title: The Nuclear Matrix Regulates Gene Induction By Maintaining the Chromatin-Speckle Association and Compartmentalization [RNA-Seq]

city: Daejeon

first: Wonki

last: Cho

address: 291 Daehak-ro Yuseong-gu

institute: KAIST

summary: Emerging evidence reveals the critical role of the nuclear RNA-protein meshwork complex, termed nuclear matrix, in stabilizing chromatin architecture. While chromatin associates with transcriptional machinery within nuclear bodies to regulate gene expression through hierarchical architecture formation, how the nuclear matrix mediates chromatin-nuclear body associations and their spatial organization remains unclear. Here, we demonstrate that depletion of nuclear matrix factor SAF-A leads to genome-wide chromatin compaction and enhanced chromatin-speckle associations. Using super-resolution imaging and genomic analyses, we show that these chromatin organizational changes alter the inducibility of speckle-associated genes. Mechanistically, we reveal that nuclear matrix exhibits a layered spatial distribution, forming distinct compartments with RNA polymerase II clusters and chromatin in the perispeckle region. Our findings demonstrate that nuclear matrix maintains chromatin architecture and regulates gene expression through spatial coupling with nuclear bodies, providing new insights into the hierarchical organization of nuclear structure-function relationships.

overall_design: RNA-seq profiling of HCT116 osTIR1(F74G) SAF-A-mAID-Halo cells and their acute depletion by 5-Ph-IAA treatment for 3hr and 12hr.


title: Chemical inhibition of exon junction complex assembly impairs mRNA localization and neural stem cells ciliogenesis

status: Public on Nov 29 2025

city: Rehovot

first: David

last: Dierks

state: Central District

address: Herzl St 234, Weizmann Institute of Science to the Department of Biomolecular Sciences, Laboratory of Dr. Scherz-Shouval

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

type: Expression profiling by high throughput sequencing

summary: The Exon Junction Complex (EJC) is formed by the essential eIF4A3, MAGOH and Y14 core proteins. It is universally deposited during splicing at exon-exon junctions. The EJC is known to impact almost every post-transcriptional regulatory step throughout the life of mRNAs including their modifications, splicing, decay and trafficking. Its dysregulation leads to neurodevelopmental pathologies. Here we show that EJC-i, a compound known to block the ATPase activity of eIF4A3, inhibits de novo EJC assembly. EJC-i and targeted knockdown of either eIF4A3 or Y14 core EJC subunits lead to very similar phenotypes by impacting the destiny of mRNAs due to alterations in alternative splicing, nonsense-mediated mRNA decay, genome-wide m6A methylation and proper intracellular addressing of specific transcripts, in particular to the centrosome. Both EJC impairment methods disrupt the centrosome structure that might be responsible for mitotic arrest at prometaphase. However, as a small molecule that readily diffuses into cells, EJC-i is a particularly attractive easy to use and versatile tool to investigate EJC functions in live cells or whole organism that are not prone to genetic manipulation. Indeed, this property was used to disrupt ciliogenesis in primary neural stem cells.

overall_design: Two biological replicates of human HEK293T cells were treated with a 20 µM dose of EJC-i for 0, 2, 4, 8, and 16 hours. Total RNA from the time-coursed samples, was extracted using TRI reagent was poly-A selected, and a total of 200 ng of poly-A selected mRNA per sample was used to prepare m6A-seq2 libraries as previously described (Dierks et al., 2021).

first: Tommaso

last: Villa

first: Oriane

last: Pourcelot

first: Marion

last: Faucourt

first: Cindy

last: Burel

first: Floric

last: Slimani

first: Léa

last: Guyonnet

first: Nathalie

last: Spassky

first: Shraga

last: Schwartz

first: Edouard

last: Bertrand

first: Olivier

last: Bensaude

first: Hervé

last: Le Hir


title: A conserved transcriptional backbone and rewiring of gene-regulatory networks in activated human CD4⁺ T cells

status: Public on Nov 25 2025

city: Umeå

first: Johan

last: Henriksson

address: Sjukhusområdet Umeå universitet

country: Sweden

institute: Umeå University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: CD4+ T cells are components of the adaptive immune system with a plethora of subtype-specific functions. In order to further dissect the  activation and differentiation  regulatory program(s) of individual CD4+ T cell subsets, we performed an in vitro activation and differentiation of human primary naive CD4+ T cells towards Th1, Th2, Th17 and Treg subtypes followed by the single-cell RNA-seq and ATAC-seq (multiome) analysis.  Resulting multiome data were used for constructing the subtype-specific gene regulatory networks, which were next assessed for their differences/similarities among the subtypes.  Surprisingly, a conserved set of 8 “backbone” transcription factors (TFs) was identified as highly central in all subtypes, however, with  unique differentiation-driven rewiring tendency.  Subtype-specific “driver” TFs were identified in the case of Th1-Th1_17-Th17 lineage (EOMES, HLF), naive Tregs (ESR1, DACH1), and memory Tregs (SOX13). Finally, we applied community detection algorithms to identify potential non-obvious groups of genes that regulate diverse molecular functions within the differentiated subtypes, linked to the backbone TFs. Our atlas aims at providing a high resolution understanding of the gene regulatory networks and their  rewiring in human primary CD4+ T cells, upon activation and differentiation.

overall_design: Human naive CD4+ T cells were negatively selected, stimulated under lineage-specific cytokines, and profiled using 10x Multiome; data processed with Cell Ranger ARC.

first: Ionut S

last: Mihai

first: Martin

last: Selinger

first: Iker

last: Nunez-Carpintero

first: Davide

last: Cirillo

last: Trygg

first: Mattias

last: Forsell


title: The Nuclear Matrix Regulates Gene Induction By Maintaining the Chromatin-Speckle Association and Compartmentalization [TSA-Seq]

status: Public on Nov 24 2025

first: Wonki

last: Cho

country: South Korea

overall_design: TSA-seq profiling of HCT116 osTIR1(F74G) SAF-A-mAID-Halo cells and their acute depletion by 5-Ph-IAA treatment for 3hr and 12hr.


title: Transcriptional profiling of HYF1 overexpression strain.

city: San Francisco

first: Mark

last: Voorhies

state: CA

address: 513 Parnassus, S472

department: Microbiology and Immunology

country: USA

institute: University of California

summary: Heritable phenotypic switches are fundamental to the ability of cells to respond to specific conditions. Such switches are key to the success of environmental pathogens, which encounter disparate conditions as they transition between the environment and host. We determine that the copy number of chromosome seven in the thermally dimorphic fungus Histoplasma dramatically affects the rate of transition. Though Histoplasma is haploid, a second copy of this chromosome is present in natural isolates of multiple Histoplasma species and is gained and lost at a high rate. Cells carrying two copies of this chromosome exhibit aspects of the environmental transcriptome even under host-like conditions and have a competitive advantage in the transition to the environmental form. Conversely, these cells are considerably less virulent than euploid cells and have a competitive disadvantage in the mouse model of infection. Chromosome seven contains a previously unstudied transcription factor that, when overexpressed in euploid Histoplasma, is sufficient to promote some of the key phenotypes of aneuploidy. We hypothesize that rapid gain and loss of this chromosome benefits Histoplasma by increasing phenotypic variation, thus helping populations of cells survive abrupt transitions between environment and host.  This series contains expression profiling of increased copy number constructs for the HYF1 and HYF2 transcription factors.

overall_design: Three replicates for each of two genotypes for yeast cultures with or without a two day shift from 37°C to 25°C for a total of 12 samples.

first: Sarah

last: Heater

first: Anita

last: Sil


title: Beckwith-Wiedemann syndrome and large offspring syndrome involve alterations in methylome, transcriptome, and chromatin configuration

city: Columbia

first: Rocío

middle: Melissa

last: Rivera

state: MO

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: University of Missouri, Columbia

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Transciptional response to hypoxia in SKNAS cells

status: Public on Nov 26 2025

city: Liverpool

first: Sonia

last: Rocha

address: Crown Street

country: United Kingdom

institute: University of Liverool

summary: RNA-seq analysis investigating transcriptional response following hypoxia stimulation in SKNAS cells.

overall_design: SKNAS cells were grown at 21% oxygen and exposed to 0 hours or 24 hours 1% oxygen (hypoxia).

first: Chun-Sui

last: Kwok

first: Michael

last: Batie


title: The Nuclear Matrix Regulates Gene Induction By Maintaining the Chromatin-Speckle Association and Compartmentalization [Hi-C]

overall_design: Hi-C profiling of HCT116 osTIR1(F74G) SAF-A-mAID-Halo TetOn-SAF-A(WT or RBD del) cells and dox treatment for 24hr followed by acute depletion with 5-Ph-IAA treatment for 3hr and 12hr.


title: The Nuclear Matrix Regulates Gene Induction By Maintaining the Chromatin-Speckle Association and Compartmentalization [CLIP-Seq]

overall_design: RNA binding landscape profiling by CLIP-seq of HCT116 cells of wild type SAF-A.


title: The Nuclear Matrix Regulates Gene Induction By Maintaining the Chromatin-Speckle Association and Compartmentalization [ATAC-Seq]

overall_design: Open chromatin landscape profiling of HCT116 afte racute depletion by 5-Ph-IAA treatment for 3hr and 12hr.


title: The Nuclear Matrix Regulates Gene Induction By Maintaining the Chromatin-Speckle Association and Compartmentalization [CUT&Tag]

overall_design: DNA binding landscape of SAF-A profiling of HCT116 after transcriptin inhibition by DRB and THZ1 for 3hr.


title: MicroRNA Profiling Identifies Diagnostic and Prognostic Markers in Pediatric Sarcoma

city: Seattle, WA

first: Leonid

middle: M

last: Yermakov

state: WA

address: 1959 NE Pacific St, Box 357470

institute: University of Washington

summary: MicroRNAs are small non-coding RNA molecules that play a significant role in many physiologic processes in the body, including regulation of gene expression. Their expression in cancer cells can become dysregulated where they can promote tumorigensis or function as tumor suppressors.  In this article, we define the microRNA profile associated with three common pediatric sarcomas. Using multiple tissue samples from different sources including tissue microarray slides and two methods, we have detected the differential expression of miR-9-5p, miR-206 and miR-140 in Ewing’s sarcoma, rhabdomyosarcoma, and osteosarcoma respectively. NanoString nCounter profiling method exhibited higher sensivity in detecting microRNA profiles and differentially expressed microRNAs compared to microRNAscope which identified in situ hybridization of specific microRNA molecules. MicroRNA expression correlated with adverse patient outcome. Our findings demonstrate that distinct miRNA profiles can differentiate pediatric sarcoma types and provide clinically relevant insights into potential diagnostic and prognostic applications.

overall_design: NanoString nCounter profiling was performed on pediatric (ages 0-18 years) patients who were diagnosed and treated for Ewing sarcoma, osteosarcoma and rhabdomyosarcoma at Children’s Mercy Hospital (CMH) in Kansas City, Missouri, USA, and the Instituto Nacional de Pediatría (INP) in Mexico City, Mexico between May 2012 to May 2019. RNA was extracted from archived formalin-fixed paraffin embedded (FFPE) tumor blocks. 108 tumor cases were selected: 32 osteosarcoma, 26 Ewing sarcoma, and 50 rhabdomyosarcoma (22 alveolar and 28 embryonal subtypes).

