title: Chemically modified CRISPR-Cas9 enables targeting of individual G-quadruplex and i-motif structures, revealing ligand-dependent transcriptional perturbation

city: London

first: Marco

last: Di Antonio

state: United Kingdom

address: 80 Wood Lane

department: Chemistry

institute: Imperial College London

summary: The development of selective ligands to target DNA G-quadruplexes (G4s) has been pivotal in revealing their role in transcriptional regulation. However, most of the ligands described to date lack intra-G4 selectivity, severely limiting their potential for uncovering the biological function of individual G4s across the genome. To overcome these limitations, we developed ATENA (Approach to Target Exact Nucleic Acid alternative structures). ATENA relies on the chemical modification of established G4-ligands to enable their conjugation onto a catalytically inactive Cas9 protein (dCas9) using HaloTag, allowing for the targeting of individual G4s in living cells. We have systematically screened the length of the PEG-linkers connecting the G4-ligands to the HaloTag and sgRNA sequences to attain optimal G4 engagement both in vitro and in cells. Using optimized conditions, we leveraged ATENA to demonstrate how the selective targeting of the well-studied G4 in the promoter of the oncogene c-MYC suppresses its transcription exclusively from the P1 promoter. We also show that positioning ligands in the proximity of regulatory elements suppresses c-MYC transcription in a G4-independent manner, highlighting the importance of appropriate design to measure genuine G4-mediated transcriptional changes. We also demonstrate that selective targeting of a G4 in the PVT1 promoter can either stimulate or repress its transcription depending on the type of G4-ligand used, indicating that functional responses associated with G4-stabilization can highly depend on the type of ligand used. We further harnessed ATENA to study transcriptional perturbation associated with cell-specific G4s, revealing that the functional responses associated with these structures are tightly linked with the expression levels of the targeted gene. Our study provides critical insights into G4-based therapeutic design, offering an innovative platform to investigate G4 biology with high precision.

overall_design: To investigate the intra-G4 selectivity provided by ATENA against DC-34 and PyPDS, we performed  RNA-Seq analysis.

first: Sabrina Pia

last: Nuccio

first: Enrico

last: Cadoni

first: Roxani

last: Nikoloudaki

first: Silvia

last: Galli

first: An-Jie

last: Ler

first: Thomas

middle: E

last: Maher

first: Ella

last: Fan

first: Ling Sum

last: Liu

first: Christopher

middle: R

last: Fullenkamp

first: John

middle: S

last: Schneekloth Jr


title: Targeting the histone methyltransferase DOT1L rewires CD8 T cells and enhances their intrinsic cytotoxic activity towards tumor cells [RNAseq_WT_KO_DMSO_EPZ]

status: Public on Nov 03 2025

city: Amsterdam

first: Fred

last: van Leeuwen

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Institute

type: Expression profiling by high throughput sequencing

summary: Insights into the epigenetic mechanisms of CD8 T cell differentiation are delivering novel opportunities for modulating fate decisions and immune responses. The histone methyltransferase DOT1L is emerging as a central epigenetic regulator in immune cells. However, its cell-intrinsic role in CD8 T cell programming remains unclear as positive as well as negative roles have been ascribed to DOT1L. Here, we determined the cell-intrinsic role of DOT1L in mouse CD8 T cells using conditional ablation. In contrast to deletion of Dot1L early in the T cell lineage, conditional ablation of Dot1L in isolated mature CD8 T cells in vitro did not compromise the in vivo proliferative capacity and anti-tumor reactivity. In vitro, Dot1L knock-out CD8 T cells showed accelerated and enhanced antigen-specific cytotoxic activity towards tumor cells. Mechanistically, transcriptome and proteome profiling revealed that loss of DOT1L results in an altered cell-identity program with loss of T-cell and gain of NK-cell features. This role of DOT1L was linked to its catalytic activity since treatment with specific DOT1L inhibitors phenocopied genetic deletion of Dot1L. Our findings show that ablation of DOT1L activity is well-tolerated in mature CD8 T cells, rewires their cell identity in a tunable way towards the NK-cell lineage and enhances their cytolytic activity cell intrinsically.

overall_design: RNAseq on expanded murine CD8 T cells (day 8) to investigate the effect of DOT1L genetic ablation (n=3 biological replicates) or catalytic inhibition (n=4 biological replicates) on the transcriptome. For catalytic inhibition, cells were treated for 8 days with either EPZ-5676 (DOT1L inhibitor; 10 mM) or DMSO (vehicle control).

first: Muhammad

middle: A

last: Aslam

first: Muddassir

last: Malik

first: Eliza

middle: M

last: Kwesi-Maliepaard


title: Transcriptomic Profiling Reveals the Role of Hedgehog Signaling as a Biomarker and in the Pathogenesis of Ménétrier’s Disease

city: New Haven

first: Won Jae

last: Huh

state: CT

address: 310 Cedar Street

country: USA

institute: Yale University

summary: Both Ménétrier’s disease (MD) and juvenile polyposis syndrome (JPS) are rare premalignant conditions that can lead to gastric cancer. MD is an acquired disease without known causative mutations that is characterized by increased expression of an EGF receptor (EGFR) ligand, transforming growth factor-alpha (TGFα), in the stomach. JPS is inherited in an autosomal dominant pattern and is caused by BMPR1A or SMAD4 mutations. Although there are distinct clinico-pathological features that differ between the two diseases, they also share similar features that often lead to misdiagnosis. To identify diagnostic markers for MD and to better understand the pathogenesis of the disease, we performed transcriptomic profiling of stomach tissues from normal (NL), MD, and JPS patients. Comparative analysis between MD and JPS revealed both common and differential gene signatures. Common gene signatures included estrogen receptor signaling, integrin signaling, mTOR signaling, and others, which may be responsible for histopathological similarities. Among differential gene signatures, we found that Hedgehog (Hh) signaling is upregulated in MD and confirmed that protein expression of Hh signaling downstream targets, GLI1 (glioma-associated oncogene homolog 1) and HHIP (Hedgehog-interacting protein), is higher in MD than in JPS, particularly in foveolar cells by immunohistochemistry. We also showed that treatment with an Hh pathway inhibitor partially rescued the histopathological phenotypes in an MD mouse model. This study provides valuable insights into the potential mechanisms underlying the similar clinico-pathological features observed in MD and JPS. We also identified GLI1 and HHIP as diagnostic markers that can help to distinguish MD from JPS. Furthermore, Hh signaling was shown to play an important role in the pathogenesis of MD and can function as a potential therapeutic target.

overall_design: To compare the transcriptomic profile between MD and JPS, total RNA was extracted from the stomachs of  3 MD, 3 JPS, and 3 normal (NL) individuals. Then RNA sequencing was performed.

first: Miyoung

last: Shin

first: Tryston

middle: T

last: Gabriel

first: Fred Kwame

last: Ofosu

first: Jiali

last: Zhang

first: Tricia

last: Wang

first: Matthew

last: Bechard

first: Robert

middle: J

last: Coffey


title: Targeting the histone methyltransferase DOT1L rewires CD8 T cells and enhances their intrinsic cytotoxic activity towards tumor cells [ChIPSeq_DMSO_EPZ_SGC]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Chromatin immunoprecipitation DNA sequencing (ChIP-seq) for H3K79me2 on isolated CD8 T cells (N=2 biological replicates) expanded for 8 days in medium containing 0.1% DMSO, 10 mM EPZ-5676 or 10 mM SGC-0946. Chromatin from S. cerevisiae containing HA tagged H3 and lacking H3K79 methylation was spiked into all samples and co-immunoprecipitated to normalize and quantify the data.

first: Teun

last: van der Brand

first: Willem-Jan

last: de Leeuw

first: Tibor

last: van Welsem


title: MeCP2 Interacts with the Super Elongation Complex to Regulate Transcription (ChIP-Seq)

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

summary: Loss-of-function mutations in methyl-CpG binding protein 2 (MECP2) cause the neurodevelopmental disorder, Rett syndrome (RTT). The molecular mechanisms underlying MeCP2 function remain poorly understood. Here, using a MECP2 gain-of-function Drosophila model, we screened for genetic modifiers of MECP2-induced toxicity. Our approach identified several subunits of the Drosophila super elongation complex (SEC), a P-TEFb containing elongation factor that releases promoter-proximally paused RNA polymerase II (RNA pol II), as genetic interactors of MECP2. MeCP2 directly interacts with AFF4, the scaffold of the SEC, and facilitates its binding on a subset of genes that regulate neuronal development and synaptic function in the mouse cortex. Furthermore, genes with reduced AFF4 binding showed reduced RNA pol II binding in their genebody and decreased RNA expression in Mecp2 null mice. Taken together, we propose that MeCP2 interacts with the SEC to facilitate the release of RNA pol II and thereby support gene expression.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) of AFF4 and total RNA Pol II in wildtype and Mecp2 null cortex at 7-weeks of age

first: Jun

middle: Y

last: Sonn

first: Marta

last: Iwanaszko

first: Huda

last: Zoghbi


title: MeCP2 Interacts with the Super Elongation Complex to Regulate Transcription (RNA-Seq)

overall_design: Gene expression profiling in wildtype and Mecp2 null cortex at 7-weeks of age


title: MeCP2 Interacts with the Super Elongation Complex to Regulate Transcription

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

overall_design: Refer to individual Series


title: MMP-12 blockade in B lymphocytes inhibits the formation of inducible BALTs and alleviates neutrophilic allergic airway inflammation

city: Nanjing

first: Xijie

address: 300 Guangzhou Road, Gulou District

department: Department of Respiratory and Critical Care Medicine

country: China

institute: the First Affiliated Hospital of Nanjing Medical University

summary: Inducible Bronchus-Associated Lymphoid Tissue (iBALTs), the tertiary immune organs in the lungs, have been implicated in various pulmonary diseases. The formation and roles of iBALTs related to severe asthma, however, remain unclear. iBALTs was located near the area of bronchi and vessels in the severe asthma murine model induced by  house dust mite (HDM) extract and lipopolysaccharides (LPS). Repeated sensitizations promoted the formation of iBALTs, which disappeared 2 weeks post last HDM challenge. The neutralizing antibody of CXCL13 prevented the formation of iBALTs but failed to relieve the airway inflammation. B lymphocytes dominated in iBALTs. Compared with the control group, severe asthma group had increased IgE secreting cells. Bulk RNA-seq reveled the elevated MMP-12 in pulmonary B cells. MMP408, a specific MMP-12 inhibitor, reduced iBALTs formation. Moreover, AAV-6 targeting down MMP-12 in B lymphocytes blocked iBALTs and ameliorated the inflammation. These results indicated that MMP-12 from B lymphocytes motivated the aggregation of B lymphocytes, promoted the formation of iBALTs and further sharpened the inflammation of severe asthma.

overall_design: To investigate the possible effect of pulmonary B cells on the formation of iBALTs in severe asthma mice, we isolated the murine B cells from single-cell suspension of lung tissue via B220+ microbeads (130-049-501, Miltenyi Biotec). Then, we explored the differetial expressed genes between control mice and asthma mice by RNA-seq.

