title: Transcriptional effects of VIP on murine intestinal stem cells

city: Munich

first: Hans

middle: Carlo

last: Maurer

state: Bavaria

address: Ismaninger Str. 22

department: II. Medizinische Klinik

country: Germany

institute: Klinikum rechts der Isar

summary: In our study, we investigated the effect of Vasoactive intestinal peptide (VIP) on murine intestinal stem cell (ISC) activity and differentiation in homeostatic conditions and following irradiation-induced injury. We utilized a model of murine intestinal organoids and observed that VIP promotes epithelial differentiation towards a secretory phenotype predominantly via the p38 MAPK pathway. Moreover, VIP prominently modulates epithelial proliferation as well as the number and proliferative activity of Lgr5-EGFP+ ISC under homeostatic conditions. Further analysis revealed that in vitro acute irradiation injury renders Lgr5-EGFP+ ISC even more susceptible to modulations by VIP, which results in the strong promotion of epithelial regeneration by VIP. Finally, these effects by VIP translate into an in vivo model of abdominal irradiation, where VIP was shown to prominently mitigate radiation-induced injury. Taken together, our findings indicate a prominent role of VIP in modulating ISC behavior in intestinal homeostasis and its potential to promote intestinal regeneration following acute irradiation injury.

overall_design: Bulk gene expression data are presented for whole VIP-treated (n=4) or untreated (n=3) organoids, for sorted Lgr5-EGFP+ cells from VIP-treated (n=4) or untreated (n=4) organoids and for sorted Lgr5-EGFP+ cells from VIP-treated (n=4) or untreated (n=4) organoids exposed to irradiation.

first: Tatiana

last: Agibalova

first: H

first: Moritz

last: Middelhoff


title: Transcriptome changes of OA rat synovium before and after the injection of human SyMSCs and AdMSCs

status: Public on Sep 30 2024

city: Bunkyo-ku

first: Kentaro

last: Endo

state: Tokyo

address: 1-5-45 Yushima

country: Japan

institute: Institute of Science Tokyo

type: Expression profiling by high throughput sequencing

summary: To clarify the effect of factors produced by human SyMSCs and AdMSCs on OA synovium, we performed RNA sequencing for OA rat synovium before and after the injection of human SyMSCs and AdMSCs.

overall_design: Rat synovium was collected the next day of human SyMSCs and AdMSCs injection.

first: Seiya

last: Matsuta


title: Transcriptomics of PBMC from women with PCOS

status: Public on Sep 26 2024

city: Rancagua

first: Nicolas

last: Santander

address: Libertador Bernardo O'Higgins 611

country: Chile

institute: Universidad de O´Higgins

summary: PCOS is a condition that affects a large proportion of women and is associated with impared fertility and metabolism. Here, we explore gene expression changes in these women using PBMC as marker cells.

overall_design: We obtained total RNA from peripheral blood mononuclear cells from control women and women with PCOS. We further divided each group based on the use of oral contraceptives.

first: Alejandro

last: González

first: Francisca

last: Salas


title: Unveiling Cancer-Related Metaplastic Cells in Both Helicobacter pylori Infection and Autoimmune Gastritis

status: Public on Sep 25 2024

city: St. Louis

first: Richard

last: DiPaolo

state: MO

address: 1100 S Grand Ave

country: USA

institute: Saint Louis Univeristy

summary: We used 10X 5' single cell RNA sequencing (scRNAseq) technology to examine the transcriptional profiles of distinct gastric metaplastic cell types within the gastric corpus of mice chronically infected with Helicobacter pylori or chronically inflamed with autoimmune gastritis and humans with autoimmune gastritis.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Using 5' 10X scRNAseq we transcriptionally profiled cells derived from the corpora of 2-7 mice either chronically infected with H. pylori (Hp) or chronically inflamed with autoimmune gastritis (TxA23) and patients with autoimmune gastritis (AIG). Replicates are of the same disease state. In analysis, metaplastic cells were identified by signature score and isolated for a further phenotypic comparative analysis.

first: Stella

middle: G

last: Hoft

middle: J

first: Jose

middle: B

last: Saenz

first: Tarin

middle: M

last: Bigley


title: Individual RNA-seq for different prostate cancer cells and Lucap35CR PDX treated by SR8278,JQ1,AZD5153,ENZ or by FOXA1 and NR1D1 gene knockdown or NR1D1 overexpression.

city: Sacramento

first: yatian

last: yang

state: CA

institute: UC Davis

summary: Gene expression profile of different prostate cancer PDX tumor, and cell models to study tumorigenic programs.

overall_design: RNA-seq for C42B, 22RV1, Lucap35CR with different treatment.

first: Yatian

last: Yang

first: Xiong

last: Zhang

first: Demin

last: Cai

first: Hong-wu

last: Chen


title: Single-cell m6A profiling in the mouse brain uncovers cell type-specific RNA methylomes and age-dependent differential methylation [GLORI]

status: Public on Sep 24 2024

city: Durham

first: Matthew

last: Tegowski

state: NC

address: 153 Research Dr.

department: Biochemistry

institute: Duke University

type: Methylation profiling by high throughput sequencing

summary: N6-methyladenosine (m6A) is an abundant mRNA modification in the brain which plays important roles in neurodevelopment and brain function. However, due to technical limitations, global profiling of m6A sites within the individual cell types that make up the brain has not been possible. Here, we develop a mouse model that enables transcriptome-wide m6A detection in any tissue of interest and at single-cell resolution. We use these mice to map m6A across different brain regions and within single cells of the mouse cortex and discover a high degree of shared methylation across brain regions and cell types. However, we also identify a small number of differentially methylated mRNAs in neurons that encode important regulators of neuronal signaling, and we discover that microglia have lower levels of m6A compared to other cell types. Finally, we perform single-cell m6A mapping in aged mice and identify many transcripts with age-dependent changes in m6A.

overall_design: Samples are from flow-sorted cortical microglia and astrocytes. Then, total RNA was extracted and GLORI performed to deaminate non-methylated adenosine residues. RNA-seq libraries prepared. m6A sites were identified using GLORI-Tools.

first: Anna

middle: K

last: Prater

first: Christopher

middle: L

last: Holley

first: Kate

middle: D

last: Meyer


title: Single-cell m6A profiling in the mouse brain uncovers cell type-specific RNA methylomes and age-dependent differential methylation [aged study]

relation:
Reanalysis of: GSM8255387
Reanalysis of: GSM8255388
Reanalysis of: GSM8255389
Reanalysis of: GSM8255390

overall_design:
Samples are from flow-sorted cortical Neurons. Nuclei were isolated and fixed with ethanol prior to staining with anti-NeuN antibody and flow sorting. Then, total RNA was extracted, and RNA-seq libraries prepared. m6A sites were identified using to Bullseye pipeline to find sites of C-to-U conversion.
Differentially methylated RNAs examined between aged and young mice.  The young mice data are contained in GSE266876.


title: Prenatal vitamin D deficiency alters immune cell proportions of offspring in young adult age [RNA-seq]

city: College Station

first: Masako

last: Suzuki

state: TX

address: 498 Olsen Blvd, Norman E. Borlaug Building 202C

department: Nutrition

institute: Texas A&M University

summary: Vitamin D deficiency is a common micronutrient deficiency worldwide, especially among reproductive-age women, and vitamin D deficiency during pregnancy increases the risks of offspring’s immune-related diseases later in life. The mechanisms of how our body remembers the exposure status of an adverse environment during development have not been fully elucidated yet. Here we show that prenatal vitamin D deficiency exposure alters the immune cell proportion of the offspring at the prenatal and adult stage, which is attributed to transcriptional alterations of vitamin D receptor downstream genes. Further, we assessed the association between maternal vitamin D status and cord blood immune cell profiles from 75 healthy mother and their term baby pairs and found that maternal vitamin D deficiency significantly alters immune cell proportion in cord blood. Our findings demonstrate that prenatal vitamin D deficiency alters the immune cell compositions of offspring by changing the transcriptional properties of stem cells and altering long-term stem cell fate decisions.

overall_design: To investigate the effects of maternal vitamin D deficiency on the hematopoietic system of offspring, we performed RNA-seq analyses on the liver at postnatal day 1 and the isolated multipoint progenitor 4 cells (MPP4) at 16 weeks of age of prenatal vitamin D deficiency exposed (VDD) and not exposed (VDS) male mice.


title: Single-cell m6A profiling in the mouse brain uncovers cell type-specific RNA methylomes and age-dependent differential methylation

overall_design: Samples are from flow-sorted cortical Neurons. Nuclei were isolated and fixed with ethanol prior to staining with anti-NeuN antibody and flow sorting. Then, total RNA was extracted, and RNA-seq libraries prepared. m6A sites were identified using to Bullseye pipeline to find sites of C-to-U conversion.


title: Single-cell m6A profiling in the mouse brain uncovers cell type-specific RNA methylomes and age-dependent differential methylation [neuronuclei]

overall_design: Samples are from flow-sorted cortical Neurons. Nuclei were isolated and fixed with ethanol prior to staining with anti-NeuN antibody and flow sorting. Then, total RNA was extracted, and RNA-seq libraries prepared. m6A sites were identified using Bullseye pipeline to find sites of C-to-U conversion.


title: Single-cell m6A profiling in the mouse brain uncovers cell type-specific methylomes and age-dependent differential methylation [m6A]

overall_design: Mice expressing tamoxifen-inducible APOBEC1-YTH were used to identify sites of m6A methylation across three different brain regions in bulk. Since the APOBEC1-YTH transgene induces C-to-U mutations at sites of m6A methylation, these raw files consist of RNA-seq data. Sequening data from APOBEC1-YTHmut expressing mice are used in the m6A site calling process as a background control for C-to-U edits. Additionally, whole cortexes from APOBEC1-YTH and APOBEC1-YTHmut were used for single-cell RNA-seq. Split-pool barcoding (Parse Biosciences) was used to generate these libraries and they were sequenced as a pool, with cellular barcodes used to identify replicates and transgene expression.

first: Chistopher


title: RNA-Sequencing Analysis of LNCaP Wildtype (WT)  and RB-p53 CRISPR-Cas9 Double Knockout (DKO) Cells Treated with Enzalutamide

city: London

first: Fred

last: Dick

state: Ontario

address: 1151 Richmond St

department: Pathology and Laboratory Medicine

country: Canada

institute: Western University

summary:
To investigate differential gene expression between LNCaP wild type (WT) cells and cells deficient for RB and p53 in the presence of absence of enzalutamide
To investigate differential gene expression between LNCaP wild type (WT) cells and cells deficient for RB and p53 (generated using CRISPR-Cas9) in the presence of absence of enzalutamide

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of both cell lines in 2 different treatment conditions.

first: Michael

last: Roes


title: CHD7 promotes anti-viral short-lived effector CD8+ T cells

status: Public on Sep 23 2024

city: Boston

first: Martin

middle: Wallace

last: LaFleur

state: MA

address: 4 Blackfan Circle Room 140

institute: Harvard Medical School

type: Genome binding/occupancy profiling by high throughput sequencing

summary: CD8+ T cells differentiate into two subpopulations in response to acute viral infection: memory precursor effector cells (MPECs) and short-lived effector cells (SLECs). MPECs and SLECs are epigenetically distinct; however, the epigenetic regulators required for formation of these subpopulations are mostly unknown. Here we performed an in vivo CRISPR screen in murine naive CD8+ T cells to identify the epigenetic regulators required for MPEC and SLEC formation, using the acute lymphocytic choriomeningitis virus (LCMV) Armstrong infection model. We identified the ATP-dependent chromatin remodeler chromodomain-helicase-DNA-binding-protein-7 (CHD7) as a positive regulator of SLEC formation, as knockout (KO) of Chd7 reduced SLECs numerically. In contrast, KO of Chd7 increased the formation of central memory T cells following pathogen clearance yet attenuated memory cell expansion following a rechallenge. These findings establish CHD7 as a novel positive regulator of SLEC and negative regulator of central memory T cell formation.

