title: RNA-seq profiling of left atrial remodeling in a minimally invasive echocardiography-guided mouse model of degenerative mitral regurgitation

city: Tainan

first: Wei-Ting

last: Chang

state: Tainan

address: 901 ZhongHua Rd. YongKang Dist

institute: Chi-Mei Medical Center

summary: Degenerative mitral regurgitation (MR) leads to progressive atrial enlargement, fibrosis, calcium-handling abnormalities, and arrhythmogenesis. To investigate transcriptomic remodeling associated with MR, we established a minimally invasive, transthoracic echocardiography-guided mouse model by puncturing the anterior mitral leaflet through a closed-chest apical approach.  Left atrial (LA) tissues were harvested two weeks after MR induction from adult C57BL/6J mice and compared with sham-operated controls. Bulk RNA sequencing was performed to characterize molecular pathways associated with atrial remodeling and arrhythmogenic remodeling.  Transcriptomic analysis revealed enrichment of calcium signaling, apoptosis, extracellular matrix remodeling, and shear stress–related pathways in MR atria, consistent with structural remodeling, fibrosis, and enhanced arrhythmogenic susceptibility observed in functional and histological assessments.  This dataset provides a reproducible murine transcriptomic resource for studying atrial remodeling and calcium-handling dysregulation in valvular heart disease.

overall_design: Adult male C57BL/6J mice (10 weeks old) underwent either: MR induction via echocardiography-guided anterior mitral leaflet puncture Sham procedure (apical puncture without leaflet disruption) Left atrial tissues were collected at 2 weeks post-surgery. Biological replicates: Sham: n = 3 MR: n = 3 Bulk RNA-seq was performed using poly(A)-selected libraries with paired-end sequencing.

first: WeiTing


title: Transcription analysis of primary dermal fibroblasts with different genotypes for CTGF rs9399005 SNP after irradiation or sham irradiation

status: Public on Jun 25 2026

city: Mannheim

first: Ahmad

last: Sami

state: Baden-Württemberg

address: Theodor-Kutzer-Ufer 1-3

department: Department of Radiation Oncology

country: Germany

institute: Medical Faculty Mannheim, Heidelberg University

type: Expression profiling by high throughput sequencing

summary: A predictive model for skin fibrosis following radiotherapy in breast cancer patients was previously developed, and the rs9399005 non-coding candidate SNP associated with reduced risk was identified within a high-risk subgroup, determined by the functional RILA assay. The SNP was located downstream of the CTGF gene, but its biological function is poorly understood. The purpose of this work was to investigate its functional impact at the transcriptional level. Patient-derived dermal fibroblasts, previously genotyped for the candidate SNP, were obtained from a local biobank. Initially, six fibroblast strains for each major homozygote (CC), heterozygote (CT), and minor homozygote (TT) genotype were cultured to passage 6 and exposed to 4 Gy of irradiation or sham irradiation, but one TT fibroblast was excluded from the study due to poor quality and slow growth. Total cellular RNA was collected before irradiation (day-0) and on day-2 post-treatment for gene expression quantification using RNA-seq. After data trimming with Trimmomatic, pseudo- alignment with Kallisto and data normalization (voom function, limma), differential gene expression (DGE) analysis was carried out using the limma package (FDR<0.05). Pathway enrichment analysis was conducted using the ReactomePA package in R. Results: Few differentially expressed genes (DEGs) were identified at baseline (day-0) between the genotypes (TT vs CC: n=5; TT vs CT: n=2; CT vs CC: n=1). Transcriptome changes on day-2 were assessed by comparing irradiated and untreated samples of each genotype to the untreated CC genotype at baseline (day-0) as a common control. Significant differences in the number of DEGs were observed between fibroblasts of different genotypes (p<0.001, Chi-squared test). The highest number of DEGs on day-2 was found in CC fibroblasts (0 Gy: n=2372, 4 Gy: n=9576), while fibroblasts with the TT genotype showed significantly fewer DEGs (0 Gy: n=523, 4 Gy: n=3538), with CT fibroblasts showing intermediate levels (0 Gy: n=788, 4 Gy: n=5471). Pathway analysis after irradiation revealed similar expected responses across all genotypes, consistent with previous reports. However, pathways related to cell cycle regulation, metabolism, and signal transduction were underrepresented in TT fibroblasts at baseline but overrepresented on day-2 post-irradiation, compared to CC fibroblasts. Distinct genes were leading these under- and over-representations. A significant influence of the candidate SNP on fibroblast responses to irradiation was demonstrated, primarily through the modulation of pathways related to growth and stress regulation. Personalized approaches to managing fibrosis risk may be guided by these findings.

overall_design: Patient-derived dermal fibroblasts, previously genotyped for the rs9399005 SNP, were obtained from a local biobank. The experiment was performed in two batches. Batch-1 contained six fibroblast strains with the TT genotype and three fibroblast strains from each CC and CT genotypes (total number of strains n=12). However, one TT fibroblast was excluded from the study due to poor quality and slow growth. Batch-2 contained three fibroblast strains from each CC and CT genotypes (total number of strains n=6). The fibroblasts were cultured to passage 6 and exposed to 4 Gy of irradiation or sham irradiation, but total cellular RNA was collected before irradiation (day-0) and on day-2 post-treatment. After data trimming with Trimmomatic, pseudo- alignment with Kallisto, and data normalization (voom function, limma), differential gene expression (DGE) analysis was carried out using the limma package (FDR<0.05). The batch effect was included as a covariate in the design matrix model.

first: Carsten

last: Sticht

first: Marlon

last: Veldwijk

last: Herskind


title: Selection of cord-blood donors for NK cell-based anti-tumor immunotherapy

status: Public on Jun 26 2026

city: Houston

first: Katayoun

last: Rezvani

state: Texas

address: 1515 Holcombe Blvd

department: Department of Stem Cell Transplantation and Cellular Therapy

country: USA

institute: The University of Texas MD Anderson Cancer Center

summary: Donor heterogeneity in cord blood?derived NK cells can influence the efficacy of NK cell?based anti-tumor immunotherapy. Here, we profile single-cell gene expression in ex vivo-expanded cord blood NK cells and primary cord blood to determine how baseline NK-cell subset composition shapes subsequent immune effector activity.

overall_design: Single cell RNA sequencing with antibody-derived tag (ADT) detection was performed on expanded human NK cells. NK cell subsets were directly isolated from cord blood and, in parallel, expanded ex vivo for two weeks using uAPC feeder cells in the presence of 200 U/mL IL-2. Primay cord blood was sequenced using 3' 10x Genomics protocol.

first: Katy


title: 3-(4-Hydroxy-3-methoxyphenyl) propionic acid prevents renal fibrosis and inflammation in CKD mice induced by adenine

city: Higashi-Hiroshima

first: Yanaka

last: Noriyuki

address: Kagamiyama 1-4-4

department: Graduate School of Biosphere Science

country: Japan

institute: Hiroshima University

summary: Transcriptional profiling of mouse kidney. The objective of this study is to explore gene expression profiles of kidney of an adenine-induced chronic kidney disease model in response to 3-(4-Hydroxy-3-methoxyphenyl) propionic acid (HMPA) supplementation by DNA microarray analysis.

overall_design: Two-condition experiment, kidney of five adenine diet mice at 12W weeks of age with and without HMPA supplementaion

first: Noriyuki

last: Yanaka


title: Endothelial PIEZO1 activation impairs osteogenesis via GREM1-mediated inhibition of BMP signaling [MC3T3_RNA-seq]

city: Harbin

first: Haoran

last: Zhang

state: Heilongjiang

address: 246 Xuefu Road

country: China

institute: Harbin Medical University

summary: The mechanosensitive ion channel PIEZO1 has emerged as a key regulator of vascular and skeletal biology. Here, we show that systemic activation of PIEZO1 using the chemical agonist Yoda1 in 3-week-old mice disrupts bone homeostasis by impairing type H endothelial cells and inhibiting osteogenic differentiation. In vivo, Yoda1 treatment significantly reduced the abundance of CD31hiEMCNhi type H vessels and altered trabecular bone microarchitecture without affecting total bone mass. In vitro, Yoda1 inhibited osteogenic gene expression and alkaline phosphatase activity in MC3T3-E1 preosteoblasts. Transcriptomic analysis of Yoda1-treated human bone microvascular endothelial cells (hBMECs) revealed a shift from an angiogenic H-type to a quiescent L-type, accompanied by upregulation of BMP signaling antagonists, particularly GREM1. Functional assays confirmed that GREM1 secreted from Yoda1-stimulated endothelial cells suppresses BMP4-induced osteoblast differentiation via paracrine signaling. Together, these findings uncover a novel endothelial-to-osteoblast regulatory axis mediated by PIEZO1-GREM1-BMP4 signaling, and underscore the context-dependent effects of PIEZO1 activation on bone regeneration.

overall_design: Human bone microvascular endothelial cells (hBMECs) were obtained from Sunncell (Cat#SNP-H101) and maintained in the corresponding growth medium (Sunncell, Cat#SNPM-H101). After treated with 10μM Yoda1 (MedChemExpress, Cat#18723) or DMSO as a vehicle control for 24 hours, total RNA was extracted from four biological replicates per condition and subjected to bulk RNA sequencing.

first: Bowen

last: Wang

first: Jing

last: He

first: Shengyi

last: Zhou

first: Juan

last: Song

first: Ziwen

last: Liu

first: Xiangyu

last: Zeng

first: Ying

last: Xing

first: Feng

last: Guo

first: Jianyu


title: Gene expression profile at single cell level of atrial tissue in atrial fibrillation

city: Bengbu

first: Pinfang

last: Kang

address: 801 Zhihuai Road

institute: Bengbu Medical University

summary: Atrial tissues contain endothelial cells, myofibroblasts, cardiomyocytes, and immune cells

overall_design:
Human left atrial appendage samples from atrial fibrillation patients and control individuals undergoing cardiac surgery were collected and sorted for live cells

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


title: Single-Nucleus Analysis of the Adult Human Olfactory Epithelium Uncovers Shared Neurogenesis Programs with the Brain

city: NEW YORK

first: Panos

last: Roussos

state: NY

address: 1411 Madison Ave Apt 4E

institute: Icahn School of Medicine at Mount Sinai

summary: Neurogenesis, a critical process implicated in diverse brain disorders, is greatly diminished in the adult human brain, complicating direct investigations into its mechanistic role in disease. In the olfactory epithelium (OE), olfactory sensory neurons (OSNs) maintain homeostasis via continual neurogenesis throughout life, providing a niche to investigate neurogenesis in vivo. However, the molecular mechanisms underlying this process and its similarities to brain neurogenesis remain largely unknown. Here, we performed single-nucleus RNA-seq (snRNA-seq from the human OE of 6 living adult donors, yielding 145,720 high-quality transcriptomics. Integrating with an independent OE dataset from 4 adults, different developmental stages of OSNs were identified, including neural precursor cells (globose basal cells, GBCs), as well as immature and mature OSNs. We inferred trajectories and assessed the transcriptional and regulatory dynamics of OSN development. Genes and transcription factors involved in regulating neuronal differentiation and neurogenesis were highly expressed in GBCs and early immature OSNs, but were downregulated in mature neurons. OSNs and cortical excitatory neurons exhibited convergence during early developmental stages, including dynamically expressed genes, biological processes, transcription factors, as well as polygenic enrichment for psychiatric disorders. In addition, highly matched expression dynamics of autism risk genes between OSNs and cortical excitatory neurons further validated their convergence. Overall, OSNs cells in the olfactory neuroepithelium represent a potential proxy to study gene programs involved in neurogenesis in the human brain, providing an accessible model for investigating neurodevelopmental dysfunction in psychiatric disorders.

overall_design: snRNA-seq profiling of olfactory epithelium at adult human.

