title: Cancer cells avoid ferroptosis induced by immune cells via fatty acid binding proteins [ATAC-seq]

city: Dallas

first: Maria

last: Freitas-Cortez

state: Texas

address: 6000 Harry Hines Blvd

institute: UT Southwestern

summary: Background Cancer creates an immunosuppressive environment that hampers immune responses, allowing tumors to grow and resist therapy. One way the immune system fights back is by inducing ferroptosis, a type of cell death, in tumor cells through CD8+ T cells. This involves lipid peroxidation and enzymes like lysophosphatidylcholine acyltransferase 3 (Lpcat3), which makes cells more prone to ferroptosis. However, the mechanisms by which cancer cells avoid immunotherapy-mediated ferroptosis are unclear. Our study reveals how cancer cells evade ferroptosis and anti-tumor immunity through the upregulation of fatty acid-binding protein 7 (Fabp7).  Methods To explore how cancer cells resist immune cell-mediated ferroptosis, we used a comprehensive range of techniques. We worked with cell lines including PD1-sensitive, PD1-resistant, B16F10, and QPP7 glioblastoma cells, and conducted in vivo studies in syngeneic 129 Sv/Ev, C57BL/6, and conditional knockout mice with Rora deletion specifically in CD8+ T cells, Cd8 cre;Rorafl mice. Methods included mass spectrometry-based lipidomics, targeted lipidomics, Oil Red O staining, Seahorse analysis, quantitative PCR, immunohistochemistry, PPARγ transcription factor assays, ChIP-seq, untargeted lipidomic analysis, ROS assay, ex vivo co-culture of CD8+ T cells with cancer cells, ATAC-seq, RNA-seq, Western blotting, co-immunoprecipitation assay, flow cytometry and Imaging Mass Cytometry.  Results PD1-resistant tumors upregulate Fabp7, driving protective metabolic changes that shield cells from ferroptosis and evade anti-tumor immunity. Fabp7 decreases the transcription of ferroptosis-inducing genes like Lpcat3 and increases the transcription of ferroptosis-protective genes such as Bmal1 through epigenetic reprogramming. Lipidomic profiling revealed that Fabp7 increases triglycerides and monounsaturated fatty acids (MUFAs), which impede lipid peroxidation and ROS generation. Fabp7 also improves mitochondrial function and fatty acid oxidation (FAO), enhancing cancer cell survival. Furthermore, cancer cells increase Fabp7 expression in CD8+ T cells, disrupting circadian clock gene expression and triggering apoptosis through p53 stabilization. Clinical trial data revealed that higher FABP7 expression correlates with poorer overall survival and progression-free survival in patients undergoing immunotherapy.

overall_design: ATACseq profiling of T cells co-cultured with Res cells control and Res-shFabp7.

first: Fatemeh

last: Masrorpour


title: Temporal profiling of human lymphoid tissues reveals coordinated defence against viral challenge

status: Public on Jan 31 2025

city: Cambridge

first: Menna

last: Clatworthy

address: Cambridge Biomedical Campus, Francis Crick Ave, Trumpington

department: Department of Medicine

country: United Kingdom

institute: University of Cambridge

type: Expression profiling by high throughput sequencing

summary: Adaptive immunity is generated in lymphoid organs, but how these structures defend themselves during infection in humans is unknown. The nasal epithelium is a major site of viral entry, with adenoid nasal-associated lymphoid tissue (NALT generating early adaptive responses. Here, using a nasopharyngeal biopsy technique, we investigated longitudinal immune responses in NALT following viral challenge, using SARS-CoV-2 infection as a natural experimental model. In acute infection, infiltrating monocytes formed a subepithelial and peri-follicular shield, recruiting NET-forming neutrophils, whilst tissue macrophages expressed pro-repair molecules during convalescence to promote the restoration of tissue integrity. Germinal centre B cells expressed anti-viral transcripts that inversely correlated with fate-defining transcription factors. Among T cells, tissue-resident memory CD8 T cells alone showed clonal expansion and maintained cytotoxic transcriptional programmes into convalescence. Together our study provides unique insights into how human nasal adaptive immune responses are generated and sustained in the face of viral challenge.

overall_design: Nasal and peripheral blood samples were taken at a single timepoint from three groups of subjects for scRNAseq (10x Genomics 5') for single cell gene expression, scTCR and scBCR sequencing. The gene expression data is included here. Groups were: 1. Active: subjects within 14 days of primary SARS-CoV-2 infection and 7 days of first positive swab, 2. Convalescent: subjects between 21 and 28 days of first positive SARS-CoV-2 swab, 3. Uninfected healthy control subjects.

first: Matthew

middle: L

last: Coates

first: Nathan

last: Richoz

first: Zewen

middle: K

last: Tuong

first: Georgina

last: Bowyer

first: Colin

middle: Y

last: Lee

first: John

middle: R

last: Ferdinand

first: Eleanor

last: Gillman

first: Mark

last: McClure

first: Lisa

last: Dratva

first: Sarah

middle: A

last: Teichmann

first: David

last: Jayne

first: Rafael

last: Barros

first: Benjamin

middle: J

last: Stewart


title: Cancer cells avoid ferroptosis induced by immune cells via fatty acid binding proteins [ChIP-seq]

country: USA

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Chip-seq of histone modification H3K27ac and H3K9ac in Sen, Res, Res_ctrl and Res_shFabp7 cells

first: Jiang

last: Hong

first: Yue

last: Lu


title: Analysis of piRNA production in meioc (moto) mutant zebrafish testis

status: Public on Jan 28 2025

city: Mainz

first: Emil

last: Karaulanov

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology

type: Non-coding RNA profiling by high throughput sequencing

summary: We isolated a novel zebrafish mutant denoted meioc (moto) in which germ cells arrest at the early stage of spermatogonia. The protein encoded by the mutated gene interacts with Piwil1 and affects its intracellular localization. Thus, it is interesting to explore piRNA production in meioc (moto) mutants.

overall_design: Small RNA-seq analysis of piRNA production in testes from 6 heterozygote and 5 homozygote moto mutant 10-month old zebrafish animals.

first: Noriyoshi

last: Sakai

first: Kellee

last: Siegfried

first: René

last: Ketting


title: RBM10 loss promotes metastases by aberrant splicing of cytoskeletal and extracellular matrix mRNAs.

status: Public on Feb 17 2025

city: New York

first: Gnana

middle: P

last: Krishnamoorthy

state: New York

address: 1275 York Avenue

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering cancer center

summary: RBM10 modulates transcriptome-wide cassette exon splicing.  Loss-of-function RBM10 mutations are enriched in thyroid cancers with distant metastases. Analysis of transcriptomes and genes mis-spliced by RBM10 loss showed pro-migratory and RHO/RAC signaling signatures. RBM10 loss increases cell velocity. Cytoskeletal and ECM transcripts subject to exon-inclusion events included vinculin (VCL), tenascin C (TNC) and CD44.  Knockdown of the VCL exon inclusion transcript in RBM10-null cells reduced cell velocity, whereas knockdown of TNC and CD44 exon-inclusion isoforms reduced invasiveness.  RAC1-GTP levels were increased in RBM10-null cells. Mouse HrasG12V/Rbm1OKO thyrocytes develop metastases that are reversed by RBM10 or by combined knockdown of VCL, CD44 and TNC inclusion isoforms. Thus, RBM10 loss generates exon inclusion in transcripts regulating ECM-cytoskeletal interactions, leading to RAC1 activation and metastatic competency. Moreover, a CRISPR-Cas9 screen for synthetic lethality with RBM10 loss identified NFkB effectors as central to viability, providing a therapeutic target for these lethal thyroid cancers.

overall_design: Differential splicing analysis was performed as previously described (Dvinge et al., 2014), from RNA-sequencing of the following isogenic RBM10-overexpressing or -Knockdown (KD) thyroid cancer cell lines: KTC1, KTC1-RBM10, PE121410, PE121410-RBM10, 8305C-sh.Ctrl, 8305C-sh.RBM10, SW1736-sh.Ctrl, SW1736-sh.RBM10 and HTH83-sh.Ctrl, HTH83-sh.RBM10.

first: Jose

middle: M

last: Pineda

first: Robert

last: Bradley

first: James

last: Fagin


title: Unraveling Morphogenesis, Starvation, and Light Responses in a Mushroom-Forming Fungus, Coprinopsis cinerea, Using Long Read Sequencing and Extensive Expression Profiling

status: Public on Jan 30 2025

city: Szeged

first: Botond

last: Hegedüs

state: Csongrád-Csanád

address: Temesvári krt. 62

department: Institute of Biochemistry

country: Hungary

institute: Biological Research Center

summary: Mushroom-forming fungi (Agaricomycetes) are emerging as pivotal players in several fields, as drivers of nutrient cycling, sources of novel applications, or as the group that includes the most morphologically complex fungi. Genomic data for Agaricomycetes are accumulating at a steady pace, however, this is not paralleled by improvements in the quality of genome sequence and associated functional gene annotations, which leaves gene function notoriously poorly understood in comparison with other fungi and model eukaryotes. We set out to improve our functional understanding of the model mushroom Coprinopsis cinerea by integrating a new, chromosome-level assembly with high-quality gene predictions and functional information derived from gene-expression profiling data across 67 developmental, stress, and light conditions. The new annotation includes 5′- and 3′-untranslated regions (UTRs), polyadenylation sites (PAS), upstream ORFs (uORFs), splicing isoforms, conserved sequence motifs (e.g., TATA and Kozak boxes) and microexons. We found that alternative polyadenylation is widespread in C. cinerea, but that it is not specifically regulated across the various conditions used here. Transcriptome profiling allowed us to delineate core gene sets corresponding to carbon starvation, light-response, and hyphal differentiation, and uncover new aspects of the light-regulated phases of life cycle. As a result, the genome of C. cinerea has now become the most comprehensively annotated genome among mushroom-forming fungi, which will contribute to multiple rapidly expanding fields, including research on their life history, light and stress responses, as well as multicellular development.

overall_design: Gene-expression profiling data across 67 developmental, stress and light conditions. The growth conditions and the experimental design are described in detail in the file growth_protocol.pdf.

first: Neha

last: Sahu

first: Balázs

last: Bálint

first: Sajeet

last: Haridas

first: Viktória

last: Bense

first: Zsolt

last: Merényi

first: Máté

last: Virágh

first: Hongli

last: Wu

first: Xiao-Bin

last: Liu

last: Riley

first: Anna

last: Lipzen

first: Maxim

last: Koriabine

first: Emily

last: Savage

first: Jie

last: Guo

first: Kerrie

last: Barry

first: Vivian

last: Ng

first: Péter

last: Urbán

first: Attila

last: Gyenesei

first: Michael

last: Freitag

first: Igor

middle: V

last: Grigoriev

first: László

middle: G

last: Nagy


title: Drug and single-cell gene expression integration identifies sensitive and resistant glioblastoma cell populations

city: Washington, DC

first: Nagi

last: Ayad

state: District Of Columbia

address: 3970 Reservoir Rd NW

department: Department of Oncology

institute: Georgetown University

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

overall_design: Refer to individual Series


title: Transient gene melting governs the timing of oligodendrocyte maturation [siRNA ATAC-seq]

status: Public on Jan 20 2025

city: Cleveland

first: Paul

last: Tesar

state: Ohio

address: 10900 Euclid Ave.

department: Genetics & Genome Sciences

institute: Case Western Reserve University

summary: Cellular maturation is a crucial step for tissue formation and function, distinct from the initial steps of differentiation and cell fate specification. In the central nervous system, failure of oligodendrocyte maturation is linked to diseases such as multiple sclerosis. Here, we report a transcriptional mechanism that governs the timing of oligodendrocyte maturation. After progenitor cells differentiate into immature oligodendrocytes, the transcription factor SOX6 redistributes from super enhancers to cluster across specific gene bodies. These sites exhibit extensive chromatin decondensation and transcription, which abruptly turn off upon maturation. Suppression of SOX6 deactivates these immaturity loci, accelerating the transition to mature, myelinating oligodendrocytes. Notably, cells harboring this immature SOX6 gene signature are enriched in multiple sclerosis patient brains. Antisense oligonucleotide-mediated Sox6 knockdown drives precocious oligodendrocyte maturation in mice. Our findings establish SOX6 as a key regulator of oligodendrocyte maturation and highlight its potential as a therapeutic target to promote myelination in disease.