first: Chen

last: Yang

first: Min

first: Qi

last: Yuan

first: Xinyu

last: Jia

first: Tingting

last: Xu

first: Zhengxia

first: Ningfei

last: Ji

first: Mao

last: Huang

first: Mingshun


title: FUNCTIONAL AND TRANSCRIPTOMIC ANALYSIS OF EXTRACELLULAR VESICLES IDENTIFIES CALPROTECTIN AS A NEW PROGNOSTIC MARKER IN PERIPHERAL ARTERIAL DISEASE (PAD)

city: Pamplona

first: Goren

last: Saenz-Pipaon

state: Navarra

address: Av. Pio XII 55

department: Atherothrombosis

country: Spain

institute: CIMA University of Navarra

summary:
Rationale: Peripheral arterial disease (PAD) is associated with a high risk of cardiovascular events and death and is postulated to be a critical socioeconomic cost in the future. Extracellular vesicles (EVs) have emerged as potential candidates for new biomarker discovery related to their protein and nucleic acid cargo.
Objective: To study prothrombotic activity, cellular origin and transcriptomic profile of circulating EVs and to assess them as prognostic and therapeutic targets in PAD.
Methods and Results: This prospective study included control and PAD patients. Coagulation time (Procoag-PPL kit), EVs cellular origin and phosphatidylserine exposure were determined by flow cytometry in platelet-free plasma (n=45 PAD). Transcriptomic profiles of medium/large EVs were generated using the MARS-Seq RNA-Seq protocol (n=12/group). The serum concentration of the differentially expressed gene calprotectin was validated by ELISA in control (n=100) and PAD patients (n=317). Calprotectin was also determined in EVs and tissues of human atherosclerotic plaques (n=3). Circulating EVs of PAD patients were mainly of platelet origin, predominantly AnnexinV positive and were associated with the procoagulant activity of platelet-free plasma. Transcriptomic analysis of EVs identified 15 differentially expressed genes. Among them, serum calprotectin was elevated in PAD patients (p<0.05) and associated with increased amputation risk before and after covariate adjustment (mean follow-up 3.6 years, p<0.01). The combination of calprotectin with hs-CRP in the multivariate analysis further improved risk stratification (p<0.01). Furthermore, calprotectin was also expressed in femoral plaque derived EVs and tissues.
Conclusions: We found that PAD patients release EVs, mainly of platelet origin, highly positive for AnnexinV and rich in transcripts related to platelet biology and immune responses. Amputation risk prediction improved with calprotectin and was significantly higher when combined with hs-CRP. Our results suggest that EVs can be a promising component of liquid biopsy with prognostic implications in PAD.

overall_design: RNA-Seq was performed in plasma derived extracellular vesicles from controls, PAD patients with intermittent claudication (IC, Fontaine class IIa) and PAD patients with critical limb ischemia (CLI, Fontaine class IV). n=12/group.

first: Patxi

last: San Martín

first: Núria

last: Planell

first: Alberto

last: Maillo

first: Susana

last: Ravassa

first: Amaia

last: Vilas-Zornoza

first: Esther

last: Martínez-Aguilar

first: José

last: Rodriguez

first: Daniel

last: Alameda

first: David

last: Lara-Astiaso

first: Felipe

last: Prosper

last: Paramo

first: Josune

last: Orbe

last: Gomez-Cabrero

first: Carmen

last: Roncal


title: Conserved heat shock factors control barley heat stress memory through diverged mechanisms - extended replicate

status: Public on Nov 02 2025

city: Potsdam

first: Isabel

last: Bäurle

address: Karl-Liebknecht-Str. 24-25

department: Institut für Biochemie und Biologie

country: Germany

institute: Universität Potsdam

summary: Climate change requires optimizing stress responses in crops. Priming and memory of heat stress (HS) allow plants to improve their tolerance against high temperatures. Here, we investigate HS memory in cultivated barley (Hordeum vulgare) to assess whether the mechanisms underlying priming by and memory of HS are conserved between dicots and monocots. Mutation of the barley orthologs of two key transcriptional regulators of HS memory, HvHSFA2 and HvHSFA3, reduced HS memory. This correlated with altered transcriptional responses of heat-induced genes in the mutants after recurrent HS. Conversely, overexpression of HvHSFA2 increases HS tolerance with no penalty on productivity. While the biological role of HSFA2 and HSFA3 is conserved, their mechanistic functions appear to have diverged, as we did not find evidence that HvHSFA2 is involved in H3K4me-mediated priming. Instead, both factors are globally required to boost induction of HS-responsive genes after recurrent HS. In summary, while barley HS memory depends on the highly conserved HvHSFA2 and HvHSFA3, the underlying transcriptional wiring is different. Our findings provide a tangible route to improve HS tolerance in temperate cereals.

overall_design: Gene expression analysis for Barley wild-type, hsfa2 and hsfa3 mutants with and without heat priming and heat treatment.

first: Loris

last: Pratx

first: Christian

last: Kappel


title: DRUG-seq of high-density neutrophils (HDNs), mature low-density neutrophils (M-LDN), and immature low-density neutrophils (IM-LDN) in patients with colorectal cancer

city: Shanghai

first: Zhuoqing

last: Xu

address: No. 197, Ruijin Er Road, Shanghai,

department: Ruijin Hospital

institute: Department of General Surgery

summary: High-density neutrophils (HDNs), mature low-density neutrophils (M-LDN), and immature low-density neutrophils (IM-LDN) were isolated from peripheral blood of nine treatment-naïve colorectal cancer (CRC) patients with histologically confirmed diagnoses, followed by gene expression profiling of these neutrophil subsets using Digital RNA with pertUrbation of Genes (DRUG) sequencing.

first: Haoran

last: Feng

first: Wenqing

first: Yuchen

last: Zhang

first: Jianting

last: Huo

first: Zifeng

first: Fangqian

last: Chen

first: Han

last: Gao

first: Zeping

last: Lv

first: Wangyi

last: Liu

first: Abudumaimaitijiang

last: Tuersun

first: Suyue

last: Yu

first: Wenchang

last: Li

first: Yaping

last: Zong

first: Xiaohui

last: Shen

first: Xi

last: Cheng

first: Jingkun

last: Zhao

first: Aiguo

last: Lu


title: Single-cell RNA sequencing of tumor tissues from 12 colorectal cancer (CRC) patients.

first: Zhuoqing

summary: Surgical specimens of tumor tissues from 12 colorectal cancer (CRC) patients were included.  All cases were consecutively enrolled and cytologically or histologically confirmed as rectal adenocarcinoma by at least two pathologists, with no history of prior neoadjuvant anti-tumor therapy.

first: Haoran

first: Zichao

last: Guo

last: Jia

first: Tao

first: Kun

first: Ren


title: DRUG-seq of High-Density Neutrophils (HDNs) from Colorectal Cancer Patients with or without GM-CSF Stimulation

last: Xu

summary: High-density neutrophils (HDNs) were isolated from peripheral blood of three treatment-naïve colorectal cancer (CRC) patients with histologically confirmed colorectal adenocarcinoma, then divided into PBS-treated controls (Ctrl) and GM-CSF-treated groups (GMCSF, 10 ng/mL, 16 hours) prior to Digital RNA with pertUrbation of Genes (DRUG) Sequencing analysis of stimulation-dependent gene expression profiles.

last: Feng

first: Wenqing

first: Yuchen

first: Jianting

first: Zifeng

first: Fangqian

first: Han


title: Inhibition of the inflammasome ameliorates orthologous polycystic kidney disease

city: Freiburg

first: Katharina

last: Moos

address: Breisacherstr. 153

department: Medical Faculty

institute: University of Freiburg

summary: ADPKD is the most common genetic renal disease, leading to renal failure in the vast majority of affected individuals. Standard therapy consists of blood pressure control and salt restriction. Tolvaptan further delays renal failure but side effects prevent its widespread use. Novel therapeutic approaches are needed. Recent evidence has identified inflammation as an important driver of ADPKD. Here we show a strong inflammatory signature in transcriptomes of early ADPKD in the mouse. IL1β and IL18, effectors of inflammasome activation, are among the top upregulated transcripts. Inflammasomes act as part of the innate immune response to danger signals, including crystals. Induction of calcium oxalate crystals through dietary intervention in Pkd1 mutant mice aggravated the cystic phenotype. Treatment of Pkd1 mutant mice with the inflammasome inhibitor MCC950 significantly ameliorated the ADPKD phenotype. Analogous results were obtained through genetic silencing of the essential inflammasome component Asc in ADPKD mice. Interference with inflammasome activation in the ADPKD animals resulted in better renal function and decreased IL18 excretion in the urine. These findings identify inflammasome inhibition as a promising concept for the treatment of ADPKD.

overall_design: We performed a transcriptional screen in mice with a time dependent targeted deletion of Pkd1. Pkd1flox/flox.Pax8rtTA.Tet-O-Cre mice underwent tetracycline induced tubular deletion of Pkd1 during postnatal week 5 and 6. At 10 weeks, the kidneys were analyzed by RNAseq and the transcripts compared to kidneys from non-cystic Pkd1flox/flox.Tet-O-Cre control animals lacking Pax8rtTA.

first: Junwei

first: Manuel

last: Rogg

first: Shaya

last: Sasanpour

first: Vera

last: Strassl

first: Manaswita

last: Jain

first: Sato

last: Magassa

first: Björn

last: Neubauer

first: Benedikt

last: Kloos

first: Simone

last: Braeg

last: Saller

first: Svenja

last: Wöhrle

first: Frank

last: Bienaimé

first: Oliver

last: Gorka

first: Melanie

last: Boerries

first: Amandine

last: Viau

first: Olaf

last: Gross

first: Christoph

last: Schell

first: Wolfgang

last: Kuehn


title: Conserved heat shock factors control barley heat stress memory through diverged mechanisms

first: Isabel

last: Bäurle

first: Loris

last: Pratx

first: Christian

last: Kappel


title: transcriptomic differences between ACMs stimulated with a high LCAC C16 concentration and control

status: Public on Nov 01 2025

city: Beijing

first: Rui

last: Lin

address: Chaoyang District

institute: Capital Medical University Affiliated Anzhen Hospital

summary: About 20% of acute myocardial infarction (AMI) patients with multivessel disease experience adverse outcomes after complete revascularization. We aim to investigate the underlying metabolic mechanism of ischemia-reperfusion injury responsible for abnormal hemodynamic stresses of in high-risk patients undergoing complete revascularization. Elevated preoperative serum levels of long-chain acylcarnitine (LCAC) 16:1 was associated with an increased risk of poor prognosis following complete revascularization. Multi-omics analyses revealed reperfusion injury activates fatty acid degradation and carnitine palmitoyltransferase 1A (CPT1A) was identified as a key regulator of LCACs in the interaction network in the porcine models. In the early stages of reperfusion injury in non-culprit lesions, the release and prolonged elevation of circulating LCACs primarily depend on the activation of endothelial CPT1A through hemodynamic injury, which can be reduced using inhibitor (etomoxir). Excess LCACs entered cardiomyocytes via the organic cation transporter 2, leading to imbalanced mitochondrial quality control and causing cardiomyocyte death.

overall_design: To determine how LCACs affect mitochondrial dysfunction in cardiomyocytes, we investigated the transcriptomic differences between ACMs stimulated with a high LCAC C16 concentration (150 µM) and control cells by transcriptome sequencing.

first: Yuan

last: Wang


title: Position-Specific Methylation of Benzo[a]pyrene Drives AHR-Dependent Fin Duplication in Zebrafish

city: Corvallis

first: Robyn

middle: Leigh

last: Tanguay

state: Oregon

address: 28645 east hwy 34

department: Environmental and Molecular Toxicology

institute: Oregon State University

summary: Polycyclic aromatic hydrocarbons (PAHs) are an environmental contaminant class characterized by fused aromatic rings. PAHs are released through the incomplete combustion of organic materials as well as petrogenic sources like oil and gas. Benzo[a]pyrene (BaP) is one of the most well-studied PAHs and is known to cause cancer through the formation of DNA adducts and strand breaks. In larval zebrafish exposed from 6 hpf, BaP caused behavioral effects by 4 µM but no morphological effects up to 50 µM by 120 hours post-fertilization (hpf). In contrast, 8-methylbenzo[a]pyrene caused a distinct fin duplication phenotype by 0.26 µM and severe edema and mortality 1 µM. Alkyl substitutions in different positions (7-, 6-, 9-, and 10-MBaP) did not elicit morphological effects at similar concentrations. Utilizing knock-out lines, we determined that the effects of 8-MBaP were Ahr2 dependent and that Cyp1a served a protective role. To identify transcriptomic changes underlying the observed phenotypic effects, larvae were exposed to three concentrations of BaP, 6-MBaP, and 8-MBaP. Whole larvae were collected at 48 and 72 hpf which was before and during phenotype onset, respectively. A systematic approach allowed us to identify the concentration-dependent transcriptional responses linked to the downstream morphological phenotypes unique to BaP methylation at the eight position. This study improves environmental and human health hazard assessment by identifying critical structural features and mechanisms of action contributing to the toxicity of PAH mixtures in the environment.