first: Liting

first: John

last: Fullard

first: Claire

last: Coleman

first: Evelyn

last: Hennigan

first: Clara

last: Casey

first: Xinyi

first: Stathis

last: Argyriou

first: Steven

last: Kleopoulos

first: Samuel

last: DeMaria

first: Jaroslav

last: Bendl

first: Alfred

last: Marc Iloreta

first: Pengfei

last: Dong


title: Evaluation of potential immune-related adverse events in mouse lung tissues after anti-PD1 or anti-PD1 nanocapsule treatment

city: Los Angeles

first: Jeffrey

last: Harding

state: CA

address: 405 Hilgard Avenue

institute: University of California Los Angeles

summary: Immune-releated adverse events is a common side effect in immune-checkpoint bloakade therapy like anti-PD1. Here, we performed RNA sequencing of lung tissues after treatment of anti-PD1 or anti-PD1 nanocapsules to evaluate their transcriptomic change related to adverse events. Our analysis has revelaed that nanocapsules which can target tumor tissue more effectively rather than accumulating in healthy tissues cause less transcriptomic change and can potentially prevent immune0related adverse events in lung tissues.

overall_design: Three lung samples from each group (PBS, anti-PD1, and anti-PD1 nanocapsules) were analyzed through RNA sequencing.


title: Ubiquitin-like proteins NEDD8 and SUMO2 control epithelial homeostasis, regeneration, and inflammation [RNA-Seq SUMO2, NEDD8]

city: Stanford

first: Paul

last: Khavari

address: 269 Campus Dr

department: Dermatology

institute: Stanford University

summary: Stratified epithelial differentiation involves incompletely understood transcriptional and proteomic remodeling. Multi-omic profiling implicated ubiquitin and related networks in differentiation dynamics. Systematic perturbation of ubiquitin-like machinery uncovered opposite functions of NEDD8 and SUMO2. Knockout mice established essential roles for NEDD8 in progenitor maintenance, skin regeneration, and inflammation, whereas SUMO2 was required for differentiation. Beyond ubiquitin-proteasome-concordant changes, NEDD8 directed proteomic regulation correlated with RNA abundance. Integration of IP-MS with genome-wide suppressor screening revealed context-specific NEDDylated dependencies. Among effectors, HNRNPU emerged as a post-transcriptional regulator of epithelial cell state, whose binding repertoire was modulated by NEDDylation, linking NEDD8 induced proteomic remodeling to RNA regulation. Together, these findings define opposite roles for NEDD8 and SUMO2 in orchestrating epithelial homeostasis, regeneration, and inflammation, underscoring how ubiquitin-like networks govern tissue fate.

overall_design: NEDD8 or SUMO2 knockout mice (and K14-CreERT negative littermate controls) were induced with topical tamoxifen

first: Carl Gustaf Marten

last: Winge

first: Leandra

middle: V

last: Jackrazi


title: Hypertonicity induced changes in gene expression in mpkCCD cells and the contribution of  NFAT5 activity on these changes.

city: Halle

first: Bayram

last: Edemir

address: Ernst-Grube-Str. 20

institute: University Hospital Halle (Saale)

summary: The corticomedullary osmotic gradient between renal cortex and medulla induces a specific spatial gene expression pattern. The factors that control these differences are not fully addressed. The hypertonic environment leads to activation of the nuclear factor of activated T-cells 5 (NFAT5), which regulates the expression of osmoprotective genes. While NFAT5 function under hypertonic conditions has been extensively studied, its contribution to basal gene 28 regulation remains incompletely understood. We used murine principal kidney cortical collecting duct (mpkCCD) cells and induced functional deletion of NFAT5 and performed gene expression profiling to identify genes that are differentially expressed under isotonic and hypertonic cell culture conditions. Hypertonic stress induced extensive transcriptional changes in control cells, which were markedly altered in NFAT5-deficient cells. Furthermore, the comparison of the mpkCCD transcriptomes with gene expression profiles from renal cortex and inner medulla of control and principal cell-specific NFAT5 knockout mice revealed partial overlap in hypertonicity-associated and NFAT5-dependent gene expression patterns. In both conditions, the expression of known NFAT5 target genes, like Aqp2 or Ranbp3l, was downregulated. These findings support the use of mpkCCD cells as a complementary model to study NFAT5-associated gene regulation under controlled in vitro conditions.

overall_design: In this study, we used RNA-seq to assess gene expression profiles in mpkCCD cells with CRISPR/Cas9 mediated deletion of NFAT5 in the same cells (Nfat5-KO).

first: Kristina

last: Engel

first: Dmitry

last: Chernyakov

first: Moritz

last: Pernecker


title: Ubiquitin-like proteins NEDD8 and SUMO2 control epithelial homeostasis, regeneration, and inflammation [scRNA-seq]

overall_design: Nedd8fl/fl, Sumo2fl/fl and Nedd8fl/fl, Nrf2-/-, NEDD8fl/fl Nrf2-/-,  with or without K14-Cre (littermate controls) were treated with tamoxifen, and post-recombination full thickness skin samples were isolated as single cell suspensions then processed according to 10x genomics workflow for scRNA sequencing

first: Benjamin

last: Pham

first: Dayan

last: Li


title: Shaping Gut Immunity with Intestinal Epithelial-Immune Dynamics in Peyer's Patches

city: Brisbane

first: M. Zeeshan

last: Chaudhry

state: Queensland

address: 37 Kent Street

country: Australia

institute: The University of Queensland

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

overall_design: Refer to individual Series


title: Transcriptomic profiling of epigenetic regulators and metabolic reprogramming in human cholangiocarcinoma

city: Pamplona

first: Maite

middle: G

last: Fernandez-Barrena

address: Pio XII 55

country: Spain

institute: CIMA

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Transcriptomic profiling of neonatal mouse ventricular myocytes (NMVMs) under hypoxia and recombinant Serglycin stimulation

city: tianjin

first: lifeng

last: feng

state: State...

address: china

institute: nankai university

summary: To investigate the direct regulatory effects of Serglycin (SRGN) on cardiomyocytes under ischemic conditions, we performed bulk RNA-sequencing on primary neonatal mouse ventricular myocytes (NMVMs). The study includes three experimental groups: Control (Con), Hypoxia, and Hypoxia + recombinant SRGN (rSRGN). NMVMs in the Hypoxia and Hypoxia+rSRGN groups were subjected to oxygen-glucose deprivation (glucose-free and serum-free DMEM) in an anaerobic environment (AnaeroPack-MIC, Mitsubishi A-07) for 6 hours. This dataset identifies the transcriptional alterations driven by SRGN in cardiomyocytes during hypoxic stress.

overall_design: Comparative gene expression analysis of primary NMVMs. The experiment consists of 3 groups: Control, Hypoxia (6h), and Hypoxia + rSRGN (6h). Total RNA was extracted for library construction and sequencing.

first: Lifeng

last: Feng

first: Hanmo

last: Zhang

first: Xin

last: Qi

first: Zhi


title: Fusarium graminearum grown in vitro and challenged with F. avenaceum filtrate leads to the strong induction of a F. graminearum ABC transporter.

city: Ottawa

first: Linda

middle: J

last: Harris

state: Ontario

address: 960 Carling Ave.

department: Eastern Cereal & Oilseed Research Centre

country: Canada

institute: Agriculture & Agri-Food Canada (AAFC)

summary: Fusarium cereal pathogens are known to produce a diverse array of mycotoxins and other secondary metabolites which may act together to cause plant disease and adverse effects on human and animal health. To study the impact of Fusarium interactions, we chose F. graminearum and F. avenaceum, which are known to co-contaminate Canadian durum wheat samples resulting in the deposition of trichothecenes, enniatins, moniliformin, and other bioactive compounds. We are studying the interaction of a F. graminearum (3-ADON-producer) and a F. avenaceum strain (both isolated from the same wheat sample) in durum wheat spikes. To study the impact of F. avenaceum secondary metabolites on F. graminearum, we conducted transcriptomic profiling of F. graminearum grown in the presence of F. avenaceum culture filtrate extracts in vitro.  A F. graminearum ABC transporter gene was strongly induced in vitro upon exposure to F. avenaceum culture filtrate.

overall_design: 13 samples were collected of Fusarium graminearum strain LH03 (DAOM242075) grown in liquid culture and collected six hours and 2 days after the addition of Fusarium avenaceum mixed filtrate extracts or the control DMSO. F. graminearum LH03 macroconidia (8x104 spores/mL) were used to inoculate 4 mL of GYEP media in each well of 6-well plates. Sterile Miracloth circles were added to each well, plates sealed with air pore tape, and incubated at 170 rpm at 28 °C in the dark. After two days, the media was removed and replaced with 4 mL of second stage media. At this time, either 10 µL of DMSO or 10 µL of mixed FaLH03/FaLH27 MeOH fraction re-suspended in DMSO were added to each well and incubated at 170 rpm, 28 °C in the dark. Miracloth circles and associated mycelia were harvested after 6 h and 2 days. Samples from three biological replicates of each treatment and time were analyzed (except for four biological replicates of FgLH03 + FaLH03/LH07 filtrate 6h). Single-dye hybridizations.

first: Anne

last: Johnston

first: Rachel

last: Kwan

first: Whynn

last: Bosnich

first: Danielle

last: Schneiderman


title: Effect of intravenous poly(lactide-co-glycolide) nanoparticles on bleomycin pulmonary fibrosis

city: Ann Arbor

first: Hannah

last: Viola

state: Michigan

address: 1600 Huron Parkway

department: Biomedical Engineering

institute: University of Michigan - Ann Arbor

summary: Organ fibrosis presents a substantial disease burden with few therapeutic options. Innate immunity mediates fibrinogenesis, but also plays a major role in fibrinolysis. Here, we show that immunomodulatory nanoparticles (NPs) can harness this endogenous antifibrotic capacity by catalyzing monocyte activation leading to resolution of bleomycin-induced pulmonary fibrosis in vivo. Cargo-free NPs comprised of the degradable biopolymer poly(lactide-co-glycolide) (PLG) induce a transcriptional shift toward antifibrotic immune activation in profibrotic M2 macrophages (MΦs) in vitro. NPs stimulate M2 MΦs toward a glycolytic, rather than fatty acid oxidative, metabolism; suppress canonical M2 markers like arginase-1 (Arg1) and periostin (Postn); and upregulate collagenases, hyaluronidases and immunoregulatory factors. When delivered intravenously in vivo, NPs resolve established bleomycin-induced pulmonary fibrosis and invert the trajectory of over 1,000 genes from pre- to post-treatment according to bulk RNA-sequencing. NPs also suppress profibrotic signaling and increase expression of repair-associated pathways like peroxisome proliferator-activated receptor gamma (PPAR-γ), nuclear retinoic acid receptor (RAR), vascular endothelial growth factor (VEGF), and sphingolipid signaling in fibrotic lungs. Flow cytometry confirms that NPs induce monocyte recruitment to fibrotic lungs via enhanced integrin expression. Altogether, NPs induce a robust pro-regenerative signature comprised of ECM degradation, inflammation resolution, and tissue repair pathways, concomitant with increased NP+ monocyte recruitment to fibrotic lungs. This work demonstrates that monocytes are not intrinsically profibrotic, but rather, their effects are context-dependent, and they retain a capacity for fibrotic resolution under conditions that can be induced by materials with translational potential.

overall_design: Bulk RNA-sequencing was conducted on whole lung homogenates from 3 conditions: Day 14 (pre-treatment, n=4), Day 21 NP (n=4), and Day 21 Vehicle (n=4) (mean 44 ± 7.7 million reads/sample).

