title: Analysing the Noncoding RNAs Involved in Rehabilitation Exercise Ameliorating Acute Myocardial Infarction-induced Cardiac Remodelling

city: Jining

first: xueying

last: Chen

state: Shandong

address: No.89 Guhuai Road

department: Department of Cardiology

institute: Affiliated Hospital of Jining Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: Rehabilitation exercise (RE) can reduce cardiac remodeling and improve cardiac function in patients with acute myocardial infarction (AMI). However, the molecular mechanisms are not fully understood. The noncoding ribonucleic acid (ncRNA)  have been reported to play important roles in various cardiovascular diseases. The specific functions of ncRNAs in the process by which RE improves AMI patients’ cardiac remodeling remain largely unknown. In this study, whole-transcriptome sequencing was performed to investigate the expression patterns of ncRNAs in the myocardium in AMI mice with or without RE. A total of 100 long ncRNAs (lncRNAs), 14 microRNAs (miRNAs), 131 circular RNAs (circRNAs), and 1028 messenger RNAs (mRNAs) were significant. Bioinformatics tools and databases were used to explore potential ncRNA functions and relationships. Our data revealed that the most prominent pathways involved in RE-mediated improvement of cardiac remodeling after AMI are the PI3K-Akt signaling pathway, cytokine−cytokine receptor interaction, chemokine signaling pathway and MAPK signaling pathway. In addition, lncRNA‒miRNA-mRNA and circRNA-miRNA‒mRNA networks of RE-mediated improvement of cardiac remodeling after AMI were constructed. This is the first study to comprehensively identify regulated ncRNAs involved in RE-mediated improvement of cardiac remodeling after AMI and to demonstrate the involvement of different ncRNA expression patterns in the physiological processes by which RE improves cardiac remodeling after AMI pathogenesis by sequence analysis. This information will provide a theoretical foundation and test basis for further research on how RE improves cardiac remodeling after AMI.

overall_design: The present study analyzed RNA expression in AMI mice with or without Rehabilitation exercise by whole-transcriptome sequencing.

first: Xueying

first: Mingrui

first: Yugang

last: Yan

first: Lijun

last: Gan


title: Transcriptomic signatures induced by single versus dual lipoparticle-formulated adjuvants

status: Public on Aug 14 2026

city: Lyon

first: Pierre-Olivier

last: Vidalain

address: 21 Avenue Tony Garnier

country: France

institute: CIRI

type: Expression profiling by high throughput sequencing

summary: Adjuvant delivery using lipid-polymer hybrid nanoparticles (Lipoparticles) represents a promising strategy to modulate immune cell activation. This study investigates whether the combination of two adjuvants encapsulated within Lipoparticles induces distinct transcriptional responses compared with individual adjuvant formulations. Bone marrow-derived macrophages (BMDMs) generated from five independent mice were treated with single or dual adjuvant formulations, and RNA sequencing was performed to characterize genome-wide gene expression changes. Differential gene expression and functional enrichment analyses were conducted to identify biological pathways modulated by these formulations, with a particular focus on immune-related responses.

overall_design: RNA was extracted from five independent biological replicates (five mice) for each culture condition (LP; LP PIC; LP 3M; LP 3M PIC).

first: Valentine

last: Ginet

first: Bernard

last: Verrier


title: Mouse neocortical transcriptome of layer 2/3 cortical projection neurons

city: Baltimore

first: Alex

middle: L.

last: Kolodkin

state: MD

address: 600 N. Wolfe St.

department: Neuroscience

country: USA

institute: Johns Hopkins School of Medicine

summary: Bulk RNA expression is analyzed in layer 2 and layer 3 cortical projection neurons (CPNs) at postnatal day 3 (P3) and P7.

overall_design: Layer 2 and 3 CPNs were labeled with mCherry via timed in utero electroporation. Neurons were isolated from P3 and P7 cortices and FACS-sorted. Neurons micro-dissected from 2 – 3 pups correspond to one biological replicate (n=3 replicates for each condition).

first: Jakub

last: Ziak

middle: L


title: RNA-seq of Ishikawa and KLE cells following CuCl₂ treatment

city: Nantong

first: Li

last: Ji

state: 江苏 / 江苏

address: No. 20 Xisi Street

country: China

institute: Nantong University

summary: We conducted bulk RNA-seq analyses for both Ishikawa and KLE cells, comparing untreated control cells with those treated with CuCl₂ (200 μM).

overall_design: Bulk RNA sequencing was performed in two human endometrial cancer cell lines, Ishikawa and KLE. For each cell line, untreated control cells and cells treated with 200 µM CuCl₂ for 24 h were analyzed using three independent biological replicates per condition, yielding 12 libraries in total. Libraries were sequenced as 150-bp paired-end reads on an Illumina NovaSeq 6000 platform.

first: Ronghui

last: Qiang

first: Yi

last: You

first: Yilang

last: Wang

first: Jun

last: Yu

first: Xiaoqing

last: Yang


title: Single-nucleus and bulk transcriptomic atlas of human visceral adipose tissue across metabolic disease states identifies THBS1 as a fibro-inflammatory driver

city: Seongnam city

first: SungHee

last: Choi

address: Dolmaro 172, Bundang dist

department: Internal Medicine, Division of Endocrinology and Metabolism

country: South Korea

institute: Seoul National University Bundang Hospital

summary: The cellular complexity of adipose tissue plays a critical role in the pathogenesis of metabolic disease; however, mechanisms underlying adipose dysfunction remain poorly understood. Here, we constructed a single-nucleus and bulk transcriptomic atlas of human visceral adipose tissues from an ethnically homogeneous cohort with defined metabolic states: lean with normal glucose tolerance, obesity, and obesity with type 2 diabetes. Single-nucleus RNA sequencing (snRNA-seq) revealed a fibro-inflammatory subpopulation of adipose stem cells and adipocytes characterized by high THBS1 expression, which were enriched in individuals with obesity and obesity with type 2 diabetes compared to lean controls. Through complementary in vitro, ex vivo, and in vivo experiments, we demonstrated that THBS1 promoted adipose fibrosis and inflammation via macrophage-mediated TGFbeta activation, impairing adipogenesis and adipocyte function. Inhibition of THBS1 attenuated fibro-inflammatory features in metabolically dysfunctional adipose tissues. Collectively, this dataset provides a cellular atlas of human visceral adipose tissue across metabolic disease states and identifies THBS1 as a key pathogenic driver and potential therapeutic target.

overall_design: Visceral adipose tissue was obtained from 21 Korean adults undergoing abdominal surgery and stratified into three metabolic groups: lean with normal glucose tolerance (Lean; BMI <23 kg/m2, HbA1c <6.5%; n=8, living kidney donors), obesity (Ob; BMI >=30 kg/m2; n=5) and obesity with type 2 diabetes (Ob-DM; BMI >=30 kg/m2, HbA1c >=6.5%; n=8), the latter two undergoing laparoscopic sleeve gastrectomy.  Two assay types were generated from these donors. (1) Bulk RNA-seq of whole visceral adipose tissue from 20 donors (Lean n=8, Ob n=5, Ob-DM n=7). (2) snRNA-seq of nuclei isolated from snap-frozen visceral adipose tissue, distributed across 11 10x Genomics channels: 4 channels each loaded with a single donor, and 7 channels each loaded with nuclei from 2-3 donors of the same metabolic condition pooled in equal proportions. Pooled channels carried no exogenous labelling; donor identity was resolved after sequencing from natural genetic variation, using Souporcell genotype clustering matched to donor-specific germline sequencing data.  In addition, paired bulk RNA-seq was generated from ex vivo visceral adipose tissue explant cultures of 4 donors with obesity and type 2 diabetes, each cultured for 5 days with an anti-THBS1 monoclonal antibody or left untreated (8 libraries, 4 matched pairs).

first: Jisu

last: Jung

first: Eun Seo

last: Park

first: Na Keum

last: Lee

first: Jung-Jae

first: Uijin

last: Juang

first: Qingzhi

last: Huang

first: Young Suk

first: Hyung Joon

last: Kim

first: Jung-Kwon

first: Tae Jung

last: Oh

first: Jae Myoung

last: Suh

first: Jae Bum

first: Joon Ho

last: Moon

first: Jong Kyoung

first: Sung Hee


title: circRNA Microarray Service for 6 mouse eWAT samples

city: GUANGZHOU

first: ZHU

last: TIANXIN

address: 107 Yanjiang West Road

institute: Sun Yat-sen Memorial Hospital

summary: We have completed the Arraystar Mouse circRNA Array V2 analysis of the 6 samples that you submitted. Total RNA from each sample was quantified using the NanoDrop ND-1000. The sample preparation and microarray hybridization were performed based on the Arraystar’s standard protocols. Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were hybridized onto the Arraystar Mouse circRNA V2 Array (8x15K, Arraystar). After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C

overall_design: A total of 6 samples, three control groups and three experimental (obese) groups

first: YANRUI

last: HUANG

first: TIANXIN

last: ZHU


title: circRNA BRAKE on eWAT after specific knockdown in adipose tissue

summary: Mice homozygous for the circRNA BRAKE conditional allele and the Adipo-Cre transgene were generated. Adipose tissue was collected from 8-week-old animals, and primary adipocyte progenitor cells (APCs) were isolated. Following adipogenic differentiation into mature adipocytes, transcriptomic profiling was performed.

overall_design: Detection of different RNA expression after APCs induced maturation in AKD mice and their littermate control mice.


title: RtmR is a membrane-embedded RRM-family RNA-binding protein

city: Madison

first: Mark

middle: J

last: Mandel

state: WI

address: 1550 Linden Drive

department: Medical Microbiology and Immunology

institute: University of Wisconsin-Madison

summary: The animal symbiont Vibrio fischeri has served as a model organism for molecular processes underlying bacterial group behaviors, including quorum sensing and biofilm development. Here, using a genetic approach to identify negative regulators of biofilm formation in V. fischeri, we identified a membrane-bound RNA-binding protein, RtmR (VF_2432), that acts as an inhibitor of the symbiosis polysaccharide (SYP) biofilm. Membrane localization of the protein seems to be required for protein stability or expression, as truncation of the transmembrane helices led to an inability to detect the protein. The conserved RNP1 and RNP2 motifs in RtmR’s cytoplasmic RNA recognition motif (RRM) domain are required for function, and we demonstrate binding to RNA substrates. Identification of RtmR RNA ligands was conducted with a iiCLIP-seq approach that revealed a large interactome. One transcript identified was that of the biofilm regulatory histidine kinase RscS. We found that RtmR biofilm inhibition depends on RscS activity and that RtmR negatively regulates levels of RscS. Overall, this work characterizes a novel type of bacterial RNA-binding protein.

overall_design: RNA-seq to perform differential expression analysis at early stationary phase (OD600 ~1.8) to compare wild-type to ∆rtmR and  rscS* ArtmR to. rscS* ArtmR rtmR-3XFLAG+ (mutant vs complement in biofilm induced background).