overall_design: Poly-A tail bulk RNA sequencing was performed for three chemicals (8-MBaP, 6-MBaP, and BaP) at three concentrations and two timepoints to elucidate transcriptomic changes unique to 8-MBaP exposure and development of the x-fin phenotype. Embryonic zebrafish were exposed to three concentrations (0.133, 1.33, and 13.3 µM) of 3 chemicals (8-methylbenzo[a]pyrene, 6-methylbenzo[a]pyrene, and benzo[a]pyrene) and a DMSO control at 6 hpf.  Embryos were exposed to chemical in 100µL of embryonic medium in 96-well plates. Pools of 6 embryos were collected at 48 hpf and 72 hpf. RNA sequencing was performed by Alithia Genomics (Epalignes, Switzerland) using their Mercurius™ BRB-SEQ service, which is a multiplexed 3’ RNA sequencing library preparation technique.

first: Mackenzie

middle: L

last: Morshead

first: Lisa

last: Truong


title: Genomic Profiling of Sirt6 binding sites in the neuroblastoma cell line ShSy-5y under normal culture conditions.

city: Beer sheva

first: Debra

last: Toiber

state: Beer sheva

address: David Ben Gurion Blvd 1

department: Life Sciences

country: Israel

institute: Ben Gurion University of the Negev

summary: Histone deacetylases are important regulators of gene expression and chromatin conformation. Sirt6 is a histone deacetylase that regulates gene expression by deacetylating histone H3 on the specific lysine residues K9 and K56. Notably, Sirt6 expression and activity negatively correlate with biological aging and the onset of age-related diseases, such as Alzheimer’s disease. Moreover, Sirt6 also binds to DNA double-strand breaks, as a DSB-sensor protein, and regulates the DNA damage response, promoting non-homologous end-joining (NHEJ) or homologous recombination (HR) pathways. Therefore, Sirt6 functions as a stress signaling epigenetic regulator capable of coordinating the cellular response to several cytotoxic stimuli, including DNA damage, as one of its main regulatory outputs. We performed Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) to investigate the Sirt6 genomic-binding profile in the neuroblastoma cell line ShSy-5y under normal culture conditions. This experiment allows the scientific community and us to identify the Sirt6 targets at the gene level, and predict a possible regulatory role on its expression. The study on Sirt6 binding to specific genes was further confirmed and analyzed by ChIP-qPCR under specific experimental conditions.

overall_design: For the ChIPseq experiments, we did three independent biological replicates of the next experiment, including input samples and negative controls. We transduced Sh-Sy5y cells with a Myc-tagged Sirt6 protein. After transduction and puromycin selection, we performed the Chromatin Immunoprecipitations. The cells were plated for all the experimental conditions at an equal confluence, fixed with 1% formaldehyde for 10 minutes, quenched, and collected. After cell pellet resuspension in RIPA buffer, the lysates were sonicated using a vibracell needle sonicator (Sonics & Materials Inc, USA) to break the chromatin. Chromatin immunoprecipitations were carried out using anti-myc antibodies coated magnetic beads (MedChemExpress, Cat# HY-K0206) to isolate Sirt6-bound DNA. The negative controls consisted of untransduced ShSy-5y cells used for the same ChIP procedure, and the input samples were taken from the Sirt6-transduced samples used for Sirt6 ChIPs. The entire experiment was repeated on three independent occasions, and each one was validated by ChIP-qPCR using known Sirt6 target sequences. Immunoprecipitated DNA was then sequenced on a Novaseq 6000 sequencer (Illumina) using an SP 100 cycles kit, allocating 20M reads per sample, paired-end sequencing. Peaks were called using the MACS2 software, and the resulting peak files are included as processed data.

first: Alfredo

last: Garcia-Venzor

first: Shai

last: Shai Kaluski-Kopatch

first: Nili

last: Tickotsky-Moskovitz


title: KROX20-Notch1 Network Transcriptionally Regulates Meibomian Gland Stem Cells for Its Development and Homeostasis [ChIP-Seq]

city: Charlottesville

first: Yumeng

last: Zhang

state: Virginia

address: 1726 Webland Park

institute: University of Virginia

summary: Meibomian gland dysfunction is the leading cause of Evaporative Dry Eye Disease (EDED), and accounts for approximately 90% of dry eye disease cases worldwide. The transcription factor Krox20 has been shown to mark stem cells that play a critical role in Meibomian gland (MG) development and homeostasis, however, the molecular mechanisms underlying these processes are not well understood. In this report, we used multiple Krox20 lineage tracing and ablation studies to investigate the process that governs lineage commitment during MG morphogenesis and homeostasis. Krox20 marks MG stem/progenitor cell pools, and it regulates cellular contributions to the glands, as loss of Krox20 leads to MG atrophy, while its overexpression results in MG enlargement. We also found that Notch1 signaling is regulated by KROX20 and that ablation of the Notch1 gene in KROX20-expressing cells leads to MG atrophy, while Notch1 overexpression partially rescues MG atrophy caused by the loss of Krox20. Together, these results reveal a critical KROX20-Notch1 regulatory pathway in MG stem/progenitor cells. Activation of Notch1 signaling may offer a novel approach to preventing and treating EDED caused by the depletion of the MG stem cell pool that can occur with aging.

overall_design: ChIP-seq of transcription factor KROX20 binding sites in IHMGECs infected by pLenti-Krox20.

first: Edem

last: Tchegnon

first: Elnaz

last: Ghotbi

first: Zhiguo

last: Chen

first: Stefanie

last: Moye

first: Yi

last: He

first: Renee

last: McKay

first: Lu

middle: Q

last: Le


title: Variant-specific interaction of kinectin 1 with the multi–tRNA synthetase complex regulates ER sheet organization

city: Sendai

first: Masaki

last: Hosogane

state: Miyagi

address: 2-1 Seiryo-machi, Aoba-ku

country: Japan

institute: Tohoku university

summary: Kinectin 1 (KTN1) is an integral endoplasmic reticulum (ER) sheet protein that functions in ER organization and translation elongation. Alternative splicing introduces sequence diversity into the cytoplasmic region of KTN1, but the functional relevance of these variants has remained unclear. Here we show that the multi–tRNA synthetase complex (MSC), composed of eight aminoacyl-tRNA synthetases and three nonenzymatic proteins, specifically interacts with KTN1 in a manner dependent on the alternative exon V2 and glutamine-tRNA synthetase (QARS). Using V2 exon-specific knockout cells and KTN1 knockout cells with variant-specific resucue, we found that the V2 exon is required for KTN1-mediated recruitment of the MSC to the ER, where it promotes the formation of rough ER stacks. These findings define a variant-specific role for KTN1 in anchoring the MSC to the ER, and suggest that this interaction underlies a noncanonical activity of the MSC in regulating ER sheet organization.

overall_design: Ribo-seq together with RNA-seq (for normalization of Ribo-seq reads) of KTN1 knockout HeLa cells rescued by doxycycline(dox)-inducible one single variant of KTN1, either KTN1 V2 exon(+) or KTN1 V2 exon(-).


title: Histone 2B Monoubiquitylation regulates elongation-to-termination transition in RNA Polymerase II transcription

city: Bronx

first: Pabitra

middle: Kumar

last: Parua

state: NY

address: 1300 Morris Park Avenue, Forchheimer/236

department: Molecular Pharmacology

institute: Albert Einstein College of Medicine

summary: RNA Polymerase II (Pol II)-dependent transcription is meticulously regulated during initiation, elongation, termination, and two pivotal transitions: from initiation to elongation and from elongation to termination 1. The successful transition from elongation to termination is vital for accurate transcription termination 2,3. While elongation and termination have been extensively studied, the regulatory mechanisms governing the transition between these stages are not fully understood. Here we report that, in fission yeast Schizosaccharomyces pombe (S. pombe) and human cells, Cdk9 and its cyclin partner (Cyclin T in humans, and Pch1 in S. pombe) disengage from the elongation machinery near gene 3'-ends, as Pol II crosses the cleavage and polyadenylation signal (CPS). Concurrently, chromatin immunoprecipitation (ChIP) data shows an increased association of Dis2 (the PP1 ortholog in S. pombe)4 beyond the CPS. Additionally, ChIP-seq indicates that histone 2B monoubiquitylation (H2Bub1) is pivotal for Cdk9 occupancy but serves differential roles along the gene. H2Bub1 facilitates Cdk9 chromatin recruitment during elongation but prompts Cdk9 dissociation from the elongation complex as Pol II traverses the CPS. Furthermore, in S. pombe, disruptions of H2Bub1 in htb1-K119R 5 and sustained levels in ubp8D 6 inversely affect the chromatin occupancy of Pol II, Pol II CTD phosphorylation within the heptad repeats, Spt5, phosphorylated Spt5 (pSpt5), Dis2, components of the mRNA 3’-end processing complex (Pfs2 and Pla1), and termination factors Rhn1 (Rtt103) and Pcf1 around the CPS—diminishing with H2Bub1 loss and increasing with H2Bub1 stabilization. In essence, our data indicates that the H2Bub1-mediated eviction of Cdk9 as Pol II navigates the CPS precipitates a rise in PP1 binding, which, in turn, dephosphorylates pSpt5, slowing Pol II to facilitate efficient termination. The unique modulation of Cdk9 occupancy by H2Bub1 during transcription progression presents a compelling, novel concept requiring further exploration.

sample_organism:
Schizosaccharomyces pombe
Homo sapiens

platform_organism:
Schizosaccharomyces pombe
Homo sapiens

overall_design: ChIP-seq and RNA-seq: Data represent thirteen different ChIP-seq and 3 different RNA-seq experiments in S. pombe and human colon carcinoma (HCT116) cells, performed in biological replicates. There are raw and processed files (bigWig) for all biological replicates.

first: Tirthankar

last: Bandyopadhyay

first: Baidehi

last: Basu

first: Nayem

last: Haque


title: Role of STAT3 in Human Esophageal Epithelial Development

city: New York

first: Yosuke

last: Mitani

state: New York

address: 1130 St Nicholas Ave, 3rd floor

department: HICCC

institute: Columbia University

summary: The transcription factor STAT3 plays broad roles in epithelial biology, yet its function in human esophageal development remains undefined. Using 2D and 3D human induced pluripotent stem cell (hiPSC)-derived platforms, we investigated how STAT3 regulates esophageal epithelial differentiation.

overall_design: We established CRISPR/Cas9-engineered STAT3-knockout (KO) hiPSCs (BU3 NGST). These cells, along with control hiPSCs, were differentiated into esophageal epithelial progenitor cells (EPCs) using a previously reported protocol (Zhang et al., Cell Stem Cell, 2018). After 16 days on the differentiation protocol, the resulting human EPCs were harvested, and total RNA was extracted. The RNA samples were submitted to Azenta for RNA sequencing.