first: Bethany

middle: B

last: Moore

first: Lonnie

last: Shea


title: Ubiquitin-like proteins NEDD8 and SUMO2 control epithelial homeostasis, regeneration, and inflammation [RNA-Seq epithelial]

first: Paul

last: Khavari

overall_design: RNA sequencing of primary human cell types (cervical, corneal) treated with DMSO or NEDD8i

first: Carl Gustaf Marten

last: Winge

first: Leandra

last: Jackrazi


title: Cardiopedia-Ligand: a Ligand Stimulation Atlas for Cardiac Function and Transcriptional Response

first: James

last: Hudson

address: 300 Herston Rd, Herston QLD 4006

institute: QIMR Berghofer Medical Research Institute

summary: Large-scale perturbation atlases have transformed systems biology, yet no equivalent resource exists for the human heart, where contractile function and transcriptomic state must be measured together. Here, we establish Cardiopedia-Ligand, a comprehensive perturbation–function–transcriptome atlas generated by stimulating human cardiac organoids (hCOs) with 87 ligands targeting 98 cell-membrane receptors expressed in the human heart. We developed an automated high-throughput pipeline enabling individualized contractility measurements and single-organoid mRNA-sequencing. We use this pipeline to define both recognized and previously unrecognized functional and transcriptional clusters, including inotropes, endothelin peptides, extracellular matrix regulators, and multiple inflammatory clusters. Clustering analysis, machine learning, and ‘fingerprinting’ of human heart failure biopsies revealed previously underappreciated similarities between ligands and an interferon-γ signaling signature driving heart failure with preserved ejection fraction (HFpEF). Together this comprehensive Cardiopedia-Ligand dataset provides a valuable and accessible resource to interrogate cardiac biology and human disease.

overall_design: Human cardiac organoids (hCO) were stimulated with a library of 87 ligands and 2 compounds targetting 98 receptors expressed in the human heart and hCO. Contractile function was recorded at 4 hours and 24 hours after ligand stmulation. hCO were then lysed for RNAseq for a matched gene epression signature for the 24 hour function timepoint.

first: Janice

middle: D

last: Reid

middle: E


title: Ubiquitin-like proteins NEDD8 and SUMO2 control epithelial homeostasis, regeneration, and inflammation [RNAseq mouse topical NEDD8i]

overall_design: Wild type mice were treated with topical NEDD8i or DMSO on the dorsal skin for 3 days


title: Single-cell spatial transcriptomics reveals sex-dependent gene expression and intercellular signaling in the mouse adrenal cortex

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embriology

country: Poland

institute: Poznan University of Medical Science

summary: Sexual dimorphism profoundly influences adrenal physiology and disease susceptibility, yet its molecular and spatial basis remains poorly understood. The female-predominant X-zone, a transient cortical structure recognized for nearly a century, has lacked comprehensive molecular characterization. Here we use high-resolution Visium HD spatial transcriptomics with Cellpose-based cell segmentation to generate ~203,000 near-single-cell-resolution transcriptomic profiles from sexually mature mouse adrenal glands (four male, four female). We identify ten distinct cell populations with sex differences spatially restricted to inner cortical zones. The X-zone exhibits pronounced sexual dimorphism, with Akr1c18 (20α-hydroxysteroid dehydrogenase) as the definitive marker (log₂FC = −16.28, female-enriched), establishing the X-zone as a specialized progesterone-catabolizing endocrine compartment. Female adrenal glands exhibit greater intercellular communication complexity (435 vs 369 interactions) and higher aggregate signalling strength, with SPP1-integrin pathways enriched in the female X-zone microenvironment. Spatial trajectory inference reveals a dominant centripetal transcriptional gradient from the CT capsule toward the middle zona fasciculata conserved across both sexes, and a secondary centrifugal axis emanating from the JMZ/X region that is prominent in females and reflects the transcriptionally active X-zone. This spatial atlas establishes spatial restriction as a fundamental organizing principle of endocrine sexual dimorphism and provides a foundational resource for investigating sex-specific adrenal physiology, with implications for precision medicine approaches to adrenal disorders.

overall_design: Animals were housed under SPF conditions (21-23°C, 55-60% humidity, 12h light/dark cycle) with standard chow and water ad libitum. Animals were euthanized by decapitation at 7 weeks of age. Adrenal glands were immediately excised and fixed in 10% neutral buffered formalin.

first: Małgorzata

last: Blatkiewicz

first: Szymon

last: Hryhorowicz

first: Marta

last: Szyszka

first: Joanna

last: Suszyńska-Zajczyk

first: Andrzej

last: Pławski

first: Anna

last: Olechnowicz

first: Andrea

last: Porzionato

first: Ludwik K.

last: Malendowicz


title: Cancer cachexia induces senescent reprogramming of brown adipose tissue and pro-cachectic S100A9 secretion by adipocytes

city: Rome

last: Ninni

address: Via della ricerca scientifica 1

department: Biology

country: Italy

institute: University of Rome "Tor Vergata"

summary: Cancer-associated cachexia (CAC) is a multifactorial wasting syndrome characterized by the progressive loss of fat and lean mass, systemic inflammation, and poor therapeutic responsiveness. While brown adipose tissue (BAT) is traditionally considered a protective, energy-dissipating organ, its qualitative remodelling in CAC remains poorly characterized.

overall_design: Here, we demonstrate that CAC induces a senescent conversion of BAT, marked by thermogenic failure, fibrosis, inflammation, and acquisition of a senescence-associated secretory phenotype (SASP). Through integrative transcriptomic, proteomic, and secretomic analyses in a murine model of lung cancer-induced cachexia, we identify S100A9 as a key factor selectively upregulated and secreted by brown adipocytes. Functional assays reveal that the BAT secretome exerts deleterious paracrine effects on white adipocytes and skeletal myotubes, promoting lipolysis and atrophy, while also impairing brown adipocyte identity in an autocrine manner. Co-culture and gain-of-function experiments with S100A9 recapitulate these phenotypes in vitro in mouse and human brown adipocytes, whereas pharmacological blockade of S100A9 signalling partially restores thermogenic and metabolic features.

first: Katia

last: Aquilano

first: Claudia

last: Di Biagio

first: Flavia

last: Tortolici


title: ZMAT3 alleviates cell death in Fanconi anemia via adaptation of sphingolipid metabolism

city: Paris

first: Camille

last: Lobry

address: 16 rue de la Grange aux Belles

department: IRSL Inserm U944 / CNRS UMR7212

country: France

institute: Inserm

summary: Fanconi anemia (FA) is characterized by defective DNA repair and chronic p53 activation, predisposing to acute myeloid leukemia through persistent genomic instability. The molecular adaptations enabling cell survival under chronic stress remain poorly understood. This study investigates the role of ZMAT3, a p53 responsive RNA binding protein overexpressed in FA deficient cells, to elucidate its role in cellular adaptation. Using FA patient fibroblasts and Fancg KO mouse models, we launched transcriptomic profiling, lipidomic, and functional analyses. RNA-seq and lipidomic analyses revealed unexpected alterations in sphingolipid metabolism upon ZMAT3 depletion, linked to ceramide accumulation and downregulation of ASAH1 (acid ceramidase). Functionally, ZMAT3 depletion increased DNA damage and enhanced ferroptosis susceptibility, an iron dependent cell death mechanism. Mechanistically, our results showed that ZMAT3 promotes ASAH1 expression, limits ceramide accumulation and protects cells from ferroptosis induced death which could participate to preleukemic clonal evolution and pointing to areas for further exploration in FA-associated malignancies.

overall_design: Stable cell line (PD20) with inducible shRNA(ZMAT3 or control) treated or not by MMC

first: Dominique

last: Bluteau


title: Fetal erythropoiesis and hemoglobin regulation in the context of maternal obesity

city: Pullman

first: Min

last: Du

state: WA

address: 1815 Ferdinand's Ln

department: Animal Science

institute: Washington State University

summary: We employed single-cell RNA sequencing (scRNA-seq) to investigate the impact of maternal obesity (MO) on embryonic erythropoiesis across multiple hematopoietic organs during mouse development. Tissues including E13.5 placenta, yolk sac, and liver, as well as E17.5 fetal liver, were collected from embryos of obese and control dams. Our analysis revealed dynamic changes in erythroid lineage composition, maturation states, and hemoglobin gene regulation under MO conditions. This dataset provides a comprehensive single-cell transcriptional map of developing erythroid cells across distinct anatomical sites and developmental stages in response to maternal metabolic stress, offering insights into how maternal obesity disrupts embryonic hematopoiesis.

overall_design: To investigate the effects of maternal obesity (MO) on embryonic erythropoiesis, we performed single-cell RNA sequencing (scRNA-seq) on hematopoietic tissues isolated from mouse embryos at different developmental stages. The C57/BL6 female mice were randomly separated into two groups which were fed either a control (CT)diet (10% energy from fat) or a high-fat diet (45% energy from fat), respectively. When the difference in body weight between the two groups exceeded 20%, female mice were mated with males fed a regular diet. Embryonic tissues including the placenta, yolk sac, and liver were harvested at embryonic day 13.5 (E13.5), and fetal livers were additionally collected at E17.5. Single-cell suspensions were prepared from each tissue and subjected to 10x Genomics 3’ scRNA-seq. Samples were processed separately by tissue type, developmental stage, and maternal diet condition (CT vs. MO). The dataset includes biological replicates from multiple litters, with one embryo per litter used per condition.

first: Zhongyun

last: Kou


title: LUCAT1 Drives Arecoline-Induced Head and Neck Cancer Progression via STAT1-Mediated Transcriptional Regulation

city: Taoyuan City

first: Ann-Joy

last: Cheng

address: 259 Wen-Hua 1st Road

country: Taiwan

institute: Chang Gung University

summary: Background: Areca nut chewing is a major environmental risk factor for head and neck cancer (HNC), particularly in Southeast Asia. However, the molecular mechanisms that link areca nut exposure to malignant progression remain poorly understood. Long noncoding RNAs (lncRNAs) have emerged as critical regulators of oncogenesis, but their role in areca nut-associated HNC remains unexplored. Methods: We performed functional assays, transcriptomic profiling, and bioinformatic analyses to investigate the role of the lncRNA LUCAT1 in arecoline-treated HNC cells. Cell motility, epithelial–mesenchymal transition (EMT), reactive oxygen species (ROS) levels, and therapeutic resistance were assessed following LUCAT1 knockdown or overexpression. We identified upstream regulators of LUCAT1 through promoter analysis, transcription factor knockdown, and pharmacological inhibition. Results: LUCAT1 expression was significantly upregulated by arecoline exposure and promoted cell motility, EMT, ROS clearance, and resistance to radiotherapy and chemotherapy. Knockdown of LUCAT1 reversed these malignant phenotypes and suppressed antioxidant enzyme expression, partly through modulation of the p38 MAPK pathway. Transcriptomic and promoter analyses identified STAT1 as a key transcription factor activated by arecoline through muscarinic acetylcholine receptor (mAChR) signaling. Functional rescue experiments confirmed that LUCAT1 acts downstream of STAT1 to sustain arecoline-induced tumor aggressiveness. Conclusion: Our findings define a novel mAChR–STAT1–LUCAT1 regulatory axis that mediates areca nut-induced malignant progression in HNC. This study not only reveals a critical molecular pathway linking environmental carcinogen exposure to oncogenic transcriptional reprogramming but also highlights LUCAT1 as a promising target for therapeutic intervention in high-risk HNC patients.

overall_design: Two human head and neck cancer cell lines (CGHNC9 and OECM1) were used to investigate transcriptomic changes induced by stable LUCAT1 knockdown. For each cell line, parental control and LUCAT1 knockdown cells were subjected to poly(A)-selected, strand-specific RNA sequencing. Differential expression analysis was performed to identify genes regulated by LUCAT1.

