title: hMDM infection with different bacteria

first: Itai

last: Yanai

address: 430 East 29th St., Office 510

department: Biochemistry and Molecular Pharmacology

institute: New York University, School of Medicine

summary: During an intracellular bacterial infection, the host cell and the infecting pathogen interact through a progressive series of events that may result in many distinct outcomes. To understand the specific strategies our immune system employs to manage attack by diverse pathogens, we sought to identify the unique and the core host and pathogen interactions that occur during infection: We compared in molecular detail the pathways induced across infection by seven diverse bacterial species that constitute many of the main human pathogens: Staphylococcus aureus, Listeria monocytogenes, Enterococcus faecalis, Group B Streptococcus, Yersinia pseudotuberculosis, Shigella flexneri and Salmonella enterica. We infected primary human macrophages with each species and used scRNA-Seq to generate a comprehensive dataset of gene expression profiles during bacterial infection. Examining the expression profiles of the infected macrophages across the pathogens, we discovered different modules of infection representing different states through which the infection progresses. The early module captures intra-cellular activity such as lysosome and degranulation, followed by type I IFN signaling, from which results in a cell death module, with a last mode of inflammatory response through response to IL-1. Comparing these modules across the pathogens, we found that their dynamics differ, with some modules active in all species and others which are present in some, but not all pathogens. Our work defines the hallmarks of host-pathogen interactions by identifying recurring properties of infection that can provide insight into diagnostics and therapeutic timing.

overall_design: single cells were infected with diverse bacteria, and harvested after 2 or 4 hors of infection, tagged using cell hashing and processed using 10X scRNA-Seq protocol

first: Gal

last: Avital

first: Felicia

last: Kuperwaser


title: Small RNA sequencing of plasma cells of multiple myeloma patients with extramedullary disease

status: Public on Dec 14 2022

city: Brno

first: Jana

last: Gregorova

address: Kamenice 5

country: Czech Republic

institute: Masaryk University

type: Non-coding RNA profiling by high throughput sequencing

summary:
Background: Extramedullary disease (EM) in multiple myeloma (MM) is defined by escape of malignant plasma cells out of the bone marrow. The mechanisms of extramedullary spread are not well understood. MicroRNAs (miRNA) were proven to be involved in the pathogenesis of MM; nevertheless, there is a lack of knowledge about their role in EM.
Methods: Using NGS analysis, we identified ten differentially expressed miRNA in plasma cells of MM versus EM patients. We performed qPCR in validation phase, using TaqMan Advanced MiRNA Assays.
Results: In this study, we identified 10 miRNAs differentially expressed between MM and EM patiens.

overall_design: Expression miRNA profile of 36 multiple myeloma patients and 9 patients with extramedullary disease.

first: Petra

last: Vychytilova-Faltejskova

first: Natalia

middle: A

last: Gablo

first: David

last: Vrabel

first: Lenka

last: Radova

first: Lucie

last: Brozova

first: Jiri

last: Jarkovsky

first: Martina

last: Almasi

first: Renata

last: Bezdekova

first: Martin

last: Stork

last: Minarik

first: Zdenek

last: Adam

first: Marta

last: Krejci

first: Tereza

last: Popkova

first: Roma

last: Hajek

first: Ondrej

last: Slaby

first: Ludek

last: Pour

first: Sabina

last: Sevcikova


title: Dual Roles for CND1 in Maintenances of Nuclear and Chloroplast Genome Stability in Plants

status: Public on Dec 13 2022

city: 广州市

first: 柳

last: 洪

state: 广东省

address: 番禺区

department: 中药学院

country: China

institute: 广州中医药大学

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Regulation of the alveolar regenerative niche by amphiregulin-producing Treg cells (AT2)

city: New York

first: Nicholas

last: Arpaia

state: NY

address: 701 W 168TH ST HHSC 910C

department: Microbiology & Immunology

country: USA

institute: Columbia University Irving Medical Center

summary: This study investigates the role of regulatory T cell–derived Areg in driving epithelial repair following influenza infection. We use RNA sequencing to probe the gene expression changes within epithelial cells in wildtype mice and in mice that conditionally lack Areg from T cell sources (CD4-cre Areg-flox). Further, we identify a population of damage-associated transitional alveolar epithelial cells that are induced in reponse to acute injury and exhibit gene expression changes reflective of AT2 transdifferentiation to AT1.

overall_design: Alveolar epithelial cells were isolated by FACs prior to RNA extraction and RNA sequencing. Wild-type type II alveolar epithelial cells (AT2)  isolated from mock treated (PBS) mice and mice treated with PR8/H1N1 influenza at day 7 post infection; n= 4 per group.  Intermediate alveolar epihtelial cells isolated at day 5 post infection with PR8/H1N1 influenza from CD4-cre Areg-fl/fl and Areg-fl/fl controls; n=4 per group.

first: Katherine

last: Kaiser

first: Lucas

last: Loffredo

first: Kenia

last: de los Santos


title: MTA mediated m6A modification promotes chilling tolerance by regulating gene translation efficiency in Arabidopsis

city: Nanjing

first: Wang

last: Haiyan

state: Jiangsu

address: Weigang NO.1

department: State Key Laboratory for Crop Genetics and Germplasm Enhancement

institute: Nanjing Agricultural University

summary: Plants can respond to low temperatures with diverse mechanisms occurred at transcriptional and translational levels. N6-methyladenosine (m6A) is the most prevalent mRNA modification in eukaryotes that acts as a new emerging layer of epitranscriptomic gene regulation. However, the cellular roles of m6A in plant response to low temperatures remain largely unknown. Here we show that mRNA m6A modification is indispensable for Arabidopsis growth under chilling conditions.

overall_design: Gene expression,translation efficiency and m6A peaks were identified from wild type Columbia-0 and AmiR-mta mutant under chilling and normal conditions in two biological replicates.

first: Shuai

last: Wang

first: Haiyan

first: Zhihui

last: Xu


title: Effect of Activin A on gene expression in atherosclerotic liver in LDLR-/- mice

city: Boston

first: Huan

last: Liu

state: Massachusetts

address: 185 Cambridge Street

department: CVRC

institute: Massachusetts General Hospital

summary:
To investigate the mechanism of hepatic Activin A in atherosclerosis, we studied LDLR-/- mice on a Western diet for 12 weeks and used adeno-associated viral vectors with a liver-specific thyroxine binding globulin (TBG) promoter to express Activin A or GFP (control)
We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different livers in each group

overall_design: Comparative gene expression profiling analysis of RNA-seq data for liver from AAV-TBG-Control and AAV-TBG-Activin A

first: Anthony

last: Rosenzweig


title: An ectopic enhancer restores CFTR expression through de novo chromatin looping.

city: Cleveland

first: Ann

last: Harris

state: OH

address: 2109 Adelbert Rd

department: Genetics and Genome Sciences

institute: Case Western Reserve University


title: An ectopic enhancer restores CFTR expression through de novo chromatin looping [ATAC-seq]

summary: Transcription of the cystic fibrosis transmembrane conductance regulator (CFTR) gene is regulated by a set of ubiquitous and cell-type selective cis-regulatory elements (CREs). These elements include extragenic and intronic enhancers that bind cell-type specific transcription factors, as well as architectural protein bound structural elements. We previously reported that loss of the airway-selective -35kb enhancer in 16HBE14o- airway epithelial cells disrupts normal enhancer-promoter looping at the CFTR locus and nearly abolishes its expression. Here we expand on previous work, and explore the effect of relocation of the 500bp -35kb enhancer core to an ectopic site in intron 1 of CFTR on gene expression and chromatin dynamics. We find that although genomic relocation of this element is not able to fully restore CFTR expression to wild-type levels, the -35kb sequence is able establish a de novo enhancer signature at chromatin at the site of insertion. Additionally, the relocated -35kb enhancer is able to form chromatin contacts with known CFTR CREs. These studies reveal important direct chromatin effects, as well as limitations, of CFTR enhancers, and provide important considerations when targeting the CFTR locus for novel therapeutic gene editing.

overall_design: ATAC-seq to examine open chromatin in WT and modified 16HBE14o- cells

first: Jenny

middle: L

last: Kerschner

first: Alekh

last: Paranjapye


title: Transcriptome signatures preceding the induction of anti-stalk antibodies elicited by a chimeric hemagglutinin-based universal influenza virus vaccine

first: Ana

middle: S.

last: Gonzalez-Reiche

state: New York

address: 1 Gustave L. Levy Pl

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: A phase 1 clinical trial to test the immunogenicity of a chimeric group 1 HA (cHA) universal influenza virus vaccine targeting the conserved stalk domain of the hemagglutinin of influenza viruses was carried out. Vaccination with adjuvanted-inactivated vaccines induced high anti-stalk antibody titers. We sought to identify gene expression signatures that correlate with such induction. Messenger-RNA sequencing in whole blood was performed on peripheral blood of 53 vaccinees, at early and late time points after priming and boosting. We generated longitudinal data on peripheral blood of 53 volunteers, at early (days 3 and 7) and late (28 days) time points after priming and boosting with cHAs. Differentially expressed gene analysis showed no differences between placebo and live-attenuated vaccine groups. However, an upregulation of genes involved in innate immune responses and type I interferon signaling was found at day 3 after vaccination with inactivated adjuvanted formulations. Cell type deconvolution analysis revealed a significant enrichment for monocyte markers and different subsets of dendritic cells as mediators for optimal B cell responses and significant increase of anti-stalk antibodies in sera. A significant upregulation of immunoglobulin related genes was only observed after administration of adjuvanted vaccines (either as primer or booster) with specific induction of anti-stalk IGVH1-69. This approach informed of specific immune signatures that correlate with robust anti-stalk antibody responses, while also helping to understand regulation of gene expression induced by cHA proteins under different vaccine regimens.

overall_design: A randomized, placebo-controlled, observer-blind, phase I clinical study was conducted at Cincinnati Children’s Hospital Medical Center (Cincinnati, OH, USA) and Duke Early Phase Clinical Research Unit (Durham, NC, USA). This clinical trial was designed to assess the safety and immunogenicity of a chimeric hemagglutinin-based vaccine approach; and its ability to elicit broadly cross-reactive antibodies against the hemagglutinin stalk domain of influenza viruses. Briefly, 66 participants were block-randomized in each site and received LAIV8-IIV5/AS03 (Group 1, G1), LAIV8-IIV5 (Group 2, G2), SALINE-PBS (Group 3, G3), IIV8/AS03-IIV5/AS03 (Group 4, G4) or PBS-PBS (Group 5, G5). To note, LAIV8 was administered intranasal while the IIV5 and IIV5/AS03 vaccines were given intramuscularly. The Cincinnati Children’s Hospital Medical Center Institutional Review Board (IRB) served as the central IRB of record for review, approval and oversight of this study on behalf of the Icahn School of Medicine at Mount Sinai IRB, Duke IRB and PATH Research Ethics Committee. All patients provided written informed consent prior to participation. ClinicalTrials.gov identifier NCT03300050. De-identified samples were made available for this analysis (Icahn School of Medicine at Mount Sinai IRB approval #IRB-17-01779).