first: Jacob

middle: A

last: Vander Griend

first: Denise

last: Ludvik

first: Hunter

middle: C

last: Nottage

first: Andrew

last: Mehle


title: Methylated eEF1A Selectively Decodes mRNA to Shape Cancer Proteomes

city: Stockholm

first: Krzysztof

middle: Jan

last: Szkop

state: Solna

address: SciLifeLab, Tomtebodavägen 23

department: Department of Oncology and Pathology

country: Sweden

institute: Karolinska Institutet

summary: Differences in mRNA decoding efficiency influence protein synthesis. However, whether the translation elongation machinery harbors an intrinsic mechanism that selectively decodes codons—and how this shapes proteomes in homeostasis and disease—remains unknown. Here we find that METTL13-catalyzed dimethylation of the elongation factor eEF1A at lysine 55 (eEF1AK55me2) enhances decoding of select codons, thereby preferentially increasing synthesis of pro-oncogenic proteins, including KRAS, to promote tumorigenesis and targeted therapy resistance. Proteomic profiling and single-molecule imaging reveal that eEF1AK55me2 increases decoding efficiency, particularly for underrepresented codons with weak wobble-position basepairing. In cancer cells, METTL13 knockdown reduced synthesis of oncogenic proteins encoded by genes enriched in eEF1AK55me2-dependent codons—including KRAS—an effect reversed by synonymous recoding with eEF1AK55me2-independent codons. KRAS recoding also attenuated anti-neoplastic effects of METTL13 depletion. Loss of METTL13 inhibited growth of KRASG12Cinhibitor(sotorasib)-resistant syngeneic and patient-derived lung adenocarcinoma (LUAD) xenografts. Further, METTL13 ablation in relapsed autochthonous KRASG12C-driven LUAD tumors mitigated sotorasib resistance, significantly extending survival in vivo. Finally, in clinical trial patients treated with the KRASG12C-inhibitor adagrasib, inferred METTL13 activity was associated with inferior clinical response. These findings identify an eEF1AK55me2-mediated mRNA decoding mechanism that promotes selective oncogenic protein synthesis and suggest that METTL13 targeting may counteract tumor resistance to KRAS inhibitors.

overall_design: T3M4 cells expressing a non-targeting control sgRNA (sgControl) or an sgRNA targeting METTL13 (sgMETTL13) were subjected to RNA-seq and Ribo-seq.

first: Shuo

last: Liu

first: F

last: Cruz-Navarrete

first: Simone

last: Hausmann

first: Ryan

last: Brady

first: Xiaoyin

last: Lu

first: Rui

last: Dong

first: Julia

last: Vu

first: Natasha

middle: M

last: Flores

first: Sabeen

last: Ikram

first: Emily

last: Zahn

last: Thompson

first: Ben

last: Garcia

first: Ola

last: Larsson

first: Ivan

last: Topisirovic

first: Scott

last: Blanchard

first: Or

last: Gozani

first: Pawel

middle: K

last: Mazur


title: Brain perivascular macrophages regulate endothelial cell function via a cMAF-dependent transcriptional program in mouse and human [RNA-seq BEC]

city: Stanford

last: Belk

state: California

address: 450 Serra Mall

institute: Stanford University

summary: Brain perivascular macrophages maintain brain physiology, yet their transcriptional regulation and functions in health and disease remain unclear. Using single-cell multi-omics and functional experiments, we identify cMAF as a key transcription factor for brain perivascular macrophages. Conditional deletion of cMAF disrupts the phenotype of perivascular macrophages, while sparing microglia. Functionally, cMAF drives IGF1 expression in perivascular macrophages, enabling communication with endothelial cells. Consistently, cMAF deletion in perivascular macrophages causes transcriptional alterations in cerebral arteries affecting vascular functions. Notably, cMAF emerges as the main transcription factor for human perivascular macrophages, suggesting conservation of this transcriptional module. During Alzheimer’s Disease (AD), human perivascular macrophages upregulate cMAF and IGF1 to enhance communications with vascular cells, and this response is abrogated in APOE4 carriers. Lastly, we explore an uncharacterized polymorphism in cMAF providing evidence that this program is protective against AD. Targeting cMAF in perivascular macrophages may offer new therapeutic strategies for cerebrovascular and neurodegenerative diseases.

overall_design: Bulk RNA-seq of primary endothelial cells stimulated with IGF1 and GAS6

last: Brioschi

first: Marco

last: Colonna


title: Brain perivascular macrophages regulate endothelial cell function via a cMAF-dependent transcriptional program in mouse and human [CUT&Run]

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Brain perivascular macrophages maintain brain physiology, yet their transcriptional regulators and functions in health and disease remain unclear. Using single-cell multi-omics and functional experiments, we identify cMAF as a key transcription factor for brain perivascular macrophages. Conditional deletion of cMAF disrupts the phenotype of perivascular macrophages, while sparing microglia. Functionally, cMAF drives IGF1 expression in perivascular macrophages, enabling communication with endothelial cells. Consistently, cMAF deletion in perivascular macrophages causes transcriptional alterations in cerebral arteries affecting vascular functions. Notably, cMAF emerges as the main transcription factor for human perivascular macrophages, suggesting conservation of this transcriptional module. During Alzheimer’s Disease (AD), human perivascular macrophages upregulate cMAF and IGF1 to enhance communications with vascular cells, and this response is abrogated in APOE4 carriers. Lastly, we explore an uncharacterized polymorphism in cMAF providing evidence that this program is protective against AD. Targeting cMAF in perivascular macrophages may offer new therapeutic strategies for cerebrovascular and neurodegenerative diseases.

overall_design: CUT&RUN for cMAF in microglia and BAMs from Bl6 mice


title: Brain perivascular macrophages regulate endothelial cell function via a cMAF-dependent transcriptional program in mouse and human [scRNA-seq APOE4]

overall_design: 10x Genomics single-cell RNA sequencing of brain macrophages sorted from APOE3 and APOE4 knock-in mice.


title: SNAI1 ablation alters integrin-mediated adhesion and endocytic fate

city: Uppsala

first: Mohamad

middle: Moustafa

last: Ali

state: Uppsala län

address: husargatan 3, Biomedical Center

department: IMBIM

institute: Uppsala University

summary: Transcription factor SNAI1 guides plasticity and invasiveness in cancer. Using a complete SNAI1 knockout in mesenchymal, triple-negative breast cancer cells, unbiased genome-wide transcriptomic analysis revealed a marked under-expression of integrin-based adhesion and endocytic components. Utilizing this knockout cell model, complementary breast cancer cell models and functional screening of multiple differentially expressed genes, we found that the pioneering transcription factor FOXA1, whose expression is repressed by SNAI1, associates with several key mediators of the cellular phenotype. FOXA1 represses the small GTPase ARF6 and its exchange factor PSD4, in addition to integrin and matrix metalloprotease genes. Accordingly, SNAI1 knockout cells presented poor adhesion to collagen type I or fibronectin, formed defective invadopodia and focal adhesions with weakened FAK/SRC signaling. SNAI1 knockout cells performed ineffective receptor-mediated internalization, including nanoparticle and extracellular vesicle (EV) uptake, exhibited reduced lysosomal content, lacked multivesicular bodies enriched in intraluminal vesicles and showed decreased EV secretion. Gain-of-function experiments demonstrated that SNAI1 has an impact on the PSD4/ARF6 signaling module, using FOXA1 as an intermediate factor to regulate EV release by tumor cells. We propose that the SNAI1-FOXA1 transcriptional mechanism operates at the level of membrane and vesicular trafficking control, which interlinks cell plasticity, adhesion and invasiveness through the extracellular environment, with the associated process of EV secretion.

overall_design: MDA-MB-231 cells were treated with TGFb1 for 48 hours and collected together with corresponding untreated control samples and subjected to RNA extraction and sequencing.

first: Chrysoula

last: Tsirigoti

first: Aristidis

last: Moustakas

first: Dorival

last: Rodrigues-Junior


title: Single cell RNA sequencing of the small intestine epithelium during Xenopus tropicalis metamorphosis reveals the involvement of epithelial-mesenchymal transition in the development of adult epithelial stem cells

city: Bethesda

first: Caroline

last: Esnault

state: md

address: 9000 Rockville Pike,

institute: NICHD NIH

summary: Intestinal remodeling during thyroid hormone-dependent Xenopus metamorphosis involves degeneration of the larval epithelium through apoptosis and de novo formation of adult stem cells followed by their proliferation and differentiation to establish a multi-fold adult epithelium.  This offers an opportunity to study how adult organ-specific stem cells are formed during vertebrate development. Here, we have carried out single cell RNA-sequencing (scRNA-seq) analyses of the intestinal epithelium at stage 56, a larval stage, and stage 61, a climax stage when larval epithelial cells undergo apoptosis and adult epithelial stem cells are formed and proliferating, and stage 66, the completion of metamorphosis. By distributing cells on a UMAP, where the locations of individual cells on a 2-dimensional plot are dictated by their transcriptomes relative to other cells, we found that most known cell types in the intestinal epithelium, such as goblet and enteroendocrine cells, are colocalized at the two stages, suggesting little changes in the transcriptomes of these cells between the two stages.  On the other hand, the location of the major cell type, the enterocytes, shifts significantly at stage 61.  Importantly, stem cells and a novel cell type, epithelial-mesenchymal transition (EMT) cells, are found almost exclusively at stage 61.  Bioinformatics analyses of the differentially expressed genes (DEGs) between stages 56 and 61 for the enterocytes, EMT cells, and stem cells reveal that many more DEGs are for EMT cells and stem cells compared to the enterocytes. Interestingly, nearly 40% of the DEGs are common between EMT cells and stem cells.  Pathway analyses of these common DEGs suggest that the EMT cells are the precursors of the adult stem cells and are derived from larval epithelial cells, most likely the enterocytes.

overall_design: At three developmental stages during Xenopus tropicalis metamorphosis (stage 56, stage 61, and stage 66), small intestinal epithelium was isolated and analyzed using single-cell RNA sequencing to investigate intestine epithelial remodeling across development.

first: Divine

last: Ayichi

first: Paisley

last: Thomson

first: Yun-Bo

last: Shi

first: Liezhen

last: Fu

first: Ryan

last: Dale


title: Single Nucleus RNA sequencing Identifies PLXNA4 Upregulation in End Stage Arrhythmogenic Right Ventricular Cardiomyopathy

city: Cambridge

first: Mark

last: Chaffin

state: MA

address: 75 Ames Street

department: Cardiovascular Disease Initiative

institute: Broad Institute of MIT and Harvard

summary: Arrhythmogenic right ventricular cardiomyopathy (ARVC) is a rare genetic form of heart disease often caused by mutations in desmosomal proteins. We carried out single-nucleus RNA sequencing (snRNA-seq) on 11 non-failing and 8 ARVC patient right ventricular samples and transcriptionally profiled 139,347 nuclei. We identified over 4,400 differentially expressed protein coding genes between non-failing and ARVC samples across cell types. When compared to dilated, hypertrophic and ischemic cardiomyopathy, we found that end stage ARVC is transcriptionally similar to other forms of end stage heart failure. Despite broad transcriptional similarities, we identified seven cardiomyocyte genes and six fibroblast genes that were uniquely dysregulated in ARVC and validated PLXNA4 as a gene with uniquely increased expression in cardiomyocytes in ARVC compared to other cardiomyopathies. Overexpression of PLXNA4 in hiPSC-derived ventricular cardiomyocytes induced immune response gene expression, suppressed calcium signaling, and altered cardiomyocyte electrophysiology, suggesting PLXNA4 may contribute to these pathways in ARVC.