first: Terrie

middle: G

last: Flatt

first: Atif

last: Ahmed


title: Regulation of murine follicle-stimulating hormone β subunit transcription by newly identified enhancers [ChIP-seq; LβT2 cells]

city: Los Angeles

first: Michel

middle: A

last: Zamojski

state: California

address: 8700 Beverly Boulevard

department: Regenerative Medicine Institute

institute: Cedars-Sinai Medical Center

summary: Activin-class ligands of the TGFβ family induce follicle-stimulating hormone (FSH) production by pituitary gonadotrope cells in mice via the actions of the transcription factors SMAD3, SMAD4, and FOXL2, which bind to cis-elements in the FSHβ subunit (Fshb) promoter. An enhancer region for murine Fshb transcription was identified in vitro. The region, however, did not significantly alter basal or activin-stimulated murine Fshb promoter-reporter activity in LβT2 cells. In contrast, three other open chromatin regions enhanced basal and activin A-stimulated Fshb promoter-reporter activity in LβT2 cells, with the two most distal showing the greatest effects. Using ChIP-seq we show that these two regions exhibit enrichment of the enhancer mark H3K27ac, and are bound by SMAD2/3 and FOXL2 in response to activin A in LβT2 cells. These data are part of a SuperSeries that includes ATAC-seq data also showing these regions to be open in response to activin A in LβΤ2 cells, as well as scATAC-seq data of whole mouse pituitaries indicating that there may be as many as four activin-sensitive enhancers upstream of murine Fshb. The data of this series were generated with the help of Next Gen and Bioinformatics Core services at the Salk Institute.

overall_design: LβT2 cells stably expressing FLAG-tagged FOXL2 (FLAG-mFoxL2) were generated by lentivirus transduction of a cassette that permits constitutive GFP expression and tetracycline/doxycycline (DOX)-inducible, IRES-mediated tandem expression of a fluorescent reporter.  LβT2-FLAG-mFoxL2 cells were cultured in plates, and DOX-induction was initiated, followed by treatment with either vehicle or activin A.  Cross-linked complexes suitable for ChIP-seq were produced and enriched for SMAD2/3-, FLAG-FOXL2- and H3K27ac-bound complexes, the DNA of which was then isolated and prepared for sequencing.

first: Alissa

last: Blackler

first: Sven

last: Heinz

first: Christopher

last: Benner

first: German

last: Nudelman

first: Hailey

last: Schultz

first: Stuart

last: Sealfon

first: Daniel

last: Bernard

first: Louise

last: Bilezikjian


title: Targeting the MEK/ERK Pathway to Suppress P-glycoprotein and Reverse Carfilzomib Resistance in Multiple Myeloma

status: Public on Nov 23 2025

city: Moscow

first: Natalia

last: Moiseeva

state: Moscow

address: Kashirskoe Shosse 24

country: Russia

institute: N.N. Blokhin National Medical Research Center of Oncology

summary: Carfilzomib (CFZ) is a cornerstone in the treatment of relapsed multiple myeloma (MM). However, its efficacy is limited by resistance mediated by the overexpression of the ABC-transporter P-glycoprotein (P-gp).The signaling pathways driving emergence of P-gp in MM remain unclear. To investigate this, we generated CFZ-resistant AMO-1/CFZ cells with P-gp overexpression by long-term selection. RNA sequencing of control AMO-1 and AMO-1/CFZ, sorted into two subpopulations P-gp HIGH and P-gp LOW, implicated the Ras/MEK/ERK pathway as the most likely signaling cascade involved in P-gp upregulation. We therefore evaluated two clinically used MAPK pathway inhibitors, cobimetinib and ulixertinib, for their ability to re-sensitize AMO-1/CFZ cells to CFZ. Co-administration at non-toxic concentrations enhanced sensitivity 5-fold with cobimetinib and 17-fold with ulixertinib. Analysis of combined MTT assay results, rhodamine efflux experiments, molecular docking, and western blotting revealed distinct actions. Ulixertinib primarily functions as a potent direct P-gp inhibitor. Conversely, non-toxic concentrations of cobimetinib sensitizes cells by suppressing MAPK signaling, though it also exhibits P-gp inhibition at higher concentrations. Both inhibitors at the IC₅₀ concentration reduced P-gp expression. In conclusion, combining CFZ with MAPK pathway inhibitors like cobimetinib or ulixertinib represents a promising strategy to overcome P-gp-mediated resistance in ММ.

overall_design: RNA sequencing was performed on the multiple myeloma cell line AMO-1, including the parental control (n=4) and a carfilzomib-resistant derivative (AMO-1/CFZ). The resistant cells were sorted into two subpopulations based on P-glycoprotein (P-gp) expression: P-gp HIGH (n=4) and P-gp LOW (n=4).

first: Lidia

last: Laletina

first: Anastasiia

last: Cherkasova

first: Ekaterina

last: Scherbakova

first: Pavel

last: Iamshchikov

last: Koroleva

first: Anna

last: Lushnikova

first: Alexey

last: Komissarov

first: Nikolay

last: Kalitin


title: Heterochromatin epimutations impose mitochondrial dysfunction to confer antifungal resistance

status: Public on Nov 20 2025

city: Edinburgh

first: Andreas

last: Fellas

address: Swann Building, Max Born Crescent

department: Institute of Cell Biology

institute: University of Edinburgh

summary:
Antifungal resistance in pathogenic fungi endanger global health and food supply. Wild-type fission yeast,
Schizosaccharomyces pombe, can gain resistance to insults including caffeine and antifungal compounds through reversible
epimutations. Resistant epimutants exhibit ectopic histone-H3K9 methylation-dependent heterochromatin islands, repressing
underlying genes. Two genes whose heterochromatin island-induced repression causes resistance encode mitochondrial
proteins: LYR-domain protein Cup1 and Cox1 translation regulator Ppr4. Genetic mutations, cup1-tt and ppr4Δ, that
phenocopy epimutants, cause mitochondrial dysfunction, including respiratory deficiency, poor growth on non-glucose carbon
sources, and elevated reactive oxygen species. Transcriptomic analyses indicate cup1-tt and ppr4Δ cells activate Pap1
transcription factor-dependent oxidative stress response and mitonuclear retrograde pathways. Pap1 nuclear localisation and
recruitment to promoters of oxidoreductase and membrane transporter genes is increased, causing increased efflux activity.
cup1 and ppr4 epimutants likewise show mitochondrial dysfunction phenotypes and increased efflux, explaining how
heterochromatin-island epimutations cause drug resistance. Thus, wild-type cells harness epimutations that impose
mitochondrial dysfunction to bypass external insults. As mitochondrial dysfunction is linked to antifungal resistance in several
fungi, similar epimutations likely contribute to development of resistance in fungal pathogens.

overall_design: Comparison of transcriptional profiles of cup1-tt and ppr4Δ with wildtype 972 strain

first: Alison

middle: L

last: Pidoux

first: Pin

last: Tong

first: Harriet

middle: H

last: Hewes

first: Emma

middle: C

last: Wallace

first: Robin

last: Allshire


title: Deciphering Precursor Cell Dynamics in Esophageal Preneoplasia via Genetic Barcoding and Single-Cell Transcriptomics

city: Houston

first: Kyung Pil

last: Ko

state: Tx

address: 1515 Holcombe Blvd

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

summary: Esophageal preneoplastic cells, despite appearing histologically normal, exhibit early genetic alterations and lineage plasticity, yet their origins and trajectories remain unclear. This study employs genetic barcoding combined with single-cell RNA sequencing to trace the lineage of esophageal preneoplastic cells and identify a distinct progenitor-like population with high plasticity. Through a newly developed scoring system, high-plasticity cells are mapped, revealing their contributions to proliferative and basal cell populations. The study identifies key molecular markers, including Nfib and Qk, that define these precursor cells. These findings provide critical insights into early tumorigenesis, highlighting the potential of precursor cells as biomarkers for early cancer detection and therapeutic targeting. By elucidating the cellular dynamics underlying esophageal cancer initiation, this research lays the foundation for strategies to prevent malignant progression, offering broader implications for improving cancer diagnostics and treatment approaches.

overall_design: For Xenium In Situ experiment, a single FFPE block was prepared from normal esophagus and Trp53, Cdkn2a dKO cell-derived subcutaneous tumor samples and placed onto a Xenium slide.  Mouse 5K gene panel was used.


title: An integrated multi-omics and network analysis of neutrophil differentiation from initial- to late-stage

city: Beijing

first: Cheng

last: Li

state: Beijing

address: No.5 Yiheyuan Road, Haidian District

department: School of Life Sciences

country: China

institute: Peking University

summary: The goal of this study is to study the gene regulation mechanism during ATRA-induced HL-60 cell neutrophil differentiation especially in the early time-point. We demonstrated the striking early changes event that trigger the whole differentiation process. We also identified the pioneer TFs (Transcription factors) that ignite the differentiation process with the corresponding TF correlation networks.

overall_design: Genome-wide mapping of transcriptomic, chromatin accessibility, and chromatin interaction in differenti time-points during neutrophil differentiation.

first: Wei

first: Minglei

last: Shi

first: Qing

last: Chen


title: CTCF couples long-range loop extrusion and diffusion to mediate a diverse Igk repertoire [3C-HTGTS]

city: East Lansing

first: Yu

last: Zhang

state: MI

address: 567 Wilson Rd, Biomedical and Physical Sciences Building, Rm 5176

department: Microbiology, Genetics and Immunology

institute: Michigan State University

summary: Dynamic genome folding is important for V(D)J recombination at the immunoglobulin kappa (Igk) locus, which recombines Jk and Vk gene segments across a 3.2 Mb region in both deletional and inversional orientations. Chromatin loop extrusion and diffusion are considered two key mechanisms underlying Igk folding, but how they coordinate remains unclear. Here we show that CTCF is a key regulator coupling loop extrusion and diffusion during Igk V-J rearrangement, promoting recombination in both orientations across long genomic distances. Mechanistically, the CTCF N-terminus promotes long-range loop extrusion that facilitates distal Vk usage by stabilizing cohesin against WAPL release, and also forms loop barriers enabling chromatin diffusion for inversional Vk joining. In CTCF N-terminal-deficient B cells, defects in inversional Vk joining are not restored by WAPL depletion but are instead largely rescued by a dCas9-blockade targeted to the Vk-Jk intergenic region, mimicking the CTCF barrier. Our findings thus highlight how CTCF coordinates distinct genome-folding mechanisms through its dual roles in cohesin stabilization and extrusion barrier formation to ensure the generation of a diverse Igk repertoire.

overall_design: We performed 3C-HTGTS in v-Abl transformed pro-B cells and the various mutant derivatives to study the molecular basis of CTCF's role in Igk recombination


title: Hyperosmotic stress induces a large-scale rewiring of 3D chromatin interactions [Hi-C]

city: Chapel Hill

first: John Patrick

last: Flores

state: NC

address: 104 Manning Dr

institute: UNC Chapel Hill

summary: Cells rapidly adapt to hyperosmotic stress through coordinated molecular responses. To determine how three-dimensional (3D) chromatin structure contributes to this process, we profiled chromatin interactions, architectural protein occupancy, and transcriptional dynamics in human cells exposed to sorbitol-induced hyperosmotic stress. We performed time-resolved Hi-C to measure stress-induced remodeling of chromatin loops and domains, CUT&Tag to quantify CTCF, RAD21, YAP1, and H3K27ac occupancy at loop anchors, and RNA-seq to capture stress-responsive transcriptional programs. These data reveal global loss of pre-existing chromatin contacts and concurrent formation of de novo, transient loops enriched for retained CTCF and cohesin, as well as transcriptional responses that are temporally layered and largely decoupled from loop remodeling. This dataset provides a resource for investigating how nuclear architecture and transcriptional regulation respond to hyperosmotic stress.