first: Secunda

middle: W

last: Kariuki

first: Joel

last: Gabre

first: Ricardo

last: Cruz-Acuña


title: Mapping CMV-Related Immune Signatures in Blood, Aorta, and Adipose Tissue

city: Nashville

first: Lindsey

middle: "Joey"

last: Stolze

state: TN

address: 1211 Medical Center Dr

institute: Vanderbilt University Medical Center

summary: Cytomegalovirus (CMV) is a chronic herpes virus infection humans have co-evolved with. CMV infects immune and non-immune cells and alters the immune cell repertoire. CMV seropositivity has been associated with diseases of aging, including cardiovascular diseases. This study aims to deeply phenotype immune cell changes in blood, large arterial blood vessels, and perivascular adipose tissue to understand the role of CMV in cardiovascular disease.

overall_design: Thoracic aorta were obtained from patients undergoing cardiothoracic surgery. Blood and adipose tissue was also collected at the time of surgery. CMV antibody titers were measured in the plasma of all participants. Single cells isolated from aorta, adipose tissue and peripheral blood mononuclear cells were anlyzed using scRNA-seq.

first: Celestine

middle: N

last: Wanjalla


title: Loss of METTL3 potentiates transposable element expression and drives inflammation-induced cell plasticity in the mammary epithelium [scRNA-seq]

city: Boston

first: Xintao

last: Qiu

state: MA

address: 440 brookline ave

institute: Dana Faber Cancer Institute

summary: Sustained proliferation and aberrant cellular plasticity are the hallmarks of breast premalignancy, yet the mechanisms driving this process remain unclear. Using CRISPR knockout screens, we systematically characterized the regulators of cellular fitness in the normal mammary epithelium. We found that loss of RNA methyltransferase METTL3 initiates mammary epithelial proliferation and reprograms gene expression, which depends on its catalytic activity. Single-cell analysis in normal breast organoids revealed that METTL3 ablation causes disruption of the mammary cellular hierarchy through increased aberrant luminal differentiation. Mechanically, METTL3 loss reduces the RNA m6A modification of transcribed transposable elements leading to their increased expression and upregulating interferon-STAT signaling. This inflammatory response leads to the crosstalk between STAT and GATA3 transcription factors, resulting in transcriptional activation of luminal genes in the mammary epithelium. These findings identify a cell-intrinsic epigenetic loop contributing to mammary epithelial plasticity and highlight a potential role of METTL3-dependent m6A modification during neoplastic transformation.

overall_design: To systematically understand the cellular and molecular changes that associated with aberrant mammary epithelial differentiation upon METTL3 loss, we performed single-cell RNA sequencing in the normal breast organoids with or without METTL3 sgRNA-mediated depletion


title: A ketogenic diet improves memory in females in the APOE4 mouse model of Alzheimer’s disease.

city: PADOVA

first: GIUSEPPE

last: PERSICO

state: PD

address: VIA UGO BASSI 58/B

country: Italy

institute: UNIVERSITA' DI PADOVA

summary: The 𝜀4 allele of Apolipoprotein E (APOE4) is the strongest genetic risk factor for Alzheimer’s disease (AD), affecting approximately 68 million Americans. APOE4 carriers exhibit cerebral metabolic deficits decades before clinical onset. We previously demonstrated that ketogenic diet (KD), a low-carbohydrate, high-fat diet promoting ketone metabolism, confers cognitive benefits in aged and PS1/APP mice. Here, we evaluated the effects of KD in a humanized APOE4 AD mouse model. KD significantly improved composite cognitive performance and spatial working memory, with pronounced effects in females. Synaptic plasticity, measured via long-term potentiation (LTP), was likewise enhanced exclusively in females. Transcriptomic and protein analyses revealed KD-induced activation of CREB pathway, marked by increased phosphorylation of ERK and CREB in female brains. Moreover, KD selectively reduced pro-inflammatory cytokine levels in females. These findings demonstrate sex-specific neuroprotective effects of KD in APOE4 mice and suggest its potential therapeutic role in mitigating AD risk in APOE4-positive women.

overall_design: RNA was isolated from 10 mg of frozen murine brain cortex (N = 4–6 per group; 22-month-old ApoE4 males/females on control or ketogenic diet), using the RNeasy Mini Kit (QIAGEN) according to the manufacturer’s instructions. Extracted RNA was used for NGS library preparation following Illumina’s instruction (TruSeq Stranded Total RNA Library Prep Gold), while sequencing was performed on NovaSeq 6000 (Illumina) running in a 50-bp paired-end mode.

first: Jacopo

last: Di Lucente

first: Jennifer

last: Rutkowsky

first: Alfredo

last: Errico Provenzano

first: Giuseppe

last: Persico

first: Zeyu

last: Zhou

first: Lee-Way

last: Jin

first: Jon

last: Ramsey

first: Claire

last: Montgomery

first: Kyoungmi

last: Kim

first: Marco

last: Giorgio

first: Izumi

last: Maezawa

first: Gino

last: Cortopassi


title: KROX20-Notch1 Network Transcriptionally Regulates Meibomian Gland Stem Cells for Its Development and Homeostasis

first: Yumeng

last: Zhang

overall_design: RNA-seq profiling of widetype IHMGECs and their derivatives (pLenti-GFP and pLenti-Krox20 infected cells) after 18 hour, 42 hour and 66 hour infection.

first: Edem

last: Tchegnon

first: Elnaz

last: Ghotbi

first: Zhiguo

last: Chen

first: Stefanie

last: Moye

first: Yi

last: He

first: Renee

last: McKay

first: Lu

last: Le


title: Loss of METTL3 potentiates transposable element expression and drives inflammation-induced cell plasticity in the mammary epithelium [ChIP-seq]

first: Xintao

last: Qiu

overall_design: GATA3 is a critical transcription factor in the mammary epithelium, which coordinately regulates ESR1 and FOXA1 mediated transcription, and drives luminal epithelial differentiation and breast cancer progression. We therefore performed GATA3 ChIP-seq to examine GATA3-bound DNA regions in MCF10A cells upon METTL3 depletion.


title: Loss of METTL3 potentiates transposable element expression and drives inflammation-induced cell plasticity in the mammary epithelium [RNA-seq]

overall_design: To identify the regulatory mechanisms that contribute to increased cell fitness in mammary epithelial cells upon METTL3 depletion, we assessed the RNA expression profile in control and METTL3 KO cells.


title: Loss of METTL3 potentiates transposable element expression and drives inflammation-induced cell plasticity in the mammary epithelium [ATAC-seq]

overall_design: we performed ATAC-seq in control or METTL3 depleted MCF10A cells to evaluate whether changes in chromatin state are associated with the transcription of mammary epithelial luminal genes.


title: Acetyl transferase EP300 deficiency leads to chronic replication stress mediated by defective fork protection at stalled replication forks

city: New Brunswick

first: Advaitha

last: Madireddy

state: NJ

address: Little Albany Street

institute: Rutgers Cancer Institute

summary: Mutations in the epigenetic regulator and global transcriptional activator, E1A binding protein (EP300), is being increasingly reported in aggressive hematological malignancies including adult T-cell leukemia/lymphoma (ATLL). However, the mechanistic contribution of EP300 dysregulation to cancer initiation and progression are currently unknown. Independent inhibition of EP300 in human cells results in the differential expression of genes involved in regulating the cell cycle, DNA replication and DNA damage response. Nevertheless, specific function played by EP300 in DNA replication initiation, progression and replication fork integrity has not been studied. Here, using ATLL cells as a model to study EP300 deficiency and an EP300-selective PROTAC degrader, as a pharmacologic tool, we reveal that EP300-mutated cells display prolonged cell cycle kinetics, due to pronounced dysregulations in DNA replication dynamics leading to persistent genomic instability. Aberrant DNA replication in EP300-mutated cells is characterized by elevated replication origin firing due to increased replisome pausing genome-wide. We demonstrate that EP300 deficiency results in nucleolytic degradation of nascently synthesized  DNA at stalled forks due to a prominent defect in fork stabilization and protection. This in turn results in the accumulation of single- single-stranded DNA gaps at collapsed replication forks, in EP300-deficient cells.  Inhibition of Mre11 nuclease rescues the ssDNA accumulation indicating a dysregulation in downstream mechanisms that restrain nuclease activity at stalled forks. In addition, Importantly, we find that the absence of EP300 results in decreased expression of BRCA2 protein expression and a dependency on POLD3-mediated error-prone replication restart mechanisms. The overall S-phase abnormalities observed lead to under-replicated DNA in G2/M that instigates mitotic DNA synthesis. This in turn is associated with mitotic segregation defects characterized by elevated micronuclei formation, transmission of unrepaired inherited DNA lesions in the subsequent G1-phase and accumulation of cytosolic DNA in EP300-deficient cells. However, EP300 deficient cells show a significant defect in innate immune system activation. Importantly, EP300Mut cells are sensitive treatments (PARPi, POLQi and Rev1i) that are cytotoxic to BRCA-deficient cancers. Overall, we demonstrate that the DNA replication dynamics of EP300-mutated cells recapitulate features of BRCA-deficient cancers. Altogether, these results suggest that mutations in EP300 cause chronic DNA replication stress, persistent genomic instability and innate immune system evasion underlie aggressive chemo-resistant tumorigenesis in humansdue to the inability to protect stalled replication forks from collapse.

overall_design: We utilize Adult T-cell leukemia/lymphoma (ATLL) cell lines as a model system to investigate the consequences of EP300 deficiency. We also employ an EP300-selective PROTAC degrader as a pharmacologic tool to selectively degrade EP300 in wild-type cell lines to understand the effects on EP300 loss.

first: Mrunmai

last: Niljikar


title: RNA sequencing of human monocyte-derived dendritic cells stimulated with CLEC10A ligand glycodendrimers in the presence of Pam3CysK4

city: Amsterdam

first: Nadia

last: van der Meijs

address: De Boelelaan 1108

department: MCBI

institute: Amsterdam UMC

summary: To investigate ligand-specific responses via CLEC10A in human monocyte-derived dendritic cells, five CLEC10A ligands were coupled to dendrimers. The ligands consist of alfa-GalNAc and the GalNAc-containing structures Forssman antigen, blood group A antigen, asialo GM2, and GM2. The human dendritic cells of 4 independent donors were stimulated with these glycodendrimers or a control dendrimer (coupled to C6 chain) for 5 hours in the presence of TLR stimulus Pam3CysK4. Total RNA was isolated and sequenced.

overall_design: Human monocyte-derived dendritic cells of 4 donors were each stimulated with 5 CLEC10A ligand glycodendrimers or a control glycodendrimer as reference. All 24 samples were included in the RNA sequencing.

first: Mike

last: de Kok

first: Sandra

last: van Vliet


title: Insulin resistance alters cortical inhibitory neurons and microglia to exacerbate Alzheimer’s knock-in mouse phenotypes

city: New Haven

first: Stephen

last: Strittmatter.

state: Connecticut

address: 295 Congress Ave, BCMM Rm433

department: Neurology

institute: Yale University

summary: Clinically, patients with diabetes have a higher risk of suffering from Alzheimer's disease (AD), with increased severity of cognitive decline upon disease onset. Several studies have reported on the metabolic impact of chronic hyperglycemia using various mouse models of AD, with varying results and behavioral outcomes. Furthermore, the underlying cellular mechanisms driving any observable increases in cognitive impairments remain unclear. In this study, we induced either Type-1 (streptozotocin, STZ) or  Type-2 (chronic high-fat diet,  HFD)  diabetes on either wild type or a double knock-in AD mouse model. We found that there was no observable difference in behavioral defect between AD and AD mice with STZ-induced diabetes. However, AD mice on a chronic high-fat diet displayed increased impairments in memory and learning. Histological and transcriptomic analysis of these mice revealed an increase in glial-mediated synapse due to an altered metabolic state of microglia.