overall_design: ATAC-seq of induced pluripotent stem cell derived oligodendrocytes (OLs) treated with siRNA targeting Sox6

first: Jesse

last: Zhan

first: Anushka

last: Nikhil


title: Single nucleus RNA-seq reveals the process from onset to chronic kidney disease in IgA nephropathy

status: Public on Jan 18 2025

city: Zhengzhou

first: Junpeng

last: You

state: Henan

address: No.1, Jianshe Road, Erqi District

department: Department of Nephrology

country: China

institute: The First Affiliated Hospital of Zhengzhou University

summary: IgA nephropathy (IgAN) is a common form of glomerulonephritis, according to the established multi-hit theory of IgAN pathogenesis, the final hit is the mesangial deposition of IgA1-containing immune complexes, leading to characteristic pathological features such as mesangial cell proliferation and expansion of extracellular matrix. We analyzed several public transcriptomic datasets, including microarray and bulk RNA-sequencing, to identify pathway alterations in IgAN patients and progressors. We also generated our own single-nucleus RNA-sequencing dataset from IgAN kidney biopsies with normal or reduced estimated glomerular filtration rate and integrated it with a publicly available healthy control dataset to comprehensively examine cell type specific changes during IgAN progression. Pathways related to complement activation, focal adhesion, and collagen formation were significantly enhanced in IgAN compared to healthy controls. Our snRNA-seq data identified two mesenchymal stromal cell (MSC) clusters with higher scores in these pathways than other cell types, which were progressively perturbed as eGFR declined. We observed a potential transition from mesangial cells to myofibroblasts within MSCs, accompanied by increased expression of genes involved in complement activation, humoral immunity, collagen organization, and extracellular matrix assembly. This transition could be partially reversed through in silico knockdown of certain transcription factors, such as PRRX1.

overall_design: We collected renal biopsy samples from 20 IgAN patients at the Zhengzhou University First Hospital and stored them in liquid nitrogen until pathology analysis. Based on the eGFR, we grouped the samples into 9 with normal eGFR (>90 mL/min/1.73m²) and 11 with low eGFR (<90 mL/min/1.73m²). We then pooled the samples into 3 normal eGFR and 3 low eGFR IgAN groups, and sent them for standard 10X Genomics snRNA-seq.

first: Genyang

last: Cheng

first: Xiaoxue

last: Zhang

first: Zheng

last: Wang

first: Wei

last: Ning

first: Yuanyuan

last: Qi

first: Zhanzheng

last: Zhao


title: Antigen-specific CD4+ T cells promote monocyte recruitment and differentiation into glycolytic lung macrophages to control Mycobacterium tuberculosis.

status: Public on Jan 27 2025

city: Minneapolis

first: Samuel

last: Becker

state: MN

address: 2101 6th St SE

institute: University of Minnesota

summary: Although lung myeloid cells provide an intracellular niche for Mycobacterium tuberculosis (Mtb), CD4+ T cells limit Mtb growth in these cells to protect the host. Here, we show that monocyte-derived macrophages (MDMs), instead of phenotypically similar dendritic cells, are preferentially infected with Mtb in murine lungs. Mtb-specific CD4+ T cells recruited monocyte precursors of MDMs into the lungs via interferon-γ (IFN-γ). Although the CD4+ T cells increased the number of Mtb-infectable cells in the lungs, they then attenuated Mtb growth by engaging in MHC class II (MHCII)-mediated cognate interactions with monocyte-derived cells to promote their disinfection. Specifically, cognate CD4+ T cell help via MHCII enhanced MDM expression of glycolytic genes independently of IFN-γ. These results indicate that CD4+ T cells recruit infectable MDMs to the lungs and trigger glycolysis-dependent bacterial control within them by engaging MHCII-bound Mtb peptides on their surfaces.

overall_design: Tamoxifen-fed Cre negative, H2-Ab1-flox/flox (samples 1 and 2, 2 biological replicates) and Ccr2-CreERT2, H2-Ab1-flox flox mice (samples 3 and 4, 2 biological replicates) were infected with Mycobacterium tuberculosis strain H37Rv via standard low-dose aerosol inoculation (~100 colony forming units/mouse). At 3 weeks post-infection, lung single cell suspensions were generated, sorting was performed to enrich for monocytes, macrophages and dendritic cells, and single cell RNA sequencing was performed using the 10X Genomics 3' Single Cell Gene Expression kit.

middle: H

first: Christine

middle: E

last: Ronayne

first: Tyler

middle: D

last: Bold

first: Marc

last: Jenkins


title: Single-cell sequencing of murine small intestinal dendritic cells

status: Public on Jan 15 2025

city: Aachen

first: Hieu

middle: Trong

last: Nguyen

address: Pauwelstrasse 30

institute: RWTH Aachen University Hospital

summary: This study was designed to analyse the transcriptomes of dendritic cell populations from the lamina propria of the small intestine in order to identify transcriptomic changes along their maturation towards a migratory phenotype.

overall_design: Transcriptomic profile of dendritic cells isolated from the lamina propria of the murine small intestine

first: Fabian

middle: T

last: Hager

first: Lydia

last: Kopplin

first: Vuk

last: Cerovic

first: Anna

last: Andrusaite


title: Single cell RNA-seq data of Arabidopsis roots

status: Public on Jan 26 2025

city: Los Angeles

first: Rachel

last: Shahan

state: California

address: 610 Charles E. Young Dr. S

institute: University of California, Los Angeles

summary: We report both raw and processed scRNA-seq data that were used to construct a reference atlas of the cell cycle in the Arabidopsis root and profile opsopl2 mutant roots.

overall_design: scRNA-seq of 11 wild-type and 2 opsopl2 double mutant Arabidopsis root samples. Root tips were harvested from 5-7 day-old plants and scRNA-seq performed using 10X genomics 3` kits. The supplemtary file also contains 7 WT samples from our and others previously published work (GSE152766: Samples GSM4625995, GSM4625996, GSM4625997 and GSM4625998) and (GSE123818: Samples GSM3511858 and GSM3511859)

first: Nemanja

last: Vukašinović

first: Che-Wei

last: Hsu

first: Marco

last: Marconi

first: Shaopeng

last: Li

first: Pablo

last: Szekley

first: Christopher

last: Zachary

first: Ziv

last: Aardening

first: Isabelle

last: Vanhoutte

first: Ma

last: Qian

first: Lucrezia

last: Pinto

first: Pavel

last: Krupař

first: Nathan

last: German

first: Jingyuan

first: Jessica

last: Perez-Sancho

first: José

last: Cana Quijada

first: Emmanuelle

last: Bayer

first: Asaph

last: Aharoni

first: Matyáš

last: Fendrych

first: Elisabeth

last: Truernit

first: Yu

last: Zhou

first: Sigal

last: Savaldi-Goldstein

first: Krzysztof

last: Wabnik

first: Trevor

last: Nolan

first: Eugenia

last: Russinova


title: miR-381-3p contribution in mouse spontaneous abortion via targeting VEGFA

city: Nanjing

first: Chao

last: Ding

state: Jiangsu

address: 138 Xianlin Avenue

institute: Nanjing University of Chinese Medicine

summary: Recurrent spontaneous abortion (RSA) affects 1-5% of pregnant women, yet the mechanisms behind the disease remain unknown. It is well acknowledged that insufficient blood flow and placental abnormalities are key factors contributing to RSA. The abortive mouse model was constructed by intraperitoneal injection of β2-GPI. miRNA expression profiles in placental tissues of aborted and normal pregnant mice were detected by high-throughput sequencing. We found that miR-381-3p was highly expressed in the placenta of aborted mice and may bind to VEGFA

overall_design: Placentas from 3 normal pregnant mice and 3 placentas from β2-GPI-induced aborted pregnant mice

first: Fukang

last: Liu

first: Huayue

last: Shi

first: Jing

last: Zuo

first: Lei

last: Bi

first: Longgang

last: Shao

first: Yanqiu

last: Pan


title: Inhaled Xenon modulates microglia and ameliorates disease in mouse models of amyloidosis and tauopathy [Xenon PK in APP.PS1 microglia -mice]

city: Boston

first: Wesley

last: Nogueira Brandao

state: Massachusetts

address: 60 Fenwood Rd

department: Neurology

institute: Brigham and Women's Hospital

summary: Alzheimer’s disease (AD) is the most prevalent neurodegenerativedisorder. Currently, anti-amyloid antibody treatments modestly slow disease progression in milddementia due to AD.Emerging evidence shows that homeostatic dysregulation of the brainimmune system, especially that orchestrated by microglia, plays a significant role in the onset andprogression of the disease, including an increase in neuroinflammation and oxidative stress.Thus,a major question is how to modulate the phenotype and function of microglia to treat AD.Xenongas (Xe) is a noble gas used in human patients as an anesthetic and neuroprotectant in treatingbrain injuries. Xe penetratestheblood-brain barrier, which can make it an effective therapeutic.WeidentifiedthatXeinhalationpolarizesmouse and human microglia towards an intermediatestate of activation that we have termedas‘pre-MGnD’ in anacute neurodegeneration model andmouse models with AD-like pathology, i.e.,5xFAD (amyloid) and P301S (tau). This microglialphenotypic transition enhanced amyloid plaque compaction and reduced dystrophic neurites.Moreover, Xe inhalation reduced brain atrophy neuroinflammationand improved nest-buildingbehavior in APOE4:P301S mice. Mechanistically, Xe inhalation polarizes homeostatic microgliatoward a pre-MGnD state via IFNsignaling that maintains the microglial phagocytic responsewhile suppressing its pro-inflammatory properties. These resultssupport the translation of Xeinhalation as a novel approach to treatingAD.

overall_design: We treated 3-month-old APP/PS1 mice with a single dose of 30% Xe for 40 minutes. Animals were euthanized 3-, 7- or 14 days post-treatment, and isolated Microglia were evaluated by RNA-seq.

last: Brandao

first: Nimansha

last: Jain

first: Zhuoran

last: Yin

first: Kilian

last: Kleemann

first: Madison

last: Carpenter

first: Xin

last: Bao

first: Javier

last: Serrano

first: Eric

last: Tycksen

first: Ana

last: Durao

first: Jen-Li

last: Barry

first: Caroline

last: Baufeld

first: Dilansu

last: Guneykaya

first: Xiaoming

last: Zhang

first: Alexandra

last: Litvinchuk

first: Hong

last: Jiang

first: Neta

last: Rosenzweig

first: Kristen

last: Pitts

first: Michael

last: Aronchik

first: Taha

last: Yahya

first: Tian

last: Cao

first: Saef

last: Izzy

first: Marcelo

last: Takahashi

first: Rajesh

last: Krishnan

first: Hayk

last: Davtyan

first: Jason

last: Ulrich

first: Matthew

last: Blurton-Jones

first: Ilya

last: Ilin

first: Howard

last: Weiner

first: David

last: Holtzman

first: Oleg

last: Butovsky


title: ARM-X: an adaptable mesenchymal stromal cell-based vaccination pltform suitable for solid tumors.