overall_design: eGFP-YAP HEK293 cells were serum-starved for 1 hour and then exposed to 200 mM sorbitol to induce hyperosmotic stress. Chromatin organization was profiled by in situ Hi-C at eight time points (0 min, 10 min, 30 min, 1 h, 3 h, 6 h, 12 h, and 24 h) to capture the formation, loss, and recovery of chromatin interactions. To assess the generality of chromatin remodeling, additional Hi-C experiments were performed in HEK293 wild-type and HCT116 cells with and without 1 hour of sorbitol treatment. To probe the requirement for architectural proteins, we also performed Hi-C in HCT116 mAID2-CTCF and mAID2-RAD21 degron cell lines treated with 1 μM 5-Ph-IAA to rapidly and reversibly degrade CTCF or RAD21 prior to sorbitol exposure. Transcriptional responses were measured by stranded RNA-seq across a time course (0 h, 1 h, 3 h, 6 h, 9 h, 12 h, and 24 h). To quantify changes in architectural protein occupancy, CUT&Tag for CTCF and RAD21 was performed in untreated and 1-hour sorbitol-treated HEK293 cells.

first: JP

first: Andrea A.

last: Perreault

first: Zack

last: Drum

first: Chenxi

last: Xu

first: Doris

last: Cruz Alonso

first: Gelila

last: Petros

first: Yijia

last: Wu

first: Ivana Y.

last: Quiroga-Barber

first: Isha

last: Sahasrabudhe

first: Justin

last: Demmerle

first: Gang Greg

last: Wang

first: Danfeng

last: Cai

first: Douglas

last: Phanstiel


first: Jinho

last: Jang

state: Texas

address: 1755 Wyndale Street

institute: MD Anderson Cancer Center

summary: Cancer cell lineage plasticity complicates tumor initiation and progression. Using genetic barcoding and single-cell RNA sequencing (scRNA-seq), we mapped esophageal preneoplastic cell lineages and developed the eXamined Ridge (XR) score to identify high-plasticity cells. We discovered preneoplastic precursor cells (PNPCs) as key progenitors and identified Nfib and Qk as conserved markers, highlighting potential biomarkers for early cancer detection and intervention.

overall_design: For scRNA-seq analysis, esophageal organoids were derived from Trp53^floxed/floxed mice, with Ad-Cre-EGFP introducing Trp53 knockout, followed by CRISPR/Cas9-mediated Cdkn2a or Notch1 knockout to generate PC and PCN organoids. Organoid cells were dissociated, cultured in DMEM + 10% FBS with Y-27632, and maintained without Y-27632 after three passages before single-cell analysis.

first: Kyung-Pil

last: Ko

first: Jie

first: Sohee

last: Jun

first: Jae-Il

last: Park


title: CTCF couples long-range loop extrusion and diffusion to mediate a diverse Igk repertoire [ChIP-Seq]

first: Yu

last: Zhang

overall_design: We performed CTCF and SMC3 ChIP-Seq in WT and CTCF N-terminal mutant v-Abl transformed pro-B cells to study the molecular basis of CTCF's role in Igk recombination


title: Pyroptosis modulates multiple immune cell populations in targeted therapy-treated melanoma

city: Philadelphia

first: Andrew

middle: E

last: Aplin

state: PA

address: 233 South 10th St.

institute: Thomas Jefferson University

summary: Treatment of melanoma with BRAF inhibitors plus MEK inhibitors (BRAFi + MEKi) stimulates an intratumoral immune response, in part through pyroptosis mediated by the pore-forming protein gasdermin E (GSDME/Gsdme). How GSDME-mediates effects on tumoral immunity is not well characterized. Using single-cell RNA-sequencing (scRNA-seq) and flow cytometry, we show that Gsdme knockout (KO) tumors have decreased infiltration of T cells, natural killer (NK) cells and regulatory T cells (Tregs) following BRAFi + MEKi-treatment compared to control tumors.  Infiltrated Tregs in Gsdme KO tumors displayed decreased expression of the interleukin 2 receptor and phenotypic markers that are associated with a suppressive function of Tregs. Furthermore, intratumoral, phenotypically suppressive Tregs were decreased after BRAFi + MEKi treatment in Gsdme KO tumors expressing a pyroptosis-defective mutant form of Gsdme (T6E) compared to tumors expressing wild-type Gsdme. Use of a TLR9 agonist, which alters the tumor immune microenvironment, decreased the regrowth of Gsdme KO tumors on BRAFi + MEKi treatment, correlating to a further decrease in intratumoral Tregs. Overall, we show a critical role of GSDME in the modulation of intratumoral immune cells, particularly Tregs, in BRAFi + MEKi-treated melanoma.

overall_design: YUMM1.7 CTL and Gsdme KO cells were injected intradermally into the shaved right flank of C57BL/6J mice. When tumors reached approximately 100-200 mm3, animals were administered BRAFi + MEKi or vehicle control chow. On day 4, BRAFi + MEKi-treated tumors (n=5) and control-treated tumors (n=3) were harvested and pooled into single samples.

first: Nicole

last: Wilski-Cronin

first: Timothy

middle: J

last: Purwin


title: Developmental regulation of ERK signaling by mitotic kinases

status: Public on Nov 19 2025

city: Bern

state: Bern

address: Freiestrasse 3

country: Switzerland

institute: Department of Chemistry, Biochemistry and Pharmaceutical Sciences

summary: The morphogenesis of the mouse epiblast during implantation can be recapitulated by culturing its counterpart ES cells in growth factor reduced Matrigel. We analysed the transcripts level changes using Next-generation sequencing (NGS) technique with ES cells grown in Matrigel in N2B27 medium supplemented with 2iLif, FGF2/Activin, PD03259021, Aurka inh and PD032+ Aurka inh for 2 days.  We found cells delayed exit of naïve pluripotency by inhibiting Aurka activity and this effect can be strengthened by combing Mek and Aurka inhibitors. By further pathways enrichment analysis, we found down regulation of MAPK signalling pathway after Aurka inhibition which is validated by Q-PCR and immunofluorescence. Our findings demonstrate the pluripotent cells continuously generate and perceive two types of Erk-mediated pro-differentiation cues - autocrine signals of the Fgf/Mek cascade and cell-intrinsic cues via the mitotic kinase Aurka.

overall_design: We performed bulk RNA-sequencing on ES cells grown in growth factor reduced Matrigel with 5 different culture conditions and each culture condition has 3 replicates.

first: Fei

last: Chen

first: Jan

last: Bruder

first: Niraimathi

last: Govindasamy

first: Rui

first: Devila

last: Prit

first: Hannes

last: Drexler

first: Sebastian

last: Leidel

first: Hans

middle: R

last: Schöler

first: Ivan

last: Bedzhov


title: Multiscale profiling of tyrosine kinase inhibitor cardiotoxicity reveals mechanosensitive ion channel PIEZO1 as cardioprotective [bulk RNA-seq]

city: Palo Alto

last: Liu

address: 1215 Welch Road

department: CVI

institute: Stanford University

summary: Tyrosine kinase inhibitors (TKIs) have improved cancer outcomes but are limited by cardiovascular toxicity, most notably hypertension and heart failure. The underlying mechanisms remain poorly understood, hindering the development of protective strategies. Here, we investigated the role of endothelial mechanotransduction in mediating vascular and cardiac injury caused by the VEGFR-targeting TKI sunitinib. Using patient-specific induced pluripotent stem cell-derived endothelial cells (iPSC-ECs) and a mouse model of TKI-induced hypertension, we identified downregulation of PIEZO1, a mechanically activated ion channel, as a central driver of endothelial dysfunction. Restoring PIEZO1 expression, either pharmacologically with Yoda1, a selective agonist, or through inducible overexpression in iPSC-ECs, reversed sunitinib-induced endothelial dysfunction and mitigated its hypertensive effects, providing both mechanistic and genetic validation of PIEZO1’s protective role against vascular toxicity. In mice, Yoda1 co-treatment prevented the long-term cardiac dysfunction observed following sunitinib exposure, and normalized elevations in circulating cardiac stress biomarkers. Single-nuclei multiomic profiling of mouse hearts revealed that sunitinib exposure activated chromatin remodeling and fibrogenic programs, which were reversed with PIEZO1 activation. Human engineered cardiac organoids further demonstrated that sunitinib impaired cardiomyocyte function only in the presence of endothelial cells, confirming a role for disrupted endothelial-cardiomyocyte crosstalk in TKI cardiotoxicity. Together, these findings identify endothelial PIEZO1 as a critical mediator of TKI-induced hypertension and cardiac dysfunction and highlight PIEZO1 activation as a potential therapeutic strategy for protecting cardiovascular health during cancer therapy.

overall_design: RNA-seq of patient-specific iPSC-ECs, primary endothelial cells, and iPSC-derived cardiac organoids

first: Nazish

last: Sayed


title: Sex-Specific Angiogenic Responses in Endothelial Cells – Role of the Pluripotency Factor OCT4

city: Cleveland

first: Olga

last: Cherepanova

state: OH

address: 9500 Euclid Ave

department: Cardiovascular and Metabolic Sciences

institute: Cleveland Clinic

summary: The study investigates the sex-specific effects of the pluripotency factor OCT4 deficiency in endothelial cells (ECs) on angiogenesis. OCT4 is known for its role in embryonic stem cells, but we recently found that it plays a protective role in ECs during atherosclerosis. Herein, we utilized cultured mouse aortic ECs (MAECs) and several in vivo models, including skin wounding, melanoma tumor implantation, and hindlimb ischemia, to explore the role of OCT4 in angiogenesis in both male and female mice. Our findings show significant sexual dimorphism in angiogenic responses to OCT4 deficiency. Male mice with endothelial Oct4 knockout had faster skin wound healing, increased vascularization, and quicker blood flow recovery after hindlimb ischemia than wild-type mice. In contrast, female mice with endothelial Oct4 knockout experienced delayed wound healing, no significant change in blood flow recovery after hindlimb ischemia, and increased tumor growth. Mechanistically, MCP1, a key angiogenic chemokine, was differentially regulated in male and female Oct4 knockout compared to wild-type MAECs, suggesting OCT4-dependent regulation of MCP1 as a critical mechanism for sex differences in angiogenic responses. RNA sequencing (RNAseq) analysis revealed distinct gene expression profiles in male and female MAECs upon OCT4 deficiency, with female ECs showing upregulation of pro-inflammatory genes and male ECs exhibiting increased cell cycle and angiogenesis-related gene expression. Overall, the research provides novel insights into the sex-specific functional role of OCT4 in ECs during angiogenesis and emphasizes the need for developing sex-specific EC-targeting therapeutic strategies for cardiovascular diseases and cancer.

overall_design: To investigate the role of the pluripotency factor OCT4 in endothelial cells, we isolated endothelial cells from aortas of endothelial cell specific OCT4 knockout male and female mice. We established mouse aortic primary cultured endothelial cells. We then performed bulk RNA-seq. The wild-type male and female aortic endothelial cells were isolated from the littermate mice and cultured, processed, and sequenced in parallel. Raw data for wild type control cells can be found in GSE247364.


title: Astrocytic FABP5 drives cerebellar white matter dysfunction in multiple system atrophy by promoting TNF signaling and ferroptosis

city: Shenzhen

first: Chuantao

last: Wu

state: Guangdong

address: Gongchang Street No.66

institute: Sun Yat-sen University

summary: This study identifies astrocytic FABP5 as a critical mediator linking glial inflammation, ferroptosis, and mitochondrial dysfunction in multiple system atrophy pathogenesis.

overall_design: Primary mouse astrocytes were treated with LPS or subjected to shFABP5 silencing under LPS stimulation to investigate transcriptomic alterations associated with FABP5-regulated neuroinflammation and ferroptosis.