overall_design: snRNA-seq on the right ventricle from patients with arrhythmogenic right ventricular cardiomyopathy (n = 8) and non-failing controls (n=11). Libraries were prepared using the 10X Genomics platform.

first: Bridget

last: Simonson

first: Patrick

middle: T

last: Ellinor


title: Conditional overexpression of PPARα in intestinal epithelium diminishes GIP enteroendocrine cells and circulating hormone levels

city: Cincinnati

first: Kelli

last: VanDussen

state: OH

address: 3333 Burnet Ave, MLC 2010

institute: Cincinnati Children's Hospital Medical Center

summary: PPARα transcriptional programs have tissue-dependent features, yet there is a lack of genetic research tools to study tissue-specific signaling activation without the addition of a systemic agonist. Our aim was to investigate intestinal epithelial-specific roles of PPARα signaling using a novel transgenic mouse that enables spatial and temporal control of Ppara overexpression. CAG-Ppara,-EGFP mice were bred to Villin-CreERT2 to establish the IEC-Ppara mouse, which was compared to littermate controls 2 weeks after tamoxifen exposure. Transcriptional analysis of intestinal tissue from IEC-Ppara mice showed upregulation of PPARα target genes and functional enrichment for fatty acid catabolic processes. Unexpectedly, the enteroendocrine hormone Gip was among the most downregulated genes. GIP-positive enteroendocrine cell number, GIP circulating hormone, and the incretin response were also reduced in IEC-Ppara mice. These findings reveal PPARα as a regulator of GIP and support a new framework in which PPARα signaling influences glucose homeostasis via a gut hormone axis

overall_design: RNA-seq of ileal tissue from adult mice conditionally overexpressing Ppara in the intestinal epithelium and controls two weeks after tamoxifen administration

first: Jacob

last: Socha


title: Single Nucleus RNA sequencing Identifies PLXNA4 Upregulation in End Stage Arrhythmogenic Right Ventricular Cardiomyopathy [RNA-seq]

overall_design: RNA-sequencing of 4 groups of iPSC-CMs: 1. PLXNA4 Overexpression (n=3), 2. PLXNA4 Overexpression virus control (n=3), 3. PLXNA4 siRNA Knockdown (n=3), 4. PLXNA4 siRNA scramble control (n=3).


title: Methylome profiling of cartilage tumors: a promising new diagnostic tool?

city: Bern

first: Jon

last: Brugger

address: Private Address

country: Switzerland

institute: Private

type: Methylation profiling by genome tiling array

summary: DNA methylation and copy number variation (CNV) profiling has emerged as a promising tool for the classification of bone and soft tissue tumors. We evaluated its utility in cartilage tumors, where distinguishing low-grade from high-grade conventional central chondrosarcoma (CS) as well as atypical cartilaginous tumors (ACT) from enchondromas are frequent diagnostic challenges, particularly on biopsy material. We analyzed 214 chondrogenic tumors, including enchondromas, ACT, conventional central, dedifferentiated, and clear cell chondrosarcomas, and determined their IDH1/2 mutation status. Unsupervised dimensionality reduction of genome-wide DNA methylation patterns revealed four clusters among IDH-mutant tumors (IDH-MUT-1: mostly enchondromas and ACT and some high-grade CS; IDH-MUT-2: predominantly high-grade CS; IDH-MUT-3: largely dedifferentiated CS; IDH-MUT-HN: distinct head and neck group with markedly different methylation pattern) and two clusters among IDH-wildtype tumors (IDH-WT-1 and IDH-WT-2: both primarily high-grade CS, with IDH-WT-2 showing higher tumor grade and more extensive CNVs). Clear cell chondrosarcomas formed a separate cluster (CC). The amount of CNVs, including loss of CDKN2A, increased with tumor grade, reflecting increased genomic instability during chondrosarcoma progression. Supervised classifiers trained separately, both on methylation and CNV data, distinguished low- and high-grade cartilaginous tumors with AUC values of 0.87–0.97 and 85–90% accuracy. Furthermore, we tested whether dedifferentiated chondrosarcoma (DDCS) can be distinguished from metastatic carcinomas and other high-grade sarcomas of bone. Across 246 reference samples, a supervised classifier achieved 97.2% accuracy (AUC 99.8%) and correctly identified 30/32 (93.8%) DDCS. These results indicate that DNA methylation and CNV data analysis provide a valuable tool for distinguishing most low- and high-grade chondrosarcomas, with additional utility also in differentiating DDCS from morphologic mimics.

overall_design: 169 specimens were analyzed using the MethylationEPIC v1.0 and v2.0 BeadChips


title: mTORC1 inhibition upregulates CD20 and enhances anti-CD20 antibody efficacy in B-ALL

city: Łódź

first: Zuzanna

last: Nowicka

address: Mazowiecka 15

department: Department of Biostatistics and Translational Medicine

country: Poland

institute: Medical University of Łódź

summary: B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is characterized by impaired B-cell maturation and poor prognosis in relapsed/refractory (R/R) cases. While CD20-targeted immunotherapies offer clinical benefit, their efficacy is limited by low and heterogeneous CD20 expression on BCP-ALL cells. In this study, we demonstrate that overexpression of wild-type IKZF1, a tumor suppressor frequently mutated in high-risk BCP-ALL, upregulates CD20 and promotes leukemic cell maturation. Using a transcriptional mimicry approach, we identified mTORC1 inhibitors as functional IKZF1 mimetics that induce CD20 expression both in vitro and in vivo. mTORC1 inhibition enhanced the antitumor efficacy of anti-CD20 monoclonal antibodies and promoted B-lineage antigen expression, including CD22, while downregulating immature markers. Mechanistically, CD20 upregulation was mediated via the AKT–FOXO1 axis, with transient AKT phosphorylation being essential for this effect. Importantly, this phenotypic shift was observed in BCP-ALL models with IKZF1 deletions, highlighting the relevance to high-risk disease. Our findings support the use of mTORC1 inhibitors to sensitize BCP-ALL cells to CD20-directed immunotherapies and suggest a broader role for these agents in enhancing antigen stability and preventing immune escape. These results provide a strong rationale for clinical evaluation of mTORC1 inhibitors as adjuncts to immunotherapy in BCP-ALL.

overall_design: RNA-seq profiling of BV-173 cells after 48 hours of incubation with 1 nM rapamycin (RAPA) or vehicle control (DMSO) with 2 biological replicates per condition.

first: Firczuk

last: Małgorzata

first: Nowicka

last: Zuzanna

first: Dabkowska

last: Agnieszka

first: Pastorczak

last: Agata

first: Domka

last: Krzysztof


title: IL1A promotes inflammation while safeguarding epithelial basal cell identity and barrier function

first: Maria

last: Genander

address: Tomtebodavägen 16

department: Department of Cell and Molecular Biology

summary: The ability of barrier epithelia to sense physiological changes and initiate local inflammation is essential, as this process facilitates subsequent progenitor-mediated epithelial repair. Herein, we combine analysis of single-cell transcriptional RNA-sequencing from the human adult esophageal epithelium with spatially resolved characterization of epithelial cell populations. Using NGFR and P73, we define a layer of human basal progenitor cells spanning both papillary and interpapillary epithelial regions. In contrast, cycling basal progenitor cells are enriched within the papillary epithelium and a subset of papillary basal progenitor cells are marked by the differentiation marker YAP, revealing spatially organized human progenitor cell heterogeneity. When challenged, NGFR-positive basal cells outcompete NGFR-negative suprabasal cells in primary organoid-forming capacity and suppress NOTCH signaling to maintain their basal identity. Examining changes in progenitor cell states associated with esophageal regeneration and inflammation, we identify upregulation of IL1A in primary human organoids and find an intraepithelial apical-to-basal IL1A signaling loop active in human eosinophilic esophagitis patients. Mechanistically, IL1A activates downstream NF-kB, inducing epithelial expression of secreted mediators that recruit inflammatory immune cells, thereby amplifying and extending the inflammatory response. Notably, IL1A also expands the basal progenitor cell pool and enhances epithelial barrier integrity. Together, these findings demonstrate how inflammatory signals can be harnessed to promote regeneration of the human esophageal epithelium.

overall_design: RNA-sequencing of human primary NGFR+ or NGFR- epithelial cells, as well as NGFR+ and NGFR- cells isolated from human organoids (+/- IL1A treatment) at day 7.

first: Evelien

last: Eenjes

first: Li

last: Lei


title: Targeting DKC1-mediated pseudouridylation combined with PARPi induces synthetic lethality in HR-proficient tumors [ATAC-seq]

city: Beijing

first: Xiaoyang

last: Liu

address: 5th Yiheyuan road

institute: Peking University

summary: Poly(ADP-ribose) polymerase inhibitors (PARPi) have revolutionized the treatment landscape of BRCA-mutant tumors by exploiting synthetic lethality arising from homologous recombination (HR) deficiency. Yet, a substantial proportion of solid tumors remain HR-proficient and thus less responsive to PARPi, underscoring the need to develop strategies that extend their therapeutic scope. Here, we uncover a previously unrecognized synthetic lethal interaction between PARPi and dyskerin (DKC1), an RNA pseudouridine synthase. By analyzing a publicly available genome-wide CRISPR-Cas9 screen conducted in the presence of niraparib, we identified DKC1 as a top candidate whose loss synergized with PARP inhibition to selectively kill HR-proficient cancer cells. Mechanistically, DKC1 depletion impaired pseudouridylation of chromatin-associated RNAs, particularly promoter-associated RNAs, resulting in reduced chromatin accessibility and compromised recruitment of DNA repair factors, including BRCA1 and RAD21. This chromatin remodeling phenocopies HR deficiency, rendering HR-proficient cells vulnerable to PARPi. Notably, co-targeting DKC1 and PARP elicited potent antitumor effects in vitro and in multiple HR-proficient xenograft models. These findings identify DKC1-mediated pseudouridylation as a critical determinant of chromatin structure and DNA repair fidelity, and extend the conceptual framework of synthetic lethality from genetic HR defects to epigenetic regulation, offering a promising strategy to broaden the clinical utility of PARPi.

overall_design: ATAC-seq profiling of wildtype HeLa cells and their knockdown derivatives (shDKC1) after 48 hours of culture.