overall_design: To investigate the open chromatin regions in CD8+ T cells responding to LCMV Armstrong infection we performed ATACseq.

middle: W


title: HCC spatial transcriptomic profiling reveals significant and potentially targetable cancer-endothelial interactions

first: Joseph

last: Franses

state: Massachusetts

department: Cancer Center

institute: Massachusetts General Hospital

summary: HCC is a highly vascular tumor, and many effective drug regimens target the tumor blood vessels. Prior bulk HCC subtyping data used bulk transcriptomes, which contained a mixture of parenchymal and stromal contributions. Using cell type–specific spatial transcriptomics techniques to separate cancer cells and endothelial cells applied to a set of 41 resected HCC tissue specimens, we report that the prior Hoshida bulk transcriptional subtyping schema is driven largely by an endothelial fraction, show an alternative tumor-specific schema has potential prognostic value, and use spatially paired ligand-receptor analyses to identify known and novel (LGALS9 tumor-HAVCR2 vessel) signaling relationships that drive HCC biology in a subtype-specific and potentially targetable manner. Our study leverages spatial gene expression profiling technologies to dissect HCC heterogeneity and identify heterogeneous sig- naling relationships between cancer cells and their endothelial cells. Future validation and expansion of these findings may validate novel cancer- endothelial cell interactions and related drug targets.

overall_design: We used cell type–specific spatial transcriptomics techniques (Nanostring GeoMx) to separate cancer cells and endothelial cells applied to a set of 41 resected HCC tissue specimens.

first: Chenyue

last: Lu

first: Amaya

last: Pankaj

last: Raabe

first: Cole

last: Nawrocki

first: Ann

last: Liu

first: Nova

last: Xu

first: Bidish

last: Patel

last: Emmett

first: Avril

last: Coley

first: Cristina

middle: R

last: Ferrone

first: Vikram

last: Deshpande

first: Irun

last: Bhan

first: Yujin

last: Hoshida

first: David

middle: T

last: Ting

last: Aryee


title: CHD7 promotes anti-viral short-lived effector CD8+ T cells [RNA-seq]

last: LaFleur

overall_design: To investigate the differentially expressed genes in CD8+ T cells responding to LCMV Armstrong infection we performed RNAseq.


title: Paving the way to a neural fate - RNA signatures in naive and trans-differentiating Mesenchymal Stem Cells

city: Saarbrücken

first: Annika

last: Engel

state: Saarland

address: Campus E2 1

department: Center for Bioinformatics

institute: Saarland University

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

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

overall_design: Refer to individual Series


title: PGLYRP-1 Confers Immune Evasive Properties to Pancreactic Cancer Stem Cells [2015]

city: Madrid

first: Susana

last: García-Silva

state: madrid

address: Melchor Fernandez Alamgro

department: Molecular Oncology

country: Spain

institute: Spanish national Cancer Research Centre

summary: The crosstalk between tumor and immune cells has important implications for cancer treatment, in particular for immunotherapies. Pancreatic ductal adenocarcinoma (PDAC) generally displays a chemoresistant phenotype and is refractory to immune-based therapies. Highly tumorigenic and stem-like cells known as cancer stem cells (CSCs) within PDAC tumors have been demonstrated to contribute to its aggressiveness, metastatic capacity and chemoresistance. Here, we show that CSCs could be also relevant to establish an immunosuppresive environment. Using genetically engineered mouse models (GEMMs) of PDAC we isolated a triple positive (EpCAM+, Sca-1+ and CD133+) population of tumor cells, functionally validated these cells as bona fide CSCs and probed their transcriptional profile by microarray analysis. In addition to stem pathways, signatures related to tumor immune evasion, immune modulation, invasiveness, and innate immune response were enriched in this population. Peptidoglycan recognition protein 1 (Pglyrp1), an innate immune response anti-bacterial protein expressed primarily by neutrophils, was highly expressed in this triple-positive population and in CSC-enriched spheres from human cell lines. Interestingly, modulation of Pglyrp1 expression in murine PDAC primary cultures affected their immune evasive properties, specifically their ability to escape macrophage- and T-cell-mediated killing in vitro and to establish tumors in immunocompetent hosts. Pglyrp1 expression in tumor cells seemed to interfere with TNFα-mediated killing by T cells and to promote activated T-cell cytotoxicity. Importantly, these results could be validated in CSCs from human patient-derived xenografts, and PGLYRP1 protein levels were also significantly higher in PDAC patient samples versus healthy controls. Thus, our study demonstrates a hierarchical organization of cancer cells in a murine model of PDAC, validating the CSC concept, and identifies Pglyrp1 as a putative PDAC biomarker that confers immune privilege properties to CSCs which could have important therapeutic implications.

overall_design: Tumor cells from mouse pancreatic tumors were isolated using enzymatic digestion with collagenase P and trypsin. Cells were grown  in RPMI medium with 10%fetal bovine serum and 50units/ml penicillin/streptomycin. Epithelial clones were picked and expanded. For adherent conditions, cells were grown for 4 days in RPMI medium with 10%fetal bovine serum and 50units/ml penicillin/streptomycin in regular culture dishes. For sphere conditions, cells were grown for 4 days in ultra-low attachment plates using serum-free RPMI supplemented with B27 1:50, 20 ng/mL bFGF, L-Glutamine and 50 units/ml penicillin/streptomycin.

first: Jorge

last: Dorado

last: Silva

first: Christopher

last: Heeschen

first: Bruno

last: Sainz


title: Cell autonomous role of nuclear FGF in gene expression patterning during organogenesis

city: Zurich

first: Darren

last: Gilmour

address: Winterthurerstrasse 190

department: Department of Molecular Life Sciences

country: Switzerland

institute: University of Zurich

summary: Cell signaling molecules are essential drivers of gene expression patterns, which are crucial for the development of multicellular organisms. Although prior research has established the importance of the levels and distribution of these molecules for gene expression patterns during embryonic development, a complete understanding of the specific targets influenced by their activity remains elusive. This study investigates how the fibroblast growth factor (FGF), a key developmental signal, orchestrates gene expression during the organogenesis of the zebrafish lateral line. Our analysis provides a detailed catalog of genes mediated by FGF signaling and identified dose-dependent genes that consistently respond to varying levels of extracellular FGF signaling in vivo. Notably, we uncovered an unexpected group of target genes that show suppressed expression at increased levels of FGF ligand, independent of changes in extracellular signaling. Experiments utilizing mosaic mis-expression of FGF ligands demonstrate that this gene regulation occurs autonomously within individual cells. In embryos with endogenous FGF levels, these target genes are suppressed in FGF-producing cells that shows nuclear accumulation of the FGF ligand. Targeted degradation of nuclear FGF confirms its role in this suppression, while not interfering with the activity of extracellular FGF signaling in the neighboring cells. Thus, we propose a novel mechanism of gene expression patterning in which the FGF ligand is directed to the nucleus within source cells. This process autonomously regulates its signaling targets, which are induced by extracellular FGF, leading to a self-organized symmetry-breaking in FGF signaling targets. Our findings of consistent gene expression patterns across multiple tissues, together with the nuclear localization of other paracrine FGF ligands, indicate that the cell-autonomous gene regulation by nuclear-targeted ligands could be a more widespread mechanism.

overall_design: Zebrafish lateral line primordium treated with SU5402 (FGFR1 inhibitor) and FGF ligand overexpression

first: Sevi

last: Durdu

first: Murat

last: Iskar

first: Alicia

last: Roig-Merino

first: Elisa

last: Gallo

first: Ezgi

last: Karaca

first: Andreas

last: Kunze

first: Erika

last: Donà

first: Peer

last: Bork


title: Paving the way to a neural fate - RNA signatures in naive and trans-differentiating Mesenchymal Stem Cells - transcriptome data

summary: We conducted a detailed time-course RNA expression profiling during the early trans-differentiation of human bone marrow-derived MSCs (hBMSCs).

overall_design: Human BMSCs (C-12974) were obtained from PromoCell GmbH (Heidelberg, Germany). The cells were grown on fibronectin coated flasks and time-course samples were collected at 0, 3, 6, 9, 12, 24 and 48 h after addition of a neurogenic differentiation medium.

first: Caroline

last: Diener

first: Konstantin

last: Thüre

first: Martin

last: Hart

last: Keller

first: Eckart

last: Meese

first: Ulrike

last: Fischer


title: Lipid droplet-loaded macrophages as a targetable pro-tumorigenic immune cell entity in human glioblastoma

status: Public on Sep 27 2024

city: Lund

first: Mattias

last: Belting

state: Skåne

address: Barngatan

department: Clinical Sciences Lund

country: Sweden

institute: Lund University

summary: Glioblastoma (GBM) presents a formidable clinical challenge due to its complex microenvironment. Here, we introduce tumor-associated foam cells (TAFs), a previously unidentified immune cell entity of lipid droplet (LD)-loaded macrophages, in GBM. Through extensive analyses of patient tumors, together with in vitro and in vivo investigations, we reveal that TAFs exhibit distinct pro-tumorigenic characteristics related to hypoxia, mesenchymal transition, angiogenesis, and impaired phagocytosis. Moreover, TAF presence correlates with worse patient outcome. Our mechanistic investigations demonstrate that TAF formation is facilitated by lipid cargo transfer from extracellular vesicles released by GBM cells. Importantly, we demonstrate that targeting key enzymes involved in LD formation, such as DGAT1 or ACSL, effectively disrupts TAF functionality. This study establishes TAFs as a prominent immune cell entity in GBM and provides valuable insights into their interplay within the microenvironment. Disrupting LD form

overall_design: scRNA of GBM tumors

first: Valeria

last: Governa

first: Kelin

last: de Oliveira

first: Svenja

last: Offer

first: Myriam

middle: C

last: Magaña

first: Anna

last: Rudenstam

first: Jiaxin

last: Li

first: Sarah

last: Beyer

first: Maria

last: Johansson

first: Ann-Sofie

last: Månsson

first: Charlotte

last: Edvardsson

first: Faris

last: Durmo

first: Axel

last: Boukredine

first: Emelie

last: Gezelius

first: Julien

middle: A

last: Menard

first: Raquel

last: Garza

first: Johan

last: Jakobsson

first: Therese

last: de Neergaard

first: Pia

last: Sundgren

first: Pontus

last: Nordenfelt

last: Darabi

first: Karin

last: Forsberg-Nilsson

first: Hugo

last: Talbot

last: Bengzon


title: Paving the way to a neural fate - RNA signatures in naive and trans-differentiating Mesenchymal Stem Cells - miRNome data

first: Annika

last: Engel

first: Caroline

last: Diener

first: Konstantin

last: Thüre

first: Martin

last: Hart

first: Andreas

last: Keller

first: Eckart

last: Meese

first: Ulrike

last: Fischer


title: Loss of synovial tissue macrophage homeostasis precedes Rheumatoid Arthritis clinical onset.