first: Teresa

last: Aydillo

middle: S

first: Daniel

last: Stadlbauer

first: Mary

last: Amper

first: Venugopalan

middle: D

last: Nair

first: Chiara

last: Mariottini

first: Stuart

middle: C

last: Sealfon

first: Harm

last: van Bakel

first: Peter

last: Palese

first: Florian

last: Krammer

first: Adolfo

last: García-Sastre


title: Dual Roles for CND1 in Maintenances of Nuclear and Chloroplast Genome Stability in Plants [RNA-seq]

first: 柳

last: 洪

summary: The coordination of chloroplast and nuclear genome status are critical for plant cell function, but the mechanism remain largely unclear. In this study, we report that Arabidopsis thaliana CHLOROPLAST AND NUCLEUS DUAL-LOCALIZED PROTEIN 1 (CND1) maintains genome stability in both the chloroplast and the nucleus.

overall_design: We performed transcriptome deep sequencing (RNA-seq) to compare the differences of gene expression between cnd1-3 and wild type plants

first: Sujuan

last: Duana

first: Ziyue

last: Yang

first: Yunping

last: Zeng


title: An ectopic enhancer restores CFTR expression through de novo chromatin looping [4C-seq]

first: Ann

last: Harris

overall_design: Analysis of the 3D chromatin architecture with 4C-seq at the CFTR locus to determine interaction frequencies between elements in response to deletion or relocation of -35kb CRE in 16HBE14o- cells

first: Jenny

last: Kerschner


title: Molecular dissection of somatic NF1 pseudarthrosis

city: Dallas

first: Jonathan

last: Rios

state: TX

address: 2222 Welborn Street

institute: Scottish Rite for Children

summary: Neurofibromatosis Type 1 (NF1) is a tumor predisposition syndrome with pleiotropic somatic manifestations, including formation of bone pseudarthrosis after fracture. The pathogenesis of NF1 pseudarthroses remains unclear, though defects in osteogenesis have been posited. Here, we applied time-series single-cell RNA-sequencing (scRNAseq) to patient-matched control and pseudarthrosis-derived primary bone mesenchymal stromal cells (MSCs). We show that osteogenesis occurs in NF1-/- MSCs. In contrast, expression of genetic pathways associated with skeletal mineralization were reduced in NF1-/- cells compared to co-cultured NF1+/- fracture-derived cells.

overall_design: Control bone-derived primarry MSCs underwent time-series scRNAseq prior to differentiation and after 3-days and 9-days of osteogenesis. Patient-matched pseudarthrosis-derived primary MSCs underwent time-series scRNAseq prior to differentiation and following 3-, 6-, and 9-days of osteogenesis. All experiments were performed using the Fluidigm C1 instrument.

middle: J


title: Chromatin accessibility in T-ALL cells upon USP7 inhibitor with or without dexamethasone (ATAC-Seq)

first: Sonali

last: Narang

address: 435 east 30th street

institute: NYU Langone

summary: We report chromatin accessibility changes in DND41 cells upon USP7 inhibitor with or without dexamethasone. DND41 cells were treated with USP7 inhibitor with or without dexamethasone. ATAC-seq were performed to detect chromatin accessibility change

overall_design: Examination of chromatin accessibility in DND41 cells

first: Qi

last: Jin

first: Blanca

middle: G

last: Diaz

first: Yalu

last: Zhou

first: Panagiotis

last: Ntziachristos


title: Chromatin organization in T-ALL cells upon USP7 inhibitor with or without dexamethasone (Hi-C)

summary: We report chromatin organization changes in DND41 cells upon USP7 inhibitor with or without dexamethasone. DND41 cells were treated with USP7 inhibitor with or without dexamethasone. ATAC-seq were performed to detect chromatin organization change

overall_design: Examination of chromatinorganization in DND41 cells


title: Controlling organoid symmetry breaking uncovers an excitable system underlying human axial elongation

status: Public on Dec 12 2022

city: Newton

first: Giridhar

last: Anand

state: MA

address: 31 Cross Street

institute: Harvard University

summary: The human embryo breaks symmetry to form the anterior-posterior axis of the body. As the embryo elongates along this axis, progenitors in the tailbud give rise to tissues that generate the spinal cord, skeleton, and musculature. This raises the question of how the embryo achieves axial elongation and patterning. While ethics necessitate in vitro studies, the variability of organoid systems has hindered mechanistic insights. Here we developed a bioengineering and machine learning framework that optimizes symmetry breaking by tuning the spatial coupling between human stem cell-derived organoids. This framework enabled the reproducible generation of axially elongating organoids, each possessing a tailbud and neural tube. We discovered that an excitable system composed of WNT/FGF signaling drives elongation through induction of a neuromesodermal progenitor (NMP)-like signaling center. We discovered that instabilities in the excitable system are suppressed by secreted WNT inhibitors. Absence of these inhibitors led to ectopic tailbuds and branches.  Our results identify mechanisms governing stable human axial elongation.

overall_design: Single-cell mRNA sequencing of day 4 human ESC-derived organoids

first: Anand

last: Giridhar

first: Weis

last: Theresa

first: Ramanathan

last: Sharad


title: Genome-wide gain-of-function screening characterized lncRNAs as tumor immune response regulators [CRISPR_screen]

city: Pittsburgh

first: Da

address: 308 Salk Pavilion

institute: University of Pittsburgh

summary: The majority of lncRNAs’ roles in tumor immunology remain elusive. In this project, we performed a CRISPR activation screening of 9744 lncRNAs in melanoma cells co-culturing with human CD8+ T cells. We identified 16 novel lncRNAs potentially regulating tumor immune response. Further integrative analysis using tumor immunogenomics data revealed that IL10RB-DT and LINC01198 are significantly correlated with tumor immune response and survival in melanoma and breast cancer. Specifically, IL10RB-DT suppresses CD8+ T cells activation via inhibiting IFN-γ-JAK-STAT1 signaling and antigen presentation in melanoma and breast cancer cells. On the other hand, LINC01198’s upregulation sensitizes the killing of tumor cells by CD8+ T cells. Mechanistically, LINC01198 interacts and activates NF-κB component p65 to trigger the type I and type II interferon responses in melanoma and breast cancer cells. Our study systematically characterized novel lncRNAs involved in tumor immune response.

overall_design: CRISPR activation sgRNA library targeting lncRNAs was transduced in MEL-526 cells and co-cultured with T cells before sequencing to determine sgRNA distribution

first: Yifei

last: Wang

first: Yueshan

last: Zhao

first: Min

last: Zhang


title: Chromatin organization in T-ALL cells upon USP7 inhibitor with or without dexamethasone


title: Microglial pattern recognition via IL-33 promotes synaptic refinement in developing corticothalamic circuits in mice (FOS ChIP-seq)

city: San Francisco

first: Ilia

middle: D.

last: Vainchtein

state: California

address: 1550 4th street

department: Psychiatry

institute: UCSF

summary: To determine whether FOS is involved in the IL-33 microglial gene expression response, we have FOS ChIP-sequenced cortical microglia 4 hours after IL-33 i.c.v. injection.

overall_design: FOS ChIP-sequencing data from cortical microglia 4 hours after i.c.v injection of IL-33 in P30 mice.

first: Rafael

middle: T

last: Han

first: Johannes

last: Schlachetzki

first: Anna

middle: V

last: Molofsky


title: Microglial pattern recognition via IL-33 promotes synaptic refinement in developing corticothalamic circuits in mice (H3K27ac ChIP-seq)

summary: To determine the direct effect of IL-33 on microglial gene expression, we have H3K27ac ChIP-sequenced cortical microglia 4 hours after IL-33 or vehicle i.c.v. injection.

overall_design: H3K27ac ChIP-sequencing data from cortical microglia 4 hours after i.c.v injection of IL-33 or vehicle in P30 mice.


title: Chromatin accessibility in T-ALL cells upon USP7 inhibitor with or without dexamethasone (RNA-Seq)

first: Sonali


title: Microglial pattern recognition via IL-33 promotes synaptic refinement in developing corticothalamic circuits in mice (scRNAseq)

summary: To determine the effect of IL-33 on microglial gene expression, we have scRNA-sequenced cortical microglia from ST2KO and WT mice 4 hours after IL-33 or vehicle i.c.v. injection.

overall_design: scRNA-sequencing data from CD45+ cells from ST2KO and WT mice 4 hours after IL-33 or vehicle i.c.v. injection.

first: Leah

last: Dorman


title: Differential gene expression in sporadic and genetic forms of Alzheimer’s disease and frontotemporal dementia in brain tissue and lymphoblastoid cell lines.

city: Barcelona

last: Antonell

state: Barcelona

address: C/Casanova, 143

department: Neurosciences

country: Spain

institute: Fundacio Clinic per a la Recerca Biomèdica

summary: We have performed gene expression microarray analysis of two types of dementia, Alzheimer's disease (AD) and frontotemporal dementia (FTD), using two kind of samples, frozen brain tissue and lymphoblastoid cell lines.

overall_design: 60 samples were included: 35 brain samples and 23 lymphoblastoid cell lines. AD group was divided in sporadic early onset and familial due to mutation in PSEN1 gene. FTD was divided in genetic by mutation in MAPT, GRN and C9orf72 genes, and sporadic with tau and TDP43 deposition. Gene expression was analyzed with Clariom D microarray (Affymetrix). Differentially expressed genes (DEG) were obtained adjusting a linear model with empirical Bayes moderation of the variance. Significance threshold was set at p-value <0.05 and fold change >1.5 and <1/1.5. In the final analysis, two samples FTD.M2.B1 and AD.MF.L3 were discarded as outliers, and thus are not included in the records.

first: Oscar

last: Ramos-Campoy

first: Albert

last: Llado

first: Beatriz

last: Bosch

first: Mireia

last: Ferrer

first: Agnes

last: Perez-Millan

first: Miguel

last: Vergara

first: Laura

last: Molina-Porcel

first: Guadalupe

last: Fernandez-Villullas

first: Mircea

last: Balasa

first: Raquel

last: Sanchez-Valle


title: PALI1 Promotes Tumor Growth through Competitive Recruitment of PRC2 to G9A-target Chromatin for Dual Epigenetic Silencing [ChIP-seq]

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

summary: PALI1 is a newly identified accessory protein of the Polycomb Repressive Complex 2 (PRC2) that catalyzes H3K27 methylation. However, the roles of PALI1 in cancer are yet to be defined. Here we report that PALI1 is upregulated in advanced prostate cancer (PCa) and competes with JARID2 for binding to PRC2 core subunit SUZ12. PALI1 further interacts with the H3K9 methyltransferase G9A, bridging the formation of a unique G9A-PALI1-PRC2 super-complex that occupies a subset of G9A-target genes to mediate dual H3K9/K27 methylation and gene repression. Many of these genes are developmental regulators induced upon cell differentiation, and their loss in PCa predicts poor prognosis. Accordingly, PALI1 and G9A drive PCa cell proliferation and invasion in vitro and xenograft tumor growth in vivo. Collectively, our study shows that PALI1 harnesses two central epigenetic mechanisms to suppress cellular differentiation and promote tumorigenesis, which can be targeted by dual EZH2 and G9A inhibition.

overall_design: Examination of H3K27me3 and H3K9me2 modification along with SUZ12, PALI and G9a bound chromatin loci in human prostate cancer cells. There are 27 ChIP-Seq samples with pLKO/siCtrl as the control/reference.

first: Ka

middle: W

last: Fong


title: Microglial pattern recognition via IL-33 promotes synaptic refinement in developing corticothalamic circuits in mice (bulk RNA-seq)

first: Ilia

last: Vainchtein

summary: To determine the direct effect of IL-33 on microglial gene expression, we have bulk RNA-sequenced cortical microglia 4 hours after IL-33 or vehicle i.c.v. injection.

