title: Impact of thermal treatment, pulsed electric fields, and high-pressure processing on the transcriptome of Escherichia coli ATCC 8739

status: Public on Dec 03 2024

city: Hamburg

first: Astrid

last: Gedas

address: Ohnhorststrasse 18

department: Department of Chemistry

institute: Universität Hamburg

summary: Red fruits are valued for their vitamin C and polyphenol content, but traditional heat preservation methods used in juice and nectar production can significantly reduce these components. Therefore, alternative non-thermal methods are explored to inactivate foodborne pathogens like Escherichia coli while maintaining the nutritional value. However, knowledge about the effects of these technologies on bacterial cells is limited. This study analyzed differentially expressed genes of E. coli ATCC 8739 inoculated in strawberry nectar after exposure to three treatments with two sets of parameters each, namely thermal treatment, high-pressure processing (HPP), and moderate-intensity pulsed electric field (MIPEF). The highest inactivation efficiency was achieved with HPP at 400 MPa, 1 min, reducing microbial counts by 5.0±0.3 log cfu/mL, and thermal treatment at 60°C, 200 s, achieving a reduction of 4.4±0.2 log cfu/mL, while no inactivation was observed with MIPEF at 6 kV/cm. Transcriptomic analysis showed that thermal and HPP treatments caused similar molecular stress responses in E. coli. In both cases, the most overexpressed genes encoded outer membrane proteins, which may lead to the activation of the envelope stress response. Despite no microbial inactivation was revealed after MIPEF treatment, strong transcriptomic responses were observed, particularly in genes related to membrane integrity and metabolic activity. Numerous overexpressed genes associated with ABC transporters, outer membrane proteins, and lipoproteins were identified, which could increase the strain’s virulence. This study provides insights into the stress response mechanisms induced by conventional and novel treatments. Nevertheless, further research is needed to investigate the long-term effects on bacterial populations.

overall_design: RNA-seq profiling of E. coli ATCC 8739 inoculated in strawberry nectar after exposure to six different treatments, including thermal treatment, high pressure processing, and pulsed electric field (3 replicates)

first: Gędas

last: Astrid

first: Levante

last: Alessia

first: Cattani

last: Luca

first: Bottari

last: Benedetta

first: Weiss

last: Agnes


title: AAV-CYP46A1 gene therapy  in mouse models of Huntington’s disease

status: Public on Dec 31 2024

city: paris

first: farah

last: CHALI

address: 47 Boulevard de l’Hôpital  75013 Paris, FRANCE

country: France

institute: AskBio

type: Expression profiling by high throughput sequencing

summary: To evaluate the effect of CYP46A1 treatment in R6/2 mice, we performed gene expression profiling analysis using data obtained from RNA-seq of 6 different conditions

overall_design: To evaluate the effect of CYP46A1 treatment in HD mice Vs control mice, 27 samples were analyzed (n= 4 or 5 per groups)

first: Farah

first: Justine

last: GUEGAN

first: Louis

last: PARSAI

first: Sandro

last: ALVES

first: Nathalie

last: CARTIER


title: Proteogenomics Study of Lung Cancer

status: Public on Dec 02 2024

city: Houston

first: Sung Wook

last: Kang

state: TX

address: one plaza

department: Surgery

country: USA

institute: Baylor college of medicine

summary: Lung cancer remains the leading cause of cancer-related mortality worldwide, with limited treatment options for advanced stages. This proteogenomics study aims to integrate multi-omics approaches, including proteomics, genomics, and transcriptomics, to elucidate the molecular mechanisms underlying lung cancer progression and treatment resistance. By leveraging cutting-edge technologies, this study seeks to identify novel biomarkers and therapeutic targets, enabling personalized medicine strategies to improve patient outcomes. The integration of proteogenomic data will provide a comprehensive understanding of tumor biology, revealing critical pathways and interactions that drive tumorigenesis and immune evasion.

first: Hyun-Sung

last: Lee


title: Vg1+ gd T cells promote DC activation and CD8 T cell expansion via IL-4

status: Public on Dec 07 2024

city: Parkville

first: Jan

last: Schroeder

state: Victoria

address: Peter Doherty Institute Melbourne

department: DMI

country: Australia

institute: University of Melbourne

summary: Classically, dendritic cells (DC) capture pathogen material and upon activation by pathogen products (or damage), initiate adaptive immunity. Here, we describe an additional layer to this process, required when the pathogen-derived signals themselves do not provide effective DC activation.  Immunisation with sporozoites from Plasmodium leads to the generation of protective anti-malarial immunity mediated by liver resident memory T (TRM) cells, in a complex response that is crucially dependent upon gd T cells.  Here, we show that CD40L signals to antigen-presenting DC are CD4 T cell derived, but Vg1 gd T cells play an initiating role by providing essential IL-4 signals to DC. IL-4 acts together with IFNg to induce IL-12 and promote CD8 T cell expansion. This study shows that responses to some pathogens, such as Plasmodium, require help from innate-like T cells to pass the initiation threshold, and demonstrates the critical role of IL-4 in this process.

overall_design: Dendritic cells were isolated from spleens of B16.Flt3L tumour-bearing mice. Briefly, spleens were finely minced in 1mg/ml Collagenase Type 3, 20 µg/ml DNase I and continuously agitated for 15 minutes. DC-T cell complexes were disrupted with the addition of 0.1M EDTA (pH7.2). Undigested fragments were removed by filtering through a 70 µM mesh before light-density separation with 1.077g/cm3 Nycodenz medium via centrifugation at 1700rpm at 4°C for 12min. To increase the purity of cDC1 precursors, the light density fraction was collected, and cDC1s/pre-cDC1s were negatively enriched for through incubation with rat mAb against CD3ε (KT3), Thy1.1 (T24/31.7), Gr-1 (RB6-8C5), B220 (RA3-6B2), Ter-119 and CD11b (M1/70) prior to incubation with BioMag goat anti-rat IgG coupled magnetic beads (Qiagen) and magnetic separation. Target cells were characterised as CD11c+, MHC-IIint/+, CD11b−, CD24hi, CD8a+ with purities from 60-80%. CD11c+, MHC-IIint/+, CD11b−, CD24hi, B220−, CD172− cells were then sorted using a BD FACSAriaTM III Cell Sorter into filtered RPMI supplemented with 50% heat-inactivated FCS and pelleted. In a 24-well plate, 5 x 105 cells were plated in complete Kenneth D Shortman RPMI (KDS-RPMI 1640, 10% FCS, 2mM L-glutamine, 100 U/ml penicillin, 100 mg/ml streptomycin and 50 mM 2-mercaptoethanol). To assess cDC1 gene expression in response to IL-4, cells were incubated in the presence of -CD40 (10g/ml), IL-4 (60ng/mL), IFN- (20ng/mL), or LPS (1g/ml). Plates were then incubated at 37°C and 5% CO2 for 4 hours. For RNA isolation, cells were washed and resuspended using TRIzol (Life Technologies), snap frozen and stored at -80°C.

first: Lynette

last: Beattie


title: Functional analysis of plant translation regulation (on the tomato model) under cold stress

status: Public on Nov 29 2024

city: Moscow

first: Alexander

last: Tyurin

address: Botanicheskaya st., 35, building 1

country: Russia

institute: Timiryazev Institute of Plant Physiology, Russian Academy of Sciences

summary: In the presented study, we analyzed the physiological, biochemical and molecular responses of experimental plants under low temperature conditions. The aim of the study was to investigate the differences in expression profiles in the total transcriptome and in its translated fraction. To more fully cover possible strategies for plant acclimation to cold, we selected the following experimental conditions: control (intact plants), stress, hardening, and a combination of hardening and stress. Since the goal of this work was to study the differences in expression profiles at both the transcription and translation stages, we used separate approaches to obtain these experimental data: for transcription -- sequencing of the total transcriptome, for translation -- sequencing of transcriptome fractions obtained during polysome profiling and corresponding to the translated mRNAs: monosomes and polysomes. Thus, for 4 experimental conditions and 3 types of mRNA libraries, 12 samples were obtained. Sequencing was performed in duplicate. The obtained data will allow us to evaluate the contribution of transcription and translation separately to the regulation of cold acclimation in tomato plants and, probably, to identify the molecular mechanisms responsible for this.

overall_design:
The experimental design included 4 types of temperature conditions:
- control (intact plants) : Control
- stress : Stress
- hardening : Hardening
- combination of hardening and stress : Combo and 3 different mRNA fractions:
- total transcriptome : total
- polysomes : poly
- monosomes : mono
Total: 12 different samples

middle: A

first: Aleksandra

middle: V

last: Suhorukova


title: Time-series single-cell transcriptomic profiling of luteal-phase endometrium uncovers dynamic characteristics and its dysregulation in recurrent implantation failures

status: Public on Nov 18 2024

city: Shenzhen

first: zhu

last: kongfu

address: NanShan

country: China

institute: The Hong Kong University - Shenzhen Hospital

summary: Understanding human endometrial dynamics remains a challenge, limiting early diagnosis and treatment of reproductive disorders. Here, we decoded the normal endometrial dynamics across the window of implantation (WOI) and its deficiency in endometrium from women with recurrent implantation failure (RIF) by analyzing data from over 220,000 cells, together with developing a computational model StemVAE that is capable of both temporal prediction and pattern discovery. Our time-series atlas highlighted a two-stage stromal decidualization process whereas a gradual epithelial transitional process across the WOI allowing the identification of a time-varying gene set regulating epithelial receptivity. The epithelial receptivity genes were able to stratify the RIF endometrium into two classes of receptivity-deficiency involving early and late implantation. Further investigation uncovered epithelial cell dysfunction under hyperinflammatory microenvironment in RIF endometrium. The holistic characterization of physiological and pathophysiological WOI, and a computational tool trained on this temporal atlas provide a platform for future therapeutic developments.

overall_design: To generate a high-resolution cellular map of human endometrium across WOI and to characterize the endometrial cellular profiles affecting embryo implantation, endometrial aspirates from fertile women and women with RIF were collected and subjected to droplet-based scRNA-seq. In total, 28 endometrial biopsies spanning 5 time points designated as LH+3 (Day 3 post-luteinizing hormone surge), LH+5, LH+7, LH+9, LH+11 were included. The time-point LH+7 contains two types of donors including fertile women (n=6), and women with RIF (n=10). The remaining time-points post LH surge contain samples only from fertile women (n=3 for each timepoint). All the recruited women had regular menstrual cycle. Dates of menstrual cycle were relative to LH surge as determined by serial blood tests for LH. The collected endometrial biopsies were enzymatically dispersed and single cells were captured using a 10X Chromium system.

first: Dandan

last: Cao

first: Yuanqing

last: Yao


title: Anterior cingulate cortex mediates the comorbidity between colorectal cancer and depression-like behaviors

status: Public on Nov 20 2024

city: Guangzhou

first: pei

last: xia

state: Guangdong

address: No. 74, Zhongshan 2nd Road, Yuexiu District, Guangzhou City, Guangdong Province

institute: Sun Yat-Sen University

summary: In this study, we established mice with orthotopic colorectal cancer (CRC mice) and observed depression-like behaviors in the CRC mice.    Through whole-brain c-FOS mapping, functional connectivity analysis, gut-brain inverse mapping, and correlation analysis, combined with chemogenetic manipulation, we identified the anterior cingulate cortex (ACC) as a key hub in the depression-related brain network.    we performed whole transcriptome sequencing of key neural nuclei to identify molecular changes associated with CRC-depression comorbidity.    Furthermore, chemogenetic modulation of neuronal excitability not only alleviated depression-like behavior but also reduced CRC progression in these mice.    Importantly, our findings suggest that targeting the ACC, in addition to conventional colorectal cancer therapies, could offer therapeutic and quality-of-life benefits for patients with both CRC and depression.