status: Public on Jan 24 2025

city: Montreal

first: Moutih

last: Rafei

address: Montreal

country: Canada

institute: Universite de Montreal

summary: Background: In addition to triggering endosomal escape, the Accum® platform was recently reported for its ability to instill antigen cross-presentation properties in mesenchymal stromal cells (MSCs). Despite the promising results obtained with the first-generation vaccine using the A1 Accum® derivative (ARM vaccine), large quantities of cancer antigens were required to achieve meaningful therapeutic effects. Given this limitation, additional Accum® variants were engineered and tested for their ability to lower the need for large antigen quantities. A leading variant, AccuTOX®, was selected for that purpose. Methods: Several functional studies, including a series of antigen cross-presentation assays, were conducted using the SIINFEKL-specific T-cell clone B3Z. Analysis of endosomal escape and the effect of various anti-oxidant compounds were used to decipher the AccuTOX® mode of action in MSCs. The potency of the AccuTOX®-reprogramed MSCs (ARM-X) cells was evaluated in the context of therapeutic vaccination using immunocompetent C57BL/6 mice with three different pre-established solid tumor models. Various depletion studies were also conducted in animals to identify effector cells involved in the therapeutic response mediated by the ARM-X cells. Finally, the effect observed on murine ARM-X cells was validated on human MSCs along with an immunopeptidome study reflecting the cross-presentation potency of these reprogrammed human cells. Results: AccuTOX® can indeed trigger MSCs to cross-present, even if pulsed with low dose tumor antigens while retaining most of the innate properties of A1, including increased antigen uptake and processing, production of reactive oxygen species, endosomal escape and induction of the unfolded protein response (UPR). When tested against melanoma, pancreatic and colon cancer, therapeutic administration of the ARM-X vaccine, in combination with anti-PD-1, impairs tumor growth. Mechanistically, the ARM-X vaccine relies on efferocytosis by endogenous phagocytes and requires both CD4 and CD8 T cells, as their depletion leads to a loss in therapeutic function. Conclusion: Altogether, this second-generation ARM-X vaccine represents a platform adaptable to multiple solid tumors. In addition, our data clearly allude to a direct link between AccuTOX®-mediated UPR activation and antigen cross-presentation by MSCs. The fact that these modulated MSCs become antigen-presenting cells via UPR stimulation opens-up a new line of investigation to search for additional agents capable of specifically activating this pathway to convert culture-adapted MSCs to a cellular vaccination tool adaptable to various cancer indications.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Comparative gene expression profiling analysis of RNA-seq data for untreated mesenchymal stromal cells and AccuTOX-treated cells, co-treated with the antigen ovalbumin,tumor lysate or not.

first: Jean Pierre

last: Bikorimana

first: Nehme

last: El-Hachem


title: Inhaled Xenon modulates microglia and ameliorates disease in mouse models of amyloidosis and tauopathy [Xenon PK in APP.PS1 Tcells - mice]

first: Wesley

last: Nogueira Brandao

overall_design: We treated 3-month-old APP/PS1 mice with a single dose of 30% Xe for 40 minutes. Animals were euthanized 3-, 7- or 14 days post-treatment, and isolated splenic T cells were evaluated by RNA-seq.

last: Brandao

first: Nimansha

last: Jain

first: Zhuoran

last: Yin

first: Kilian

last: Kleemann

first: Madison

last: Carpenter

first: Xin

last: Bao

first: Javier

last: Serrano

first: Eric

last: Tycksen

first: Ana

last: Durao

first: Jen-Li

last: Barry

first: Caroline

last: Baufeld

first: Dilansu

last: Guneykaya

first: Xiaoming

last: Zhang

first: Alexandra

last: Litvinchuk

first: Hong

last: Jiang

first: Neta

last: Rosenzweig

first: Kristen

last: Pitts

last: Kenzo Takahashi


title: Inhaled Xenon modulates microglia and ameliorates disease in mouse models of amyloidosis and tauopathy [Xenon PD in MGnD paradigm]

first: Wesley

last: Nogueira Brandao

overall_design: C57BL/6 (WT) mice receive injection of apoptotic neurons in cortex and hippocampus. Two hours after the injection of apoptotic neurons, the mice were treated with Xe at four different concentrations, starting with 6%, 12%, 30%, and 35% for 40 minutes and euthanized 14 hours later. Microglia were isolated to RNAseq analysis.

last: Brandao

last: Jain

first: Michael

last: Aronchik

first: Taha

last: Yahya

first: Tian

last: Cao

first: Saef

last: Izzy

first: Marcelo

last: Takahashi

first: Rajesh

last: Krishnan

first: Hayk

last: Davtyan

first: Jason

last: Ulrich

first: Matthew

last: Blurton-Jones

first: Ilya

last: Ilin

first: Howard

last: Weiner

first: David

last: Holtzman

first: Oleg

last: Butovsky


title: Inhaled Xenon modulates microglia and ameliorates disease in mouse models of amyloidosis and tauopathy [Xenon in IFNy blocker - mice]

overall_design: we injected fluorescently labeled apoptotic neurons into the cortex and hippocampus of C57BL/6 mice previously treated with an IFNg neutralizing antibody or an IgG isotype control followed by a Xe inhalation and microglia isolation

first: Nimansha

first: Zhuoran

last: Yin

first: Kilian

last: Kleemann

first: Madison

last: Carpenter

first: Xin

last: Bao

first: Javier

last: Serrano

first: Eric

last: Tycksen

first: Ana

last: Durao

first: Jen-Li

last: Barry

first: Caroline

last: Baufeld

first: Dilansu

last: Guneykaya

first: Xiaoming

last: Zhang

first: Alexandra

last: Litvinchuk

first: Hong

last: Jiang

last: Rosenzweig

last: Pitts


title: Substrate Stiffness Dictates Unique Doxorubicin-induced Senescence-associated Secretory Phenotypes and Transcriptomic Signatures in Human Pulmonary Fibroblasts

status: Public on Jan 21 2025

city: novato

first: HUIXUN

last: DU

state: CALIFORNIA

address: 8001 Redwood Blvd

institute: Buck Institute

summary: Cells are subjected to dynamic mechanical environments which impart forces and induce cellular responses. In age-related conditions like pulmonary fibrosis, there is both an increase in tissue stiffness and an accumulation of senescent cells. While senescent cells produce a senescence-associated secretory phenotype (SASP), the impact of physical stimuli on both cellular senescence and the SASP is not well understood. Here, we show that mechanical tension, modeled using cell culture substrate rigidity, influences senescent cell markers like SA-β-gal and secretory phenotypes. Comparing human primary pulmonary fibroblasts (IMR-90) cultured on physiological (2 kPa), fibrotic (50 kPa), and plastic (approximately 3 GPa) substrates, followed by senescence induction using doxorubicin, we identified unique high-stiffness-driven secretory protein profiles using mass spectrometry and transcriptomic signatures, both showing an enrichment in collagen proteins. Consistently, clusters of p21+ cells are seen in fibrotic regions of bleomycin induced pulmonary fibrosis in mice. Computational meta-analysis of single-cell RNA sequencing datasets from human interstitial lung disease confirmed these stiffness SASP genes are highly expressed in disease fibroblasts and strongly correlate with mechanotransduction and senescence-related pathways. Thus, mechanical forces shape cell senescence and their secretory phenotypes.

overall_design: Bulk mRNA-sequencing of IMR90 fibroblasts treated with 250nM or 100nM doxorubicin that were cultured on either plastic culture plate or 2 kPa hydrogel.

first: Huixun

last: Du

first: Daniel

last: Winer


title: Native nucleosome-positioning elements for the investigation of nucleosome repositioning.

status: Public on Jan 16 2025

city: State College

first: Shane

middle: Douglas

last: Stoeber

state: Pennsylvania

address: 406 South Frear Building

department: BMMB

institute: Penn State

summary: Nucleosome repositioning is essential for establishing nucleosome-depleted regions (NDRs) to initiate transcription. This process has been extensively studied using structural, biochemical, and single-molecule approaches, which require homogenously positioned nucleosomes. This is often achieved using the Widom 601 sequence, a highly efficient nucleosome positioning element (NPE) selected for its unusually strong binding to the H3-H4 histone tetramer. Due to the artificial nature of 601, a library of native NPEs is needed to explore the role of DNA sequence in nucleosome repositioning. Here, we characterize the position distributions and nucleosome formation free energy for a set of yeast native nucleosomes (YNNs) from Saccharomyces cerevisiae. We show these native NPEs can be used in biochemical studies of nucleosome repositioning by transcription factors (TFs) and the chromatin remodeler Chd1. TFs could directly reposition a fraction of nucleosomes containing native NPEs, but not 601-containing nucleosomes. In contrast, partial unwrapping was similar for 601 and native NPE sequences. The rate of ATP-dependent remodeling by Chd1 was within the range of the fast and slow directions of the 601 nucleosomes. This set of native NPEs provides an alternative to the 601 NPE that can be used for probing the repositioning of nucleosomes that contain native DNA sequences.

overall_design: MNase-seq to determine nucleosome positioning of YNN candidates or 601 with and without yeast transcription factors.

first: Ruo-Wen

last: Chen

first: Ilana

last: Nodelman

first: Hengye

first: Lloyd

last: Yang

first: Gregory

last: Bowman

first: Lu

last: Bai

first: Michael

last: Poirier


title: RetS-Mediated Environmental Sensing Coordinates TetR-Dependent Regulation of Type III Secretion System and Virulence in Pseudomonas syringae pv. actinidiae

city: Guiyang

first: Muhammad

last: Asif

state: Guizhou

address: college of agriculture, Guizhou university

department: Plant Pathology

institute: Guizhou University

summary: Kiwifruit bacterial canker, caused by Pseudomonas syringae pv. actinidiae (Psa), is an emerging global concern in kiwifruit production. Successful Psa infection in kiwifruit relies on the type III secretion system (T3SS), which is governed by the HrpR/S-HrpL regulatory pathway. However, the mechanisms by which certain transcriptional factors regulate this pathway remain poorly understood. In this study, we identified the TetR/AcrR family transcription factors C_22735 (tetR1) and C_04700 (hybrid histidine kinase; retS) in the P. syringae pv. actinidiae (biovar 3) strain S26 using transposon libraries and a DNA pull-down strategy. Both the mutant strains tetR1 and retS exhibited significantly reduced pathogenicity in kiwifruit leaf discs and a diminished ability to induce hrpRS, hrpL, and hrpA expression in vitro and showed a reduced hypersensitive response in Nicotiana benthamiana. Moreover, transcriptomic studies showed a considerable overlap in down-regulated genes between the tetR1 and two-component system (TCS) retS mutant, highlighting the intertwined regulatory roles of both genes. This overlap suggests a tightly coordinated regulatory system, where tetR1 serves as the response regulator of the hybrid histidine kinase retS to regulate T3SS and virulence. The electrophoretic mobility shift assays, and luciferase-based promoter activity detection further revealed that TetR1 positively regulates the T3SS by directly binding to the promoter regions of hrpR/S and hrpL. This study identifies the tetR1 gene as the first TetR-family transcription factor directly linking the hybrid TCS retS to HrpR/S-HrpL -mediated T3SS regulatory pathway activation in Psa for regulation.

overall_design:
RNA-seq profiling of wild type strain S26 and its knockout strains (C_22735, C_4700) induced by HDM (hrp-depress) for 8h.