overall_design: Bulk RNA-sequencing data from cortical microglia 4 hours after i.c.v injection of IL-33 or vehicle in P30 mice.


title: Genome-wide gain-of-function screening characterized lncRNAs as tumor immune response regulators

first: Da

last: Yang

summary: RNA-seq data for candidate genes identified from CRISPR activation screen for tumor response regulators

overall_design: Total RNA-seq data for candidate genes activation/siRNA knockdown in MEL-526/ MCF-7 cells

first: Yifei

last: Wang

first: Min

last: Zhang

first: Yueshan

last: Zhao


title: Functional Characterisation of the Core Autophagy Protein ATG5 in Dictyostelium discoideum

city: Cologne

first: Ludwig

last: Eichinger

state: NRW

address: Joseph-Stelzmann-Str. 52

department: Biochemistry Medical Faculty

country: Germany

institute: Centre for Biochemistry Medical Faculty University of Cologne

summary:
Purpose: Global survey of the transcriptome in autophagy-deficient strains of D. discoideum
Results: Our RNAseq analysis of ATG5‾, ATG5‾/12‾ and ATG5‾/12‾/16‾ cells revealed major transcriptional changes in a large number of genes in comparison to AX2
Conclusions: Our study presents a first detailed analysis of the transcriptome in autophagy-deficient strains of D. discoideum. The data were generated by RNA-seq technology. The optimised data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell. We conclude that RNA-seq based transcriptome characterisation would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: Total RNA from vegetative Dictyostelium discoideum cells (AX2 wild-type and ATG5‾, ATG5‾/12‾, ATG5‾/12‾/16‾ mutant strains) was isolated as described [49], n=6, Illumina Genome Analyzer IIx

first: Malte

last: Karow

first: Sarah

last: Fischer

first: Susanne

last: Meßling

first: Ramesh

last: Rijal

first: Roman

last: Konertz

first: Prerana

last: Wagle


title: A β-catenin-regulated RNA processing transcriptional program imposes chemotherapy resistance and predicts T-ALL patient survival associated with high BRCA1 levels [RNA-Seq]

first: Anna

last: Bigas

address: Dr. Aiguader 88

department: Cancer Research

institute: Institut Hospital del Mar d'Investigacions Mèdiques

summary: De novo acquisition or subclonal selection of chemotherapy resistant cell populations are at the base of relapse in cancer. We have now investigated the role of ß-catenin in the evolution of T-ALL patients. We identified an RNA-processing signature that is directly regulated by ß-catenin in T-ALL cell lines. This signature was sufficient to identify T-ALL patients with poorest prognosis, together with high ß-catenin levels in an outdated discovery cohort with high incidence of refractory patients. In an independent validation cohort of T-ALL patients treated with current protocols and a 5-years survival >90%, neither ß-catenin-dependent signatures nor ß-catenin mRNA levels were predictive of patient outcome. However, further analysis of data demonstrated the prognosis value of the ß-catenin RNA-processing signature specifically in tumors carrying high BRCA1 levels. Finally, we show that both ß-catenin and BRCA1 enhanced the recovery of T-ALL cells after chemotherapy thus providing a mechanistic explanation for the prognosis value of ß-catenin and BRCA1.

overall_design: 12 RNA-Seq samples (triplicates per condition)

first: David

last: Arambilet

first: Violeta

last: Garcia-Hernandez

first: Yolanda

last: Guillen


title: Changes in gene expression in Pan02 tumors after TGFb-derived peptide vaccination

city: Odense

first: Lars

last: Grøntved

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: To investigate changes in the tumor microenvironment at a gene expression level induced by TGFb-derived peptide vaccination in a murine model of PDAC (Pan02)

overall_design: Pan02 tumor-bearing mice were either left untreated or vaccinated with TGFβ vaccine on days 10 and 17 post-inoculation. Tumors were harvested (n=3-4 per group) on day 30, RNA was extracted, and bulk RNAseq was performed.

first: Maria

last: Perez-Penco

first: Mads

last: Hald Andersen


title: RNA-seq of cardiomyocytes exposed to glucose deprivation with or without empagliflozin treatment

city: Shanghai

first: Yixiang

last: Xu

address: 130 Meilong Road

institute: East China University of Science and Technology

summary: Glucose-lowering drugs sodium-glucose cotransporter 2 (SGLT2) inhibitors reduce the risk of serious heart failure events, regardless of diabetes status, but the underling mechanism of this cardioprotective benefit is unknown. Here, we performed RNA-seq screening in cardiomyocytes to determine the potential cardioprotective mechanism of empagliflozin (EMPA).

overall_design: Examination of control group, GD-treated without EMPA treatment group, GD-treated with EMPA 100μM treatment group, GD-treated with EMPA 200μM treatment group  in H9c2 cells by RNA-seq, in triplicate

first: Xu

last: Yixiang

first: Li

last: Jian


title: PALI1 Promotes Tumor Growth through Competitive Recruitment of PRC2 to G9A-target Chromatin for Dual Epigenetic Silencing [RNA-Seq II]

first: Jindan

last: Yu

overall_design: Gene expression profiling from LNCaP cells were performed by RNA-seq. There are 4 treatment groups in triplicate with DMSO as a control/reference group.

first: Ka

last: Fong


title: Methylation-sequencing in prostate cancer cells

first: Bic

last: MSKCC

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

type: Methylation profiling by high throughput sequencing

summary: Methylation-sequencing was performed in prostate cancer cells to detect methylation status of SNAI2 gene.

overall_design: To understand the methylation status of SNAI2 gene in prostate cancer cells, we isolated genomic DNA from four prostate cancer cell lines (22Rv1, ABL, LAPC4, VCaP).

first: Ying

middle: Z

last: Mazzu

first: Philip

last: Kantoff


title: Next Generation Sequencing Facilitates Quantitative Analysis of  in 14-day-old wt and  val1 val2 pkl seedlings.

city: Guangzhou

first: Liang

last: Zhenwei

state: Guangdong

address: Xingang West Road

department: School of Life Science

institute: Sun Yat-sen University

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis
Methods: RNA from 14-day-old seedlings of wild-type and pkl was isolated using the RNAprep Pure Plant Kit as described above. RNAs from three biological replicates was sequenced separately at Novogene, using Illumina Hiseq X-Ten (Sequencing method: Hiseq-PE150).
Results: Reads were mapped to the TAIR10 Arabidopsis genome using TopHat (Galaxy V2.1.1 in usegalaxy.org) with default settings, except that a minimum intron length of 20 bp and a maximum intron length of 5,000 bp were required (Paired-end). Then, mapped reads were assembled according to TAIR10 version of genome annotation using cufflinks (version 2.1.1) with default settings. To analyze differential expression, the assembled transcripts from three independent biological replicates in Col and other mutants were included and compared using Cuffdiff (version 2.1.1) with default settings.
14-day-old seedling of WT and val1 val2 pkl were performed RNA-seq to analyzed their differential expression genes in Arabidopsis.

overall_design: Examination of global RNA expression in 14-day-old wt and val1 val2 pkl seedlings.

first: Zhenwei

last: Liang

first: Chenlong

last: Li


title: PALI1 Promotes Tumor Growth through Competitive Recruitment of PRC2 to G9A-target Chromatin for Dual Epigenetic Silencing [RNA-seq]

overall_design: Gene expression profiling from LNCaP cells were performed by RNA-seq. There are 5 treatment groups in triplicate with pLKO as a control/reference group.


title: Transcriptome analysis of mutant p53 rescued by arsenic trioxide (ATO)

first: Yigang

last: Tang

address: No 197 RUIJIN ER RD

institute: Shanghai Jiaotong University

summary: The goals of this study are to compare transcriptome of mutant p53 rescued by arsenic trioxide

overall_design: Treat isogenic HCT116 p53-/- cells (infected with p53-M133T, p53-R273H, vector, wild-type p53) with ATO

first: Min

last: Lu


title: PALI1 Promotes Tumor Growth through Competitive Recruitment of PRC2 to G9A-target Chromatin for Dual Epigenetic Silencing

overall_design: Refer to individual Series


title: Microglial pattern recognition via IL-33 promotes synaptic refinement in developing corticothalamic circuits in mice.

first: Ilia

last: Vainchtein

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


title: Analysis of the impact of FOXA1 expression on MDA::ER E2-sensitive transcriptomes and ER cistromes [ChIP-Seq data]

status: Public on Dec 11 2022

city: Rennes

first: Raphaël

last: Métivier

address: Campus de Beaulieu

country: France

institute: CNRS UMR 6290

summary: The primordial actions of the estrogen receptor alpha (ER) in controlling breast cancer cells proliferation rate are particularly documented. However, reintroducing ER into ER-negative cells does not reprogram their transcriptome towards an estrogen-sensitive growth phenotype. Member of the Forkhead (FKH) family of transcription factors, FOXA1 has been characterized to be essential for the appropriate binding of ER onto chromatin in MCF-7 cells. FOXA1 pioneering actions involve modulations of histone post-translational modifications (HPTMs) and local depletion in methylated CpGs. Using MDA-MB231 cells which are ER and FOXA1 negative, we aimed at determining whether the introduction of ER and FOXA1 would be sufficient to restore an estrogen-sensitive growth and to coincidently reprogram chromatin. We used ChIP-seq experiments to map ER and FOXA1 binding sites (BSs) and to profile H3K4me2 and H3K27ac marks, and surprisingly observed that FOXA1 had rather a global negative impact on ER actions, associated with an inhibition of growth and a reorientation of the transcriptome of the cells towards cell death. We demonstrate that the re-introduction of FOXA1 in these cells actually competes for the binding and pioneering actions of FOXA2, another FKH protein, on a number of ER BSs. As demonstrated for its alter ego FOXA1 in MCF-7 cells, abrogating FOXA2 expression drastically diminished ER binding onto its cognate sites, associated with a local loss of HPTMs for active chromatin.

overall_design: Whole-genome analysis of estrogen receptor (ER) and its FOXA1 and/or FOXA2 pioneering factors binding events associated with the cartography of two histone marks (H3K4me2 and H3K27ac) in four ER/FOXA1 positive or negative breast cancer cells.

first: Justine

last: Quintin

first: Christine

last: Le Péron

first: Elise

last: Mahé

first: Aurélien

last: Seérandour

first: Gaëlle

last: Palierne

first: Maud

last: Bizot

first: Frédéric

last: Percevault

first: Stéphane

last: Avner

first: Gilles

last: Salbert


title: Analysis of the impact of FOXA1 expression on MDA::ER E2-sensitive transcriptomes and ER cistromes


title: RNA-seq of suspension-grown vs. adherent Neisseria gonorrhoeae under conditions of zinc sequestration or zinc excess

city: Charlottesville

first: Eugene

last: Ke

state: Virginia

address: P.O. Box 800734, 1340 Jefferson Park Avenue

department: MIC

institute: University of Virginia

summary: Deep sequencing of cDNA of Neisseria gonorrhoeae bacteria that were grown in suspension or adherent to acid-washed glass coverslips, in media where zinc was sequestered or available in excess.

overall_design: Total RNA was isolated from Neisseria gonorrhoeae strain FA1090 grown for four hours either in suspension or adherent to acid-washed glass coverslips. Three media conditions were tested: Keratinocyte serum-free medium (KSFM) without additives, KSFM with 3 μM recombinant murine calpotectin, or KSFM with 3 μM mouse calprotectin and 6 μM ZnSO4. Ribosomal RNA was depleted, and remaining RNA was reverse-transcribed into a cDNA library for Illumina sequencing. Reads were mapped to the FA1090 genome.