city: Dublin

first: Conor

last: Smith

address: TBSI

country: Ireland

institute: Trinity COllege Dublin

summary: This study performed an in-depth investigation into the myeloid cellular landscape in the synovium of Rheumatoid Arthritis (RA) patients, ‘individuals-at-risk’ of RA and healthy controls (HC). Flow-cytometric analysis demonstrated for the first time, the presence of a CD40-expressing CD206+CD163+ macrophage population dominating the inflamed RA synovium, associated with disease-activity and treatment response. RNAseq/metabolic analysis demonstrated that this macrophage population is transcriptionally distinct, displaying unique inflammatory, and tissue-resident gene signatures, has a stable bioenergetic profile, and regulates stromal cell responses. scRNAseq profiling of 67908 RA and HC synovial-tissue cells identified nine transcriptionally distinct macrophage-clusters. IL- 1B+CCL20+ and SPP1+MT2A+ are the principal macrophage clusters in RA synovium, displaying heightened CD40 gene expression, capable of shaping stromal cell responses, and importantly are enriched pre-disease onset. Combined these findings identify the presence of an early pathogenic myeloid signature that shapes the RA joint microenvironment and represents a unique opportunity for early diagnosis and therapeutic intervention.

overall_design: Following arthrosopic surgery, single cell suspension of ~15 biopsies per individual were generated. 4 RA and 5 PsA synovial tissue samples were analysed and 4 healthy control synovial tissue samples. Healthy individuals undergoing arthroscopy during anterior cruciate ligament (ACL) reconstruction surgery were included in this study. Healthy subjects were defined as those who had no evidence of any form of arthritis on history or examination and had no cartilage damage or synovitis on knee arthroscopy.


title: The H3K9me3 heterochromatin integrity and function are sustained by H3K9me3 methyltransferases-HP1 dependencies [H4K20me3 ChIP-seq]

status: Public on Sep 19 2024

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

summary: H3K9me3-heterochromatin, compacted by HP1 proteins, restricts transcription factor binding and functions as a barrier to cell fate changes in development and reprogramming1,2. To investigate principles underlying H3K9me3-heterochromatin maintenance in mammalian cells, we applied degron engineering3,4 on mouse ESCs to conditionally deplete all three H3K9me3-methyltransferases within one hour and found an unexpectedly dynamic nature of heterochromatin maintenance. Following H3K9me3 methyltransferases degradation, HP1β dissociates from heterochromatin within three hours, and transcription factors quickly access the de-compacted heterochromatin, activating transcription of their targets, which then promotes H3K9me3 decay. Both passive dilution and active removal contribute to the H3K9me3 decay. Mathematical modeling reveals distinct H3K9me3 heterochromatin states with diverse chromatin features which influence initial H3K9me3 levels and the stability of H3K9me3 domains, thereby expanding our understanding of distinct heterochromatin domains. Rampant transposable element de-repression interferes with transcription of poised early developmental and signaling genes outside H3K9me3-domains, highlighting the intricate roles of dynamic H3K9me3-heterochromatin maintenance in safeguarding developmental programs. Our findings deconvolve the hierarchical relationships between H3K9me3 marks, methyltransferases, HP1 and transcription factors to reveal principles of H3K9me3-heterochromatin maintenance and how its remodeling enables transcription and cell fate change.

overall_design: A time-course experiment in which histone lysine 9 methyltransferases are ablated in mESCs and the decay of heterochromatin protein H4K20me3 is examined genome-wide by chIP-seq. The time-course runs 48hrs with collection points at 0hrs, 12hrs, 24hrs, and 48hrs. Three biological repeats were sequenced in three separate sequencing runs (of the same libraries) for additional genome coverage at each time point. The 0hrs time point is taken to be the baseline against which decay is measured. Matched inputs for all samples (sequenced and uploaded in GSE231845) were used to control for sonication efficiency. A drosophila chromatin spike-in is employed to properly adjust sample signal between different time points.

first: Jingchao

last: Zhang

first: Greg

first: Tomer

last: Lapidot

first: Dario

last: Nicetto

first: Kenneth

last: Zaret


title: PGLYRP-1 Confers Immune Evasive Properties to Pancreactic Cancer Stem Cells

first: Susana

last: García-Silva


title: Cross-tissue human fibroblast atlas reveals myofibroblast subtypes with distinct roles in immune modulation

city: Shenzhen

first: Yang

last: Gao

address: Guangqiao Road, Guangming District

country: China

institute: Shenzhen Bay Laboratory


title: Single-cell transcriptomic analysis reveals dynamic cellular processes in corneal epithelium during wound healing in cynomolgus monkeys

status: Public on Sep 20 2024

city: guangzhou

first: ming

last: zhou

address: jinsui road 7

institute: Sun Yat-sen University,

summary: we employed single-cell RNA sequencing (scRNA-seq) to analyze the cellular activities and transcriptional changes of corneal limbal epithelial cells at different stages after wound healing in cynomolgus monkeys

overall_design: Corneal limbal tissues were collected during uninjured, 1-day and 3-day healing stages, dissociated into single cells, and subjected to scRNA-seq using the 10× Genomics platform.

first: Ming

last: Zhou

first: Zhuo-Xing

last: Shi

first: Zhong

last: Liu

first: Ying-Feng

last: Zheng


title: Regulation of gene expression by Hcm1 in chronic LiCl stress

status: Public on Sep 18 2024

city: Worcester

first: Jennifer

last: Benanti

address: 364 Plantation St., LRB 525

department: Molecular, Cell and Cancer Biology

institute: University of Massachusetts Medical School

summary: Gene expression was quantified in S. cerevisiae cells after 40 hours of LiCl treatment or control conditions. Cells expressing wild type (WT) Hcm1, a stable Hcm1 mutant (Hcm1-3N), or a consitutitvely active, phosphomimetic mutant (Hcm1-8E)  were compared to allow the identification of genes whose expression depends upon dynamic phosphorylation of Hcm1.  We found that dynamic phosphorylation of Hcm1 is required for expression of Hcm1 target genes in LiCl stress.

overall_design: Gene expression was measured in cells expressing wild type (WT) Hcm1, Hcm1-3N (3N) or Hcm1-8E (8E). Each strain was innoculated into both control medium and medium containing 150mM LiCl. After 24 hours of growth, saturated cultures were diluted into the same growth media. Samples were collected after an additional 16 hours (40 hours total of total growth) when cells were in logarithmic phase. Biological triplicate experiments were performed.

first: Michelle

last: Conti

first: Rui

last: Li

first: Lihua

last: Zhu


title: The H3K9me3 heterochromatin integrity and function are sustained by H3K9me3 methyltransferases-HP1 dependencies

first: Gregory


title: The H3K9me3 heterochromatin integrity and function are sustained by H3K9me3 methyltransferases-HP1 dependencies [ATAC-Seq]

overall_design: A time-course experiment in which histone lysine 9 methyltransferases are ablated in mESCs and newly open chromatin is examined genome-wide by ATAC-seq. The time-course runs 48hrs with collection points at 0hrs, 3hrs, 6hrs, 12hrs, 24hrs, and 48hrs. Three biological repeats were sequenced per time point. The 0hrs time point is taken to be the baseline against which decay is measured.

first: Jingchao


title: An alveolus lung on a chip model of Mycobacterium fortuitum lung infection

city: Dallas

first: Victoria

middle: Anette

last: Ektnitphong

address: 5323 Harry Hines Blvd.

department: Internal Medicine

institute: UTSW Medical Center

summary: Lung disease due to non-tuberculous mycobacteria (NTM) is rising in incidence. While both 2D cell culture and animal models exist for NTM infections, a major knowledge gap is the early responses of human alveolar and innate immune cells to NTM within the human lung microenvironment. Here we describe development of a humanized, 3D, alveolus lung-on-a-chip (ALoC) model of Mycobacterium fortuitum infection that incorporates only primary human cells such as pulmonary vascular endothelial cells in a vascular channel, and type I and II alveolar cells and monocyte-derived macrophages in an alveolar channel along an air-liquid interface. M. fortuitum introduced into the alveolar channel primarily infected macrophages, with rare bacteria inside alveolar cells. Bulk-RNA sequencing of infected chips revealed marked upregulation of transcripts for cytokines, chemokines and secreted protease inhibitors (SERPINs). Our results demonstrate how a humanized ALoC system can identify critical early immune and epithelial responses to M. fortuitum infection. We envision potential application of the ALoC to other NTM and for studies of new antibiotics

overall_design: Alveolar lung-on-a-chips (ALoCs) that were seeded with primary human alveolar epithelial cells & human monocyte-derived macrophages in the apical channel and human microvascular pulmonary endothelial cells in the basal channel were either infected with M. fortuitum at an MOI of ~1 to the epithelial cells or left uninfected.   24 hours post-infection, control and infected chips were lysed with TriZol and RNA was isolated using phenol & the Qiagen RNeasy Mini Kit.  We performed bulk RNA-sequencing of the apical channel on uninfected and infected chips 24 hours after infection.

first: Beatriz

last: Dias

first: Priscila

last: Campos

first: Michael

last: Shiloh


title: RNA-sequence facilitates analyze changes of signaling pathways after  cell reprogramming

city: Nanjing

first: Guoqiang

last: Wan

address: Xuefu Road

institute: Nanjing University

summary: Cochlear hair cells are the sensory cells responsible for transduction of acoustic signals. In mammals, damaged hair cells do not regenerate, resulting in permanent hearing loss. Reprogramming of the surrounding supporting cells to functional hair cells represent a novel strategy to hearing restoration. However, cellular processes governing the efficient and functional hair cell reprogramming are not completely understood. Employing the mouse cochlear organoid system, we performed detailed metabolomic characterizations of the expanding and differentiating organoids. We found that hair cell differentiation is associated with increased mitochondrial electron transport chain (ETC) activity and reactive oxidative species generation. Transcriptome and metabolome analyses indicate reduced expression of oxidoreductases and tricyclic acid (TCA) cycle metabolites. The metabolic decoupling between ETC and TCA cycle limits the availability of the key metabolic cofactors, α-ketoglutarate and NAD+. Reduced expression of NAD+ in cochlear supporting cells by PGC1α deficiency further impairs hair cell reprogramming, while supplementation of α-ketoglutarate and NAD+ promotes hair cell reprogramming both in vitro and in vivo. Our findings reveal metabolic rewiring as a central cellular process during hair cell differentiation, and highlight the insufficiency of key metabolites as a metabolic barrier for efficient hair cell reprogramming.

overall_design: We perform transcriptomic analysis using cochlear organoids during proliferation and differentiation, and then it find oxidoreductases changes.We verify the results in cochlear organoid,cochlear explant and in vivo.

first: Qing

first: Linqing

last: Zhang

first: Zhen

last: Chen

first: Chengwen


title: Systems biology profiling reveal changes following short-term exposure of an epithelial-endothelial coculture to secondary organic aerosols

city: Neuherberg

first: Sebastiano

last: Di Bucchianico

address: Ingolstädter Landstraße 1

institute: Helmholtz Zentrum München

summary: To investigate the toxicological mechanisms induced by an antrhopogenic SOAs (SOANAP-SP) and a biogenic SOAs (SOAβPIN-SP), as well as, fresh soot particles (SPs) in either the directly exposed A549 cells cultured at the air-liquid interphase or in the indirectly exposed EA.hy926 cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of a coculture cell model system (A549 and EA.hy926 cells) that have ben exposed to different aerosols (SOANAP-SP, SOAβPIN-SP, SPs) and clean air (CA) as control.

first: Svenja

last: Offer

first: Michal

last: Pardo-Levin


title: Cross-tissue human fibroblast atlas reveals myofibroblast subtypes with distinct roles in immune modulation [RNA-seq]

first: Yang

last: Gao

summary: Fibroblasts hold pivotal roles in tissue homeostasis and disease progression. However, a systematic study addressing the functional heterogeneity of fibroblasts, their dynamic shifts along disease progression, as well as their impact to tumor immune microenvironment is currently lacking. Here, we performed integrated analyses on fibroblasts spanning multiple tissues and disease conditions, especially cancer. Our study provides novel insights into fibroblast cell heterogeneity and highlights the potential clinical utilities of fibroblast cell subsets as therapeutic targets.

overall_design:
We generated RNA-seq data using fibroblasts from adjacent normal tissues in colon and lung cancer patients to investigate the impact of 6 different ligands stimulation on fibroblasts.