Grant awarded to Zhao Zhibo: National Key Research and Development Program of China (Grant No. 2022YFD1400200)
Grant awarded to Zhao Zhibo: National Natural Science Foundation of China (Grant No. 31860486, 32001864)
Grant awarded to Zhao Zhibo: Fund for the China Agriculture Research System (Grant No. CARS-26-04A)

first: Renjian

last: Hu

first: Fu

last: zhao

first: Zhibo

last: Zhao

first: Asif

last: Muhammad


title: Combinatorial phosphorylation on CTD of RNA polymerase II selectively controls transcription and export of protein-coding mRNAs

city: Austin

first: Svetlana

last: Panina

state: TX

address: 101 East 21st St.

department: Molecular Biosciences

institute: The University of Texas at Austin

summary: C-terminal domain (CTD) of RNA polymerase II is crucial for recruiting transcription regulators via specific post-translational modifications (PTM), especially phosphorylation. The hypothesis of combination of PTMs, or ‘CTD code’, that can allow precise and dynamic recruitment of transcription machinery is highly attractive, yet the experimental evidence to support this hypothesis has been scarce. Here, despite lacking specific antibodies for combinatorial CTD phosphorylation, we developed an innovative approach that detects double phosphorylation patterns on the CTD in a whole-genomic fashion by leveraging the antibody masking effect with selectively removing the flanking interference. Using this method, we detected pT4pS5 double phosphosites occurring exclusively during the transcription of protein-coding genes. Furthermore, we showed that pT4pS5 marks recruit the Transcription and Export complex (TREX), which specifically facilitates mRNA processing and nucleocytoplasmic export of protein-coding mRNAs. The recruitment of TREX by pT4pS5 phosphosites is particularly important for the processing of lengthy neurogenesis-related genes. Our results provide experimental support for the notion that CTD coding system can function combinatorially and in a gene-specific manner, which encodes an exact information about the transcription of specific gene clusters. This method can be broadly applied to map all combinatorial PTM patterns on RNA polymerase II, paving the way for a deeper understanding of gene-specific transcription regulation at the molecular level.

overall_design: ChIP-Sequencing of pThr4-CTD upon treatment with active Ssu72 phosphatase or inactive enzyme (Mutant/Mut), two biological replicates per sample (HEK293 cells).

middle: B

first: Qian

last: Zhang

first: Seema

last: Irani

first: Haley

last: Hardtke

first: Renee

last: Stephenson

first: Brendan

last: Floyd

first: Rosamaria

last: Moreno

first: Edward

last: Marcotte

first: Jessie


title: Inhaled Xenon modulates microglia and ameliorates disease in mouse models of amyloidosis and tauopathy [Tau]

first: Wesley

last: Nogueira Brandao

overall_design: Starting at 6 months of age until 9.5 months of age TE4 (P301S APOE4) mice either received weekly 40-minute-long treatments with 30% Xe or atmospheric air (control).  At 9.5 months of age, mice were sacrificed, and tissue was harvested.

last: Brandao

first: Nimansha

last: Jain

first: Zhuoran

last: Yin

first: Kilian

middle: L

last: Kleemann

first: Madison

last: Carpenter

first: Xin

last: Bao

first: Javier

last: Serrano

first: Eric

last: Tycksen

first: Ana

last: Durao

first: Jen-Li

last: Barry

first: Caroline

last: Baufeld

first: Dilansu

last: Guneykaya

first: Xiaoming

first: Alexandra

last: Litvinchuk

first: Hong

last: Jiang

first: Neta

last: Rosenzweig

first: Kristen

last: Pitts

last: Aronchik

first: Taha

last: Yahya

first: Tian

last: Cao

first: Saef

last: Izzy

first: Marcelo

last: Takahashi

first: Rajesh

last: Krishnan

first: Hayk

last: Davtyan

first: Jason

last: Ulrich

first: Matthew

last: Blurton-Jones

first: Ilya

last: Ilin

first: Howard

last: Weiner

first: David

last: Holtzman

first: Oleg

last: Butovsky


title: Inhaled Xenon modulates microglia and ameliorates disease in mouse models of amyloidosis and tauopathy [Xenon scRNAseq Myeloid]

first: Wesley

last: Nogueira Brandao

overall_design: We initiated treatment with xenon (30%) or air for 40 minutes in female APP/PS1 mice at 2 months of age and continued for 8 weeks with once-a-week treatments for 40 minutes each. At the end, we euthanized the animals and isolated CD45+ Cd11b+ cells for scRNAseq

last: Brandao

first: Nimansha

last: Jain

first: Zhuoran

last: Yin

first: Kilian

last: Kleemann

first: Madison

last: Carpenter

first: Xin

last: Bao

first: Javier

last: Serrano

first: Eric

last: Tycksen

first: Ana

last: Durao

first: Jen-Li

last: Barry

first: Caroline

last: Baufeld

first: Dilansu

last: Guneykaya

first: Xiaoming

last: Zhang

last: Litvinchuk

first: Michael

middle: K


title: Inhaled Xenon modulates microglia and ameliorates disease in mouse models of amyloidosis and tauopathy [Xenon-iMGL in vitro]

overall_design: Human iPSC-derived microglia (iMG) expressing GFP+ were treated with Xenon 75% for 24h fallowed by RNA isolation.

first: Alexandra

first: Hong

last: Jiang

first: Neta

last: Rosenzweig

first: Kristen

last: Pitts

last: Aronchik

first: Taha

last: Yahya

first: Tian

last: Cao

first: Saef

last: Izzy

first: Marcelo

last: Kenzo Takahashi

first: Rajesh

last: Krishnan

first: Hayk

last: Davtyan

first: Jason

last: Ulrich

first: Matthew

last: Blurton-Jones

first: Ilya

last: Ilin

first: Howard

last: Weiner

last: Holtzman


title: Inhaled Xenon modulates microglia and ameliorates disease in mouse models of amyloidosis and tauopathy [Xenon in APPPS1 - Mice]

first: Wesley

last: Nogueira Brandao

overall_design: We initiated treatment with xenon (30%) or air for 40 minutes in female APP/PS1 mice at 2 months of age and continued for 8 weeks with once-a-week treatments for 40 minutes each. At the end, we euthanized the animals and isolated microglia cells for RNAseq.

last: Brandao

first: Nimansha

last: Jain

first: Zhuoran

last: Yin

first: Kilian

last: Kleemann

first: Madison

last: Carpenter

first: Xin

last: Bao

first: Javier

last: Serrano

first: Eric

last: Tycksen

first: Ana

last: Durao

first: Jen-Li

last: Barry

first: Caroline

last: Baufeld

first: Dilansu

last: Guneykaya

last: Zhang

first: David

first: Oleg

last: Butovsky


title: Inhaled Xenon modulates microglia and ameliorates disease in mouse models of amyloidosis and tauopathy [Xenon in IPSMG H5xFAD]

overall_design: Human iMGL were transplanted into the brains of early postnatal (P1) immunodeficient MITRG mice. Xe treatment (Xe 30%, 40 minutes once a week) was initiated in 5xFAD-MITRG mice at 4 months of age and continued once a week until the animals reached 6 months of age. The cells were isolated, and RNAseq was performed with total RNA.

first: KilianL

first: Xiaoming

first: Alexandra

last: Litvinchuk

first: Hong

last: Jiang

first: Neta

last: Rosenzweig

first: Kristen

last: Pitts

first: Michael

last: Aronchik

first: Taha

last: Yahya

first: Tian

last: Cao

first: Saef

last: Izzy

first: Marcelo

last: Kenzo Takahashi

first: Rajesh

last: Krishnan

first: Hayk

last: Davtyan

first: Jason

last: Ulrich

first: Matthew

last: Blurton-Jones

last: Ilin

last: Weiner


title: Inhaled Xenon modulates microglia and ameliorates disease in mouse models of amyloidosis and tauopathy [Tdt Tomato - mice]

first: Wesley

last: Nogueira Brandao

overall_design: APP/PS1”Clec7a-CreERT2:ROSA26TdTomato mice at 3 months of age were treated with Tamoxifen (TAM) 75mg/kg. One month later, the animals were euthanized, and microglia expressing TdTomato fluorescence (TdT) or not (DN) were isolated by FACS. The cells signature were analyzed by RNAseq.

last: Brandao

first: Nimansha

last: Jain

first: Zhuoran

last: Yin

first: Kilian

last: Kleemann

first: Madison

last: Carpenter

first: Xin

last: Bao

first: Javier

last: Serrano

first: Eric

last: Tycksen

first: Ana

last: Durao

first: Jen-Li

last: Barry

first: Caroline

last: Baufeld

first: Dilansu

last: Guneykaya

last: Zhang

first: Ilya

first: Howard

first: David

last: Holtzman


title: Bisulfite sequencing libraries from opossum male immortalised fibroblasts

status: Public on Jan 12 2025

city: London

first: James

last: Turner

address: The Francis Crick Institute, 1 Midland Road

institute: The Francis Crick Institute

type: Methylation profiling by high throughput sequencing

summary: Decades of work in placental (eutherian) species have constructed a paradigm of mammalian development, wherein the genome-wide erasure of parental DNA methylation is required for embryogenesis1-10. Whether such DNA methylation reprogramming is, in fact, conserved in other mammals is unknown. To resolve this point, we generated base-resolution DNA methylation maps in gametes, embryos and adult tissues of the opossum marsupial Monodelphis domestica, revealing extensive variations from the eutherian-derived model. In stark contrast with eutherians, the marsupial genome remains hypermethylated during the cleavage stages and in the embryo proper of the blastocyst. In the extra-embryonic trophectoderm DNA methylation is reduced, suggesting an important evolutionary conserved function for DNA hypomethylation in formation of the mammalian placenta. Furthermore, unlike in eutherians, the inactive X chromosome becomes globally DNA hypomethylated during embryogenesis. Using our DNA methylation profiles, we identify a candidate mechanism for imprinted X-inactivation in marsupials, via maternal promoter DNA methylation of the Xist-like non-coding RNA RSX11. How mammalian embryos employ DNA methylation to regulate their development is therefore more mechanistically diverse than current models can accommodate.

overall_design: BS-seq was performed on three replicates of WT and DNMT1-KO (mosaic) opossum male immortalised fibroblasts at day4 after the DNMT1-KO.

first: Bryony

last: Leeke

first: Wazeer

last: Varsally

first: Sugako

last: Ogushi


title: Bulk mRNA sequencing of adult opossum tissues

overall_design: From each animal the same three tissues were extracted: brain, liver, spleen. There are six animals, three female and three male, so 18 samples in total. All tissue was snap frozen in liquid nitrogen and stored at -80°C until library preparation.

first: Jasmin

last: Zohren

first: John

last: Vandeberg


title: Whole genome bisulfite sequencing of adult opossum tissues

first: Turner

last: James

first: Leeke

last: Bryony

first: Zohren

last: Jasmin

first: Vandeberg

last: John


title: Whole genome bisulfite sequencing of opossum embryos and gametes

overall_design: BS-seq libraries were prepared from embryos and gametes of the opossum Monodelphis domestica.


title: Inhaled Xenon modulates microglia and ameliorates disease in mouse models of amyloidosis and tauopathy [5xFAD-MITRG-iMGL 6M]

first: Wesley

last: Nogueira Brandao

overall_design: Xe treatment (Xe 30%, 40 minutes once a week) was initiated in 5xFAD-MITRG mice at 4 months of age and continued once a week until the animals reached 6 months of age. The mouse microglia were isolated by FACS Aria, and RNAseq was performed with total RNA.

last: Brandao

first: Nimansha

last: Jain

first: Zhuoran

last: Yin

first: KilianL

last: Kleemann

first: Madison

last: Carpenter

first: Xin

last: Bao

first: Javier

last: Serrano

first: Eric

last: Tycksen

first: Ana

first: Xiaoming

first: Alexandra

last: Litvinchuk

first: Hong

last: Jiang

first: Neta

last: Rosenzweig

first: Kristen

last: Pitts

first: Michael

last: Aronchik

first: Taha

last: Yahya

first: Tian

last: Cao

first: Saef

last: Izzy

first: Marcelo

last: Kenzo Takahashi

first: Rajesh

last: Krishnan

first: Hayk

last: Davtyan

first: Jason

last: Ulrich

first: Matthew

last: Blurton-Jones

last: Ilin

last: Weiner

first: Oleg

last: Butovsky


title: Inhaled Xenon modulates microglia and ameliorates disease in mouse models of amyloidosis and tauopathy [Xenon in IFNgr1 cKO]

first: Wesley

last: Nogueira Brandao

overall_design: Cx3cr1-CreERT2/+:Ifngr1Flox mice were treated with tamoxifen (TAM) to delete Ifngr1 one month before the injection of apoptotic neurons. Two hours after the injection of apoptotic neurons, the mice were treated with Xe (30%) for 40 minutes and euthanized 14 hours later. Phagocytic and non-phagocytic microglia were isolated for RNAseq analysis

last: Brandao

first: Nimansha

last: Jain

first: Zhuoran

last: Yin

first: KilianL

last: Kleemann

first: Madison

last: Carpenter

first: Xin

last: Bao

first: Javier

last: Serrano

first: Eric

last: Tycksen

last: Durao

first: Jen-Li

last: Barry

first: Caroline

last: Baufeld

first: Dilansu

last: Guneykaya

last: Zhang

first: Ilya

first: Howard

first: David

last: Holtzman


title: Inhaled Xenon modulates microglia and ameliorates disease in mouse models of amyloidosis and tauopathy [5xFAD-MITRG Astrocytes 6M]

overall_design: Xe treatment (Xe 30%, 40 minutes once a week) was initiated in 5xFAD-MITRG mice at 4 months of age and continued once a week until the animals reached 6 months of age. The astrocytes were isolated by FACS Aria, and RNAseq was performed with total RNA.