first: Alison

middle: K

last: Criss

first: Jocelyn

last: Ray

first: Asya

last: Smirnov

first: Stavros

last: Maurakis

first: Walter

last: Chazin

first: Simone

last: Harrison

first: Cynthia

middle: N

last: Cornelissen


title: Gene expression profile at single cell level of tdTomato+ DRG cells from Nav1.8-Cre R26CAG-floxStop-tdTomato mice

city: Wellington

first: Sotaro

last: Ochiai

address: Gate 7 Victoria University, Keburn Parade

country: New Zealand

institute: Malaghan Institute of Medical Research

summary: We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of Nav1.8+ sensory neurons from DRG.

overall_design: Dorsal root ganglin (DRG) cells of naïve Nav1.8-Cre R26CAG-floxStop-tdTomato mice were FACS sorted according to the presence of tdTomato signal and analyzed using scRNAseq.

first: Ochiai

last: Sotaro

first: Takahashi

last: Sonoko

first: Jin

last: Jianshi

first: Shiroguchi

last: Katsuyuki

first: Okada

last: Takaharu


title: A β-catenin-regulated RNA processing transcriptional program imposes chemotherapy resistance and predicts T-ALL patient survival associated with high BRCA1 levels [ChIP-Seq]

first: Anna

last: Bigas

overall_design: 24 ChIP-Seq samples (duplicates or triplicates for each condition) and 1 Input

first: David

last: Arambilet

first: Violeta

last: Garcia-Hernandez

first: Yolanda

last: Guillen


title: Transcriptional expression of different grafting combinations during healing

status: Public on Dec 10 2022

city: qingdao

first: ji

last: piyu

address: changcheng road

institute: Qingdao Agricultural University

summary: Grafting was widely used in pear cultivation as an ancient cultivation technique, the use of rootstocks could improve the resistance of pear trees, make pear trees early fruit. The healing process of plant grafting involves complex signal transduction and material accumulation.We used two different grafting combinations, include ‘Qingzhen D1’ on ‘QAUP-1’ and ‘Qingzhen D1’ on ‘Qingzhen D1’.The samples which are the part of graft union of those two combinations were collected om 1 day, 5 days , 9 days and 30 days after grafting. We performed an in-depth RNA-seq analysis to observe the  transcriptional changes that occur during the development of two combinations.

overall_design: Transcriptional analysis of two grafting combinations which are‘Qingzhen D1’ on ‘QAUP-1’ and ‘Qingzhen D1’ on ‘Qingzhen D1’ on four stages during the grafting healing process.

first: Liding

last: LI


title: Identification of glutamine-regulated genes in Arabidopsis seedlings

city: Taipei

first: Ming-Hsiun

last: Hsieh

state: Taiwan

address: 128 Sec. 2, Academia Rd, Nankang

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

summary: To understand the global effect of Gln on gene expression, we performed RNA-seq analysis to compare the gene expression profiles between 12-day-old Arabidopsis seedlings grown on 5 mM NH4NO3 and 5 mM Gln as the sole N source.

overall_design: Total RNA extracted from 12-day-old Arabidopsis seedlings grown on medium containing 1/2 MS-modified basal salt mixture without N (M531, PhytoTechnology Laboratories) plus 0.5% sucrose and supplemented with 5 mM NH4NO3 or 5 mM Gln as the sole N source was used for RNAseq analysis.

first: Hong-Sheng

last: Liao

first: Sang-Chu

last: Lin


title: Single cell analysis of senescent cells of old p16-FDR mice  (heart)

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

summary: We report the analysis of single cell based sequencing to understand the cellular and molecular heterogeneity of senescent cell populations in vivo in multiple organ types. The findings will help characterise the roles different cell types play during the aging process.

overall_design: Examination of FACS sorted p16-FDR mCherry+ heart cells collected from aged mice (20-22 months) (n = 2)

first: Virinder

last: Reen

first: Husayn

last: Pallikonda

first: Jodie

last: Birch

first: Scott

last: Haston

first: Jesus

last: Gil

first: Juan Pedro

last: Martinez-Barbera


title: Transcriptomic analysis of testis and epididymis tissues from Banna mini-pig inbred line (BMI) boars with single-molecule long-read sequencing

city: Kunming

first: Jinlong

last: Huo

state: Yunnan

address: Jin-hei

department: Faculty of Animal Science and Technology

institute: Yunnan Agricultural University

summary: The testis and epididymis tissues collected from 12-month-old adult BMI boars were carried out PacBio Iso-Seq sequencing and Illumina RNA-seq sequencing. The full-length isoforms, extensive alternative splicing events, lncRNAs, some genes and novel isoforms related to spermatogenesis were evaluated.

overall_design: PacBio Iso-Seq sequencing and Illumina RNA-seq sequencing of testis and epididymis from Banna mini-pig inbred line (BMI) boars.

first: Yu

middle: H

last: Sun


title: Single cell analysis of senescent cells of old p16-FDR mice  (kidney)

overall_design: Examination of FACS sorted p16-FDR mCherry+ kidney cells collected from aged mice (20-22 months) (n = 2)


title: Transcriptomic profile of MIN6 beta cells exposed to deficient and excessive arginine supply

city: Qingdao

first: Lianbin

last: Xu

address: No.700, Changcheng Road

department: College of Animal Science and Technology

summary: Purpose: The objective of this study was to evaluate the transcriptomic consequence of chronic exposure to deficient and excessive arginine supply in MIN6 pancreatic beta cells and reveal the molecular mechanisms underlying beta cell function and insulin secretion to arginine administration. Methods: After overnight adhesion, the medium was removed, and the cells were incubated in fresh DMEM medium containing low-, standard- or high-arginine concentration (LA, SA and HA) for 24 h. Following the treatment, RNA was extracted from cells for transcriptome sequencing. Results: Transcriptomics analysis allowed the detection of 23,620 and 22,939 transcripts in the LA and HA samples, among which 7,591 (3,736 up- and 3,855 down-regulated) and 197 (111 up- and 86 down-regulated) genes were expressed differently compared with the SA treatment. One hundred and forty one DEGs were overlapped between LA vs. SA and HA vs. SA comparisons, which were mainly involved in DNA replication, organic hydroxy compound metabolism and cellular response to oxidative stress. GO functional enrichment analysis demonstrated that terms related to proteasomal protein catabolic process, mRNA processing and ATP metabolic process were highly disturbed by LA administration, while DEGs induced by HA were mainly enriched to ammonium ion metabolic process, mRNA export and sterol biosynthetic process. Morever, KEGG pathway analysis revealed that DEGs between LA and SA treatments were mainly functionally classified as involved in protein processing in endoplasmic reticulum and oxidative phosphorylation, while DNA replication, steroid biosynthesis and cell cycle had more counts and reached significant difference levels according to the DEGs triggered by HA. Conclusions: These results suggested that the disturbed carbohydrate, lipid and amino acid metabolisms as well as the decreased cell proliferation, increased apoptosis and elevated oxidative stress contributed to the reduced insulin secretion in beta cells induced by LA or HA administrations.

overall_design: After preliminary selection of concentration according to the cell viability, the MIN6 pancreatic beta cells were randomly assigned to culture in low, standard or high-arginine medium (0.1×, 1× or 20× the standard arginine concentration, LA, SA and HA) for 24 h. Following the treatment, RNA was extracted from cells for transcriptome sequencing.

first: Lian

middle: B

first: Xue

middle: Y

first: Zhi

last: Hu

first: Qiu

last: Hou

first: Yun

last: Wang

first: Zhong


title: ATAC-seq of purified immune cell populations

city: Headington

first: Damien

last: Downes

state: Oxfordshire

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Medicine

institute: The University of Oxford

summary: ATAC-seq was carried out to identify regions of nucleosome depletion – marking sites of enhancers and promoters – in the MACS populations of CD4, CD8, CD14, CD19 and Natural Killer (NK) immune cells

overall_design: Three donors (two male, one female) provided peripheral blood for the isolation by magnetic activated cell sorting (MACS) of immune cells. A total of 5 populations of cells were isolated per donor and two technical replicates were performed.

first: Matthew

last: Gosden

first: Jessica

last: Davies

first: Calliope

last: Dendrou

first: Jim

middle: R

last: Hughes


title: Effect of Doxorubicin on gene expression of HS578T cells with or without heterozygous chromosomal 17p deletion [RNA-seq]

city: Indianapolis

first: Kun

last: Huang

state: IN

address: 410 W 10th street

institute: Indiana University

summary: Our preliminary data found that TNBC cells with Chrom 17p loss are more resistant to chemotherapy drug treatment, compare to cell with 17p intact.To investigate the role of cancer stemness, weg performed this gene expression profiling analysis

overall_design: Comparison of total RNA expression profile of HS578T cells with or without 17p loss, treated with doxorubincin or not

first: Xiongbin

last: Lu

first: Tianhan

last: Dong


title: Effect of Doxorubicin on gene expression of HS578T cells with or without heterozygous chromosomal 17p deletion [scRNA-seq]


title: Next Generation Sequencing Analysis of control and knockdown of hnRNPU in RKO cells

first: Yuguo

last: Liu

address: 320 Yue Yang Road

department: Institute for Nutritional Sciences, SIBS

institute: Chinese Academy of Sciences

summary: We knockdown the control and the hnRNPU gene in the RKO cells, then extracted the total RNAs and performed the next generation sequencing. By comparing sequencing data from control and knockdown of hnRNPU cells,we profield the downstream targets of the hnRNPU gene.

overall_design: The control and knockdown of hnRNPU gene in RKO cells mRNA profiles were generated by deep sequencing


title: Analysis of the impact of FOXA1 expression on MDA::ER E2-sensitive transcriptomes and ER cistromes [Transcriptome data]

first: Raphaël

last: Métivier

overall_design:
A 12 chip study aiming to characterize Estradiol (E2)-sensitive genes in MDA::ER cells conditionnally expressing FOXA1 following a 4h treatment with E2. RNAs were prepared from three independent triplicate experiments. Each of the three technical replicate correspond to pooled RNAs from 1 experiment. Controls for these experiments are 6 arrays corresponding to vehicle-treated cells.