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Submitter states that missing raw files are due to patient privacy concerns.
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first: Y

first: J

first: W

last: Cheng

last: Hou

first: Z


title: The H3K9me3 heterochromatin integrity and function are sustained by H3K9me3 methyltransferases-HP1 dependencies [ChIP-Seq]

first: Gregory

last: Donahue

overall_design: A time-course experiment in which histone lysine 9 methyltransferases are ablated in mESCs and the decay of heterochromatin proteins H3K9me3 and HP1b is examined genome-wide by chIP-seq. The time-course runs 48hrs with collection points at 0hrs, 1hr, 3hrs, 12hrs, 24hrs, and 48hrs. Three biological repeats were sequenced in three separate sequencing runs (of the same libraries) for additional genome coverage at each time point. The 0hrs time point is taken to be the baseline against which decay is measured. Matched inputs for all samples were used to control for sonication efficiency. A drosophila chromatin spike-in is employed to properly adjust sample signal between different time points.

first: Jingchao

first: Greg

first: Tomer

last: Lapidot

first: Dario

last: Nicetto

first: Kenneth

last: Zaret


title: PRDM16 is required for proper specification of the working ventricular myocardium by suppressing alternative cardiomyocyte cell fates.

city: Leuven

first: Jore

last: Van Wauwe

address: Herstraat 49 bus911

country: Belgium

institute: KU Leuven

summary: PRDM16 is a transcription factor with histone methyltransferase activity expressed at the earliest stages of cardiac development. Pathogenic mutations in humans lead to cardiomyopathy, conduction abnormalities and heart failure. PRDM16 is specifically expressed in ventricular but not atrial cardiomyocytes and declines in expression postnatally. Since in other tissues PRDM16 is best known for its role in binary cell fate decisions, we hypothesized a similar decision-making function in cardiomyocytes. Here, we demonstrated that cardiomyocyte-specific deletion of Prdm16 during cardiac development results in contractile dysfunction and abnormal electrophysiology of the postnatal heart, resulting in premature death. By combined RNA+ATAC single-cell sequencing we found that PRDM16 favors ventricular working cardiomyocyte identity, by opposing the activity of master regulators of atrial and ventricular conduction fate. Myocardial loss of Prdm16 during development resulted in hyperplasia of the ventricular conduction system. Hence, PRDM16 plays an indispensable role during cardiac development by driving ventricular working cardiomyocyte identity.

overall_design: 10X multiome RNA + ATAC sequencing of left ventricle of Prdm16_WT versus Prdm16_KO 7-day old pups.

first: Aernout

last: Luttun


title: Transcriptomic analysis reveals Streptococcus agalactiae activation of oncogenic pathways in cervical adenocarcinoma

city: Daegu

first: Hyung Soo

last: Han

state: Daegu

address: 680 Gukchaebosang-ro

country: South Korea

institute: Kyungpook National University

summary: Cervical adenocarcinoma (AC), a subtype of uterine cervical cancer (CC), poses a challenge due to its resistance to therapy and poor prognosis compared with squamous cervical carcinoma. Streptococcus agalactiae [group B Streptococcus (GBS)], a Gram-positive coccus, has been associated with cervical intraepithelial neoplasia in CC. However, the underlying mechanism interaction between GBS and CC, particularly AC, remains elusive. Leveraging The Cancer Genome Atlas public data and time-series transcriptomic data, the present study investigated the interaction between GBS and AC, revealing activation of two pivotal pathways: ‘MAPK signaling pathway’ and ‘mTORC1 signaling’. Western blotting, reverse transcription-quantitative PCR and cell viability assays were performed to validate the activation of these pathways and their role in promoting cancer cell proliferation. Subsequently, the present study evaluated the efficacy of two anticancer drugs targeting these pathways (binimetinib and ridaforolimus) in AC cell treatment. Binimetinib demonstrated a cytostatic effect, while ridaforolimus had a modest impact on HeLa cells after 48 h of treatment, as observed in both cell viability and cytotoxicity assays. The combination of binimetinib and ridaforolimus resulted in a significantly greater cytotoxic effect compared to monotherapy, even though the synergy score indicated an additive effect. Furthermore, this drug combination may enhance the effect on HeLa cells exposed to GBS compared to those without exposure. In general, the MAPK and mTORC1 signaling pathways were identified as the main pathways associated with GBS and AC cells. The combination of binimetinib and ridaforolimus could be a potential AC treatment.

overall_design: To elucidate the underlying mechanism between host adenocarcinoma cells and GBS, we conducted a time-series experiment involving Hela cells infected with GBS for 0, 2, 6, and 24 hours, alongside corresponding control groups treated solely with a bacteria-free human medium. The experimental design included triplicate replicates. Subsequently, we performed transcriptomic time-series analysis across the four time points, comparing treatment and control groups to pinpoint clusters linked with the impact of GBS. Furthermore, pathway enrichment analysis was employed to delineate transcriptome profiles of pathways involved in the interaction between host cervical cancer cells and GBS.

first: Hyung

middle: S


title: Gene expression profiles at the single-cell level of Peyer's patch CD19-negative cells in an antigen-free condition.

city: Yokohama

first: Takaharu

last: Sasaki

state: Kanagawa

address: 1-7-22 Suehiro-cho, Thurumi-ku

department: Center for Integrative Medical Sciences

institute: RIKEN

summary: CD19-negative cells contain T cells, innate lymphoid cells and dendritic cells.

overall_design: These cells were isolated from wild-type C57BL/6 mice placed on a normal chow diet (NCD) or an antigen-free diet (AFD) under specific pathogen-free (SPF) or germ-free (GF) conditions using collagenase digestion and FACS sorting for live CD19-negative cells.

first: Yui

last: Takikawa

first: Takashi

last: Kanaya

first: Masumi

last: Takahashi

first: Naoko

last: Tachibana

first: Haruka

last: Yabukami

first: Aki

last: Miinoda

first: Hiroshi

last: Ohno


title: mTOR activity paces human blastocyst stage developmental progression

city: Vienna

first: HEIDAR

last: HEIDARI KHOEI

address: Dr. Bohr-Gasse 3

country: Austria

institute: Institute of Molecular Biotechnology

summary:
Many mammals can temporally uncouple conception from parturition by pacing down their
development around the blastocyst stage. In mice, this dormant state is achieved by decreasing
the activity of the growth-regulating mTOR signaling pathway. It is unknown whether this ability
is conserved in mammals in general and in humans in particular. Here we show that decreasing
the activity of the mTOR signaling pathway induces human pluripotent stem cells (hPSCs) and
blastoids to enter a dormant state with limited proliferation, developmental progression, and
capacity to attach to endometrial cells. These in vitro assays show that, similar to other species,
the ability to enter dormancy is active in human cells around the blastocyst stage and is reversible
at both functional and molecular levels. The pacing of human blastocyst development has
potential implications for reproductive therapies

overall_design: To test the effect of mTOR inhibition on the developmental timeline and morphology of human blastoids, these were first formed and then further cultured in the presence of the mTOR inhibitor RapaLink-1 and to test whether Rapalink-1 treated blastoids are reversible, we reactivated blastoids after 3 days of Rapalink-1 treatment and further cultured them on matrigel-coated plates.

first: Heidar

last: Heidari Khoei

first: Saurabh

last: Pradhan

first: Nicolas

last: Rivron


title: Chromatin conformation dynamics during CD4+ T cell activation implicates 2 autoimmune disease-associated genes and regulatory elements

first: Andrew

last: Wells

address: 3615 Civic Center Blvd

institute: Children's Hospital of Philadelphia

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

overall_design: Refer to individual Series


title: Cross-tissue human fibroblast atlas reveals myofibroblast subtypes with distinct roles in immune modulation [scRNA-seq]

first: Yang

last: Gao

overall_design:
We generated scRNA-seq data from 38 cancer patients to investigate fibroblast cells across multiple cancer types.

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Submitter states that missing raw files are due to patient privacy concerns.
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first: Y

first: J

last: Li

first: W

last: Cheng

last: Hou

first: Z

last: Zhang


title: Chromatin conformation dynamics during CD4+ Tcell activation implicates autoimmune disease associated genes and regulatory elements (RNA-Seq)

summary: We used ATAC-seq, RNA-seq, and HiC to create atlases of the regulatory elements to provide context to autoimmune disease associated variants from publically available Genome-wide association studies

overall_design: We performed ATAC-seq, RNA on 3 donors, and HiC on data from 2 donors

first: Matthew

last: Pahl

first: Prahbat

last: Sharma


title: Chromatin conformation dynamics during CD4+ Tcell activation implicates autoimmune disease associated genes and regulatory elements (ATAC-Seq)


title: Pre-ciliated tubal epithelial cells are prone to initiation of high-grade serous ovarian carcinoma

city: Ithaca

first: Coulter

last: Ralston

state: NY

address: 237 Tower Rd

department: Biomedical Engineering

institute: Cornell University

summary: The distal region of the uterine (Fallopian) tube is commonly associated with high-grade serous carcinoma (HGSC), the predominant and most aggressive form of ovarian or extra-uterine cancer. Specific cell states and lineage dynamics of the adult tubal epithelium (TE) remain insufficiently understood, hindering efforts to determine the cell of origin for HGSC. Here, we report a comprehensive census of cell types and states of the mouse uterine tube. We show that distal TE cells expressing the stem/progenitor cell marker Slc1a3 can differentiate into both secretory (Ovgp1+) and ciliated (Fam183b+) cells. Inactivation of Trp53 and Rb1, whose pathways are commonly altered in HGSC, leads to elimination of targeted Slc1a3+ cells by apoptosis, thereby preventing their malignant transformation. In contrast, pre-ciliated cells (Krt5+, Prom1+, Trp73+) remain cancer-prone and give rise to serous tubal intraepithelial carcinomas and overt HGSC. These findings identify transitional pre-ciliated cells as a previously unrecognized cancer-prone cell state and point to pre-ciliation mechanisms as novel diagnostic and therapeutic targets.

overall_design: Mouse uterine tubes were split into distal and proximal sections for single cell expression and transcriptome analysis. We isolated tubes from groups of C57BL6 adult estrous female mice to characterize the cell states present.