first: Jiejing

last: Lin

first: Yi

first: Nozomi

last: Takahashi

first: Qikai

first: Baiyao

first: Fangmeng

last: Dai

first: Wenxue

last: Zhao

first: David

middle: I

last: Finkelstein

first: Ichiro

last: Kawahata

first: Kohji

last: Fukunaga

first: An

last: Cheng


title: Single-nucleus transcriptomic profiling of human lung tissue in chronic obstructive pulmonary disease (COPD) [snRNA-seq]

status: Public on Nov 17 2025

city: New Haven

first: Maor

last: Sauler

state: CT

address: 300 Cedar Street

department: Section of Pulmonary, Critical Care, and Sleep Medicine

institute: Yale School of Medicine

summary: Chronic obstructive pulmonary disease (COPD) is clinically and molecularly heterogeneous. To investigate COPD heterogeneity, we performed single-nucleus RNA sequencing (snRNA-seq) on lung tissue from individuals with and without COPD spanning the full disease spectrum. We generated 1,516,727 high-quality cell transcriptomes from 146 lung lobes obtained from 141 subjects. The dataset captures broad shifts in cellular composition and disease-associated cell states in epithelial, stromal, and immune populations. These data define the cellular landscape of COPD heterogeneity, revealing molecular drivers and biomarkers that could inform therapeutic strategies.

overall_design: Snap-frozen lung tissues from 146 lobes of 141 subjects were processed for snRNA-seq. Lung tissues were obtained from participants in the Lung Transplant Research Consortium, including never-smokers, smokers without COPD, and individuals with COPD across GOLD stages I-IV. Nuclei were isolated and loaded onto the 10x Genomics Chromium platform for library construction, and sequencing was performed on the Illumina NovaSeq 6000.

first: Yuening

last: Zhang

first: Huanhuan

last: Wei

first: Jessica

last: Nouws


title: Characterisation of TET function during indirect flight muscle development

status: Public on Nov 18 2025

city: clermont ferrand

first: yoan

last: renaud

address: place henri dunand

country: France

institute: igred

summary: Enzymes of the Ten Eleven Translocation (TET) family play a key role in the regulation of gene expression in many species by oxidizing 5-methylcytosine (5mC), a prominent epigenetic mark, into 5-hydroxymethylcytosine (5hmC). Yet, TET proteins also have non-canonical modes of action beyond 5mC oxidation, notably in Drosophila, whose genomes is devoid of 5mC. Here, we assessed TET function during the development of the adult indirect flight muscles which are derived from a population of progenitors located on the larval wing imaginal discs.

overall_design: All experiments were performed with biological replicates using dissected third instar larval wing discs or dissected pupal indirect flight muscles. w1118 (wt) or TET-GFP knock-in flies were used as control lines. Drosophila homozygous for Tet null or Tet catalytic dead alleles were used as test lines.

first: Lucas

last: WALTZER

first: Yoan

last: RENAUD

first: Vincent

last: GERDY


title: Small Molecule ITK and Pan-TRK Kinase Inhibitor (PF-07245303) for the Potential Topical Treatment of Atopic Dermatitis

city: Cambridge

first: Samir

last: Lal

address: 1 Portland St

institute: Pfizer Inc

summary: Atopic dermatitis (AD) is a chronic inflammatory skin disease driven by cytokines interleukin-4 (IL-4) and interleukin-13 (IL-13) and associated with skin barrier disruption and pruritis. Interleukin-2-inducible T cell kinase (ITK) is a tyrosine kinase expressed by T cells which functions to amplify T cell receptor (TCR)-dependent signals, and ITK deletion or kinase inhibition reduces TCR-induced IL-4 and IL-13 production. Nerve growth factor (NGF) is a neurotrophic factor which signals via the receptor tropomyosin-related kinase A (TRKA) and can promote pruritis in the skin.  The expression of both NGF and TRKA are enhanced in atopic dermatitis skin lesions, and levels of NGF in AD skin lesions correlated with itch severity. Here we describe a compound, PF-07245303, which potently inhibits ITK and TRK kinases (TRKA, B, and C). This compound demonstrated inhibition of TCR-induced, ITK-dependent phosphorylation of PLCγ1 and potently inhibits TCR stimulated IL-2 production from purified human T cells. Moreover, this ITK/TRK kinase inhibitor suppressed production of inflammatory cytokines from Th1, Th2, Th17, and CD8 T cells. In biochemical and cell-based assays PF-07245303 inhibited receptor kinases TRKA, TRKB, and TRKC and suppressed NGF-induced human basophil activation.  Using a human skin explant model of atopic dermatitis, PF-07245303 demonstrated pharmacological activity by inhibiting phosphorylation of TRKA and suppressed expression of cytokines from TCR-activated resident dermal T cells. These results suggest that dual inhibition of ITK and TRKs with PF-07245303 suppress(es) dermal T cell activation and NGF-dependent responses which contribute to atopic dermatitis.

overall_design: Skin explants were stimulated with CD3/CD28/TH2 cytokine cocktail and a ITK/TRK inhibitor

first: Jelinsky

last: Scott


title: Dietary sulfur amino acid restriction elicits a cold-like transcriptional response in inguinal but not epididymal white adipose tissue of male mice

city: Ithaca

first: Philip

last: Ruppert

state: NY

address: 244 Garden Avenue

department: Division of Nutritional Sciences

institute: Cornell University

summary: Introduction: About 1 billion people are living with obesity worldwide. GLP-1-based drugs have massively transformed care, but long-term consequences are unclear in part due to reductions in energy expenditure with ongoing use. Diet-induced thermogenesis (DIT) and cold exposure (CE) raise EE via brown adipose tissue (BAT) activation and beiging of white adipose tissue (WAT). Methionine restriction (MetR) is a candidate DIT stimulus, but its EE effect has not been benchmarked against CE, nor have their tissue-level interactions been defined. Objective & Methods: In a 2×2 design (Control vs. MetR; room temperature, RT: 22 °C vs. CE: 4 °C for 24 h), we used male C57BL/6N mice to benchmark MetR-induced thermogenesis against CE and mapped how diet and temperature interact across tissues. Bulk RNA-seq profiled liver, iBAT, iWAT, and eWAT. Differential expression was modeled with main effects and a diet×temperature interaction. KEGG GSEA was used to assess pathway-level enrichment. Results: MetR increased EE at RT and shifted fuel use towards lipid oxidation, supporting MetR as a bona fide DIT stimulus. CE elevated EE across diets and blunted diet differences. Transcriptomic responses were tissue-specific: in liver, CE dominated gene induction while MetR and CE cooperatively repressed genes. The combination enriched glucagon/AMPK-linked and core metabolic pathways. In iBAT, CE dominated thermogenic and lipid-oxidation programs with minimal MetR contribution. In iWAT, MetR and CE acted largely additively with high concordance, enhancing fatty-acid degradation, PPAR signaling, thermogenesis, and TCA cycle pathways. In eWAT, robust co-dependent and synergistic differential expression emerged only with MetR+CE. Conclusion: MetR is a genuine DIT stimulus that remodels metabolism in a tissue-specific manner. Our study provides a tissue-resolved transcriptomic resource that benchmarks diet-induced (MetR) against cold-induced thermogenesis and maps their interactions across liver, iBAT, iWAT, and eWAT.

overall_design: RNA-seq profiling of Liver, iWAT, iBAT and eWAT from C57BL/6N mice (Taconic) exposed to Sulfur amino acid restriction (0.12% Methionine, 0% Cysteine) or Control diets (0.86% Methionine, 0% Cysteine) (Research diets cat no. A11051301B and A11051302B) for 7 days +/- 24h of Cold exposure (22°C to 4°C).

first: Philip M

first: Aylin

middle: S

last: Güller

first: Marcus

last: Rosendal

first: Natasa

last: Stanic

first: Jan-Wilhelm

last: Kornfeld


title: Leveraging Two Novel Droplet-Based Single-Cell RNA Sequencing Platforms: a Comparative Study With 10x Genomics

first: Alesya

last: Maluchenko

address: Kulakova str. 20

institute: Moscow Center for Advanced Studies

summary: Here we performed a comparison of two droplet-based high-throughput single-cell platforms, namely, SeekOne and MobiDrop with a widely-used commercial platform from 10x Genomics. The use of different types of samples allowed us to evaluate the performance of the platforms on cell suspensions of varying complexity and quality. 10x showed generally superior performance, although all platforms compared in this study showed acceptable gene yield and allowed identification of all expected cell types. Taking into account the cost and availability of devices and reagents required for each platform and the flexibility in the number of samples loaded onto the chip, SeekOne and MobiDrop might serve as a good alternative. The results of the current comparison will support the community's efforts to compare different aspects, including sample amount requirements, throughput, cell quality, gene capture efficiency and cell type representativeness.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
We analyzed the samples of human peripheral blood mononuclear cells, murine adrenal glands and human tumors to compare performance of the three scRNA-seq platforms (10x, SeekOne, MobiDrop).
To compare 3-primed assays of 10x, SeekOne and MobiDrop pooled PBMC derived from 4 patients and murine adrenal gland samples obtained from two-week-old or three-day-old mice were used. Human tumor tissue samples were obtained from two operated patients with non-functioning pancreatic neuroendocrine tumors to compare 10x and MobiDrop 5-primed assays.

first: Alesia

first: Ekaterina

last: Avsievich

first: Iaroslava

last: Zvorygina

first: Zoia

last: Antysheva

first: Denis

last: Maksimov

first: Margarita

last: Boytsova

first: Dmitry

last: Tabakov

first: Natalia

last: Bodunova

first: Olga

last: Glazova

last: Tychinin

first: Alexander

last: Bolbat

last: Petriaikina

last: Svetlichnyy

first: Sergey

last: Yudin

first: Anton

last: Keskinov

first: Vladimir

first: Mary

last: Woroncow

first: Veronika

last: Skvortsova

first: Julia

last: Krupinova

first: Pavel

last: Volchkov


title: Junctional adhesion molecule-C contributes to vascular lumenization through promoting endothelial cell adhesion and matrix deposition

city: Guangzhou

first: Keli

last: Liu

address: 7 Jinsui Road

summary: Bulk RNAseq was performed using control or JAM3 siRNA treated human umbilical vein endothelial cells (HUVECs)

overall_design: Treated cells were detached and lysed. Total RNAs were extracted and then subjected to RNAseq analysis

first: Feng

last: Zhang

first: Lechun

last: Ou

first: Weifa

last: Wang


title: NAT10 promotes cancer metastasis by modulating p300/CBP activity through chromatin-associated tRNA

city: Bethesda

first: Maxwell

last: Lee

state: MD

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

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

overall_design: Refer to individual Series


title: NAT10 promotes cancer metastasis by modulating p300/CBP activity through chromatin-associated tRNA [RNA-ChIP]

summary: Acetylation of proteins and RNA is crucial for development and cancer progression. NAT10 is the sole RNA acetylase responsible for N4-acetylcytidine (ac4C) modification of various RNAs. Our study reveals that NAT10 loss significantly reduces lung metastasis in breast cancer mouse models. NAT10 interacts with a mechanosensitive, metastasis-susceptibility protein complex at the nuclear pore. Mechanistically, NAT10-mediated acetylation of chromatin-associated tRNAs enhances p300/CBP activity. Without NAT10, acetylation of these tRNAs decreases, leading to p300/CBP inactivation and mislocalization. As a result, NAT10 depletion disrupts enhancer organization, altering gene transcription critical for metastasis, including reduced chemokines that recruit myeloid cells and create a less metastasis-prone tumor microenvironment. Our findings highlight the distinct role of NAT10 in acetylated tRNA-dependent regulation of enhancer function in metastatic tumor cells and its impact on tumor-immune interactions influencing metastasis.