overall_design: Transcriptomic characteristics of ACC brain regions in mice before and after regulation


title: Chromosome engineering to correct a complex rearrangement on Chromosome 8 reveals the effects of 8p syndrome on gene expression and neural differentiation

status: Public on Nov 15 2024

city: New Haven

first: Jason

last: Sheltzer

state: CT

address: 300 George Street

institute: Yale University

summary: Chromosomal rearrangements on the short arm of chromosome 8 cause 8p syndrome, a rare developmentaldisorder characterized by neurodevelopmental delays, epilepsy, and cardiacabnormalities.While significantprogress has been made in managing the symptoms of 8p syndrome and otherconditionscaused by large-scalechromosomalaneuploidies, no therapeutic approach has yet been demonstrated to target the underlyingdisease-causingchromosome.Here, we establish a two-step approachto eliminate theabnormalcopy ofchromosome 8and restore euploidy in cells derived from an individual with a complex rearrangement ofchromosome 8p.Transcriptomic analysis revealed 361 differentially expressed genes between the proband andthe euploid revertant, highlighting genes both within and outside the 8p region that may contribute to 8psyndrome pathology. Our work demonstrates the feasibilityof using chromosome engineering to correct complexaneuploidies invitro and suggests a potential therapeutic avenue for disorders caused by chromosomalrearrangements.

overall_design:
Application of pharmacologic and CRISPR based strategies to invdupdel(8p) iPS cells to induce chromosome scale changes to generate a euploid derivative, and subsequent phenotypic comparison between original proband and revertant cell line. Processed RNA-seq and low pass WGS data used for analysis is provided for all cell lines

** Submitters state that there are privacy concerns regarding public access to the raw WGS data, therefore WGS raw data is not provided ***

first: Sophia

middle: N

first: Erin

middle: C

last: Banda

first: Lu

last: Qiao

first: Sarah

middle: L

last: Thompson

first: Karan

last: Singh

first: Ryan

last: Hagenson

first: Teresa

last: Davoli

first: Stefan

middle: F

last: Pinter

middle: M


title: Engrafted hPSC-Derived Nitrergic Neurons Improve Gut Dysmotility in Mice

status: Public on Dec 01 2024

city: San Francisco

first: Faranak

last: Fattahi

state: California

department: Cellular and Molecular Pharmacology

institute: University of California San Francisco

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

overall_design: Refer to individual Series


title: Heart tube morphogenesis is regulated by segment-specific gene regulatory networks controlled by MEF2C  [snRNA-Seq]

status: Public on Nov 04 2024

first: Jonathon

last: Muncie-Vasic

state: CA

address: 1650 Owens St

institute: Gladstone Institutes

summary: The transcription factor MEF2C plays a critical role in the development of the linear heart tube, but the specific transcriptional networks controlled by MEF2C remain largely undefined. To address this, we performed combined single-nucleus RNA- and ATAC- sequencing on wild type and MEF2C-null embryos at distinct stages of development. We identified a broadly “posteriorized” cardiac gene signature and chromatin landscape throughout the heart tube in the absence of MEF2C. By integrating our gene expression and chromatin accessibility data in a deep-learning based model, we were able to construct developmental trajectories for each of the outflow tract, ventricular, and inflow tract lineages and determined how each of these segment-specific trajectories were distinctly altered in the MEF2C-null embryos. We computationally identified potential segment-specific MEF2C-dependent enhancers. Using transgenesis in zebrafish embryos, we identified novel MEF2C-dependent enhancers with activity in the developing heart tube from among these candidates. Finally, using inferred gene regulatory networks we discovered a genetic interaction between MEF2C and the atrial nuclear hormone receptor NR2F2, revealing that the MEF2C-null heart malformations are partly driven by a transcriptional network with increased NR2F2 activity. These studies not only provide a rich description of the genomic regulation of early heart tube development, but provide a generalizable framework for using genetic mutants to dissect the transcriptional networks that govern developmental processes.

overall_design: We collected WT and MEF2C KO mouse embryos at E7.75, E8.5, and E9. At each developmental stage we collected two replicate WT and two replicate MEF2C KO embryos. Embryos were processed through the 10x Multiome kit to produce snRNA-seq and snATAC-seq libraries. Each sample in the dataset corresponds to an individual embryo. This dataset contains the snRNA-seq data from that experiment.

first: Benoit

middle: G

last: Bruneau


title: Heart tube morphogenesis is regulated by segment-specific gene regulatory networks controlled by MEF2C

type: Genome binding/occupancy profiling by high throughput sequencing


title: Heart tube morphogenesis is regulated by segment-specific gene regulatory networks controlled by MEF2C [snATAC-seq]

overall_design: We collected WT and MEF2C KO mouse embryos at E7.75, E8.5, and E9. At each developmental stage we collected two replicate WT and two replicate MEF2C KO embryos. Embryos were processed through the 10x Multiome kit to produce snRNA-seq and snATAC-seq libraries. Each sample in the dataset corresponds to an individual embryo. This dataset contains the snATAC-seq data from that experiment.


title: Integration of transcriptional and epigenetic regulation of TFEB reveals dual functional roles in Pan-cancer [RNA-seq]

status: Public on Nov 10 2024

city: Avenida da Universidade Taipa

first: Chen

last: Ming

address: Macau

department: Faculty of Health Sciences

country: Macau

institute: the University of Macau

summary: Transcription factor EB (TFEB) mainly regulates the autophagy-lysosomal pathway, associated with many diseases, including cancer. However, the role of TFEB in pan-cancer has not been investigated systematically. In this study, we comprehensively analyzed TFEB targets under three stresses in Hela cells by cross-validation of RNA-seq and ChIP-seq. 1,712 novel TFEB targets have not been reported in the Gene Set Enrichment Analysis and ChIP Enrichment Analysis databases. We further investigated their distributions and roles among the pan-cancer co-expression networks across 32 cancers constructed by multiscale embedded gene co-expression network analysis (MEGENA) based on the Cancer Genome Atlas (TCGA) cohort. Specifically, TFEB might serve as a hidden player with multifaceted functions in regulating pan-cancer risk factors, e.g., CXCL2, PKMYT1, and BUB1, associated with cell cycle and immunosuppression. TFEB might also regulate protective factors, e.g., CD79A, related to immune promotion in the tumour microenvironment. We further developed a Shiny app website to present the comprehensive regulatory targets of TFEB under various stimuli, intending to support further research on TFEB functions. Summarily, we provided references for the TFEB downstream targets responding to three stresses and the dual roles of TFEB and its targets in pan-cancer, which are promising anticancer targets that warrant further exploration.

overall_design: To investigate  regulatory targets of TFEB under three different stresses , we did RNA sequencing for Hela cells expressing 3×Flag-TFEB without treatment or with treatment of CCCP, sucrose and Torin1. Each group has three replicates. We then performed gene expression profiling analysis using RNA-seq data from the four groups, i.e., Ctrl, CCCP-stimuli, Sucrose-stimuli, and Torin-1 stimuli. By comparing the differential expressed genes between three stimuli groups and the Ctrl group, we identified the potential TFEB regulatory target genes.

first: Jing-Fang

last: Luo

first: Shijia

last: Wang

first: Jiajing

last: Fu

first: Peng

last: Xu

first: Ningyi

last: Shao

first: Jia-Hong

last: Lu


title: Single nuclei sequencing of the nodose ganglia

status: Public on Nov 01 2024

city: Richardson

first: Catherine

last: Thorn

address: 800 W Campbell Rd

department: Neuroscience

institute: The University of Texas at Dallas

summary: The vagus nerves are important carriers of sensory information from the viscera to the brain. Emerging evidence suggests that sensory signaling through the right, but not the left, vagus nerve evokes striatal dopamine release and reinforces appetitive behaviors. However, the extent to which differential gene expression within vagal sensory neurons may underlie this asymmetric reward-related signaling is unknown. Here, we use single-nucleus RNA sequencing, in situ hybridization, and calcium imaging to identify a single cluster of neurons, defined by co-expression of Chrna3 (nicotinic acetylcholine receptor subunit 3) and Cckar (cholecystokinin 1 receptor), that is preferentially expressed in the right nodose ganglia of rats. This neuronal population also expresses several genes implicated in digestive signaling, including Glp1r and Sctr, consistent with a gut-innervating subtype. Our results suggest that right-biased expression of this unique chemosensing vagal cell type may contribute to asymmetric encoding of interoceptive rewards by the vagus nerves.

overall_design: The right and left NG of experimentally naïve, 8-week-old male and female rats were dissected, and single-nuclei RNA sequencing (snRNA-Seq) was performed.

first: Hailey

last: Welch

first: Ishwarya

last: Sankaranarayanan

first: Khadijah

last: Mazhar

first: Theodore

middle: J

last: Price


title: Gene expression of exosomes from human umbilical cord mesenchymal stem cells

city: yantai

first: he

last: yu

address: gaoxin

institute: he

summary: To determine the gene expression of exosomes in human umbilical cord mesenchymal stem cells

overall_design: Three samples of hUMSC-exo, respectively. Three independent experiments were performed.

first: Yanlian

last: Xiong

first: Qianqian

first: Yu

last: He

first: Chengen

last: Liu


title: scnasRNA-seq resolves in vivo single-cell RNA dynamics of immune cells during Salmonella infection [small intestine]

status: Public on Oct 31 2024

city: Beijing

first: Zhen

address: 15 Datun Road, Beijing 100101, China

department: Institute of Biophysics

institute: Chinese Academy of Sciences

summary: The immune response against pathogens involves multiple cell state transitions and complex gene expression changes. Here we established an in vivo single-cell nascent RNA labeling sequencing method (scnasRNA-seq) and applied it to survey time-resolved RNA dynamics during immune response to acute enteric infection with Salmonella. We showed that detection of nascent RNA synthesis reflects more realistic information on cell activation and gene transcription than total RNA level. Interplay of nascent RNA synthesis and RNA degradation together modulate dynamics of total RNA. We found that bone marrow macrophages are first primed at very early stage upon Salmonella infection. In contrast, the innate immune response of macrophages in intestine is limited. Notably, intestinal CD8+ T cells and plasma cells are rapidly and specifically activated at early stage post infection. Intestinal late enterocytes quickly express MHC-I molecules and present Salmonella antigen to CD8+ T cells for their activation, serving as antigen presenting cells for initiation of adaptive immunity. Our findings unveil novel RNA control strategies of immune cells and dynamic time course of immune response activation upon Salmonella infection, challenging the doctrine boundary between innate immunity and adaptive immunity against bacterial infection.

overall_design: To measure newly transcribed RNA in vivo, we administrated mice with S4U through tail vein injection to label nascent RNA. Bone marrow cells and small intestinal cells were collect and perform scRNA-seq.