This submission represents transcriptome component of study.

first: Justine

last: Quintin

first: Christine

last: Le Péron

first: Elise

last: Mahé

first: Aurélien

middle: A

last: Sérandour

first: Gaëlle

last: Palierne

first: Maud

last: Bizot

first: Frédéric

last: Percevault

first: Stéphane

last: Avner

first: Gilles

last: Salbert


title: Effect of Doxorubicin on gene expression of HS578T cells with or without heterozygous chromosomal 17p deletion


title: Mediterranean diet and fiber supplementation change the whole blood DNA methylation pattern of NAFLD patients

status: Public on Dec 09 2022

city: Szczecin

first: Tomasz

last: Wojdacz

state: Zachodniopomorskie

address: Unii Lubelskiej 1

department: Independent Clinical Epigenetics Laboratory

country: Poland

institute: Pomeranian Medical University

type: Methylation profiling by genome tiling array

summary: Genome-wide patterns of DNA methylation were quantified using the Illumina Infinium HumanMethylationEPIC BeadChip in DNA samples extracted from whole blood samples taken from 18 participants with NAFLD.

overall_design: In this study, we recruited 18 participants with NAFLD. All of them were instructed to change their dietary habits to a Mediterranean diet and to eat high-fiber rolls with no change of physical activity. From all participants we took whole blood samples 3 times: before diet change, 1 month after a diet change, and 2 months after the diet change. DNA methylation analyses were performed on 54 whole blood samples.

first: Katarzyna

middle: E

last: Sokolowska

first: Dominika

last: Maciejewska-Markiewicz

first: Jan

last: Bińkowski

first: Joanna

last: Palma

first: Olga

last: Taryma-Leśniak

last: Kozlowska-Petriczko

first: Konrad

last: Borowski

first: Magdalena

last: Baśkiewicz-Hałasa

first: Viktoria

last: Hawryłkowicz

first: Patrycja

last: Załęcka

first: Marcin

last: Ufnal

first: Dominik

last: Strapagiel

first: Justyna

last: Jarczak

first: Karolina

last: Skonieczna-Żydecka

first: Karina

last: Ryterska

first: Ewa

last: Stachowska


title: The protumor function of UHRF1 is linked to both the Akt signaling cascade and the epithelial-mesenchymal transition in esophageal cancer

city: Luzhou

first: xu

last: liu

address: 25th Taiping Street

institute: The Affiliated Hospital of Southwest Medical University

summary: The epigenetic factor UHRF1 is highly expressed in many types of cancers, however, the underlying mechanism remains elusive. Here we report an oncogenic function of UHRF1 in esophageal cancer(EC). UHRF1 was observed to be robustly expressed in EC cells. Knockdown of UHRF1 was achieved in two EC cell lines TE-10 and Kyse410 using a shRNA-mediated lentivirus system. Silencing of UHRF1 led to the inhibition of the proliferation and the mesenchymal phenotype as determined by the wound-healing and the invasion-in-matrigel assays. Transcriptome profile analysis revealed that two groups of the genes are significantly suppressed upon the UHRF1-shRNA expression. One group is linked to Akt signal pathway and the other is linked to the epithelial-mesenchymal transition. MK2206, an Akt inhibitor, could also inhibit the growth and the mesenchymal phenotype of EC cells. But interestingly, while UHRF1 deficiency resulted in the downregulation of EMT-associated genes such as ZEB2, vimentin and twist1, MK2206 inhibition of Akt activity only suppressed the expression of snail, suggesting that the control of the mesenchymal phenotype by UHRF1 does not rely on the AKT cascade. We conclude that the oncogenic function of UHRF1 is linked to the synergistic effect on the Akt signal cascade and the EMT-specific genes in EC cells.

overall_design: We examined the mRNA expresssion in the clinical samples obtained from 20 of EC patients using qRT-PCR and IHC. We then utilized these two EC cell lines TE10 and Kyse410 in the following gene-silencing experiment and evaluated the ability of the migration and invasion in UHRF1-shRNA-cells as determined by the wound-healing and the invasion-in-matrigel assays. RNA-seq was performed from the cells expressing UHRF1-shRNA and the scramble control. UHRF1-shRNA expressed TE10 and Kyse410 celle or their scramble controls were treated with MK2206 and tested the change of migration and invasion and EMT markers.

first: Yan

last: Li

first: Xiaoyan

last: Wang

first: Li

last: Tang

first: Yong

last: Cao

first: Xueqin

last: Song

first: Xu

last: Liu

first: Mingying

first: Fang

last: Huang

first: Minglan

last: Yu

first: Feng

last: Chen

first: Haisu

last: Wan


title: ATAC-seq of H1 Human Embryonic Stem Cells (hESC)

first: Damien

last: Downes

summary: ATAC-seq was carried out to identify regions of nucleosome depletion – marking sites of enhancers and promoters – in the H1 human embryonic stem cell line (H1-hESC)

overall_design: Four separately grown flasks of H1-hESC cells were used to generate ATAC-seq data with two technical replicates per flask.

first: Yavor

last: Bozhilov

first: Andrew

last: King

first: Jim

last: Hughes


title: Massively parallel engineering of persistent CAR-Ts [GEO_CLASH_Integration_off_targets]

city: West Haven

first: Sidi

state: CT

address: 850 West Campus Drive

institute: Yale University

summary: To identify immune-related gene perturbations that enhance CAR-T cell persistence in in vitro and in vivo settings, we generated thousands of CAR-T variants using the CLASH platform and evaluated crRNA representation across time in in vitro and in vivo cancer models.

overall_design: First round PCR primers (CP-1) were designed to target unique regions of CAR vector. Second round PCR 3' primers (CP-2) were designed to targeting LHA.

first: Xiaoyun

last: Dai

first: Jonathan

last: Park


title: Single cell RNA sequence presents atlas analysis for chondrocyte in the talus and reveals potential mechanism in coping with mechanical stress

first: Junjie

address: The Affiliated Hospital of Qingdao University, No.59，Haier Road

summary: Chondrocytes are indispensable for the function of cartilage because they provide extracellular matrix. Therefore, gaining insight into the chondrocytes may be helpful in understanding the cartilage function and pinpointing potential therapeutical target for diseases. The talus is a part of ankle joint, which serves as the major large joint that bears body weight. Compared with distal tibial and fibula, the talus bears much more mechanical loading, which is risk factor for osteoarthritis (OA). However, in most individuals, OA seems to be absent in ankle, and cartilage of the talus seems to function normally. This study applied single-cell RNA sequencing to demonstrate atlas for chondrocyte subsets in healthy talus cartilage obtained from five volunteers, and chondrocyte subsets were annotated. Gene ontology and Kyoto encyclopedia of genes and genomes pathway enrichment analyses for each cell type, cell-cell interactions, and single-cell regulatory network inference and clustering for each cell type were conducted, and hub genes for each cell type were identified. Immunohistochemical staining was used to confirm the presence and distribution of each cell type. Two new chondrocyte subsets were annotated as MirCs and SpCs. The identified and speculated novel microenvironment may pose different direction in chondrocyte composition, development and metabolism in the talus.

overall_design: Five cartilage samples of talus from healthy volunteers

first: Tianrui

first: Zewen

last: Sun

first: Lu

last: Zhang


title: Conserved and cell type-specific transcriptional responses to IFN-γ in the ventral midbrain

city: New York

first: Peter

last: Sims

state: NY

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

summary: Dysregulated inflammation within the central nervous system (CNS) contributes to neuropathology in infectious, autoimmune, and neurodegenerative disease. With the exception of microglia, major histocompatibility complex (MHC) proteins are virtually undetectable in the mature, healthy central nervous system (CNS). Neurons have generally been considered incapable of antigen presentation, and although interferon gamma (IFN-γ) can elicit neuronal MHC class I (MHC-I) expression and antigen presentation in vitro, it remains unclear whether similar responses occur in vivo. Here we directly injected IFN-γ into the ventral midbrain of mature mice and analyzed gene expression profiles of specific CNS cell types. We find that IFN-γ induces cellular proliferation and expression of MHC-II and associated genes only in microglia. However, IFN-γ upregulated MHC-I and associated mRNAs in ventral midbrain microglia, astrocytes, oligodendrocytes, and GABAergic, glutamatergic, and dopaminergic neurons. The core set of IFN-γ-induced genes and their response kinetics were conserved across neurons and glia, with a lower amplitude of expression in neurons. A diverse repertoire of genes was upregulated in glia, particularly microglia, while no neuron-specific responses to IFN-γ were observed. Using mutant mice to selectively delete the IFN-γ-binding domain of IFNGR1 in dopaminergic neurons, we demonstrate that dopaminergic neurons respond directly to IFN-γ. Our results suggest that most neurons are capable of responding directly to IFN-γ and upregulating MHC-I and related genes in vivo, but their expression amplitude and repertoire is limited compared to oligodendrocytes, astrocytes, and microglia.

overall_design: Bulk and single-nucleus RNA-seq comparing murine midbrain samples that are treated with IFNG or vehicle control.

first: B

middle: D

last: Hobson

first: P

first: D

last: Sulzer


title: Effect of radiation therapy

first: Achraf

last: Shamseddine

address: 1275 York Avenue

department: Radiation Oncology

institute: Memorial Sloan Kettering Cancer Center

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

overall_design: Refer to individual Series


title: Effect of radiation therapy on gene expression of different murine cardiac cell lineage at different time points post radiation [RNA-seq]

summary:
To investigate the pathways affected by radiation at the cellular levels in the heart, we radiated WT mice with 12 Gyx1 RT and isolated constituents cell lineages
We then performed gene expression profiling analysis using data obtained from RNA-seq of endothelial cells, fibroblasts and myocytes at 3 different time points

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Sham and WT treated heart cells at different time points

first: Shamseddine

last: Achraf

first: Patel

last: Suchit

first: Schmitt

last: Adam


title: Effect of radiation therapy on CD45+ murine cardiac cells in wild type and STING KO mice [scRNA-seq]

summary:
To investigate the changes in CD45+ cardiac murine cells, we radiated WT mice with 12 Gyx1 RT and isolated constituents cell lines
We then performed expression profiling using scRNA sequencing obtained from CD45+ cells

overall_design: Comparative gene expression profiling analysis of CD45+ scRNA-seq data for Sham and RT treated hearts in WT and STING KO mice 28 days post RT


title: Massively parallel engineering of persistent CAR-Ts [GEO_CLASH_Nextera]

last: Chen

type: Genome variation profiling by high throughput sequencing

overall_design: After genomic DNA was collected from CAR-Ts, designed primers near the cutting site and performed PCR to generate a sequenceable guide library. Raw counts were processed using custom bash and R scripts.


title: Massively parallel engineering of persistent CAR-Ts [GEO_CLASH_MIPS]

overall_design: MIPS probe were designed according to previously published protocols,(https://github.com/shendurelab/MIPGEN)

first: Yaying

last: Du


title: A Nile Rat Transcriptomic Landscape Across 22 Organs By Ultra-deep Sequencing and Comparative RNA-seq pipeline (CRSP)

city: Cleveland

first: Peng

last: Jiang

state: OH

address: 2121 Euclid Ave

institute: Cleveland State University

summary: We generated the first ultra-deep Nile grass rat RNA-seq data from 60 biopsy samples representing 22 major organs, providing a unique resource and spatial transcriptomic reference (e.g., tissue gene expression baseline) for using Nile grass rat as a model to study human diseases.

overall_design: We collected 59 biopsy samples from 4 Nile grass rats representing 22 major organs (testis, brain, eye, pancreas, bone, thymus, bone marrow, spleen, heat, muscle, adipose, nerve, trachea, bladder, ovary, uterus, esophagus, stomach, liver, intestine, and kidney). Samples were prepared via the Illumina TruSeq RNA protocol. PolyA+ selection was undertaken via RNA purification beads followed by fragmentation for 6 minutes. We performed first and second strand cDNA synthesis and purified with Agencourt AMPure XP beads. We then performed an end repair step. We next adenylated the 3’ ends, ligated Illumina adapters and purified the libraries with AMPure XP beads. Then, we performed cDNA enrichment via PCR (15 cycles). Finally, we validated our libraries via PicoGreen quantification on a Synergy plate reader. Samples were then barcoded and sequenced as paired-end reads on the Illumina HiSeq 3000 sequencer.

