immune responses, possibly linked to early clearance in high-dose and prolonged viremia in low-dose infections. In particular, pathways associated with innate and adaptive immune responses, as well as inflammatory responses, were more strongly upregulated in high-dose infections than in lower doses. Hence, inoculation with low doses may enable EqHV to evade strong immune responses in the early phase and therefore promote robust, long-lasting infection.

overall_design: Transcriptomic analysis of equine liver biopsies pre- and post-EqHV infection

first: André

last: Gömer

first: Julien

last: Delaroquce

first: Christina

last: Puff

first: Maximilian

middle: K

last: Nocke

first: Reinecke

last: Birthe

first: Wolfgang

last: Baumgärtner

first: Jessika

middle: M

last: Cavalleri

first: Karsten

last: Feige

first: Eike

last: Steinmann


title: Next generation sequencing to identify PNISR regulating alternative splicing in CRC

city: Guangzhou

first: Zhenxing

last: Liang

state: Guangdong

address: 26 Yuancun Erheng Rd

institute: The Sixth Affiliated Hospital, Sun Yat-sen University

summary: We performed next generation sequencing between control CRC cells and CRC cells with PNISR knockdown to identify PNISR regulating alternative splicing

first: Huashan

last: Liu


title: Effect of bryostatin-1 on gene expression profile of Raji cells

city: Seattle

first: Rimas

last: Orentas

state: Washington

address: 1100 Olive Way NE

department: BTCCCR

institute: Seattle Children's Research Institute

summary: To investigate bryostain's effect on Raji , we performed a whole-transcriptome RNA sequencing experiment for Raji cells treated with Bryostatin and established differntial expression profile comparing to raji treated with DMSO.

overall_design: Raji cells were treated with 1nM Bryostatin or DMSO and whole transcriptome sequencing was performed.

first: Yue

last: Zhang-Wong


title: Utomilumab in Refractory Melanoma and NSCLC (NCT01307267)

city: Houston

first: David

middle: S

last: Hong

state: TX

address: 1515 Holcombe Boulevard Unit 455

institute: University of Texas M.D. Anderson Cancer Center

summary: The paper reports clinical and translational results from patients with non-small-cell lung cancer (NSCLC) or melanoma dosed once every 4 weeks with either 0.24 mg/kg or 1.2 mg/kg of single-agent utomilumab, a 4-1BB/CD137 agonist mAb. The dose levels tested were well-tolerated but clinical efficacy was low. Analysis of gene expression in tumor biopsies suggested utomilumab efficacy was associated with immune-active tumor microenvironments, and pharmacodynamic activity may be reduced at higher doses. In vitro models of stimulated human T cells showed loss of pharmacodynamic activity at higher doses of utomilumab.

overall_design: Tumor biopsies collected either before or after utomilumab treatment were subjected to RNA-seq analysis

first: Ajay

last: Gopal

first: Alexander

middle: N

last: Shoushtari

first: Sandip

middle: P

last: Patel

first: Aiwu

middle: R

last: He

first: Toshihiko

last: Doi

first: Suresh

last: Ramalingam

first: Amita

last: Patnaik

first: Shahneen

last: Sandhu

first: Ying

last: Chen

first: Craig

middle: B

last: Davis

first: Timothy

last: Fisher

first: Bo

last: Huang

first: Kolette

middle: D

last: Fly

first: Antoni

last: Ribas


title: Regulation of Host Gene Expression by Gastrointestinal Tract Microbiota

city: Windsor

first: Javad

last: Sadeghi

state: Ontario

address: 2990 Riverside Dr W

department: GLIER

country: Canada

institute: University of Windsor

summary: Difference in gut microbiome is linked with health, disease and eventually host fitness, however, the molecular mechanisms by which this variation affects the host fitness are not well characterized. Here, we modified the fish gut microbiota by using antibiotic and probiotic to address the effect of host microbiome on gene expression pattern by using transcriptome.

overall_design: Chinook salmon (Oncorhynchus tshawytscha) gene expression was evaluated using transcriptome sequencing (RNA-Seq) on hindgut mucosa samples from individuals reared in the presence of antibiotics and probiotics and healthy controls to determine differentially expressed (DE) host genes.

first: Subba

last: Chaganti

first: Daniel

last: Heath


title: Heterogeneous Expression of Alternatively Spliced lncRNA mediates Vascular Smooth Cell Plasticity

city: San Diego

first: Jaimie

last: Mayner

address: 9500 Gilman Dr.

department: Bioengineering

institute: UCSD

summary: 9p21 locus polymorphisms have the strongest correlation with coronary artery disease, but as a non-coding locus, disease connection is enigmatic. The lncRNA ANRIL found in 9p21 may regulate vascular smooth muscle cell (VSMC) phenotype to contribute to disease risk. We observed significant variability in induced pluripotent stem cell-derived VSMCs from patients homozygous for risk versus isogenic knockout or non-risk haplotypes. Sub-populations of risk haplotype cells exhibited variable morphology, proliferation, contraction, and adhesion. When sorted by adhesion, risk VSMCs parsed into synthetic and contractile sub-populations, i.e., weakly adherent and strongly adherent, respectively. >90% of differentially expressed genes co-regulated by haplotype and adhesion were associated with Rho GTPases, i.e., contractility. Weakly adherent sub-populations expressed more short isoforms of ANRIL, and when overexpressed in knockout cells, ANRIL suppressed adhesion, contractility, and αSMA expression. These data are the first to suggest that variable lncRNA penetrance may drive mixed functional outcomes that confound pathology.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for iPSC derived VSMCs from RR Patient 1 (cell line-"1-5") sorted into weakly aderent (WA) and strongly adherent (SA) populations using a microfluidic device. Unosrted (US) control from Risk Patient 1 ("1-5) and an isogenic comparison of its TALEN edited Knock-Out ("1-9") also included.

first: Evan

last: Masutani

first: Elena

last: Demeester

first: Aditya

last: Kumar

first: Gail

last: Macapugay

first: Pranjali

last: Beri

first: Valentina

middle: L

last: Sardo

first: Adam

middle: J

last: Engler


title: acRIP-seq to identify NAT10 mediates  mRNA ac4C modification in colorectal cancer

first: Zhenxing

last: Liang

summary: We performedacRIP-seq between control CRC cells and CRC cells with NAT10 knockdown to identify NAT10 mediates  mRNA ac4C modification

first: Huashan

last: Liu

first: Li

last: Xiong


title: Gene expression in self-activating- and non-self-activationg CAR-T cells with CD28 or 4-1BB costimulatory domain.

city: Yokohama

first: Taku

last: Kouro

state: Kanagawa

address: 2-3-2 Nakao, Asahi-ku

department: Division of Cancer Immunotherapy

country: Japan

institute: Kanagawa Cancer Center Research Institute

summary:
We observed self-activation of SKM-CAR-T cells which target novel mesothelioma antigen. CAR-T with CD28 costimulatory domain showed signs of exhaustion while those with 4-1BB costimulatory domain did not.
To elucidate molecules responsible for self-activation-induced exhaustion, we performed RNA-seq analysis of SKM-CAR-T cells with CD28 or 4-1BB and CD19-CAR-T cells with CD28 or 4-1BB.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for SKM-28z CAR-T cells, SKM-28TM-BBz CAR-T cells and respective controls with CD19-CAR-T cells.

first: Tetsuro

last: Sasada


title: Adipocyte-derived lactate is a signalling metabolite that potentiates adipose macrophage inflammation via targeting PHD2

city: Hong Kong

first: Hui

last: Xiaoyan

address: Chinese University of Hong Kong (CUHK), Shatin, Hong Kong.

department: school of biomedical sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: To investigate whether lactate concentration is associated with proinflammatory responses.

overall_design: Gene expression profiling was performed in 14 human adipose tissues with high or low lactate by RNA-seq.

first: HUI

last: XIAOYAN


title: Differential Requirement for DICER1 Activity during the Development of Mitral and Tricuspid Vlaves

city: Augusta

first: Kai

last: Jiao

state: GA

address: 1462 Laney Walker Blvd.

department: Center for Biotechnology and Genomic Medicine

institute: Medical College of Georgia at Augusta University

summary: Mitral and tricuspid valves are essential for unidirectional blood flow in the heart. They are derived from similar cell sources, and yet congenital dysplasia affecting both valves is clinically rare, suggesting the presence of differential regulatory mechanisms underlying their development. We specifically inactivated Dicer1 in the endocardium during cardiogenesis and found that Dicer1-deletion caused congenital mitral valve stenosis and regurgitation, while it had no impact on other valves. We showed that hyperplastic mitral valves were caused by abnormal condensation and extracellular matrix (ECM) remodeling. Our single-cell RNA Sequencing analysis revealed impaired maturation of mesenchymal cells and abnormal expression of ECM genes in mutant mitral valves. Furthermore, expression of a set of miRNAs that target ECM genes was significantly lower in tricuspid valves compared to mitral valves, consistent with the idea that the miRNAs are differentially required for mitral and tricuspid valve development. We thus reveal miRNA-mediated gene regulation as a novel molecular mechanism that differentially regulates mitral and tricuspid valve development, thereby enhancing our understanding of the non-association of inborn mitral and tricuspid dysplasia observed clinically.