overall_design: The impact of chronic elevated glucose levels on synapse loss was tested in homozygous AppNL-G-F/hMapt double knock-in (DKI) mouse model of Alzheimer's Diease. DKI mice on a sustained control diet, containing low sucorse, or high fat diet, were compared to wild type mice under going the same treatment.  Mice in all groups were evaluated for behavioral deficits, synapse loss by immunohistology, tau pathology, gliosis, inflammatory markers, and snRNA-seq transcriptomic profiling.

first: LaShae

middle: K

last: Nicholson

first: Si Jie

last: Tang

first: Tejaswini

last: Karra

first: Habiba

last: Abouelatta

last: Strittmatter


title: Transient inhibition of MEK/ERK and WNT pathways enhances direct differentiation of primed hPSCs into functional trophoblast stem cells

status: Public on Oct 31 2025

city: Guangzhou

first: Qifan

last: Jiang

state: Guangdong

address: No.1023,South Shatai Road, Baiyun District

institute: Southern Medical University

summary: The placenta plays a pivotal role in human pregnancy, yet research into placental development has been hindered by limited access to early-stage embryos and ethical constraints. Here, we developed a simplified and efficient strategy that enables direct, efficient conversion of primed hPSCs into stable, self-renewing hTSCs.

overall_design: Transcriptional profiles in primed PSCs (H1-ES), primed PSCs-derived cells induced by different strategies at two timepoints, YP medium-derived hTSCs (TS-YP).


title: Bulk RNA sequencing for gene expression profiling of iPSC-derived liver sinusoidal endothelial cells treated with Antithymocyte globulin compared with normal rabbit IgG

city: Kamakura

first: Shuntaro

last: Kawamura

state: Kanagawa

address: Tamanawa 1-6-42, Oak Tree Kamakura 103

institute: Institute of Science Tokyo

summary: Antithymocyte globulin (ATG) is a widely used immunosuppressive agent, yet its off-target vascular effects remain a clinical challenge in part due to a lack of relevant human models. To elucidate the effects of ATG on liver sinusoidal endothelial cells, we performed bulk RNA-seq analysis of iPSC-derived liver sinusoidal endothelial cells (iLSECs) exposed to ATG or normal rabbit IgG (rIgG) for 4 or 24 hours. We here report that ATG induces a proinflammatory program in iLSECs, characterized by upregulation of chemokines and prothrombotic factors. While minimal differences were observed at 4 hours, expression patterns clustered separately at 24 hours between rIgG- and ATG-treated cells. At 24 hours, ATG upregulated gene expressions, including chemokines such as CCL2, CXCL1, and CXCL5, as well as prothrombotic mediators SPP1 and SERPINE1, with downregulation of the vasoprotective gene NOS3. Gene set enrichment analysis identified that the gene set "Overview of Proinflammatory and Profibrotic Mediators" was significantly enriched in ATG-treated iLSECs at 24 hours compared to rIgG controls. This dataset provides critical insight to uncover the direct mode of action of ATG on LSEC beyond its immunosuppressive function.

overall_design: RNA-seq profiling of iLSECs differentiated from iPSCs for 14 days. Cells were treated with vehicle control, normal rabbit rIgG as antibody control, or ATG, and harvested at baseline (0 h), 4 h, and 24 h post-treatment.

first: Yosuke

last: Yoneyama

first: Norikazu

last: Saiki

first: Takanori

last: Takebe


title: Phenotypically Anchored Transcriptomics of Diverse Agrichemicals Revealed Congruent Pathways and Unique Gene Expression Signatures

first: Robyn

last: Tanguay

state: OR

address: 28645 East Hwy 34

summary: Transcriptomic data for 48 hour post-fertilization (hpf) wildtype zebrafish developmentally exposed to 45 different agrichemicals.

overall_design: mRNA sequencing was performed on four biological replicates of the five collected for each treatment. Collections of 8 animals performed over 28 different days with a single day match control collected to form a global control dataset compared to treated samples.The samples underwent PrepX Robotic RNA PolyA enrichment combined with NEBNext UltraII Directional RNA Library Prep/Illumina Stranded mRNA library preparation. Samples were split between three P3 flow cells (1.2 billion reads per run) and a P2 (400 million reads per run), and samples were sequenced usii an Illumina NextSeq 2000 (100 bp single end) resulting in 20 million read counts for each sample.

first: Lindsey

last: St Mary

first: Ryan

last: McClure

first: Lisa

last: Truong

first: Katrina

last: Waters

first: Steven

last: Carrell


title: NF-κB-dependent redistribution of the GR cistrome recruits GR to inflammatory gene loci and correlates with reduced repression by glucocorticoid [RNAP2_ChIPseq]

city: Calgary

first: Alex

last: Gao

state: Alberta

address: 3330 Hospital Dr NW

department: Physiology and Pharmacology

country: Canada

institute: University of Calgary

summary: While ligand-activated glucocorticoid receptor (GR) binds DNA to activate transcription, glucocorticoids, including budesonide, reduce inflammatory gene expression, yet recruit GR to many such gene loci. In epithelial cells, the inflammatory cytokine, interleukin-1β (IL1B), activates NF-κB to induce gene expression and co-treatment with budesonide produces nanoscale GR-RELA nuclear co-localization. Such co-stimulation orchestrated reciprocal genome-wide redistribution of GR and RELA binding regions (GBRs and RBRs, respectively) relative to each mono-treatment to produce widespread GBR RBR overlap. This correlated with increased RNA polymerase-2 presence and required NF-κB for GR cistrome remodeling. Mapping transcription start sites to the nearest GBR or RBR both revealed associations with upregulated, but not repressed, genes. Importantly, RBR proximity to budesonide upregulated genes and GBR proximity to IL1B-upregulated genes correlated with attenuated repression on co-treatment. As this occurred on a background of glucocorticoid-induced repression, GR presence at specific IL1B-induced gene loci may reduce, or protect, from an otherwise prevalent glucocorticoid induced repression.

overall_design: To understand the impact of NF-κB on GR cistrome redistribution, A549 cells were infected with Ad5-GFP (control), or Ad-IκBαΔN (NF-κB inhibitor) before no treatment, or treatment with IL1B, budesonide, or both for 1h. ChIP was performed using RNAP2 antibody, and sequenced using Illumina NovaSeq 6000.

first: Mahmoud

last: Mostafa

first: Robert

last: Newton

first: Amandah

last: Necker-Brown


title: NF-κB-dependent redistribution of the GR cistrome recruits GR to inflammatory gene loci and correlates with reduced repression by glucocorticoid

summary: While ligand-activated glucocorticoid receptor (GR) binds DNA to activate transcription, glucocorticoids, including budesonide, reduce inflammatory gene expression, yet recruit GR to many such gene loci. In epithelial cells, the inflammatory cytokine, interleukin-1β (IL1B), activates NF-κB to induce gene expression and co-treatment with budesonide produces nanoscale GR-RELA nuclear co-localization. Such co-stimulation orchestrated reciprocal genome-wide redistribution of GR and RELA binding regions (GBRs and RBRs, respectively) relative to each mono-treatment to produce widespread GBR_x0002_RBR overlap. This correlated with increased RNA polymerase-2 presence and required NF-κB for GR cistrome remodeling. Mapping transcription start sites to the nearest GBR or RBR both revealed associations with upregulated, but not repressed, genes. Importantly, RBR proximity to budesonide_x0002_upregulated genes and GBR proximity to IL1B-upregulated genes correlated with attenuated repression on co-treatment. As this occurred on a background of glucocorticoid-induced repression, GR presence at specific IL1B-induced gene loci may reduce, or protect, from an otherwise prevalent glucocorticoid_x0002_induced repression.

overall_design: To understand transcriptional interactions between GR and NF-κB, mammalian airway epithelial (A549) cells were not stimulated or treated with IL1B, budesonide, or both for 1, 2, 6, 12, and 24h before harvesting for RNA sequencing.


title: Winter temperature affects fatty acid composition and gene expression, but not fat content and survival in a northern population of a range-expanding spider

city: Greifswald

first: Carolina

last: Ortiz Movliav

state: Mecklenburg-Vorpommern

address: Loitzer Straße 26

department: Zoological Institute and Museum

institute: University of Greifswald

summary: Species expand their geographic distribution when environmental conditions are favorable or when mutations arise that allow them to live in previously unfavorable conditions. The European wasp spider, Argiope bruennichi, has expanded its range poleward, and populations at the northern edge show higher tolerance to cold and are genetically differentiated from the core populations. We aimed to investigate the degree and limits of plasticity in a recently cold-adapted Estonian population by exposing overwintering juveniles (spiderlings) to three fixed winter regimes over the course of three months. These regimes differed in absolute and relative day and night temperature: cold (5°C day, −15°C night), moderate (5°C day, −5°C night), and warm (15°C day, −5°C night). We expected a differential response to the winter regimes in survival, lipid content, metabolites, and gene expression patterns. The survival probability of the spiderlings decreased over winter by approximately 20% and their lipid content by 28%, with no significant differences between groups. Spiderlings also did not differ in content of saturated and monounsaturated fatty acids per dry weight. However, in spiderlings exposed to the warm winter regime, short-chain omega-3 PUFAs were less abundant (~57%) and long-chain omega-3 PUFAs more abundant (~66%) compared to the other regimes. The gene expression response was low under the cold regime and much higher under the warm regime, as compared to the moderate regime. The affected pathways suggest a more pronounced stress response under warmer winter temperatures. Taken together, our findings demonstrate that A. bruennichi spiderlings from a northern population can endure very different winter regimes. However, the observed physiological responses to the warmer regime suggest metabolic costs that may reduce spiderling survival probability after emergence from the egg sac. We conclude that, despite remarkable tolerance to different winter regimes, warmer winters have nuanced effects on spiderling physiology beyond survival probability.

overall_design: RNAseq of winter treatments cold (5°C day, -15°C night), moderate (5°C day, -5°C night), and warm (15°C day, -5°C night) after three months of exposure.

last: Ortiz-Movliav

first: Andreas W.

last: Kuss

first: Lars R.

last: Jensen

first: Corinna

first: Alexander

last: Wacker

first: Gabriele

last: Uhl


title: NF-κB-dependent redistribution of the GR cistrome recruits GR to inflammatory gene loci and correlates with reduced repression by glucocorticoid [GR_RELA_ChIPseq]

overall_design: To understand interactions between the GR and NF-κB cistromes, A549 cells were not treated, or treated with NS, IL1B, budesonide, or both before ChIP was performed using GR and RELA antibodies, and sequenced using Illumina NovaSeq 6000.

first: Andrew

last: Thorne

first: Akanksha

last: Bansal


title: Next-Generation Sequencing Facilitates Quantitative Analysis of WT and Mpp8/Tasor double knockout Embryonic Stem Cells Transcriptomes

city: Nanjing

first: Yuzhuo

last: Xu

address: 12 Xue-fu Road, Pukou District

institute: Nanjing University

summary: Purpose: The goals of this study are to compare Mpp8/Tasor-dko with wildtype embryonic stem cells transcriptome profiling (RNA-seq) to evaluate the target genes regulated by HUSH complex.

overall_design: mRNA profiles of WT and MPP8/Tasor-dko embryonic stem cells were generated by deep sequencing, in triplicate, using Illumina Novaseq6000.

first: Bowen

last: Wang

first: Jinzhong

last: Qin


title: Comparison of gene expression in HeLa cells after treatment with IFN-b, IFN-g, or VPgEMCV.