first: Huishi

last: Toh


title: Stress responses elicited by glucose withdrawal in Aspergillus fumigatus

city: Debrecen

first: Tamas

last: Emri

address: Egyetem ter 1

country: Hungary

institute: University of Debrecen

summary: Glucose is a widely used carbon source in laboratory practice to culture Aspergillus fumigatus, however, glucose availability is often low in its “natural habitats” including the human body. We used a physiological–transcriptomical approach to reveal differences between A. fumigatus Af293 cultures incubated on glucose, glucose and peptone, peptone (carbon limitation), or without any carbon source (carbon starvation). Autolytic cell wall degradation was upregulated by both carbon starvation and limitation. The importance of autolytic cell wall degradation in adaptation to carbon stress was also highlighted by approximately 12.4% of the A. fumigatus genomes harbor duplication of genes involved in N-acetyl glucosamine utilization. Glucose withdrawal increased redox imbalance, altered both the transcription of antioxidative enzyme genes and oxidative stress tolerance, downregulated iron acquisition, but upregulated heme protein genes. Transcriptional activity of the Gliotoxin cluster was low in all experiments, while the Fumagillin cluster showed substantial activity both on glucose and under carbon starvation, and the Hexadehydro-astechrome cluster only on glucose. We concluded that glucose withdrawal substantially modified the physiology of A. fumigatus including processes that contribute to virulence. This may explain the challenge of predicting the in vivo behavior of A. fumigatus based on data from glucose rich cultures.

overall_design: The Af293 reference strain was studied under four culturing conditions differing in the available carbon/energy source: cultures incubated in glucose rich or carbon source free media as well as cultures growing on casein peptone or glucose plus casein peptone.  Each culturing condition was examined with three biological replicates.

first: Tamás

first: Barnabas

middle: C

last: Gila

first: Karoly

last: Antal

first: Andrea

middle: P

last: Jónás

first: Istvan

last: Pocsi


title: Microglial pattern recognition via IL-33 promotes synaptic refinement in developing corticothalamic circuits in mice (ATACseq)

city: San Francisco

first: Ilia

last: Vainchtein

address: 1550 4th street

institute: UCSF

summary: To determine the direct effect of IL-33 on microglial gene expression, we have bulk ATAC-sequenced cortical microglia 4 hours after IL-33 or vehicle i.c.v. injection.

overall_design: Bulk ATAC-sequencing data from cortical microglia 4 hours after i.c.v injection of IL-33 or vehicle in P30 mice.

first: Rafael

last: Han

first: Johannes

last: Schlachetzki

first: Anna

last: Molofsky


title: Massively parallel engineering of persistent CAR-Ts

first: Sidi


title: SIRT1 activation attenuates microglia-mediated synaptic engulfment in postoperative cognitive

city: Beijing

first: Yi

last: Sun

address: No.8 Gongti Nanlu, Chao-Yang District

institute: Beijing Chao-Yang hospital

summary: Background: Postoperative cognitive dysfunction (POCD) is a debilitating neurological complication in surgical patients. Current research has focused mainly on microglial activation, but less is known about the resultant neuronal synaptic changes. Recent studies have suggested that silent information regulator 1 (SIRT1) plays a critical role in several different neurological disorders via its involvement in microglial activation. In this study, we evaluate the effects of SIRT1 activation in a POCD mouse model.  Methods: Exploratory laparotomy was performed in mice aged 12-14 months under sevoflurane anesthesia to establish our animal POCD model. Transcriptional changes in the hippocampus after anesthesia and surgery were evaluated by RNA sequencing. SIRT1 expression was verified by Western Blot. Mice were treated with SIRT1 agonist SRT1720 or vehicle after surgery. Changes in microglia morphology, microglial phagocytosis, presence of dystrophic neurites, and dendritic spine density were evaluated. Cognitive performance was evaluated using the Y maze and Morris water maze.  Results: SIRT1 expression levels were downregulated in POCD. Exposure to anesthesia and surgery lead to alteration in microglia morphology, increased synaptic engulfment, dendritic spine loss, and cognitive deficits. These effects were alleviated by SRT1720 administration.  Conclusion: This study suggests an important neuroprotective role for SIRT1 in POCD pathogenesis. Increasing SIRT1 function represents a promising therapeutic strategy for prevention and treatment of POCD.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control and surgery hippocampus in mice

first: Yuzhu

last: Wang

first: Fan

last: Ye

first: Victoria

last: Cui

first: Dandan

last: Lin

first: Hui

last: Shi

first: Yan

last: Zhang

first: Anshi

last: Wu

first: Changwei

last: Wei


title: To investigate the mechanisms of CDCA regulates proliferation of Porcine Small Intestinal Epithelial Cells (IPEC-J2)

city: Nanjing

first: Yu

last: Pi

state: Jiangsu

address: NO. 1 Weigang, Nanjing Agricultural University

institute: Nanjing Agricultural University

summary: The objective of this study was to investigate the effects of CDCA on the gene expression of IPEC-J2 cells. The control group (CON) treated with PBS and the CDCA group treated with both CDCA. Compared with the CON group, CDCA group could regulate the gene expression related proliferation genes.

overall_design: There are two groups in this stduy. The control group IPEC-J2 treated with PBS and the CDCA group IPEC-J2 treated with both CDCA (n = 3).

first: Xilong

last: Li


title: Polymer thin film promotes tumor spheroid formation via JAK2-STAT3 signaling primed by fibronectin-integrin 5ɑ and sustained by LMO2-LDB1 complex

city: Daejeon

first: Yoonjung

last: Choi

address: 7-12, Daehak-ro 179beon-gil, Yuseong-gu

country: South Korea

institute: Yoonjung

summary: Cancer stem-like cells (CSCs) are considered as a tempting target due to their role in tumor progression. Although recent studies attempted to obtain and analyze patient-derived CSCs ex vivo, there are limitations in supplying diverse and large quantity of CSCs. Previously, functional polymer thin film (PTF) platform which induces cancer cells transformation into tumorigenic CSCs was invented. Here, we verified the functionality of polymer X, new PTF with a streamlined production process. Polymer X induced tumor spheroid formation and the spheroids showed increase in the expression of CSC-related genes. STAT3 phosphorylation was upregulated by fibronectin-integrin 5α-JAK2 axis and maintained by the cytosolic LMO2/LBD1 complex. In addition, STAT3 signaling was critical in spheroid formation on polymer X. By allowing the generation of CSCs from cancer cells, the PTF platform will enable to overcome the previous limitation of patient-derived CSC.

overall_design: mRNA profiles of 8 day-SKOV3-ssiCSC spheroids and 2D-cultured SKOV3 control were generated by deep sequencing, in duplicate, using Novaseq-600

first: Sunyoung

last: Seo

first: Nayoung

last: Hong

first: Junhyuk

last: Song

first: Dohyeon

last: Kim

first: Daeyoup

last: Lee

first: Sangyong

last: Jon

first: Hyunggee


title: Expression data from Saccharomyces cerevisiae

city: Chengdu

first: Yajing

state: Sichuan

address: No. 24, South Section 1, First Ring Road

department: College of Architecture and Environment

institute: Sichuan University

summary:
Industrial bioethanol production may involve a low pH environment,improving the tolerance of S. cerevisiae to a low pH environment caused by inorganic acids may be of industrial importance to control bacterial contamination, increase ethanol yield and reduce production cost.
Through analysis the transcriptomic data of Saccharomyces cerevisiae with different ploidy under low pH stress, we hope to find the tolerance mechanism of Saccharomyces cerevisiae to low pH.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: In order to comprehensively analyze the tolerance mechanism of Saccharomyces cerevisiae to low pH stress, we selected four yeast strains (KF7, B3, C3,BC3), each of them was exprement with two pH conditions (pH 2.5 and pH 4.5), respectively.


title: BI 456906: a dual glucagon-like peptide-1/glucagon agonist promoting bodyweight reduction

city: Biberach a.d. Riss

first: Eric

last: Simon

address: Birkendorfer Str. 65

institute: Boehringer Ingelheim Pharma GmbH & Co KG

summary: Glucagon and glucagon-like peptide-1 (GLP-1) are hormones involved in energy homeostasis. GLP-1 receptor (GLP-1R) agonism reduces food intake and delays gastric emptying, and glucagon receptor (GCGR) agonism increases energy expenditure by thermogenesis. BI 456906 is a subcutaneous, once-weekly injectable dual GLP-1R/GCGR agonist in development for the treatment of obesity or non-alcoholic steatohepatitis. Here we show that BI 456906 is a potent dual agonist with an extended half-life in human plasma. Key GLP-1R-mediated mechanisms of reduced food intake, delayed gastric emptying and improved glucose tolerance were confirmed in GLP-1R knockout mice. GCGR activity was confirmed by reduced plasma amino acids, increased hepatic expression of nicotinamide N-methyltransferase and increased energy expenditure. BI 456906 produced greater bodyweight reductions than maximally efficacious semaglutide doses and modulated gene expression, including genes involved in amino acid metabolism. BI 456906 is a potent dual agonist that produces bodyweight-lowering effects through both GLP-1R and GCGR agonism.

overall_design: Male C57BL6/J mice pre-fed with 60% high-fat diet were obtained from The Jackson Laboratories (Bar Harbour, ME, USA) at >16 weeks of age. Upon arrival, mice were single-housed to obtain accurate and individual food intake measurements for each animal. During the entire study, animals had ad libitum access to food (high-fat diet D12492; Research Diets, Inc., New Brunswick, NJ, USA) and tap water. Before the start of the study, animals were randomised based on their bodyweight measured 1 week prior to the start of treatment (n=11/group). At the study start, the age of mice was 22 weeks. Mice were administered chronic repeated SC dosing of vehicle, BI 456906 (3, 10, 20 or 30 nmol/kg) or semaglutide (20 or 100 nmol/kg) daily for 30 days, with bodyweight and food intake measured every day.

first: Tina

last: Zimmermann

first: Leo

last: Thomas

first: Tamara

last: Baader-Pagler

first: Peter

last: Haebel

first: Heike

last: Neubauer

first: Wolfgang

last: Reindl

first: Besnik

last: Bajrami

last: Rist

first: Ingo

last: Uphues

first: Daniel

last: Drucker

first: Holger

last: Klein

first: Rakesh

last: Santhanam

first: Robert

last: Augustin


title: Transcriptome analysis of graft liver provides insight into the immune response of rat liver transplantation

city: shanghai

first: jing

last: lu

state: State...

address: Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201600, China

institute: shanghai jiaotong university

summary:
Background: As an “immune-privileged organ”, the rate of spontaneous and operational tolerance was higher after liver transplantation (LT) compared with other solid organs. However, modern immunosuppression regimens still have multiple complications, which require a deeper understanding of the real mechanism of inducing immune tolerance.
Methods: Homogenic and allogeneic rat LT models were established, and recipient tissue was collected on postoperative day 7. The degree of LT rejection was evaluated by liver pathological changes and liver function. Differentially expressed genes (DEGs) were detected by transcriptome sequencing and identified by RT-PCR. The functional properties of DEGs were characterized by the Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and Reactome pathway analyses. The cells infiltrating the graft and recipient spleen and peripheral blood were evaluated by immunofluorescence assays and flow cytometry.
Result: A total of 1465 DEGs were screened, including 1177 up-regulated genes and 288 down-regulated genes. GO enrichment and KEGG pathway analysis indicated that DEGs were involved in several immunobiological processes, including immune system process, immune response, regulation of immune response, T cell activation, cytokine-cytokine receptor interaction, allograft rejection, Th1,Th2 and Th17 cell differentiation. Reactome results showed that PD-1 signaling was also enriched. Further research confirmed that the expression of multiple immune cell markers increased, and most marker of T cell exhaustion changed significantly. Flow cytometry results showed that the proportion of Treg decreased in the allogeneic group, while CD4+PD-1+ T and CD8+PD-1+ T cells increased.
Conclusion: This study, to our knowledge, was the first to reveal the impact of liver transplantation rejection on the liver at the omics level. Our results revealed that the progression of LT rejection involves multiple immune cells, activation of various immune pathways and special changes of immune checkpoints, which provides potential reference for potential risk assessment and pathogenesis. However, further clinical validation is also needed.