first: Hung-Han

last: Huang

first: Guo-Rung

last: You

first: Joseph T

last: Chang


title: Solamargine induces apoptosis and ferroptosis through the ROS/p38 MAPK signalling pathway in intrahepatic cholangiocarcinoma

city: Dalian

first: Xiang

last: Wang

address: No. 467, Zhongshan Road, Shahekou District

institute: The Second Hospital of Dalian Medica

summary: For exploring the potential mechanism of the effects of SM on ICC cells, samples were sent for transcriptome sequencing, and RNA-seq was applied to analyze the effect of SM treatment on transcriptional changes in ICC cell lines.

overall_design: HUCCT-1 cells were treated with or without SM for 24h, and samples were collected for total RNA extraction and sequencing.

first: Kai

last: Luo

first: He

last: Bai

first: Xudong

last: Zhang

first: Jialin

last: Qu

first: Xiaoqing

first: Xu

last: Sun

first: Yuting

last: Zhao

first: Bin

first: Guixin


title: Transcriptomic profiling of epigenetic regulators and metabolic reprogramming in human cholangiocarcinoma [liver]

first: Maite

last: Fernandez-Barrena

summary: To study the expression of epigenetic and metabolic genes in cholangiocarcinoma (CCA) tumor progression, CCA was induced in C57BL/6J mice by hydrodynamic tail vein injection (HTVI) of plasmids coding for Notch Intracellular Domain 1 (NICD1, 10 µg per mouse) in combination with myr-AKT (10 µg/mouse) and the sleeping beauty transposase (NICD1AKT). C57BL/6J mice without HTVI injection were used as healthy controls (C). Mice were sacrificed at 2 and 3 weeks to evaluate the expression landscape of epigenetic and metabolic genes in tumor progression. We then performed gene expression profiling using RNA-seq data from 3 mice per group.

overall_design: CCA was induced in C57BL/6J mice by hydrodynamic tail vein injection (HTVI) of plasmids coding for Notch Intracellular Domain 1 (NICD1, 10 µg per mouse) in combination with myr-AKT (10 µg/mouse) and the sleeping beauty transposase (NICD1AKT). C57BL/6J mice without HTVI injection were used as healthy controls (C). Mice were sacrificed at 2 and 3 weeks after HTVI.

first: Amaya

last: Lopez-Pascual

first: Jasmin

last: Elurbide

first: Emiliana

last: Valbuena-Goiricelaya

first: M Ujue

last: Latasa

first: Elena

last: Anaya

last: Adan-Villaescusa

first: Borja

last: Castelló-Uribe

first: Luz

middle: A

last: Martínez-Pérez

first: Iker

last: Uriarte

first: Maria

last: Arechederra

first: Sergio

last: Ciordia

first: Fernando

last: Corrales

first: Sona

last: Frankova

first: Eva

last: Sticova

first: Ondrej

last: Fabian

first: Leticia

last: Colyn

first: Patricia

last: Inacio

first: Juan

last: Bayo

first: Meritxell

last: Huch

first: Carmen

last: Berasain

last: Fernández-Barrena

first: Matías

last: Avila


title: Transcriptomic profiling of epigenetic regulators and metabolic reprogramming in human cholangiocarcinoma [HuCCT-1]

first: Maite

last: Fernandez-Barrena

summary: Epigenetic alterations play an increasingly recognized role in carcinogenesis and in the development of resistance to anticancer therapies. In this study, we examined the expression of epigenetic genes to investigate their interplay in cholangiocarcinoma (CCA). We examined 257 epigenetic genes (EpiGs) in transcriptomic data from HuCCT-1 iCCA cells under hypoxia (1% O₂) for 24 h. We observed that exposing the HuCCT-1 iCCA cell line to hypoxia increased the expression of key epigenetic regulators. Our results suggest that hypoxia may contribute to the activation of a shared epigenetic program associated with malignant transformation and poor prognosis.

overall_design: Human iCCA cell culture (HuCCT-1; RRID:CVCL_0324) under hypoxia (1% O₂) or normoxia (21% O₂) for 24 h. Three technical replicates for each condition.

first: Amaya

last: Lopez-Pascual

first: Jasmin

last: Elurbide

first: Emiliana

last: Valbuena-Goiricelaya

first: M Ujue

last: Latasa

last: Anaya

last: Adan-Villaescusa


title: RNA-Seq analysis of Leptospira interrogans serogroup Icterohaemorrhagiae and Pomona strains

first: Rania

last: Ouazahrou

address: 28 rue docteur Roux

institute: Institut Pasteur Paris

summary: Zoonotic pathogens account for the majority of emerging and re-emerging infectious diseases, yet the evolutionary mechanisms underlying their host specialization remain largely unexplained. Here, by combining comparative genomics and transcriptomics and the response of macrophages of varying hosts, we investigated the adaptive host evolution in the Bacterial celll zoonotic pathogen model Leptospira interrogans. Genomic analyses reveal that specialized genogroups exhibit specific signatures, characterized by reduced nucleotide diversity and restricted pangenome openness. We identify adaptive hotspots in genes encoding virulence factors, membrane proteins and environmental sensors, suggesting that positive selection in these genes is likely the primary drivers behing the emergence of genogroups. Focusing on the predominant genogroups associated with serogroups Icterohaemorrhagiae and Pomona, we uncover unique protein domain acquisitions linked to host adaptation, as well as a genogroup-specific gene expression programs potentially affecting virulence, secretion systems and metabolic pathways. Finally, infection of macrophages of different hosts elicits distinct immune responses, further validating ecological specialization of certain genogroups. Together, our findings suggest that intraspecies heterogeneity in L. interrogans is driven by niche specialization through differences in gene content, mutation rate variation and regulation of transcriptional programs.

overall_design: RNA sequencing was performed on Leptospira interrogans serogroup Icterohaemorrhagiae (5 strains) and serogroup Pomona (4 strains) in EMJH medium at 30°C during the exponential phase or in complete cell medium (EMEM medium supplemented with 5% rabbit serum and 0.72 nM FeSO4) at 37°C under 5% CO2 for 3 days.

first: Alexandre

last: Giraud-Gatineau

first: Marc

last: Monot

first: Nadia

last: Benaroudj

first: Frederic

last: Veyrier

first: Helena

last: Petrosova

first: Mathieu

last: Picardeau


title: The MUC1 extracellular domain and cytoplasmic tail play distinct roles during Salmonella invasion of enterocytes

city: Utrecht

first: Karin

last: Strijbis

state: Utrecht

address: Yalelaan 1

department: Biomolecular Health Sciences

country: Netherlands

institute: Utrecht University

summary: The intestinal mucus layer consists of secreted and transmembrane (TM) mucins that are expressed on the apical surface of enterocytes and goblet cells. The TM mucin has a complex domain structure consisting of an extended highly O-glycosylated extracellular domain (ED) and a cytoplasmic tail (CT) with signaling potential. The enteropathogenic bacterium Salmonella expresses a giant adhesin called SiiE that interacts with the MUC1, resulting in invasion at the apical surface of the intestinal epithelium.  Here, we determined the contributions of the MUC1 ED and CT to Salmonella invasion and subsequent immune responses. To investigate the role of the MUC1 ED in Salmonella invasion, the mucin-selective protease StcE was used to remove the glycosylated ED from the surface of intestinal HT29-MTX cultures. StcE-mediated removal of the MUC1 ED blocked Salmonella invasion to levels comparable to MUC1 knockout cells. To study the contribution of the MUC1 CT, a targeted CRISPR/Cas9 approach was used that resulted in the removal of the CT but left the ED and transmembrane domain intact. Salmonella invasion into these MUC1-ΔCT cultures was comparable to wild type cells. These results demonstrate that MUC1 ED, but not the MUC1 CT, is essential for apical Salmonella invasion. To determine the contributions of MUC1 domains, we performed a transcriptomics analysis of uninfected MUC1-WT, MUC1-ΔCT, and ΔMUC1 cultures and cultures that were infected with Salmonella for 6-hour. Deletion of the full MUC1 protein led to a large number of differentially expressed genes, while a smaller group of 132 genes was differentially expressed in infected MUC1-WT cultures compared to  MUC1-ΔCT cultures. Amongst these genes were many NFκB-regulated genes that showed reduced expression in the absence of the MUC1 CT. Immunoblot analysis demonstrated that expression of the NFκB inhibitory cytoplasmic subunits p100, p105, and IκBα was significantly reduced in MUC1-WT cultures compared to MUC1-ΔCT and ΔMUC1 cultures. We conclude that the MUC1 ED is essential for Salmonella invasion, and that the MUC1 CT plays a role in activation of the NFκB pathway.

overall_design: To investigate the effect of Salmonella infection mediated through MUC1 apical invasion in HT29-MTX cells. We demonstrate that Salmonella employs MUC1-ED as an entry receptor into polarized epithelial cells; however, the contribution of the distinct MUC1 domains during the invasion remains unknown. We performed gene expression profiling analysis using data obtained from bulk RNA-seq of uninfected and Salmonella-infected HT29-MTX MUC1-WT, MUC1-ΔCT, and ΔMUC1 cells. Comparative gene expression analysis of RNA-seq data for distinct genotypic HT29-MTX cultures and alteration of the gene expression upon Salmonella infection.

first: Jinyi

last: Su

first: Xinyue

last: Li

first: Evelien

last: Floor

first: Jos

last: van Putten


title: Systems biology approach unveils the cellular and molecular mechanisms of formalin-killed vaccine-induced protective immunity against Coxiella burnetii in mice

city: San Antonio

first: Venkatesh

last: Kumaresan

state: TX

address: 3.230, BSE Building, One UTSA circle

department: Molecular Microbiology and Immunology

institute: The University of Texas at San Antonio

summary: The formalin-inactivated Coxiella burnetii virulent phase I vaccine (PIV) was demonstrated to be more protective than the avirulent phase II vaccine (PIIV) against virulent C. burnetii challenge in animal models. However, the cellular and molecular mechanism underlying the difference between PIV and PIIV in their ability to induce protective immunity remains unidentified. In this study, we confirmed that regardless single or multiple immunization, PIV and PIIV derived from the axenic (ACCM-D) culture retained their different protectivities, which PIV provided robust protection but PIIV did not. In addition, PIV elicited earlier PI-specific IgM and sustained higher IgG responses than PIIV, suggesting the immunogenicity is different between PIV and PIIV. We also used bulk-RNA-seq and flow cytometry to compare the immune responses between PIV- and PIIV-vaccinated mice. Interestingly, PIV elicited prolonged neutrophil response in the spleen, which accompanied with upregulation of genes involved in neutrophil degranulation, metal sequestration, and TLR-dependent innate immune pathways. In contrast, PIIV-induced neutrophil response was transient, which did not persist until the later stage of vaccination. These findings suggest that PIV-induced protection might be partially dependent on its ability to activate neutrophil-mediated effector functions. Furthermore, depletion of neutrophils in PIV-vaccinated mice before challenging with virulent C. burnetii significantly reduced the ability of PIV to confer protection in mice. Collectively, this study provides novel evidence to support that the ability of PIV to modulate neutrophil’s function may play an important role in PIV-mediated protective immunity against C. burnetii infection.

overall_design:
PIV and PIIV were generated from axenic (ACCM-D) cultures and administered to mice using single or multiple immunization regimens. Protective efficacy was evaluated following challenge with virulent C. burnetii. Humoral immune responses were assessed by measuring phase I–specific IgM and IgG antibodies. Bulk RNA sequencing of splenocytes from PIV and PIIV vaccinated mice (pooled triplicates) and flow cytometry (triplicates) were used to compare immune responses in PIV- and PIIV-vaccinated mice. The role of neutrophils in vaccine-mediated protection was examined through neutrophil depletion prior to challenge.