first: Runyuan

last: Wu

first: Yanxin


title: NR4A1 and NR4A2 orphan nuclear receptors regulate endothelial to hematopoietic transition in mouse hematopoietic stem cell specification

city: Memphis

first: Jasmine

last: Plummer

state: TN

address: 262 Danny Thomas Pl

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

summary: Hematopoietic stem cells (HSCs) sustain life-long hematopoiesis and emerge during mid-gestation from hemogenic endothelial (HE) progenitors via an endothelial to hematopoietic transition (EHT). The full scope of molecular mechanisms governing this process remains unclear. The NR4A subfamily of orphan nuclear receptors act as tumour suppressors in myeloid leukemogenesis and have never been implicated in HSC specification. Here, we report that Nr4a1 and Nr4a2 expression is upregulated in hemogenic endothelium during EHT. Progressive genetic ablation of Nr4a gene dosage results in a gradual decrease in numbers of nascent c-Kit+ hematopoietic progenitors in developing embryos, c-Kit+ cell cluster size in the dorsal aorta, and a block in HSC maturation, revealed by an accumulation of pro-HSCs and pre-HSC-type I cells and decreased numbers of pre-HSC-type II cells. Consistent with these observations, cells isolated from E11.5 Nr4a1-/-; Nr4a2-/- aorta-gonads-mesonephros (AGM) are devoid of in vivo long-term hematopoietic repopulating potential.  Molecularly, employing spatial transcriptomic analysis we determined that the genetic ablation of Nr4a1 and Nr4a2 prevents NOTCH signaling from being downregulated in intra-aortic clusters and thus for pro-HSCs to mature into HSCs. Interestingly, this defect is partially rescued via ex vivo culture of dissected AGMs with SCF, IL3 and FLT3L, which may bypass NOTCH-dependent regulation. Overall, our data reveal a novel role for the NR4A family of orphan nuclear receptors in EHT.

overall_design: CosMxTM technology [CosMxTM Human Universal Cell Characterization RNA Panel (1000-plex) + 50 custom genes; Nanostring, USA] was applied to 2 FF mouse embryo samples: 1 double knockout within 13 sections, 1 wild type within 9 sections .

first: Diana

last: Sa da Bandeira

first: Chris

middle: D

last: Nevitt

first: Felipe

last: Segato Dezem

first: Maycon

last: Marção

first: Yutian

first: Zakiya

last: Kelley

first: Hannah

last: DuBose

first: Ashley

last: Chabot

first: Trent

last: Hall

first: Claire

last: Caprio

first: Victoria

last: Okhomina

first: Guolian

last: Kang

first: Shannon

last: McKinney-Freeman

first: Wilson

middle: K

last: Clements

first: MIGUEL

last: GANUZA


title: The single-molecule accessibility landscape of newly replicated mammalian chromatin

status: Public on Nov 12 2024

city: Los Angeles

first: Marty

last: Yang

address: 615 Charles E Young Dr S

department: Biological Chemistry

institute: University of California, Los Angeles

summary: We present replication-aware single-molecule accessibility mapping (RASAM), a method to nondestructively measure replication status and protein-DNA interactions on chromatin genome-wide. Using RASAM, we uncover a genome-wide state of single-molecule "hyperaccessibility" post-replication that resolves over several hours. Combining RASAM with cellular models for rapid protein degradation, we demonstrate that histone chaperone CAF-1 reduces nascent chromatin accessibility by filling single-molecular "gaps" and generating closely spaced dinucleosomes on replicated DNA. At cis-regulatory elements, we observe unique modes by which nascent chromatin hyperaccessibility resolves: at CCCTC-binding factor (CTCF)-binding sites, CTCF and nucleosomes compete, reducing CTCF occupancy and motif accessibility post-replication; at active transcription start sites, high chromatin accessibility is maintained, implying rapid re-establishment of nucleosome-free regions. Our study introduces a new paradigm for studying replicated chromatin fiber organization. More broadly, we uncover a unique organization of newly replicated chromatin that must be reset by active processes, providing a substrate for epigenetic reprogramming.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single-molecule methyltransferase footprinting of protein-DNA contacts from nascent chromatin fibers in BrdU-treated mESCs and K562 cells with third-generation PacBio sequencing.

first: Megan

last: Ostrowski

first: Vijay

last: Ramani


title: scRNAseq and CITEseq of aged HSPCs derived from FlkSwitch mouse model

status: Public on Oct 29 2024

city: Santa Cruz

first: Paloma

last: Medina

address: 1156 High St.

institute: University of California Santa Cruz


title: Proliferation and differentiation of intestinal stem cells depends on the zinc finger transcription factor BCL11/Chronophage

status: Public on Oct 28 2024

city: Heidelberg

first: Stefan

last: Peidli

state: BW

address: Meyerhofstraße 1

department: Genome Biology

country: Germany

institute: European Molecular Biology Laboratory

summary: The molecular programs that drive proliferation and differentiation of intestinal stem cells (ISCs) are essential for organismal fitness. Notch signalling regulates the binary fate decision of ISCs, favouring enterocyte commitment when Notch activity is high and enteroendocrine cell (EE) fate when activity is low. However, the gene regulatory mechanisms that underlie this process on an organ scale remain poorly understood. Here, we find that the expression of the C2H2-type zinc-finger transcription factor Chronophage (Cph), homologous to mammalian BCL11, increases specifically along the ISC-to-EE lineage when Notch is inactivated. We show that the expression of Cph is regulated by the Achaete-Scute Complex (AS-C) gene, scute, which directly binds to multiple sites within the Cph locus to promote its expression. Our genetic and single-cell RNA sequencing experiments demonstrate that Cph maintains the ISC and EE populations and is necessary to remodel the transcriptome of progenitor cells with low Notch activity. By identifying and functionally validating Cph target genes, we uncover a novel role for sugar free frosting (sff) in directing proliferative and lineage commitment steps of ISCs. Our findings provide mechanistic insight into how Cph maintains intestinal epithelial homeostasis, and together with our evolutionary analysis of Cph/BCL11, suggests that it may represent a general mechanism used by adult somatic stem cells in other tissues to balance proliferation and differentiation.

overall_design: To gain insights into regulatory targets of Chronophage (Cph) in the intestine we performed NanoDam sequencing of the Drosophila melanogaster intestine under The experiments were preformed in duplicates.

first: Siamak

last: Redhai

first: Nick

last: Hirschmüller

first: Wolfgang

last: Huber

first: Michael

last: Boutros


title: scnasRNA-seq resolves in vivo single-cell RNA dynamics of immune cells during Salmonella infection

status: Public on Oct 17 2024

first: Zhen

last: Xiong

first: Runyuan

last: Wu

first: Yanxin

last: Wang


title: Single-cell nascent transcription reveals sparse genome usage and plasticity [EU_seq]

status: Public on Oct 09 2024

first: Xiaohua

last: Shen

state: Beijing

address: China, Tsinghua university, school of medicine

department: Medical School

institute: Tsinghua University

summary: Understanding cell diversification from a common genome in metazoans requires single-cell transcriptional analysis. We introduce scFLUENT-seq, a single-cell nascent RNA sequencing method using brief 10-minute metabolic labeling to capture genome-wide transcription. Surprisingly, individual cellsfrom splenic lymphocytes to pluripotent stem cellstranscribe only 0.02~3.1% of the genome, versus >80% in bulk, revealing limited genome engagement and profound cell-type and cell-to-cell heterogeneity. Intergenic transcription, especially from heterochromatin, is pervasive and stochastic. Promoter-associated antisense and genic transcription rarely co-occur in the same cell. Proximal intergenic transcription involves both gene readthrough and independent initiation, while distal intergenic transcription is largely independent of neighboring genes and correlates with increased transcriptional diversity, a hallmark of cellular plasticity. Although global RNA sysnthesis and turnover are coupled in bulk, individual mRNA transcription and decay are poorly coordinated in single cells, suggesting noise-buffering mechanisms. Overall, scFLUENT-seq uncovers complex coding and noncoding transcriptional dynamics that underlie single-cell heterogeneity and state transitions.

overall_design: For 5-ethynyl uridine (EU) labeling, mouse embryonic stem cells (ESCs) were cultured for 10 min with the medium containing 2 mM EU, washed with ice-cold PBS, and then collected by centrifugation after ice-cold trypsin digestion. 106 fixed nuclei of mouse ESCs were prepared for in-situ click and reverse transcription, followed by biotinylated RNA pull-down and RNA library contruction.

first: Shaoqian

last: Ma


title: Single-cell nascent transcription reveals sparse genome usage and plasticity [pro-seq]

overall_design: We used mouse ESCs for precision nuclear run-on (PRO-seq). Nascent RNA in mouse ESCs were labelled with biotin-11-CTP, and enriched by biotin pull-down twice. NGS library was prepared and sequenced for the nascent RNAs.


title: Single-cell nascent transcription reveals sparse genome usage and plasticity [single_cell]

overall_design: For 5-ethynyl uridine (EU) labeling, mouse embryonic stem cells (ESCs) or primary cells were cultured for 10 min with the medium containing 2 mM EU, washed with ice-cold PBS, and then collected by centrifugation after ice-cold trypsin digestion. 20,000 fixed nuclei of mouse ESCs were prepared in PBS solution for uploading to the droplet platform. We used Pol II CTD-AID ESCs with or without IAA addition (1 hour), spleic cells and mouse embryonic fibroblasts isolated from mouse.


title: Analysis of gene expression in Mel Z cells grown on plastic (MP).

status: Public on Oct 08 2024

first: Nickolai

last: Tchurikov

address: 32, Vavilova str.

department: Department of Epigenetic Mechanisms of Gene Expression Regulation

institute: Engelhardt Institute of Molecular Biology

summary: RNA-Seq procedure was used for analysis of expression in melanoma cells. Cells were separately lysed with Trizol reagent (Invitrogen). Total RNA was extracted from cell lysed with Trizol reagent and PureLink RNA Micro Kit (Invitrogen) according to manufacture instruction. RNA quality was checked with  BioAnalyser and  RNA 6000 Nano Kit (Agilent). Poly(A)+ RNA was purified with Dynabeads® mRNA Purification Kit (Ambion). Illumina library was prepared from poly(A)+RNA with NEBNextNEBNext® Ultra™II RNA Library Prep Kit for Illumina® (NEB) according to manual. Sequencing was performed on HiSeq1500 with 50 bp read length. At least 14.8 millions of reads were generated for each sample.

overall_design: Analysis of gene expression in Mel Z cells grown on plastic (MP), Matrigel (MM), and on Matrigel in the presence of inhibitor(MMI).

first: Yuri

last: Kravatsky

first: Amalia

last: Vartanian


title: Effect of p.E475G mutation in the PNPT1 gene on 293T global transcriptome

status: Public on Oct 07 2024

city: Milano

first: Federico

last: Zambelli

address: Via Giovanni Celoria 26

department: Department of Biosciences

country: Italy

institute: University of Milan

summary: We genereted via genome editing 293T cell lines with the heterozygous and homozygous nucleotide substitution c.1424A>G in the PNPT1 gene (namely EK81 and EK81.8, respectively), causing the amino acidic variation p.E475G, and studied their transcriptomes before and after 6 hours of treatment with 1 µM staurosporine to induce apoptosis

overall_design: Comparative RNA expression analysis of RNA-seq data for 293T cells and its derivatives EK81 and EK81.8

first: Federica

last: Briani

first: Roberto

last: Pizzoccheri

first: Giulio

last: Pavesi

first: Tania

last: Camboni


title: Drosophila and Commensal Bacteria Synergistically Compete with Opportunistic Pathogens at Bulk and Single-Cell Resolutions [scRNA-seq]

status: Public on Oct 01 2024

city: Hefe

first: sheng

last: zhang

state: Anhui Province

address: Shushan District

institute: anhui agriculture university

summary: A challenging task to reveal health and disease-associated microbiome signatures is to disentangle regulatory networks of microbes among themselves and with their host. Using the integrated Drosophila-commensal-pathogen model system, we here reported that Drosophila and commensal bacterium L. plantarum cooperated to compete with the opportunistic pathogen S. marcescens. At first, we found that Drosophila larvae and L. plantarum efficiently antagonized S. marcescens in the coexisting niche by suppressing population size and altering metabolism. Drosophila and L. plantarum synergistically enforced the transcriptional reprogramming of S. marcescens, including lipopolysaccharide synthesis, peptidoglycan synthesis, and cationic antimicrobial peptide (CAMP) resistance. More importantly, bacterial single-cell RNA sequencing reveals that larvae and L. plantarum modulated carbon utilization and resistance heterogeneity of S. marcescens. On the other hand, L. plantarum adjusted the transcriptional reprogramming in adaption to the alliance with larvae for colonization resistance to S. marcescen. Altogether, our findings provide amenable insight into the host–microbe–microbe interplays at both bulk and single-cell resolutions, advancing fundamental concepts of interactome and precise manipulation of bacterial communities.