city: Kyoto

first: Takashi

last: Fujita

state: Kyoto

address: 53 Shogoin Kawahara-cho, Sakyo-ku

department: Biosystems Science

institute: Kyoto University

summary: We uncovered that cells infected with the encephalomyocarditis virus (EMCV) release soluble factors that induce apoptosis in uninfected cells. These factors were identified as the cytokine TNF-α and the viral protein VPgEMCV, which is necessary for viral RNA synthesis. Intriguingly, we discovered that VPgEMCV also acts as a functional mimic of IFN-γ, activating its canonical signaling pathway. This includes phosphorylation of STAT1 and the induction of IRF-1 and iNOS, leading to increased nitric oxide (NO) production. The synergy of NO accumulation and TNF-α signaling initiates powerful apoptosis. To compare gene sets regulated by IFN-I signaling (IFN-b), IFN-II signaling (IFN-g), and VPgEMCV signaling, we utilized RNA-seq analysis. From the deep sequencing data, we further discovered that VPgEMCV induces a gene expression profile similar to IFN-II signaling (IFN-γ), while also uniquely downregulating a distinct subset of genes. Our findings reveal that this cytokine-mimicry function of VPgEMCV regulates genes to control both viral replication and disease pathogenesis.

overall_design: RNA-seq analysis comparing wildtype HeLa cells treated with IFN-b, IFN-g, or VPgEMCV 24h post-treatment.

first: Yutaro

last: Shirasaka


title: Inflammation associated microglial expansion disrupts hippocampal glial network communication, driving postoperative neurocognitive impairment

city: Beijing

first: Yuxiang

last: Zheng

address: No. 17, Panjiayuan Nanli, Chaoyang District

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

summary: Postoperative neurocognitive impairment (PNCI) significantly affects the recovery and long-term outcomes of elderly patients, with central nervous system (CNS) inflammation serving as the key pathogenic driver of its development. As the resident immune cells of the CNS, microglia play a crucial role in regulating perioperative inflammation and maintaining homeostasis. However, the contribution, phenotypic heterogeneity, and communication network of perioperative microglia in the development of PNCI remain insufficiently characterized. In this study, 18-month-old mice underwent surgery and developed PNCI. Single-cell RNA sequencing was performed, which identified eight microglial subpopulations and six astrocytic subpopulations in hippocampus. Postoperatively, the percentage of microglial subpopulations underwent dramatic changes, with inflammation associated microglia (IAM) increasing more than 14-fold and transition state microglia (TSM) increasing more than 33-fold. These alterations were accompanied by a marked enhancement of intercellular communications among glial cells, particularly driven by the activation of TNF signaling pathway in IAM. This pathway, along with its associated regulatory network, critically modulated the function of astrocytes and endothelial cells, thereby playing a pivotal role in CNS inflammation and the subsequent development of PNCI. Notably, administration of TNF inhibitor etanercept attenuated IAM activation and glial network communication in the hippocampus, which was associated with improved cognitive performance in PNCI mice.

relation:
Reanalysis of: GSM8281758
Reanalysis of: GSM8281759
Reanalysis of: GSM8281760
Reanalysis of: GSM8281761
Reanalysis of: GSM8281762
Reanalysis of: GSM8281763

overall_design:
In this study, six aged mice were randomly assigned to two groups: control group and surgery group. The mice in surgery group received anesthesia and laparotomy, while control group received 50% oxygen for 30 minutes. All mice were sacrificed by decapitation 24 hours after procedure. The brain tissue was rapidly removed, and the hippocampi were dissected out and immediately frozen in liquid nitrogen.

This study represents a re-analysis of all of the raw data generated for GSE267933.

***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.
***************************************************************

first: Wenjie

first: Zizheng

last: Suo

first: Yinyin

last: Qu

first: Lina

last: Lin

first: Enze

last: Zhang

first: Dengyang

last: Han

first: Meikui

last: Wu

first: Hongyi

last: Li

first: Hui

first: Ting

last: Xiao

first: Cheng

last: Ni


title: Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs

city: Kansas City

first: Melanie

last: Weilert

state: MO

institute: Stowers Institute for Medical Research

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

overall_design: Refer to individual Series


title: Cooperativity between head-to-head dimerization and head-to-tail multimerization of FoxP3 transcription factor

first: Sun

last: Hur

address: 3 Blackfan St

department: Howard Hughes Medical Institute and Program in Cellular and Molecular Medicine

institute: Boston Children's Hospital

summary: FoxP3, an essential transcription factor for regulatory T cells (Tregs), forms higher-order multimers on TnG microsatellites in the genome. Although a previous study has shown that FoxP3 can form head-to-head (H-H) dimers on inverted repeats of forkhead motifs (IR-FKHM), in vivo evidence for this configuration was elusive. An unbiased FoxP3 pull-down sequencing approach identified a wide range of sequences supporting H-H dimerization, enabling systematic genomic analysis. This work revealed that FoxP3 binds DNA in Tregs as both H-H dimers and higher-order multimers, often incorporating one half-site of the H-H dimer into TnG repeats. A robust H-H interaction can seed multimerization on adjacent TnG repeats, enhancing assembly even on suboptimal sequences. Unlike other FoxP transcription factors, H-H dimerization is unique to FoxP3. Chimeric construct analyses identified a loop adjacent to the forkhead domain as the determinant for this distinctive function, underscoring a unique synergism between two binding modes.

overall_design:
In vitro pulldown assay using a synthetic dsDNA oligonucleotide library to identify FoxP3-binding motifs. MBP-tagged FoxP3 and FoxP1 were used to pull down DNA sequences with potential binding affinity. The input library was included as a control. Pulldown-enriched DNA was PCR-amplified and sequenced using paired-end 150 bp reads on an Illumina NovaSeq 6000 platform.
Follow-up in vitro pulldown experiment using the same synthetic dsDNA library, focused on comparative binding between FoxP3 and FoxP1. Samples were sequenced using single-end 130-cycle reads on an Illumina NextSeq 2000 platform.

first: Fangwei

last: Leng

first: Ryan

last: Clark

first: Wenxiang

first: Thibault

last: Viennet

first: Haribabu

last: Arthanari

first: Xi


title: Identification of strong constitutive promoters in Burkholderia to activate natural product production in Gram-negative bacteria

city: Khlong Luang

first: Wuttichai

last: Mhuantong

state: Pathum Thani

address: National Center for Genetic Engineering and Biotechnology (BIOTEC)

country: Thailand

institute: BIOTEC

summary: Gram-negative bacteria are an emerging source of natural products with pharmaceutical potential. However, the limited availability of essential genetic tools for drug discovery and sustainable production remains a challenge. Burkholderia serves as a promising source for such tools, as it produces diverse natural products and can be experimentally manipulated in the laboratory. Hence, this study aimed to identify strong and constitutive promoters from Burkholderia stagnalis TBRC 18363 for unlocking the potential of cryptic biosynthetic genes and enhance natural product production. Highly expressed genes were identified through transcriptomic analysis. Twenty-six promoters were evaluated in Escherichia coli and Pseudomonas putida reporter systems. Among all, promoters p2035 and p5642 exhibited superior performance in both systems. These promoters were selected for further investigation and were found to enhance the production titer of icosalide in B. stagnalis TBRC 18363 and FR900359, a Gq/11 protein inhibitor depsipeptide, in Chromobacterium vaccinii. This research emphasizes efficient promoters for target gene overexpression in Gram-negative bacteria.

overall_design: RNA of B. stagnalis TBRC 18363 was extracted using RiboPure™ RNA Purification Kit, bacteria (Invitrogen, U.S.A.). Cells were harvested from 250–600 microliter cultures in LS2 medium by centrifugation and resuspended with 300 microliter RNAwiz solution. Then, RNA extraction was performed following the kit protocol. RNA eluted from the kit columns were treated with DNaseI. Concentration and quality of RNA was measured by using nanodrop and 0.8% agarose gel electrophoresis, respectively. Approximately 6 microgram RNA of each samples was submitted for RNAseq analysis service at NovogeneAIT Genomics, Singapore. The integrity of RNA samples was analyzed by using Agilent 2100 bioanalyzer. The RNA sequencing was performed on Illumina NovaSeq 6000 with paired end 150 bp and acquired 3 GB data per samples.

first: Chayaphat

last: Wongsombat

first: Jindaporn

last: Kongsee

first: Thapanee

last: Pruksatrakul

first: Kitlada

last: Srichomthong

first: Pisut

last: Yotbuntueng

first: Piyanat

last: Charoenyingcharoen

first: Umaporn

last: Uawisetwathana

first: Pattaraporn

last: Yukphan

first: Vanicha

last: Vichai

first: Aiyada

last: Aroonsri


title: Bulk RNA sequencing for gene expression profiling of iPSC-derived liver sinusoidal endothelial cells and arterial endothelial cells

first: Shuntaro

last: Kawamura

summary: Liver sinusoidal endothelial cells (LSECs) line liver sinusoids and regulate exchanges between blood and liver tissue, while maintaining hepatic vascular homeostasis through coagulation control, immune cell recruitment, and barrier function. To compare endotheial lineage markers, we performed bulk RNA-seq analysis of iPSC-derived LSECs (iLSECs) and arterial endotheial cells (iAECs). We here show that venous/LSEC programs in iLSECs (NR2F2, APLNR, CD36; STAB1, LYVE1, FCGR2B), whereas iAECs expressed higher pan-endothelial and arterial markers (PECAM1, CDH5; DLL4, HEY2, NRP1).

overall_design: RNA-seq profiling of iLSECs and iAECs differentiated from iPSCs for 21 days.

first: Norikazu

last: Saiki

first: Takanori

last: Takebe


title: Gene expression of hippocampus from 17-month-old wildtype mice with sham/400 mGy X-ray irradiation treatment and 17-month-old 3xTg-AD mice with sham/400 mGy  X-ray irradiation treatment.

city: Hong Kong

first: MA

last: Chi Him Eddie

address: Tat Chee Avenue, Kowloon, Hong Kong

department: Department of Neuroscience

country: Hong Kong

institute: City University of Hong Kong

summary: Current study aimed to identify the 400 mGy X-ray irradiation-induced unique gene expression changes in the hippocampus of the 17-month-old 3xTg-AD mice.

overall_design: The 13.5-month-old 3xTg-AD mice and the age-matched wildtype mice received biweekly X-ray irradiation at 50 mGy/sham irradiation 8 times. When the mice reached 17 months old, the hippocampus from the different groups was harvested for bulk RNA sequencing (n=3-6 from each treatment group), and a total of 18 samples were analyzed.

first: Chi

middle: H

last: Ma

first: Yi

last: Xu

first: Tan

last: Wu

first: Xin

last: Wang


title: Gene expression of hippocampus from 9-month-old wildtype mice with sham/400 mGy X-ray irradiation treatment and 9-month-old 3xTg-AD mice with sham/400 mGy  X-ray irradiation treatment

summary: Current study aimed to identify the 400 mGy X-ray irradiation-induced unique gene expression changes in the hippocampus of the 9-month-old 3xTg-AD mice.

overall_design: The 5.5-month-old 3xTg-AD mice and the age-matched wildtype mice received biweekly X-ray irradiation at 50 mGy/sham irradiation 8 times. When the mice reached 9-month-old, the hippocampus from different treatment groups was harvested for bulk RNA sequencing (n=3 from each treatment group), and a total of 12 samples were analyzed.