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first: Duolin

last: Wang

first: Yan

last: Zhang

first: Dong

last: Xu

first: Guoquan


title: Effect of induced conditional knockout of Satb1 in thymocyte subsets [CUT&RUN]

city: Greater Noida

first: Sanjeev

last: Galande

state: Uttar Pradesh

address: Center of Excellence in Epigenetics  Department of Life Sciences  School of Natural Sciences  Shiv Nadar Institute of Eminence  NH91, Tehsil Dadri

country: India

institute: Shiv Nadar University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Three-dimensional (3D) genome folding, which is highly cell type-specific, plays a crucial role in orchestrating spatiotemporal gene expression. Although factors such as CTCF have been extensively studied in the hierarchical regulation of 3D chromatin organization, the mechanisms driving dynamic genome folding during T cell fate transitions remain incompletely defined. In this study, we reveal that Satb1, a chromatin organizer enriched in the T cell lineage, co-occupies genomic regions with the cohesin complex and Ctcf in double-positive (DP) thymocytes, where chromatin interactions are notably increased. We show that Satb1 physically interacts with the cohesin subunit Smc1a, and its deletion results in aberrant Smc1a binding and reduced chromatin contacts at sites co-occupied by Satb1 and cohesin. In both DP and immature CD4 single-positive (SP) T cells, Satb1 is essential for proper T cell activation and cytokine signaling. At the Cd3 locus, Satb1 and cohesin collaboratively regulate gene expression, with Satb1 loss leading to disrupted Smc1a occupancy and compromised chromatin interactions. Furthermore, Satb1 shows in vitro properties consistent with liquid-liquid phase separation, and disease-associated mutations impair these properties. Together, our findings uncover a molecular mechanism in which Satb1 facilitates chromatin looping through direct interaction with the cohesin complex and its ability to form nuclear condensates, thereby governing transcriptional regulation during T cell development.

overall_design: CUT&RUN profiling of sorted DP thymocytes from WT and tamoxifen induced Satb1 KO samples.

first: Ayush

last: Madhok


title: L-Glutamic acid negatively regulates extracellular ATP-induced reactive oxygen species signaling

city: Columbia

first: Sameep

last: Dhakal

state: MO

address: 1201 Rollins St.

department: Institute for data science and Informatics

institute: University of Missouri

summary: Extracellular ATP (eATP) and L-Glutamic acid (L-Glu) are important damage associated molecular pattern (DAMP) molecules released from cells following injury. Both molecules trigger wound-associated signal transduction pathways, as well as the enhanced production of reactive oxygen species (ROS) by the RESPIRATORY BURST OXIDASE HOMOLOG D (RBOHD) protein. However, whether eATP and L-Glu trigger overlapping or distinct pathways is mostly unknown. Here we report that Arabidopsis thaliana responses to eATP or L-Glu are distinct from each other in terms of tissue specificity and transcriptomic responses. Thus, although both DAMPs trigger the expression of multiple wounding and hormone response transcripts, systemically induced eATP and L-Glu response transcripts have little overlap between them. We further show that wounding of different tissues may result in ROS responses that are controlled by different DAMP receptors. Thus, activation of ROS production following injury of non-vascular tissues primarily depended on the eATP receptors PURINORECEPTOR 2 KINASE 1 and 2 (P2K1P2K2), while activation of ROS responses in vascular tissues primarily dependent on the L-Glu receptors GLU-LIKE RECEPTORS 3.3 and 3.6 (GLR3.3GLR3.6). Interestingly, we found that in the absence of the GLR3.3GLR3.6 receptors (i.e., in the glr3.3glr3.6 double mutant), the ROS response to eATP application is enhanced. This finding suggests that during wounding the L-Glu pathway may suppress the eATP pathway.  Taken together, our findings suggest that the DAMP molecules eATP and L-Glu have complex interactions that appear to be both partly complementary and partly antagonistic, as well as tissue dependent.

overall_design: 27 systemic samples from three different genotypes (Col-0, glr3.3glr3.6, and p2k1p2k2) were analyzed; each sample was collected and analyzed at the 30-minute timepoint post chemical application (extracellular ATP, L-Glutamate, or a mock consisting of the buffer solution without eATP or L-Glu); 3 pooled repeats consisting of 8 plants per repeat were taken for each treatment type and genotype; the respective 30-minute mock treatment was used as controls for each genotype

first: Ronald J

last: Myers

first: Abdul

last: Ghani

first: Trupti

last: Joshi

first: Gary

last: Stacey

first: Ron

last: Mittler


title: Effect of induced conditional knockout of Satb1 in thymocyte subsets [RNA-seq]

overall_design: RNA seq profiling of sorted DP and CD4 thymocytes from WT and tamoxifen induced Satb1 KO samples.


title: RNA-Seq Analysis of Fibroblast-Like Synoviocytes Treated With Lutein in a Rheumatoid Arthritis Context

city: Taipei

first: Tsung Ming

last: Chang

state: Please Select

address: Wuxing street No.250

institute: Taipei Medical University

summary: Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by synovial inflammation and progressive joint destruction. Although lutein is known for its antioxidant and anti-inflammatory properties, its effects on gene expression in RA-associated synoviocytes remain unclear. In this study, we performed RNA sequencing to investigate transcriptomic changes in fibroblast-like synoviocytes (FLS) treated with lutein. Differentially expressed genes were identified and analyzed using Gene Set Enrichment Analysis (GSEA) and Ingenuity Pathway Analysis (IPA) to explore relevant biological processes and molecular networks. The results revealed that lutein treatment altered the expression of genes involved in extracellular matrix remodeling and inflammation. Enrichment analyses suggested modulation of signaling pathways associated with RA pathogenesis. These transcriptomic findings provide insights into the potential molecular effects of lutein on RA-related synovial cells and serve as a basis for further functional investigation.

overall_design: MH7A cells were treated with lutein (10 μM) or vehicle control for 24 hours. Total RNA was extracted and subjected to RNA sequencing using the Illumina NovaSeq 6000 platform (paired-end 150 bp). Sequencing reads were aligned using HISAT2, and gene expression data were normalized using RLE and TMM methods. Differentially expressed genes were identified based on p-value < 0.05 and absolute fold change > 2.

first: Chi-Jen

first: Tsung-Ming

first: Ying-Sui

last: Sun

first: Ji-Fan

last: Lin

first: Chiang-Wen

last: Lee

first: Mei-Ling

last: Fang

first: Ju-Fang

last: Liu


title: Novel ribomethylation changes in multiple myeloma

city: Copenhagen

first: Nicolai

last: Krogh

address: Blegdamsvej 3B

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

summary: A sequencing-based profiling method (RiboMeth-seq) for ribose methylations was applied to study rRNA methylation patterns in Multiple Myeloma patient and derived cell line

overall_design: Tumor samples were analysed  in technical triplicates or duplicates, cell lines in singlicates

first: Maral

last: Halladjian

first: Siv

last: Nielsen

first: Magdalena

last: Vavakova

first: Fazila

last: Asmar

first: Kirsten

last: Grønbæk

first: Annette

last: Juul Vangsted

first: Henrik


title: Spliceosomal proteins direct RNA methylation to modulate gene expression and silence retrotransposons [RIP-seq]

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: 9000 Rockville Pike

department: National Cancer Institute

institute: National Institutes of Health

summary: RNA modifications play indispensable roles in RNA processing and gene regulation, but the mechanistic diversity and transcript specificity of RNA-modifying activities remain unclear. Using genetic screening and biochemical analyses in S. pombe, we identified the RNA methyltransferase Tgs1 as a component of a protein complex called TEaM, which is specifically recruited by spliceosomal proteins to transcripts containing inefficiently spliced cryptic introns. Strikingly, the presence of cryptic introns alone can trigger TEaM-dependent silencing of stress-inducible genes and repetitive elements, including retrotransposons, while Tgs1 is also directed to gametogenic transcripts via a YTH-domain RNA-binding protein. In both contexts, Tgs1 catalyzes trimethylguanosine (TMG) capping, a modification that recruits the conserved Pir2/ARS2 protein and promotes RNA processing through the RNAi pathway. Our findings uncover how splicing machinery and YTH proteins converge on a common regulatory mechanism—TMG capping—that facilitates RNAi-mediated silencing via Pir2/ARS2, providing new insights into gene silencing pathways across eukaryotic species.

overall_design: RIP Seq- Sequencing of RNA immunoprecipitated with the epitope tagged protein.

first: Drisya

last: Vijayakumari

first: Xander

last: Gottfried

first: Brent

last: Groubert

first: Jothy

last: Dhakshnamoorthy

first: Shweta

last: Jain

first: Hua

last: Xiao

first: Anupa

middle: T

last: Anil

first: Martin

last: Zofall

first: David

last: Wheeler


title: Investigations into the biological activity of avobenzone as part of a Next Generation Risk Assessment

city: Mason

first: Yuqing

last: Shan

state: Ohio

address: 8700 mason montgomery road

institute: Procter & Gamble

summary:
We show how New Approach Methodologies and functional analogues were used to identify the mode of action (MoA) for the sunscreen Avobenzone (AVB) and increase confidence in the selected Point of Departure (PoD) for NGRA.
There were no structural analogues for AVB, therefore a read-across safety assessment was not possible. To confirm the MoA for AVB in the safety assessment, potential functional analogues (PFAs) were identified using ToxCast and literature data, whereby AVB showed activity at 17 µM in the “TOX21_MMP_ratio down” assay, suggesting mitochondrial depolarisation is a target mechanism. Chemicals with the same potential bioactivity were 2-, 3- and 4-hydroxybenzophenone (HDBP), kaempferol and myricetin. To compare bioactivities, transcriptional profiles of AVB and PFAs were generated and used for connectivity map (CMap) analysis. AVB was also tested in an adapted pharmacology profiling panel (APPP). 100 µM AVB and myricetin both elicit transcriptional profiles consistent with a non-specific MoA, namely mitochondrial dysfunction, hypoxic stress and apoptosis. This aligns with effects observed for AVB in a repeated dose toxicity study. The remaining substances elicited a different response to AVB, showing instead similarity to chemicals acting via ER and AR. All toxicological targets in the APPP panel, including ER and AR, were unaltered by 5 µM AVB and gene expression in multiple cell types was unaltered by 10 µM AVB.
In conclusion, the MoA of AVB is non-specific and of low potency. When PoDs are compared to human AVB plasma concentrations after sunscreen application, AVB exhibits a low risk to the consumer.

overall_design: Four cell types were used for the transcriptomic experiments: MCF-7 (breast epithelial adenocarcinoma), A549 (lung epithelial carcinoma), HepG2 (hepatocellular carcinoma) and iCell cardiomyocytes (derived from induced pluripotent stem cells, FujiFilm Cellular Dynamics, Madison, WI). MCF-7, A549 and HepG2 cells were purchased from American Type Culture Collection (Manassas, VA) and grown in phenol red-free DMEM media containing 10% serum (Invitrogen, Carlsbad, CA). The iCell cardiomyocytes were grown in a proprietary maintenance medium (FujiFilm Cellular Dynamics, Inc.). Cells were seeded on 96-well plates and after 24 h of culture (for MCF-7, A549 and HepG2 cells) or 7 days for the iCell cardiomyocytes, cells were treated with one of three concentrations of each chemical, 10, 100 and 1000 µM, or vehicle (DMSO) for 6 h. The total cells seeded were 10,000 cells/well for A549 and HepG2 cells; 20,000 cells/well for MCF7 cells; and 50,000 cells/well for iCell cardiomyocytes. The final DMSO concentration in treated and DMSO vehicle control incubations was 0.1% (v/v). All cell cultures were performed in 96-well plates with 6 empty wells for TempO-Seq assay controls, 5 vehicle controls and a positive control, trichostatin-A on each plate. Cells were seeded on 96 well plates and treated with 3 concentrations of each chemical or vehicle (DMSO) for 6 h. Following 6 h treatment, cell lysates were harvested according to a protocol provided by Biospyder (TempO-Seq Workflow-BioSpyder) and then stored at −80 °C until analysis. Each treatment condition was performed in 4 biological replicas. Cell lysate plates were shipped frozen to BioSpyder (BioSpyder Technologies, Inc., Carlsbad, CA) and Tempo-Seq human whole transcriptome (version 2.0) assay was performed at BioSpyder as previously described by Biospyder, Inc. (Yeakley et al., 2017).