sample_organism:
Serratia marcescens
Lactiplantibacillus plantarum

overall_design: To investigate the antagonistic interactions of S. marcescens and L. plantarum, we constructed six gene expression sequencing libraries.

first: Sheng

last: Zhang

first: Ziguang

first: Anqi

last: Liu

first: Wei


title: Drosophila and Commensal Bacteria Synergistically Compete with Opportunistic Pathogens at Bulk and Single-Cell Resolutions [bulkRNA-seq]

platform_organism:
Serratia marcescens
Lactiplantibacillus plantarum


title: Proximity mediated effects of RNA regulatory proteins (mRNA as a proxisome).

status: Public on Dec 11 2024

city: Chapel Hill

first: Breanne

middle: Marie

last: Hatfield

state: North Carolina

address: 125 South Rd, CB#3290 Kenan Labs

department: Chemistry

institute: UNC - Chapel Hill

summary: Extensive RNA-protein interactions occur during the lifecycle of mRNA. Proteins DCP2, ZFP36L2, and CNOT7, which induce mRNA degradation, are normally targeted to the 5′ cap, 3′ untranslated region (UTR), and 3′ poly(A) tail, respectively. We directed these proteins to unconventional sites spanning the coding and non-coding regions of a reporter mRNA using an MS2 coat proteinRNA hairpin interaction. DCP2 reduced expression only when targeted to the 5′-UTR, as expected. ZFP36L2 reduced expression when targeted to either the 3′-UTR or the 3′ half of the coding sequence, the latter a region outside its cognate site. Strikingly, CNOT7 reduced expression when targeted anywhere in the mRNA, most strongly at both "ends" of the RNA, in the 3′- and 5′-UTRs. Induction of mRNA degradation by CNOT7 when bound far from the the poly(A) tail supports a model in which global folding juxtaposes many mRNA regions, creating a functional proxisome.

overall_design: To determine the RNA structure of exogenous mRNAs (expressed from a plasmid) encoding NanoLuc and containing a single MS2 stem-loop (C varient) HEK293 cells were chemically probed with dimethyl sulfate (DMS) and exogenous RNAs were subjected to mutational profiling. The resulting DNA libraries were sequenced and analyzed for DMS-MaP experiments.

first: Chase

last: Weidmann

first: Christina

last: McCutchin

first: Patrick

middle: S

last: Irving

first: Kevin

last: Weeks


title: Drosophila and Commensal Bacteria Synergistically Compete with Opportunistic Pathogens at Bulk and Single-Cell Resolutions

overall_design: Refer to individual Series


title: A human organoid drug screen identifies α2-adrenergic receptor signaling as a therapeutic target for cartilage regeneration [scRNA-seq]

status: Public on Sep 30 2024

first: zhijie

last: Lin

address: Baiyun Jingxi road

institute: Southern Medical University

summary: Directed differentiation of stem cells toward chondrogenesis in vitro and in situ to regenerate cartilage suffers from off-target differentiation and hypertrophic tendency. Here, we generated a cartilaginous organoid system from human expanded pluripotent stem cells (hEPSCs) carrying a COL2A1mCherry and COL10A1eGFP double reporter, enabling real-time monitoring of chondrogenesis and hypertrophy. After screening 2,040 FDA-approved drugs, we found that α-adrenergic receptor (α-AR) antagonists, especially phentolamine, stimulated chondrogenesis but repressed hypertrophy, while α2-AR agonists reduced chondrogenesis and induced hypertrophy. Phentolamine prevented cartilage degeneration in hEPSC cartilaginous organoid and human cartilage explant models and stimulated microfracture-activated endogenous skeletal stem cells toward hyaline-like cartilage regeneration without fibrotic degeneration in situ. Mechanistically, α2-AR signaling induced hypertrophic degeneration via cyclic guanosine monophosphate (cGMP)-dependent secretory leukocyte protease inhibitor (SLPI) production. SLPI-deleted cartilaginous organoid was degeneration resistant, facilitating large cartilage defect healing. Ultimately, targeting α2-AR/SLPI was a promising and clinically feasible strategy to regenerate cartilage via promoting chondrogenesis and repressing hypertrophy.

overall_design: Day 28 hEPSC derived-cartilaginous pellets were treated with hypertrophic induction medium containing 1 μM PM in compared with vehicle. After 14 days of incubation, the D42 pellets with or without PM treatment were digested and analyzed using scRNA-seq.

first: Xiaochun

last: Bai


title: The RNA binding protein HNRNPA2B1 regulates IFNG signaling in macrophages

first: Susan

last: Carpenter

address: Red Hill Rd, Biomedical Sciences

department: MCD

institute: UC Santa Cruz

summary: Heterogeneous nuclear ribonucleoprotein A2B1 (HNRNPA2B1) is a well known RNA binding protein but the mechanisms by which it contributes to innate immune gene regulation is poorly understood. Here we report that HNRNPA2B1 functions in macrophages to regulate IFNG signaling through alternative splicing of the IFNG receptor. Specific deletion of HNRNPA2B1 in macrophages using our newly developed conditional mice crossed to LysMCre resulted in altered cytokine responses in both an endotoxic shock model and following Salmonella infection. Interestingly, while HNRNPA2B1 can function as a viability gene, we observed increased macrophage and neutrophil numbers in the KO mice following LPS induced endotoxic shock.  HNRNPA2B1 KO mice were more susceptible to Salmonella and Mycobacterium Tuberculosis infections and failed to effectively clear the pathogens. Mechanistically, loss of HNRNPA2B1 resulted in an increase in No-GO transcripts of the IFNG receptor (Ifngr) leading to lower expression of the receptor at the cell surface impacting the downstream IFNG signaling cascade. Collectively, our data highlights an important role for HNRNPA2B1 in regulating IFNG signaling in macrophages.

overall_design: HnrnpA2B1 was knocked out in mouse myeloid lineage cells using a LysM-Cre coupled with a Cre-loxp system with loxp sites flanking exons 2 and 7. Bone marrow derived macrophages from control (loxp/loxp) mice and KO mice were isolated and stimulated with LPS for 0 or 5 hours. Experiments were performed in biological triplicate.

first: Mays

last: Mohammed Salih


title: A human organoid drug screen identifies α2-adrenergic receptor signaling as a therapeutic target for cartilage regeneration


title: Infinium EPIC Array data for desmoid tumors

status: Public on Sep 29 2024

city: Stanford

first: Joanna

last: Przybyl

address: 300 Pasteur Drive

department: Department of Pathology

institute: Stanford University

type: Methylation profiling by genome tiling array

summary: Desmoid tumors are bland fibroblastic tumors with little histologic variation in different regions of the tumor. While desmoid tumors do not metastasize, they have a high rate of local recurrence after complete resection and no reliable predictors of clinical behavior exist. The presence of molecular intra- and inter-tumor heterogeneity has been well established in other, higher grade, sarcomas but little is known about molecular variability within histologically bland lesions. In this study, we sought to examine the extent of intra- and inter-tumoral clonal heterogeneity of desmoid tumors, which may contribute to their pathogenesis and possible relapse.  We performed analysis of DNA methylation, DNA copy number alterations, point mutations and gene expression on 24 specimens from different areas from primary and recurrent desmoid tumors from 3 patients (7-9 specimens per patient).  The studies showed a remarkable heterogeneity of DNA methylation, DNA copy number alterations, point mutations or gene expression in different regions in primary or recurrent tumors in each patient. We discovered the evidence for subclonal alterations in different areas of individual tumors. Among the four types of data, the transcriptomic profiles showed the highest degree of variability within tumors and between different tumors from the same patient. Gene expression signatures associated with favorable and unfavorable outcome were detected in different regions within the same tumor.  This study shows an unexpected degree of intra- and inter-tumor heterogeneity in desmoid tumors. Our analysis indicates that even in this histologically monotonous lesion, molecular analysis of a single tumor biopsy may underestimate the magnitude of molecular alterations. We demonstrate that molecular intra- and inter-tumor heterogeneity is an important consideration in drug development and validation of prognostic and predictive biomarkers for these tumors.

overall_design: Five hundred nanograms of genomic DNA from 20 desmoid tumor specimens was used for genome-wide DNA methylation profiling with the Infinium MethylationEPIC microarrays (Illumina).


title: The Transcriptomic Analysis of Profibrinolytic (PLAUR) and Fibrinolytic Inhibitor (SERPINE1, A2M) Genes in COVID-19 Patients and Its Relationship with D-Dimer Levels

status: Public on Sep 14 2024

city: Padang

first: Ika

middle: Kurnia

last: Febrianti

state: West  Sumatra

address: Perinstis Kemerdekaan No.94, Jati

department: Doctoral Programme of Biomedical

country: Indonesia

institute: Universitas Andalas

summary: There is a statistically significant difference in the expression of the PLAUR and fibrinolytic inhibitor genes (SERPINE1, A2M) in mild and moderate-to-severe cases. There is a relationship between serum D-dimer levels and the expression of the PLAUR and fibrinolytic inhibitor genes (SERPINE1, A2M).

overall_design: The research data was obtained through observational analytical methods, using a cross-sectional method on COVID-19 patients. The samples consisted 25 patients each for the mild and moderate-to-severe COVID-19 groups who were receiving treatment at Dr. M. Djamil General Hospital and BMC Padang Hospital, Indonesia. The inclusion criteria were patients aged ≥18 years with confirmed COVID-19 through RT-PCR testing, exhibiting clinical symptoms ranging from mild asymptomatic to moderate to severe, and willing to participate in this research by signing an informed consent form. The exclusion criteria for the samples included HIV(+) positive patients, those with hemophilia, other immunocompromised conditions, liver cirrhosis, and pregnant individuals.