overall_design: Mitral leaflets from E17.5 control and mutant embryos were dissected out and undergo scRNA-Seq

first: Shun

last: Yan

first: David

last: Crossman

first: Shanrun


title: Extracellular matrix interactions provide an escape mechanism for commitment to differentiation in cancer

city: Copenhagen

first: Malte

last: Thodberg

address: Blegdamsvej 3B, Building 7 (Maersk Tower)

department: CBMR

country: Denmark

institute: University of Copenhagen

summary: We report the new role that the interaction of cells with the surrounding extracellular matrix can exert on the differnetiation patterns controlled by the BMP pathway. In cells bearing Apc mutations, modulation of this pathway triggers cells irresponsive to  normal differentiation cues which offers a posible therapeutic anchor for anti-cancer therapies.

overall_design: Expression profiles from RNA-seq of Lrig1-high and Lrig1-low cells obtained from mouse colonic tumors and normal epithelium.

first: Pawel

last: Schweiger

first: Marie

last: Le Bouteiller

first: Shiro

last: Yui

first: Ditte

last: Clement

first: Kim

last: Jensen


title: Cellular Heterogeneity Analysis of the Sinoatrial Node Region Identifies Novel His-bundle-like Cell and Endothelial Progenitor Subtypes

first: yiwen

last: li

address: Yueyang road No.320

institute: Chinese Academy of Sciences

summary:
Aims: To gain insight into heterogeneity of pacemaker and conduction cells within the sinoatrial node (SAN) and characterize the transcriptome of cardiac endothelial cells (ECs) at single-cell resolution.
Methods and results: Single-cell transcriptome analysis of fluorescence activated cell sorting (FACS)-purified SAN cells and surrounding atrial cells from HCN4-GFP knockin mice at postnatal day 2 were performed. Subcluster analysis of SAN cardiomyocyte cluster identified three HCN4+ cell subtypes, including pacemaker cells (PCs), recently identified transitional cells (TCs), and a novel population of His-like conduction cells marked by His-bundle specific marker genes. We additionally refined the molecular signatures of PCs and TCs, and identified Vsnl1, Myl2 and Kcne1 as biomarkers of PCs, TCs and His-like respectively that persistently expressed in the SAN from E15.5 to adult. Furthermore, we observed three endothelial progenitor subtypes (endocardial progenitors, coronary vascular endothelial progenitors, and transitional endothelium migrated from endocardium to coronary vessels) in mouse heart and human fetal heart. These endothelial progenitor subtypes were further identified by mouse lineage tracing analysis.
Conclusion: Our study provides a more comprehensive understanding of molecular and cellular signatures underlying pacemaking and conduction of the SAN, and offers new insight into lineage differentiation and diversification of cardiac ECs.

first: Yi

middle: W

last: Li


title: Identification of a drug-response gene in multiple myeloma through longitudinal single-cell transcriptome sequencing.

city: Fukuoka

first: Yasuhiro

last: Nakashima

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Medicine and Bioregulatory Science

institute: Kyushu University

summary: Multiple myeloma (MM) is a life-threatening, chronic, and incurable hematological malignancy, which is characterized by clonal proliferation of malignant plasma cells. Despite recent therapeutic advances, relapse is very common during a long-term exposure to drugs with no therapeutic effects. Here, we conducted longitudinal single-cell transcriptome sequencing (scRNA-seq) of bone marrow cells from a single patient with relapsed and refractory MM, who had been treated with multiple anti-myeloma drugs, and found five UMAP subclusters (clusters 0-4) of MM cells, which appeared and/or disappeared in response to the therapeutic pressure. A small cell cluster 3, which emerged during lenalidomide treatment and disappeared after the addition of a proteasome inhibitor (PI), ixazomib. Among the differentially expressed genes in cluster 3, we found a candidate drug-response gene; pellino E3 ubiquitin protein ligase family member 2 (PELI2), which is responsible for PI-induced cell death in in vitro cell cultured assay. Kaplan-Meier survival analysis of datasets from pan-cancer prognostic database revealed that higher expression of PELI2 is associated with better prognosis. The data of this study suggest that PELI2 is a predictive biomarker of the PI response in patients with MM. Our integrated strategy combining longitudinal scRNA-seq analysis, in vitro functional assay, and database analysis would facilitate the understanding of clonal dynamics of MM in response to anti-myeloma drugs and identification of drug response genes.

overall_design: Longitudinal scRNA-seq of myeloma cells from a patient with relapse and refractory disease.

first: Toru

last: Masuda

first: Shojiro

last: Haji

first: Yoshihiro

last: Ogawa


title: Iron-dependent switch in MPN-phenotype

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

summary: Iron is a modifier of the phenotypes of JAK2-mutant myeloproliferative neoplasms

overall_design: LT-HSCs, pre-MegEs and MkPs were FACS-sorted from JAK2-WT and JAK2-mutant mouse strains after induction with tamoxifen.

first: Jan

last: Stetka

first: Tata

last: Rao

first: Radek

middle: C

last: Skoda


title: Bulk RNAseq of AB1-HA murine mesothelioma tumors from immunocompetent or CD4+ T cell depleted mice.

city: Nedlands

first: Caitlin

last: Tilsed

state: WA

address: 6 Verdun St

country: Australia

institute: NCARD,UWA

summary: Purpose: To compare the gene expression profiles of tumors with or without the infiltration of CD4+ T cells.

overall_design: BALB/c mice bearing AB1-HA murine mesothelionma were treated with PBS (n=6) or 100 ug anti-CD4 monoclonal antibody (n=6) on day -3, day 0 (day of innoculation) and day 7. Tumors were excised on day 9 and RNA extracted for sequencing.

first: Joost

last: Lesterhuis


title: Single Cell Transcriptome Analysis of Regenerating RGCs Reveals Potent Glaucoma Neural Repair Genes

city: Palo Alto

first: Xue

last: Feng

address: 1651 Page Mill road

institute: Stanford

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

overall_design: Refer to individual Series


title: MicroRNA-based signatures obtained from endometrial fluid identify implantative endometrium

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

type: Non-coding RNA profiling by high throughput sequencing

summary: Improving embryo implantation rates has become one of the greatest challenges in assisted reproduction techniques. Implantation process requires a synchrony between the development of the embryo and the endometrium, but also, an adequate embryo-endometrial crosstalk. MicroRNAs (miRNAs) and extracellular vesicles (EVs) from endometrial fluid (EF) have been described to be mediators of this communication. Therefore, the molecular analysis of the miRNA content of EF could provide a non-invasive method to recognize an implantative endometrium and consequently improve the implantation rates. In this work, we optimized EF sample collection procedure and performed a comparative analysis of five different methodologies to enrich miRNA content of EF with the purpose of identifying a simple, sensitive, reproducible and non-invasive method that allow the quick identification of an implantative endometrium. Then, we applied the selected methodology in a set of real samples with different implantation outcome. Our results showed that EVs enrichment protocols permit to detect a higher number of miRNAs. In addition, we obtained two predictive models based on three miRNAs that allow us to differentiate between an implantative and non-implantative endometrium. Model 1 (Area under the curve (AUC)=0.93; p-value=0.0033): hsa-miR-200b-3p, hsa-miR-24-3p and hsa-miR-148b-3p. Model 2 (AUC=0.92; p-value=0.0002): hsa-miR-200b-3p, hsa-miR-24-3p and hsa-miR-99b-5p. This work supports the feasibility to analyze EVs and EVs-associated miRNAs from a small volume of EF sample and the development of EV-miRNAs based assays as low-invasive tools for the detection of an implantative endometrium.

sample_organism:
Homo sapiens
blank sample

platform_organism:
Homo sapiens
blank sample

overall_design: Comparison of methods for the characterization of miRNAs from 400uL (1:30 dilution) of endometrial fluid

first: Jone

last: Ibañez-Perez

first: María

last: Díaz-Nuñez

first: Marc

last: Clos-García

first: Lucía

last: Lainz

last: Iglesias

first: Miren

last: Díez-Zapirain

first: Aintzane

last: Rabanal

first: Laura

last: Bárcena

first: Monika

last: González

first: Juan

last: Lozano

first: Urko

last: Marigorta

first: Esperanza

first: Félix

last: Royo

first: Nerea

last: Subiran

first: Roberto

last: Matorras

last: Falcón-Pérez


title: RNA-sequencing for leaves of three garlic varieties

status: Public on Aug 17 2022

city: Changsha

first: Touming

last: Liu

address: NO.348, western road of xianjia lake

department: Institute of Bast Fiber Crops

summary: To explore the clove enlarging growth-related genes, we compared the transcriptome of bulbs whose cloves are before enlargement and under enlarging-growth, respectively, using three garlic accessions, Chalingzipisuan, Ershuizao, and Yuanjiangyangsuan. Consequently, 4,658 genes were identified with a differential expression in at least two of three examined accessions.

overall_design: For each accession, bulbs of five plants were pooled as a sample. In addition, three varieties, Chalingzipisuan, Ershuizao, and Yuanjiangyangsuan, were planted in the farm of Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, China, in Oct. of 2019; and in the Feb. and Mar. of 2020, when the bulbs had not initiated to enlarge and were under enlarging growth, respectively, the parts of bulbs were collected. Three individuals were used as three replications


title: Gene expression study of 21d old Col-0 and tpt-2 shifted at the end of night to 500µmol photons m-2 s-1 for 9h and 18h

city: Rostock

first: Andreas

middle: Sven

last: Richter

address: Albert-Einstein-Strasse 3

department: Institute for Biosciences

institute: University of Rostock

summary: Analysis of Expression changes in tpt-2 mutant upon high light shift.

overall_design: Per timepoint (9h and 18h) three biological replicates of Col-0 and tpt-2 were analysed. Plants have been shifted to the HL at the end of the night.