first: Jane

last: Rose

first: Jorge

last: Naciff

first: Bastian

last: Selman

first: Xiahong

last: Wang

first: Cathy

last: Lester

first: Catherine

last: Mahony

first: Nicky

last: Hewitt


title: Single-cell transcriptome profiling of tracheal epithelium in basal cell-specific Mettl3 conditional knockout mice

city: Guangzhou

first: Kechen

last: Chen

state: Guangdong

address: Shatai South Road

institute: Southern Medical University

summary: The airway epithelium plays critical roles in respiratory function and is implicated in various pulmonary diseases. To investigate the role of the RNA methyltransferase Mettl3 in airway basal cell homeostasis, we generated a comprehensive single-cell RNA sequencing atlas of tracheal epithelial cells from Mettl3 conditional knockout (M3-CKO) mice and littermate controls. Our dataset specifically focuses on Krt5-lineage traced basal cells,  comparing tdTomato+ (traced) and tdTomato- (non-traced) populations from both genotypes.We present a comprehensive single-cell RNA-sequencing atlas of tracheas, comprising diverse populations of cells, epithelial cell, myeloid cells, B lymphocytes, T lymphocytes, endothelial cells, fibroblasts and glandular mucous cells.

overall_design: We performed single-cell RNA sequencing (10x Genomics) on tracheal epithelial cells from 3-month-old Mettl3 conditional knockout mice (Krt5-CreER; Mettl3fl/fl; R26-tdtomato) and littermate controls (Krt5-CreER;Mettl3fl/+; R26). Cells were collected after tamoxifen induction and pulsed labeling with tdTomato reporter, with each sample containing a 1:1 mixture of lineage-traced (tdTomato+) and non-traced (tdTomato-) populations. Two biological replicates per genotype were processed simultaneously

first: Xinlong

first: Zhili

last: Rong


title: Spliceosomal proteins direct RNA methylation to modulate gene expression and silence retrotransposons [smallRNA-seq]

first: Shiv

last: Grewal

type: Non-coding RNA profiling by high throughput sequencing

overall_design: Small RNA Seq: Sequencing of small RNA isolated from the listed strains

first: Drisya

last: Vijayakumari

first: Xander

last: Gottfried

first: Brent

last: Groubert

first: Jothy


title: Spliceosomal proteins direct RNA methylation to modulate gene expression and silence retrotransposons [RNA-seq]

sample_organism:
Schizosaccharomyces pombe
Homo sapiens

platform_organism:
Schizosaccharomyces pombe
Homo sapiens

overall_design: RNA sequencing : Sequencing of total RNA after ribodepletion

last: Dhakshnamoorthy

first: Shweta

last: Jain

first: Hua

last: Xiao

first: Anupa

last: Anil

first: Martin

first: David


title: Corticosterone-linked microglial activity underpins sexually dimorphic neuroplasticity after ketamine anesthesia.

city: Seattle

first: Cindy

last: van Velthoven

address: 615 Westlake Ave N

institute: Allen Institute

summary: Anesthesia recovery is critical for resuming normal physiological and neuronal functions; however, the mechanisms involved remain elusive. Here, we identify a female-selective corticosterone-mediated microglia-neuron interaction in vivo during ketamine anesthesia recovery, absent in males. This microglia-neuron interaction induces plastic and functional neuronal changes, as evidenced by increased spine density and mEPSC frequency, which is occluded upon microglia depletion. We show that this process is driven through upregulation of the stress-responsive co-chaperone Fkbp5 mRNA and its protein, FKBP51, in female microglia. Fkbp5/FKBP51 is a key intermediary in a corticosteroid-induced stress response, and its involvement points towards a critical interface between endocrine signaling and microglia. Thus, to counteract the observed KXA-mediated corticosterone increase in the blood, we remove the primary source of corticosterone through adrenalectomy. Close microglia-neuron interaction was absent, but was reinstated after corticosterone injection. Our findings offer a new mechanism of microglia-mediated neuronal plasticity during anesthesia recovery, which is mediated through corticosterone, enhancing our understanding of sex differences in brain function.

overall_design: The primary visual cortex (VISp) region was extracted from the brains of saline- or ketamine treated mice. Single nuclei were isolated and snRNA-seq and snATAC-seq libraries were prepared using the 10x Genomics Multiome kit.

first: Alessandro

last: Venturino

first: Mohammad

last: Amin Alamalhoda

first: Thomas

last: Negrello

first: Kelly

last: Jin

first: Ryan John

last: Cubero

first: Jake

last: Yeung

first: Peter

last: Koppensteiner

first: Bosiljka

last: Tasic

first: Sandra

last: Siegert


title: Spliceosomal proteins direct RNA methylation to modulate gene expression and silence retrotransposons [ChIP-seq]

first: Shiv

last: Grewal

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for lysine 9 dimethylated histone H3

first: Drisya

last: Vijayakumari

first: Xander

first: Brent

last: Zofall

last: Wheeler


title: BMAL1 and YAP cooperate to hijack enhancers and promote inflammation in the aged epidermis [RNA-seq Col14]

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

institute: IRB Barcelona

summary: Ageing is characterised by persistent low-grade inflammation that is linked to impaired tissue homeostasis and functionality. However, the molecular mechanisms driving age-associated inflammation remain poorly understood. The mammalian skin is a clinically relevant target of age-driven inflammation associated with compromised barrier function, inefficient wound healing, elevated oxidative stress, and DNA damage accumulation. Here, we show that upon ageing a previously uncharacterised BMAL1–YAP transcriptional complex is hijacked from chromatin regions associated with homeostatic genes in adult epidermis and redirected to inflammation-related enhancers, amplifying the transcription of their target genes. Independently of its known role as a core circadian clock component, BMAL1 partners with the mechanosensitive transcriptional cofactor YAP at enhancer regions to regulate epidermal identity genes. In contrast, in aged skin, BMAL1–YAP complexes bind to enhancers of inflammation-related genes, co-regulated by NF-κB. Interestingly, aged pro-inflammatory signals from the IL-17 pathway activate YAP in a Hippo-independent manner. These findings unveil a transcriptional mechanism underlying epidermal ageing, linking chromatin dynamics to inflammatory transcriptional programs through BMAL1–YAP-bound enhancer rewiring. By elucidating how ageing reprograms transcriptional networks, our work highlights potential strategies to counteract chronic inflammation and restore tissue homeostasis across age-related loss of functionality.

overall_design: Bulk RNA-seq profiling of 47 weeks old ColXIV KO and ColXIV WT mouse epidermis at Zeitgeber time 0 (ZT0), ZT4, ZT8, ZT12, ZT16 and ZT20.

first: Guiomar

last: Solanas

first: Júlia

last: Bonjoch


title: CD44 IN MYELOID CELLS IS A MAJOR DRIVER OF LIVER INFLAMMATION AND INJURY IN ALCOHOL-RELATED LIVER DISEASE [CD44_KO_Ethanol]

city: Nice

first: Philippe

last: Gual

address: 151 Route de Saint-Antoine

institute: INSERM U1065

summary: Background and Aims: Alcohol-related liver disease (ALD) is one of the leading causes of severe liver disease with limited pharmacological treatments for alcohol-related steatohepatitis (ASH). CD44, a glycoprotein mainly expressed in immune cells, has been implicated in multiple inflammatory diseases but has never been studied in the ALD context. We therefore studied its contribution to ASH development in mice and its expression in ALD patients. Approach and Results:  Here, we report that liver CD44 expression is associated with liver injury and inflammation and its deficiency (Cd44-/-) partially protected mice upon chronic plus binge ethanol feeding (CPB-EtOH). CD44 deletion in myeloid cells (Cd44myel-KO) recapitulated the same protective effects associated with reduced inflammatory monocyte infiltration and neutrophil activation in the liver and diminished blood neutrophil-lymphocyte ratio (NLR). CD44-deficient neutrophils displayed reduced PMA-induced inflammatory mediator expression and increased phagocytosis of live bacteria. Cd44myel-KO mice were also protected against hepatic steatosis mediated by CPB-EtOH or chronic ethanol feeding, due in part to increased SIRT1 mediated fatty acid beta-oxidation. CD44 neutralization with antibodies strongly decreased liver injury and inflammation (hepatic neutrophil frequency) and blood NLR upon CPB-EtOH. In samples from ALD patients, hepatic CD44 expression increased with ALD severity, correlated with hepatic TNFα and CD11b expression, and CD44-expressing neutrophils were enriched in alcohol-associated hepatitis. Conclusions: Human and experimental evidence supports CD44 as a marker of hepatic inflammation in ALD. In addition, CD44 modulates neutrophil mobilization and functions and its targeting partially prevents liver inflammation and injury in the context of acute-on-chronic alcohol drinking.

overall_design: RNA seq profiling of CD44-deficient mice (Cd44-/-)(B6.Cg-Cd44tm1Hbg/J). After acclimation to a liquid diet, mice were allowed free access to the ethanol Lieber-DeCarli diet (SSNIFF) containing 5% (vol/vol) ethanol for 10 days. On day 11, mice received a single dose of ethanol by gavage (5 g/kg body weight) in the early morning and sacrificed 9 hours later.

first: Déborah

last: ROUSSEAU

first: Stéphanie

last: BONNAFOUS

first: Frédéric

last: SOYSOUVANH

first: Dorian

last: SARRAIL

first: Manon

last: BOURINET

first: Axelle

last: STRAZZULLA

last: PATOURAUX

first: Arnaud

last: BORDERIE

first: Bastien

last: DOLFI

first: Alexandre

last: GALLERAND

first: Marwin

last: FARRUGIA

first: Véronique

last: ORIAN-ROUSSEAU

first: Yingzheng

last: Xu

first: Jesse

middle: W

last: WILLIAMS

first: Stoyan

last: IVANOV

first: Albert

last: TRAN

first: Rodolphe

last: ANTY

first: Carmelo

last: LUCI

last: GUAL


title: CD44 IN MYELOID CELLS IS A MAJOR DRIVER OF LIVER INFLAMMATION AND INJURY IN ALCOHOL-RELATED LIVER DISEASE [CD44_Myelo_KO_Ethanol]

first: Philippe

last: Gual

overall_design: RNA seq profiling of C57BL/6J/Rj LysMcre/+ Cd44flox/flox and littermate control LysM+/+ Cd44flox/flox mice. After acclimation to a liquid diet, mice were allowed free access to the ethanol Lieber-DeCarli diet (SSNIFF) containing 6% (vol/vol) ethanol for 10 days. On day 11, mice received a single dose of ethanol by gavage (5 g/kg body weight) in the early morning and sacrificed 9 hours later.

first: Déborah

last: ROUSSEAU

last: BONNAFOUS

last: SOYSOUVANH


title: EV miRNA Profiles from Nipple Discharge, Intracystic Fluid, and Tumor Tissue Surface in Breast Cancer

city: Nagoya

first: Kosuke

last: Yoshida

state: Aichi

address: 65 Tsuruma-cho

institute: Nagoya University

summary: Breast cancer is the most common cancer among women worldwide, and nipple discharge (ND) is one of its major symptoms. In this study, we investigated extracellular vesicles (EVs) in ND as potential biomarkers. We developed novel EV collection methods using cellulose nanofiber (CNF) sheets, which capture EVs within the porous nanopaper and require only 10 microliters of liquid (Yokoi A, et al. Nat Commun. 2023;14(1):6915).