first: Febrianti

last: Ika Kurnia

first: Putra

last: Andani Eka

first: Raveinal

last: Raveinal

first: Elliyanti

last: Aisyah


title: Stroma reprogramming by FAK synergizes with MAPK inhibition and renders PDAC responsive to cytotoxic- and immuno-therapies II

status: Public on Sep 04 2024

city: Saint Louis

first: David

last: DeNardo

address: 425 South Euclid Ave

institute: Washington University in Saint Louis

summary: Pancreatic ductal adenocarcinoma(PDAC) is a highly lethal malignancy with poor response rate to therapy. An immune suppressive tumor microenvironment (TME) and oncogenic mutations in KRAS have been implicated as drivers of resistance to both conventional and immune therapies.  As such, targeting RAS/MAPK signaling is an attractive strategy. However, in practice, MAPK inhibition has not yet shown clinical efficacy, likely due to rapid acquisition resistance in PDAC cells. Tumor intrinsic mechanisms of resistance to RAS/MAPK have been studied, however, the unique PDAC TME may also be a key driver in resistance. Previous studies have shown that FAK inhibition can reprogram the PDAC TME and delay PDAC progression in animal models. Herein, we found that long-term FAK inhibitor treatment leads to hyperactivation of the MAPK pathway in both genetically engineered mouse models and in post-treatment PDAC tissues from FAK inhibitor clinical trials. Concomitant inhibition of both FAK (VS4718) and RAF/MEK (V6766) signaling dramatically suppressed tumor cell growth, leading to increased survival across multiple PDAC mouse models. The mechanisms of synergy include both changes in tumor-intrinsic signaling and modulation of tumor/stroma interactions that drive MEK resistance. In the TME, we found that cancer associated fibroblasts (CAFs) can impair the downregulation of cMyc by MEK inhibition in PDAC cells. This results in de-novo resistance to MEK inhibition in fibrotic conditions. By contrast, FAK inhibitors reprogram CAFs to suppress the production of key growth factors, including FGF1, that drives resistance to RAF/MEK inhibition. While combined FAK and RAF/MEK inhibition only leads to disease stasis, the addition of chemotherapy to the combination led to tumor regression and improved long-term survival in PDAC mouse models. Analysis of tumor immunity showed that the combination of FAK and MEK inhibition improved anti-tumor immunity and improved priming of T cell responses, which was further improved with the addition of chemotherapy. These findings led to testing of FAK (Defactinib) plus RAF/MEK (Avutometinib) inhibition in combination with gemcitabine and nab-paclitaxel in advanced pancreatic cancer patients (NCT05669482). Finally, we tested if the addition of immunotherapy could enhance the efficacy of the FAKi/MEKi/chemotherapy and found adding in either PD1 or CTLA4/PD1 blockade led to long term disease control in PDAC animal models.  Together, these studies identified novel FAK inhibition as a route to overcome both tumor intrinsic and stromal-derived resistance to MAPK inhibition and showed that this combination can be exploited to increase the efficacy of cytotoxic and immunotherapy approaches.

overall_design: Total RNA  from KP2 (p48-Cre;LSL-KrasG12D;Trp53flox/flox) organoids treated by Vehicle, FAKi, MEKi, FAKi+MEKi, Gemcitabine and Gemcitabine+FAKi+MEKi for 24 hours and analyzed

first: Xiuting


title: PolySUMOylation of PCNA and Rad52 restricts centromeric recombination in fission yeast

status: Public on Sep 15 2024

city: Wroclaw

first: Karol

last: Kramarz

address: Kanonia 6/8

department: Faculty of Biological Sciences

country: Poland

institute: University of Wrocław

summary: SUMOylation, a conserved post-translational modification in eukaryotes, regulates protein function, localization, and stability. However, the role of SUMO chains in genome maintenance is still emerging. Using Schizosaccharomyces pombe, we show that loss of SUMO chains results in spontaneous replication stress, DNA damage, and elevated centromeric recombination. To investigate SUMO-dependent interactome at the sites of Rad52 repair, we used split-SUMO-ID proteomics approach. It allowed analysis of local SUMOylation content at the Rad52 repair sites, and enabled identification of the essential replication factor PCNA. We found that SUMO chain-modified PCNA antagonizes Rad8-mediated PCNA polyubiquitination, modulating the choice of post-replication repair pathways at stalled forks within centromeres. In the absence of polySUMOylation, excessive PCNA polyubiquitination drives elevated recombination at centromeres. Artificial tethering of a SUMO chain to Rad52 suppresses this defect. Our findings uncover an essential role for SUMO chains in centromere maintenance by modulating DNA repair pathway choice under endogenous replication stress.

overall_design:
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for CFP-Cnp1 histone variant (human CENP-A) from fission yeast Schizosaccharomyces pombe.

Please note that additional data processing was carried out to remove background more stringently for the GSM8506073, GSM8506075, and GSM8506077 ChIP-seq samples. The processed data files and data processing description have been updated on May 29, 2025.

first: Katarzyna

last: Markowska

first: Ireneusz

last: Litwin

first: Julia

last: Kończak

first: Dorota

last: Misiorna

first: Aleksandra

last: Broczkowska

first: Paulina

last: Tomaszewska

first: Michał

last: Tracz

first: Mika

last: Haenen


title: Comprehensive transcriptome characterization deciphers mechanisms underpinning the positive selection of B cells in germinal centers.

status: Public on Oct 04 2024

city: Cambridge

first: Louise

last: Matheson

address: Babraham Research Campus

department: Laboratory of Lymphocyte Signalling and Development

country: United Kingdom

institute: The Babraham Institute

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


title: A human organoid drug screen identifies α2-adrenergic receptor signaling as a therapeutic target for cartilage regeneration [bulk RNA-seq]

city: Guangzhou

first: zhijie

last: Lin

overall_design:
To analyze the overall transcriptome features of cultured cells and dissect subpopulations of hypertrophic cartilaginous organoids, we used FCM-sorted cells to conduct RNA sequencing (RNA-seq) on COL2+COL10- and COL2+COL10+ cell populations generated from day 42 organoids.
We next performed RNA sequencing of D42 PM-treated and vehicle-treated pellets to comprehensively understand the effects of targeting a-AR on chondrogenic phenotypes.
To identify downstream targets through which SLPI promoted hypertrophic differentiation, we conducted RNA-seq of day 42 SLPI KO and control pellets.

first: Xiaochun

last: Bai


title: Functional characterization of the SDR42E1 reveals its role in vitamin D biosynthesis

status: Public on Aug 22 2024

city: Doha

first: Georges

middle: Michel

last: Nemer

state: Qatar

department: CHLS

country: Qatar

institute: HBKU

summary: Vitamin D deficiency poses a widespread health challenge, shaped by environmental and genetic determinants. A recent discovery identified a genetic regulator, rs11542462, in the SDR42E1 gene, though its biological implications remain largely unexplored. Our bioinformatic assessments revealed pronounced SDR42E1 expression in skin keratinocytes and the analogous HaCaT human keratinocyte cell lines, prompting us to select the latter as an experimental model. Employing CRISPR/Cas9 gene-editing technology and multi-omics approach, we discovered that depleting SDR42E1 showed a 1.6-fold disruption in steroid biosynthesis pathway (P-value = 0.03), considerably affecting crucial vitamin D biosynthesis regulators. Notably, SERPINB2 (P-value = 2.17 × 10−103), EBP (P-value = 2.46 × 10−13), and DHCR7 (P-value = 8.03 × 10−09) elevated by ∼2–3 fold, while ALPP (P-value <2.2 × 10−308), SLC7A5 (P-value = 1.96 × 10−215), and CYP26A1 (P-value = 1.06 × 10−08) downregulated by ∼1.5–3 fold. These alterations resulted in accumulation of 7-dehydrocholesterol precursor and reduction of vitamin D3 production, as evidenced by the drug enrichment (P-value = 4.39 × 10−06) and total vitamin D quantification (R2 = 0.935, P-value = 0.0016) analyses. Our investigation unveils SDR42E1's significance in vitamin D homeostasis, emphasizing the potential of precision medicine in addressing vitamin D deficiency through understanding its genetic basis.

overall_design: To investiage global transcriptomic changes associated with SDR42E1, a suggested modulator of serum vitamin D levels, we performed bulk RNA sequencing on HaCat cell lines subjected to CRISPR/Cas9-induced SDR42E1 homozygous knockout, mimicking genetic mutation in patients, alongside wild-type HaCat cells serving as negative controls, all sampled simultaneously. Each sample in this study comprises three biological replicates.

first: Nagham

last: Hendi


title: Alzheimer’s disease-linked risk alleles elevate microglial cGAS-associated senescence and neurodegeneration in a tauopathy model [snRNAseq]

status: Public on Aug 21 2024

city: New York

first: Li

last: Gan

state: NY

address: 413 East 69th Street, 9th Floor BB904

department: Helen and Robert Appel Alzheimer’s Disease Research Institute

institute: Weill Cornell Medicine

summary: The strongest risk factors for Alzheimer’s disease (AD) include the 4 allele of apolipoprotein E (APOE), the R47H variant of triggering receptor expressed on myeloid cells 2 (TREM2), and female sex. Here, we combine APOE4 and TREM2R47H (R47H) in female P301S tauopathy mice to identify the pathways activated when AD risk is the strongest, thereby highlighting disease-causing mechanisms. We find that the R47H variant induces neurodegeneration in female APOE4 mice without impacting hippocampal tau load. The combination of APOE4 and R47H amplified tauopathy-induced cell-autonomous microglial cGAS-STING signaling and type-I interferon response, and interferon signaling converged across glial cell types in the hippocampus. APOE4-R47H microglia displayed cGAS- and BAX-dependent upregulation of senescence, showing association between neurotoxic signatures and implicating mitochondrial permeabilization in pathogenesis. By uncovering pathways enhanced by the strongest AD risk factors, our study points to cGAS-STING signaling and associated microglial senescence as potential drivers of AD risk.

overall_design: Droplet-based single nuclear RNA sequencing of hippocampus from a) female mice with APOE3_NTG_TREM2-WT (n=3), APOE3_P301S_TREM2-WT (n=3), APOE3_P301S_TREM2-R47H (n=3), APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3); b) male mice with APOE4_NTG_TREM2-WT (n=3), APOE4_P301S_TREM2-WT (n=3), APOE4_P301S_TREM2-R47H (n=3).

first: Gillian

last: Carling

last: Fan

first: Nessa

middle: R

last: Foxe

first: Kendra

last: Norman

first: Pearly

last: Ye

first: Man

middle: Y

last: Wong

first: Daphne

last: Zhu

first: Fangmin

last: Yu

first: Jielin

last: Xu

first: Allan

last: Yarahmady

first: Hao

last: Chen

first: Yige

last: Huang

first: Sadaf

last: Amin

first: Emmanouil

last: Zacharioudakis

first: Xiaoying

last: Holtzman

first: Sue-Ann

last: Mok

first: Evripidis

last: Gavathiotis

first: Subhash

last: Sinha

first: Feixiong

last: Cheng

first: Wenjie

last: Luo

first: Shiaoching

last: Gong


title: Ribo-seq reveals translational landscapes during yak testicular development process and cattle-yak.

status: Public on Aug 30 2024

city: Lanzhou

first: shaoke

last: guo

state: Gansu

address: West Lake Street

department: Lanzhou institute of husbandry and pharmaceutical sciences

institute: Chinese Academy of Agricultural Sciences

summary: This study used yak and cattle-yak testes from different developmental stages as materials to construct a complete translation map of the testes, and integrated transcriptome and translation results to explore gene expression changes during the sexual maturation process of yak testes. This study utilized Ribo seq technology to construct a transcriptome map of yak testicular development, revealing that the expression of genes related to spermatogenesis is specifically translated and regulated at different developmental stages. In addition, many unknown open reading frames (ORFs) in the testes have been newly identified.

sample_organism:
Bos grunniens
Bos grunniens x Bos taurus

overall_design: Construction of ribosomal footprint map of yak and cattle-yak testes

first: Shaoke

last: Guo

first: Menglki

last: Cao

first: Xingdong

last: Wang

first: Xian


title: Rhesus immune reference atlas (RIRA): a comprehensive single-cell atlas of rhesus macaque immune cells

status: Public on Sep 24 2024

city: Beaverton

first: Benjamin

last: Bimber

state: OR

address: 505 NW 185th Ave

summary: This is a single-cell RNA-seq atlas comprised of 10x genomics data from 47 macaques and 7 tissues

overall_design:
This dataset contains single-cell RNA-seq from bulk immune cells from rhesus macaque tissues
Please note that the series supplementary .rds data files have been updated on Feb 7, 2025.