overall_design: We performed  p300 RNA immunoprecipitation followed by sequencing of chromatin-associated RNAs (RNA-ChIP) of WT and Nat10 knockout (KO-c43) 4T1 mouse mammary tumor cells. We followed the protocol described in RNA Chromatin Immunoprecipitation (RNA-ChIP) kit (Active Motif). Briefly, 4T1 cells were cultured in 15 cm dishes at a seeding density of 4 × 10⁶ cells per dish. After 48 hours, the cells were fixed with 1% formaldehyde for 15 minutes at room temperature. The fixation was quenched by adding 1x Glycine Stop-Fix solution. Cells were then harvested by scraping, followed by centrifugation at 3,500 rpm for 10 minutes at 4°C. For nuclei isolation, the cell pellets were lysed in 1 ml of ice-cold Complete Lysis Buffer for 30 minutes and then homogenized using a Dounce homogenizer with 50 strokes. The release of nuclei was confirmed under a brightfield microscope. The lysates were centrifuged at 5,000 rpm for 10 minutes at 4°C, and the nuclear pellet was resuspended in Complete Shearing Buffer containing RNase inhibitors. Chromatin was sheared using a Bioruptor Plus sonicator (Diagenode) for 3 cycles (30 seconds on, 30 seconds off) at 4°C. The sheared chromatin samples were then centrifuged at 18,000 x g for 10 minutes at 4°C, and the supernatant containing the chromatin fraction was transferred to fresh tubes. The concentration of chromatin was determined by isolating RNA from an aliquot of the chromatin preparation. RNA-ChIP reactions were performed using three biological replicates for both WT and KO samples, with each reaction containing the equivalent of 6 μg of RNA from chromatin. Immunoprecipitation was conducted in a 150 μl reaction volume, consisting of 25 μl of pre-washed Protein G Magnetic Beads, RNA-IP buffer, RNase inhibitors, Protease Inhibitor Cocktail, and 2 μg of rabbit p300 antibody (Abcam). The reaction mixture was incubated overnight on a rotator at 4°C. The beads were then washed four times with Complete RNA-ChIP Wash Buffer 1, followed by two washes with Complete RNA-ChIP Wash Buffer 2. RNA was eluted from the beads with Complete RNA-ChIP Elution Buffer by rotating on an end-to-end rotator for 15 minutes at room temperature. The supernatant containing the eluted RNA was transferred to a fresh tube after magnetic separation of the beads. Both the immunoprecipitated RNA and input RNA samples were treated with proteinase K and reverse cross-linked at 65°C for 1.5 hours. The RNA was then purified using TriPure Isolation Reagent (Millipore-Sigma). To remove residual DNA, the purified RNA was treated with DNase I, followed by further purification using the RNA Clean & Concentrator-5 Kit (Zymo).

first: Ruhul

last: Amin

first: Ngoc-Han

last: Ha

first: Tinghu

last: Qiu

first: Ronald

last: Holewinski

first: C Lam

last: Khiem

first: Amélie

last: Daugherty-Lopès

first: Huaitian

first: Andy D

last: Tran

first: Maxwell P

first: Thorkell

last: Andresson

first: Romina S

last: Goldszmid

first: Kent W

last: Hunter


title: NAT10 promotes cancer metastasis by modulating p300/CBP activity through chromatin-associated tRNA [ChIP-seq]

overall_design: We performed ChIP-seq of H3K27ac, H4K20ac, and H3K27me3 in WT and Nat10 knockout (KO-c43) 4T1 mouse mammary tumor cells. In addition, we also performed ChIP-seq of Nat10, Pan Brd4, V5-tagged Brd4-short isoform, endogenous RRP1B, HA-tagged Rrp1b and Sipa1 in parental 4T1 cells.

first: Andy

middle: D

middle: P

first: Supuni

middle: T

last: Gamage

first: Jordon

last: Meier

first: Kent

middle: W


title: Antioxidant program of islet-resident macrophages preserves β cell physiology

city: Paris

first: Nicolas

last: Venteclef

address: 156 rue de Vaugirard

institute: Institut Necker Enfants Malades, INSERM U1151

summary: Macrophages residing inside mouse pancreatic islets have an activated phenotype at steady-state. To explore the molecular pathways involved in their polarization, we compared the transcriptomic signatures of islet-resident macrophages with autologous epididymal adipose tissue (EpiWAT)-resident macrophages. Our data confirmed the pro-inflammatory profile of islet marophages and revealed also strong anti-oxidant capacities compared to EpiWATcells.

overall_design: Single cells were obtained from pancreatic islets and EpiWAT of autologous 12-week-old chow diet-fed C57BL/6J males. Resident marcrophages were sort-purified as live DAPI-CD45+F4/80+CD64+ cells with a FACS ARIA III cell sorter (BD Biosciences) using FACS Diva software (BD Biosciences) and lysed for mRNA extraction and librairie preparation.

first: E

last: Dalmas

first: M

last: Diedisheim

first: LG

last: Baudrin

first: S

last: Baulande


title: RNA regulation in satellite cell differentiation(RNA-seq)

status: Public on Nov 16 2025

city: shanghai

first: hong

last: cheng

address: yueyang road

institute: ucas

overall_design: Zfc3h1 knock-out and wild-type stellate cells, as well as myotubes, were profiled under normal conditions in two biological replicates.


title: RNAseq data of frontal cortex of 4 months high fat diet fed WT, AKO,  4 months high fat diet fed conditional human amylin expressing mice followed by vehicle and Tamoxifen injection, and 2 months high fat diet fed WT mice

status: Public on Nov 15 2025

city: Lexington

first: Nirmal

last: Verma

state: Kentcuky

address: 900 S Limestone

department: Pharmacology and Nutritional Sciences

institute: University of Kentucky

summary: We performed gene expression profiling analysis using data from RNAseq of brain frontal cortex from four months high fat diet fed WT (n=10), AKO (n=10), four months high fat diet fed condition human amylin mice followed by vehicle (n=10) or Tamoxifen (n=10) injection for another two months, and 2 months high fat diet fed WT mice (n=10).

overall_design:
Expression profiling by high throughput sequencing
CreVE: four months high fat diet fed condition human amylin mice followed by vehicle
CreTM: four months high fat diet fed condition human amylin mice followed by Tamoxifen
4MHFW: four months high fat diet fed WT
4MHFA: four months high fat diet fed AKO
2MHF: 2 months high fat diet fed WT mice

first: Davargaon

last: Ravichandra

first: verma

last: nirmal

first: Kotiya

last: Deepak

first: Leibold

last: Noah

first: Despa

last: Sanda

first: despa

last: florin


title: RNA regulation in satellite cell differentiation(quant-seq)


title: NAT10 promotes cancer metastasis by modulating p300/CBP activity through chromatin-associated tRNA [RNA-seq]

first: Maxwell

last: Lee

overall_design: We performed total RNA-seq of WT and Nat10 knockout (KO-c19 and KO-c43) 4T1 mouse mammary tumor cells. 4T1 cells were grown on 6cm dish at a seeding density of 300, 000 cells/dish. 3 biological replicates were performed per condition. 48h later, cells were lysed with TriPure isolation reagent (sigma). RNA was isolated using RNEasy mini kit (Qiagen). On column DNase I digestion was performed to eliminate genomic DNA contamination.

first: Ruhul

last: Amin

first: Ngoc-Han

last: Ha

first: Tinghu

last: Qiu

first: Ronald

last: Holewinski

first: Huaitian

last: Liu

first: Andy

last: Tran

first: Thorkell

last: Andresson


title: Single cell analysis reveals the myeloid-biased hematopoiesis and leukemic evolution programs initiated by Brd4 in HSPCs of mice with disuse osteoporosis

status: Public on Nov 14 2025

city: Xi'an

first: Chen

last: Zhang

address: Xinsi road

department: Department of hematology

institute: Tangdu Hospital

summary: To understand the molecular changes driving the myeloid-biased hematopoiesis and the potential of leukemia evolution by restricting the differentiation and apoptosis in HSPCs of OP-HU mice, single cell RNA sequencing was performed to analyze the transcriptional changes of Lin-/c-kit+ HSPCs from the femur and tibia of OP-HU and control mice.

overall_design: Lin-/c-kit+ HSPCs from the femur and tibia of OP-HU and control mice were enriched repectively by combination of lineage depletion kit (Miltenyi Biotech, 130-090-858) and CD117 MicroBeads (Miltenyi Biotech, 130-091-224). Lin- CD117+ enriched HSPCs were dispelled into single cell for further single-cell RNA sequencing analysis (Singleron Biotech Co., Ltd, Nanjing, China)

first: Li

first: Weiwei

last: Qin


title: Homozygous deletion of the epigenetic regulator PHF20 in individuals with neurodevelopmental disorder

city: Grand Rapids

first: Xiaobing

last: Shi

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

summary: PHF20 encodes plant homeodomain finger protein 20 (PHF20), a component of the KAT8-containing non-specific lethal (NSL) complex that deposits acetylation on histone H4 to activate gene expression. We report two unrelated individuals with developmental delay, microcephaly and distinctive facial features, in whom exome sequencing and chromosomal microarray analysis revealed a homozygous deletion of PHF20 that segregated with the disease phenotype in their families. Breakpoint junction sequencing revealed an Alu-Alu mediated deletion event. Western blot in cells from an affected individual showed undetectable PHF20, while levels of other NSL complex subunits were unaltered.  Transcriptomic and epigenomic analysis revealed significant downregulation of gene pathways related to cell projection and neuronal development, associated with reduced histone H4K16 acetylation at these genes. In conclusion, our data suggest that homozygous deletion of PHF20 leads to a neurodevelopmental syndrome, potentially through targeted epigenetic dysregulation and altered gene expression essential for neuronal development. Identifying additional families with biallelic PHF20 variants will further delineate the phenotypic spectrum, and molecular studies in neuronal cell lines will be essential for understanding the disease mechanism.

overall_design: H4K16ac ChIP profiles of lymphoblastoid cell lines (LCLs) from EBV-transformed PHF20 -/- patient lymphocytes.

first: Shira

middle: Y

last: Dagan

first: Hongwen

last: Xuan

first: Yonatan

last: Rips

first: Emuna

last: Paz-Ebstein

first: Talia

last: Baer

last: Gross

first: Ayala

last: Frumkin

first: Tamar

last: Harel


title: Methylome dataset by Whole-genome bisulfite sequencing (WGBS) using whole blood of dogs

city: Fujimino

first: Miyuki

last: Nakamura

state: Saitama

country: Japan

institute: KDDI research Inc


title: Single-cell sequencing unveils a novel cluster of mesenchymal cells in the rat subcutaneous fascia

city: Nanjing

first: Haixiang

last: Huang

state: 江苏

address: No.1, Weigang, Xuanwu district

department: College of veterinary

institute: Nanjing Agricultural University

summary: ScRNA data of the abdominal skin and subcutaneous fascia

overall_design: we performed scRNA-seq to compare the cellular constitution of the skin(n=2) and subcutaneous fascia (n=2)

first: Zhenwei

first: Jianming

last: Yue

first: Lu

last: Mei

first: Qiusheng

last: Chen


title: Targeting AASS improves neurotoxicity and  mitochondrial function in astrocyte models for  pyridoxine dependent epilepsy

status: Public on Nov 13 2025

city: Nijmegen

first: Sofia

last: Puvogel

address: Geert Grooteplein Zuid 10

country: Netherlands

institute: RadboudUMC

summary: Pyridoxine-dependent epilepsy (PDE) is a rare neurometabolic disorder of lysine catabolism, which is caused by pathogenic variants in ALDH7A1. In this study, we performed RNA sequencing on differentiated astrocytes derived from patient and isogenic knock-out iPSC lines. We identified a reduced expression of genes associated with oxygen response, which correlates with heightened oxidative stress in PDE astrocytes.

overall_design: Transcriptomic profiling of human iPSC-derived astrocytes was performed using two control lines (C1, C4), two Pyridoxine-dependent epilepsy (PDE) patient lines (P1, P3), and an isogenic ALDH7A1-/- line derived from C1. Each cell line included three biological replicates.