last: Gu

first: Zhangxian

last: Zhou


title: Transcriptomic Characterisation of Transitional B Cells Reveals Four Subsets with Perturbed Activation Profiles in Systemic Sclerosis

city: London

first: Claire

last: Beesley

address: Royal Free Hospital

country: United Kingdom

institute: UCL

summary: We have previously shown that patients with systemic sclerosis (SSc) exhibit increased frequencies of autoreactive transitional B cells, including those with anti-topoisomerase I (ATA+) specificity, an autoantibody associated with progressive interstitial lung disease. This suggests that defective transitional B cell tolerance drives autoimmunity in SSc, however, the mechanism underpinning reduced censorship of these early B cells remains undefined. To investigate this, we applied single-cell transcriptomic and B cell receptor (BCR) sequencing to dissect the molecular and repertoire features of transitional B cells isolated from early-stage ATA+ treatment-naive SSc patients. This revealed four distinct transitional B cell clusters: T1, T2, CD27+ and marginal zone precursors (MZP). Novel marker genes were identified within these clusters, including the pro-apoptotic gene HRK which was specifically enriched in the MZP cluster. These findings were validated using a publicly available single-cell dataset. Among these transitional clusters, T1 B cells were significantly expanded in SSc patients, with a two-fold increase compared with matched healthy controls, suggesting elevated bone marrow output or increased exodus of transitional B cells in SSc. Additionally, pro-survival genes such as IL4R, TCL1A and S100A10 were significantly upregulated in SSc, whilst a key negative regulator of PI3K/AKT signalling, FOX01 was significantly reduced. Interferon responsive genes (IFITM1 and IFITM2) were also significantly increased in SSc transitional B cells, consistent with dysregulated interferon signalling in SSc. BCR analysis revealed significantly increased CDR3 hydrophobicity in SSc, notably in the T2 cluster, where a trend towards increased usage of the autoimmunity-associated gene IGHV4-39 was also observed. Furthermore, the κ/λ light chain ratio was elevated in the majority of SSc patients, perhaps implying incomplete receptor editing. Collectively, our findings support divergent transitional B cell development and activation in SSc, with an AKT-driven pathway likely promoting autoreactive transitional B cell survival.

overall_design:
Transitional B cells were sorted from 4 SSc patients and 4 healthy controls and analysed via 5' single cell immune profiling with GEX (gene expression) libraries and VDJ BCR (B cell receptor) libraries. Bulk RNA-sequencing of sorted T1 and T2 transitional B cells was performed in a subset of patients.
NOTE: The processed data files generated from both *L001 and *L002 samples are linked to the corresponding *L001 sample records.


title: Transcriptomic and chromatin accessibility profiling of liver from Midn XTR conditional knockout mice

city: Grand Forks

first: Motoki

last: Takaku

state: ND

address: W221 Biomedical Sciences 1301 N. Columbia Road

institute: University of North Dakota

summary: This study investigates the role of Midnolin (Midn) in regulating hepatic transcriptional and chromatin landscapes in vivo. Midn is a ubiquitin-like domain–containing nuclear protein that mediates ubiquitin-independent proteasomal degradation of transcription factors. Although Midn has been implicated in metabolic regulation and liver disease, its physiological function in normal liver remains poorly understood. To address this, we generated a liver-specific Midn conditional depletion mouse model using an eXpressed–Trapped–Restored (XTR) gene-trap strategy. In this system, Cre recombination converts the XTR allele into a Trapped (Midn-T) state, resulting in disruption of Midn expression and activation of a GFP reporter. Liver tissues from wild-type (WT) and Midn-T mice of both sexes were collected for genomic analysis. Transcriptomic profiling was performed using RNA sequencing (RNA-seq), and chromatin accessibility was assessed using ATAC sequencing (ATAC-seq). Differential gene expression and chromatin accessibility analyses were conducted to identify Midn-dependent regulatory changes in liver tissue. These data provide insight into the role of Midn in hepatic gene regulation and chromatin organization and reveal sex-dependent effects on metabolic gene expression programs.

overall_design:
Liver-specific Midn conditional knockout mice were generated using the XTR (eXpressed–Trapped–Restored) gene-trap system. In this model, Cre-mediated recombination converts the XTR allele to the Trapped (Midn-T) state, leading to loss of Midn expression and induction of GFP. Midn-XTR mice were crossed with Albumin-Cre mice to achieve hepatocyte-specific recombination.
Liver tissues were collected from male and female mice aged 11–14 weeks. For each sex, wild-type (WT) and Midn-T samples were analyzed. Total RNA was isolated from liver tissue and used for RNA-seq library preparation following ribosomal RNA depletion. Libraries were sequenced on an Illumina NovaSeq 6000 platform to generate paired-end 150 bp reads.
For chromatin accessibility analysis, ATAC-seq libraries were prepared from isolated nuclei from frozen liver tissue. Libraries were sequenced on an Illumina NovaSeq 6000 platform to generate paired-end 150 bp reads.
RNA-seq reads were aligned to the Mus musculus reference genome (GRCm39/mm39) using STAR, and gene counts were generated using HTSeq. Differential expression analysis was performed using DESeq2. ATAC-seq reads were aligned to the same reference genome, and peaks were identified using MACS2. Differential accessibility analysis was performed using edgeR.
All samples include biological replicates for each condition (WT and Midn-T) and sex (male and female). These datasets enable comparative analysis of transcriptional and chromatin accessibility changes associated with Midn loss in liver.

first: Lakshmi

middle: S

last: Nissankararao

first: Gayeoun

last: Kim

first: Soo-Mi

last: Kweon

first: Vaisnavii

last: Mohanraj

first: Damien

last: Parrello

first: Walter

last: Tsark

first: Keane

last: Lai


title: Characterization of DNA methylation patterns in early‑stage NSCLC

city: Shanghai

first: Leiqin

address: 320 Yueyang Road

institute: CAS Center for Excellence in Molecular Cell Science (CEMCS)

type: Methylation profiling by high throughput sequencing

summary: Early-stage lung cancer offers a critical window for therapeutic intervention, yet the epigenetic alterations underlying disease initiation remain incompletely defined. DNA methylation is a central regulator of gene expression and a well-recognized contributor to tumorigenesis, but methylation profiling in stage I disease has largely relied on array-based platforms with limited genomic coverage. Here we systematically characterized the DNA methylation landscape of stage I lung cancer at base resolution. We first identified differentially methylated regions (DMRs) distinguishing stage I tumors from adjacent normal lung tissue, and compared these with alterations observed at later stages. We then examined the functional consequences of these DMRs by testing their associations with differential gene expression, thereby linking epigenetic alterations to transcriptional dysregulation in early disease. Finally, we mapped regions of coordinated methylation (co-methylation) and assessed their relationship with cancer-associated gene dysregulation, with the aim of identifying epigenetically regulated gene networks that operate from the earliest detectable stage of tumorigenesis.

overall_design:
To characterize DNA methylation patterns in early-stage lung cancer, we performed whole-genome bisulfite sequencing (WGBS) on primary tumor specimens and adjacent non-malignant lung tissue. The discovery cohort comprised 39 clinical specimens: 26 stage I lung cancers (14 lung adenocarcinomas [LUAD] and 12 lung squamous cell carcinomas [LUSC]) and 13 adjacent normal samples.

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Raw data(FASTQ files) are controlled to protect patient privacy.
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first: Rui

last: Hou

first: Jiantao

last: Shi


title: Targeting DKC1-mediated pseudouridylation combined with PARPi induces synthetic lethality in HR-proficient tumors [RNA-Seq]

overall_design: RNA-seq profiling of wildtype HeLa cells and their knockdown derivatives (shDKC1) after 48 hours of culture.


title: Targeting DKC1-mediated pseudouridylation combined with PARPi induces synthetic lethality in HR-proficient tumors

overall_design: PRAISE-seq profiling of wildtype HeLa cells and their knockdown derivatives (shDKC1) after 48 hours of culture.


title: Enrichment of CD4-CD8- cytotoxic Vδ1/3 T cells in pulmonary tuberculosis disease

city: La Jolla

first: Kendall

last: Kearns

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

summary: Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a leading cause of global morbidity and mortality. Although gamma-delta (γδ) T cells have increasingly been suggested to contribute to the TB immune response, quantitative and qualitative differences in this immune cell compartment between healthy and diseased individuals are not well-characterized. In this study, we used single-cell RNA sequencing to provide a high-resolution characterization of CD4-CD8- γδ T cells in peripheral blood across healthy Mtb-(non-)sensitized and TB disease pre-/post-treatment cohorts. We found an activated and cytotoxic gene signature in γδ T cells of TB disease compared to both healthy cohorts. Strikingly, these differences persisted through one year following TB disease diagnosis.  These transcriptomic differences were largely mediated by an NK-like cytotoxic Vδ1 and Vδ3 subset that was enriched in TB disease. Our findings suggest long-lasting changes in the CD4-CD8- γδ T cell compartment and highlight specific subsets as potentially important in TB.

overall_design:
PBMCs were isolated from 112 samples - 20 IGRA- donors, 20 IGRA+ donors, and 18 donors with TB across 4 timepoints. PBMCs were thawed and prepared to isolate CD4-CD8- T cells via fluorescence-activated cell sorting, which then underwent 10x single-cell RNA sequencing.

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raw data cannot be provided due to patient privacy concerns
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first: Rashmi

last: Tippalagama

first: Ashu

last: Chawla

first: Jason

last: Greenbaum

first: Aruna Dharshan

last: De Silva

first: Wathsala

last: Gunasinghe

first: Judy

last: Perera

first: Hansani

last: Gunasekera

first: Darsha

middle: D

last: Senevirathne

first: Thomas

last: Scriba

first: Julie

middle: G

last: Burel

first: Cecilia

last: Lindestam Arlehamn

first: Bjoern

last: Peters


title: Physiological UPR induction drives gametogenesis through coordination of protein synthesis and ER structure

city: Atherton

first: Constantine

last: Bartolutti

address: 69 Santiago Avenue

summary: Although stress responses, such as the unfolded stress response (UPR), have been extensively studied upon induction by harsh stressors, endogenous functions of these protective pathways remain less well understood. We previously found that the UPR is activated during meiosis in budding yeast, and here we investigate its role. We find that endogenous UPR activation during the meiotic divisions does not lead to a broad transcriptional program as reported for drug-triggered UPR activation and is dispensable for gamete formation. In contrast, we find that the endogenous UPR activation that occurs just prior to meiosis is required for meiotic entry and thus gamete production. Only a small subset of known UPR transcriptional targets are part of this response, and the role of the pre-meiotic UPR can be replaced by increasing ER chaperone levels, reducing bulk translation, or reducing expression of the translocation factor Sec61. Together, these findings indicate that physiological meiosis-associated UPR activation supports normal proteostasis in multiple ways to prepare cells for meiotic entry, including by reducing expression of translation factors. In support of a model that ER function is compromised in pre-meiotic cells lacking the UPR, foci of reticulon proteins are present in these cells and their presence correlates with an inability of cells to enter meiosis. Overall, our study reveals surprising features of a physiological UPR activation event, including that its critical targets are minimal and that they support normal ER structure.