middle: Q

first: Alex

middle: Y

last: Nikitin

first: Benjamin

last: Cosgrove


title: Chromatin conformation dynamics during CD4+ Tcell activation implicates autoimmune disease associated genes and regulatory elements (HiC)

overall_design: We performed ATAC-seq  and HiC on data from 3 donors


title: Longitudinal transcriptome analysis of high risk cattle to determine host expressional changes associated with BRD development

city: Canyon

middle: Adam

last: Scott

address: 3201 Russell Long Blvd

department: Large Animal Clinical Sciences

institute: Texas A&M University

summary: Whole blood samples from 36 cattle, across two independent populations, were sequenced via a Illumina NovaSeq 6000 system. Samples were bioinformatically processed in a HISAT2/StringTie pipeline, and stratified based on treatment frequency for BRD (healthy, treated once, treated twice or more and/or died). Differential expression analysis was conducted in R, utilizing an additive, multifactor generalized linear model and blocking for paired samples and year. Genes were considered differentially expressed with an FDR cutoff of 0.10. The objective of this study was to identify differentially expressed genes and mechanisms within and across treatment cohorts overtime, and determine host expressional changes influenced by BRD within the first 28 days of facility arrival.

overall_design: 73 whole blood mRNA samples from 36 individual cattle, taken at days 0, 28, and end of study (~63).


title: Expression changes in mouse proximal tubules during primary culture

status: Public on Sep 17 2024

city: Ann Arbor

first: Jeffrey

last: Beamish

state: MI

address: 1500 E. Medical Center Drive, SPC 5364

department: Department of Internal Medicine, Division of Nephrology

institute: University of Michigan

summary: Primary cultures of proximal tubule cells are widely used to model the behavior of kidney epithelial cells in vitro. De-differentiation of primary cells upon culture has been observed and appreciated for decades, yet the mechanisms driving this phenomenon remain poorly understood. The goal of this experiment was to quantitatively measure the changes in expression of purified proximal tubules as they enter primary culture.

overall_design: Jeffrey, A, Beamish


title: A Spatiotemporal Transcriptome Revealed Stalk Development in Pearl Millet

status: Public on Sep 15 2024

city: Fuzhou

first: mao

last: fei

state: Fujian

address: Shangxiadianlu NO.15

department: National Engineering Research Center of JUNCAO

institute: Fujian Agriculture and Forestry University

summary: Pearl millet is a major cereal crop that feeds more than 90 million people worldwide in arid and semi-arid regions. The stalk phenotypes of Poaceous grasses are critical for their productivity and stress tolerance, however, the molecular mechanisms governing stalk development in pearl millet remained to be deciphered. In this study, we spatiotemporally measured 19 transcriptomes for stalk internodes of four different early developmental stages. Data analysis of the transcriptomes defined 4 developmental zones on the stalks and identified 12 specific gene sets with specific expression patterns across the zones. Using weighted gene co-expression network analysis (WGCNA), we found that 2 co-expression modules together with candidate genes were involved in stalk elongation and thickening of pearl millet. Among the elongation-related candidate genes, we established by SELEX that a MYB-family transcription factor PMF7G02448 can bind to the promoters of three cell wall synthases genes (CesAs). In summary, these findings provide insights into stalk development and offer potential targets for future genetic improvement of pearl millet.

overall_design:
To understand the dynamics of gene expression during stalk elongation of pearl millet, we collected 19 internodes for stalks of four early developmental stages.
To verify the regulatory role of the MYB-family TF PMF7G02448 on the PmCesAs, we performed SELEX for PMF7G02448 to examine its specificity.

first: Fei

last: Mao

first: Lin

last: Luo

first: Fangjie

last: Zhu

first: Dongmei

last: Lin


title: An atlas of the aging mouse transcriptome and proteome reveals the features of age-related post-transcriptional dysregulation

city: Osaka-shi

first: Masaki

last: Takasugi

state: Osaka

address: 1-4-3 Asahimachi, Abeno-ku

institute: Osaka Metropolitan University

summary: We've collected bulk RNA-Seq and TMT-labeled proteomic data of aorta, brain, heart, kidney, liver, lung, muscle (gastrocnemius muscle), and skin of 6-, 15-, 24-, and 30-months old male C57BL/6J mice. The tissues used for  transcriptomic analysis and proteomic analysis were collected from the same mice. All analyses were conducted with 4 biological replicates.

overall_design: Comparative gene expression profiling analysis of aorta, brain, heart, kidney, liver, lung, muscle (gastrocnemius muscle), and skin of 6-, 15-, 24-, and 30-months old male C57BL/6J mice.


title: 129-derived passenger mutations confound phenotype of ACKR1-deficient mice

city: Munich

first: Johan

last: Duchene

state: - Please Select -

address: Pettenkoferstrasse, 9

department: IPEK

institute: LMU

summary:
A majority of genetically modified mice carry passenger mutations, originating from the 129-derived embryonic stem (ES) cells, near the targeted gene. Unintended retention of these mutations can introduce confounding phenotypes and affect conclusions.
We show that Ackr1-/-129ES mice retained approximately 6 Mb of 129 ES cells-derived genomic material in chromosome 1 near Ackr1 in bone marrow derived monocytes (Mono), nucleated erythroblasts (NECs), and polymorphonucleated neutrophils (PMN), notably affecting the expression of PYHIN genes.

overall_design: C57BL/J (n = 3, WT CTRL) and ACKR1-deficient mice (n = 3, KO); no technical replicates

first: Zoe

last: Möller-Ramon


title: Transcriptome of Mycobacterium abscessus in response to transition metals

status: Public on Sep 13 2024

city: London

first: Gerald

middle: J

last: Larrouy-Maumus

address: South Kensington Campus

country: United Kingdom

institute: Imperial College London

summary: Antimicrobial resistance (AMR) is one of the major challenges that humans are facing this century. Understanding the mechanisms behind the rise of AMR is crucial to tackle this global threat. Among the triggers of phenotypic antimicrobial resistance, the contribution of transition metals has been understudied in Mycobacterium abscessus (Mabs), a fast-growing non-tuberculous mycobacterium known for its extreme AMR levels. Deeper understanding of the effects of transition metal ions will be beneficial for our knowledge in AMR and the discovery of potential therapeutic targets. Here, we investigated the impact of transition metal ions, nickel, cobalt and copper on the physiology and drug susceptibility of Mabs.

overall_design: M. abscessus ATCC19977 strain was grown to mid-exponential phase (OD600=0.8) and treated with one of the transition metal ions at pre-defined stress concentrations (Cu2+: 0.156 mM; Co2+: 0.625 mM; Ni2+: 2.5 mM) for two hours, together with an untreated group. Three biological replicates in each group were prepared for RNA extraction.

first: Nadia

last: Fernandes

first: Yi

last: Liu

first: Richard

last: Williams


title: SARS-CoV-2 spike protein induces the cytokine release syndrome by stimulating T cells to produce more IL-2

city: Changchun

first: Chao

last: Niu

state: Jilin

address: Xinmin Street #1

institute: The First Hospital of Jilin University

summary: Cytokine release syndrome (CRS) is one of the leading causes of mortality in COVID-19 patients caused by the SARS-CoV-2 coronavirus. However, the mechanism of CRS induced by SARS-CoV-2 is vague. This study shows that dendritic cells loaded with spike protein of SARS-CoV-2 stimulate T cells to release much more IL-2, which subsequently cooperates with spike protein to facilitate peripheral blood mononuclear cells to release IL-1β, IL-6, and IL-8. The aim of this sequencing is to find the key molecular of IL-2 synergistic spike protein releasing much more inflammatory factors in PBMCs and to explore the molecular mechanism.

overall_design: Gene expression profiling analysis of RNA-seq data of human peripheral blood mononuclear cells treated with SARS-CoV-2 spike protein, IL-2 combining with spike protein, IL-2 and PBS.

first: Jiuwei

last: Cui

first: Xin

last: Zhou


title: TCA metabolism regulates DNA hypermethylation in LPS and Mycobacterium tuberculosis–induced immune tolerance

status: Public on Sep 12 2024

city: Chicago

first: Abhimanyu

state: Illinois

address: 920 E 58th Street

institute: University of Chicago

type: Methylation profiling by genome tiling array

summary: Severe and chronic infections, including pneumonia, sepsis, and tuberculosis (TB), induce long-lasting epigenetic changes that are associated with an increase in all cause post-infectious  morbidity and mortality. We show that TCA cycle also regulates  epigenetics, specifically DNA methylation, after infection induced immune tolerance. This data from TB patients who received everolimus with standard of care antibiotics, and have less DNA hypermethylation demonstrating proof of concept that metabolic manipulation can mitigate epigenetic scars.

overall_design: Bisulphite converted DNA was evaluated from a TB cohort from South Africa. TB patients were treated with standard of care (SOC) anti-TB Therapy with or without Everolimus . DNA methylation was evaluated from cryopreserved PBMCs at the end of TB treatment (day 180).

last: Abhimanyu

first: S

last: Longlax

first: T

last: Nishiguchi

first: M

last: Ladki

first: D

last: Sheikh

first: A

last: Martinez

first: E

last: Mace

last: Grimm

last: Caldwell

last: Portillo Varela

first: R

middle: V

last: Sekhar

last: Mandalakas

last: Mlotshwa

last: Ginidza

first: J

last: Cirillo

last: Wallis

middle: G

last: Netea

last: van Crevel

first: C

last: Coarfa

last: DiNardo


title: Differential gene expression of orthotopic breast tumor in  Nod2-/- and WT mice

city: Gary

first: Dipika

last: Gupta

state: IN

address: 3400 Broadway

department: School of Medicine

institute: Indiana University

summary: We report that Nod2, a pattern recognition receptor, protects from orthotopic breast cancer and this protection is accompanied by changes in gene expression for cell proliferation, lipid metabolism and adipogenesis.

overall_design: We compared RNA populations in the tumors from WT and Nod2-/- mice injected 4T1 mamary carcinoma cells.

first: Gupta

last: Dipika

first: Gurses

last: Serdar


title: TCA metabolism regulates DNA hypermethylation in LPS and  Mycobacterium tuberculosis–induced immune tolerance

summary: Severe and chronic infections, including pneumonia, sepsis, and tuberculosis (TB), induce long-lasting epigenetic changes that are associated with an increase in all cause post-infectious  morbidity and mortality. We show that TCA cycle also regulates  epigenetics, specifically DNA methylation, after infection induced immune tolerance. The following data is DNA methylation from lipopolysaccharide (LPS) in presence of by inhibitors of cellular metabolism (rapamycin, everolimus, metformin)  and the TCA cycle (IDH inhibitors). DNA methylation profiles were also generated from exogenous supplementation with TCA metabolites (succinate and itaconate) in Monocyte derived Macrophages

overall_design: Bisulphite converted DNA from the four sample across 6 conditions;  23samples and 6 samples from metabolite treated cells total 29 samples were hybridised to the Illumina EPIC 850K

last: Abhimanyu

last: Longlax

last: Nishiguchi

last: Ladki

last: Sheikh

last: Martinez

middle: M

last: Mace

first: SL


title: Transcriptomics-based anti-tuberculous mechanism of traditional Chinese polyherbal preparation NiuBeiXiaoHe intermediates

city: beijing

last: Wang

address: Tuberculosis Prevention and Control Key Laboratory, Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, Eighth Medical Center of PLA General Hospital

institute: People's Liberation Army General Hospital

summary: To further investigate the therapeutic potential of NBXH in treating tuberculosis, we employ whole genome microarray expression profiling as a discovery platform. The study aimed to explore the impact of NBXH treatment on the gene expression profile of tuberculosis-infected animal models. The animal models were treated with high, medium, and low doses of NBXH. Following three months of treatment, PBMCs from each treatment group were used for whole genome microarray expression profiling analysis, alongside a control group. With a screening criterion of P <0.05 and an absolute log2FC value >1, 3454 up-regulated and 3597 down-regulated DEGs were respectively identified in the gene expression profiles of the mouse TB model treated with NBXH.