title: OncoScan™ CNV FFPE Assay data for desmoid tumors

first: Joanna

last: Przybyl

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

overall_design:
OncoScan™ CNV FFPE Assay was performed according to the manufacturer's directions on DNA extracted from FFPE desmoid tumor specimens
Genomic DNA from 23 desmoid tumor specimens was used for genome-wide copy number and allelic ratio profiling with the OncoScan FFPE Assay (Affymetrix, Santa Clara, CA). Sample preparation and hybridization were performed by the Affymetrix Research Services Laboratory (Affymetrix, Santa Clara, CA). Results were visualized and analyzed with NexusExpress for OncoScan3 software (BioDiscovery, El Segundo, CA).


title: Development of a First-in-Class DNMT1/HDAC Inhibitor with Improved Therapeutic Potential and Potentiated Antitumor Immunity

status: Public on Sep 10 2024

first: Huahui

address: 190 Kaiyuan Avenue, Huangpu District, Guangzhou

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

summary: Epigenetic therapies have emerged as an up-and-coming strategy avenue for treating cancer treatmentmalignancies. In this study, a series of DNMT1/HDAC dual inhibitors were obtained by merging pharmacophores. Among them, compound (R)-23a stood out due to balanced inhibition of DNMT1 and HDAC, along with excellent anti-tumor effects in vitro by stimulating both histone acetylation and DNA methylation. Notably, treatment with compound (R)-23a resulted in a significant anti-tumor effect (TGI = 98%) on MV-4-11 xenograft models, surpassing that achieved with combination therapy. Additionally, compound (R)-23a demonstrated the ability to dramatically reduce tumor volume or even induce tumor regression in MC38 murine colon cancer models. However, this effect was compromised under conditions of immune deficiency. In conclusion, the novel DNMT1/HDAC dual inhibitor (R)-23a holds promise for the development of multiple-target anti-AML agents and tumor immunotherapy.

overall_design: To decipher the molecular mechanism underlying the enhanced anti-AML activities of (R)-23a, we conducted RNA sequencing (RNA-seq) on MV-4-11 cells treated with (R)-23a, GSK5032, SAHA, and the combination of GSK5032 and SAHA (COMBO).


title: Expression data from mouse meninges - home cage (HC) and chronic social defeat (SD) stress mice

status: Public on Aug 29 2024

first: Stacey

last: Kigar

address: Puddicombe Way

institute: University of Cambridge

summary: CSD stress leads to transcriptional changes in the meninges indicative of increased immune system activation. We have characterized lymphopenia (B cell depletion) and possible fibroblast contribution to neutrophil trafficking at arachnoid barrier cells (ABCs) with this data set.

overall_design: 14 samples were analyzed, 7 per group. xCell was used to deconvolve microarray gene expression values for cell count estimations. Limma was used to test for differential expression of genes; genes ranked by t-statistic were used for gene set enrichment analysis using R-based cluster-Profiler

first: Mary-Ellen

last: Lynall


title: De novo gene synthesis by an antiviral reverse transcriptase [RIP-seq]

status: Public on Aug 11 2024

first: Samuel

last: Sternberg

address: 701 W. 168th Street, HHSC 726

institute: Columbia University

summary: Bacteria defend themselves from viral predation using diverse immune systems, many of which sense and target foreign nucleic acids. Defense-associated reverse transcriptase (DRT) systems provide an intriguing counterpoint to this immune strategy by instead leveraging DNA synthesis, but the identities and functions of their DNA products remain largely unknown.  Here we show that DRT2 systems execute an unprecedented immunity mechanism that involves de novo gene synthesis via rolling-circle reverse transcription of a non-coding RNA (ncRNA). Unbiased profiling of RT-associated RNA and DNA ligands uncovered constitutive synthesis of concatenated cDNA repeats through programmed template jumping on the ncRNA. The presence of phage then triggers second-strand cDNA synthesis, leading to the production of long double-stranded DNA. Remarkably, this nascent ‘gene’ is efficiently transcribed, generating messenger RNAs that encode a stop codon-less, never-ending ORF (neo) whose translation causes potent growth arrest. Phylogenetic analyses and screening of diverse DRT2 homologs further revealed broad conservation of rolling-circle reverse transcription and Neo protein function. Our work highlights an elegant expansion of genome coding potential through RNA-templated gene creation, and challenges conventional paradigms of genetic information encoded along the one-dimensional axis of genomic DNA.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: We performed RNA immunoprecipitation and sequencing (RIP-seq) on the KpnDRT2 reverse transcriptase in E. coli cells to systematically profile its RNA substrate specificity in vivo. We also performed RIP-seq in the context of KpnDRT2 RT or ncRNA mutants.

first: Stephen

last: Tang

first: Valentin

last: Conte

first: Dennis

last: Zhang

first: Rimantė

last: Žedaveinytė

first: George

last: Lampe

first: Tanner

last: Wiegand

first: Lauren

first: Megan

first: Matt

middle: W

last: Walker

first: Jerrin

middle: T

last: George

first: Luke

middle: E

last: Berchowitz

first: Marko

last: Jovanovic

middle: H


title: De novo gene synthesis by an antiviral reverse transcriptase [RNA-seq]

platform_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: We performed differential RNA sequencing (dRNA-seq) and Term-seq on E. coli cells expressing the KpnDRT2 reverse transcriptase to determine the start and end coordinates of the KpnDRT2 ncRNA.

middle: C


title: Sequencing experiments on poly(U) polymerase mutants in C. elegans [srna]

status: Public on Jul 17 2024

city: Bloomington

first: Leanne

last: Kelley

state: IN

address: 1001 E Third St

institute: Indiana University

type: Non-coding RNA profiling by high throughput sequencing

summary: To investigate sRNAs and mRNAs that are targeted by poly(U) polymerases in C. elegans.

overall_design: We performed Illumina-based sRNA-seq and Oxford Nanopore Technologies-based mRNA-seq on various poly(U) polymerase deletion mutants.

first: Kelley

last: Leanne

first: Maine

last: Eleanor


title: Sequencing experiments on poly(U) polymerase mutants in C. elegans [mrna]


title: Decoding Heterogeneous and Coordinated Tissue Architecture in Glioblastoma Using Spatial Transcriptomics

status: Public on Jul 03 2024

city: Tianjin

first: xuejiao

last: lv

state: Tianjin

address: No.22 Qixiangtai Rd

institute: Tianjin Medical University

summary: Glioblastoma multiforme (GBM) stands as a devastating human malignancy known for its aggressive nature and resistance to multiple therapeutic interventions. Despite extensive intra-tumor heterogeneity unveiled by single-cell transcriptomic studies, the spatial intricacies of this heterogeneity remain largely unknown. This study leveraged clinical GBM specimens to explore gene expression heterogeneity using spatial transcriptomics technology. Our findings unveiled a prominent enrichment of the tissue stem cell signature in the region between necrosis and the peritumoral area, exhibiting a positive correlation with the signature of the mesenchymal subtype. Additionally, the upregulated genes in these regions demonstrated associations with ECM-receptor interaction, Proteoglycans, as well as the VEGF and ANGPT signaling pathways. In contrast, signature genes linked to Glycogen metabolism and Oxidative Phosphorylation were prominently expressed across all samples, irrespective of pathological zoning. Notably, Creatine metabolism showed enrichment in various cell populations except for the vascular-enriched areas. These spatial profiles not only serve as a reference but also provide a profound guide for future functional and mechanistic investigations into the progression of GBM.

overall_design: Tumor tissues were procured from patients diagnosed with treatment-naive GBM (WHO Grade IV). For ST sequencing, 16 fresh tissue samples were extracted via surgery from 3 glioblastoma patients.

first: Xuejiao

last: Lv

first: Xianfu

last: Yi

first: Bo

last: Wang

first: Mulin

last: Li

first: Xudong

last: Wu


title: De novo gene synthesis by an antiviral reverse transcriptase [cDIP-seq]

first: Samuel

last: Sternberg

overall_design: We developed a new technique, termed cDNA immunoprecipitation and sequencing (cDIP-seq), and applied it to the KpnDRT2 reverse transcriptase in E. coli cells to systematically profile its cDNA production in vivo. We also performed cDIP-seq in the context of KpnDRT2 RT or ncRNA mutants.

first: Stephen

last: Tang

first: Valentin

last: Conte

first: Dennis

last: Zhang

first: Rimantė

first: George


title: Targeting Immune-Fibroblast Crosstalk in Myocardial Infarction and Cardiac Fibrosis VI

status: Public on Jul 01 2024

city: South San Francisco

first: Xin

last: Luo

address: 750 Gateway Blvd

department: Research and Development

institute: Amgen Inc

summary: Inflammation and tissue fibrosis co-exist and are causally linked to organ dysfunction. However, the molecular mechanisms driving immune-fibroblast crosstalk in human cardiac disease remains unexplored, and there are currently no approved treatments that directly target cardiac fibrosis. Here, we performed multi-omic single-cell gene expression, epitope mapping, and chromatin accessibility profiling in 45 donors, acutely infarcted, and chronically failing human hearts. We identified a disease-associated fibroblast trajectory marked by cell surface expression of fibroblast activator protein (FAP), which diverged into distinct myofibroblasts and pro-fibrotic fibroblast populations, the latter resembling matrifibrocytes. We lineage traced FAP fibroblasts in vivo and showed that they contribute to the POSTN lineage but not the myofibroblast lineage. We assessed the applicability of experimental systems to model tissue fibrosis and demonstrated that 3 different in vivo mouse models of cardiac injury were superior compared to cultured human heart and dermal fibroblasts in recapitulating the human disease phenotype. Ligand-receptor analysis and spatial transcriptomics predicted that interactions between C-C chemokine receptor type 2 (CCR2) macrophages and fibroblasts mediated by interleukin 1 beta (IL-1β) signaling drove the emergence of pro-fibrotic fibroblasts within spatially defined niches. In vivo, we deleted the IL-1 receptor on fibroblasts, the IL-1β ligand in CCR2 monocytes and macrophages, and inhibited IL-1β signaling using a monoclonal antibody and showed fewer pro-fibrotic fibroblasts, decreased cardiac fibrosis, and improved cardiac function. Herein, we characterize fibroblast lineage diversification in the failing heart and showed a subset of macrophages signal to fibroblasts via IL-1β and rewire their gene regulatory network and differentiation trajectory towards a pro-fibrotic fibroblast phenotype. These findings highlight the broader therapeutic potential of targeting inflammation to treat tissue fibrosis and preserve organ function.