overall_design: We performed ChIP-seq on budding yeast cells growing under a variety of conditions including mitosis, mitosis with external folding inhibition, meiosis, and premeiotic starvation

first: Alena

last: Bishop

first: Gloria

last: Brar


title: Physiological UPR induction drives gametogenesis through coordination of protein synthesis and ER structure [meiosis]

overall_design: We performed mRNA-seq on budding yeast cells progressing through meiosis with or without the presence of exogenously-driven high levels of spliced HAC1 mRNA

first: Kelsey

last: Van Dalfsen


overall_design: We performed mRNA-seq on budding yeast cells growing under a variety of conditions including mitosis, mitosis with external folding inhibition, meiosis, and premeiotic starvation


title: Targeting PPAR-γ Mitigates Fibrosis and Arrhythmia in DSG2-Linked Arrhythmogenic Cardiomyopathy

city: Taoyuan

first: Jang-Hau

last: Lian

address: No. 5, Fuxing Street

country: Taiwan

institute: Chang Gung Memorial Hospital

summary: Background:Arrhythmogenic right ventricular cardiomyopathy (ARVC) is an inherited heart muscle disorder characterized by fibrofatty myocardial replacement and ventricular arrhythmias. While desmosomal gene mutations, including DSG2, are well-established causes, the mechanisms by which specific missense mutations contribute to disease progression remain poorly understood. Methods:We generated a physiologically relevant Dsg2F536C knock-in (KI) mouse model using CRISPR/Cas9 to mimic the human DSG2p.Phe531Cys mutation. Comprehensive phenotyping included histopathology, immunostaining, transcriptomic profiling, in vitro cardiomyocyte and fibroblast assays, in vivo image and ECG analysis, and ex vivo optical mapping. Therapeutic potential was assessed using the PPAR-γ antagonist GW9662. Results:Dsg2F536C/F536C mice developed progressive cardiac hypertrophy, interstitial fibrosis, lipid accumulation, and inducible ventricular arrhythmias following isoproterenol infusion and programmed electrical stimulation. These changes resulted in severe cardiac dysfunction and were associated with reduced survival. Mechanistically, the mutation led to decreased DSG2 expression and nuclear accumulation of β-catenin and PPAR-γ, promoting triacylglycerol biosynthesis, oxidative stress, cardiomyocyte death, and calcium-handling abnormalities. We also identified activation of epicardial epithelial-to-mesenchymal transition (EMT) and paracrine fibroblast activation via IL-6 and PDGF-BB as key contributors to fibrotic remodeling. Optical mapping revealed prolonged and heterogeneous action potential duration and demonstrated both reentrant and focal ectopic mechanisms of ventricular tachycardia. Treatment with GW9662 attenuated lipid accumulation, fibrosis, ROS production, and arrhythmogenic susceptibility. Conclusions:This study establishesdsg2F536C KI mice as a robust genotype-specific ARVC model and uncovers a mechanistic link between desmosomal dysfunction, metabolic remodeling, epicardial EMT, and arrhythmia. Pharmacological inhibition of PPAR-γ mitigated structural and electrophysiological abnormalities, identifying it as a promising therapeutic target. These findings support a precision medicine framework for the treatment of desmosome-related cardiomyopathies.

overall_design: we employed a physiologically relevant dsg2F536C knock-in (KI) mouse model—homologous to the human F531C mutation—to elucidate the contribution of PPAR-γ signaling to ARVC pathogenesis. We further tested whether pharmacologic inhibition of PPAR-γ could attenuate myocardial fibrosis, lipid accumulation, and arrhythmogenic susceptibility

first: Yung-Hsin

last: Yeh

first: Yu-Shien

last: Ko

first: Yi-Hsin

last: Chan

first: Ying-Ju

last: Lai

first: Gwo-Jyh

last: Chang

first: Chi-Jen

first: Lung-An

last: Hsu


overall_design: We performed mRNA-seq on budding yeast cells growing vegetatively with or without the presence of exogenously-driven high levels of spliced HAC1 mRNA


title: Nanostraw Electroporation for Temporal RNA Sampling from Living 2D and 3D Cell Culture Systems - RNA sequencing data

city: Singapore

first: Andy

last: Tay

address: 4 Engineering Drive 3

department: Biomedical Engineering

country: Singapore

institute: National University of Singapore

summary: Traditional gene expression studies extract RNA through destructive cell lysis, restricting analysis to single timepoints and requiring parallel samples. This limits the ability to track transcriptomic changes within the same cell population and poses challenges for experiments with scarce primary samples. To address this, we developed a minimally perturbative, unbiased RNA sampling approach — nano-electroextraction (NEE) — which uses hollow nanostraw membranes with mild electroporation to extract intracellular RNA without compromising cell viability or gene expression.

overall_design: This GEO submission contains RNA-seq datasets from two experimental arms:  Timepoint arm — RNA sequencing of A549 monolayers and spheroids harvested at four different timepoints relative to NEE treatment: before NEE, immediately after NEE, 2 hours after NEE, and 24 hours after NEE. Two biological replicates were collected for each condition, resulting in a total of 16 samples. NEE-derived RNA reproducibility arm — RNA sequencing of NEE-sampled RNA from A549 cells, with 3 technical replicates to assess reproducibility and technical variability in RNA profiles obtained through NEE. For both arms, cultures were grown under matched conditions, and all libraries were prepared using the Smart-Seq2 protocol. Sequencing was performed on an Illumina NovaSeq X platform. In total, the dataset includes 19 samples. Raw paired-end sequencing reads and gene-level count matrices are provided.

first: Ying Jie

last: Quek

first: Arun RK

last: Kumar

first: Giulia

last: Adriani


title: Effect of maternal social isolation rearing (SIR) on adult offspring gene expression in the thalamus

city: Zürich

first: Juliet

last: Richetto

address: Winterthurerstrasse 260

institute: University of Zürich

summary: Antenatal depression affects 10–20 % of pregnancies worldwide and contributes to maternal morbidity, pre-term birth, and long-term neuropsychiatric vulnerability in children. Yet the neural circuits and molecular programs through which maternal mood disturbance shapes offspring brain development are poorly defined. Depression that predates conception and continues through pregnancy confers enduring vulnerability to mood and cognitive disorders in offspring, yet its neuroanatomical and molecular footprints remain elusive. To address this knowledge gap, we employed a model of prenatal depression based on social isolation rearing in female mice that induces a depressive-like phenotype before conception that persists during pregnancy.  Female C57BL/6 N mice were subjected to social-isolation rearing (SIR) from weaning through gestation and lactation. Adult offspring underwent standard anxiety testing and thalamic bulk RNA sequencing. SIR offspring of both sexes exhibited pronounced anxiety in light–dark, open-field, Y-maze and novelty-suppressed-feeding assays. RNA sequencing uncovered extensive, sex-divergent transcriptional re-programming: males were enriched for pathways governing protein synthesis and synaptic organisation, whereas females showed signatures associated with neuronal plasticity and glial development.

overall_design: Bulk thalamic RNA-seq profiling of control and SIR offspring in adulthood (PND90)

first: Monica

last: Iachizzi

first: Urs

last: Meyer

first: Lennart

last: Opitz


title: Brain perivascular macrophages regulate endothelial cell function via a cMAF-dependent transcriptional program in mouse and human [scRNA-seq brain macrophages]

first: Julia

last: Belk

address: 450 Serra Mall

summary: Brain perivascular macrophages maintain brain physiology, yet their transcriptional regulators and functions in health and disease remain unclear. Using single-cell multi-omics and functional experiments, we identify cMAF as a key transcription factor for brain perivascular macrophages. Conditional deletion of cMAF disrupts the phenotype of perivascular macrophages, while sparing microglia. Functionally, cMAF drives IGF1 expression in perivascular macrophages, enabling communication with endothelial cells. Consistently, cMAF deletion in perivascular macrophages causes transcriptional alterations in cerebral arteries affecting vascular functions. Notably, cMAF emerges as the main transcription factor for human perivascular macrophages, suggesting conservation of this transcriptional module. During Alzheimer’s Disease (AD), human perivascular macrophages upregulate cMAF and IGF1 to enhance communications with vascular cells, and this response is abrogated in APOE4 carriers. Lastly, we explore an uncharacterized polymorphism in cMAF providing evidence that the cMAF program is protective against AD. Targeting cMAF in perivascular macrophages may offer new therapeutic strategies for neurodegenerative and cerebrovascular diseases.

overall_design: 10x Genomics single-cell RNA sequencing of brain macrophages sorted from Maf-flox and Maf-flox : Crybb1-Cre mice

first: Simone

last: Brioschi

first: Marco

last: Colonna


title: Brain perivascular macrophages regulate endothelial cell function via a cMAF-dependent transcriptional program in mouse and human [ChIP-Seq]

overall_design: ChIP-seq for cMAF in bone-marrow derived macrophages (BMDMs) from Bl6 mice


title: Brain perivascular macrophages regulate endothelial cell function via a cMAF-dependent transcriptional program in mouse and human [scRNA-seq brain vascular cells]

overall_design: 10x Genomics single-cell RNA sequencing of CD45 negative cells sorted from Maf-flox and Maf-flox : Crybb1-Cre mice


title: Brain perivascular macrophages regulate endothelial cell function via a cMAF-dependent transcriptional program in mouse and human [RNA-seq BMDMs]

overall_design: Bulk RNA-seq of bone-marrow derived macrophages (BMDMs) from Bl6 mice carrying CRISPR/Cas9-mediated deletion of Maf and Mafb.


title: Metabolic reprogramming modulates cardiomyocyte hypertrophy via GLS1 in chronic kidney disease

status: Public on Aug 13 2026

city: Hangzhou

first: Linnan

last: Bai

address: 3 East Qingchun Road

institute: Zhejiang University School of Medicine Sir Run Run Shaw Hospital

summary: Left ventricular hypertrophy (LVH) is critical in chronic kidney disease (CKD), but its mechanisms remain unclear. This study employed multi-omics approaches, including RNA-seq and integrated metabolomics, to characterize metabolic alterations in cardiomyocytes (CM) of CKD mice, revealing enhanced glutaminolysis and impaired oxidative phosphorylation. We identified that glutaminase 1 (GLS1), the rate-limiting enzyme of glutaminolysis, is significantly upregulated and enzymatically activated in CM under CKD conditions. A multi-center cohort study confirmed that serum-induced GLS1 activity was associated with LV hypertrophic remodeling. Cardiomyocyte-specific deletion or pharmacological inhibition of GLS1 attenuated CKD-induced cardiac hypertrophy. Proteomic analysis revealed that multiple circulating proteins in the serum of CKD patients are associated with GLS1 enzymatic activity. Furthermore, phosphate (Pi), a representative uremic toxin, functions as a critical modulator of GLS1 activity and expression, compromising mitochondrial bioenergetics by promoting ammonia production and reducing mitochondrially encoded respiratory chain proteins. These integrated metabolic effects underscore the pivotal role of GLS1 in orchestrating myocardial energy reprogramming, thereby contributing to CKD-induced LVH.

overall_design: CKD was induced using a two-step 5/6 subtotal nephrectomy (STNx) procedure, which was performed as previously described1. Briefly, mice were anaesthetized with intraperitoneal injection of ketamine (100 mg/kg body weight) and xylazine (5 mg/kg body weight), placed on a warming pad and subjected to sterile surgery. During the first operation, the upper and lower poles of the left kidney were surgically removed, leaving approximately one-third of the left kidney. Haemostasis was achieved by gentle compression and packing with absorbable gelatin sponge. Seven days later, the right kidney was completely removed; this second operation was defined as week 0. Sham-operated mice underwent the same anaesthesia, laparotomy and kidney exposure without renal tissue excision. Mice were monitored until recovery from anaesthesia and at least once daily during the immediate postoperative period.