first: Imke

last: Schuurman

first: Udo

last: Engelk

first: Sofía

first: Rachel

last: Mijdam

first: Gijs-Jan

last: Scholte

first: Astrid

last: Oudakker

first: Dirk

last: Lefeber

first: Clara

last: van Karnebeek

first: Nael

last: Nadif Kasri

first: Alejandro

last: Garanto


first: Nicolas

last: Venteclef


title: Molecular and epistatic interactions between pioneer transcription factors shape nucleosome dynamics and cell differentiation [MNase-seq]

city: paris

first: Pablo

last: Navarro

address: 25 rue du Docteur Roux

institute: Institut Pasteur

summary: Pioneer transcription factors (TF) bind nucleosome-embedded DNA motifs to activate new regulatory elements and promote differentiation. However, the complexity, binding dependencies and temporal effects of their action remain unclear. Here, we dissect how ectopic induction of the pioneer TF GATA6 triggers Primitive Endoderm (PrE) differentiation from pluripotent cells. We show that transient GATA6 binding exploits accessible regions to decommission enhancers and promote pluripotency gene silencing. Simultaneously, GATA6 targets closed chromatin and initiates extensive remodeling culminating in the establishment of fragile nucleosomes flanked by ordered nucleosome arrays and increased accessibility. This is enhanced by rapidly expressed PrE TFs (SOX17) and by pluripotency TFs repurposed for differentiation (OCT4/SOX2). Accordingly, depletion of OCT4 during GATA6 induction decreases Gata6 expression, alters GATA6 and SOX17 binding and impairs differentiation. Therefore, pioneer TFs orchestrate complex regulatory networks involving many if not all available pioneer TFs, including those required to support the original identity of differentiating cells.

overall_design: differentiation of ES cells carrying a dox-inducible GATA6 transgene was induced using doxycycline, MNase-seq was carried out at various differentiation time points

first: Rémi-Xavier

last: Coux


title: Molecular and epistatic interactions between pioneer transcription factors shape nucleosome dynamics and cell differentiation [ATAC-seq]

overall_design:
differentiation of ES cells carrying a dox-inducible GATA6 transgene was induced using doxycycline
ATACseq was carried out at various differentiation time points


title: Virus Entry is a Major Determinant of HCMV Latency in Monocytes

status: Public on Nov 27 2025

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

institute: Weizmann Institute

summary: Human Cytomegalovirus (HCMV) infection can result in either productive or latent infection, the latter being the basis for the virus life-long persistence. Intriguingly, monocytes, which support latent infection, become permissive to productive infection upon differentiation to macrophages. However, the molecular factors explaining these differentiation-driven differences are not fully understood and have been so far attributed to chromatin-mediated repression of the viral genome. Here, by using metabolic labeling of newly synthesized RNA early in monocyte and macrophage infection, we discover a major early block in viral gene expression, and viral transcripts are barely detected in infected monocytes. By unbiasedly analyzing the changes between monocytes and their differentiated counterparts, we reveal that the levels of several cell surface proteins involved in HCMV entry are upregulated upon monocyte to macrophage differentiation, and correspondingly we uncover HCMV entry into monocytes compared to macrophages is extremely inefficient. Remarkably, ectopic expression of a canonical HCMV entry receptor in monocytes facilitates productive infection of these cells, demonstrating that given efficient viral entry, monocytes, like macrophages, have the capacity to support productive infection. Among the cell surface proteins that are upregulated upon monocyte differentiation are several integrins, which we show play an important role in HCMV entry into macrophages, partially explaining the differences in viral entry. Overall, our findings reveal that a previously unrecognized major barrier for productive infection in monocytes is entry, adding a critical layer to the paradigm of HCMV latency.

overall_design: Slam-seq: We directly measure early transcription of viral genes using slam-seq on primary and THP1 monocytes and macrophages.  RNA-seq: 1. We performed RNA-seq on primary monocytes, THP1 monocytes and Kasumi-3 myeloid progenitor cells, as well as on macrophages derived from the same cells. 2. We sequence THP1 control and THP1 overexpressing PDGFRa.  CRISPR-screen: THP1-PDGFRα monocytes were transduced with the GeCKO CRISPR/Cas9 genome-wide knockout library (targets 19,050 human genes with three guides per gene and one thousand non-targeting gRNA as controls). We infected these cells with HCMV-GFP and at 2 days post infection sorted them to GFP-bright and GFP-dim populations, reflecting productive and non-productive infection, respectively. gRNAs were sequenced and aligned using MAGeCK.

first: Kitsberg

last: Yaarit

first: Nachshon

last: Aharon

first: Arazi

last: Tamar

first: Schwartz

last: Michal

first: Stern-Ginossar

last: Noam


title: MASTR-seq: Multiplexed Analysis of Short Tandem Repeats with sequencing

city: St. Louis

first: Jennifer

middle: E.

last: Phillips-Cremins

state: MO

address: 4515 McKinley Ave

department: Bioengineering

institute: Washington University in St. Louis

summary: More than 60 human disorders have been linked to unstable expansion of short tandem repeat (STR) tracts. STR length and the extent of DNA methylation is linked to disease pathology and can be mosaic in a cell type-specific manner in several repeat expansion disorders. Mosaic phenomenon have been difficult to study to date due to technical bias intrinsic to repeat sequences and the need for multi-modal measurements at single-allele resolution. Nanopore long-read sequencing accurately measures STR length and DNA methylation in the same single molecule but is cost prohibitive for studies assessing a target locus across multiple experimental conditions or patient samples. Here, we describe MASTR-seq, Multiplexed Analysis of Short Tandem Repeats, for cost-effective, high-throughput, accurate, multi-modal measurements of DNA methylation and STR genotype at single-allele resolution. MASTR-seq couples long-read sequencing, Cas9-mediated target enrichment, and PCR-free multiplexed barcoding to achieve a >ten-fold increase in on-target read mapping for 8-12 pooled samples in a single MinION flow cell. We provide a detailed experimental protocol and computational tools and present evidence that MASTR-seq quantifies tract length and DNA methylation status for CGG and CAG STR loci in normal-length and mutation-length human cell lines. The MASTR-seq protocol takes approximately eight days for experiments and one additional day for data processing and analyses.

overall_design: Multiplexed STR analysis by target nanopore sequencing in human iPSC or  ESC samples modeling human pathological STR expansion related neurological diseases, like fragile-X-syndrome and huntington diseases.

first: Chuanbin

last: Su

first: Han-Seul

last: Ryu

first: Keerthivasan

last: Chandradoss

first: Thomas

last: Malachowski

first: Ravi

last: Boya

first: Kristen

last: Brennand


title: Single-Cell Analysis of Heterogeneity in Reverted Human iPSC-Derived Hepatic Stellate Cells

status: Public on Nov 12 2025

city: Cleveland

first: Xianfang

last: Wu

state: Ohio

address: 9500 Euclid Avenue/NE20, Office NE2-308, Office NE2-308

department: Infection Biology

institute: Cleveland Clinic

summary: We employed a single-cell RNA sequencing (scRNA-seq) approach using the 10x Genomics platform to investigate the heterogeneity of reverted hepatic stellate cells (HSCs) derived from human induced pluripotent stem cells (hiPSCs). HSCs are key mediators of liver fibrosis; although their activation is well known to drive fibrogenesis, their fate following removal of the fibrogenic insult remains poorly understood. To address this, we utilized a hiPSC-derived liver culture system comprising hepatocytes, HSCs, and macrophages. HSCs were activated by hepatitis C virus (HCV) infection and subsequently treated with antivirals to achieve viral clearance. Reverted HSCs were then characterized through gene expression profiling, vitamin A quantification, functional assays, and scRNA-seq. Our data reveal that activated HSCs exhibit plasticity and can revert to a quiescent-like state upon removal of the activating stimulus, although they retain heightened sensitivity to re-stimulation. These findings enhance our understanding of HSC dynamics and highlight potential therapeutic strategies targeting HSC reversion to treat liver fibrosis.

overall_design: HSCs were activated through hepatitis C virus (HCV) infection and subsequently treated with antiviral agents to achieve viral clearance. To enable single-cell RNA sequencing (scRNA-seq), reverted HSCs were isolated by depleting co-cultured hepatocytes.

first: Xinjia

last: Wang

first: Eun Hee

last: Ha

first: Yifei

last: Zheng


title: FET-Rearranged Soft Tissue Myoepithelial Tumors Span a Broad Clinicopathologic and Molecular Spectrum that is Epigenetically Distinct from Cutaneous and Head and Neck Myoepithelial Tumors

status: Public on Nov 09 2025

city: New York

first: Cristina

last: Antonescu

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

type: Methylation profiling by genome tiling array

summary: DNA methylation profiling from a multi-institutional cohort of 52 fusion-positive MET cases were analyzed. Pooled clinicopathological and outcome analysis with new and published cases (total 185 and 69 cases, respectively) was performed. The MET subgroups, EWSR1::KLF15, EWSR1/FUS::KLF17, EWSR1::PBX1, EWSR1::PBX3, EWSR1/FUS::POU5F1, SS18::POU5F1, and EWSR1::ZNF444, showed significant heterogeneity in age group, site, and histology. DNA methylation analysis revealed that fusion-positive MET were epigenetically related to each other and EWSR1/FUS::NFATC2 sarcomas, but entirely distinct from the epigenetically-related PLAG1-rearranged and salivary gland MET.

overall_design: Genomic DNA was extracted from formalin-fixed paraffin-embedded tissue sections for each of the samples. Next, 250 ng of genomic DNA was subjected to bisulfite conversion and processed on the Illumina Infinium Methylation EPICv2 platform. IDAT processing and data analysis on all 407 samples was performed using the R software (version 4.4.1) and the “minfi” package (version 1.52.1). Raw IDAT files were normalized by preprocessSWAN function and filtered in for detection P value < 0.05.

first: Josephine

last: Dermawan

first: Michael


title: Transcription factor occupancy is affected by genetic variation in the white adipose tissue of C57BL6/j and 129S1/SvImJ mice

city: Kuopio

first: Juho

middle: Mikael

last: Mononen

address: Yliopistonranta 1E

department: Faculty of Health Sciences

country: Finland

institute: University of Eastern Finland

overall_design: Refer to individual Series


title: Molecular and epistatic interactions between pioneer transcription factors shape nucleosome dynamics and cell differentiation [ChIP-Seq]

first: Pablo

last: Navarro

overall_design:
differentiation of ES cells carrying a dox-inducible GATA6 transgene was induced using doxycycline
ChIPseq against GATA6, SOX17, OCT4, SOX2 and ESRRB were carried out at various differentiation time points

ES cells carrying a dox-inducible GATA6 transgene were nucleofected with control or oct4 siRNA and plated in doxycycline containing media. ChIPseq against SOX17 and GATA6 was carried out 48h after nucleofection.

first: Remi-Xavier

last: Coux


title: Altered thymopoiesis in thymoma is associated with defects in negative selection machinery and decreased Treg abundance

first: Alexandre

last: Lanau

address: 26 rue d'Ulm

department: Unité 830

institute: Institut Curie

summary: Thymomas are rare thymic epithelial tumors harboring a high but variable proportion of lymphocytes without obvious function. Auto-immunity is present in one third of patients at diagnosis. Herein, we performed a phenotypic, scRNAseq, and spatial analysis of both the T cells and tumoral cells. All stages of T cell development -from immature to mature- were present in the tumor suggesting active thymopoiesis in thymoma. However, multiple approaches suggest a maturation blockade at the DN-DP stages. In the mature T cell compartment, the frequency of Tregs was strongly decreased. Notably according to scRNAseq, the transcriptome of tumoral Thymic Epithelial Cells (tTEC) was most similar to that of non-tumoral medullary TEC but the expression of key molecules involved in positive and negative selection was defective. Multiplexed Immunohistochemical Consecutive Staining evidenced a loss of the cortex-medulla zoning in thymoma which may be related to a decrease expression of T cell targeted chemokines by tTEC. Altogether, these results suggest that the thymopoiesis present in thymoma is abnormal and may provide the grounds for the prevalent auto-immunity observed in this disease.