overall_design: scRNA-seq on DRAQ5+/DAPI- cells in Ang II/PE day 7 isotype treated and anti-IL1b mAb treated mice

first: Junedh

last: Amrute

first: Kory

last: Lavine


title: Targeting Immune-Fibroblast Crosstalk in Myocardial Infarction and Cardiac Fibrosis V

overall_design: scRNA-seq on gated Fap+ and Fap- fibroblasts in Ang II/PE day 7 isotype treated and anti-IL1b mAb treated mice


title: De novo gene synthesis by an antiviral reverse transcriptase

overall_design: Refer to individual Series


title: Single cell chromatin accessibility allows analysis of the transposable element landscape, revealing shared features of immune tissue residency

status: Public on Jul 22 2024

city: Regensburg

first: LIT

last: NGS-Core

address: Franz-Josef-Strauß-Allee 11

department: NGS-Core

institute: Leibniz Institute for Immunotherapy

summary: Tissue adaptation is a necessary process for immune cells to function within tissues and organs. Whether this process shares similarities between different tissue-localized immune cell populations is not yet well understood. Here, we addressed this by generating single cell ATAC-sequencing data of CD45+ tissue-localized immune cells from different tissues from mice and human donors. T cells, B cells, NK cells, and myeloid cells all showed bZIP transcription factor motif enrichment in tissue-localized cells. Tissue adaptation by regulatory T cells served as a reference program and comparisons unraveled shared features with other immune cell subsets, specifically with amphiregulin-producing Th17 and ILC2 cells. The ancient landscape of transposable elements (TE) revealed an enrichment of transcription factor binding motifs, especially bZIP family members, in accessible TE regions and identified individual TEs and TE families to be associated with tissue adaptation. Understanding tissue adaptation will help to harness immune cells in different disease contexts.

overall_design:
scATAC-seq of CD45+ hematopoietic cells from murine tissues such spleen, colon, visceral adipose tissue, and skin

Treg naive 3 replicates, Tregs isolated from mice Foxp3tm1(CD2/CD52)Shori 3 replicates for tissue Treg and 1 (ATAC) 2 (ChIP) replicates for IL2 treated cells.

first: Simon

last: Malte

first: Philipp

last: Stueve

first: Lisa

last: Schmidleithner

first: Andreas

last: Eigenberger

first: Lukas

last: Prantl

first: Nicholas

last: Strieder

first: Claudia

last: Gebhard

first: Michael

last: Rehli

first: Christian

last: Schmidl

first: Thomas

last: Hehlgans

first: Benedikt

last: Brors

first: Charles

last: Imbusch

last: Delacher

first: Markus

last: Feuerer


title: Inhibition of DUSP18 impairs cholesterol biosynthesis and promotes anti-tumor immunity in colorectal cancer

status: Public on Jun 21 2024

city: Zhengzhou

first: Xiaojun

last: Zhou

state: Henan

address: 100 Lianhua Street

department: College of Bioengineering

institute: Henan University of Technology

summary: We discovered, through mining TCGA data and conducting CRISPR screens, that DUSP18 expression within tumor cells significantly influences the immune microenvironment of colorectal cancer.To explore the role of DUSP18 in regulating the immune microenvironment of colorectal cancer (CRC), we established MC38 and HCT116 cell lines with targeted gene knockdown via shRNA and performed RNA-Seq.

first: Youjun

last: Li


title: MGA deletion leads to Richter's transformation via modulation of mitochondrial OXPHOS

status: Public on Jun 27 2024

city: Monrovia

first: Lili

last: Wang

state: CALIFORNIA

address: 1218 South Fifth Ave.

department: Systems biology

institute: City of Hope

summary: Richter’s transformation (RT) is a progression of chronic lymphocytic leukemia (CLL) to aggressive lymphoma. MGA (Max gene associated), a functional MYC suppressor, is mutated at 3% in CLL and 36% in RT. The, genetic models and molecular mechanisms of MGA deletion driving CLL to RT remain elusive. We established a RT mouse model by knockout of Mga in the Sf3b1/Mdr CLL model via CRISPR-Cas9. Murine RT cells exhibit mitochondrial aberrations with elevated oxidative phosphorylation (OXPHOS). We identified Nme1 (Nucleoside diphosphate kinase) as a Mga target through RNA sequencing and functional characterization, which drives RT by modulating OXPHOS. As NME1 is also a known MYC target without targetable compounds, we found that concurrent inhibition of MYC and ETC complex II significantly prolongs the survival of RT mice in vivo. Our results suggest that Mga-Nme1 axis drives murine CLL-to-RT transition via modulating OXPHOS, highlighting a novel therapeutic avenue for RT.

overall_design: To investigate the role of MGA in mouse CLL and Richters transformation. We adoptively transfer in-vitro edited via sgRNA-Mga/control early LSK (Lin-Sca1+ Kit+) progenitors (CD19-Cre+/--Mdrfl/+-Sf3B1fl/+-Cas9fl/+) in the recepient mice and followed the mice by serial bleeding for the development of CLL by flow cytometry for 22 months. After the mice developed CLL, we subsequenlty transplanted the CLL cells in other recepient mice and  developed RT.  We isolated the donor splenic B cells from Mga deleted mouse CLL and RT  having SF3B1 K700E mutation and 13q(MDR) deletion and performed RNA seq on the donor splenic B cells.


title: Targeting Immune-Fibroblast Crosstalk in Myocardial Infarction and Cardiac Fibrosis III

first: Xin

last: Luo

overall_design: To dissect the epigenetic landscape of MI and HF, we performed Multiome (paired single nucleus RNA and ATAC) sequencing of 23 samples including donors, AMI, ICM, and NICM.

first: Junedh

last: Amrute

first: Tracy

last: Yamawaki

first: Xue

last: Zeng

first: Chi-Ming

first: Brandon

last: Ason

first: Kory

last: Lavine


title: Effects of Monocyte/Macrophages on the Severity of Hand, Foot, and Mouth Disease Patients due to Enterovirus

status: Public on Jun 20 2024

city: Xian

first: Yaping

state: Shaanxi

address: Xincheng District

institute: Xi'an Jiaotong University

summary: To elucidate alterations in immune cells during enterovirus 71 (EV-A71) infection and explore potential interaction mechanisms.Single-cell sequencing technology was used to sequence peripheral blood monocytes (PBMCs) obtained from a severe hand, foot and mouth disease (HFMD) patient due to EV-A71 and a healthy control.

overall_design: Single-cell sequencing technology was used to sequence peripheral blood mononuclear cells from a severe hand, foot and mouth disease patient infected with EV-A71 and healthy controls to clarify the differences in their immune status and the potential mechanism affecting EV71 infection.

first: Muqi

first: Meng

last: Zhang

first: Shuangsuo

last: Dang


title: Targeting Immune-Fibroblast Crosstalk in Myocardial Infarction and Cardiac Fibrosis IV

overall_design: scRNA-seq on DRAQ5+/DAPI- cells from saline or Ang II/PE infused pumps at day 28


title: Harnessing the microbiome to regulate systemic innate immunity II

city: Avon

first: Beiyan

state: Connecticut

address: 263 Farmington Ave, Immunology

department: Immunology

institute: UCONN Health

summary:
Mechanisms through which the microbiome communicates with the systemic immune system remain unclear. We have identified a family of microbiome Bacteroidota-derived lipopeptides – the serine-glycine (S/G) lipids, and specifically L654 – that are TLR2 ligands, access the systemic circulation, and potentially link the microbiome and systemic innate immunity. We have previously postulated that L654 and the S/G lipids regulate systemic innate immunity by entering the systemic circulation and mediating weak TLR2 interactions that maintain “normal” levels of innate immune signaling feedback inhibitors. In proof-of-concept studies, we reported that increasing systemic L654 levels in mice by administering exogenous L654 intravenously significantly diminishes systemic innate immune responses and attenuates murine autoimmunity. In the present study, our goal was to confirm the role of the microbiome in mediating this mode of immunoregulation by decreasing the microbiome-based production of S/G lipids.
We now report that decreasing microbiome Bacteroidota in mice using a specific oral antibiotic/rest protocol reduces fecal and plasma S/G lipids levels and significantly enhances systemic innate immune responses. Replenishing systemic levels of S/G lipids after antibiotic treatment through exogenous administration of L654 returns innate immune responses to normal levels, confirming the regulatory role of S/G lipids in this mode of microbiome regulation. Finally, RNAseq analysis of splenic monocytes derived from antibiotic-treated and control mice with or without exogenous L654 prior to ex vivo stimulation demonstrates that the antibiotic/rest protocol and the concomitant decrease in microbiome S/G lipids and Bacteroidota has significant downregulatory effects on normal homeostatic pro-inflammatory pathways. These effects are also associated with downregulation of specific proinflammatory pathway inhibitors, which may suggest a potential mechanism underlying the enhancement in ex vivo innate immune stimulated responses of these monocytes.
Overall, our results suggest that S/G lipids are microbiome-derived bacterial factors capable of regulating systemic innate immunity and as such are manipulatable targets with therapeutic potential for enhancing or decreasing innate immunity in the context of infectious, malignant, and autoimmune diseases.

overall_design: We performed RNA-Seq analysis on splenic monocytes from vancomycin or water gavaged mice with or without reintroduction of exogenous L654 lipid to determine gene expression dynamics driving enhanced pro-inflammatory response following vancomycin treatment. Splenic monocytes were isolated via EasySep Mouse Monocyte Isolation Kit (Stemcell) from 3 biological replicates per treatment. RNA-Seq libraries were generated using Illumina TruSeq Stranded mRNA library prep kit and sequenced on Illumina NovaSeq S4 v1.5 for 200 cycles at 10M total pair end reads of length 100 base-pairs. Reads in Fastq files were aligned using HISAT2 v2.2.1 on the GRCm38 index, with SAMtools v1.9 for BAM conversion. A matrix of fragments per kilobase of transcript per million fragments mapped (FPKM) was calculated using Stringtie v2.1.3 with Ballgown on the GRCm38 index. FPKM data was converted to gene count data matrix using tximport v1.26.1 R package.

first: Alyssa

last: Matz

first: Robert

last: Clark


title: Spatial transcriptome sequencing of the rat corpus cavernosum with normal erectile function

status: Public on Jun 12 2024

city: Zhuhai

first: Liangyu

last: Zhao

state: Guangdong

address: 52th Meihua Road, Zhuhai, China

institute: Shanghai Jiao Tong University School of Medicinethe Fifth Affiliated Hospital of Sun Yat-sen University

summary: The composition and cellular heterogeneity of the corpus cavernosum (CC) microenvironment have been characterized, but the spatial heterogeneity at the molecular level and the evolutionary differences among species remain unexplored. In this study, we integrated single-cell RNA sequencing (scRNA-seq) and spatial transcriptome sequencing to comprehensively charted the spatial cellular landscape of human and rat CC under normal and disease conditions. We partitioned CC on the basis of special structures such as cavernous arteries, septum pectiniforme, and tunica albuginea, and described the spatial heterogeneity of cell composition and signaling networks in different regions. Additionally, we observed differences in the proportion of cell subtypes and marker genes among endothelial cells (EC), smooth muscle cells (SMC), and fibroblasts (FB) between humans and rats. Although many signalings involved in the basic biological processes such as translation are relatively conserved between human and rat, they show significant species differences in the pathways such as inflammatory response. Based on the analysis of FB niche, we also found that mechanical force signaling have significant spatial heterogeneity within CC and correlated with the spatial distribution of different FB subtypes. In vitro, soft and hard extracellular matrix (ECM) induced the differentiation of FB into APO+FB or COMP+FB subtype, respectively, and reprogrammed their lipid metabolism. In summary, our study provided a cross-species and physio-pathology transcriptomic atlas of the CC at the single-cell level with high spatial resolution, contributing to further understanding of the molecular anatomy and regulation of penile erection.

overall_design: Spatial transcriptome of rat CC tissue with normal function, we cropped the tissue cross-sections and coronal-section.


title: Targeting Immune-Fibroblast Crosstalk in Myocardial Infarction and Cardiac Fibrosis

state: CA

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


title: Single cell RNA seq data of the third DMED patients corpus cavernosum

summary: we profiled the scRNA-seq of one DMED patients, it is belong to one of the scRNA-seq of normal and DMED human CC atlas.