first: Yi

last: Wang

first: Junnan

last: Wu


title: CITE-seq of circulating CD4+ T cells and monocytes from BMT recipients treated with or without Tocilizumab

city: Herston

first: Cameron

middle: Gerard

last: Williams

state: QLD

address: 300 Herston Road

department: Infection and Inflammation

country: Australia

institute: QIMR Berghofer

summary: Allogeneic hematopoietic stem cell transplantation (SCT) is a curative treatment for hematological cancers but outcomes are limited by graft-versus-host disease (GVHD). IL-6R expression and IL-6 signaling are most pronounced in CD4 T cells and monocytesand promote acute GVHD (aGVHD) in preclinical models by inducing Th17 and Th22 differentiation. To understand the effect of IL-6 signaling on T cell responses in humans, we performed CITE-seq on circulating CD14+ monocytes and CD4+ T cells from HSCT recipients in a randomized controlled clinical trial receiving tocilizumab (TCZ) or placebo who did not develop acute GVHD. A third placebo treated group were analyzed prior to their development of aGVHD. IL-6 inhibition promoted Type I IFN-associated transcriptional programs in both CD4+ T cells and CD14+ monocytes relative to those from placebo-treated recipients

overall_design: CITE-seq of circulating CD4+ T cells and monocytes from BMT recipients who (1) developed GvHD, (2) did not develop GvHD, or (3) did not develop GvHD and received IL-6R blockade via Tocilizumab.

first: Hyun Jae

last: Lee

first: Jessica

last: Engel

first: Antiopi

last: Varelias

first: Geoffrey

middle: R

last: Hill

first: Ashraful

last: Haque


title: Imaging and Molecular Mechanisms of Pelvic Floor Electrical Stimulation in Improving Pelvic Floor Muscle Injury in Stress Urinary Incontinence Rats

first: Chen

last: Li

state: Beijing

address: No. 10 North Jiaomen Road

department: School of Rehabilitation

institute: Capital Medical University

summary: Purpose: This study aimed to investigate the imaging characteristics and molecular mechanisms by which pelvic floor electrical stimulation (PFES) improves pelvic floor muscle injury in a rat model of stress urinary incontinence (SUI). Methods: An SUI model was established in female Sprague-Dawley rats via vaginal distension combined with bilateral ovariectomy. One week post-modeling, the stimulation group received intravaginal PFES for 2 weeks. Evaluations included 9.4 T MRI, urodynamic tests, histopathological staining, qPCR, Western blotting, and RNA-seq. Results: PFES significantly elevated ALPP compared with controls, indicating improved urinary continence. MRI demonstrated that PFES attenuated focal hyperintensity, muscle edema, and fiber disorganization in the pubococcygeus muscle. Histological analyses confirmed that PFES restored dense muscle fiber arrangement and collagen distribution, and immunohistochemistry showed upregulated expression of COL1A1, COL3A1, and CD34. RNA-seq revealed that differentially expressed genes were prominently enriched in ECM organization, focal adhesion, ECM-receptor interaction, and the PI3K-Akt pathway. Western blotting verified that PFES increased COL1A1, COL3A1, and VEGFA, while suppressing the atrophy-related ubiquitin ligase FBXO32. Conclusion: PFES effectively repairs pelvic floor muscle structure and function by reducing muscle edema and fiber disruption, upregulating type I and III collagens to promote ECM remodeling, inducing VEGF-mediated angiogenesis, and downregulating FBXO32 to counteract atrophy. These findings elucidate PFES mechanisms and support its clinical application.

overall_design: Twenty-four female Sprague-Dawley rats were randomly divided into three groups with 8 rats per group. The blank group received no intervention. The control group only underwent stress urinary incontinence (SUI) modeling via bilateral ovariectomy combined with vaginal distension: an 8-Fr Foley balloon catheter was inflated with 3 mL normal saline and loaded with a 120 g weight suspended for 4 hours, without any subsequent treatment. One week after modeling, the stimulation group received transvaginal pelvic floor electrical stimulation (PFES) with the following parameters: 50 Hz frequency, 20 mA current, 200 μs pulse width, and monophasic square wave. The stimulation was administered 5 days per week for 30 minutes each day over a 2-week period. Following treatment, four rats were randomly selected from each group for magnetic resonance imaging (MRI) examination. Afterwards, all rats underwent urodynamic testing to detect the abdominal leak point pressure (ALPP). After euthanasia, pubococcygeus muscle tissues were collected for subsequent experiments, including RNA sequencing (RNA-seq), histopathological staining, quantitative real-time polymerase chain reaction (qPCR), and western blotting (WB).


title: RNA-seq analysis of FOXA1 and TRIM28 knockdown in LNCaP prostate cancer cells

city: Nanchang

first: Bin

last: Fu

address: The First Affiliated Hospital of Nanchang University

summary: This study investigates transcriptomic changes following knockdown of FOXA1 or TRIM28 in LNCaP prostate cancer cells. LNCaP cells were transduced/transfected with shRNAs targeting FOXA1 or TRIM28, along with corresponding negative control shRNAs. Total RNA was extracted from biological replicates and subjected to high-throughput RNA sequencing. Differential gene expression analysis was performed to identify genes and pathways affected by FOXA1 or TRIM28 depletion. This dataset provides a resource for studying the transcriptional regulatory roles of FOXA1 and TRIM28 in prostate cancer cells.

overall_design: LNCaP prostate cancer cells were divided into four experimental groups: negative control for FOXA1 knockdown, FOXA1 knockdown, negative control for TRIM28 knockdown, and TRIM28 knockdown. Each group included three biological replicates. Cells were treated with negative control shRNA or shRNAs targeting FOXA1 or TRIM28. Total RNA was collected from each sample and analyzed by RNA sequencing. The resulting transcriptomes were compared between knockdown and corresponding negative control groups to identify genes regulated by FOXA1 or TRIM28.


title: Whole-brain transcriptomic profiling of control, diabetic neuropathic pain, and baclofen-treated mice

city: Dongguan

first: Kaisheng

last: Ye

address: No. 111 Humen Avenue, Humen Town, Dongguan City

institute: Binhaiwan Central Hospital of Dongguan

summary: This study investigated central transcriptional alterations associated with diabetic neuropathic pain and baclofen treatment. Whole-brain RNA sequencing was performed in control mice, untreated diabetic neuropathic pain mice, and baclofen-treated diabetic neuropathic pain mice. The dataset was used to assess GABAergic and inhibitory synaptic signaling, neuroinflammation, glial activation, and treatment-associated transcriptional modulation.

overall_design: Whole-brain RNA sequencing was performed using nine male C57BL/6 mice divided into three experimental groups: normal control, diabetic neuropathic pain, and baclofen-treated diabetic neuropathic pain, with three biological replicates per group. Diabetic neuropathic pain was induced using a high-fat diet and streptozotocin protocol. Mice in the baclofen-treated group received baclofen at 8 mg/kg by intraperitoneal injection once daily for 7 days. Total RNA was extracted from whole-brain tissues, poly(A)-enriched RNA was used for library construction, and non-strand-specific paired-end mRNA sequencing was performed.

first: Qun

first: Haishao

last: Chen

first: Sizhuang

last: Xie

first: Kangyu


title: Epitranscriptomic Profiling Reveals N7-Methylguanosine Modification as a Novel Regulator in Recurrent Spontaneous Abortion

city: fuzhou

first: Jianping

last: Tang

state: fujian

address: No. 18 Daoshan Road, Gulou District

institute: fujian women and child health hospital

summary: Recurrent spontaneous abortion (RSA) is a severe pregnancy disorder with heterogeneous etiologies. Emerging evidence has suggested a functional role of epigenetic modification in RSA development. N7-methylguanosine (m7G) in mRNA is one of the frequently reported epigenetic modifications closely associated with various human diseases. However, the role of m7G modification in the development of RSA remains poorly understood. In this study, we perform multi-omics analyses of decidua from RSA patients and healthy controls (HC), and report for the first time that m7G modification was associated with RSA development. MeRIP-seq verifies that the m7G modification features, such as sequence motifs, distribution regions, and distribution densities, were significantly different between the two groups. Notably, genes with altered m7G modification were mostly enriched in embryonic and systemic morphogenesis and development. Moreover, we found an increased expression of the m7G methyltransferase METTL1 in the RSA decidua. RNA sequencing (RNA-seq) further revealed a vastly changed transcriptome in the RSA decidua. Conjoint analysis of MeRIP-seq and RNA-seq further showed that the methylation levels and expression levels of 48 genes changed simultaneously in the RSA decidua. Furthermore, we identified 7 RSA-related genes such as SOCS3, RASA1, FLT1, and JUNB were downregulated, while GNLY was up-regulated in RSA decidua. More importantly, METTL1 showed high-affinity binding to target mRNAs harboring altered m7G modification, indicating dysregulated RSA-genes may be driven by METTL1-mediated m7G modification. These findings provide novel insight into the functional role of m7G modification in RSA pathogenesis.

overall_design: Decidual tissues were collected from RSA patients and healthy control (HC) individuals at the Fujian Provincial Maternity and Children’s Hospital. The HC individuals were women who had healthy pregnancies and underwent selective pregnancy terminations for non-medical reasons. The exclusion criteria were as follows: a) symptoms of endocrine or metabolic diseases; b) karyotype abnormality; c) viral infectious diseases; and d) uterine or and cervix abnormality. Immediately after collection, the collected tissues were flash-frozen in liquid nitrogen and then stored at -80℃ until analysis. The study was approved by the Institutional Ethics Committee of Fujian Provincial Maternity and Children’s Hospital (NO. 2021KRD09001).

first: Jiangping

first: Shuqiong

last: He

first: Yuhong

last: Guo

first: Hailong

last: Huang

first: Xiaoqing

first: Liangpu

last: Xu

first: Shixin


title: Chronic bacterial infection caused by Staphylococcus aureus does not promote atherosclerotic progression in hyperlipidemic mice

city: Little Rock

first: ryan

last: allen

state: Arkansas

address: 4301 W. Markham St

department: Physiology and Cell Biology

institute: University of Arkansas for Medical Sciences

summary: Atherosclerosis is a disease of mid-to-large arteries characterized by lipid accumulation, chronic inflammation, and pathologic remodeling of the vessel wall. Rupture of atherosclerotic plaques can generate thrombi that occlude blood flow and cause acute myocardial infarction (AMI) and acute ischemic stroke (AIS) that are leading causes of death and disability. Patients that develop severe bacterial infections are at increased risk of AMI and AIS, but the mechanisms underlying this association have not been well-characterized. Previous studies have reported that low-density lipoprotein (LDL) carries bacterial small (s)RNAs that can influence macrophage polarization within plaques, but whether infection alters LDL-associated sRNA or atherosclerotic plaque characteristics to promote AMI/AIS is unclear. Here, we tested whether chronic infection by the Gram-positive pathobiont Staphylococcus aureus was sufficient to alter LDL-associated bacterial sRNA and promote pathogenic changes in atheromatous plaques. Using a mouse model of injury-associated S. aureus osteomyelitis, we report minimal changes in the bacterial sRNA composition of LDL with no obvious changes in pathogen-derived sRNA on LDL of either normolipidemic or hyperlipidemic mice. Unexpectedly, hyperlipidemic mice with chronic osteomyelitis showed a reduction in plaque area within the aortic root relative to sham mice. Although these results do not explain increased risk of AMI/AIS in patients, we observed that hyperlipidemic mice had reduced bacterial burden and reduced bone disease relative to normolipidemic mice infected with S. aureus. Together, these findings highlight unresolved questions regarding the origin of bacterial sRNA associated with LDL and suggests that hyperlipidemia contributes to host protection against invasive S. aureus infection.