title: Mutated KLF4(K409Q) in meningioma binds STRs and activates FGF3 gene expression

city: Oklahoma City

first: Alla

last: Tsytsykova

state: OK

address: 1122 NE 13th Street

department: Neurosurgery

institute: OUHSC

summary:
Meningiomas are the most common primary tumors of the central nervous system. The genetic landscape of the most common subtype of meningioma involves mutation or copy loss of the NF2 gene in approximately 50% of cases. Other recurrent canonical somatic mutations are present in ~40% of sporadic meningiomas and are not defined by NF2 inactivation. These genes include TRAF7, AKT1, SMO, and KLF4, among others. Tumors with KLF4 and TRAF7 mutations share a unique secretory phenotype, which is characterized by glandular lumina with secretory globules, and tend to cause disproportional peritumoral edema, which can cause severe medical and neurological complications in pre- and post-operative management. The K409Q mutation in KLF4 is found in ~15% of meningiomas. The mutated allele KLF4K409Q is the same in all affected patients and occurs together with TRAF7 missense mutations. The contribution of the meningioma-specific KLF4 mutation to tumorigenesis and mechanism of action is unknown.
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) analysis was performed to investigate different DNA recognition sequences by ectopically expressed KLF4 and KLF4(K409Q) proteins in transiently transfected HEK293 cells.

overall_design: ChIP-seq was performed using HEK293 cells transfected with p3XFLAG-CMV™-7.1 vector (E7533, Sigma-Ardrich) expressing human KLF4 or KLF4(K409Q) proteins and anti-FLAG antibody. Six independent biological replicates for each ChIP-seq condition were analyzed.

first: Graham

last: Wiley

first: Richard

last: Pelikan

first: Ian

last: Dunn


title: Expression Data from ST2 cells treated with Wnt1

city: Hamburg

first: Thorsten

last: Schinke

address: Martinistr. 52

department: Department of Osteology and Biomechanics

institute: University Medical Center Hamburg-Eppendorf

summary:
Wnt1 has major anabolic functions in bone metabolism. We investigated the effect of recombinant murine Wnt1/Sfrp1 complex on the mesenchymal cell line ST2.
We used microarray analysis to detail the global gene expression of ST2 cells in response to 6 hour of treatment with 100 ng recombinant Wnt1/Sfrp1 complex.

overall_design: 3 samples generated from pools of 3 independent experiments each were analyzed. Effects of 6h treatment with 100 ng recombinant Wnt1/Sfrp1 complex were compared to 50 ng recombinant Sfrp1 or PBS.

first: Nele

last: Vollersen

first: Wenbo

last: Zhao

first: Fabiola

last: Lange

first: Timur

last: Yorgan


title: Skin transcriptome profiles associated with black- and white-coated region  in a crossbred  goat

city: Wuhan

first: Qi

last: Xiong

address: No.1 Nanhu Yaoyuan, Shizisanjie, Hongsan D

institute: Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences

summary: we compared the skin transcriptomes of the black- and white-coated region  from the Boer and Macheng Black crossbred goat with black head and white body using the Illumina RNA-Seq method. Six cDNA libraries derived from skin samples of the white coat region (n = 3) and black coat region (n = 3) were constructed from three full-sib goats. On average, we obtained approximately 76.5 and 73.5 million reads for each skin sample of black coat and white coat, respectively, of which 75.39% and 76.05% reads were covered in the genome database. Our study provides insight into the transcriptional regulation of two distinct coat color that might serve as a key resource for understanding coat color pigmentation of goat.

overall_design: Examination of 2 different coat region  in a crossbred goat.

first: Mingxin

last: Chen


title: Maternal transcription factor TCF12 mediates fertilization and zygotic genome activation during early embryonic development

city: Hangzhou

first: Lan-Rui

last: Cao

state: Zhejiang

address: 866 Yu Hang Tang Rd

department: Life Sciences Institute

institute: Zhejiang University

summary: To investigate the physiological function of TCF12 in oocyte maturation and preimplantational development, we crossed Tcf12fl/fl mice with Gdf9-Cre mice to specifically delete Tcf12 from the primordial follicle stage. We then performed gene expression profiling analysis using data obtained from RNA-seq on Tcf12fl/fl and Tcf12fl/fl;Gdf9-Cre growing GV oocytes (gGO), fully grown GV oocytes (fGO), embryos at 2-cell and 4-cell stage.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Tcf12fl/fl and Tcf12fl/fl;Gdf9-Cre samples.

first: Chi

last: Zhang

first: Zuo-Qi

last: Deng

first: Zhi-Yan

last: Jiang

first: Yun-Wen

last: Wu

first: Jing

last: Li

first: Heng-Yu

last: Fan


title: Mucosal immune and stress responses of Neoparamoeba perurans-infected Atlantic salmon (Salmo salar) treated with peracetic acid shed light on the host-parasite-oxidant interactions

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

summary: Treatment development for parasitic infestation is often limited to disease resolution as an endpoint response, and physiological and immunological consequences are not thoroughly considered. The impact of exposing Atlantic salmon affected with amoebic gill disease (AGD) to peracetic acid (PAA), an oxidative chemotherapeutic was studied. Transcriptome profiling in the gills showed significant changes triggered by AGD and PAA treatments, and the effects of PAA were more notable 24 h after treatment. Genes related to immune pathways of B- and T- cells and protein synthesis and metabolism were downregulated, where the magnitude was more remarkable in 10ppm-15mins group. Even though treatment did not fully resolve the pathologies associated with AGD, 5ppm-30mins group showed lower parasite load at 4 weeks post-treatment. Mucous cell parameters (i.e., size and density) increased within 24 h post-treatment and were significantly higher at termination, especially in AGD-affected fish, with some treatment effects influenced by the dose of PAA. Infection and treatments resulted in oxidative stress – in the early phase in the gill mucosa, while systemic reactive oxygen species (ROS) dysregulation was evident at the later stage. Infected fish responded to elevated circulating ROS by increasing antioxidant production. Exposing the fish to a crowding stress revealed interference in the post-stress responses. Lower cortisol response was displayed by AGD-affected groups. Collectively, the study established that PAA, within the evaluated treatment protocols, could not provide a convincing treatment resolution and thus require further optimisation.

overall_design: AGD-affected fish were treated with PAA either by exposing them to 5 ppm for 30 mins or 10 ppm for 15 mins. Unexposed fish from both infected and uninfected groups were also included. Samples were collected at 24 h, 2 weeks and 4 weeks post treatment.

first: Carlo

last: Lazado


title: RNA sequencing of Cd44-positive and Cd44-negative primary osteosarcoma isolated from Nf2 - mutant mice

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

institute: Leibniz Institute on Aging - FLI

summary: Osteosarcoma is the most common type of pediatric bone tumor. Despite great advances in chem-otherapy during the past decades the survival rates of osteosarcoma patients remains usatisfacto-ry. Drug resistance is one of the main reasons leading to treatment failure and poor progno-sis. Previous reports correlated expression of cluster of differentiation 44 (CD44) with drug re-sistance and poor survival of osteosarcoma patients, however the underlying mechanisms are poorly defined. Here, we investigated the role of CD44 in the regulation of drug chemoresistance using osteosarcoma cells isolated from mice carrying a mutation of the tumor suppressor neurofi-bromatosis type 2 (Nf2) gene. CD44 expression was knocked-down in the cells using CRISPR/Cas9 approach. Subsequently, CD44 isoforms and mutants were re-introduced to investigate CD44-dependent processes. Sensitivity to doxorubicin was analyzed in the osteosarcoma cells with modified CD44 expression by immunoblot, colony formation- and WST-1 assay. To dissect the molecular alterations induced by deletion of Cd44, RNA sequencing was performed on Cd44-positive and Cd44-negative primary osteosarcoma tissues isolated from Nf2-mutant mice. Subsequently, expression of candidate genes was evaluated by quantitative reverse transcription PCR (qRT-PCR). Our results indicate that CD44 increases the resistance of osteosarcoma cells to doxorubicin by up-regulating the levels of multidrug resistance (MDR) 1 protein expression, and suggest the role of proteolytically released CD44 intracellular domain, and hyaluronan interac-tions in this process. Moreover, high throughput sequencing analysis identified differential regula-tion of several apoptosis-related genes in Cd44-positive and -negative primary osteosarcomas, in-cluding p53 apoptosis effector related to PMP-22 (Perp). Deletion of CD44 in osteosarcoma cells led to doxorubicin-dependent p53 activation and a profound increase in Perp mRNA expression. Overall, our results suggest that CD44 might be an important regulator of drug resistance and suggest that targeting CD44 can sensitize osteosarcoma to standard chemotherapy.