first: Ana

first: Xiaoming

first: Alexandra

last: Litvinchuk

first: Hong

last: Jiang

first: Neta

last: Rosenzweig

first: Kristen

last: Pitts

first: Michael

last: Aronchik

first: Taha

last: Yahya

first: Tian

last: Cao

first: Saef

last: Izzy

first: Marcelo

last: Kenzo Takahashi

first: Rajesh

last: Krishnan

first: Hayk

last: Davtyan

first: Jason

last: Ulrich

last: Blurton-Jones

last: Ilin

last: Weiner


title: Tissular chromatin states cartography based on double-barcoded DNA arrays capturing unloaded PA-Tn5 Transposase

status: Public on Jan 14 2025

city: Evry

first: Marco Antonio

last: MENDOZA-PARRA

address: 2 rue Gaston Crémieux

country: France

institute: CNRS UMR8030

summary: Recent developments in spatial omics are revoluzionating our understanding of tissue structures organization and their deregulation in disease. Here, we present a strategy for capturing chromatin histone modification signatures across tissue sections by taking advantage of a double-barcoded DNA arrays design compatible with in situ protein A-Transposase Tn5 tagmentation. This approach has been validated in presence of fresh-frozen mouse brain tissues but also in decalcified formalin-fixed paraffin-embedded (FFPE) mouse paws samples, where either the histone modification H3K4 tri-methylation or H3K27-acethylation has been used as proxy for interrogating active promoter signatures. Furthermore, since combinatorial enrichment of multiple histone modifications were shown to code for various states of gene transcriptional status (active, bivalent, repressed), we have integrated several histone modifications issued from consecutive mouse embryos to reveal changes in chromatin states across the tissue. Overall, this spatial epigenomics technology combined with the use of a spatial chromatin states analytical strategy paves the way for future epigenetics studies for addressing tissue architecture complexity.

overall_design: Tissue sections were deposited on DNA arrays presenting a MOS sequence at the 3'-end and two unique molecular barcodes associated to their physical position in the Array. After adding a 1st antibody directed to a given histone modification, and a second antibody for enhancing the signal, the ProteinA-Tn5 recombinant protein has been loaded into the DNA arrays thanks to the MOS sequence in regions enriched for the antibodies in use. Then, the use of MgCl2 allows to cleave the chromatin and allows to physically capture it into the DNA array. Finally a library preparation procedure is used for Illumina sequencing.

first: Maria-Grazia

last: Mendoza-Ferri

first: Gwendoline

last: Lozachmeur

first: Maximilien

last: Duvina

first: Laetitia

last: Perret

first: Didier

last: Merciris

first: Anne

last: Gigout

first: Marco-Antonio

last: Mendoza-Parra


title: Deep phenotyping of peripheral mononuclear blood cells in health and disease

status: Public on Jan 06 2025

city: Newcastle upon tyne

first: Tegan

last: McTaggart

address: Framlington Place

institute: Newcastle University

summary: Peripheral blood mononuclear cells (PBMCs) were isolated from healthy controls and patients with various diseases.. Cells were stained with CD45 and sample tags for identification purposes. CD45+ live cells were enriched through flow sorting and samples were pooled. Samples were then stained with 30 AbSeq antibodies and loaded onto 4 cartridges to account for interplate differences. Pooled sequencing libraries were then sequenced on NovaSeq 6000 (Illumina) using a S2 Reagent Kit v1.5 (200 cycles).

overall_design: For human scRNAseq, PBMCS were isolated from healthy controls and patients with various diseases. Cells were stained with CD45 and sample tags. CD45+ live cells were enriched through flow sorting and samples were pooled. Samples were then stained with 30 AbSeq antibodies and loaded onto 4 cartridges and subjected to Rhapsody analysis following manufacturers protocol. Pooled sequencing libraries were then sequenced on NovaSeq 6000 (Illumina) using a S2 Reagent Kit v1.5 (200 cycles).

first: Shoba

last: Amarnath

first: Jing Xuan

last: Lim


title: Inhaled Xenon modulates microglia and ameliorates disease in mouse models of amyloidosis and tauopathy [Xenon in Microglia in vitro - Mice]

first: Wesley

last: Nogueira Brandao

overall_design: To evaluate the direct effects of Xenon on microglia,we cultured adult microglia for 5 days with the following: 1) M-CSF (10ng/ml) with human TGFb (50ng/ml) to induce a homeostatic signature, or 2) GM-CSF (10ng/ml) for MGnD differentiation. On day 6, all cytokines were removed following Xe exposure for 24 hours. Thus, the RNA were extracted and samples submitted to RNAseq analysis.

last: Brandao

first: Nimansha

last: Jain

first: Zhuoran

last: Yin

first: Kilian

last: Kleemann

first: Madison

last: Carpenter

first: Xin

last: Bao

first: Javier

last: Serrano

first: Eric

last: Tycksen

first: Ana

last: Durao

first: Jen-Li

last: Barry

first: Caroline

last: Baufeld

first: Dilansu

last: Guneykaya

first: Xiaoming

last: Zhang

first: Alexandra

last: Litvinchuk

first: Hong

last: Jiang

first: Neta

last: Rosenzweig

first: Kristen

last: Pitts

first: Michael

last: Aronchik

first: Taha

last: Yahya

first: Tian

last: Cao

last: Izzy

last: Takahashi

last: Krishnan

first: Matthew

first: Ilya

first: Howard

first: David

last: Holtzman

first: Oleg

last: Butovsky


title: RNA-sequencing libraries from opossum male immortalised fibroblasts

first: James

last: Turner

overall_design: RNA-seq was performed on three replicates of WT and DNMT1-KO (mosaic) opossum male immortalised fibroblasts at day4 and day8 after the DNMT1-KO.

first: Turner

last: James

first: Leeke

last: Bryony

first: Menchero Fernandez

last: Sergio

first: Ogushi

last: Sugako


title: A reference model for circulating hematopoietic stem cells with applications to diagnostics

city: Rehovot

first: Liran

last: Shlush

address: 234 Herzl Street

country: Israel

institute: Weizmann Institute of Science

summary:
With aging, deviation of human blood counts from their normal range accompanies the transition from health to hematological and other diseases. Hematopoietic stem and progenitor cells (HSPCs) deliver life-long multi-lineage output, but their variation across healthy humans and their diagnostic utility haven’t been characterized. To address this, we introduce an HSPC reference model using single-cell profiling of circulating CD34+ cells (cHSPCs) from 148 healthy individuals. We characterize physiological cHSPC composition, link it with standard blood counts and show that the ratio between lymphoid and myeloid progenitors is decreased in ageing males. Using this new reference model, we develop sensitive tools which could be used for diagnostics of myelodysplastic syndrome (MDS) from peripheral blood without bone marrow analysis. Profiling cHSPC compositions leads to the discovery of new MDS subclasses, ranging in their lymphocyte, basophil and granulocyte progenitor frequencies. The data and methodologies presented herein highlight the role of reference modeling in promoting clinical applications of single-cell genomics in MDS and in the future for other diseases too.

This dataset can be explored as metacells at https://apps.tanaylab.com/MCV/blood_aging (for more about metacells, see https://github.com/tanaylab/metacells and https://doi.org/10.1186/s13059-022-02667-1).

overall_design:
PBMCs were isolated from fresh blood using Ficoll (Lymphoprep filled Sepmate tubes by StemCell technologies), then enriched for cHSPCs using CD34 magnetic bead-based enrichment (EasySep human CD34 positive selection kit II by StemCell technologies). scRNA-seq was performed on the enriched fraction (10x Genomics Chromium Next Gem single cell 3’ reagent kit V3.1)

***************************************************************
As our scRNA-seq data contain SNPs allowing donor identification, our IRB does not allow publishing raw data, and so we publish only processed data.
***************************************************************

first: Nili

last: Furer

first: Nimrod

last: Rappoport

first: Oren

last: Milman

first: Sigal

last: Tavor

first: Aviezer

last: Lifshitz

first: Akhiad

last: Bercovich

last: Ben-Kiki

first: Adi

last: Danin

first: Merav

last: Kedmi

first: Zohar

last: Shipony

first: Doron

last: Lipson

first: Eti

last: Meiri

first: Gila

last: Lithwik Yanai

first: Shiran

last: Shapira

first: Nadir

last: Arber

first: Svetlana

last: Berdichevsky

first: Jeffrey

last: Tyner

first: Sunil

last: Joshi

first: Dan

last: Landau

first: Saravanan

last: Ganesan

first: Neville

last: Dusaj

first: Paulina

last: Chamely

first: Nathali

last: Kaushansky

first: Noa

last: Chapal-Ilani

first: Ron

last: Shamir

first: Amos

last: Tanay


title: Antimicrobial action of t-cinnamaldehyde on Escherichia coli MG1655

status: Public on Jan 03 2025

city: Gdansk

first: Dariusz

last: Nowicki

state: pomorskie

address: Wita Stwosza 59

department: Bacterial Molecular Genetics

country: Poland

institute: University of Gdansk

summary: Antimicrobial resistance pose a global thread nowadays. Compounds of natural origin are an important source of drugs used in clinical practice. However, it is important to understand both their principles of efficacy and their molecular mechanism of action. In this study we evaluated antimicrobial potential of t-cinnamaldehyde which is an organic compound found in many plant species, especially in the Cinnamomum genus, such as Cinnamomum zeylanicum and cassia. Cinnamon oil extracted from the bark of these plants contains up to 80% trans-cinnamaldehyde. Although CNMA has shown antimicrobial properties against numerous Gram+ and Gram- species, its mode of action against pathogens remains not fuly elucidated. Therefore, this project aims to determine CNMA activity at the level of gene expression. Total RNA was isolated and checked for quality using the Bioanalyzer 2100. The sequencing run was conducted on the Illumina NovaSeq6000 platform. 30 million pair-end reads per samples were assessed with 101 pb read length. Reference E. coli MG1655 genome sequence and annotations were downloaded from GenBank. Differentially expressed analysis of 0.25 x MIC CNMA was performed against untreated control in indicated time with p ≤ 0.001 and log2FC ≥ 1.5. We have discovered many changes bacterial transcriptome. For instance: following the treatment with 0.25×MIC of CNMA, we found 292 and 140 upregulated and 107 and 96 downregulated genes at time points 30 and 60 min, respectively. Among the most enriched genes, were those related to the tricarboxylic acid (TCA) cycle, flagellum synthesis, amino acid transport, and oxidoreductase activity. According to these findings we can conclude that observed transcriprional pattern indicates severe metabolic downshift in treated cells, and consequently activation of stress processes. These was in line with our secondary experiments which revealed drop in growth kinnetic, cytoplasm shrinkage, NAD/NADH level alteration and elevation of stringent response alarmones ((p)ppGpp). Taken together, this suggests that CNMA-treated E. coli bacteria undergo major metabolic changes that finally result in cell death.

overall_design: To obtain a overview of the impact of t-cinnamaldehyde (CNMA) on bacterial fitness, we analyzed the transcriptome changes in cells treated with sub-inhibitory concentration (0.25xMIC). Total RNA sequencing was performed to assess the changes in gene expression pattern at 30 and 60 min post t-cinnamaldehyde treatment. Experiment was performed in three independent repeats, untreated cultures where used as a control.