overall_design: Either tumor cells (CD45- Epcam+) or thymocytes (T cells selection kit milteny) were isolated. Thymocytes were sequenced using 10x 5’scRNA-seq paird with scTCR-seq kit. Tumor cells were sequenced using 10X 3’ scRNA-seq kit.

first: Clemence

last: Basse

first: Joshua

last: Waterfall

first: Olivier

last: Lantz

first: Nicolas

last: Girard


title: Small-molecule inhibition of MuRF1 protects against early disuse-induced diaphragmatic dysfunction and atrophy: Underlying cellular and molecular mechanisms

city: Stockholm

first: Paulo

middle: R.

last: Jannig

address: Solnavägen 9

department: Department of Physiology and Pharmacology

institute: Karolinska Institutet

summary: Background: Disuse-induced diaphragmatic dysfunction and atrophy (DIDD) is characterized by a rapid  and progressive loss of diaphragm muscle fibers size and contractile function. Patients undergoing mechanical ventilation or diaphragm paralysis can develop DIDD, which correlates with worse clinical outcomes, morbidity and mortality. We hypothesize tha Muscle RING-finger protein-1 (MuRF1) activity plays an important role in DIDD onset and pathophysiology. Aim: To evaluate the effect of small-molecule inhibition of MuRF1 (MyoMed-205) on early DIDD in an experimental model in rats.

overall_design: Male Wistar rats (n = 24) were divided into three experimental groups (n = 8): Sham 12h, Denervated 12h + vehicle, and Denervated 12h + MuRF1 inhibitor (205). Unilateral diaphragm denervation was performed, followed by intravenous treatment with vehicle or MuRF1 inhibitor (50 mg/kg bw) for 12h. The Sham operated group underwent no diaphragm denervation or aditional interventions apart from sedation and anesthesia. Diaphragm muscle (costal portion) was used for morphological, functional, gene (RNA-seq) and protein expression analyses.

first: Fernando

last: Ribeiro

first: Siegfried

last: Labeit

first: Anselmo

last: Moriscot


title: Transcriptomes of classical monocytes in post-COVID patients suggest predisposing condition or innate memory from SARS-CoV-2 infection

status: Public on Nov 07 2025

city: Rostock

first: Brigitte

last: Müller-Hilke

address: Schillingallee 70

department: Core Facility for Cell Sorting and Cell Analysis

country: Germany

institute: Rostock University Medical Center

summary: Despite extensive global research efforts, predisposing conditions and mechanisms leading to post-COVID remain poorly understood. While age and sex have most frequently been cited as predispositions, perturbations of the peripheral immune system have been associated with its pathogenesis. To deepen the current knowledge, we here investigated the immunological landscapes of 44 post-COVID patients and 44 sex-, age-, and vaccine-matched convalescents using single-cell RNA sequencing (scRNA-seq) of peripheral blood mononuclear cells (PBMCs). To validate the mRNA-based findings, we measured plasma cytokine levels via Luminex technology. Our analysis revealed only minor differences in immune cell composition between the cohorts. In contrast, we identified numerous differently expressed genes (DEGs) that allowed for a clear clustering of patients and controls. These transcriptomic changes were predominantly observed in classical monocytes and were characterized by the downregulation of inflammation-associated genes, including IL1B, CCL3, -4, and -20 as well as CXCL1, -2, -3, and -8. Further analysis of transcription factor activity hinted at reduced inflammasome activity via SNAI1 and impaired differentiation of classical monocytes due to reduced ATF2. RNA velocity corroborated the findings of pre-mature classical monocytes in post-COVID patients. Based on these results, we hypothesize that patients either developed a state of SARS-CoV-2-induced immune tolerance that contributed to subsequent symptoms, or they possessed a predisposition of impaired innate immunity prior to infection, that facilitated the development of post-COVID.

overall_design: Immmune profiling of 44 post-COVID patients and 44 controls via scRNA-seq and validation with plasma cytokines measurements via Luminex technology.

first: Florian

last: Fricke

first: Franz

last: Mai

first: Christine

last: Wossidlo

first: Felix

last: Steinbeck

first: Wendy

last: Bergmann-Ewert

first: Marcel

last: Kordt

first: Emil

last: Reisinger


title: The growth factor FGF21 maintains neuromuscular junction through histone deacetylase HDAC4 in denervation-induced skeletal muscle atrophy

status: Public on Nov 06 2025

city: Tokyo

first: Lirong

last: Zheng

address: kanto

institute: The University of Tokyo

summary: Skeletal muscles undergo atrophy in response to denervation and neuromuscular diseases. Understanding the mechanisms by which denervation drives muscle atrophy is crucial for developing therapies against neurogenic muscle atrophy. Here, we identify muscle-secreted fibroblast growth factor 21 (FGF21) as a key inducer of atrophy following muscle denervation. In denervated skeletal muscles, Fgf21 is the most robustly upregulated member of the Fgf family and acts in an autocrine/paracrine manner to promote muscle atrophy. Silencing Fgf21 in muscle prevents denervation-induced muscle wasting by preserving neuromuscular junction (NMJ) innervation. Conversely, forced expression of FGF21 in muscle reduces NMJ innervation, leading to muscle atrophy. Mechanistically, TGFB1 released by denervated fibro-adipogenic progenitors (FAPs) upregulates Fgf21 through the JNK/c-Jun axis. The resulting increase in FGF21 protein reduces the cytoplasmic level of histone deacetylase 4 (HDAC4), culminating in muscle atrophy. HDAC4 knockdown abolishes the atrophy-resistant effects observed in Fgf21-deficient denervated muscles, resulting in muscle atrophy. Our findings reveal a novel role and heretofore unrecognized mechanism of FGF21 in skeletal muscle atrophy, suggesting that inhibiting muscular FGF21 could be a promising strategy for mitigating skeletal muscle atrophy.

overall_design: adult male WT and whole body FGF21KO mice were anesthetized with isoflurane. The sciatic nerve of the left leg was exposed and a 2 mm piece was removed. The right leg remained innervated and was used as a control. Mice were sacrificed and the TA muscles were then prepared and snap frozen in liquid nitrogen 14 days after denervation.

first: Takashi

last: Sasaki


title: An AINTEGUMENTA phosphoswitch controls bilateral stem cell activity during secondary growth

city: ghent

first: Wei

last: Xiao

address: Technologiepark-Zwijnaarde 71 - 9052 Ghent - Belgium

country: Belgium

institute: VIB-UGent Center for Plant Systems Biology

summary: Plant stem cells have the remarkable ability to give rise to distinct organs and tissues throughout development. Two concentric cylinders of actively dividing stem cells are the main drivers of radial thickening during secondary growth, each producing distinct vascular cell types towards the inside and the outside. While the molecular mechanisms underlying their initiation have been well studied, it remains unclear how these stem cell layers determine which cell type is generated. Here, we demonstrate that the crosstalk between the ERECTA (ER) receptor pathway and auxin signalling controls the amount and choice of output tissue in these two stem cell regions. Mechanistically, we show that the ER pathway phosphorylates the transcription factor ANTEGUMENTA, thereby modulating bilateral stem cell activity and favouring the differentiation of only one type of cell. Our results thus show that the phosphorylation status of ANT regulates root girth and biomass accumulation by influencing bilateral stem cell production. This highlights the critical role of post-translational modifications in plant growth and development.

overall_design: To investigate how auxin control bilateral stem cell activity, we performed RNA seq with pPER15::slr-GR and pPXY::shy2-2-GR roots. We transfer 12-day-old plants to either Mock or DEX plates for another 24 hours. Next, we collected only the uppermost 1.5 cm of roots (plants were grown in vitro 1/2 MS in continuous light at 22 Celsius degrees). 3 biological replicates. Each biological is from at least 100 plants

first: Laura

last: Ragni


title: GPC2-CAR T-cells have potent preclinical activity against orthotopic medulloblastoma xenografts

city: New Brunswick

first: Xiyuan

last: Zhang

state: NJ

address: 195 Little Albany St.

department: Pediatric Hematology/Oncology

institute: Rutgers Cancer Institute

summary: Medulloblastoma (MB) is the most common malignant brain tumor in children. Patients with high-risk features, such as MYCN aberrations, and relapsed/refractory disease have poor clinical outcomes. This underscores the urgent need for new therapies. Glypican-2 (GPC2) is a MYCN-regulated and recently discovered oncofetal antigen. Given that GPC2 is also expressed in brain tumors, we evaluated the preclinical activity of our GPC2-CAR (CT3-CD28HTM-BBζ) against MB and compared it to two existing CARs targeting GD2 and B7-H3. A newly generated patient-derived xenograft (PDX) MAF1433, with MYCN aberrations, were used to test CAR T-cells in vivo. Single-cell RNA-sequencing were used for mechanistic studies. MB patient samples express intermediate to high levels of GPC2 and can be targeted with a GPC2-CAR, leading to significant in vivo tumor regression in orthotopic tumor models. GPC2-CAR T-cells had equivalent activity to the B7-H3-CAR and enhanced activity compared to the GD2-CAR in vivo. T-cell kinetic studies revealed that GPC2-CAR T-cells home to the TME, expand, and upregulate genes critical for cytotoxicity and T-cell homing to induce MB cell death. CT3-CD28HTM-BBζ GPC2-CAR can regress GPC2+ MB with MYCN aberrations in preclinical studies, providing a preclinical rationale for including children with GPC2+ MB in our upcoming clinical GPC2-CAR T-cell trial.

overall_design: To investigate the difference in tumor microenvironment status between MB PDX treated with GPC2-CAR T cells, GD2-CAR T cells, and B7-H3-CAR T cells, we inoculated mice orthotopically with a new MB PDX; MAF1433. Around 2 weeks after the tumor injection, mice underwent IVIS bioluminescence imaging (BLI) and were randomized to receive either 5 × 10^6 CAR+ T-cells or matched total numbers of untransduced mock T-cells or PBS. On day 10 post CAR injection, the cerebella were extracted and dissociated.  The cells were analyzed using scRNA seq.

first: Reona

last: Okada

first: Rosa

last: Nguyen


title: IL-17A stimulates erythropoiesis by tuning the Erythropoietin-feedback circuit

city: Boston

first: Qiu Chang

last: Wu

state: MA

address: 220 Longwood Ave

department: Systems Biology

institute: Harvard University

summary: Feedback control of erythropoiesis exemplifies conflicting goals in tissue homeostasis: maintaining fast reactivity to stress while minimizing proliferative burden on progenitors in the steady state. Here we show that these conflicting goals are tuned through the combinatorial action of cytokines. We find that IL-17A, a pro-inflammatory cytokine, mediates striking synergism with the negative feedback signal erythropoietin (Epo) in vivo, accelerating the erythropoietic response to hypoxia. A model of erythropoietic control shows increased reactivity may occur through two cell circuit designs, with one having far lower constitutive progenitor burden in normoxia. IL-17A acts through this optimal design by sensitizing progenitors to Epo, a model supported by multiple experimental observations. We suggest that IL-17A signals impending hypoxia during infections, tuning erythropoiesis in favor of a faster stress response. Our study highlights IL-17A as a potential erythropoietic therapeutic agent and serves as a model of homeostatic tuning in stem and progenitor cell circuits.