overall_design: Mice transduced with AAV-GFP and fed a chow diet or AAV-PCSK9-D377Y and fed a western diet. Fourteen weeks after transduction, mice were anesthetized and received a surgical unicortical defect in the right femur that was inoculated with 1x10^6 CFU of methicillin-resistant S. aureus (MRSA) USA300 (LA. County strain) or PBS (SHAM). Mice were euthanized two weeks after surgery and plasma was collected from blood at harvest. Plasma from each of four groups were fractionated by size-exclusion chromatography to isolate APOB-containing lipoproteins (LDL and TRL). Total RNA was isolated from APOB-containing lipoproteins and small RNA sequencing libraries were constructed using a splint adapter ligation strategy and Illumina primers. Sequencing was performed on a NextSeq2000 Instrument.

first: Anisha

last: Neupane

first: Ryan

last: Allen


title: Brain perivascular macrophages regulate endothelial cell function via a cMAF-dependent transcriptional program in mouse and human [RNA-seq Aorta]

city: Stanford

first: Julia

last: Belk

institute: Stanford University

overall_design: Bulk RNA-seq of primary endothelial cells stimulated with IGF1 and GAS6

first: Simone

last: Brioschi

first: Julia A

first: Marco

last: Colonna


title: The role of the NADPH oxidase complex in the defense against Aspergillus nidulans clinical isolates

city: Ribeirão Preto

first: Matheus

middle: Mertz

last: Ribeiro

state: São Paulo

address: Av. Prof. Dr. Zeferino Vaz - Vila Monte Alegre, Ribeirão Preto - SP, 14040-900

department: Faculty of Pharmaceutical Sciences of Ribeirão Preto

country: Brazil

institute: University of São Paulo

summary: Epidemiological data indicate that Aspergillus nidulans shows a unique association with patients with chronic granulomatous disease (CGD), accounting for the prevalence of fungal infections in this population. The mechanisms underlying this association remain poorly understood. We characterized 24 clinical A. nidulans isolates through genomic sequencing, phenotypic profiling, and host-pathogen interaction studies using wild-type and gp91phox⁻/⁻ (CGD) murine macrophages, complemented by in vivo apocynin-treated murine models. Pangenome analysis revealed a predominantly closed genome (82.2% core) with geographic population structure and strain-specific biosynthetic gene clusters. Phenotypic characterization showed substantial strain-to-strain variability in stress responses, antifungal susceptibility, and cell wall architecture. While CGD macrophages exhibited reduced ROS and increased conidial survival, only a subset of A. nidulans isolates demonstrated virulence comparable to A. fumigatus. Transcriptional profiling identified strain-specific immune modulation, with one isolate exhibiting distinct immune-evasion signatures. Apocynin treatment paradoxically protected against A. fumigatus (70% to 40% lethality) but not A. nidulans, reflecting differential inflammatory responses. Our findings challenge the notion that A. nidulans possesses unique virulence attributes predisposing it to CGD. The epidemiological association likely reflects strain-specific determinants, species misidentification within the A. nidulans complex, and host immune context. Virulence appears to be a distributed property rather than a species-level trait, emphasizing the need for individualized isolate characterization.

overall_design:
RNA sequencing was performed to characterize the transcriptional responses of fungal isolates during interaction with murine macrophages. Three clinical *Aspergillus nidulans* isolates (65_034, 77_054, and 84_25) and one *Aspergillus fumigatus* reference strain (A1160) were cultured under three experimental conditions: DMEM medium alone (control), co-culture with wild-type (WT) murine macrophages, and co-culture with chronic granulomatous disease (CGD; gp91phox−/−) murine macrophages. Each condition was performed in biological triplicate. Following incubation, total RNA was extracted from the fungal cells, sequencing libraries were prepared, and samples were subjected to high-throughput RNA sequencing. The dataset was generated to compare fungal transcriptional responses among *A. nidulans* clinical isolates and *A. fumigatus* under different host immune environments and to identify genes and pathways associated with adaptation to macrophage interaction and NADPH oxidase deficiency.

Raw data were uploaded to SRA under BioProject PRJNA1457744. SRA Accessions are listed in Series supplementary file (SRA_Run_accessions.xlsx, SRR contains raw data for three replicates).

first: Peter

last: Rocha

first: Renan

middle: V

last: Graça-Filho

first: Endrews

last: Delbaje

first: Ana

last: Izquierdo

first: Camila

middle: F

last: Pinzan

first: Larissa

last: Cunha

first: Gustavo

middle: H

last: Goldman


title: Epigenetic repressor TRIM28 coordinates myocardial trabeculation and compaction for cardiac chamber formation [CUT&Tag]

first: Yuze

last: Wang

address: Shanghai Minhang District Dongchuan Road No. 800

institute: Shanghai Jiao Tong University

summary: BACKGROUND: Left ventricular non-compaction (LVNC) is a prevailing subtype of cardiomyopathy manifested with excessive trabeculation and spongy-like ventricular wall. LVNC is associated with severe clinical presentations-including arrhythmias, thromboembolic events and heart failure-yet its etiopathology is heterogenous and remains poorly understood.  METHODS: We generated a cardiomyocyte-specific TRIM28 (Tripartite motif containing 28) knockout mouse (TRIM28nCKO) by crossing TRIM28 flox mouse with NKX2.5-Cre mouse. The LVNC phenotype was assessed by combined histologic assays including H&E and immunofluorescence to calculate the thickness of trabeculae versus compact myocardium. We leveraged the RNA-seq and CUT&Tag epigenomic profiling technology to identify molecular pathway mediated by TRIM28 in the trabecular and compact myocardium of developing hearts. Furthermore, we generated TRIM28 and Hey2 (hes-related family bHLH transcription factor with YRPW motif 2) whole-body single and double heterozygous knockout mice to evaluate their cooperative roles on P21Cip1/Waf1 (Cyclin-Dependent Kinase Inhibitor 1A) repression and myocardial compaction. RESULTS: TRIM28nCKO mouse embryos died before the age of E16.5 and developed a mid-gestational LVNC phenotype manifested by excessive trabeculation and insufficient myocardial compaction. TRIM28nCKO hearts displayed reciprocal proliferative profiles: hyperproliferation in the trabecular myocardium versus hypoproliferation in the compact layer. Mechanically, TRIM28 depletion in the trabecular myocardium promoted the expression of zinc finger transcription factor of EGR1 (Early Growth Response 1) to increase the deposition of subendocardial extracellular matrix (ECM) and induced the trabecular overgrowth. In contrast, TRIM28 in the compact layer cooperated with transcription repressor Hey2 to suppress the expression of cell cycle inhibitor P21Cip1/Waf1 (Cyclin-Dependent Kinase Inhibitor 1A) and ensure the normal compaction, whereas TRIM28 ablation disrupted this mechanism and lead to compact insufficiency by removing the inhibition of p21. These distinct compartment-specific mechanisms collectively drive the defective cardiac chamber morphogenesis underlying left ventricular noncompaction (LVNC) in TRIM28  TRIM28nCKO heats. CONCLUSIONS: Our study identifies TRIM28 and its compartmentalized downstream pathways as the critical epigenetic regulatory axis governing the cardiac chamber development and underlying LVNC pathogenesis.

overall_design: CUT&Tag assays for Trim28, Hey2 and H3K9me3 in mouse embryonic hearts

first: Xing

last: Liu

first: Shasha

last: Zhang

first: Juntao

last: Lin


title: 3D high-grade serous ovarian cancer models reveal unique gene expression and proliferation dynamics

city: Ljubljana

first: Vesna

last: Kokondoska Grgič

address: Brnčičeva ulica 31, Kemomed

department: R&D Kemomed

country: Slovenia

institute: kemomed d.o.o

summary: High-grade serous ovarian cancer (HGSOC) is the most lethal gynaecological malignancy, largely due late diagnosis and tumor heterogeneity. Accurate preclinical modelling of HGSOC biological complexity is essential to improve translational research outcomes and therapeutic development; however, traditional 2D models have limited translational relevance. We therefore compared the morphological, proliferative, and molecular characteristics of four HGSOC cell lines (OVCAR-4, OVSAHO, COV362, and Kuramochi) in 2D versus 3D culture environments. To support systematic interrogation of 3D models, we developed reproducible protocols for 3D spheroid generation and optimized a dissociation method for downstream analysis. We observed significant differences in cellular behaviour, morphology, cell cycle regulation, and gene expression. Kuramochi cells showed upregulated EMT markers WNT11B and VIM, suggesting an increased invasive phenotype, i.e., enhanced epithelial–mesenchymal transition and signalling pathways. In OVSAHO cells, MMP2 was significantly downregulated while VEGFA was upregulated, highlighting alterations in matrix remodelling and angiogenesis, characterizing this cell line as proliferative rather than invasive. COV362 cells showed an initial decrease followed by an increase in KI67 expression. Downregulation of BRCA1 and KI67 indicates reduced cell proliferation in 3D environments. Proliferation kinetics were also altered in 3D environments: Kuramochi and OVCAR-4 adopted a more quiescent phenotype, while COV362 remained more proliferative with significant KI67 overexpression. These proliferation dynamics were confirmed with immunocytochemistry. Alignment of expression data showed that different cell types align with distinct HGSOC subtypes: OVASHO with immunoreactive, OVCAR4 with mesenchymal and differentiated, COV362 with differentiated and proliferative, and Kuramochi with proliferative subtype. The described 3D models can serve as high-throughput platforms for drug testing and functional studies, as well as for studying the complex molecular dynamics of ovarian cancer. Moreover, co-culturing systems can enhance their translational potential for the development of more effective therapeutic strategies.

overall_design: Comparison of the morphological, proliferative, and molecular characteristics of four HGSOC cell lines (OVCAR-4, OVSAHO, COV362, and Kuramochi) cultured under 2D and 3D conditions using optimized spheroid generation and dissociation protocols.

first: Kokondoska Grgič

last: Vesna

first: Pavlič

last: Renata

first: Janev

last: Aleksandar

first: Erdani Kreft

last: Mateja

first: Kološa

last: Katja

first: Černigoj

last: Lana

first: Levatić

last: Jurica

first: Džeroski

last: Sašo

first: Sinreih

last: Maša

first: Lanišnik Rižner

last: Tea

first: Jovčevska

last: Ivana


title: Targeting a novel double-stranded DNA-binding protein of Plasmodium falciparum impairs parasite growth by repressing global gene expression.