first: Monika

last: Karczewska

first: Agnieszka

last: Szalewska-Pałasz


title: Infiltrating lipid-rich macrophage subpopulations identified as a regulator of increasing prostate size in human benign prostatic hyperplasia

status: Public on Jan 13 2025

city: West Lafayette

first: Nadia

middle: Marie

last: Atallah

state: IN

address: 201 S. University St

department: Center for Cancer Research

institute: Purdue University

summary: Macrophages exhibit marked phenotypic heterogeneity within and across disease states. Lipid metabolic reprogramming critically regulates macrophage activation. Chronic inflammation has been observed in human benign prostatic hyperplasia (BPH) tissues, however macrophage activation states and their contributions to this hyperplastic disease have not been defined. We postulated that a shift in macrophage phenotypes with increasing prostate size could involve metabolic alterations resulting in prostatic epithelial or stromal hyperplasia. Single-cell RNA-seq of CD45+ transition zone leukocytes from 10 large (>90 grams) and 10 small (<40 grams) human prostates was conducted. Macrophage subpopulations were defined using marker genes. BPH macrophages do not distinctly categorize into M1 and M2 phenotypes. Instead, macrophages with neither polarization signature accumulate in large versus small prostates. Specifically, macrophage subpopulations with altered lipid metabolism pathways, demarcated by TREM2 and MARCO expression, significantly accumulate as prostate size increases. No T cell subclusters specifically accumulate in large versus small prostates. TREM2+ and MARCO+ macrophage abundance positively correlates with patient body mass index and prostatic symptom scores. TREM2+ macrophages have significantly higher neutral lipid than TREM2- macrophages from BPH tissues. Lipid-rich macrophages localize to the stroma in BPH tissues. In vitro studies indicate that lipid-loaded macrophages increase prostate epithelial and stromal cell proliferation compared to control macrophages. These data define new BPH immune subpopulations, TREM2+ and MARCO+ macrophages, and suggest that lipid-rich macrophages may exacerbate lower urinary tract symptoms in patients with large prostates. Further investigation is needed to evaluate the therapeutic benefit of targeting these cells in BPH.

overall_design: Single-cell RNA-seq of CD45+ transition zone leukocytes from 10 large (>90 grams) and 10 small (<40 grams) human prostates was conducted. The small samples and 4 large samples were submitted to GEO previously in GSE164695.

last: Lanman

first: Era

last: Meco

first: Philip

last: Fitchev

first: Andree

last: Kolliegbo

first: Meaghan

last: Broman

first: Yana

last: Filipovich

first: Harish

last: Kothandaraman

first: Gregory

last: Cresswell

first: Pooja

last: Talaty

first: Malgorzata

last: Antoniak

last: Brumer

first: Alexander

last: Glaser

first: Andrew

last: Higgins

first: Brian

last: Helfand

first: Omar

last: Franco

first: Susan

last: Crawford

first: Timothy

last: Ratliff

first: Simon

middle: W

last: Hayward

first: Renee

last: Vickman


title: NEDD4-binding protein 1 suppresses HBV replication by regulating HBV RNAs

status: Public on Jan 08 2025

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

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

summary: Background and Aims  Chronic infection with hepatitis B virus (HBV) has been known to cause liver cirrhosis and hepatocellular carcinoma. Although nucleos(t)ide analogs are mainly used for the treatment of HBV, they require long-term administration and may lead to the emergence of drug resistance. Therefore, to identify targets for the development of novel anti-HBV therapies, we screened HBV-suppressive host factors using RNA-bnding protein (RBP) expression plasmids library.   Approach and Results  We screened the RBP library by generating overexpressing RBP cell lines and observing anti-HBV effect. As a result, we identified NEDD4-binding protein 1 (N4BP1) as a candidate showing anti-HBV effect. In hepatocellular carcinoma cell lines, overexpression of N4BP1 decreased the relaxed circular DNA (rcDNA) levels, while suppression of N4BP1 expression increased rcDNA levels. Restoring N4BP1 expression in N4BP1 knockout cells regained the anti-HBV effect of N4BP1. Next, we constructed KH-like and RNase domain-deficient mutants of N4BP1 and examined their effects on HBV replication, and found that both the KH-like and RNase domains are required for its anti-HBV effect. N4BP1 suppresses the step where pregenomic RNA (pgRNA) is synthesized in the HBV life cycle by promoting degradation of pgRNA. Transcriptome analyses of primary human hepatocytes overexpressing N4BP1 suggested that N4BP1 may have anti-HBV activity independent of other host factors.   Conclusions  In summary, N4BP1 was found to be a novel anti-HBV factor. N4BP1 inhibited HBV replication by promoting pgRNA degradation.

overall_design: We performed a transcriptome analyses to determine whether other factors are involved in the anti-HBV activity of N4BP1. GFP or N4BP1 overexpressing PHHs were infected with HBV (5 Geq/cell). At 3 dpi, total RNA in PHHs was extracted using RNeasy Mini Kit following the manufacturer's protocol.

first: Nobuhiro

last: Kobayashi

first: Saori

last: Suzuki

first: Rigel

first: Tomokazu

last: Tamura

first: Yuki

last: Sakamoto

first: Tomoya

last: Saito

first: Takuma

last: Izumi

first: Kisho

last: Noda

last: Okuzaki

first: Yumi

last: Kanegae

first: Yoshiharu

last: Matsuura

first: Osamu

last: Takeuchi

first: Akinobu

last: Taketomi

first: Takasuke

last: Fukuhara


title: Inhaled Xenon modulates microglia and ameliorates disease in mouse models of amyloidosis and tauopathy [Xenon in APPPS1 IFNy blocker-Mice]

first: Wesley

last: Nogueira Brandao

overall_design: We treated APP/PS1 mice at 6 months of age once a week for 2 weeks with the anti-IFNγ neutralizing antibody, administered 24 hours intraperitoneally before Xe exposure. After 14 days, we euthanized the animals and assessed microglial signatures and disease pathology

last: Brandao

first: Nimansha

last: Jain

first: Zhuoran

last: Yin

first: Kilian

last: Kleemann

first: Madison

last: Carpenter

first: Xin

last: Bao

first: Javier

middle: R

last: Serrano

first: Eric

last: Tycksen

first: Ana

last: Durao

first: Jen-Li

last: Barry

first: Caroline

last: Baufeld

first: Dilansu

last: Guneykaya

first: Xiaoming

last: Zhang

first: Alexandra

last: Litvinchuk

first: Hong

last: Jiang

first: Neta

last: Rosenzweig

first: Kristen

last: Pitts

first: Michael

last: Aronchik

first: Taha

last: Yahya

first: Tian

last: Cao

first: Saef

last: Izzy

first: Marcelo

last: Takahashi

first: Rajesh

last: Krishnan

first: Hayk

last: Davtyan

first: Jason

last: Ulrich

first: Matthew

last: Blurton-Jones

first: Ilya

last: Ilin

first: Howard

last: Weiner

first: David

last: Holtzman

first: Oleg

last: Butovsky


title: A Blueprint of Sex-Specific Neuronal Regulation in the C. elegans Nervous System at Single-Cell Resolution

first: Rizwanul

last: Haque

state: Israel

address: Herzl St 234, Rehovot

department: Brain Sciences

summary: Sex-specific behaviors within a species are often attributed to variances in neuronal wiring and molecular signatures. However, how the genetic sex shapes the molecular architecture of the nervous system at a single neuron level is still unknown. To address this gap, we used single-cell RNA-sequencing (scRNA-seq) to profile the transcriptome of the sex-shared nervous system of adult male and hermaphrodite Caenorhabditis elegans. By ranking neurons based on the degree of molecular dimorphism, we uncover novel sexually dimorphic neurons such as PLM neurons, where functional dimorphism was corroborated by diminished posterior touch responses in hermaphrodites. We identify sex-specific regulators of mechanosensory behavior and neuronal function by combining our dataset with reverse genetic screens. While most sex-shared neurons retain their neurotransmitter identity, the male neuropeptide connectome undergoes substantial remodeling, with most of the neuropeptides showing a male-bias expression. This reinforces the notion that neuropeptides are crucial for diversifying connectome outputs. Furthermore, by correlating gene expression with outgoing synaptic connectivity, we identified regulatory candidates for synaptic wiring, including both shared and sex-specific genes. This comprehensive resource provides foundational insights into the molecular drivers of sexual dimorphism, facilitating future exploration of regulatory mechanisms and their impact on sex-specific behaviors in higher organisms.

overall_design: Single-cell RNA-sequencing profiles were generated from young adult C. elegans larvae of both sexes (hermaphrodites and males), utilizing strains with pan-neuronal labeling. Neurons were isolated using fluorescence-activated cell sorting (FACS).

first: Hagar

last: Setty

first: Ramiro

last: Lorenzo

first: Gil

last: Stelzer

first: Ron

last: Rotkopf

first: Yehuda

last: Salzberg

first: Sandeep

last: Kumar

first: Gal

last: Goldman

first: Shiraz

last: Nir Halber

first: Elad

last: Schneidman

first: Andrew

last: Leifer

first: Patrick

last: Laurent

first: Meital

last: Oren-Suissa


title: RNAseq of CD4 T cells from 83 individuals with musculoskeletal compains

status: Public on Jan 02 2025

city: Gothenburg

first: Maria

middle: I

last: Bokarewa

state: VG

address: Guldhedagatan 10A

department: Rheumatology and Inflammation Research

country: Sweden

institute: Gothenburg University

summary: RNAseq of CD4 cells from 83 individuals with musculoskeletal complains (age 51y, range 19-86. male 22%) were collected at the Rheumatology Clinic during 2022-2023 . Cells were activated with anti-CD3 for 48 hours.

overall_design: CD4 cells were isolated by positive selection on Dynabeads (cat.11331D) from human PBMC. Cells were stimulated with anti-CD3 (OKT3, Sigma-Aldrich)  for 48h

first: Karin

last: Andersson

first: Malin

middle: C

last: Erlandsson

first: Eric

last: Malmhäll-Bah


title: Identification of MUC1-C Dependence in Drug-Resistant Advanced Prostate Cancer Uncovers a New Target for Antibody-Drug Conjugate Therapy

first: Keisuke

last: Shigeta

state: MA

address: 450 Brookline Avenue

institute: Dana Farber Cancer Institute

summary: Androgen receptor positive prostate cancer (PC), castration resistant prostate cancer (CRPC) and neuroendocrine prostate cancer (NEPC) represent a spectrum of malignancies that invariably become resistant to treatment with targeted and cytotoxic agents. There is no known common pathway responsible for these pleotropic mechanisms of resistance. The MUC1 gene is aberrantly expressed in CRPC and NEPC in association with poor clinical outcomes. The present results demonstrate that the oncogenic MUC1-C protein is necessary for resistance of (i) PC cells to enzalutamide (ENZ), and (ii) CRPC and NEPC cells to docetaxel (DTX). We show that MUC1-C-mediated ENZ and DTX resistance is conferred by upregulation of aerobic glycolysis and suppression of reactive oxygen species (ROS) necessary for self-renewal capacity.  Common dependence of these drug-resistant phenotypes on MUC1-C for the cancer stem cell (CSC) state thus identified a potential new target for their treatment. cIn this context, we further demonstrate that targeting MUC1-C with an antibody-drug conjugate (ADC) is highly effective in suppressing (i) self-renewal of drug-resistant CRPC and NEPC CSCs and (ii) growth of t-NEPC tumor xenografts derived from drug-resistant cells and a patient with refractory disease. These findings reveal a shared MUC1-C-dependent pathway in drug-resistant CRPC and NEPC progression and identify MUC1-C as a target for their treatment with an ADC.

overall_design: RNA Seq in LNCaP-ER, DU-145-DR, and H660 Cell lines with MUC1-C shRNA silencing. We conpared DMSO and DOX treatment cells for differential gene expression analysis. MUC1shRNA (MISSION shRNA TRCN0000122938; Sigma, St. Louis, MO, USA)  was inserted into the pLKO-tet-puro vector (Plasmid #21915; Addgene, Cambridge, MA, USA) . Vector-transduced cells were selected for growth in 1–2 μg/ml puromycin. Cells were treated with 0.1% DMSO as the vehicle control or 500 ng/ml doxycycline (DOX; Millipore Sigma).