overall_design: 6 samples in total: 3 samples CD44+/+, 3 samples CD44-/-

first: Monika

last: Hartmann

first: Diana

last: Becker


title: Based on Transcriptomics to Explore the Mechanism of Maxing Shigan Decoction in Treating Viral Lung Injury Induced by Influenza A Virus in Mice

first: Fangguo

last: Lu

state: Hunan

address: Xueshi Road No. 300

institute: Hunan University of Chinese Medicine

summary: Objective: To explore the mechanism of MXSGD in treating viral lung injury induced by influenza A virus in mice based on Transcriptomics.  Materials & Methods: The mice were divided into MXSGD group, model group and normal group. After the intervention, the body weight, lung index, e pathological changes were detected. Transcriptomics is then used to detect differential gene expression in lung tissues and perform bioinformatics analysis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data

first: Shiying

first: Bei

first: Ling

first: Hongtao

last: Xia

first: Weiqing


title: RNAseq analysis of primary astrocyte and microglia under Aβ40WT and Aβ42WT fibrils treatment

city: Kingston

first: Willam

middle: Van

last: Nostrand

state: Rhode Island

address: 7 Greenhouse Rd

department: College of Pharmacy

institute: University of Rhode Island

summary:
To investigate the influence of Aβ40WT and Aβ42WT fibrils on astrocyte and microglia, we isolated astrocyte and microglia from P2 SD rats and treated glia cells with Aβ40WT and Aβ42WT fibrils for 24 hours.
We then performed gene expression profiling analysis using data obtained from RNA-seq of astrocyte and microglia treated with Aβ fibrils.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for primary astrocyte and microglia under the treatment of Aβ40WT and Aβ42WT fibrils

first: Xiaoyue

last: Zhu

first: William

last: Van Nostrand


title: Mitochondrial dynamics maintain stem cell regenerative competence throughout adult life by regulating metabolism and mitophagy

city: Barcelona

first: Eusebio

last: Perdiguero

address: Dr. Aiguader 88

department: Department of Medicine and Life Sciences

institute: UPF

summary: We profiled by bulk RNA-seq the transcriptional changes upon deletion of Drp1 in murine satellite cells, freshly harvested from young and old homeostatic muscle and during regeneration, after acute cardiotoxin-induced myoinjury

overall_design: Hindlimb skeletal muscles from tamoxifen-treated WT ( Pax7-CreER; ROSA26YFP) and conditional Drp1-KO (Pax7-CreER;ROSA26YFP;Drp1fl/fl) mice were collected, manually minced, and mechano-enzymatically dissociated with Liberase/Dispase for 1-1.5 hours at 37ºC. Tissue homogenates were filtered and red blood cells lysed. The final single-suspension cell pellets were stained and processed for FACS-sorting to isolate highly purified satellite cells based on YFP+ expression (QSC, quiescent satellite cells). Concurrently pre-injured (tibialis anterior, quadriceps, and gastrocnemius) muscles, were also harvested from equivalent groups of genotype- and age-matched animals at 1-day ('Activated' satellite cells, ASC) or 3-days ('Proliferating' satellite cells) post-cardiotoxin-injection (DPI). For these timepoint conditions, cells were FACS-sorted from the regenerating bulk homogenates based on YFP+ (1DPI) or CD34-YFP+ (3DPI) immunophenotypes. Ages for the Young and the Old animal groups were 3 and 24 months, respectively.

first: Xiaotong

last: Hong

first: Oleg

last: Deryagin

first: Joan

last: Isern

first: Pura

last: Munoz-Canoves


title: Transcriptomics analysis of gene expression at three different developmental stages of zebrafish embryos

city: xinxiang

first: chune

last: zhou

address: jian she east road 46

institute: henan normal university

summary: To investigate the expression profile of three different developental stages of zebrafish embryos, we then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different developmental of zebrafish embryos.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 3 different developmental stages of zebrafish embryos.

first: Chune

last: Zhou

first: Xiaoyu

last: Li


title: Inhibition of LSD1 with bomedemstat sensitizes small cell lung cancer to immune checkpoint blockade and T cell killing

city: Seattle

first: Joseph

middle: Brian

last: Hiatt

address: 1100 Fairview Ave N

department: Human Biology

institute: Fred Hutchinson Cancer Center

summary: The addition of immune checkpoint blockade (ICB) to platinum/etoposide chemotherapy changed the standard of care for small cell lung cancer (SCLC) treatment. However, ICB addition only modestly improved clinical outcomes, likely reflecting the high prevalence of an immunologically “cold” tumor microenvironment in SCLC, despite high mutational burden. Nevertheless, some patients clearly benefit from ICB and recent reports have associated clinical responses to ICB in SCLC with A) decreased neuroendocrine characteristics and B) activation of NOTCH signaling. We previously showed that inhibition of the LSD1 demethylase activates NOTCH and suppresses neuroendocrine features of SCLC, leading us to investigate whether LSD1 inhibition would enhance the response to PD1 inhibition in SCLC.

overall_design: Identification of differentially expressed genes regulated by exposure to the LSD1 inhibitor bomedemstat (BOM) in cultured murine SCLC cells and an immunocompetent murine flank tumor model of SCLC. Cultured cells were treated with BOM for 96h, or with BOM or control for 10d with or without IFNg for the last 48h. Flank tumors were exposed to BOM or vehicle, with or without anti-PD1 immune checkpoint inhibitor (ICI) antibody, for 16-17 days.

first: David

last: MacPherson

first: Holly

last: Sandborg

first: Henry

last: Arnold

first: Justin

last: Norton

first: Sheng-You

last: Liao


title: The histone modification change between PRC2-wt and PRC2-loss in human MPNST cancer cells

city: NEW YORK

first: Ping

last: Chi

state: NY

address: 1275 YORK AVENUE

institute: MEMORIAL SLOAN KETTERING CANCER CTR

summary: PRC2-isogenic human malignant peripheral nerve sheath tumor (MPNST) M3 cells were generated through CRISPR/Cas9-mediated knockout of the PRC2 core component, SUZ12. PRC2 loss leads to global loss of H3K27me3, which causes H3K27ac redistribution and also affect other histone modification, e.g., H3K36me2/3.

overall_design: PRC2-isogenic human MPNST M3 cells (sgCon, sgSUZ12) were usesd for CUT&RUN with H3K27me3, H3K27ac, H3K36me2, H3K36me3.

first: Yu

last: Chen

first: Juan

last: Yan


title: Hepatic unfolded protein response in liver transplant patients

city: Chicago

first: Xiaoying

last: Liu

state: IL

address: 240 E Huron St., McGaw M-319

institute: Northwestern University

summary: The hepatic unfolded protein response (UPR) is an adaptive cellular response to endoplasmic reticulum stress that is important in the pathogenesis of many liver diseases. In this study, we utilized liver biopsies from patients after liver transplantation as a disease model to determine the transcriptional profile and hepatic UPR gene expression that is associated with liver injury and cholestasis.

overall_design: RNA was extracted from liver biopsies from patients after liver transplantation. RNA-seq was performed to determine the transcriptional profile.


title: Revealing the increased stress response behavior through transcriptomic analysis of adult zebrafish brain after chronic and low to moderate dose rates of ionizing radiations

city: Saint Paul lez Durance

first: olivier

last: ARMANT

address: Cadarache BP3

department: SERIS

country: France

institute: IRSN

summary: We describe the transcriptomics data acquired on adult zebrafish after chronic exposure to low dose of IR (< 6mGy/h)

overall_design: Comparative gene expression profiling analysis of RNA-seq data from dissected telencephalon obtained after exposure of adult zebrafish to 0.05 mGy/h, 0.5 mGy/h and 5 mGy/h during 36 days

first: Elsa

last: Cantabella

first: Olivier

last: Armant


title: DBC1 is a positive regulator of enhancer epigenomic writers KMT2D and p300.

city: Seoul

first: Jeong

middle: Hoon

last: Kim

address: Irwon-dong Gangnam-gu

country: South Korea

institute: Sungkyunkwan University

summary: Genome-wide maps of DBC1, KMT2D, and p300 in SW480 WT and DBC1 KO cells

overall_design: To analyze DBC1 and DBC1-regulated histone epigenetic writers , we perfomed ChIP-seq analyses of DBC1, KMT2D, and p300 in colon cancer cell line SW480 WT and DBC1 KO cells.

first: Hwa

middle: H


title: Transcriptome analysis between PRC2-loss and PRC2-wt in human malignant peripheral nerve sheath tumor (MPNST)

summary: PRC2 loss of function occurs frequently in human MPNST. Here, we found that PRC2-loss tumors are separated from PRC2-wt ones at the transcriptome level by RNA-seq among 41 human MPNST tumor tissues.

overall_design: mRNA profiling of 41 human MPNST tumors including 15 PRC2-wt and 26 PRC2-loss tumors

first: Yuedan


title: Inhibition of mutant IDH1 promotes cycling of acute myeloid leukemia stem cells [scRNA-seq]

city: Melbourne

first: Emily

last: Gruber

state: VIC

address: 305 Grattan St

institute: Peter MacCallum Cancer Centre

summary: Acute myeloid leukemia (AML) tumors are comprised of multiple cell types with distinct capabilities to propagate the disease and resist therapy. Approximately 20% of AML patients carry gain-of-function mutations in isocitrate dehydrogenase (IDH) 1 or -2 that result in over-production of the onco-metabolite D-2-hydroxyglutarate (2-HG). Small molecule inhibitors that block 2-HG synthesis can induce complete morphological remission even in heavily pre-treated AML patients. However, almost all patients eventually relapse with analysis of clinical samples suggesting that a population of IDH mutant cells is able to persist during treatment eventually acquiring 2-HG independence and drug resistance. Herein we characterized the molecular and cellular responses to the clinical IDH1 inhibitor AG-120 (Ivosidenib) at high resolution using a novel multi-allelic mouse model of IDH1 mutant AML. We demonstrate that inhibition of mutant IDH1 exerts cell type-dependent effects on leukemic cells promoting delayed disease regression. Although single agent AG-120 treatment was not able to fully eradicate the disease, we uncovered that it increases cycling of rare leukemic stem cells (LSCs) and triggers transcriptional upregulation of the pyrimidine salvage pathway. Accordingly, AG-120 sensitized IDH1 mutant AML to the cytosine analogue hypomethylating agent azacitidine with the combination of AG-120 and azacitidine showing vastly improved efficacy in vivo. Our data highlight the impact of non-genetic heterogeneity on treatment response and provide mechanistic rationale for a drug combination that is being tested in clinical trials.