title: PURE-seq Integrates FACS and PIP-seq for Single-Cell Genomics of Ultra-rare Cells

city: San Francisco

first: Sixuan

last: Pan

state: California

address: 1450 3rd Street

department: Bioengineering

institute: UCSF

summary: We used PURE-seq with single-cell RNA-sequencing (scRNA-seq) to study murine long-term hematopoietic stem cells (LT-HSCs) and their transcriptomes in the context of hematopoietic aging.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: First, we used human and mouse cell mixtures to demonstrate the sensitivity and specificity of PURE-seq. We used mixed population of HEK/3T3 or 3T3/PBMC cells with target cell fractions of 10^-3, 10^-4, 10^-5, and 10^-6. Then, we used PURE-seq workflow to study murine LT-HSCs from young, middle-aged, and old mice. We also evaluated murine hematopoietic stem cells (HSCs) and the percentage of long-term HSCs (LT-HSCs) before enrichment, as a comparison to enriched LT-HSCs throuhg PURE-seq.

first: Kai-Chun

last: Chang

first: Inés

last: Fernández-Maestre


title: Genital herpes shedding episodes associate with alterations in the spatial organization and activation of mucosal immune cells

status: Public on Oct 30 2025

city: Seattle

first: Rachael

last: Zemek

state: Washington

address: 1100 Fairview Ave

institute: Fred Hutchinson Cancer Centre

summary:
Analysis of vaginal mucosa samples from patients that are HSV-2 seronegative or seropositive, with comparison of active vs inactive HSV-2 shedding (Anogenital Swab HSV-2 PCR Result). This unique dataset was used to define and spatially map immune cell subsets and localized gene expression via spatial transcriptomics.
Herpes Simplex Virus 2 (HSV-2) infection results in variable rates of local viral shedding in anogenital skin. The impact of episodic viral exposures on immune cells in adjacent mucosal tissues, including the genital tract, is unknown. However, any immune responses at this site could impact protective mucosal immunity, tissue homeostasis, and adverse health outcomes. To investigate the impact of HSV-2 on cervicovaginal tract immunity, we applied flow cytometry, immunofluorescent imaging, analysis of soluble immune factors, and spatial transcriptomics to cervicovaginal tissue and blood samples provided by a total of 232 HSV-2 seropositive and seronegative participants, with genital HSV-2 shedding evaluated at the time of biopsy. This unique dataset was used to define and spatially map immune cell subsets and localized gene expression via spatial transcriptomics. HSV-2 seropositivity alone was associated with minimal differences in cervicovaginal and circulating T cell phenotypes. However, the vaginal mucosa during active HSV-2 shedding was associated with alterations in T cell, macrophage, and dendritic cell localization and gene expression consistent with increased immune surveillance, with immune activating and suppressing signals potentially reinforcing mucosal tissue homeostasis.

overall_design: HSV-2 Seronegative: 6 samples. HSV-2 Seropositive: 5 samples (3 shedding, and 2 non-shedding)


title: Regional encoding of enteric nervous system responses to microbiota and type 2 inflammation [Neuron SmartSeq2]

city: CAMBRIDGE

first: Jacques

last: Deguine

state: Massachusetts

address: 415 Main Street, 415M-7175 - Xavier lab

department: Immunology Program

institute: Broad Institute

summary: Enteric neurons are essential regulators of intestinal physiology, yet their responses to varying microbial and immune environments along the intestinal tract and or during challenges remain poorly understood. Here, we regionally profile enteric neurons across gnotobiotic, allergic and parasite-infected mice. We demonstrate that timing and complexity of microbial perturbations and type 2 inflammation result in motor neuron state shifts and alter multiple functionally distinct sensory neurons, including IL-13- and leukotriene-responsive Nmu-hi cells and Grp-hi neurons, which expand in germ-free colonic tissue and interact with Grpr+ interstitial cells of Cajal. Leveraging AAV-based Perturb-seq to define genetic controllers of inhibitory motor neuron state transition, we identified Edf1 and Mitf as controllers of this program and of gastrointestinal transit time, directly linking enteric neuron states to physiology.

overall_design: Enteric neurons were isolated from submucosal and myenteric plexuses of duodenal-jejunal segments, ileum and colon from either germ free (GF), Bacteroides thetaiotaomicron (BT) colonized, altered Schaedler flora (ASF) rederived or specific-pathogen free (SPF) mice. In addition, we also examined the ENS response to a spectrum of type 2 inflammatory responses induced by food allergy or by infection with an enteric parasite.  For food allergy, mice were sensitized with ovalbumin (OVA) in alum administered intraperitoneally, and subsequently challenged by intragastric OVA. To examine responses to a parasite, we studied animals at 14 days post infection with the exclusively enteric parasite Heligmosomoides polygyrus (H. polygyrus), a helminth. We utilized the neuron-specific Uchl1 (also known as PGP9.5) reporter mouse Uchl1-H2B-mCherry/GFPgpi.

first: Peng

last: Tan

first: Alok

last: Jaiswal

first: Shane

middle: P

last: Murphy

first: Eric

last: Brown

first: Hailey

last: Wheeler

first: Chien-Wen

last: Su

first: Emily

last: Finan

first: Guadalupe

last: Jasso

first: Hai Ning

last: Shi

first: Daniel

middle: B

last: Graham

first: Toni

last: Delorey

first: Ramnik

last: Xavier


title: mTORC1 controls ILC2 activation and allergic lung inflammation through NMUR1-mediated neuronal regulation [WT-KO ILC2s RNA-seq]

city: Shanghai

first: Dongdi

last: Wang

address: 227 South Chongqing Road, Shanghai, China

institute: Shanghai Jiaotong University School of Medicine

summary: Group 2 innate lymphoid cells (ILC2s) play critical roles in allergic lung inflammation through initiating and amplifying type 2 immune responses. However, the molecular mechanisms underlying pathogenic ILC2 activation remain largely unknown. Here, we show that lung ILC2s exhibit increased mTORC1 activation in allergic asthma. Genetic ablation of RAPTOR, an adaptor protein of the mTORC1 complex, results in reduced IL-5 and IL-13 production in ILC2s and protects mice from allergic inflammation. Pharmacological inhibition of mTORC1 by rapamycin also suppresses ILC2 pathogenic activation and ameliorates allergic lung inflammation. Mechanistically, mTORC1 signaling promotes ILC2 activation through metabolic regulation of epigenetics to maintain neurointerin U receptor 1 (NMUR1) expression, which mediates neural-ILC2 interaction via the NMU-NMUR1 axis. These findings identify mTORC1 as a novel regulator to control the neural-ILC2 interaction and highlight mTORC1 as a potential therapeutic target for allergic asthma.

overall_design: lung ILC2s mRNA profiles of  R5/+ (WT) and R5/+Rptorf/f (KO) mice after papain treament

first: Lei

last: Shen


title: mTORC1 controls ILC2 activation and allergic lung inflammation through NMUR1-mediated neuronal regulation

overall_design: lung ILC2s mRNA profiles of PBS treated mice and Papain treated mice


title: Regional encoding of enteric nervous system responses to microbiota and type 2 inflammation [10xGermfree]

overall_design: To understand the cellular context in which enteric neurons reside, large intestine tissues were harvested from a total of 6 mice for each group, germ free or SPF, and isolated cells were analyzed by droplet based single-cell RNA-seq.


title: v-ATPase-mediated buffering of mitochondrial dysfunction

city: Helsinki

first: Christopher

middle: B.

last: Jackson

state: - Select -

address: Hartmanninkatu 8

department: Department of Biochemistry and Developmental Biology

country: Finland

institute: University of Helsinki, Faculty of Medicine

summary: Mitochondrial dysfunction is implicated in a broad spectrum of human disease including primary mitochondrial disorders, neurodegeneration, cancer, and ageing. Cells have evolved several mechanisms in response to mitochondrial dysfunction to maintain cellular homeostasis and face fundamental challenges orchestrating the expression of the nuclear and mitochondrial genome. Here we used genome-wide CRISPR/Cas9 knockout screening in HEK293 to identify activated cell fitness pathways in response to distorted mitochondrial protein synthesis promoting cell survival upon mitochondrial dysfunction.

overall_design: HEK293 cells were treated with low doses of actinonin, chlormaphenicol and the combination over 15-days using the Brunello GeCKO library. The samples encompass day 15 sequencing results of EtOH-treated control and the respective treatments in independent replicates.

first: Geoffray

last: Monteuuis


title: Distinct miRNA profiles in human amniotic tissue and its vesicular and non-vesicular secretome

status: Public on Oct 29 2025

city: Wien

first: Andreas

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

type: Non-coding RNA profiling by high throughput sequencing

summary: The human amniotic membrane (hAM) is a valuable tissue in regenerative medicine due to its capacity to release cell-derived bioactive factors. Among these, microRNAs (miRNAs) play a critical role in modulating gene expression. This study aimed to comprehensively characterize the miRNA landscape of native viable hAM tissue and its secretome, with a focus on distinguishing between extracellular vesicles (EV)-associated and protein-bound miRNAs. We analyzed two anatomically and functionally distinct regions of the hAM, the reflected and placental amnion. After incubation of tissue biopsies ex vivo for 72 hours, vesicular and non-vesicular components in the conditioned medium were separated by size exclusion chromatography, and small RNA sequencing was performed on tissue and secretome fractions. Our analysis identified three main clusters of miRNA expression corresponding to tissue, EV-associated, and protein-bound fractions. We observed regional differences in miRNA expression between the reflected and placental amnion and identified miRNAs selectively released into EVs or protein-bound fractions. Data of gene ontology analysis suggest distinct biological roles for miRNA depending on the sample type. This dataset provides novel insights into the spatial and functional miRNA release profile of viable hAM and contributes to a better understanding of its regenerative potential.

overall_design: This study investigates small RNA expression profiles derived from different regions of the human amniotic membrane. Placental amnion (PA) and reflected amnion (RA) were separated from human placentae obtained after cesarean sections. Two biopsy punches (26 mm diameter) from each region were cultured for 72 hours (Dulbecco Modified Eagle’s medium/high glucose, 1 % v/v L-glutamine, 1 % v/v penicillin/streptomycin, 37 °C, 5 % CO2, humidified atmosphere), and extracellular vesicle and protein fractions were isolated from the conditioned media. Small RNAs from EV fractions, protein fractions, and tissue samples were analyzed using next-generation sequencing. Four biological replicates were included for each tissue type and sample fraction to assess differences in small RNA content.

first: Nefertiti

last: Chaves-Solano

first: Silvio

last: Kau-Strebinger

first: Johannes

last: Oesterreicher

first: Marianne

last: Pultar

first: Wolfgang

last: Holnthoner

last: Grillari

first: Simone

last: Hennerbichler

last: Brandstetter

last: Spittler

first: Matthias

last: Hackl

first: Susanne

last: Wolbank

first: Asmita

last: Banerjee

first: Adelheid

last: Weidinger


title: Integrated Multiomics Profiling Uncovers miRNA-Guided Regulatory Networks After Spinal Cord Injury in Rats

city: Vestec

first: Ruslan

last: Klassen

address: Průmyslová 595

department: Institute of Biotechnology

country: Czech Republic

institute: Czech Academy of Science


title: Single-cell RNA sequencing reveals distinct senotypes and a quiescence-senescence continuum at the transcriptome level following chemotherapy

city: Boulder

first: Brianna

last: Fernandez

state: CO

address: 3415 Colorado Avenue

department: Biochemistry

institute: University of Colorado Boulder

summary: Quiescence (reversible cell-cycle arrest) and senescence (irreversible arrest) are challenging to distinguish due to a lack of specific biomarkers, yet both arise simultaneously after chemotherapy. While senescence suppresses tumors by limiting proliferation and recruiting the immune system, quiescent cancer cells evade future therapies and may resume proliferation. Here, we pair time-lapse imaging of cell-cycle dynamics with single-cell RNA-sequencing after etoposide treatment to differentiate these states, linking heterogeneous cell-cycle phenotypes to the transcriptomic landscape. We identify diverse senescent types (senotypes) and link them to two arrest pathways – a gradual path arising after a standard mitosis-to-G0 transition, and a rarer but direct path driven by a mitotic slip. Using pseudotime trajectory analysis, we find that senescent phenotypes begin to manifest early and gradually along the first trajectory, even in shallow quiescent cells. These data support a model wherein, following chemotherapy, quiescence and senescence exist on a continuum of cell-cycle withdrawal at a transcriptome-wide level.