overall_design: Lewis and Brown Norway (BN) rats were utilized as liver donors and recipients to establish allogeneic rejection models.   Lewis-rats were used to construct homogenic tolerance models. mRNA was isolated from graft  (three samples per group) and analyzed using RNA-seq.

first: Wanyue

last: Cao

first: Jing

last: Lu


title: Transcriptome changes after the transfection of cGAS specific agonist G3-YSD

city: Shanghai

first: Haiyang

last: Hu

address: 320 Yueyang Road

institute: PICB

summary: The cGAS-STING signalling has been well recognized as the major pathway response to self and non-self DNA molecule in cytoplasm. Here, we measured the temporal transcriptome dynamic changes after cGAS-STING signalling activation based on cGAS specific agonist G3-YSD transfection

overall_design: Total RNA after transfecting G3-YSD or G3-YSD control was isolated and sequenced by deep sequencing using Illumina HiSeq 4000

last: HU

first: Lele

last: Zhang

first: MingJu

last: Lv

last: Sun


title: Transcriptomics of isolated alveolar macrophages from WT and CD47 deficient mice upon influenza A virus infection

city: Braunschweig

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary: CD47 is an ubiquitously expressed surface molecule that has a significant impact on immune responses. However, its role for antiviral immunity is not fully understood. We can show that CD47 has an inhibitory role in influenza virus defense, since CD47-deficient mice (CD47-/-) display an increased viral clearance during influenza virus infection. This effect is strongly associated with alveolar macrophages, yet the underlying mechanisms are unclear. Thus, to assess the precise impact of CD47 on antiviral action of alveolar macrophages, transcriptional analysis of ex vivo isolated alveolar macrophages from CD47-/- and WT mice were performed isolated 3dpi. Surprisingly, instead of classical antiviral mediators, an increased expression of both hemoglobin α and hemoglobin β was found in CD47 deficient compared to WT alveolar macrophages upon influenza A virus infection. Importantly, antiviral activity of hemoglobin was already shown for other viruses and thus, CD47 might limit influenza virus defense via the regulation of hemoglobin, which could act as a modulator of the antiviral immune response during the infection.

overall_design: The dataset contains microarray data from alveolar macrophages of CD47-/- and WT mice, which were isolated by FACS either from naive mice  or at day 3 post influenza A virus infection. Two independent replicates were generated for each condition.

first: C

last: Wenzek

first: T

last: Knuschke

first: R


title: The molecular signature of human testicular peritubular cells revealed by single-cell analysis

city: Planegg-Martinsried

first: Artur

last: Mayerhofer

address: Großhadernerstr. 9

department: Biomedical Center

institute: LMU Munich

summary: Peritubular cells of the human testis form a small compartment surrounding the seminiferous tubules. It contrast to rodents, it is composed of several cell layers and extracellular matrix. Peritubular cells are crucial for sperm transport and emerge as contributors to the spermatogonial stem cell niche, yet testicular peritubular cells are among the least known cell types of the human body. We employed single-cell RNA sequencing of cultured human testicular peritubular cells (HTPCs) isolated from testicular samples of donors with normal spermatogenesis and compared our data with recently published ex vivo data and, if available, with immunohistochemical data of the Human Protein Atlas. We observed a significant overlap between our results and genes expressed in vivo. Based on expression of a set of smooth muscle markers, HTPCs can be classified as smooth muscle cells. Small differences between in vivo/in vitro expressed genes may be due to plasticity/phenotypic switching. Plasticity was also shown upon addition of FCS to the culture medium. Based on transcriptome similarities four cellular states were observed. Characteristics of mesenchymal stromal cells and Leydig stem cells were noted, yet differentiation attempts into fat cells, bone cells or mature Leydig cells were not successful. Further analyses confirmed known stem cell niche-relevant factors (e.g. GDNF) and identified unknown functions e.g. the ability to produce retinoic acid. The results reveal that HTPCs upon isolation and culture are a highly adequate cellular model as they retain major characteristics. They therefore allow us to define the signature and functions of human testicular peritubular cells. The data may serve as a resource for future studies to better understand male (in)fertility.

overall_design: Single-cell RNA-seq of in vitro cultured human testicular peritubular cells (HTPCs).

first: Annika

last: Missel

first: Nina

last: Schmid

first: Christina

last: Koupourtidou

first: Carola

last: Herrmann

first: Kim-Gwendolyn

last: Dietrich

first: Harald

last: Welter

first: Jovica

last: Ninkovic


title: T cell dependent bispecific antibodies (TDBs) promote T cell redistribution through organ-specific alteration of vascular endothelial cell

city: South San Francisco

first: Robert

last: Piskol

state: CA

address: 1 DNA Way

department: gRED Computational Sciences

institute: Genentech Inc.

overall_design: Refer to individual Series


title: Exploratory Study to Identify Skin Anti-Aging Biomarkers as a Result of a Non-ablative Fractional Laser Treatment

city: Baltimore

first: Luis

middle: Andres

last: Garza

state: Maryland

address: 1550 Orleans Street Suite 204 CRBII Koch

department: Dermatology

institute: Johns Hopkins University

summary: Non-ablative fractional laser can be used to treat photoaged skin by stimulating the breakdown and regeneration of dermal matrix constituents, such as collagen and elastic fibers. The objective of this study was to validate previously studied molecular mechanisms and explore yet uncharacterized biomarkers underlying the clinical efficacy of non-ablative fractional laser resurfacing.

overall_design: Seventeen white female participants with moderate-severe photoaging at baseline received treatment with 1550 nm Er:Glass non-ablative fractional laser on the face and forearm once monthly for 6 months. Punch biopsies for microarray analysis were obtained at baseline and 7 days after treatment of the face, as well as at baseline and 1, 7, 14, and 29 days after treatment of the forearm, resulting in a total of 119 samples.


title: T cell dependent bispecific antibodies (TDBs) promote T cell redistribution through organ-specific alteration of vascular endothelial cell (scRNAseq)

summary: TDBs (T cell dependent bispecific antibodies) have an agonistic anti-CD3 arm paired with a tumor-targeting arm that recognizes tumor-restricted/enriched cell-surface proteins. Preclinical and clinical studies demonstrated that TDBs can induce systemic changes in addition to their expected action in tumors, including transient loss of circulating leukocytes (margination), systemic cytokine release, and accumulation of lymphocytes in normal tissues. These reactions can lead to undesirable symptoms including cytokine release syndrome and liver enzyme elevation. Here, we report for the first-time an in-depth characterization of acute responses in tumor and liver upon TDB treatment. We observed rapid and substantial accumulation of lymphocytes around large blood vessels in normal organs such as the liver, accompanied by elevated vascular endothelial cell (EC) activation markers. We hypothesized that organ-specific EC phenotypes may account for the differential T cell accumulation in normal tissues versus tumors. Despite ongoing efforts to better characterize specific properties of ECs, the underlying transcriptional changes of specific endothelial cell subtypes influencing the T cell trafficking and accumulation in non-target-expressing organs (like here liver) upon TDB treatment are unknown. The purpose of the study is to investigate the effect of anti-HER2/CD3 TDB treatment on the endothelial cells in the liver and characterize possible transcriptional changes occurring.

overall_design: scRNA sequenced from dissociated liver tissue of three control-treated and three anti-HER2/CD3 TDB-treated mice

first: P

last: Himmels

first: W

last: Ye


title: Transcriptome analysis of primary normal fibroblasts and matched cancer associated fibroblasts

city: Tianjin

first: xudong

last: Wu

address: Qixiangtai Road

institute: Tianjin medical university

summary: To get an insight into the mechanisms for CAF-supported metastasis in breast cancers, we performed RNA-sequencing (RNA-seq) analysis with seven pairs of primary NFs and CAFs.Gene set variation analysis (GSVA) showed significant upregulated expression of genes enriched with cancer metastasis-associated signaling pathways. Besides, we identified CAF signature genes, which have similar patterns in several of these primary CAFs.

overall_design: The mRNA profiles of seven pairs of primary normal fibroblasts and matched cancer associated fibroblasts

first: Xudong

first: Qian

last: Li

first: Xuejiao

last: Lv

first: Chunyong

last: Han


title: Massively parallel engineering of persistent CAR-Ts [XDRNA]

city: West Haven

first: Sidi

last: Chen

address: 850 West Campus Drive

institute: Yale University

summary: To evaluate the immunological landscape of PRDM1-crRNA CAR-Ts, we performed timecourse RNAseq. We also compared and contrasted transcription profiles of CAR-Ts mutated by two different PRDM1-crRNAs.

overall_design: T cells were infected with CLASH vector and PRDM1-cr1 CAR22 AAV6 after electroporation with NLS6 LbCpf1mRNA. For time course data, resulting PRDM-1 edited CAR-Ts were then subject to coculture; RNA at different time points was collected and libraries were prepared. For the PRDM1-cr1 vs. PRDM2 experiment, one time point was used.

first: Stanley

last: Lam

first: Jonathan

last: Park


title: Enhancer reprogramming promotes the activation of cancer-associated fibroblasts and breast cancer metastasis

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


title: dBET57 exerts anti-cancer effects in neuroblastoma

city: Suzhou

first: Zimu

last: Zhang

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

summary: Neuroblastoma (NB) is the most common extracranial solid tumor of childhood, which is derived from primordial neural crest cells. dBET57, a new cereblon (CRBN) based inhibitor developed by PROTAC technology. It binds to the BET protein families BRD2, BRD3, and BRD4, which are recruited to the proteasome system for selective ubiquitination degradation. However, the function of dBET57 has not been assessed in NB models so far. In the present study, RNA-seq analysis was performed to explore the effect of dBET57 on NB cells.

overall_design: mRNA profiles of SK-N-BE(2) cells treated with 1200 nM or same volume DMSO for 48 h were generated by RNA sequencing, in double, using Illumina NovaSeq6000.

first: Siqi

last: Jia

first: Jian

last: Pan


title: Genome-wide maps of H3K27ac and H3K4me1 in primary normal fibroblasts and matched cancer-associated fibroblasts

summary: To understand the driving mechanisms for CAF activation, we performed H3K27ac and H3K4me1 Cleavage Under Targets and Tagmentation (CUT&Tag) analysis in six pairs of NFs and CAFs. At H3K4me1+ sites, we identified 3,333 regions with H3K27ac levels in CAFs ≥ 2-fold than matched NFs in more than 3 pairs, and defined them as CAF-activated enhancers.

overall_design: H3K27ac and H3K4me1 CUT&Tag in six pairs of NFs and matched CAFs


title: Massively parallel engineering of persistent CAR-Ts [CLASH]

summary: To identify immune-related gene perturbations that enhance CAR-T cell persistence in in vitro and in vivo settings, we generated thousands of CAR-T variants using the CLASH platform and evaluated crRNA representation across time in in vitro and in vivo cancer models.

overall_design: After genomic DNA was collected from CAR-Ts (either from in vitro or in vivo experiments), a two step PCR was performed to generate a sequenceable guide library. Raw counts were processed using custom bash and R scripts.