title: RNA sequencing libraries from NMT-seq of opossum blastocyst single cells

first: James

last: Turner

summary: Decades of work in placental (eutherian) species have constructed a paradigm of mammalian development, wherein the genome-wide erasure of parental DNA methylation is required for embryogenesis. Whether such DNA methylation reprogramming is, in fact, conserved in other mammals is unknown. To resolve this point, we generated base-resolution DNA methylation maps in gametes, embryos and adult tissues of the opossum marsupial Monodelphis domestica, revealing extensive variations from the eutherian-derived model. In stark contrast with eutherians, the marsupial genome remains hypermethylated during the cleavage stages and in the embryo proper of the blastocyst. In the extra-embryonic trophectoderm DNA methylation is reduced, suggesting an important evolutionary conserved function for DNA hypomethylation in formation of the mammalian placenta. Furthermore, unlike in eutherians, the inactive X chromosome becomes globally DNA hypomethylated during embryogenesis. Using our DNA methylation profiles, we identify a candidate mechanism for imprinted X-inactivation in marsupials, via maternal promoter DNA methylation of the Xist-like non-coding RNA RSX11. How mammalian embryos employ DNA methylation to regulate their development is therefore more mechanistically diverse than current models can accommodate.

overall_design: NMT-seq was performed on single cells isolated from blastocysts of the opossum Monodelphis domestica. RNA-seq and Bisulfite-seq libraries were generated from the same single cells.

first: Bryony

last: Leeke

first: Wazeer

last: Varsally


title: Marsupial DNA methylation

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

sample_organism:
Mus musculus
Monodelphis domestica
Mus musculus x Mus spretus

overall_design: Refer to individual Series


title: Cellular hierarchies of ETMR are shaped by oncogenic miRNAs and receptor-ligand interactions

status: Public on Dec 31 2024

first: Lisa

last: Gabler

address: Brookline Avenue 360

summary: Embryonal tumor with multilayered rosettes (ETMR) is a malignant pediatric brain tumor with a dismal prognosis. The proposed oncogenic driver is amplification and fusion of the chromosome 19 miRNA cluster (C19MC). However, the ramifications of this distinct genetic event as well as the complex tumor architecture and the interactions between malignant cell types in ETMR remain vastly understudied. Here, we have analyzed a cohort of 11 ETMR patients using single-cell transcriptomic and multiplexed spatial protein profiling. We reveal a common, spatially distinct cellular hierarchy, closely resembling normal development presenting as a highly proliferative neural stem cell-like population that gives rise to neuron-like cells. C19MC, which is predominantly expressed in the malignant stem-like population, controls a transcriptional network governing stemness and lineage commitment, indicated by high-resolution miRNA:mRNA analyses. Further, we show that FGF- and NOTCH-signaling, important for cell-cell interactions in ETMR, can be successfully targeted in preclinical ETMR models and ETMR patients. Taken together, our study provides unprecedented new insights into fundamental ETMR biology and a powerful rationale for more effective targeted therapies.

overall_design:
Single-cell / single-nucleus RNA sequencing data on embryonal tumor with multilayered rosettes (ETMR) patient samples, patient-derived xenografts in mice, and patient-derived cells were collected and analyzed.
>>>Submitter statement concerning raw data availability: 'Raw data include personalized patient information and cannot be shared at this point. Raw data will be deposited in a secure repository which can be accessible following special request.'<<<

first: Alexander

last: Beck

first: Marcel

last: Kool

first: Mariella

last: Filbin

first: Volker

last: Hovestadt


title: Whole genome bisulfite sequencing of mouse tissues, gametes, and blastocysts.

sample_organism:
Mus musculus
Mus musculus x Mus spretus

platform_organism:
Mus musculus
Mus musculus x Mus spretus

overall_design: Sperm and blastocysts were from WT C57BL/6J animals. Adult brain and liver tissues were derived from a C57BL/6J x mus spretus F1 cross carrying an Xist mutation resulting in skewed X inactivation.

first: Jasmin

last: Zohren


title: Nr4a1 Modulates Inflammation and Heart Regeneration in Zebrafish

city: Chapel Hill

first: Yiran

last: Song

state: NC

address: 111 Mason Farm Road

institute: The University of North Carolina

summary: Recent findings have highlighted the complex role of inflammation in zebrafish heart regeneration, demonstrating that while inflammation is essential for initiating transient fibrosis and tissue repair, chronic inflammation and unresolved fibrosis could impede full regenerative recovery. In this study, we identified the nuclear receptor Nr4a1 as a critical regulator of this regenerative process in zebrafish. Loss of Nr4a1 function led to a prolonged and excessive inflammatory response, disrupted neutrophil migration, delayed fibrin clearance, and ultimately impaired heart regeneration. Transcriptome-wide RNA-seq analysis at different injury stages revealed molecular disruptions associated with dysregulated inflammation and fibrosis in Nr4a1 mutants. Notably, partial inhibition of the pro-inflammatory cytokine Tnf-α rescued heart regeneration in the nr4a1 mutants, highlighting the therapeutic potential of modulating inflammation. Our findings suggest that Nr4a1 plays a crucial role in orchestrating the immune response during heart regeneration and may serve as a valuable target for enhancing cardiac repair following injury.

overall_design: To elucidate the molecular basis of the phenotypes observed in the nr4a1 mutant, we performed transcriptome-wide bulk RNA sequencing on the ventricles from both control and mutant hearts at several key time points. Baseline transcriptomic profiles were established from uninjured hearts to compare the cardiac transcriptomics of the wildtype control and nr4a1 mutant. Given the critical involvement of inflammation in heart regeneration, samples were also collected at 2 and 7 dpci, corresponding to stages marked by an active inflammatory response. Moreover, to elucidate the prolonged fibrosis phenotype in the late injury stage, we performed transcriptomic analysis on hearts collected at 21 dpci.

first: Dong

last: Feng

first: Yanhan

last: Dong

first: Yifang

last: Xie

first: Brian

last: Spurlock

first: Landry

last: Kuehn

first: Nicholas

last: Yapundich

first: Li

last: Qian

first: Jiandong

last: Liu


title: PRDM16 regulates the postnatal fate of embryonic radial glia via VCAM1-dependent mechanisms

status: Public on Dec 30 2024

city: Los Angeles

first: Jiwen

last: Li

address: 635 Charles E. Young Dr. S.

institute: UCLA

summary: Postnatally, a subpopulation of embryonic neural stem cells becomes adult neural stem cells, which primarily generate olfactory bulb interneurons in mice. Although embryonic and adult neural stem cells have been characterized, the mechanisms that regulate the transition from embryonic to adult neural stem cells remain poorly understood. We show that PR domain-containing 16 (Prdm16) promotes the transition from embryonic to adult neural stem cells. By single-cell RNA sequencing, it reveals postnatal persistence of radial glia in Prdm16 cKO mice.

overall_design: The V-SVZ of the lateral walls of the lateral ventricles from one-month old (P31-33) mice were dissected according to published protocols (Mirzadeh et al., 2010). The V-SVZs from 2-3 mice including both males and females were combined as a biological replicate. 3, 3, and 1 biological replicates from control, Prdm16 cKO, and Prdm16-Vcam1 DKO were analyzed.

first: Ye

last: Zhang


title: Next Generation sequencing Facilitates Quantitative Analysis of α-KG  and control Transcriptomes in MKN74 and AGS cell lines

city: Hohhot

first: Liu

last: Fangyuan

state: Inner Mongolia

address: No. 1 Tongdao North Street

institute: Affiliated Hospital of Inner Mongolia Medical University

summary: In recent years, gastric cancer (GC) has garnered significant attention due to its poor response to treatment, unfavorable prognosis, and the lack of reliable biomarkers for predicting disease progression and therapeutic outcomes. α-Ketoglutarate (α-KG), a critical metabolite involved in cellular energy metabolism and epigenetic regulation during tumor development, has emerged as a potential prognostic biomarker for GC. To explore this potential, we utilized publicly available datasets from the TCGA and GEO databases to analyze α-KG-related genes and establish the α-KG Index (AKGI). By evaluating the predictive performance of the AKGI model, we confirmed its robust capability to predict survival outcomes in gastric cancer patients.By analyzing signaling pathways and biological functions correlated with AKGI, we elucidated the regulatory mechanisms and biological roles of α-KG in gastric cancer. These insights were validated through cellular experiments, where α-KG treatment was shown to significantly inhibit gastric cancer cell proliferation, migration, and invasion.Taken together, our data demonstrate AKGI offers a valuable framework for advancing our understanding of the role and mechanisms of α-KG in gastric cancer.

overall_design: AGS and MKN74 cell lines treated with α-KG and the control group, with three replicates per group, were analyzed for gene expression profiles using RNA seq data..

first: Fangyuan

first: Xuemeng

last: Sun

first: Xiangyun

last: Meng


title: Dual role of circulating and mucosal Vd1 T cells in the control of and contribution to persistent HIV-1 infection

status: Public on Jan 09 2025

city: Washington

first: Natalia

last: Soriano-Sarabia

state: DC

address: 2300 I St. NW

department: Microbiology Immunology and tropical Medicine

institute: George Washington University

summary: Curative strategies for human immunodeficiency virus (HIV-1) infection are hindered by incomplete characterization of the latent reservoir and limited enhancement of anti-HIV immune responses. In this study, we identified a novel dual role for peripheral and tissue-resident Vd1 T cells within the gastrointestinal mucosa of virally suppressed people with HIV. Phenotypic analyses identified an increased frequency of highly differentiated, cytotoxic effector Vd1 T cells that exerted potent inhibition of HIV-1 replication in vitro coinciding with direct increases in cytolytic function. Conversely, we detected an enrichment of HIV-1 DNA in tissue-resident CD4+Vd1 T cells in situ. Despite low CD4 expression, we found circulating Vd1 T cells also contained HIV-1 DNA which was replication-competent. We show that TCR-mediated activation of peripheral Vd1 T cells induced de novo upregulation of CD4 providing a plausible mechanism for increased permissibility to infection. These findings highlight juxtaposing roles for Vd1 T cells in HIV-1 persistence including significant contribution to tissue reservoirs.

overall_design: Human Vd1 T cells were FACS-purified ex vivo from PBMCs isolated from three ART-suppressed people living with HIV and three HIV-seronegative donors and interrogated by ATAC-seq.

first: Brendan

last: Mann

first: Marta

last: Sanz

first: Matthew

last: Clohosey

first: Kayley

last: Langlands

first: Alisha

last: Chitrakar

first: Carles

last: Moreno

first: Joana

last: Vitalle

first: Marie

last: Iannone

first: Ezequiel

last: Ruiz-Mateos

first: Claire

last: Deleage

first: Marc

last: Siegel


title: Identification of ALEKSIN as a novel multi-IRF inhibitor of IRF- and STAT-mediated transcription in vascular inflammation and atherosclerosis [ApoEKO]

city: Poznan

first: Hans

last: Bluyssen

address: Uniwersytetu Poznańskiego 6

department: Laboratory of Human Molecular Genetics

institute: Adam Mickiewicz University

summary: Cardiovascular diseases (CVDs) include atherosclerosis, which is an inflammatory disease of large and medium vessels that leads to atherosclerotic plaque formation. Key factors contributing to onset and progression of atherosclerosis include the pro-inflammatory cytokines Interferon (IFN)α and IFNγ and the Pattern Recognition Receptor (PRR) Toll-like receptor 4 (TLR4). Together, they trigger activation of IFN Regulatory Factors (IRFs) as well as Signal Transducer and Activator of Transcription (STAT)s. Based on their promoting role in atherosclerosis, we hypothesized that combined inhibition of IRFs and STATs blocks pro-inflammatory target gene expression and may be a promising strategy to treat CVDs.  Using comparative in silico docking of multiple IRF-DBD models on a multi-million natural compound library, we identified the novel multi-IRF inhibitor, ALEKSIN. This compound targets the DBD domain of IRF1, IRF2, and IRF8 with the same affinity and simultaneously inhibits expression of multiple IRF-target genes in HMECs in response to IFNa and IFNg. Under the same conditions, ALEKSIN was also shown to inhibit phosphorylation of STATs, potentially through low-affinity STAT-SH2 binding, however  with lower potency as the known multi-STAT inhibitor STATTIC. This was in line with the common inhibition of ALEKSIN and STATTIC observed on genome-wide expression of pro-inflammatory IRF/STAT/NF-κB target genes, as well as on migration of HMECs. Finally, we identified a novel signature of 46 ALEKSIN and STATTIC commonly inhibited pro-atherogenic target genes, that was upregulated in atherosclerotic plaques in aorta's of high-fat diet fed APOE-/- mice and associated with inflammation, proliferation, adhesion, chemotaxis and response to lipid.  Together, this suggests that ALEKSIN represents a novel class of multi-IRF inhibitors, which inhibit IRF- , STAT- and NF-κB-mediated transcription and could offer great promise for the treatment of CVDs. Also, the ALEKSIN and STATTIC commonly inhibited pro-inflammatory gene signature could serve to monitor plaque progression during experimental atherosclerosis.