overall_design: MCF10A cells were treated with 2.5, 10, or 25μM etoposide for 24 h. Cells were then washed twice with PBS before being returned to full-growth media. Full-growth media was refreshed every 3d during the drug recovery period. Cells were sequenced on day 6 following etoposide washout.

first: Victor

last: Passanisi

first: Humza

last: Ashraf

first: Sabrina

last: Spencer


title: Thiolutin is a direct inhibitor of RNA Polymerase II

city: Boston

first: Chenxi

last: Qiu

state: MA

address: NRB 858, 77 Avenue Louis Pasteur

institute: Harvard Medical School

summary: Thiolutin is a well-known and long-used natural product transcription inhibitor with an unresolved mode of action. Recent studies have identified Zn2+-chelation activity for both thiolutin and the related dithiolopyrrolone holomycin, with direct inhibition of RNA polymerases ruled out as a mode of action. However, negative results for direct transcription inhibition of RNA polymerases in recent studies are contradicted by previously observed thiolutin inhibition of extract fractions containing yeast RNA Polymerases I, II, and III. Here, we present chemical genetic and biochemical approaches to investigate the mode of action of thiolutin. We identify diverse classes of mutant that alter sensitivity to thiolutin. We functionally dissect the multidrug resistance and thioredoxin pathways controlling thiolutin sensitivity. We provide genetic evidence that thiolutin causes oxidation of thioredoxins in vivo and suggest that thiolutin both induces oxidative stress and alters Zn2+, Cu2+ and Mn2+ homeostasis in vivo, recapitulating previously observed thiolutin interactions with Zn2+. Finally, our results resolve contradictory biochemical results for thiolutin inhibition of transcription by direct demonstration of thiolutin inhibition of RNA polymerase II (Pol II) in vitro. Inhibitory activity requires both appropriate reduction of thiolutin and the presence of Mn2+. Thio/Mn2+ inhibition is abrogated when template DNA is pre-bound to Pol II or when excess DTT is present, and renders Pol II pause prone in elongation if initiation is bypassed using a pre-formed Pol II elongation complex. Together, we propose that thiolutin directly inhibits Pol II transcription through a novel mechanism distinct from known transcription inhibitors.

overall_design: This is a series of processed RNA polymerase II (Pol II) ChIP-seq data after thiolutin treatment to evaluate how Pol II occupancy over the gene changes upon thiolutin treatment at a genome-wide scale, as an approach to provide insight to the mode of action of thiolutin (initiation inhibition vs elongation inhibition). Input chromatin or Chromatin IP samples using FLAG M2 antibody (Sigma) for FLAG-tagged Rpb3 from control or thiolutin treated yeast chromatin. Cells were untreated, or treated with thiolutin (in DMSO) at 10 µg/mL final concentration in the medium for 1, 2, 4, or 8 minutes or with DMSO (vehicle for thiolutin) for 8 minutes. Chromatin samples included spike-in chromatin from Schizosaccharomyces pombe also including FLAG-tagged rpb3+.

first: Payal

last: Arora

first: Craig

middle: D

last: Kaplan


title: Regional encoding of enteric nervous system responses to microbiota and type 2 inflammation [10xPerturbSeq]

first: Jacques

last: Deguine

overall_design: Adeno-associated virus (AAV)-based gene delivery was used for CRISPR screening and retrograde labeling of projecting neurons. The AAV-PHP.S capsid, tailored to infect peripheral neurons, was used for  in vivo Perturb-seq access to the ENS. In addition, the piggyBac transposon element was used for AAV-mediated stable transgene expression . We generated separate pools of guide RNAs (gRNA) for the different classes of genes discussed above and stably introduced them in Cas9-expressing animals by injecting AAV PHP.S vectors encoding gRNAs with a tdTomato-KASH reporter, and the piggyBac transposon system. The latter was used to sort nuclei from infected cells. Four weeks after AAV infection, we isolated nuclei from infected submucosal and myenteric plexuses, and subjected them to single nuclei RNA-seq to generate transcriptome profiles and gRNA sequences for individual cells.

first: Peng

last: Tan

first: Alok

last: Jaiswal

first: Shane

last: Murphy

first: Eric

middle: M

last: Brown

first: Hailey

last: Wheeler

first: Chien-Wen

last: Su

first: Emily

last: Finan

first: Guadalupe

last: Jasso

first: Hai Ning

last: Shi

first: Daniel

last: Graham

first: Toni

last: Delorey

first: Ramnik

last: Xavier


title: Chemical reprogramming of fibroblasts into functional retinal pigment epithelium cells (scRNA-seq)

city: Wenzhou

first: zhengbiao

last: zhu

state: Zhejiang

address: Ouhai District

department: The Affiliated Eye Hospital of Wenzhou Medical University

institute: Wenzhou Medical University

summary: Restoring retinal pigment epithelium (RPE) cells is crucial for treating retinal degenerative (RD) diseases, with chemical reprogramming offering a transformative, scalable solution. However, identifying key compounds for generating functional RPE cells remains challenging. Here, we present a two-step chemical reprogramming strategy to convert fibroblasts into functional RPE (ciRPE) cells. Leveraging the Single-Cell Reprogramming Compound Finder (scRCF), which integrates transcriptomics-guided predictions with advanced screening, we identified compound cocktails that precisely and efficiently reprogram fibroblasts through an intermediate state into ciRPE cells. These ciRPE cells closely mimic the structure and function of native RPE cells, and upon transplantation into RD rats, they seamlessly integrate into host tissue, protect photoreceptors, and restore visual function. Omics and mechanistic analyses revealed that the identified compounds synergistically activate core transcription factors, including Ascl1 and Olig2, orchestrating the reprogramming process. This work provides a scalable platform for RPE cell generation, advancing cell replacement therapies for RD diseases.

overall_design: Using multi-omics sequencing to examine cellular changes during the chemical reprogramming of fibroblasts into RPE cells.

first: JianZhong

first: ShaSha

last: Li

first: Hui

last: Liu

first: ZhengBiao

last: Zhu


title: Comprehensive bioinformatics analysis reveals the hub genes and pathways in a mouse model of Pierpont Syndrome

city: Amsterdam

first: Aldo

last: Jongejan

address: Meibergdreef 9

department: Epidemiology & Data Science

institute: Amsterdam University Medical Centers

summary: Unravelling molecular defects resulting from the missense mutation in TBL1XR1 using targeted mutant mice bearing the Tbl1xr1 Y446C/Y446C mutation. These mice used as an animal model of Pierpont syndrome have disturbed hearing and a trend for disturbed locomotor activity. RNA seq of cortex tissue has been performed to establish the transcriptome.

overall_design: mRNA profiles for cortex of wild type and Tbl1xr1Y446C/Y446C mice (6 mice for each genotype, 3 male and 3 female mice per genotype).

first: Yalan

last: Hu

first: Peter

last: Lauffer

first: Anita

last: Boelen


title: Chemical reprogramming of fibroblasts into functional retinal pigment epithelium cells (RNA-seq)


title: Chemical reprogramming of fibroblasts into functional retinal pigment epithelium cells (cut&tag)


title: Imaginal discs produce neuropeptide-like precursor 1 to alleviate ER stress in response to warm temperatures

city: Gwangju

first: Il-Ju

last: Kim

address: 123, Cheomdangwagi-ro, Buk-gu, Gwangju, Republic of Korea

country: South Korea

institute: GIST

summary: In mammals, prolonged heat stress induces an endoplasmic reticulum (ER) stress response that can damage internal organs. In Drosophila, larvae grow and develop into adults faster at warmer temperatures (e.g., 30°C) than at lower temperatures, but with reduced body size and fertility. In this study, we show that the neuropeptide gene neuropeptide-like precursor 1 (Nplp1) alleviates temperature-induced ER stress in imaginal discs. Warm temperatures increase production of a specific Nplp1 splice variant that inhibits PKR-like endoplasmic reticulum kinase (PERK) activation and cell death. Nplp1 inhibits Dilp8 expression through the PERK/ATF4/Yki pathway, thereby enabling imaginal disc growth and ecdysone homeostasis under warm temperature conditions. These findings provide valuable insights into how animals cope with elevated temperatures.

overall_design: For each sample, total RNA was extracted from thirty sets of larval brains and associated tissues, including salivary glands, imaginal discs, and fat bodies, dissected at 90 or 108 hours after egg laying (AEL). Dissections were performed in PBS. Total RNA was isolated using TRIzol reagent (Takara) according to the manufacturer's protocol. RNA (1 μg) was reverse transcribed using oligo(dT) primers (Promega) and Accupower RT premix (Bioneer). Sequencing libraries were generated using a poly(A)-based enrichment protocol and sequenced on the Illumina NextSeq 500 platform (single-end). Transcript-level abundance was quantified using Kallisto (v0.48.0) with the Drosophila melanogaster transcriptome index (FlyBase release r6.54)


title: In Vitro Modeling of and Automated Drug Screening in Embryonal Brain Tumors Using Tumor-Brain Organoids

status: Public on Oct 28 2025

city: Münster

first: Kornelius

last: Kerl

address: Albert-Schweitzer-Campus 1

department: Department of Pediatric Hematology and Oncology

institute: University Children’s Hospital Münster

summary: Embryonal brain tumors (EBTs), arising during early brain development, present significant challenges in understanding pathogenesis and developing of treatments. This study explores the efficacy of forebrain organoid (FBO) models in replicating the complexities of the EBT microenvironment. We established an EBT-forebrain-organoid (TBO) model, incorporating embryonal tumor with multilayered rosettes (ETMR) and atypical teratoid and rhabdoid tumor (ATRT), using a scalable liquid-handling-assisted coaggregation method. Comprehensive characterization, including wholemount immunostaining, immunohisto-chemistry, single-cell RNA sequencing, integration with existing datasets, and automated cell type-specific drug screening, validated the TBO model. TBOs closely mimicked mid-gestational fetal brain environments, and EBTs in FBOs better approximated native intratumoral heterogeneity at both histological and transcriptomic levels than tumor-only 3D approaches. Drug screening in ETMR-FBOs identified promising treatment options, including anthracyclins and triptolide, demonstrating anti-tumoral effects with minimal neurotoxicity. Scalable TBO models that incorporate immature neural microenvironments better recapitulate individual tumor heterogeneity and mark significant progress towards targeted therapy and personalized precision medicine.

overall_design: scRNA-seq (10xGenomics) of fresh tumor forbrain organoid samples (n = 2) and fixed snRNA-seq samples from tumors (n = 17) and cell lines (n = 10).

first: Riedel

last: Nicole C.

first: Walter

last: Carolin

first: de Faria

last: Flavia W.

first: Atendorf

last: Lea

first: Aust

last: Paula

first: Göbel

first: Verma

last: Archana

first: Ballast

last: Annika

first: Bedzhov

last: Ivan

first: Roy

last: Rajanya

first: Münter

last: Daniel

first: Albert

last: Thomas K.

first: Rössig

last: Claudia

first: Johann

last: Pascal

first: von Zezschwitz

last: Barbara

first: Sandmann

last: Sarah

first: Varghese

last: Julian

first: Thomas

last: Christian

first: Schüller

last: Ulrich

first: Bruder

last: Jan M.

first: Kerl

last: Kornelius