title: Transcriptome analysis of JUN overexpressed or JUN inactivated fibroblasts

summary: To examine the effects of phosphorylated JUN-mediated enhancers activation on gene expression, we conducted RNA-seq analysis in JUN wildtype (WT) or JUN inactive mutant (JUN AA) overexpressed MRC5 cells. The expression levels of genes associated with JUN-activated enhancers are significantly upregulated in JUN WT cells rather than in JUN AA cells.  To quantify the effects of JUN inactivation on gene expression, we also performed RNA-seq analysis in JNKi-treated induced CAFs (iCAFs). We observed that JNKi significantly reduced expression levels of JUN-activated enhancers-associated genes.

overall_design: RNA-seq analysis in JUN wildtype (WT) or JUN inactive mutant (JUN AA) overexpressed MRC5 cells, as well as JNKi-treated iCAFs.


title: T cell dependent bispecific antibodies (TDBs) promote T cell redistribution through organ-specific alteration of vascular endothelial cell (bulk RNAseq)

overall_design: bulk RNA sequenced from dissociated liver and tumor  tissue of three control-treated and three anti-HER2/CD3 TDB-treated mice

first: R


title: Transcriptomes of control and JAG1-deficient cochlea

city: Rochester

first: Cameron

last: Baker

address: 601 Elmwood Ave

institute: University of Rochester

summary: The aim of this study is to identify the gene targets of the Notch ligand JAG1 in the postnatal cochlea. JAG1 was conditionally deleted in mice carrying both an inducible Cre allele (Sox2CreER) and a floxed (fl) Jag1 allele.  Tamoxifen was administered to P0/P1 pups.  Cochlear tissues from 6 Sox2CreER/+Jag1fl/fl and wildtype littermate controls were dissected under the dissecting microscope in ice-cold DEPC-treated PBS and stored in RNAlater (Invitrogen) at 4C. The RNAs were purified by RNeasy Micro Kit (QIAGEN).  The quality and quantity of RNAs were measured by a 2100 bioanalyzer (Agilent). Illumina compatible sequencing libraries were generated by the University of Rochester Genomics Research Center. Libraries were hybridized to the Illumina flow cell and single-end reads of 100nts were generated. Identification of significantly differentially expressed genes was determined using DeSeq2.  We found 548 differentially expressed genes with an adjusted p-value of <0.05, 411 of those genes were significantly upregulated while 137 were significantly downregulated.  Analysis of pathways revealed novel genes involved downstream of JAG1-Notch signaling in the postnatal cochlea.

overall_design: To delete Jag1 in maturing cochlear supporting cells, we administered tamoxifen to Sox2CreER/+Jag1fl/fl (Jag1-mutant) and Sox2+/+ (control) mice at postnatal day (P)0/P1. At P6 we collected the cochlear sensory epithelium, extracted RNA and performed RNA-Seq. Six biological replicates of each genotype, Jag1-mutants and controls (wt), were compared.

first: Amy

last: Kiernan

first: Felicia

last: Gilels


title: An RNAi Screen of RNA Helicases Identifies eIF4A3 as a Regulator of Embryonic Stem Cell Identity [RNA-Seq]

city: New York

first: Jianlong

last: Wang

state: New York

department: Department of Medicine

institute: Columbia University Irving Medical Center

summary: RNA helicases are involved in multiple steps of RNA metabolism to direct their roles in gene expression, yet their functions in pluripotency control remain largely unexplored. Starting from an RNAi screen of RNA helicases, we identified that eIF4A3, a DEAD-box (Ddx) helicase component of the exon junction complex (EJC), is essential for the maintenance of embryonic stem cells (ESCs). Mechanistically, we show that eIF4A3 post-transcriptionally controls the pluripotency-related cell cycle regulators and that its depletion causes cellular differentiation via cell cycle dysregulation.  Specifically, eIF4A3 is required for the efficient nuclear export of Ccnb1 mRNA, which encodes Cyclin B1, a key component of the pluripotency-promoting pathway during cell cycle progression of ESCs. Our results reveal a previously unappreciated role of eIF4A3 and its associated EJC in the post-transcriptional cell cycle control in maintaining stem cell pluripotency.

overall_design: eIF4A3 transcriptome profiling was investigated via RNA-seq analysis in mouse embryonic stem cells.

first: Dan

first: Jihong

last: Yang

first: Xin

last: Huang


title: An RNAi Screen of RNA Helicases Identifies eIF4A3 as a Regulator of Embryonic Stem Cell Identity [Ribo-seq]


title: An RNAi Screen of RNA Helicases Identifies eIF4A3 as a Regulator of Embryonic Stem Cell Identity [CLIP-seq]


title: An RNAi Screen of RNA Helicases Identifies eIF4A3 as a Regulator of Embryonic Stem Cell Identity


title: Detailed delineation of the immune response to COVID-19 mRNA vaccination via high-temporal frequency blood transcriptomics

city: Doha

first: Darawan

last: Rinchai

state: Qatar

address: Al Gharrafa St

department: Research

country: Qatar

institute: Sidra Medicine

summary: The COVID-19 pandemic has prompted vaccine development efforts on an unprecedented scale. Vaccines based on mRNA technology have emerged as particularly attractive due to their high efficacy and short development timelines. However, relatively little is known about the factors contributing to the development of protective immunity by this new class of vaccines. We employed a high-temporal-resolution transcriptome profiling approach to investigate responses to COVID-19 mRNA vaccination. A cohort of 23 subjects was recruited and changes in blood transcript abundance were measured daily for 9 days post-priming and post-booster vaccination via RNA sequencing. Antibody responses were measured on days 7 and 14 post-vaccination using a custom multiplex assay. Marked differences were observed between responses to the priming and booster doses, with the latter inducing widespread changes in blood transcript abundance consistent with those found in patients with acute viral respiratory infections. The delineation of interferon responses at a high-temporal frequency also suggested that the priming and booster doses elicited distinct types of responses that peaked on day 2 post-priming dose and day 1 post-booster dose. The booster dose also induced inflammation on day 1 and erythroid cell signatures as well as an atypical plasmablast signature on day 4. Notably, this plasmablast signature, together with the post-booster interferon response signature, correlated with the antibody response levels induced on day 14 after the booster dose. Taken together, this work provides a detailed map of the antibody and transcriptional responses to the first and second doses of a new class of vaccine and yields important insights into the mechanisms underlying their immunogenicity. Furthermore, our results suggest that implementing high-temporal-frequency immune profiling protocols may provide an opportunity to better resolve the immune responses elicited by the growing number of available COVID-19 vaccines.

overall_design: After puncturing the skin with a finger stick, 50 µl of blood was collected in a capillary/microfuge tube assembly supplied by KABE Labortechnik (Numbrecht, Germany) containing 100 µl of tempus RNA-stabilizing solution aliquoted from a regular-sized tempus tube (designed for the collection of 3 ml of blood and containing 6 ml of solution; ThermoFisher, Waltham, MA, USA). Blood was collected prior to the vaccine being administered (day 0), on the same day, and daily thereafter over the next 10 days. This protocol was followed for both the priming and booster doses.

first: Sara

last: Deola

first: Giusy

last: Gentilcore

first: Basirudeen

last: Kabeer

first: Selma

last: Maacha

first: Igor

last: Pavlovski

first: Mohammed

last: Toufiq

first: Davide

last: Bedognetti

first: Jean-Charles

last: Grivel

first: Damien

last: Chaussabel


title: Anti-proliferative effect of Cinobufagin on acute myeloid leukemia cells with repression of c-Myc pathway associated genes (ChIP-Seq)

city: Chiba

first: Masaki

last: Fukuyo

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

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

summary: To analyse the effect of Cinobufagin to human acute myeloid leukemia cell lines, HL60 and Kasumi-1.

overall_design: 1) HL60 cells were treated with 100nM Cinobufagin for 24 hours 2) Kasumi-1 cells were treated with 100nM Cinobufagin for 24 hours

first: Yoshiro

last: Hirasaki

first: Atsushi

last: Okabe

first: Bahityar

last: Rahmutulla

first: Yasunobu

last: Mano

first: Motoaki

last: Seki

first: Takayuki

last: Hoshii

first: Takao

last: Namiki

last: Kaneda


title: Anti-proliferative effect of Cinobufagin on acute myeloid leukemia cells with repression of c-Myc pathway associated genes (RNA-Seq)


title: Anti-proliferative effect of Cinobufagin on acute myeloid leukemia cells with repression of c-Myc pathway associated genes


title: Genome-wide maps of H3K27ac, H3K4me1, JUN and p-JUN in JUN overexpressed or JUN inactivated fibroblasts

first: xudong

last: Wu

summary: To further dissect whether and how activated JUN reconfigures the chromatin landscape, we performed Chromatin Immunoprecipitation (ChIP)-seq analyses for H3K4me1 and H3K27ac. Based on the significant increase of H3K27ac levels at H3K4me1+ sites, we identified 3,017 JUN-activated enhancers in JUN WT cells. In contrast, JUN AA fails to significantly induce H3K27ac accumulation at these regions. Their enrichment levels at JUN-activated enhancers were significantly decreased after JNKi treatment. Besides, these enhancers are directly driven by JUN, especially phosphorylated JUN.

overall_design: ChIP-seq of H3K27ac, H3K4me1, JUN and p-JUN in JUN overexpressed or JUN inactivated fibroblasts

first: Xudong

first: Qian

last: Li

first: Xuejiao

last: Lv

first: Chunyong

last: Han


title: Cdh13 null mice isolated islets RNAseq

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: The pancreas islets RNA expressions were compared between WT (exon2 floxed) mice and Cdh13 KO (exon2 deleted) mice.  The islets were isolated from the mice at 8wks old, 14wks old under normal chow diet, and 14wks old under HFD conditions.

overall_design: Baseline at 8wks old. WT (n=3) and Cdh13 KO (n=3).  14wks old under normal chow. WT (n=3) and Cdh13 KO (n=3).  14wks old under HFD conditions, WT (n=3) and Cdh13 KO (n=3).HFD was started at 8wks old.

first: Shunbun

last: Kita

first: Tomonori

last: Okita


title: Differential gene expression of Wnt ligands/Wnt agonist 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: Wnt regulates various cell responses. In dental pulp cells, Wnt signaling control cell proliferation, apoptosis, migration and differentiation. Here, the differential gene expression of human dental pulp stem cells treated with Wnt ligands or Wnt agonist was examined using a high throughput RNA sequencing technique. Results demonstrated that Wnt ligands or Wnt agonist altered numerous gene expression in human dental pulp stem cells.

overall_design: Cells were treated with Wnt2B (500 ng/mL) or Tideglusib (200 nM) or IWP (25 uM) for 24 h in normal growth medium. Total RNA was isolated and subjected to RNA sequencing.

first: Chatvadee

last: Kornsuthisopon


title: RNA seq analysis of A2780 and  A2780-ADR

city: Bethesda

first: Wei

last: Zheng

state: MD

address: 9800 Medical Center Drive

institute: National Center for Advancing Translational Sciences

summary: We compared the global RNA expression level between doxorubicin-sensitive human ovarian cancer cell line A2780 and the adriamycin-resistant cell line A2780-ADR to elucidate the drug resistant related molecular mechanisms or targets.

overall_design: Three independent A2780 and A2780-ADR samples were examined.

last: Sun

first: Sima

last: Ni