overall_design: To investigate the extent of heterogeneity of AG-120 transcriptional responses, we utilized the 10X Genomics 3' single-cell RNA sequencing (scRNAseq) platform to profile gene expression from individual I1DN progenitor cells (cKit+/Cd11b-) isolated from mice following 5 days of inhibitor or vehicle treatment.

first: Lev

last: Kats


title: Acute and long-term effects of psilocybin on energy balance and feeding behavior in mice

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

institute: Copenhagen University

summary: Psilocybin, and other serotonergic psychedelics, have re-emerged as therapeutics for neuropsychiatric disorders, including addiction. Psilocybin induces long-lasting effects on behavior, likely due to its profound ability to alter consciousness and augment neural connectivity and plasticity. Impaired synaptic plasticity in obesity contributes to ‘addictive-like’ behaviors, including heightened motivation for palatable food, and excessive food seeking and consumption. Here, we evaluate the effects of psilocybin on feeding behavior, energy metabolism and as a weight-lowering agent in mice. We demonstrate that a single dose of psilocybin substantially alters the prefrontal cortex transcriptome but has no acute or long-lasting effects on food intake or body weight in diet-induced obese mice or in genetic mouse models of obesity. Similarly, sub-chronic microdosing of psilocybin has no metabolic effects in obese mice and psilocybin does not augment glucagon-like peptide-1 (GLP-1) induced weight loss or enhance diet-induced weight loss. A single high dose of psilocybin reduces sucrose preference but fails to counter binge-like eating behavior.  Although these preclinical data discourage clinical investigation, there may be nuances in the mode of action of psychedelic drugs that are difficult to capture in rodent models, and thus require human evaluation to uncover.

overall_design: Two-way ANOVA like setup in two brain regions: Hypothalamus and Frontal Cortex. The effect of Psilocybin injection is compared to saline injection at two timepoints: 3 hours post injection and 4 weeks post injection.

first: Nicole

last: Fadahunsi

first: Jens

last: Lund

first: Alberte

last: Wollesen Breum

first: Cecilie

last: Vad Mathiesen

first: Isabella

last: Beck Larsen

first: Gitte

last: Moos Knudsen

first: Anders

last: Bue Klein

first: Christoffer

last: Clemmensen


title: Inhibition of mutant IDH1 promotes cycling of acute myeloid leukemia stem cells [RRBS]

type: Methylation profiling by high throughput sequencing

overall_design: We investigated the consequences of the combined AG-120 and azacitidine treatment on DNA methylation and gene expression using reduced representation bisulfite sequencing (RRBS) and RNAseq


title: Inhibition of mutant IDH1 promotes cycling of acute myeloid leukemia stem cells [RNAseq_AG120_treatment]

overall_design: We analyzed the impact of IDH1 inhibition on gene expression by RNA sequencing (RNAseq) of sorted leukemic progenitor cells from I1DN tumor-bearing mice that had been treated with vehicle or AG-120 for 5 or 14 days, or treated for 4 weeks and subsequently relapsed


title: Enhanced hippocampal neurogenesis mediated by PGC-1α-activated OXPHOS after neonatal low-dose Propofol exposure

city: Guangzhou

first: Chen

last: Keyu

state: Guangdong Province

address: 58 Zhongshan Second Road

institute: Sun Yat-Sen University

summary: The  regulation of gene expression after low-dose Propofol exposured in neural stem / progenitor cells (NSPCs)

overall_design: One sample from NSPCs of Control and low-dose Propofol-exposured respectively

first: Xia

last: Feng

first: Keyu

last: Chen

first: Dihan

last: Lu

first: Mei

last: Jiang


title: Inhibition of mutant IDH1 promotes cycling of acute myeloid leukemia stem cells [RNAseq_AG120_AZA_treatment]


title: DBC1 is a positive regulator of enhancer epigenomic writers KMT2D and p300 [HCT116 ChIP-seq]

first: Jeong

last: Kim

summary: Genome-wide maps of H3K4me3 and H3K27ac in HCT116 WT and DBC1 KO cells

overall_design: To identify DBC1-regulated histone H3 modifications, we perfomed ChIP-seq analyses of H3K4me3 and H3K27ac in colon cancer cell line HCT116 WT and DBC1 KO cells.

first: Hwa


title: DBC1 is a positive regulator of enhancer epigenomic writers KMT2D and p300 [HCT116 RNA-seq]

summary: We identified DBC1/CCAR2 target genes using RNA-seq analysis in colon cancer cells.

overall_design: mRNA profiles of HCT116 WT or DBC1 KO cells were generated by deep sequencing, in triplicate, using illumina NovaSeq6000.


title: Regulation of type I interferon signature by VGLL3 in the fibroblast-like synoviocytes of rheumatoid arthritis patients via targeting the Hippo pathway

city: Shanghai

first: Yu

last: Du

address: 600 Yishan Road

department: Department of Rheumatology and Immunology

institute: Shanghai Jiao Tong University Affiliated Sixth People’s Hospital

summary:
To address the regulation of interferon-stimulated genes expression by VGLL3 in fibroblast-like synoviocytes (FLS) of rheumatoid arthritis (RA) patients, VGLL3 was overexpressed in RA-FLS via a lentiviral vector.
After four days of transfection, VGLL3-overexpressed RA-FLS and vector-transfected RA-FLS were subjected to RNA sequencing.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for VGLL3-overexpressed RA-FLS and vector-transfected RA-FLS.

first: Ran

last: Cui

last: Tian

first: Miao

first: Xian-Long

last: Zhang

first: Sheng-Ming

last: Dai


title: Oral microbiota shapes the gut microbiota, resulting in systemic effects

city: Niigata

first: Kazuhisa

last: Yamazaki

address: 2-110-1 Gakkocho-dori, Chu-o-ku

institute: Niigata University

summary: The effect of oral microbiota on the intestinal microbiota has garnered growing attention as a mechanism linking periodontal diseases to systemic diseases. However, the salivary microbiota is diverse and comprises numerous bacteria with a largely similar composition in healthy individuals and periodontitis patients. Thus, the systemic effects of small differences in the oral microbiota are unclear. In this study, we explored how health-associated and periodontitis-associated salivary microbiota differently colonized the intestine and their subsequent systemic effects by analyzing the hepatic gene expression and serum metabolomic profiles. The salivary microbiota was collected from a healthy individual and a periodontitis patient and gavaged into C57BL/6NJcl[GF] mice. Samples were collected five weeks after administration. Gut microbial communities were analyzed by 16S ribosomal RNA gene sequencing. Hepatic gene expression profiles were analyzed using a DNA microarray and quantitative polymerase chain reaction. Serum metabolites were analyzed by capillary electrophoresis time-of-flight mass spectrometry. The gut microbial composition at the genus level was significantly different between periodontitis-associated microbiota-administered (PAO) and health-associated oral microbiota-administered (HAO) mice. The hepatic gene expression profile demonstrated a distinct pattern between the two groups, with higher expression of Neat1, Mt1, Mt2, and Spindlin1, which are involved in lipid and glucose metabolism. Disease-associated metabolites such as 2-hydroxyisobutyric acid and hydroxybenzoic acid were elevated in PAO mice. These metabolites were significantly correlated with Bifidobacterium, Atomobium, Campylobacter, and Haemophilus, which are characteristic taxa in PAO mice. Conversely, health-associated oral microbiota were associated with higher levels of beneficial serum metabolites in HAO mice. The multi-omics approach used in this study revealed that periodontitis-associated oral microbiota is associated with the induction of disease phenotype when they colonized the gut of germ-free mice.

overall_design: Effect of salivary microbiota of a periodontitis patient and a healthy subject on the liver gen expression profile was measured in germ-free mice (N=6/group).

first: Kyoko

first: Eiji

last: Miyauchi

first: Tamotsu

last: Kato

first: Keisuke

last: sato

first: Wataru

last: Suda

first: Takahiro

last: Tsuzuno

first: Miki

last: Yamada-Hara

first: Hiroshi

last: Ohno

last: Yamazakki


title: Transcriptome analysis of different developmental stages of Daphnia similoides sinensis and screening of male sex determination candidate genes

city: Huaibei

first: Deng

last: daogui

state: Anhui

address: 100 Dongshan Road

department: College of Life Sciences

institute: Huaibei Normal University

summary:
Background: In the life history of Daphnia, the reproductive mode of parthenogenesis and sexual reproduction alternate in aquatic ecosystem, which are often affected by environmental and genetic factor. Although several functional genes on reproductive transition of Daphnia had been determined, molecular mechanism on the reproductive mode of Daphnia are still not known well, including differentially expressed genes in different developmental stages.
Results: In this study, four developmental stages, juvenile female (JF), parthenogenetic female (PF), sexual female (SF) and male (M), of D. similoides sinensis were performed for transcriptome sequence, and candidate genes related to male sex determination were screened. A total of 110437 transcripts were obtained and assembled into 22996 unigenes. In the four developmental stages (JF, PF, SF and M), the number of unique unigenes is respectively 2863, 445, 437 and 586, and the number of common unigenes is 9708. The differentially expressed genes (DEGs) between male and other three female stages (M vs JF, M vs PF and M vs SF) were obtained. The GO gene enrichment analysis showed that the up-regulated genes in male were mainly enriched in hydrolase activity and peptidase activity.
Thirty-six candidate genes related to male sex determination in male were significantly higher expression than those in the other three stages, including one Doublesex (Dsx) gene, one laminin gene, five trypsin genes and one serine protease genes, and one chitin synthase gene and two chitinase genes. In addition, in D. similoides sinensis male, the relative expression levels of two genes (Dsx1, antp) related to male sex determination observed in other Daphnia species were also significantly higher than those in other developmental stages.
Conclusions: Our results showed that thirty-six candidate genes may involve in sex differetiation of D. similoides sinensis male, and it will provide a reference for further exploring the functional genes related to sex determination mechanism in Daphnia species. Moreover, according to previous investigations, we thought that the expression level of functional genes may be related to the development stage of organisms, and may be also affected by different Daphnia species.