overall_design: We used gene expression profiling by high throughput sequencing in ApoEKO  model for understanding the mechanisms accompanying the formation of atherosclerotic plaque and the genes responsible for this process

middle: A


title: Effect of activating Wnt signalling on expression of 3' UTR spliced transcripts in colorectal carcinoma cell line HCT116

status: Public on Dec 20 2024

city: Sheffield

first: Jack

last: Riley

address: Firth Court, Western Bank

department: School of Biosciences

institute: The University of Sheffield

summary: The Wnt signalling pathway is commonly mutated or dysregulated in colorectal cancer, including approximately 93% of solid tumour samples from The Cancer Genome Atlas. Such dysregulation commonly leads to overactivation of CTNNB1, a transcription factor central to Wnt signalling. We have previously observed an increase in splicing of the 3'UTR of CTNNB1 in colon cancer samples compared to healthy samples. Additionally, we have observed isoform-specific regulation of CTNNB1 3'UTR spliced and retained isoforms in response culturing HCT116 cells with increasing concentrations of Wnt activator CHIR99021, and the opposite upon incubation with Wnt inhibitor IWR-1. By treating HCT116 cells with a high concentration of Wnt activator CHIR99021 and performing RNA sequencing, we assessed the global impact of Wnt signalling on expression of transcripts with spliced 3'UTRs. Interestingly, we observe an enrichment of alternative splicing events relating to components of the canonical Wnt signalling pathway itself, highlighting potential autoregulatory functions.

overall_design: To investigate the role that Wnt signalling has on expression of 3'UTR spliced transcripts, HCT116 cells were treated with CHIR99021, a small molecule inhibitor of GSK3B, to activate the Wnt signalling pathway. Following RNAseq, we conducted differential transcript usage and differential splicing analyses.

middle: J

first: Ian

middle: M

last: Sudbery


title: Circadian-clock independent ultradian rhythms in lipid metabolism in Drosophila fat body

status: Public on Dec 19 2024

city: Geneva

first: Blanca

middle: Lago

last: Solis

address: 30 Quai Ernest-Ansermet

department: Genetics and Evolution

country: Switzerland

institute: University of Geneva

summary: The role of circadian clocks in regulating metabolic processes has been studied extensively. Yet, the physiological impacts of the circadian system on metabolic states across species and life stages remain to be explored. This study investigates the relationship between circadian rhythms and metabolic regulation in the fat body of Drosophila larva, an organ crucial for maintaining metabolic homeostasis, growth and developmental timing. Larval fat body is analogous to the mammalian liver and adipose tissue but lacks a canonical circadian clock. Around-the-clock RNA-sequencing analysis on the fat bodies of wild-type and period clock gene null mutant larvae revealed circadian rhythms in the transcriptome of wild-type larvae. Surprisingly, period mutant exhibited 12-h rhythms in the expression of numerous genes, particularly those involved in peroxisome function, lipid metabolism, and oxidative stress response. Consistent with these transcriptomic data, peroxisome biogenesis and activity demonstrated 12-h rhythms in period mutant fat bodies. Furthermore, levels of reactive oxygen species displayed inverse-phased rhythms to that of lipid peroxidation, with 24-h rhythms in wild-type and 12-h rhythms in period mutant fat bodies. Moreover, while daily fat storage levels in wild-type larvae remained constant, period mutants exhibited fluctuations with a 12-h period and a net reduction in body fat storage. Collectively, our results identified a clock-independent ultradian rhythms in lipid metabolism, which may contribute to maintaining the metabolic, energetic, and redox homeostasis essential for larval survival and development.

overall_design: Circadian RNA-sequencing profile of the fat body of drosophila melanogaster third instar larvae in two different genotypes: w1118 and per0 mutant. It was performed at nine different timepoints (CT00-CT32) in duplicates and in constant darkness condition.

last: Lago Solis

first: Rafael

last: Koch

first: Emi

last: Nagoshi


title: AAV-HBV mouse model shows similar exhaustion marker pattern to chronic HBV patients at single-cell level.

city: Beerse

first: Nádia

last: Conceição-Neto

address: Turnhoutseweg 30

country: Belgium

institute: Janssen R&D

summary: Background and Aims: Unresolved hepatitis B virus (HBV) infection leads to a progressive state of immune exhaustion that impairs resolution of infection, leading to chronic infection (CHB). The immune-competent AAV-HBV mouse is a common HBV preclinical immune competent model, though a comprehensive characterization of the liver immune microenvironment and its translatability to human infection is still lacking. We investigated the intrahepatic immune profile of the AAV-HBV mouse model at a single-cell level and compared with data from CHB patients in immune tolerant (IT) and immune active (IA) clinical stages.  Methods: Immune exhaustion was profiled through an iterative subclustering approach for cell-typing analyses of single-cell RNA-sequencing data in CHB donors and compared to the AAV-HBV mouse model 24-weeks post-transduction to assess its translatability. This was validated using an exhaustion flow cytometry panel at 40 weeks post-transduction. Results: Using single-cell RNA-sequencing, CD8 pre-exhausted T-cells with self-renewing capacity (TCF7+), and terminally exhausted CD8 T-cells (TCF7-) were detected in the AAV-HBV model. These terminally exhausted CD8 T-cells (expressing Pdcd1, Tox, Lag3, Tigit) were significantly enriched versus control mice and independently identified through flow cytometry. Importantly, comparison to CHB human data showed a similar exhausted CD8 T-cell population in IT and IA donors, but not in uninfected individuals.  Conclusions: Long term high titer AAV-HBV mouse liver transduction led to T-cell exhaustion, as evidenced by expression of classical immune checkpoint markers at mRNA and protein levels. In both IT and IA donors, a similar CD8 exhausted T-cell population was identified, with increased frequency observed in IA donors. These data support the use of the AAV-HBV mouse model to study T-cell exhaustion in HBV infection and the effect of immune-based therapeutic interventions.

overall_design: Male C57BL/6 mice (4–5-week-old, Wuxi Apptec, Shanghai, China) were either transduced via the tail vein with 1x1011 viral genome equivalents (vge) per mouse of rAAV-HBV1.3 (n=5)  (FivePlus Molecular Medicine Institute, Beijing, China) or rAAV vector control (n=5), which contained an empty rAAV capsid and rAAV containing a short sequence of the CMV promoter and BGH poly A tail flanked with inverted AAV-ITR or kept naïve (n=5). IHICs isolated via mechanical digestion of the liver were processed according to the 10x Chromium Single-cell V(D)J Reagent Kits User Guide and loaded on to the Chromium 10x platform using the 5’ v1.1 chemistry (10x Genomics). Libraries were sequenced on a NovaSeq 6000 platform (PE150) (Illumina) to an average ~50,000 reads per cell.

first: Qinglin

last: Han

first: Zhiyuan

last: Yao

first: Wim

last: Pierson

first: Qun

last: Wu

first: Koen

last: Dockx

first: Liese

last: Aerts

first: Dries

last: De Maeyer

last: Van den Berge

first: Chris

last: Li

first: George

last: Kukolj

first: Ren

last: Zhu

first: Ondřej

last: Podlaha

first: Isabel

last: Nájera

first: Ellen

last: Van Gulck


title: Transcriptome sequencing data analysis of Bacillus methylotrophicus B-9987 wild-type strain and bm0677 mutant strain

city: Shenzhen

first: Shanshan

last: Xu

address: Xueyuan Avenue, No. 1066

institute: Shenzhen University

summary: In the pre-laboratory study, a GntR family regulatory gene bm0677 was discovered. In this study, we found that colony morphology of the bm0677 mutant strain was changed. And the ability to produce biofilm of the mutant in MSgg solid and liquid medium was repressed, which proposed that this gene was involved in regulation of biofilm formation. Then we used transcriptome sequencing (RNA-Seq) to analyze how the regulator Bm0677 was involved in the regulation of biofilm formation. For the statistically significant differential expression (P < 0.001), there were 644 genes up-regulated and 810 genes down-regulated by at least two folds when comparing Δbm0677 to the wild-type strain.

overall_design: mRNA profiles of Bacillus methylotrophicus B-9987 wild-type strain and bm0677 mutant strain

first: Wenli

first: Zengzhi

last: Liu


title: Transcriptome profile analysis in bovine blastocysts developed in vivo after intrafollicular transfer of matured or immature oocytes

city: Bonn

first: Dessie Salilew

last: Wondim

address: Endenicher Allee 15

institute: University of Bonn

summary: This study aimed to investigate the transcriptome profile of bovine blastocysts produced in three different experimental conditions, namely I) VITRO (entire in vitro production of blastocysts), II) IFOT-M (Intrafollicular transfer of in vitro matured oocytes into preovulatory follicles) and III) IFOT-IM (Intrafollicular transfer of immature oocytes into dominant follicles) and  ex vivo derived blastocysts (IV, VIVO) were used as a control. Accordingly, differentially expressed genes between in vitro and in vivo derived blastocysts which are involved in various fundamental roles including protein synthesis and protein degradation were identified. The study highlights insights about   the attainment of embryonic developmental capacity and might be useful to improve embryo in vitro culture conditions.

overall_design: Blastocysts produced in three different experimental conditions, namely I) VITRO (entire in vitro production of blastocysts), II) IFOT-M (Intrafollicular transfer of in vitro matured oocytes into preovulatory follicles) and III) IFOT-IM (Intrafollicular transfer of immature oocytes into dominant follicles) were compared with ex vivo derived blastocysts (IV, VIVO) serving as control. To determine the transcriptome profiles,  pools of 15-20 blastocysts were analyzed by Affymetrix GeneChip® Bovine 1.0 ST array. Three independent biological replicates were investigated for each of the four experimental groups.

first: Mohammad

last: Bozlur Rahman

first: Eva

last: Held-Hoelker

first: Mohammed

last: Saeed-Zidane

first: Franca

last: Rings

first: Dessie

last: Salilew-Wondim

first: Dawit

last: Tesfaye

first: Ahmed

last: Gad

first: Samuel

last: Gebremedhn

first: Ernst

last: Tholen

first: Karl

last: Schellander

first: Christine

last: Große-Brinkhaus

first: Michael

last: Hoelker


title: Gene expression profile at single-cell resolution of liver tissues from mice exposed to  electromagnetic field (EMF) after 90 and 150 days

status: Public on Dec 24 2024

city: Beijing

first: Mingming

last: ZHANG

address: Taiping Road No.27

institute: AMMU

summary: Whether radiofrequency EMF (RF-EMF) exposure affects liver function remains poorly understood. We used scRNA-seq to explore changes at transcriptional level.

overall_design: C57/BL6J mice were exposed to 2.45 GHz EMF for 6 minutes everyday. Liver tissues of mice were collected at 90 and 150 days respectively.

last: Zhang

first: Haiyang

last: Wang


title: Epigenetic programming by trithorax supports the translation capacity of Drosophila memory neurons.

status: Public on Dec 17 2024

city: Nijmegen

first: Nicholas

last: Raun

address: Geert Grooteplein 10

country: Netherlands

institute: Radboudumc