overall_design: A total of 23 ND samples were included in the analysis: normal (n = 8), intraductal papilloma (IDP, n = 1), ductal carcinoma in situ (DCIS, n = 8), and invasive ductal carcinoma (IDC, n = 6). Tissue miRNAs from three tumor samples (two cases of DCIS and one case of IDP) and EV-miRNAs from the respective tissue surfaces were analyzed. Additionally, tissue miRNAs and EV-miRNAs from three normal mammary samples from corresponding patients were also collected. Furthermore, four intracystic fluids (two cases of DCIS, one case of IDC, and one case of IDP) were also analyzed. In total, 39 samples were included in the analysis.

first: Yuri

last: Ozaki

first: Akira

last: Yokoi


title: Cartography of emergency myelopoiesis identifies conserved molecular activation modules

city: New York

first: James

last: Swann

state: NY

address: 650 W 168th Street

institute: Columbia University

summary: Hematopoietic stem and progenitor cells (HSPC) respond to infections, inflammation, and regenerative challenges using cellular and molecular mechanisms termed emergency myelopoiesis (EM) pathways. However, it remains unclear whether all parts of the hematopoietic hierarchy are similarly activated by different EM inducers. Here, we generate a generalizable and comprehensive cell annotation method together with a refined quantitative model of hematopoietic differentiation using single cell RNA sequencing (scRNA-seq) of HSPCs, which we apply to a broad range of EM contexts. We uncover multiple strategies to enhance myelopoiesis acting at different levels of the HSPC hierarchy, which are also associated with both unique and shared transcriptional response modules. In particular, we identify a myeloid progenitor-based signature associated with EM pathway engagement across multiple inflammatory challenges, which predicts outcome in both pediatric and adult human acute myeloid leukemia. Collectively, our work illuminates fundamental regulatory mechanisms in hematopoietic regeneration and identifies a common EM signature that informs outcome in disease contexts.

overall_design: Mice were treated with agents to stimuate emergency myelopoiesis (5-fluorouracil, interleukin-1 beta, polyinsolinic:polycytidylic acid) before bone marrow was collected. Hematopoietic stem and progenitor cells from the lineage-/cKit+ (LK) or lineage-/cKit+/Sca-1+ (LSK) fractions were isolated and subjected to single cell RNA sequencing.

first: Oakley

middle: C

last: Olson

first: Emmanuelle

last: Passegue


title: BMAL1 and YAP cooperate to hijack enhancers and promote inflammation in the aged epidermis [RNA-seq Aged_adult]

first: Camille

last: Stephan Otto Attolini

overall_design: Bulk RNA-seq profiling of adult (18-25 weeks old) and aged (80-90 weeks old) mouse epidermis at Zeitgeber time 0 (ZT0), ZT4, ZT8, ZT12, ZT16 and ZT20.

first: Camile

first: Guiomar

last: Solanas

first: Júlia

last: Bonjoch


title: Metadomain genome associations in mammalian T cells

city: Princeton

last: Pritykin

state: NJ

address: 245 Carl Icahn Lab

department: QCB

institute: Princeton

summary: We identified megabase-scale and inter-chromosomal interactions, including many cell type-specific meta-TAD associations (meta-domains) containing genes important for T cell function including Ctla4, Ikzf2, Ets1, Lef1, Runx1, Bach2, Foxo1 and others. Reanalysis of published data confirmed the reproducibility of these metadomain interactions in both mouse and human T cells.

overall_design: Hi-C in T-cells from secondary lymphoid organs, either in bulk or separated by activation status


title: The EZH2 and EZH1 inhibitor valemetostat derepresses p16INK4a to induce early endomitotic exit in megakaryocytes [scATAC-Seq]

city: Edogawa-ku

first: Kyungtaek

last: Lim

state: Tokyo

address: 1-16-13, Kitakasai

institute: Daiichi Sankyo Co., Ltd.

summary: Polycomb repressive complex 2 (PRC2) represses transcription by trimethylation of histone H3 at lysine 27. Valemetostat is a potent inhibitor of enhancer of zeste homolog (EZH)2 and EZH1, which are histone methyltransferases of PRC2. PRC2 inhibitors, including valemetostat, have been showing promises in multiple cancer types. PRC2 inhibitors, however, can induce thrombocytopenia as a class adverse effect. To better understand valemetostat-induced thrombocytopenia, we performed single-cell ATAC-seq and bulk RNA-seq for human bone marrow CD34+ cells that were in vitro differentiated into megakaryocytes.

overall_design: Primary human bone marrow CD34+ cells derived from three different donors were cultured StemSpan serum-free expansion medium (STEMCELL Technologies) in the presence of thrombopoietin (TPO), TPO/FLT3 ligand (FL)/SCF, interleukin 3 (IL3L)/ interleukin 6 (IL6), TPO /IL3/IL6, or TPO/FL/SCF/IL3/IL6.

first: Toshihiro

last: Banjo

first: Akiko

last: Toyota

first: Hiroki

last: Goto

first: Daisuke

last: Honma

first: Munetada

last: Haruyama

first: Hitoshi

last: Takizawa

first: Atsushi

last: Okamoto

first: Yoshimasa

last: Ono

first: Shinji

last: Tsutsumi


title: Metadomain genome associations in mammalian T cells (CD4/CD8 data)

first: Yuri

summary: There is a paucity of information regarding 3-dimensional (3D) chromatin interactions and chromosomal organization in different mammalian cell types. For example, the relationships between different topologically associating domains (TADs) and sub-TAD regulatory loops are uncertain due to the lack of appropriate computational tools and high-resolution experimental data. Herein, we developed a computational methodology for studying chromosomal organization across scales and applied it to high-resolution chromosome conformation capture (Hi-C) data using activatory and inhibitory lineages of T lymphocytes as a model. We identified shared and cell type-specific TADs and sub-TAD loops at 5 Kb resolution. Global analysis revealed megabase-scale and inter-chromosomal interactions, including many cell type-specific meta-TAD associations (meta-domains) containing multiple functionally important genes such as Ctla4, Ikzf2, Ets1, Lef1, Runx1, Bach2, Foxo1 and others. Reanalysis of published data confirmed the reproducibility of these metadomain interactions in both mouse and human T cells. Genome-wide metadomain clustering identified several intra-chromosomal and three inter-chromosomal hubs with distinct histone marks, indicating compartment-like structures, with one active hub linked to general gene activation across immune cells and another being highly specific to T cells. Building and analyzing a compendium of new and public epigenomic T cell data enabled identification of ultra-long-range meta-loop interactions underlying metadomains and inference of distinct architectural factors associated with short-range sub-TAD loops and long-range metaloops. Altogether, our study reveals new cell type-specific 3D chromosomal structures across scales in T cells. The computational methodology is broadly applicable to analyses of 3D genome organization across different cell types and experimental systems.

overall_design: Hi-C in CD4 and CD8 T-cells from secondary lymphoid organs


title: CALIPERS: Cell cycle-aware live imaging for phenotyping experiments and regeneration studies

city: Torino

first: Elisa

last: Balmas

address: via Nizza 52

institute: University of Torino

summary: We introduce CALIPERS, a Fluorescence Ubiquitin Cell Cycle Indicator enabling cell cycle-aware phenotyping based on multiplexed live-cell imaging. We validate CALIPERS in three- and four-color reporter lines (HaCaT) and human induced pluripotent stem cells (WTC-11), co-expressing genetically encoded structural and functional fluorescent sensors. To exemplify the broad applications of CALIPERS, we show cell cycle-aware phenotyping in live-cell imaging applications ranging from proliferation and migration to cardiac-specific maturation and drug testing.

overall_design: We used performed scRNAseq on CALIPERS hPSC differentiated to different lineages  and CALIPERS hPSC derived cardiac organoids. We performed a 3' 10X genomics experiment and multiplexed all these samples in one run. Then we amplified the CALIPERS construct from this library to identify the CALIPERS specific gene expression.

first: Moises

last: Di Sante

first: Melissa

last: Pezzotti

first: Julius

last: Zimmermann

first: Alessandro

last: Enrico

first: Joran

last: Deschamps

first: Silvia

last: Becca

last: Reali

last: Bertero

first: Florian

last: Jug

first: Francesco

last: Pasqualini


title: AGED CD8+ T CELLS DRIVE COGNITIVE DECLINE VIA GZMK

city: Stanford

first: Julien

last: Couthouis

state: CA

address: 279 Campus Dr

department: Genetics

institute: Stanford University

summary: Changes in peripheral CD8+ T cells are a prominent hallmark of immune aging. While infiltrating CD8+ T cells are implicated in aging and neurodegenerative disease-related pathology in the brain, the role of aged non-infiltrating CD8+ T cells has yet to be fully defined. Here, we show that targeting activated aged peripheral CD8+ T cells rescues age-related cognitive decline. Using heterochronic parabiosis and single cell transcriptomics analysis we observed that aged peripheral CD8+ T cells maintain properties intrinsic to their age, being refractory to the effects of a young or aged systemic milieu. Systemic exposure of young mice to aged CD8+ T cells elicited synaptic-related aging transcriptional signatures in the hippocampus and impaired cognition. Inhibiting migration of aged peripheral CD8+ T cells to lymph nodes mitigated pro-aging effects on the young hippocampus. Conversely, targeting aged CD8+ T cells restored synaptic-related signatures in the aged hippocampus and ameliorated cognitive impairments. Mechanistically, we identified granzyme k (GZMK) as a secreted age-associated CD8+ T cell-derived factor that impairs cognitive function. Together, our data identify activated aged CD8+ T cells and their secreted factors as potential therapeutic targets to rescue cognition in old age.

overall_design: We sought to investigate the pro-aging potential of aged circulating CD8+ T cells on the young hippocampus. For this, following CD8a depletion to remove resident CD8+ T cells, we performed an adoptive transfer of aged (22 month) CD8+ T cells into young (4 months) animals. Age-matched young animals receiving young CD8+ T cells were included as a young baseline control. To investigate molecular changes elicited in the young hippocampus by aged circulating CD8+ T cells, we performed bulk RNA-sequencing analysis of the hippocampus. Having observed pro-aging effects of aged circulating CD8+ T cells in the young hippocampus, we conversely explored the possibility that targeting CD8+ T cells can rescue cognitive function in aged mice. To selectively target aged peripheral CD8+ T cells late in life, aged (22 months) mice were given intraperitoneal injections of a CD8a depleting antibody or IgG2b isotype control. To investigate molecular changes elicited in the aged hippocampus following depletion of aged peripheral CD8+ T cells, we performed bulk RNA-sequencing analysis.

first: Juliana

last: Sucharov

first: Saul

last: Villeda


title: The EZH2 and EZH1 inhibitor valemetostat derepresses p16INK4a to induce early endomitotic exit in megakaryocytes [RNA-Seq]

first: Kyungtaek

last: Lim

first: Toshihiro

last: Banjo

first: Akiko

last: Toyota

first: Hiroki

last: Goto

first: Daisuke

last: Honma

first: Munetada

last: Haruyama

first: Hitoshi

last: Takizawa

last: Okamoto


title: Transcriptional profiling of murine germinal center (GC) B cells from GC-specific conditional Crebbp R14467H knock-in and Crebbp-knock-out mice

first: Laura

last: Pasqualucci

address: 1130 St Nicholas Avenue

department: Institute for Cancer Genetics

summary: Truncating and missense mutations of the CREBBP gene are highly prevalent in follicular lymphoma (FL) and diffuse large B cell lymphoma (DLBCL), the most common lymphoid malignancies. These mutations are acquired early during tumor evolution and lead to either complete protein loss or single amino acid substitutions in the acetyltransferase (KAT) domain. As a consequence, CREBBP is impaired in its ability to acetylate enhancer histones as well as non-histone proteins implicated in the germinal center (GC) reaction, the structure from which these tumors originate. However, whether truncating and missense mutations of the KAT domain are functionally equivalent remains unexplored. Using a conditional GC-specific knock-in mouse model for the highly frequent Crebbp-R1446H amino-acid change (CrebbpRH), here we show that, compared to complete Crebbp loss, missense mutants impose distinct quantitative and qualitative effects on the GC response. CrebbpRH mutation controls unique transcriptional programs leading to the pre-neoplastic expansion of GCs with abnormal architecture, increased percentage of Tfh cells, and a skewed immune response toward memory B cell differentiation. Expression of CrebbpRH, but not Crebbp loss, was by itself sufficient to initiate malignant transformation in vivo, indicating a stronger tumor-promoting activity. Our findings, together with the differential distribution of missense and truncating mutations in FL and DLBCL, have implications for the mechanisms underlying lymphomagenesis and their therapeutic targeting.