overall_design: RNA sequencing of different developmental stages of Daphnia similoides sinensis

first: Ziyan

last: Wang

first: Daogui

last: Deng


title: Transcriptional response of tea roots of different genotypes to potassium

city: Hangzhou

first: Li

last: Ruan

address: Meiling South Road No. 9

institute: Tea Research Institute, Chinese Academy of Agricultural Science

summary:
Purpose: We investigated root foraging strategies for K of tea plants using a multi-layer split-root system by RNA-seq.
Methods: One-year old tea cuttings were cultivated with the roots evenly planted on the two sides of the split root hydroponic box with a root canal. Three treatments were included to simulate the heterogeneous and homogeneous K environments. After 5d treatment, the roots on the two sides of the split root hydroponic box were collected separately and the RNA sequencing were analyzed by the Illumina Hiseq (2500, Illumina, San Diego, CA).
Results: RNA-seq data had a linear relationship with qRT–PCR (r2=0.76), which confirmed the reliability of the RNA-seq data.
Conclusions: Our study screened the key genes of tea root system to adapt to potassium heterogeneity.

overall_design: Transcriptomic changes in low-potassium intolerant and tolerant tea plant (Camellia sinensis) genotypes under potassium heterogeneity.

first: Jianwu

last: Li


title: Inhibition of mutant IDH1 promotes cycling of acute myeloid leukemia stem cells

first: Emily

last: Gruber

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

overall_design: Refer to individual Series


title: Estrogen induces the expression of EBV lytic protein ZEBRA, a marker of poor prognosis in nasopharyngeal carcinoma.

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University

summary: To identify the difference of lytic infection by estradiol and TPA+SB in human nasopharyngeal carcinoma, EBV-positive nasopharyngeal  cell line (HK1-EBV-eGFP) were subjected to RNA-seq analysis.

overall_design: HK1-EBV-eGFP cells were treated with none (DMSO), estradiol 10nM, or TPA+SB.

first: Hirotomo

last: Dochi

first: Satoru

last: Kondo

first: Takayuki

last: Murata

first: Asuka

last: Nanbo

first: Kousho

last: Wakae

first: Wen-Ping

last: Jiang

first: Toshihide

last: Hamabe-Horiike

first: Mariko

last: Tanaka

first: Takumi

last: Nishiuchi

first: Harue

last: Mizokami

first: Makiko

last: Moriyama-Kita

last: Kobayashi

first: Nobuyuki

last: Hirai

first: Takeshi

last: Komori

first: Takayoshi

last: Ueno

first: Yosuke

last: Nakanishi

first: Miyako

last: Hatano

first: Kazuhira

last: Endo

first: Hisashi

last: Sugimoto

first: Naohiro

last: Wakisaka

first: Shin-Hun

last: Juang

first: Masamichi

last: Muramatsu

first: Atsushi

last: Kaneda

first: Tomokazu

last: Yoshizaki


title: ELOVL5 promotes cell proliferation and invasion in renal cell carcinoma

city: Tsukuba

first: Satoshi

last: Nitta

address: 1-1-1 Tennodai

department: Urology

institute: Tsukuba University

summary: Fatty acid is a main component of lipid. The differences of chain-length and pattern of saturation / desaturation in fatty acid are essential for diversity of biological lipid functions. Elongation of very-long-chain fatty acids (ELOVL) plays a critical role in regulating the elongation of fatty acid and ELOVL 1 to 7 are reported in the present. In several cancers but renal cell carcinoma (RCC), the relationship between ELOVLs and cancer progression has been reported. In TCGA cohort, ELOVL5 expression is associated with advanced TNM stage and poor prognosis. We performed CRISPR-Cas9 targeted knockout of ELOVL5 in 2 different RCC cell lines, ACHN and 786-O, respectively. ELOVL5 knockout significantly suppressed cellular invasion, migration and proliferation in vitro and in vivo. In ingenuity Pathway Analysis, Akt signaling activation was decreased in ELOVL5-KO cells. In western blotting analysis, the phosphorylation level of Akt was inhibited in ELOVL5-KO cells. Resultantly, it was suggested that ELOVL5 is involved in the phosphorylation level of Akt and affects cancer progression in RCC.

overall_design: We knocked out ELOVL5 expression by using two independent CRISPR/Cas9 single guide RNAs (#1 and #2) in ACHN cells. RNA sequencing was performed using sgControl and sgELOVL5 cells.

first: Shuya

last: Kandori

first: Yoshiyuki

last: Nagumo

first: Hiroyuki

last: Nishiyama


title: Transcriptome sequencing and ceRNA (lncRNA-miRNA-mRNA) network construction identified the key molecular markers and signaling pathways of chronic thromboembolic pulmonary hypertension

city: Beijing

first: Min

last: Liu

state: Beijing

address: No.2 Yinghua Dong Street, Hepingli, Chao Yang District

institute: China-Japan Friendship Hospital

summary: For patients with chronic thromboembolic pulmonary hypertension (CTEPH), it can lead to death if left untreated. In this study, we attempted to identify key genes and pathways that could help in the diagnosis and treatment of CTEPH. It also provides research direction for further understanding the molecular mechanism of CTEPH.Firstly, we extract RNA from blood samples to construct the library. Then, qualified libraries were sequenced using PE100 strategy on BGIseq platform. Subsequently, the DESeq2 package in R was used to screen differentially expressed mRNAs (DEmRNAs) and differentially expressed lncRNAs (DElncRNAs) of the CTEPH patient group and the normal control group. Afterwards, we performed functional enrichment and protein-protein interaction analysis of DEmRNAs. In addition, we also performed lncRNA-mRNA co-expression analysis and lncRNA-miRNA-mRNA network construction.  A total of 437 DEmRNAs and 192 DElncRNAs were obtained. Subsequently, 205 pairs of interacting DEmRNAs and 232 pairs of lncRNA-mRNA relationship were obtained. Moreover, DEmRNAs were significantly enriched in chemokine signaling pathway, metabolic pathways, arachidonic acid metabolism and MAPK signaling pathway. In addition, only one regulation pathway of SOBP-has-miR-320b-LINC00472 was found through ceRNA network construction. In diagnostic analysis, the area under curve (AUC) of LINC00472, PIK3R6, SCN3A and TCL6 were greater than 0.7, which were 0.964, 0.893, 0.750 and 0.732, respectively. It is indicated that LINC00472, PIK3R6, SCN3A and TCL6 may as the potential diagnostic gene markers in CTEPH.

overall_design: A total of 12 blood samples were included in this study, including 7 blood samples from CTEPH patients and 5 blood samples from normal control individual. Agilent 2100 Bioanalyzer and ABI StepOnePlus Real-Time PCR System were used to detect the quality of the library. Qualified libraries were sequenced using PE100 strategy on BGIseq platform.

first: Wenqing

last: Xu

first: Mei

last: Deng

first: Wanmu

last: Xie


title: Enhanced hippocampal neurogenesis mediated by PGC-1α-activated OXPHOS after neonatal subclinical dose of Propofol exposure revealed by single-nuclei transcriptomic profiling

first: Dihan

last: Lu

state: Guangdong

address: No.58, Zhong Shan Er Lu, Guangzhou, P. R. China.

department: Department of Anesthesiology

institute: First Affiliated Hospital, Sun Yat-sen University

summary: The change of cell lineage and regulation of gene expression after low-dose Propofol exposured in hippocampal of PND10 mice

overall_design: One sample from PND10 mice of Control and low-dose Propofol-exposured respectively

first: Xia

last: Feng

last: Jiang

first: Keyu

last: Chen


title: Single-cell dissection of multiomics changes and epigenetic regulations in human high-grade serous ovarian cancer

city: Beiijing

first: haoling

last: xie

address: 5 Yiheyuan Road Haidian District Beijing

institute: Peking University

summary: To systematically characterize the underlying pathological mechanisms and intratumor heterogeneity in human high-grade serous ovarian cancer (HGSC), we profiled normal fallopian tubes (FTs), primary tumors, and matched metastases to unveil the molecular characteristics associated with tumor development. After stringent quality controls, we obtained single-cell transcriptomes for a total of 5,329 cells from 61 specimens of 16 ovarian cancer patients and 6 individuals without fallopian tube malignancy as controls. We found that the genes associated with interferon (IFN) signaling, metallothioneins, and metabolism were commonly upregulated in ovarian cancer cells. In summary, our study provides valuable resources for identifying new molecular mechanisms and potential therapeutic targets for HGSC.

overall_design:
Single cell profiles of ovarian patients

**RAW DATA not provided due to Chinese laws**

first: Fuchou

last: Tang

first: Heng

last: Cui

first: Kehkooi

last: Kee


title: The chromatin accessibility change by PRC2 inactivation with or without IFNγ stimulation in human MPNST cancer cells

first: Ping

last: Chi

summary: PRC2-isogenic human malignant peripheral nerve sheath tumor (MPNST) M3 cells were generated through CRISPR/Cas9-mediated knockout of the PRC2 core component, SUZ12. PRC2 loss led to not only significant increase, but also significant decrease of chromatin accessibility at 15,346 (16% of all ATAC peaks) and 20,099 genomic loci (21% of all ATAC peaks), respectively. PRC2 loss decreased the chromatin accessibility for IFNγ-responsive loci in M3 cells, resulting in dampened response to IFNγ stimulation.