overall_design: Single cell RNA seq data of diabetes mellitus erection dysfunction (DMED) patient corpus cavernosum


title: Analysis of chromosomal structual aberratons in NB-4 cell line

status: Public on Jun 15 2024

city: Mitaka-shi

first: Tetsuko

last: Kobayashi

state: Tokyo

country: Japan

institute: Kyorin University

summary: This Hi-C experiment was a part of a research which analyzed chromosomal structural aberrations in hematological malignancies. First, the author conducted comprehensive detection of fusion transcripts in RNA-seq data of DSMZ’s 99 cell lines, and then picked up cell lines with characteristic complex karyotype. NB-4 cell line is one of them, which shows characteristic fusion cluster in 8q24 region in the fusion detection step. This Hi-C experiment revealed amplifications of MYC, PVT1, and CCDC26 in 8q24 region. Additionally, several structural aberrations were found by scanning the whole genome.

overall_design: in situ Hi-C of DSMZ’s NB-4 cell line with no treatment

first: Kazuhiko

last: Watabe

first: Niida

last: Motoko


title: Spatial transcriptome sequencing of the human corpus cavernosum with normal erectile function

overall_design: Spatial transcriptome of human CC tissue with normal function, we cropped part of the tissue cross-sections and tried to include as more as different characteristic regions, such as cavernous arteries, septum pectiniforme, tunica albuginea and most part of cavernosal trabecular.


title: lncRNA-ZFAS1, an emerging gate-keeper in DNA damage-dependent transcriptional regulation [OE CTD ChIP-Seq]

status: Public on Jun 02 2024

first: Yuming

address: Room 512, Anatomy Building

department: School of Basic Medical Science

institute: Guangzhou medical university

summary: Numerous long noncoding RNAs (lncRNAs) are generated in response to external stimuli, but the scope and functions of such activity are not known. Here, we provide insight into how the transcription of lncRNAs are connected to DNA damage response by identifying a lncRNA ZFAS1, which is required for cell cycle arrest, transcription regulation and DNA repair. Mechanistically, ZFAS1 facilitates the changing hyperphosphorylated forms of the large subunit of RNAPII around transcription initiation sites by directly targeting the regulated genes. We revealed extensive transcription shutdown and concomitant stimulated engagement of RNAPII-Ser2P are crucial for repair and cell survival upon genotoxic stress. Finally, ZFAS1 knockout in mice dampened transcription-coupled nucleotide excision repair (TC-NER) and led to kidney dysplasia. Our study extends the understanding of lncRNAs in DNA damage repair (DDR) and implies a protective role of lncRNA against DDR-deficient developmental disorders.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for RNAPII CTD Ser2P and Ser5P in the MRC5 cells overexpressing human ZFAS1 with or without UV-C irradiation.

first: Jiena

last: Liu

first: Qing

last: Lu

first: Tingting

last: Zhu

first: Zixuan

last: Fan

last: He


title: lncRNA-ZFAS1, an emerging gate-keeper in DNA damage-dependent transcriptional regulation [H3.3 ChIP-Seq]

last: Wang

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3.3 in the MRC5 cells with or without UV-C irradiation.


title: lncRNA-ZFAS1, an emerging gate-keeper in DNA damage-dependent transcriptional regulation [CDK9 ChIP-Seq]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for CDK9 in the WT and ZFAS1-depleted cells with or without UV-C irradiation.


title: Harnessing the microbiome to regulate systemic innate immunity I

last: Zhou

summary:
Mechanisms through which the microbiome communicates with the systemic immune system remain unclear. We have identified a family of microbiome Bacteroidota-derived lipopeptides – the serine-glycine (S/G) lipids, and specifically L654 – that are TLR2 ligands, access the systemic circulation, and potentially link the microbiome and systemic innate immunity. We have previously postulated that L654 and the S/G lipids regulate systemic innate immunity by entering the systemic circulation and mediating weak TLR2 interactions that maintain “normal” levels of innate immune signaling feedback inhibitors. In proof-of-concept studies, we reported that increasing systemic L654 levels in mice by administering exogenous L654 intravenously significantly diminishes systemic innate immune responses and attenuates murine autoimmunity. In the present study, our goal was to confirm the role of the microbiome in mediating this mode of immunoregulation by decreasing the microbiome-based production of S/G lipids.
We now report that decreasing microbiome Bacteroidota in mice using a specific oral antibiotic/rest protocol reduces fecal and plasma S/G lipids levels and significantly enhances systemic innate immune responses. Replenishing systemic levels of S/G lipids after antibiotic treatment through exogenous administration of L654 returns innate immune responses to normal levels, confirming the regulatory role of S/G lipids in this mode of microbiome regulation. Finally, RNAseq analysis of splenic monocytes derived from antibiotic-treated and control mice prior to ex vivo stimulation demonstrates that the antibiotic/rest protocol and the concomitant decrease in microbiome S/G lipids and Bacteroidota has significant downregulatory effects on normal homeostatic pro-inflammatory pathways. These effects are also associated with downregulation of specific proinflammatory pathway inhibitors, which may suggest a potential mechanism underlying the enhancement in ex vivo innate immune stimulated responses of these monocytes.
Overall, our results suggest that S/G lipids are microbiome-derived bacterial factors capable of regulating systemic innate immunity and as such are manipulatable targets with therapeutic potential for enhancing or decreasing innate immunity in the context of infectious, malignant, and autoimmune diseases.

overall_design: We performed RNA-Seq analysis on splenic monocytes from vancomycin or water gavaged mice to determine gene expression dynamics driving enhanced pro-inflammatory response following vancomycin treatment. Splenic monocytes were isolated via EasySep Mouse Monocyte Isolation Kit (Stemcell) from 3 biological replicates per treatment. RNA-Seq libraries were generated using Illumina TruSeq Stranded mRNA library prep kit and sequenced on Illumina NovaSeq S4 v1.5 for 200 cycles at 10M total pair end reads of length 100 base-pairs. Reads in Fastq files were aligned using HISAT2 v2.2.1 on the GRCm38 index, with SAMtools v1.9 for BAM conversion. A matrix of fragments per kilobase of transcript per million fragments mapped (FPKM) was calculated using Stringtie v2.1.3 with Ballgown on the GRCm38 index. FPKM data was converted to gene count data matrix using tximport v1.26.1 R package.


title: lncRNA-ZFAS1, an emerging gate-keeper in DNA damage-dependent transcriptional regulation [GRO-seq]

overall_design: WT and ZFAS1-knockdown MRC5 cells were treated with DRB (100 μM, 3.5 hrs), followed by 10 J/m2 UV-C irradiation or left untreated. Cells were washed with PBS to remove DRB immediately after UV-C treatment and incubated for 10 or 40 minutes, followed by cell lysis and nuclei isolation. Nuclei were subjected to GRO-Seq.


title: Targeting Immune-Fibroblast Crosstalk in Myocardial Infarction and Cardiac Fibrosis I

first: Xin

last: Luo

summary: To define the cellular landscape of human myocardial infarction and heart failure, we performed Cellular Indexing of Transcriptomes and Epitomes by sequencing (CITE-seq) in 22 explanted human hearts from healthy donors, acute myocardial infarction (MI),and chronic ischemic and non-ischemic cardiomyopathy patients.

overall_design: CITE-Seq on explanted heart tissues from left ventricles from 6 donors, 4 acute myocardial infarction, 6 chronic ischemic and 6 non-ischemic cardiomyopathy patients

first: Kory

first: Junedh

last: Amrute

first: Tracy

last: Yamawaki

first: Chi-Ming

last: Li

first: Brandon

last: Ason


title: PKD1 mutant clones within cirrhotic livers inhibit steatohepatitis without promoting cancer [Normal Chow diet]

status: Public on May 15 2024

city: Dallas

first: Hao

state: TX

address: 6000 Harry Hines Blvd.

department: Children’s Research Institute

institute: University of Texas Southwestern Medical Center

summary: Somatic mutations in non-malignant tissues are selected for because they confer increased clonal fitness, however, it is uncertain if these clones can benefit organ health. Here, ultra-deep targeted sequencing of 150 liver samples from 30 chronic liver disease patients revealed recurrent somatic mutations. PKD1 mutations were observed in 30% of patients, whereas they were only detected in 1.3% of hepatocellular carcinomas (HCCs). To interrogate tumor suppressor functionality, we perturbed PKD1 in two HCC cell lines and six in vivo models, in some cases showing that PKD1 loss protected against HCC, but in most cases showing no impact. However, Pkd1 haploinsufficiency accelerated regeneration after partial hepatectomy. We tested Pkd1 in fatty liver disease, showing that Pkd1 loss was protective against steatosis and glucose intolerance. Mechanistically, Pkd1 loss selectively increased mTOR signaling without SREBP activation. In summary, PKD1 mutations in cirrhotic livers exert adaptive functionality without increasing transformation risk.

overall_design: Pkd1 WT, Het, and Homo litternate mice on Normal Chow diet


title: A Scaffolding Element Rewires Local 3D Chromatin Architecture During Differentiation

status: Public on May 23 2024

city: Montpellier

first: Ivana

last: Jerkovic

state: Occitanie

address: 141 rue de la Cardonille

institute: IGH, CNRS

relation:
SuperSeries of: GSE261220
SuperSeries of: GSE261221
SuperSeries of: GSE261222
SuperSeries of: GSE308227

overall_design: Refer to individual Series


title: Differential Tropisms of Old and New World Hantaviruses Influence Virulence and Developing Host-Directed Antiviral Candidates

status: Public on May 16 2024

city: Los Angeles

first: ARJIT VIJEY

last: JEYACHANDRAN

address: Tiverton Ave

institute: UCLA

summary: We report RNAseq analysis of control, calu3, astrocytes, cardiomyocytes and pulmonary endothelial cells under uninfected (mock) and Andes virus (ANDV), Sin Nombre virus (SNV), Hantaan virus (HTNV) infected and drug (synthetic 6AZA and Favipiravir, herbal Silymarin and Urolithin B) treated conditions

overall_design: Calu3, astrocytes, cardiomyocytes and pulmonary endothelial cells were either uninfected (mock) or infected with Andes virus, Sin Nombre virus or Hantaan virus and/or treated with one of the four drugs (6AZA, Favipiravir, Silymarin, and Urolithin B) components at 48 hrs

first: Arjit Vijey

last: Jeyachandran

first: Joseph Ignatius

last: Irudayam

first: Swati

last: Dubey

first: Nikhil

last: Chakravarty

first: Maria

last: Daskou

first: Anne

last: Zaiss

first: Gustavo

last: Garcia

first: Bindu

last: Konda

first: Aayushi

last: Shah

first: Aditi

last: Venkatraman

first: Cheng

first: Qi

last: Cui

first: Kevin

last: Williams

first: Sonal

last: Srikanth

first: Ashok

last: Kumar

first: Yanhong

last: Shi

first: Arjun

last: Deb

first: Robert

last: Damoiseaux

first: Barry

last: Stripp

first: Arunachalam

last: Ramaiah

first: Vaithilingaraja

last: Arumugaswami


title: Next Generation Sequencing of the transcriptomes of prostate cancer cells with or without ectopic expression of miR-5100

status: Public on May 14 2024

city: Wuhan

first: An

last: Zhang

state: Hubei

address: No.1095 Jie Fang Avenue, Hankou, Wuhan 430030, P.R. China.

institute: Tngji Hospital

summary: Gene expression profilings for prostate cancer cells after miR-5100 overexpression

overall_design: PC3 cells with miR-5100 mimic or miR-NC transfection