overall_design:
This study examines hematopoietic responses through single-cell RNA sequencing analysis of bone marrow and spleen cells from a subset of mice treated with IL-17A, Erythropoietin (Epo), or their combination over a 72-hour period.
The experiment comprised four treatment groups. The first group received IL-17A administered subcutaneously at 200 ng/g body weight every 12 hours for 72 hours, totaling six doses. The second group received Erythropoietin (Procrit) administered subcutaneously at 0.25 IU/g every 24 hours for 72 hours, totaling three doses. The third group received a combination of both treatments following the same dosing schedules. The control group received vehicle (PBS) injections at a volume of 4 µL/g body weight, with timing matched to the treatment groups.
For single-cell RNA sequencing analysis, eight mice were selected, with two mice per treatment group. From each mouse, both bone marrow and spleen tissues were collected, resulting in sixteen total samples. All tissues were harvested at 72 hours after the initial treatment and were collected in SB5 buffer containing PBS supplemented with 0.2% BSA, 0.08% glucose, and 5mM EDTA.
Bone marrow was processed by flushing bones with SB5 using a 26-gauge needle, while spleen samples were mechanically dissociated. All samples were filtered through 100 µM cell strainers and centrifuged at 2000rpm for 10 minutes. The cells were enriched for CD117-expressing cells using the EasySepTM Mouse CD117 Positive Selection Kit at 4°C, followed by live cell enrichment using OptiPrep density gradient centrifugation with 40%, 18%, 12%, and 5% gradient layers, centrifuged at 800g for 15 minutes.
Five independent single-cell RNA sequencing libraries were generated using the 10X Genomics Chromium platform. The first library contained all vehicle-treated samples (two bone marrow and two spleen samples from two mice). The second library contained all IL-17A-treated samples (two bone marrow and two spleen samples from two mice). The third library contained all Epo-treated samples (two bone marrow and two spleen samples from two mice). The fourth library contained all IL-17A plus Epo-treated samples (two bone marrow and two spleen samples from two mice). The fifth library contained all samples pooled together (eight bone marrow and eight spleen samples from all eight mice), providing technical validation through sample multiplexing.
Sample preparation for single-cell RNA sequencing involved MULTIseq labeling using MULTI-Seq Lipid-Modified Oligos with unique sample barcode oligos for multiplexing. Cells were prepared at a concentration of 1000 cells/µL in PBS with 0.04% BSA. Sequencing was performed using the 10X Genomics Chromium X instrument with Chromium Single Cell 3' v3.1 chemistry. Libraries were sequenced on the Illumina NovaSeq 6000 using S4 200 cycle and SP 100 cycle flow cells, targeting 25,000 reads per cell for gene expression and 5,000 reads per cell for sample barcodes. Quality control was performed using Agilent 2100 Bioanalyzer, Agilent Tape station, and KAPA Library Quantification.

first: Aishwarya

last: Swaminathan

first: Ashley

last: Winward

first: Logan

last: Lalonde

first: Yung

last: Hwang

first: Noah

last: Littman

first: Merav

last: Socolovsky

first: Allon

middle: M

last: Klein


title: Sensitive and unbiased genome-wide profiling of base-editor-induced off-target activity with CHANGE-seq-BE [CHANGE-seq-BE for ABE targets]

status: Public on Nov 05 2025

city: Memphis

first: Shengdar

last: Tsai

state: TN

address: 262 Danny Thomas Pl

department: Department of Hematology

institute: St Jude Children's Research Hospital

summary: To assess CHANGE-seq-BE performance, we used it to characterize ABE8e-NRCH base editor activity targeting sickle mutation (HBBS) in the HBB gene and identified additional 29 (53% more) bona fide off-targets than CIRCLE-seq. Furthermore, CHANGE-seq-BE applied for ABE8e targeting five therapeutically relevant loci (B2M, CBLB, CD7, CIITA, and PDCD1) in human primary T-cells and compared with Digenome-seq. CHANGE-seq-BE is highly sensitive and capable of detecting bona fide off-targets while requiring approximately 20-fold less sequencing reads.

overall_design: CHANGE-seq-BE applied for ABE targeting MKSR, B2M, CBLB, CD7, CIITA, PDCD1, and PCSK9 in primary human cells (CD34+ HSPCs, T-cells, and hepatocytes)

first: Cicera

last: Lazzarotto

first: Elizabeth

last: Urbina

first: GaHyun

last: Lee

first: Yichao

last: Li


title: Highly functional prolonged GC-TFH responses are associated with enhanced neutralizing antibody development

city: La Jolla

first: Ester

last: Marina-Zarate

state: California

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

summary: T follicular helper (TFH) cells are pivotal in generating high-affinity antibodies by supporting B cell survival, proliferation, affinity maturation, and differentiation into memory B cells and plasma cells. Here, we characterized TFH cell responses to HIV Env immunization longitudinally in non-human primates, analyzing > 500,000 CD4 T cells from 192 lymph node (LN) samples collected over 60 weeks, including > 36,000 vaccine-specific TFH cells. An escalating-dose priming regimen elicited significantly higher and more sustained TFH cell responses in LNs compared to conventional bolus immunization. We observed multiple GC-TFH subpopulations, including IL4hi and IL21hi GC-TFH, which were continually present in vaccine-specific GC responses over the course of a year. Clonal tracking showed the persistence of antigen-specific TFH clones within GCs for over six months, maintaining stable gene expression profiles and showing no signs of exhaustion. TFH proliferation was observed at all timepoints, with vaccine-specific TFH proliferation detectable for 27+ weeks after priming. LN TFH subpopulations correlated strongly with HIV Env-specific antibody and neutralization titers. Additionally, we provide evidence of substantial TFH clonal migration between proximal and distal LNs. Our study underscores the importance of TFH for improving antibody responses against complex pathogens like HIV, and demonstrates GC-TFH have the capacity to survive for 48 weeks in active GC responses in the absence of any new antigen delivery.

overall_design: 63-week longitudinal study with four groups of rhesus macaques. Two groups received a bolus prime of HIV Env trimer MD39  with the adjuvant SMNP, followed by boosts at either weeks 10 and 24 (Group 1) or only at week 24 (Group 2). The remaining two groups received a slow-delivery escalating dose (ED) immunization, consisting of seven incrementally increasing doses administered every other day over a 12-day period, of HIV Env with SMNP. ED group animals were boosted either at week 24 (Group 3) or week 52 (Group 4).All animals in the study were immunized bilaterally in the thighs via subcutaneous injection. Each animal received a total of 100 µg of MD39 protein and 750 µg of SMNP (50 µg/375 µg per side). The booster immunizations were given as bolus injections using the same immunogen, adjuvant, and dosage as the priming immunization. Periodic blood draws and fine needle aspirates (FNAs) from the draining inguinal LNs (iLNs) were collected.

first: Shane

last: Crotty


title: divergence in basal transcriptomes of "Wild Type" Chlamydomonas reinhardtii strains

city: Berkeley

first: Sean

middle: D.

last: Gallaher

address: 176 Stanley Hall, room 408

department: California Institute for Quantitative Biosciences

institute: UC Berkeley

summary: This is a study to compare the basal transcriptomes of several widely used laboratory strains of the Chlorophyte alga, Chlamydomonas reinhardtii. Given that there is a high degree of genetic diversity among the closely-related laboratory strains, we wished to examine how much variation there is at the transcriptome level. A panel of WT strains (CC-124, CC-125, CC-1009, CC-1690, CC-1691), all believed to be descended from a single zygospore isolated in 1945, were chosen based on their representing the oldest lineages among the standard laboratory strains. Additionally, CC-4532, which was the source for the current (v6) reference assembly, and CC-4533, which is the initial parental strain of the CLiP library collection of mutant strains, were also included in this study based on their significance to the Chlamydomonas community. All strains were grown in liquid cultures under identical, mixotrophic conditions (light + acetate) to mid-log phase before collecting mRNA for RNA-Seq analysis.

overall_design: Pre-cultures of each strain (CC-124, CC-125, CC-1009, CC-1690, CC-1691, CC-4532, and CC-4533) were used to innoculate flasks of Tris-Acetate-Phosphate (TAP) media supplemented with Kropat's trace metals at a concentration of 1.5 x 10^4 cells/mL. Flasks were placed on a shaking platform at 180 RPM under 50-70 µmol x m^-2 x s^-1 of light. Cultures were grown until they reached ~2-3 x 10^6 cells/mL, about three days, before total RNA was collected and subjected RNA-Seq analysis.

first: Anne

last: Glaesener

first: Sabeeha

last: Merchant


title: Sensitive and unbiased genome-wide profiling of base-editor-induced off-target activity with CHANGE-seq-BE [Hybrid Capture Sequencing for CBE and ABE]

summary: To assess genome-wide off-target activity of base editors and Cas9 nucleases identified by CHANGE-seq-BE, Digenome-seq, and CHANGE-seq, we performed hybrid capture sequencing for five therupatic loci (B2M, CBLB, CD7, CIITA, PDCD1) in human primary T-cells and PCSK9 in human hepatocytes. We observed high on-target editing for ABE, CBE, Cas9 mRNA edited cells and potential off-targets confirmed by hybrid capture sequencing. Our results demonstrate that CHANGE-seq-BE is highly sensitive than Digenome-seq to detect more bona fide off-targets with cellular activity ranging from 0.5% to 92.2%. Moreover, ABE exhibit more off-targets than Cas9 under same delivery conditions.

overall_design: Hybrid capture sequencing to validate bona fide off-targets sites nominated by CHANGE-seq-BE, CHANGE-seq, and Digenome-seq in primary human T-cells and hepatocytes.

first: Varun

last: Katta

first: Garret

last: Manquen


title: Sensitive and unbiased genome-wide profiling of base-editor-induced off-target activity with CHANGE-seq-BE [CHANGE-seq-BE for CBE targets]

summary: To adapt and apply for cytosone base editors (CBEs), we perfomed CHANGE-seq-BE using eA3A-BE3 to target B2M, CBLB, CD7, CIITA and PDCD1 regions at different loci. CHANGE-seq-BE identified low frequency off-target editing rates ranging from 1.7% to 7.5%  that are not identified by Digenome-seq further implies CHANGE-seq-BE is highly sensitive and can identify true off-targets while requiring 20-fold fewer sequencing reads.

overall_design: CHANGE-seq-BE applied for eA3A-BE3 (CBE) targeting B2M, CBLB, CD7, CIITA, and PDCD1 in primary human T-cells


title: Lack of Caspase 8 Directs Neuronal Progenitor-like reprogramming and Small Cell Lung Cancer Progression

city: Cologne

first: Fanyu

last: Liu

address: Joseph-Stelzmann Str. 26

institute: CECAD

summary: Mimicry of neuronal features is emerging as malignant regulator of cancer growth and metastasis. Neuroendocrine (NE) cancers including small cell lung cancers (SCLC) have been shown to share expression profiles marking various stages of neuronal differentiation. Yet, how these state changes are caused and malignant consequences thereof have remained unexplored.Here, we devise a novel mouse model of SCLC recapitulating low expression of caspase 8 as seen in humans and uncover that this allows for epigenetic reprogramming towards a more aggressive and metastasising stem-cell like neuronal state, resembling neuronal intermediate progenitor cells (nIPCs). Notably, transcriptional signatures of this cellular state are enriched in relapsed and metastatic human SCLC. Mechanistically, caspase 8 loss within the pre-tumoral niche promoted immunosuppression and metastasis via induction of immunogenic cell death. Inactivation of the necroptosis executioner Mixed lineage kinase domain-like protein (MLKL) neutralised caspase 8 loss-induced immunosuppression, metastasis and diminished the stem-cell like state providing genetic evidence for a role of necroptosis in promoting these effects. Collectively our data uncover an unexpected role for low expression of caspase 8 in directing neuronal-like reprogramming towards an immunosuppressive and highly metastatic state in SCLC.

overall_design: In order to investigate the role of low Caspase 8 in SCLC development we generated RP mice with conditional deletion of Caspase 8 (RPC mice) and induced tumor by adeno cre inhalation. Next, from endpoint SCLC tumors of RP and RPC mice we generated cell lines (four of each genotype) and perfomed Methyl-seq analysis in order to identify the effect of Caspase 8 deletion in RP tumor cells

first: Ariadne

last: Androulidaki

first: Pascal

last: Hunold

first: Vignesh

last: Sakthivelu

first: Ilmars

last: Kisis

first: Silvia

last: von Karstedt