overall_design: PRC2-isogenic human MPNST M3 cells (sgCon, sgSUZ12) were treated with PBS or 10 ng/ml IFNγ stimulation for 24 hr, followed by chromatin accessibility profiling.

first: Yu

first: Juan

last: Yan

first: Amish

last: Petal


title: Systems spatiotemporal dynamics of traumatic brain injury at single cell resolution

city: Los Angeles

last: Yang

state: CA

address: 2000A, 610 Charles E Young Dr S

institute: UCLA

summary: The etiology of mild traumatic brain injury (mTBI) remains elusive due to the tissue and cellular heterogeneity of the affected brain regions that underlie cognitive impairments and subsequent neurological disorders. This complexity is further exacerbated by disrupted circuits within and between cell populations across brain regions and the periphery, which occur at different timescales and in spatial domains. We profiled three tissues (hippocampus, frontal cortex, and blood leukocytes) at the acute (24hr) and chronic (7days) phases of mTBI at single cell resolution and demonstrated that the coordinated gene expression patterns across cell types were disrupted and re-organized by TBI at different timescales with distinct regional and cellular patterns. Gene expression-based network modeling identified astrocytes as a key regulator of the cell-cell coordination following mTBI in both hippocampus and frontal cortex across timepoints, and mt-Rnr2, which encodes the mitochondrial peptide humanin, as a potential target for intervention based on its broad regional and dynamic dysregulation following mTBI. Treatment of a murine mTBI model with humanin reversed cognitive impairment caused by mTBI through the restoration of metabolic pathways within astrocytes. Our results offer a systems-level understanding of the dynamic and spatial regulation of gene programs by mTBI and pinpoint key target genes, pathways, and cell circuits that are amenable to therapeutics.

overall_design: Ten-week old male C57BL/6 J (B6) mice were randomized to receive either FPI or Sham surgeries, with no investigator blinding. FPI was performed with the aid of a microscope. After 24 h or 7d, mice were sacrificed and fresh blood, hippocampal and frontal cortex tissue was dissected for use in Drop-seq. Humanin was injected i.p. twice at 1 and 6 h after FPI in the treatment group (n = 6 mice) at 40 µg/1 kg body weight. 1µg/100µl HNG was injected for the mice of average weight of 25g. Control FPI mice (n = 6) received vehicle (saline). The Drop-seq library molar concentration was quantified by Qubit Fluorometric Quantitation (ThermoFisher, Canoga Park, CA, USA) and library fragment length was estimated using a Bioanalyzer. Sequencing was performed on an Illumina HiSeq 4000.

first: Fernando

last: Gomez-Pinilla

first: Douglas

last: Arneson


title: SIRT3 SUMOylation confers AML chemoresistance via down-regulation of HES1 dependent fatty acid oxidation

first: JIAO

last: MA

address: No. 280 South Chongqing Road, west wing building #7 R408

department: Biochemistry and Molecular Cell Biology

institute: Shanghai Jiaotong University School of Medicine

summary: SIRT3 deacetylase is a critical mitochondrial regulator for mitochondrial metabolism reprogramming and ROS production, and is involved in the regulation of chemoresistance in AML. SIRT3 is a SUMOylated protein, with de-SUMOylation by SENP1, resulted in enhancement of its deacetylase activity. However, the molecular mechanism of de-SUMOylation mediated SIRT3 activation, which may lead to reinforced AML chemoresistance, remains poorly understood. In the current study, we demonstrated that SIRT3 SUMOylation was attenuated by cytarabine, and de-SUMOylation prevented SIRT3 from proteasome degradation. SIRT3 de-SUMOylation was capable of reprogramming mitochondrial biogenesis, and subsequently inhibited mitochondrial ROS production. Furthermore, RNA-seq revealed that expression of a collection of genes was altered by SIRT3 de-SUMOylation, among which the transcription factor HES1, a downstream substrates of Notch1 signaling pathway, was significantly downregulated by SIRT3K288R, the de-SUMOylated and constitutively active mutant of SIRT3. HES1-dependent FAO was inhibited by SIRT3 de-SUMOylation. Moreover, cytarabine synergized with the SENP1 inhibitor momodrin-Ic to eradicate AML blasts in vitro and in xenografts mice models. In summary, the current study revealed a novel role of SIRT3 SUMOylation in regulating chemoresistance in AML via HES1-dependent FAO, which may provide a rationale for SIRT3 SUMOylation-targeted intervention to improve the chemotherapies in AML.

overall_design: mRNA profiles of WT SIRT3 vs. VEC and SIRT3 K288R vs. WT SIRT3

first: Jiao

last: Ma

first: Yajie

last: Shen

first: Yirong

last: Zhang


title: Transcriptomic Profiling on Kidneys of Mice after Cecal Ligation and Puncture (CLP)  Compared to Sham Operation

city: Shenzhen

first: Boyang

last: Liu

address: 628 Zhenyuan Street, Guangming District

institute: Department of Anesthesiology, The Seventh Affiliated Hospital of Sun Yat-sen University

summary: Sepsis is a severe clinical syndrome related to an exaggerated host immune response to infection as well as systematic inflammation and serious tissue damage. Sepsis-associated acute kidney injury (SA-AKI) is one of the most frequent and serious complications of sepsis. This study aimed to identify new mechanisms in SA-AKI through transcriptome profiling (RNA-seq).

overall_design: A total of 5 C57BL/6 mice were randomly divided into 2 groups: CLP group (n=3), Sham group (n=2). In CLP group, we first anesthetized mice 2%～4% isoflurane. Under aseptic conditions, a 2-cm midline laparotomy was created below the diaphragm to expose the cecum. Two-thirds of the cecum were ligated with a 5-0 silk suture and punctured twice with a 22-gauge needle. The cecum was then squeezed gently to extrude a small amount of feces through the perforation site. Animals were resuscitated with 1 mL of saline subcutaneously after CLP. The procedures of the Sham group (controls) were the same as that of the CLP group, except for ligation and perforation. At 6 hours after CLP, the mice were sacrificed by neck fracture, and the kidneys were taken for RNA sequencing.

first: Xinjin

first: Fang

last: Tan


title: Human resting natural killer (NK) cells, activated NK cells and their secreted small EVs have a specific miRNA repertoire with a distinct pattern of non-templated post-transcriptional modifications

city: Madrid

first: Manuel

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

institute: CNIC

summary: NGS-based assesement of miRNA expression and post-transcriptional modification kinetics in human primary resting and activated natural killer (NK) cells and their released small EVs

overall_design: miRNA samples were obtained from either resting NK cells, isolated from five different healthy donors, or activated NK cells. Isolated activated NK cells were cultured for 72 hours in RPMI supplemented with 10% EV-depleted FBS (by ultracentrifugation at 100,000 g for 16 h) for EV accumulation and small EVs were isolated by culture supernatant differential ultracentrifugation for analysis.  Libraries were produced and subject to NGS with the Illumina HiSeq 2500 system, and sequencing reads processed to obtain expression estimates of known miRNA molecules described in miRBase (release 21).

first: S

middle: G

last: Dosil

last: Lopez-Cobo

first: A

last: Rodriguez-Galan

first: I

last: Fernandez-Delgado

first: M

last: Castellanos

last: Somoza

first: P

last: Milan-Rois

first: H

middle: T

last: Reyburn

last: Vales-Gomez

first: F

last: Sanchez-Madrid

first: L

last: Fernandez-Messina


title: DBC1 is a positive regulator of enhancer epigenomic writers KMT2D and p300 [ChIP-Seq]

first: Jeong

last: Kim

address: Irwon-dong Gangnam-gu

institute: Sungkyunkwan University

summary: Genome-wide maps of H3K4me3, H3K4me1, H3K27ac, H3K9/K14ac, and H3K4ac in SW480 WT and DBC1 KO cells

overall_design: To identify DBC1-regulated histone H3 modifications, we perfomed ChIP-seq analyses of H3K4me1, H3K4me3, H3K4ac, H3K9/K14ac, and H3K27ac in colon cancer cell line SW480 WT and DBC1 KO cells.


title: Differential gene expression of Wnt agonist (BIO and lithium chloride) treated human dental pulp stem cells

city: Pathumwan

first: Thanaphum

last: Osathanon

state: Bangkok

address: 34 Henri-dunant Rd. Wongmai

country: Thailand

institute: Chulalongkorn University

summary: Small molecules, BIO and Lithium chloride are widely used to activate Wnt signaling. It has been shown that these molecules induced beta-catenin accumulation and translocation, leading to the activation of Wnt signaling. These molecules also control various cell responses. Here, the differential gene expression of human dental pulp stem cells treated with BIO and Lithium chloride was examined using a high throughput RNA sequencing technique. Results demonstrated that BIO and Lithium chloride regulated the mRNA expression of various genes in human dental pulp stem cells.

overall_design: Cells were treated with BIO (800 nM) or LiCl (200 mM) for 24 h in normal growth medium. Total RNA was isolated and subjected to RNA sequencing.

first: Chatvadee

last: Kornsuthisopon


title: Chick Cranial Small RNA-seq

city: Pasadena

first: Riley

last: Galton

address: 1200 E California Blvd

department: BBE

institute: Caltech

summary: Small RNA-seq of HH9- chick embryo cranial midbrain region

overall_design: Small RNA from the cranial midbrain region of HH9- wildtype chick embryos was size selected between 19 and ~38 nucleotides. Half of each sample was oxidized to select for piRNAs, while the other half served as a total small RNA reference.