overall_design: Animals were immunized by intraperitoneal injection of sheep-red-blood-cells to induce T-cell dependent responses, and GC B cells (B220+CD95+PNA+) were sorted 12 days post immunization to extract total RNA for next generation sequencing analysis, as described in detail in the associated manuscript.

first: Antony

last: Holmes


title: S100A8/A9 contributes to inflammatory exacerbations in neutrophils and monocytes from PAMI syndrome

city: Yushima, Bunkyo-ku

first: FUMIKO

last: OZAKI

institute: Tokyo medical and dental university

summary: Proline-serine-threonine phosphatase-interacting protein 1 (PSTPIP1)-associated myeloid-related proteinemia inflammatory (PAMI) syndrome is a monogenic autoinflammatory disease characterized by progressive arthritis with neutrophilic infiltration, cytopenia, and high serum S100A8/A9 and zinc. The molecular pathophysiology of PAMI caused by particular variants of the PSTPIP1 gene, such as PSTPIP1 E250K, is still unknown, and targeted therapy based on the pathogenesis has not been developed. We established an analytical model of neutrophils and monocytes/macrophages using induced pluripotent stem cells harboring the PAMI variant and another PSTPIP1 E250Q variant observed in PSTPIP1-related disorders with milder phenotypes. Using the model cells, we demonstrated increased production of reactive oxygen species, inflammatory cytokines, S100A8/9, increased cell death in the E250K neutrophils, and increased production of cytokines and abnormal phenotype of E250K monocytes/macrophages. With these model cells, we delved into the molecular basis of the hyperinflammation and pronounced S100A8/A9 production. Our data revealed that S100A8/A9 was at the center of hyperinflammation in PAMI syndrome and its deletion can reverse functional and molecular abnormalities in the phagocytes.

overall_design: To investigate the molecular basis of neutrophil and monocyte/macrophage characteristics in PAPA syndrome with the PSTPIP1-E250Q mutation and PAMI syndrome with the PSTPIP1-E250K mutation, and their association with S100A8/A9, QuantSeq 3’ mRNA-seq analysis was performed

first: Fumiko

last: Honda-OZAKI


title: MyD88 Signaling in Trophoblasts is Necessary for Maternal High Fat Diet-Associated Developmental Programming of Obesity

city: College Station

first: Kartik

last: Shankar

email: kartik.shankar@cuanschutz.edu, kartikster@gmail.com, kartik.shankar@usda.gov, kartik.shankar@ag.tamu.edu

address: 498 Olsen Blvd TAMU 2250 TAMU 2250

department: RAFSRU

institute: USDA ARS

summary: Maternal obesity contributes to persistent programming of offspring obesity. A causal role for placental inflammatory mechanisms in developmental programming remains to be established. We examined the role of the toll-like receptor (TLR) pathway in mediating maternal obesity associated programming by trophoblast deletion of the TLR adapter protein, MyD88. Female MyD88fl/fl:Cyp19 Cre+ (MyD88-CKO) at 5 wks of age were provided control (17% fat calories, CON) or high-fat diets (HFD, 45% fat calories) for 12 wk and mated with MyD88fl/fl:Cyp19 Cre-(flox-control) males. Placenta were studied at dpc 17.5. In a subset, offspring were randomized to CON or HFD for 16 weeks. Placental weight and gene expression changes associated with HFD showed MyD88-dependence for pro-inflammatory and lipid metabolism related responses.  Male MyD88 flox offspring from HFD-dams fed postnatal HFD (HH) showed an increase in body weight, liver steatosis and gene expression. These changes were absent in MyD88 CKO HH offspring, demonstrating a causal link between placental MyD88 mediated changes and long-term changes. Overall, these findings provide the first unequivocal evidence that placental changes due to maternal HFD are causally related to offspring obesity risk.

overall_design: RNA was extracted from dpc 17.5 placenta MyD88-CKO dams fed either control or HFD. Biologically distinct pools were created in a genotype and sex-stratified manner (n = 3 per group).

first: Meghan

last: Ruebel


title: Gene expression profile of clinical ESCC tumors, matched normal tissue and lymph node metastatic tissue by RNA-seq analysis

city: 广东省

first: LI

last: ShuJun

address: 广州市番禺区新造镇新造路1号

department: 附属第五医院

institute: 广州医科大学

summary: Transcriptomic analysis of clinical tissue samples is important in the precision medicine research. Therefore, we used RNA sequencing to systematically analyze the differentially expressed genes of 17 ESCC tumor tissues and paired  normal tissue and lymph node metastatic tissue.

overall_design: RNA-seq profiles of clinical ESCC tumor tissues (n=17) and paired normal tissue and lymph node metastatic tissue generated by deep sequencing.

first: Shu-Jun

last: Li

first: Zhuo-Ran

last: Liang

first: Xiao-Mei

last: Yu


title: dCas9-KRAB CRISPRi-mediated transcriptional repression of TERT in H1299 non-small cell lung cancer cells

status: Public on Jun 24 2026

city: Seoul

first: Juyoung

last: Hong

address: 222 Wangsimni-ro, Seongdong-gu

country: South Korea

institute: Hanyang University

summary: Bulk RNA sequencing was performed to assess transcriptome-wide changes associated with dCas9-KRAB mediated CRISPR interference (CRISPRi) of telomerase reverse transcriptase (TERT) in H1299 non-small cell lung cancer cells. H1299 cells were transduced with a lentiviral vector co-expressing dCas9-KRAB and either no guide RNA (non-targeting control) or a TERT-promoter-targeting single-guide RNA, selected with puromycin, and harvested at day 33 after transduction. Differential expression analysis was used to evaluate the specificity of sustained TERT repression.

overall_design: H1299 cells under two conditions (non-targeting control expressing dCas9-KRAB without a cloned guide RNA; TERT-targeting single-guide RNA), two biological replicates per condition, four samples in total. Paired-end sequencing on an Illumina NovaSeq 6000.

first: Seong-Ho

last: Park

first: Minjeong

last: Kim

first: Hyeon-Jong

first: Taegeun

last: Bae

first: Hyomin

middle: K

last: Lee

first: Ji-Yeoun

first: Chul-kee

first: Junho

last: Hur

first: Young-Chan

first: Woochang

last: Hwang


title: Distinct driver genes and the expression of Hedgehog defines morphoeic basal cell carcinoma

city: London

first: Jun

last: Wang

address: Charterhouse Square

country: United Kingdom

institute: Barts Cancer Institute, Queen Mary, London

summary: Morphoeic basal cell carcinoma (mBCC) has a high risk of local recurrence compared to the more indolent nodular subtype. Little is known about the genetic and molecular makeup of mBCC that determines its invasive behaviour; this study represents the first comprehensive analysis of mBCC within the periocular region. A specific set of driver genes were found in mBCC including FLNB and HECTD4 leading to a loss of function. NodBCC had a different set of driver genes including TP53, FADS1 and PPM1D. BCC located within the face confers a higher risk especially within the H zone, however, this did not confer a higher UV signature or mutational burden. Wnt signalling and natural killer cell cytotoxicity (NK) were two common pathways in nodular and mBCC. NK importance may be greater in mBCC and represents a novel therapeutic target. Aberrant Hedgehog (Hh) pathway signalling was shown to be more critical in mBCC than nodBCC on three molecular levels: mutational burden, transcriptome profile and protein expression. Surrounding mBCC stroma is abnormal, containing mutations in EPHA3, ATR, and GLI3. Hh pathway over-expression is seen in the tumour and stroma of morphoeic tissue, but not nodular, with the stroma potentially contributing to the morphoeic’s aggressive nature and local recurrence risk. These findings have implications for clinical practice by highlighting novel therapeutic targets for mBCC and the potential need to remove surrounding stroma to prevent local recurrence.

overall_design: RNA-seq experiments of tumour-stroma pairs for three patients in each mBCC and nodBCC subtype were performed.

first: John

last: Bladen

first: Edel

last: O’Toole

first: Michael

middle: P

last: Philpott


title: F-actin dynamics couples sphingolipid metabolism to epithelial barrier integrity in chronic colitis

city: Novosibirsk

first: Snezhanna

last: Medvedeva

address: Acad. Lavrentiev Ave. 8/2

country: Russia

institute: Institute of Molecular and Cellular Biology SB RAS

summary: Intestinal barrier dysfunction is a hallmark of gastrointestinal disorders, including inflammatory bowel diseases (IBD). In IBD, the disruption of the gut barrier causes fluid loss and persistent immune response. Understanding the cellular events underlying epithelial barrier disruption during chronic inflammation is essential for targeting increased intestinal permeability. Filamentous actin (F-actin) destabilization accompanied by metabolic dysfunction has previously been reported in the Muc2 knockout colitis model; however, the mechanistic contribution of these defects to chronic intestinal barrier loss remains unclear. Here, we identify impaired cytoskeleton dynamics as a critical driver of intestinal barrier dysfunction in chronic colitis. An imbalance between polymeric and monomeric actin disrupts the epithelial barrier in both a 3D organoid system and in vivo. Actin and associated factors were identified as primary interactors of claudin-3, and this interaction was reduced under chronic inflammatory conditions in vivo. Further analysis revealed ceramide metabolism as a potential metabolic regulator of actin dynamics and barrier integrity during chronic inflammation. Consistently, intestinal samples from IBD patients showed concurrent disruption of tight and adherens junctions and reduced F-actin levels. Together, these findings reveal F-actin dynamics as one of the key mechanisms of barrier dysfunction in IBD and highlight ceramide metabolism as a potential therapeutic target in IBD.

overall_design: RNA-seq profiling of the descending colons of wild-type C57BL/6 and Muc2 -/- mice (n = 3) of 12 week age.

first: Elena

last: Kozhevnikova


title: RNA-seq of THP1 cells with SRSF10 knockdown

city: Nanchang

first: Fangmin

last: Zhong

address: the NO.1 Minde Road, Donghu District, Nanchang, Jiangxi, China

institute: The Second Affiliated Hospital of Nanchang University

summary: To investigate the downstream transcriptional regulatory network of the RNA-binding protein SRSF10 in acute myeloid leukemia (AML), we performed RNA sequencing (RNA-seq) in THP1 cells following SRSF10 knockdown. THP1 cells were transduced with lentivirus expressing shRNA targeting SRSF10 (shSRSF10) or a non-targeting control shRNA (shNC). Knockdown efficiency was confirmed by RT-qPCR and Western blot prior to RNA extraction. Total RNA was isolated from three biological replicates per condition (shNC and shSRSF10), and cDNA libraries were constructed using the NEBNext Ultra RNA Library Prep Kit. Paired-end 150 bp sequencing was performed on an Illumina platform. Raw reads were processed through quality filtering with fastp and aligned to the human reference genome (hg38) using STAR. Gene-level quantification was performed with featureCounts, and differentially expressed genes were identified using edgeR with thresholds of |log2FC| > 1 and adjusted P < 0.05. This dataset enables the identification of SRSF10-regulated genes and provides insights into the role of SRSF10 in AML cell survival.

overall_design: 6 samples total, comprising 3 SRSF10 knockdown samples and 3 control samples