overall_design: Once the tuberculosis infection model had been established, the tuberculosis-infected mouse models underwent treatment with high, medium, and low doses of NBXH intermediates, JHW for 87 days. Gene expression profiles in PBMCs were then measured, and each group underwent three independent experiments.

first: Xueqiong

last: Wu

first: Yan

last: Liang


title: GSK-3b in dendritic cells exerts opposite functions in regulating cross-priming and memory CD8 T cell responses independent of b-catenin

city: Detroit

first: Qing-Sheng

last: Mi

state: Michigan

address: One Ford Place

institute: Henry Ford Health

summary: GSK-3b plays a critical role in regulating the Wnt/b-catenin signaling pathway, and manipulating GSK-3b in dendritic cells (DCs) has been shown to improve anti-tumor efficacy of DC vaccines. Since inhibition of GSK-3b leads to activation of b-catenin, we hypothesize that blocking GSK-3b in DCs negatively regulates DC-mediated CD8 T cell immunity and anti-tumor immunity. Using CD11c-GSK-3b-/- conditional knockout mice in which GSK-3b is genetically deleted in CD11c-expressing DCs, we surprisingly found that deletion of GSK-3b in DCs resulted in increased anti-tumor immunity, which contradicted our initial expectation of reduced anti-tumor immunity due to presumed upregulation of b-catenin in DCs. Indeed, we found by both western blot and flow cytometry that deletion of GSK-3b in DCs did not lead to augmented expression of b-catenin protein, suggesting that GSK-3b exerts its function independent of b-catenin. Supporting this notion, our single cell RNA sequencing (scRNA-seq) analysis revealed that GSK-3b-deficient DCs exhibited distinct gene expression patterns with minimally overlapping differentially expressed genes (DEGs) compared to DCs with activated b-catenin. This suggests that deletion of GSK-3b in DCs is unlikely to lead to upregulation of b-catenin at the transcriptional level. Consistent with enhanced anti-tumor immunity, we also found that CD11c-GSK-3b-/- mice exhibited significantly augmented cross-priming of antigen-specific CD8 T cells following DC-targeted vaccines. We further found that deletion of GSK-3b in DCs completely abrogated memory CD8 T cell responses, suggesting that GSK-3b in DCs also plays a negative role in regulating the differentiation and/or maintenance of memory CD8 T cells. scRNA-seq analysis further revealed that although deletion of GSK-3b in DCs positively regulated transcriptional programs for effector differentiation and function of primed antigen-specific CD8 T cells in CD11c-GSK-3b-/- mice during the priming phase, it resulted in significantly reduced antigen-specific memory CD8 T cells, consistent with diminished memory responses. Taken together, our data demonstrate that GSK-3b in DCs has opposite functions in regulating cross-priming and memory CD8 T cell responses, and GSK-3b exerts its functions independent of its regulation of b-catenin.

overall_design: We performed  scRNA-seq on splenic dendritic cells (DCs) from  WT and CD11c-b-catenin active mice as well as WT and GSK3b-/- mice. Additionally, we conducted scRNA-seq on adoptively transferred OTI Thy1.1+ CD8+ T cells from WT vs. GSK3B-/- at day 4 and day 10.

first: Chunmei

last: Fu

first: Jie

first: Tianle

last: Ma

first: Congcong

last: Yin

first: Li

last: Zhou

first: Björn E

last: Clausen

first: Aimin

last: Jiang


title: RNA-sequencing reveals predominance of THRA splicing isoform 2 in developing human brain [treated]

city: Berlin

first: Markus

last: Schuelke

state: Berlin

address: Augustenburger Platz 1

department: Neuropediatrics

institute: Charite

summary: Thyroid Hormone Receptor α (THRα) is a nuclear hormone receptor for triiodothyronine (T3) that acts as a transcription factor. Depending on its splicing pattern, it may act either as a stimulator or inhibitor of gene transcription. The relative proportions of the THRα splicing isoforms (THRα1 versus THRα2) in different tissues are crucial for the outcome of transcription regulation. To date, the tissue-specific expression patterns of the two main isoforms in  human cortical development have not been determined. To address this gap, we generated cortical brain organoids in vitro following the STEMdiff™ Cerebral Organoid Kit guidelines. Samples were treated with 50nM T3 48h before collection to perturb the Thyroid Hormone-regulated system. We then generated the stranded bulk RNA-Seq dataset here presented. We employed a bioinformatics pipeline to ensure the quality of the dataset and to extract and quantify the read counts specific for our isoforms of interest. We observed a steady increase of THRα transcript in time and a strong predominance of THRα2 transcripts at all stages.

overall_design: bulk RNA-Seq of human cortical brain organoids treated with 50nm T3 collected at 3 different timepoints (day 26 two biological replicates; day 46 three biological replicates; day 61 three biological replicates)

first: Graceffo

last: Eugenio

first: Opitz

last: Robert

first: Krude

last: Heiko

first: Schuelke

last: Markus


title: RNA-sequencing reveals predominance of THRA splicing isoform 2 in developing human brain [untreated]

summary: Thyroid Hormone Receptor α (THRα) is a nuclear hormone receptor for triiodothyronine (T3) that acts as a transcription factor. Depending on its splicing pattern, it may act either as a stimulator or inhibitor of gene transcription. The relative proportions of the THRα splicing isoforms (THRα1 versus THRα2) in different tissues are crucial for the outcome of transcription regulation. To date, the tissue-specific expression patterns of the two main isoforms in  human cortical development have not been determined. To address this gap, we generated cortical brain organoids in vitro following the STEMdiff™ Cerebral Organoid Kit guidelines. We then generated the stranded bulk RNA-Seq dataset here presented. We employed a bioinformatics pipeline to ensure the quality of the dataset and to extract and quantify the read counts specific for our isoforms of interest. We observed a steady increase of THRα transcript in time and a strong predominance of THRα2 transcripts at all stages.

overall_design: bulk RNA-Seq of human cortical brain organoids collected at 3 different timepoints (day 26 two biological replicates; day 46 three biological replicates; day 61 three biological replicates)


title: Role of barhl1 in amphbian cerebellum

status: Public on Sep 11 2024

city: Paris

first: Mohamed

last: Doulazmi

state: Paris

address: 9 quai St Bernard

department: Neurocsiences

country: France

institute: Sorbonne Unversity

summary: Cerebellar granule neuron progenitors (GNPs) originate from the upper rhombic lip (URL), a germinative niche in which developmental defects produce human diseases. T-cell factor (TCF) responsiveness and Notch dependence are hallmarks of self-renewal in neural stem cells. TCF activity, together with transcripts encoding proneural gene repressors hairy and enhancer of split (Hes/Hey), are detected in the URL; however, their functions and regulatory modes are undeciphered. Here, we established amphibian as a pertinent model for studying vertebrate URL development. The amphibian long-lived URL is TCF active, whereas the external granular layer (EGL) is non-proliferative and expresses hes4 and hes5 genes. Using functional and transcriptomic approaches, we show that TCF activity is necessary for URL emergence and maintenance. We establish that the transcription factor Barhl1 controls GNP exit from the URL, acting partly through direct TCF inhibition. Identification of Barhl1 target genes suggests that, besides TCF, Barhl1 inhibits transcription of hes5 genes independently of Notch signaling. Observations in amniotes suggest a conserved role for Barhl in maintenance of the URL and/or EGL via co-regulation of TCF, Hes and Hey genes.

overall_design: RNA- sequencing analysis was performed on dissected Rhombomere 1 from Xenopus Laevis tadpoles depleted or not for BarH-like 1 (Barhl1), a direct target gene of Atonal 1 (Atoh1), a master regulator of cerebellar glutamatergic neurons development, and an inhibitor of T-Cell factor activity. X. laevis embryos were injected with three different conditions: MObarhl1-1; MObarhl1-2 and MOct in the two dorsal blastomeres at four cells stage. At stage 42, neural tubes were extracted in RNAse-free conditions, and the rhombomere 1 which includes the URL was carefully dissected. For each condition, three biological replicates were collected. Each replicate contains three rhombomeres. Poly A RNA was purified. Sequencing was performed using Illumina NovaSeq (paired-end sequencing) by Next Generation Sequencing Platform (NGS) (Institut Curie, Paris FR). This transcriptomic analysis identifies Barhl1 cerebellar target genes, and confirms that Barhl1 acts as a gate keeper for progenitor exit from the URL, through silencing of T-Cell Factor transcriptional activity.

first: Johnny

last: Bou-Rouphael

first: Alexis

last: Eschstruth

first: Asna

last: Abdou

first: Béatrice

last: C Durand


title: RNA-sequencing reveals strong predominance of THRA splicing isoform 2 in the developing and adult human brain

summary: Thyroid hormone receptor alpha (THRα) is a nuclear hormone receptor that binds triiodothyronine (T3) and acts as an important transcription factor in development, metabolism and reproduction. THRα has in mammals two major splicing isoforms, THRα1 and THRα2. The better characterized isoform, THRα1, is a transcriptional stimulator of genes involved in cell metabolism and growth. The less well characterized isoform, THRα2, lacks the Ligand Binding Domain (LBD) and is thought to act as an inhibitor of THRα1 action. The ratio of THRα1 to THRα2 splicing isoforms is therefore critical for transcriptional regulation in different tissues and during development. However, the expression patterns of both isoforms have not been studied in healthy human tissues or in the developing brain. Given the lack of commercially available isoform-specific antibodies, we addressed this question by analyzing four bulk RNA-sequencing datasets and two scRNA-sequencing datasets to determine the RNA expression levels of human THRA1 and THRA2 transcripts in healthy adult tissues and in the developing brain. We demonstrate how 10X Chromium scRNA-seq datasets can be used to perform splicing-sensitive analyses of isoforms that differ at the 3'-end. In all datasets, we discovered a strong predominance of THRA2 transcripts at all stages of brain development and in central nervous system from healthy human adults.

overall_design: bulk RNA-Seq of 24 different healthy adult human tissues (10 neuronal and 14 non-neuronal). Each sample was pooled from an average of 6 healthy individuals

first: Eugenio

last: Graceffo

first: Robert

last: Opitz

first: Matthias

last: Megges

first: Heiko

last: Krude


title: snRNA-Seq of optic nerve from two models of inducible demyelination.