city: Pune

first: Devatrisha

last: Purkayastha

state: Maharashtra

address: Dr Homi Bhabha Road, Pashan,

country: India

institute: Indian Institute of Science Education and Research

summary: The intricate life cycle of Plasmodium falciparum necessitates precise control of gene expression throughout its various stages of development. These developmental transitions rely on alternating gene expression, which is finely controlled by transcription factors. Here in , we characterised a novel DNA-binding small protein (PfDBSP) that harbours a nuclear localisation signal and localises to the parasite nucleus during the trophozoite and schizont stages. PfDBSP depicts a strong affinity to double-stranded DNA, and ChIP-Seq analysis of PfDBSP revealed that it binds to 1868 gene elements in the parasite genome, which mainly include genes crucial to parasite survival.

overall_design: ChIP-seq of PfDBSP to identify its genomic targets

first: Akshay

last: Munjal

first: Rawat

last: Neha

first: Parveen

last: Nida

first: Singh

last: Shailja

first: Karmodiya

last: Krishanpal


title: BKV Activates the Interferon-b response in Primary and Immortalized Microvascular Endothelial Cells Late in the Infectious Cycle Resulting in Persistence

city: Pittsburgh

first: Jim

last: Pipas

state: PA

address: 5th and Tennyson

institute: University of Pittsburgh

summary: Our previous studies have shown that the inoculation of primary endothelial cells with BKV results in a long term persistent infection with inoculated cultures surviving up to 60 days while producing low levels of infectious viral progeny. Unlike the permissive renal proximal tubule cells, infected endothelial cells activate innate immunity pathways in response to BKV infection. We hypothesized that the innate immune response limits BKV infection resulting in persistence. In this report we show that activation of innate immune pathways is not triggered by incoming virus particles but rather occurs at a late stage of the infectious cycle, when viral DNA replication, high levels of late viral transcription, and progeny virion assembly are occurring. Single cell transcriptomic data indicate that this response varies across the infected cell population with some cells showing little or no innate immune response while others appear to be highly activated. Bulk RNA-seq experiments show that the addition of interferon-β to endothelial cells results in the upregulation of a subset of known ISGs, as well as many other genes not known to be associated with the interferon response. Finally, we show that the addition of interferon-β blocks BKV infection, so long as it is added prior to or soon after inoculation. These results lead to a model in which BKV infection of endothelial cells results in interferon production and ISG induction that restrict subsequent rounds of infection and lead to a persistent state.

overall_design:
"scRNAseq: Two separate SCT experiments were conducted using VEC from two donors. Cells were either mock-infected or infected with BKV (moi = 5) and cells were harvested at 3dpi. We processed and analyzed between 6,000 and 7,000 cells per sample for both runs. The method for library construction and sequencing were performed as described in in An et al. 2021. ""Single-Cell Transcriptomics Reveals a Heterogeneous Cellular Response to BK Virus Infection"". J Virol 95:e02237-20. https://doi.org/10.1128/JVI.02237-20.

RNAseq: Eight separate RNAseq experiments were conducted using TIME cells. Cells were either mock-infected or infected with BKV as well as either untreated or treated with INFB. Cells were harvested at 16hpi or 72hpi. The RNA extraction and library construction is described in the protocols section."

first: Lindsay

last: Colgan

first: Ping

last: An

first: Paul

last: Cantalupo

first: Wenshan

last: Zheng

first: Abigail

last: Velasquez

first: Alexis

last: Duray

first: Maria

last: Sáenz-Robles

first: David

last: Weitz

first: James


title: Clonal Hematopoiesis Drives Fibrotic Remodeling of the Bone Marrow Microenvironment [dataset 3]

city: Toronto

first: Soheil

last: Jahangiri

state: Ontario

address: 610 University Ave

department: Princess Margaret Cancer Centre

country: Canada

institute: University Health Network

summary: Clonal hematopoiesis of indeterminate potential (CHIP) is associated with systemic inflammation and increased malignant risk, yet how it reshapes the bone marrow (BM) niche remains poorly understood. Using single-cell transcriptomic profiling of freshly isolated BM, we identify fibro-inflammatory remodeling as an early hallmark of CHIP. Beyond the established myeloid-biased inflammatory state, CHIP BM displayed coordinated TNFα activation spanning hematopoietic progenitors, monocytes, and stromal cells. Stromal populations showed early fibrotic remodeling, with mesenchymal and vascular cells upregulating collagen and extracellular matrix gene programs. Fibroblasts were markedly expanded regardless of mutational subtype and acquired cancer-associated fibroblast (CAF)-like transcriptional states. Histological analysis confirmed the presence of pre-fibrotic stromal remodeling in CHIP BM, representing an early and potentially disease-defining pathological change. Spatial transcriptomics further revealed discrete fiber-enriched regions populated by active and CXCL12⁺ fibroblasts, macrophages, and lymphoid cells, establishing fibroblast-immune crosstalk as a defining architectural feature of the CHIP niche. Strikingly, these regions were characterized by significant enrichment of pro-inflammatory pathways, including TGF-β and TNF signaling, identifying them as spatially confined inflammatory hubs within the BM microenvironment. Together, these findings establish fibro-inflammatory BM remodeling as a conserved early consequence of clonal expansion, linking CHIP to prefibrotic stromal changes, immune dysregulation, and a niche architecture that may prime the transition to overt malignancy.

overall_design:
We performed 10X  5' single-cell transcriptomic profiling and V(D)J sequencing on sorted T Cells from patients with and without CHIP

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Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
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first: Aguilar-Navarro

last: Alicia G.

first: Edun

last: Gibran

first: Jahangiri

last: Soheil


title: Clonal Hematopoiesis Drives Fibrotic Remodeling of the Bone Marrow Microenvironment.

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

overall_design: Refer to individual Series


title: Targeting FKBP5 Preserves Mitochondrial Homeostasis through the CaMKKβ/AMPK Pathway to Attenuate Sepsis-Induced Acute Lung Injury

city: jinan

first: yanan

last: li

state: 山东省

address: lixia

department: medicine

institute: Shandong University

summary: Background: Sepsis-induced acute lung injury (ALI) remains a leading cause of mortality in critically ill patients, with endothelial barrier disruption and mitochondrial dysfunction serving as central pathological events. FK506-binding protein 5 (FKBP5) has been implicated in various inflammatory disorders, yet its specific role and underlying mechanism in septic ALI remain elusive.

overall_design: The expression of FKBP5 was examined in GEO datasets, septic patients, and CLP-induced murine models. Endothelial cell-specific FKBP5 knockout mice (FKBP5TekKO) and human pulmonary microvascular endothelial cells (HPMVECs) with FKBP5 knockdown/overexpression were employed to assess mitochondrial function, endothelial barrier integrity, and the underlying molecular mechanisms. RNA sequencing, co-immunoprecipitation, mass spectrometry, and site-directed mutagenesis were utilized to identify the downstream targets of FKBP5.Through RNA sequencing, IP-MS, and co-IP, the downstream target of FKBP5, CaMKKβ, was identified. Point mutations were introduced at the Ser511 site of CaMKKβ to investigate its mitochondrial function and the protective mechanisms of the endothelial barrier.

first: Xinyue

last: Tian

first: Yanan

last: Li


title: Hepatocyte-derived sIL1RAP restrains chronic inflammation under dietary

city: hefei

first: xiezong

last: hu

state: anhui province

address: shushanqu huangshanlu443

institute: university of science and technology of china

summary: Metabolic dysfunction-associated steatohepatitis (MASH) is characterized by hepatic lipid accumulation, injury, inflammation, and fibrosis, but the endogenous hepatocyte-derived secretory signals that restrain hepatic inflammatory responses under dietary stress remain unclear. In this study, bulk RNA sequencing was performed on liver tissues from control mice fed a chow diet, GAN diet-induced MASH mice treated with a control AAV vector, and GAN diet-induced MASH mice treated with hepatocyte-targeted AAV-sIL1RAP. This dataset was designed to characterize GAN diet-induced hepatic transcriptional alterations and to assess whether restoration of hepatocyte-derived soluble interleukin-1 receptor accessory protein (sIL1RAP) attenuates inflammation-associated transcriptional responses. Comparative transcriptomic analysis showed that the GAN diet enhanced inflammatory transcriptional programs, including NF-κB-related signaling, whereas hepatocyte-specific restoration of sIL1RAP mitigated these changes. These data support a role for hepatocyte-derived sIL1RAP in limiting diet-induced hepatic inflammatory responses.

overall_design: This study included nine mouse liver tissue samples divided into three experimental groups, with three independent biological replicates per group. Each sample was obtained from one individual mouse. The three groups were: chow diet-fed controls, GAN diet-induced MASH mice treated with a control AAV vector, and GAN diet-induced MASH mice treated with AAV-sIL1RAP. Liver tissues were collected from each group, and total RNA was extracted. Poly(A)-enriched bulk mRNA-seq libraries were then prepared and sequenced on the DNBSEQ-T7 platform using paired-end 150 bp sequencing. Comparison between the chow control group and the GAN-AAV-Vector group was used to identify GAN diet-induced hepatic transcriptional alterations, whereas comparison between the GAN-AAV-Vector and GAN-AAV-sIL1RAP groups was used to evaluate the effect of sIL1RAP restoration on inflammation-related hepatic transcriptional programs, with a particular focus on NF-κB-related signaling pathways.

first: Xiezong

last: Hu

first: Shurao

first: Qiujing

last: Jin

first: Qingsong


title: Parallel single-cell host immune pro ling and pathogen genomic characterization in Klebsiella- associated sepsis: a pilot study

city: Rome

first: Claudia

last: Rotondo

address: Via Portuense, 292

country: Italy

institute: National Institute for Infectious Diseases "Lazzaro Spallanzani" IRCCS

summary: This study employed a single-cell RNA sequencing approach using 10x Genomics scRNA-seq to investigate peripheral blood immune responses in sepsis. Peripheral blood mononuclear cells (PBMCs) were collected from adult patients with sepsis associated with Enterobacterales bloodstream infection and from healthy controls. The study was designed to characterize the single-cell immune profile of sepsis and to compare PBMC transcriptional profiles between septic patients and healthy subjects. Processed Cell Ranger raw/unfiltered and filtered feature-barcode matrices are provided for each sample.

overall_design:
PBMCs from two adult patients with sepsis and positive blood cultures for multidrug-resistant Enterobacterales and two healthy controls were isolated from peripheral blood, cryopreserved, thawed, and processed using the 10x Genomics Chromium Next GEM Single Cell 3′ Gene Expression workflow v3.1. One single-cell gene expression library was generated for each sample, for a total of four libraries. Libraries were sequenced on an Illumina NovaSeq 6000 platform and processed with Cell Ranger v9.0.1 using intron-inclusive quantification and the GRCh38-2024-A human reference transcriptome.
Submitters state "Due to privacy concerns regarding public access to human raw sequencing data, the raw data are not included in this GEO submission."

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Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
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first: Alberto

last: Rossi

first: Michele

last: Properzi

first: Giovanni

last: Chillemi

first: Daniele

last: Pietrucci

first: Ludovica

last: Picarone

first: Lucrezia

last: Pierfederici

first: Giulia

last: Capecchi

first: Germana

last: Grassi

first: Laura

last: Loiacono

first: Eleonora

last: Cimini

first: Simona

last: Nanni

first: Carla

last: Fontana

first: Francesco

last: Messina

first: Maria Grazia

last: Bocci