first: Marianne

last: Bronner

first: Katalin

last: Fejes Toth


title: The Effects of Phytosterols Intake on Systematic and Tissue Specific Lipid Metabolism in C57BL/6J Mice

city: Chongqing China

first: Zhu

last: Qian

address: Chongqing China

institute: Chongqing Medical University

summary:
Purpose: To investigate the effects of phytosterols intake on systematic and tissue specific lipid metabolism in C57BL/6J mice.
Methods: Healthy male C57BL/6J mice were randomly divided into control diet group (CS) and phytosterols diet group (PS, 2% phytosterols). After 28 weeks of continuous feeding, livers, lungs were collected for RNA-seq analysis. All samples were paired-end sequenced on the Illumina HiSeq PE150 platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level. RT–qPCR validation was performed using SYBR Green assay.
Results: We mapped about 40 million sequence reads per sample to the mouse genome and identified 23,138 transcripts in the liver and 26,388 transcripts in the lung. Approximately 10% of the transcripts showed differentially expressed in the liver and lung between the two dietary groups, with a fold change ≥1.5 and p <0.05. Enrichment analysis revealed changes in lipid metabolic pathways. RT-qPCR confirmed the changes in related genes.
Conclusions: Phytosterols supplementation effected tissue specific lipid metabolic regulation in the liver and lung. RNA-seq provided us with data at the transcriptome level in the liver and lung of mice.

overall_design: mRNA profiles of the liver and lung of the mice fed with  control diet and 2% phytosterols diet

first: Qian

last: Zhu

first: Xuemei

last: Lian

first: Jingjing

last: Wu

first: Daxue

last: He


title: DBC1 is a positive regulator of enhancer epigenomic writers KMT2D and p300 [RNA-seq]

city: Seoul

summary: We identified DBC1/CCAR2 target genes using RNA-seq analysis in colon cancer cells.

overall_design: mRNA profiles of SW480 WT or DBC1 KO cells were generated by deep sequencing, in triplicate, using Illumina HiSeq2500.


title: Transcriptome change mediated by tumor-intrinsic PRC2 inactivation in transplant murine breast cancer AT3  tumor model in C57BL/6J mice

city: NEW YORK

first: Ping

last: Chi

address: 1275 YORK AVENUE

institute: MEMORIAL SLOAN KETTERING CANCER CTR

summary: We used CRISPR/Cas9-mediated knockout of PRC2 core components, Eed and generated PRC2-isogenic murine mammary tumor model (AT3, sgCon vs. sgEed ) amenable for syngeneic transplant in C57BL/6J mice. Transcriptome analysis of the explanted PRC2-wt (sgCon) and PRC2-loss (sgEed) AT3 tumors by RNA-seq demonstrated that PRC2 loss led to the upregulation of various developmental pathways, and the downregulation of both innate and adaptive immune response pathways.

overall_design: mRNA profiles of AT3 sgCon and sgEed tumors after mammary fat pad grafting in C57BL/6J mice

first: Yu

last: Chen

first: Juan

last: Yan

first: Yuedan


title: CSN5 inhibition in prostate cancer cells

city: New York

first: Bic

last: MSKCC

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

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

overall_design: Refer to individual Series


title: CUT&Tag of  CSN5 in prostate cancer cells

summary: DNA sequencing of libraries from CUT&Tag with three CSN5 antibodies (from SC:sc-13157; GE:GTX70207; AB: ab124720) in  prostate cancer cells

overall_design: To understand the function of CSN5 as a transcription co-factor  in Human prostan cencer cells.

first: Ying

middle: Z

last: Mazzu

first: Philip

last: Kantoff


title: DBC1 is a positive regulator of enhancer epigenomic writers KMT2D and p300

first: Jeong

last: Kim


title: To investigate the effects of PSENEN knockdown on γ-secretase subunits, biological behaviors, and related signaling pathways in keratinocytes

city: Fuzhou

first: Pengjun

last: Zhou

state: Fujian

address: St 29Xianquan

institute: the Union Hospital, Fujian Medical University

summary: The present study was designed to use small interfering RNA (siRNA) approach to identify the effects of PSENEN silencing on human immortal keratinocyte cell line, HaCaT.

overall_design: The alteration of gene expression profiles after PSENEN gene silencing in HaCaT cells was investigated employing RNA-seq sequencing

first: Xuemin

last: Xiao

first: Lihang

last: Lin

last: Liu


title: The mismatch-repair proteins MSH2 and MSH6 interact with the imprinting control regions through the ZFP57-KAP1 complex

status: Public on Aug 16 2022

city: Caserta

first: Francesco

last: Cecere

state: Caserta

address: Via A. Vivaldi, n. 43

department: DiStABiF

country: Italy

institute: University of Campania "Luigi Vanvitelli"


title: Mammalian RNase H1 directs RNA primer formation for mtDNA replication initiation and is also necessary for precise termination of mtDNA replication

city: Gothenburg

first: Claes

middle: M

last: Gustafsson

address: Medcinaregatan 9A

department: Department of Medical biochemistry and cell biology

country: Sweden

institute: Gothenburg University

summary: The exact in vivo role for RNase H1 in mammalian mitochondria has been much debated and we show here that it is essential for site-specific formation of RNA primers to allow initiation of mtDNA replication.  Without RNase H1, the RNA:DNA hybrids at the replication origins are not processed and mtDNA replication is instead initiated at non-canonical sites and becomes impaired.  Furthermore, RNase H1 is also needed for replication completion and in its absence linear deleted mtDNA molecules extending between the two origins of mtDNA replication are formed.  Finally, we report the first patient with a homozygous pathogenic mutation in the hybrid-binding domain (HBD) of RNase H1 causing impaired mtDNA replication. In contrast to catalytically dead pathological variants of RNase H1, this mutant version has enhanced enzyme activity.  This finding shows that the RNase H1 activity must be strictly controlled to allow proper regulation of mtDNA replication.

overall_design: Total or mitochondrial DNA was extracted from heart or brain mouse tissue, libraries were prepared using TruSeq Nano DNA Library Preparation Kit, and sequenced using NovaSeq 6000

first: Xie

last: Xie

first: Jelena

last: Misic


title: BET bromodomain inhibition rescues PD-1-mediated T cell exhaustion in acute myeloid leukemia

city: Guangzhou

first: Mengjun

last: Zhong

address: No.601, West Huangpu Avenue

country: China

institute: Jinan University

summary: We report that the bromodomain and extraterminal domain (BET) inhibitor JQ1 inhibits PD-1 expression in Jurkat T cells, primary T cells, and a T cell exhaustion model. Furthermore, JQ1 dramatically impaired the expression of PD-1 and T cell immunoglobulin mucin-domain-containing-3 (Tim-3), and promoted the secretion of cytokines in T cells from patients with acute myeloid leukemia (AML).

overall_design: Gene expression analysis of Jurkat T cells treated with DMSO and JQ1 in the absence or presence of PHA

first: Rili

last: Gao

first: Ruocong

last: Zhao

first: Youxue

last: Huang

first: Cunte

first: Kehan

last: Li

first: Xibao

last: Yu

first: Dingrui

last: Nie

first: Zheng

first: Xin

first: Zhuandi

first: Shaohua

first: Yuhong

last: Lu

first: Zhi

first: Liang

last: Wang

first: Peng

first: Chengwu

last: Zeng

first: Yangqiu


title: BATF3-dependent IRF4 binding inhibits FOXP3 in differentiating Tregs

city: Bryan

first: Preston

last: Arnold

state: TX

address: Health Professions Education Building 8447 Riverside Pkwy

country: USA

institute: Texas A&M School of Medicine

summary: BATF3 has been shown to inhibit FOXP3 expression in differentiating CD4 T cells, however, the role of IRF4 in this inhibition is unexplored. IRF4 binds DNA weakly on its own and requires interactions with other transcription factors. We investigated how BATF3/IRF4 interactions are necessary for IRF4 binding and BATF3-mediated FOXP3 inhibition.

overall_design: Specific BATF residues have been previously demonstrated to be necessary for BATF/IRF4. We cloned analogous mutations into BATF3 to create a BATF3Mut that does not interact with IRF4. We used a retroviral vector to overexpress the mutant and WT BATF3 in Batf/Batf3 DKO CD4 T cells, cultured the cells in iTreg-differentiating conditions for 24 hrs, and then collected cells for IRF4 ChIP-seq.

middle: R

first: Mou

last: Wen

first: Lei

last: Zhang

first: Yuanlin

last: Ying

first: Zhuyun

last: Mao

first: Xiufeng

last: Chu

first: Guangchuan

first: Xialong

first: Xiang

last: Xiao

first: Wenhao

last: Chen

first: Xian


title: LncRNA sequencing of human primary chondrocytes treated with or without inflammatory cytokines (IL-1β and TNF-α) stimulation

first: tang

last: su'an

address: 107# Yan Jiang Road West

department: Department of Orthopedics

institute: Sun Yat-sen Memorial Hospital

summary: Objectives: Long noncoding RNA (lncRNA) has been identified in numerous diseases. Inflammatory cytokines-induced activation of NF-ĸB pathway plays a critical role in the pathogenesis of osteoarthritis (OA). This study aims to explore NF-ĸB pathway related lncRNA and investigate its role and mechanism on OA development and progression.

overall_design: Examination of lncRNAs expression profiles in inflammatory cytokines stimulated human primary chondrocytes.

first: Su'an

last: Tang

first: Xiaoyu

first: Yumei

last: Cao

first: Changhai

last: Ding