city: Portland

first: Ben

last: Emery

state: Oregon

address: 3181 SW Sam Jackson Park Road

department: Neurology

institute: Oregon Health & Science University

summary: Multiple Sclerosis (MS) is a neuroinflammatory disease characterized by demyelinated lesions in the CNS. Remyelination in MS is variable between individuals and tends to become less efficient with aging. Microglia and astrocytes are known to have critical roles in MS pathogenesis, but to what extent their activity is altered by remyelination failure remains unclear.  To determine the effects of demyelination on neuroinflammation, we use two mouse models that genetically ablate myelinating oligodendrocytes. We use the Plp1-CreERT mouse line crossed with the Myrf fl/fl mouse line to induce genetic demyelination throughout the CNS following adult tamoxifen administration. Subsequent remyelination is mediated by the proliferation and differentiation of oligodendrocyte precursor cells (OPCs) to newly formed oligodendrocytes. To assess the consequences of remyelination failure, we deleted Myrf from both mature oligodendrocytes and OPCs using Myrf fl/fl; Sox10-CreERT mice, which both induces demyelination and impairs subsequent remyelination. To characterize the glial cells in these demyelinated mice, we performed single-nucleus RNA-sequencing (snRNAseq) of optic nerves at peak demyelination, generating an atlas of non-neuronal cells including oligodendrocyte lineage cells, astrocytes, microglia, endothelial cells, pericytes, arachnoid barrier cells, vascular and leptomeningeal cells.

overall_design: Optic nerves were isolated from adult Myrf fl/fl; Sox10-CreERT and Myrf fl/fl; PLP-CreERT mice and their CreERT negative control littermates at 10 weeks post tamoxifen and snap frozen. Nuclei were isolated by fluorescence-activated nuclei sorting (FANS) according to the presence or absence of RedDot signal and analyzed using snRNAseq on the 10x Genomics platform.

first: Katie

last: Emberley

first: Gregory

last: Duncan

first: Jonathan

last: Nelson


title: Comparative transcriptome analysis between hybrid and inbred lines provides molecular insights into vein ratio of leaf in Nicotiana tabacum L.

city: Guiyang

first: Renxiang

last: Liu

state: Guizhou

address: Huaxi

institute: Guizhou University

summary: Heterosis has greatly improved the yield and quality of crops. However, previous studies often focused on improving the yield and quality of the shoot system, while research on the root system was neglected. We determined the root numbers of 12 F1 hybrids, all of which showed strong heterosis, indicating that tobacco F1 hybrids have general heterosis. To understand its molecular mechanism, we selected two hybrids with strong heterosis, GJ (G70 × Jiucaiping No.2) and KJ (K326 × Jiucaiping No.2), and their parents for transcriptome analysis. There were 84.22% and 90.25% of the differentially expressed genes were overdominantly expressed. The enrichment analysis of these overdominantly expressed genes showed that "Plant hormone signal transduction", "Phenylpropanoid biosynthesis", "MAPK signaling pathway - plant", and "Starch and sucrose metabolism" pathways were associated with root development. We focused on the analysis of the biosynthetic pathways of auxin(AUX), cytokinins(CTK), abscisic acid(ABA), ethylene(ET), and salicylic acid(SA), suggesting that overdominant expression of these hormone signaling pathway genes may enhance root development in hybrids.

overall_design: 9 samples were analyzed, including 3 plant materials, each with three replicates.

first: Lili

last: Duan


title: Single nuclei RNA sequencing of murine skin in the uninjured state and 1-day post wounding

city: Washington

first: Brett

last: Shook

state: DC

address: 2300 I St NW

department: Biochemistry & Molecular Medicine

institute: George Washington University

summary: The injury response in the skin is highly complex and involves input from multiple cell types. Single nuclei RNA sequencing was performed to broadly characterize changes in gene expression from all skin cell types early after injury compared to the unwounded state.

overall_design: C57BL/6 mice were used to generate all samples. Unwounded back skin was harvested from two mice for unwounded samples 1 and 2. Full-thickness excisional wounds were made on the back skin of two mice and harvested 1-day post-wound (1dpw) for wounded samples 1 and 2. Nuclei from wound samples and uninjured back skin were isolated with mortar and pestle. Single nuclei library preparations from each sample were generated using 10X Genomics preparation kits.

first: Veronica

last: Amuso

first: Paula

last: Cooper

first: Anelia

last: Horvath


title: RNA-sequencing reveals predominance of THRA splicing isoform 2 in developing human brain

first: Markus

last: Schuelke

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

overall_design: Refer to individual Series


title: Effect of Zbtb24-depletion on gene expressions during the activation of peritoneal B1 cells

city: 苏州

first: He

last: Gao

address: 苏州市工业园区仁爱路199号

institute: Soochow University

summary: ZBTB24-null ICF2 patients suffer from recurrent infections associated with antibody defects, implying a pivitol role of ZBTB24 in B cell biology. We thus generated B-cell specific Zbtb24 knockout mice and investigated its intrinsic role in B cell development and function both in vitro and in vivo. In accordance with findings obtained in ICF2 patients, Zbtb24 is dispensable for B cell developent and maintenance in mice. Strikingly, lack of Zbtb24 does not significantly compromise the primary & secondary antibody responses against TD-Ags, but reduced TID-Ags-elicited antibodies in vivo. At the cellular level, we discovered that Zbtb24-depletion specifically impaires the plasma cell (PC) differentiation of B1, but not the conventional B2 cells comprising follicular and marginal zone B cells, without impacting their survival and proliferation. Mechanistically, ablation of Zbtb24 suppresses the biosynthesis o heme in B1 cells, and supplementation of hemin largely abrogates the differentiation defects of zbtb24-null B1 cells in vitro. Our study not only provides a plausible explanation for the recurrent respiratory and gastrointestinal infections in ICF2 patients, but is also relevant for other B1 cell-mediated barrier defenses and immune regulations.

overall_design: We generated B-cell specific knockout mice, and compared their antibody responses in vitro and in vivo.  We purified total peritoneal CD19+CD23- B1 cells and activated them in vitro by 0.1 ug/ml LPS before RNA-Seq analysis.

first: Jun

last: Wang

first: Sai

last: Zhao

first: Xiao-Qiu

last: Dai

first: Xiao-Yuan

last: Qin

first: Xiao-Ming

first: Ying


title: Clonal landscape of autoantibody-secreting plasmablasts in COVID-19 patients

city: Suita

first: Daisuke

last: Motooka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

summary: Although severe COVID-19 is often associated with elevated autoantibody titers, the underlying mechanism has been unclear. Here, we investigated repertoires and reactivities of immunoglobulins derived from blood plasmablasts (PBs) in COVID-19 patients. This uncovered robust clonal expansion of PBs secreting cardiolipin (CL)-reactive autoantibodies in humoral response to SARS-CoV-2. About half of the expanded CL-reactive clones were also reactive to SARS-CoV-2 antigens and derived from SARS-CoV-2-specific primary responses as well as seasonal coronavirus-reactive memory responses. One such clone, CoV1804, was reactive to both CL and viral nucleocapsid (N), and exhibited anti-nucleolar activity in human cells. Repertoire analysis identified antibodies sharing genetic features with CoV1804 in COVID-19 patient-derived immunoglobulins from our and other cohorts, thereby constituting a novel public antibody. These public autoantibodies had numerous mutations that enhanced anti-N reactivity. On the other hand, anti-CL reactivity fluctuated through somatic hypermutation, which instead resulted in the acquisition of additional self-reactivities, including anti-nucleolar activity in the progeny. Thus, potentially CL-reactive precursors may have developed multiple reactivities to different self-antigens through clonal expansion driven by viral antigens. Our results unraveled a unique process of autoantibody production during COVID-19 and provide novel insights into the origin of virus-induced autoantibodies.

overall_design: PBMCs from patients who were vaccinated COVID-19 vaccine were analyzed by scRNA-seq

first: Shuhei

last: Sakakibara

first: Yu-Chen

first: Masakazu

last: Ishikawa

first: Soichiro

last: Haruna

first: Marwa

last: Hussien

first: Zichang

last: Xu

first: Songling

last: Li

first: Fuminori

last: Sugihara

first: Yuko

last: Naito

first: Chao-Yuan

last: Tsai

first: Yuta

last: Yamaguchi

first: Teruaki

last: Murakami

first: Ryuya

last: Edahiro

first: Yuya

last: Shirai

first: Takayoshi

last: Morita

first: Yasuhito

last: Kato

first: Haruhiko

last: Hirata

first: Yoshito

last: Takeda

first: Chikako

last: Ono

first: Yoshiharu

last: Matsuura

first: James

middle: B

last: Wing

first: Hisatake

last: Matsumoto

first: Hisashi

last: Ogura

first: Atsushi

last: Kumanogoh

first: Yukinari

last: Okada

first: Daron

last: Standley

first: Hitoshi

last: Kikutani

last: Okuzaki


title: Immunological landscape of human lymphoid explants during measles virus infection [BulkSeq]

status: Public on Sep 10 2024

city: New York

first: Jean

last: Lim

address: 1468 Madison Ave

department: Microbiology

institute: Icahn School of Medicine at Mount Sinai

summary: In humans, lymph nodes are the primary site of measles virus (MeV) replication. To understand the immunological events that occur at this site, we infected human lymphoid tissue explants using a pathogenic strain of MeV that expresses GFP. We found that MeV infected between 5-15% of cells across donors. Using single cell RNA-Seq (scRNA-Seq) and flow cytometry, we found that while most of the 29 cell populations identified in the lymphoid culture were susceptible to MeV, there was a broad preferential infection of B cells and reduced infection of T cells.  Further subsetting of T cells revealed that this reduction may be driven by the decreased infection of naïve T cells. Transcriptional changes in infected B cells were dominated by an interferon stimulated gene (ISG) signature. To determine which of these ISGs were most substantial, we evaluated the proteome of MeV-infected Raji cells by mass spectrometry. We found that IFIT1, IFIT2, IFIT3, ISG15, CXCL10, MX2, and XAF1 proteins were the most highly induced, and positively correlated with their expression in the transcriptome. These data provide insight into the immunological events that occur in lymph nodes during infection and may lead to the development of therapeutic interventions.

overall_design: RAJI cells were infected with a fluorescent measles virus (IC323-eGFP) at an MOI = 0.01 for 3 days, before collection into TriZol. RNA was isolated using the DirectZol RNA mimiprep kit, and library preparation, QC and RNA sequencing was conducted by Azenta. The RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (New England Biolabs, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94°C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

first: Joshua

last: Acklin

first: Aum

last: Patel

middle: K


title: Beyond Basic Characterization and Omics: Immunomodulatory Roles of Platelet-Derived Extracellular Vesicles Unveiled by Functional Testing

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

institute: CIC bioGUNE

type: Non-coding RNA profiling by high throughput sequencing

summary: The proteome of anuclear platelets comprises >5000 proteins and is impacted e.g. by age and disease. The platelet secretome of over 300 proteins contains e.g. growth factors and immunomodulatory proteins and therefore, platelet products, such as platelet rich plasma are used in regenerative medicine. Platelets also release extracellular vesicles (EVs), both constitutively and upon activation. We studied 1) the tunability of platelet EVs by agonists engaging different critical platelet signaling pathways, 2) the characteristics of these EVs, and 3) macrophage responses to these EVs. Upon activating platelets, agonists have distinct impacts on the characteristics of secreted EVs, their protein and miRNA contents and functionality. These results imply that by differential activation it is possible to create tunable EVs e.g. for immunomodulatory purposes.

sample_organism:
Homo sapiens
other sequences

platform_organism:
Homo sapiens
other sequences

overall_design: The goal of this study was to compare the small RNA content of platelet derived EVs (PEVS) derived from differentially activated, or non-activated platelets, as well as platelets itself. We found that different activation routes affect the small RNA cargo of PEVS suggesting that these PEVS may have diverse impact on recipient cells.

first: Mari

last: Palviainen

first: Pia

last: Siljander

first: Juan

last: Lozano

last: Falcón-Pérez


title: Isoform-level Transcriptome Analysis of Peripheral Blood Mononuclear Cells from Breast Cancer Patients Identifies a Disease-associated RASGEF1A isoform

city: Maribor

first: Mario

middle: Smode

last: Gorenjak

address: Taborska ulica 8

country: Slovenia

institute: Faculty of Medicine, University of Maribor

summary:
Breast cancer (BC) comprises multiple subtypes with distinct molecular features, which differ in their interplay with host immunity, prognosis, and treatment. The triple-negative and HER2(+) subtypes are generally more immunogenic and associated with better immunotherapy responsiveness than the luminal subtypes. Non-invasive blood analyses can provide valuable insights into systemic immunity during cancer. The aim of this study was to analyze the expression of transcriptional isoforms in peripheral blood mononuclear cells (PBMCs) from BC patients and healthy women to identify potential BC immune biomarkers. RNA-sequencing and isoform-level bioinformatics were performed on PBMCs from 13 triple-negative and 13 luminal A patients. Isoform expression validation by qRT-PCR and clinicopathological correlations were performed in a larger cohort (156 BC patients and 32 healthy women).
Transcriptional analyses showed a significant (p<.001) decrease of the ENST00000374459 RASGEF1A isoform in PBMCs of BC compared to healthy subjects, indi-cating disease-related expression changes. The decrease was associated with higher ctDNA and Ki-67 values.
The levels of the RASGEF1A transcriptional isoform ENST00000374459 may have the potential to distinguish between BC and healthy subjects. The downregulation of ENST00000374459 in breast cancer is associated with higher proliferation and ctDNA shedding. Specialized bioinformatics analyses such as isoform analyses hold significant promise in the detection of biomarkers, since variant-indiscriminate (standard) RNA sequencing analyses may overlook specific transcriptional changes that may be disease-associated and biologically important.

overall_design: In this work, we employed transcriptional analyses to identify differences in mRNA-isoform expression in peripheral blood mononuclear cells (PBMCs) isolated from BC patients and healthy subjects. To identify isoform differences between two immunologically distinct subtypes, the more immunogenic triple-negative and the less immunogenic luminal A, RNA-seq was employed, representing the first isoform-level transcriptome analysis in peripheral blood of BC patients.

first: Helena

last: Čelešnik

first: Monika

last: Sobočan

first: Iztok

last: Takač

first: Uroš

last: Potočnik


title: SURF2 is a MDM2 antagonist in triggering the nucleolar stress response

city: PARIS

first: Simon

last: Lebaron

address: 4 avenue de l'observatoire

institute: Université Paris Descartes

summary: Cancer cells are addicted to strong ribosome production to sustain their proliferation rate. Many chemotherapies impede ribosome production which is perceived by cells as "nucleolar stress" (NS), triggering p53-dependent and independent response pathways leading to cell cycle arrest and/or apoptosis. The 5S RNP particle, a sub-ribosomal particle, is instrumental to NS response. Upon ribosome assembly defects, the 5S RNP accumulate as free form. This free form is able to sequester and inhibit MDM2, thus promoting p53 stabilization. To investigate how cancer cells can resist to NS, we purified free-5S RNP and uncovered a new interaction partner, SURF2. Functional characterization of SURF2 shows that its depletion increases cellular sensitivity to NS, while its overexpression promotes their resistance to it. Consistently, SURF2 expression level negatively correlates with the overall survival in adrenocortical and head and neck squamous cell carcinomas. Our data demonstrate that SURF2 buffers free-5S RNP particles, and can modulate their activity. SURF2 regulates NS responses, and is a key player in both ribosomopathies and oncogenic mechanisms.

overall_design: here we investigated the effect of SURF2 depletion (siSURF2) in U2OS cells compared to control (siSCR). Cells where treated twice with siRNAs at 48H inteval and after 96 hours cells were pelleted and RNA extracted using Trizol extraxtion method. 3 biological replicates were compared (siSCR-1, sSCR-2, siSCR-3 vs siSURF2-1, siSURF2-2 and siSURF2-3).We then performed gene expression differential analysis using RNAseq approach (performed by Genewiz).

first: Sophie

last: Tagnères


title: Effect of Zbtb24-depletion on gene expressions during the activation of total splenic B cells

first: He

last: Gao

address: 苏州市工业园区仁爱路199号

overall_design: We generated B-cell specific knockout mice, and compared their antibody responses in vitro and in vivo.  We purified total splenic B cells and activated them in vitro by LPS before RNA-Seq analysis.

first: Jun

last: Wang

first: Sai

last: Zhao

first: Xiao-Qiu

last: Dai

first: Xiao-Yuan

last: Qin

first: Xiao-Ming

first: Ying


title: Immunological landscape of human lymphoid explants during measles virus infection [scRNA-seq]

first: Jean

last: Lim

overall_design: Human tonsilar explants were infected with measles virus (IC323-eGFP). After 8 days of infection, tissues were homogenized with collagenase and single cell suspensions were generated. Infected (GFP+), Bystander (GFP- from infected explants) and donor matched uninfected cells (GFP- from uninfected explants) were isolated by FACS, and analyzed by single cell RNA sequencing. This study included one tonsil donor for analysis.

first: Joshua

last: Acklin

first: Aum

middle: R

last: Patel


title: Transcriptome analysis of response to exogenous trehalose and abiotic stress in grapes

city: Xinxiang

first: Ling

address: Eastern HuaLan Avenue, Xinxiang City , Henan Province , China

institute: Henan Institute of Science and Technology

summary: Grapevine is an important economic fruit tree, and European grape (Vitis vinifera L.) has been widely used in fresh food, drying, winemaking and grape seed extract. However, most European grapes have low resistance to low temperature, drought and salt stress, and these abiotic stresses will limit the growth and development of grapes, thereby affecting the grape quality and yield. Many reports have shown that exogenous or endogenous trehalose can help improve plant stress resistance. Therefore, in order to investigate the function and molecular mechanism of trehalose metabolism in grape response to stress, this project was conducted.

overall_design: Collect grape leaves from the control group, trehalose, different stresses (low temperature (4 ℃), PEG6000, NaCl), and trehalose+different stress treatments for 48 hours, and perform RNA Seq analysis. The control group and the treatment group each contain three biological replicates. 8 samples examined:  CK, 4C, NaCl，PEG6000，Tre，Tre-4C，Tre-NaCl，Tre-PEG6000.


city: Jerusalem

first: Yotam

last: Drier

state: Israel

address: Faculty of Medicine, The Hebrew University, Ein Kerem

department: Immunology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem

summary: Well-differentiated low-grade lung neuroendocrine tumors (lung carcinoids or LNETs) are histopathologically classified as typical and atypical LNETs, but each subtype is still heterogeneous at both the molecular level and its clinical manifestation. Here, we report the first genome-wide profiles of primary LNETs’ cis-regulatory elements by H3K27ac ChIP-seq with matching RNA-seq profiles. Analysis of these regulatory landscapes revealed three regulatory subtypes, independent of the typical/atypical classification. We identified unique differentiation signals that delineate each subtype. The “proneuronal” subtype emerges under the influence of ASCL1, SOX4 and TCF4 transcription factors, embodying a pronounced proneuronal signature. The “luminal-like” subtype is characterized by gain of acetylation at markers of luminal cells and GATA2 activation, and loss of LRP5 and OTP. The “HNF+” subtype is characterized by a robust enhancer landscape driven by HNF1A, HNF4A, and FOXA3, with notable acetylation and expression of FGF signaling genes, especially FGFR3 and FGFR4, pivotal components of the FGF pathway. Our findings not only deepen the understanding of LNETs' regulatory and developmental diversity but also spotlight the HNF+ subtype's reliance on FGFR signaling. We demonstrate that targeting this pathway with FGF inhibitors curtails tumor growth both in vitro and in xenograft models, unveiling a potential vulnerability and paving the way for targeted therapies. Overall, our work provides an important resource for studying LNETs to reveal regulatory networks, differentiation signals and therapeutically relevant dependences.

overall_design:
H3K27ac ChIP-seq and RNA-seq of lung neuroendocrine tumors, NCI-H727, NCI-H835 and NCI-H1770 cell lines, and an NCI-H727 xenograft, and RNA-seq after treatment of cell lines with A51.
UCSC genome browser session of the data can be accessed at: https://genome.ucsc.edu/s/yotamd/lung_NET
NOTE FROM SUBMITTER: RAW files are being deposited to the EGA

first: Simona

last: Grozinsky-Glasberg


title: Increased Autoreactivity and Maturity in EBI2+ Antibody-Secreting Cells from Nasal Polyps

city: Chicago

first: Matthew

middle: J.

last: Schipma

state: IL

address: 750 N. Lake Shore Drive

department: Biochemistry and Molecular Genetics

institute: Northwestern University

summary: Rationale: Elevated numbers of antibody secreting cells (ASCs) and anti-dsDNA antibodies are found in nasal polyp (NP) tissue. Tissue anti-dsDNA IgG prospectively predicts recurrent NP, but the characteristics of the source ASCs are unknown.     Objectives: To investigate whether NP B cells expressing the extrafollicular marker EBI2 have increased propensity for autoantibody production and to evaluate the molecular characteristics of NP ASCs.  Findings: NPs (n=8) showed increased frequencies of anti-dsDNA IgG and total IgG ASCs (34- and 9-fold, respectively, both p<0.0001) compared to tonsils (n=10), with more pronounced differences among EBI2+ cells. In NPs, EBI2+ cells were frequently double-negative (IgD-CD27-) and ASCs (36.3% and 19.5%, respectively). ScRNA-seq analysis of tonsils and NPs (both n=5) revealed substantial differences in B lineage composition: ASCs (1.2% vs 44.1%), germinal center (23.1% vs 0.2%), proliferative (12.6% vs 3.0%), and non-ASCs (63.1% vs 52.7%), respectively. NPs exhibited higher expression (>2-fold) of specific isotypes (IGHE, IGHA1, IGHA2, and IGHG4), and mature plasma genes including SDC1 and XBP1 than tonsils. GO biological processes indicated upregulated NF-κB and downregulated apoptosis pathways in NP ASCs.   Conclusions: NP EBI2+ ASCs secreted increased total and anti-dsDNA IgG compared to those from tonsils and had molecular features of mature plasma cell differentiation.

overall_design: Nasal polyp (NP) and control tonsil tissues were obtained from 5 CRSwNP patients and 5 tonsilllar patients accordingly during surgery.

first: Junqin

last: Bai

first: Atsushi

last: Kato

last: Wechsler

first: Robert

middle: P

last: Schleimer

first: Bruce

last: Tan


title: Identification of acidic extracellular pH-modulated genes

status: Public on Sep 09 2024

city: Koriyama

first: Yasumasa

state: Fukushima

address: 31-1 Misumido, Tomitamachi

department: Department of Oral Function and Molecular Biology

institute: Ohu University School of Dentistry

summary: To investigate the genes that are modulated by acidic extracellular pH, we treated the mouse B16-BL6 cells with acidic medium and then analyzed them comprehensively by cDNA microarray.

overall_design: Serum starved (overnight) cells were further incubated with serum-free growth medium at pH 7.4, 6.8, and 5.9 for 24 h. Total RNA was extracted and analyzed by Whole Mouse Genome Microarray 4x44K.