title: Arginine methylation of BAF155 regulates interactions with RNA processing machinery [TT-seq]

first: Jesse

last: Raab

address: Rm 5028 Genetic Medicine Building

institute: UNC Chapel Hill - Raab Lab

summary: Post-translational modifications (PTMs) of chromatin remodelers are abundant but functionally understudied. Here we investigate the role of asymmetric dimethylation of arginine 1064 (BAF155me2a) on the SWI/SNF core subunit BAF155, a mark deposited by CARM1/PRMT4 that has been linked to tumor progression but whose molecular function remains unclear. Using immunoprecipitation–mass spectrometry with a dimethyl-specific antibody, we found that R1064me2 selectively enhances BAF155 interactions with RNA processing factors, including the anti-termination protein SCAF4, splicing factors, and the transcription factor RFX5. CUT&RUN profiling showed that BAF155me2a, SCAF4, and RFX5 co-occupy promoter regions, and reciprocal immunoprecipitations confirmed that the SCAF4–BAF155 interaction depends on R1064 methylation. To test the functional consequences of this modification, we generated cells expressing either wild-type BAF155 or a methylation-deficient BAF155-R1064K mutant. Loss of methylation did not alter chromatin accessibility, BAF155 genomic occupancy, or SCAF4 recruitment. However, nascent transcription measured by TT-seq revealed a coordinated reduction in 5′ sense transcripts and upstream antisense transcripts (PROMPTs) at BAF155-bound promoters, with a quantitatively larger decrease in PROMPTs at SCAF4 co-bound sites. The effect was restricted to the promoter-proximal region and resolved toward the gene end, consistent with a defect in productive elongation downstream of RNA polymerase II recruitment. These data support a model in which BAF155 dimethylation provides a co-transcriptional interface coupling SWI/SNF to RNA processing machinery, and identify regulation of nascent transcription as a non-canonical function of SWI/SNF PTMs.

overall_design: TT_seq on samples from HLF cells where BAF155-WT or BAF155-R1064K was re-expressed in a knockout bakgroun


title: Arginine methylationof BAF155 regualtes interactions with RNA processing machinery [RNA-seq]

status: Public on Jun 03 2026

city: Chapel Hill

state: NC

country: USA

type: Expression profiling by high throughput sequencing

overall_design: RNA-seq on cell lines following re-expression of BAF155 WT or BAF155 R1064K that cannot be methylated.


title: Arginine methylationof BAF155 regualtes interactions with RNA processing machinery [CUT&RUN]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: CUT&RUN on cell lines following re-expression of BAF155 WT or BAF155 R1064K that cannot be methylated.


title: EpiFat Coverage: integrative multiomics analysis and machine learning modelling for heart disease

city: Lausanne

first: Andrei Alexandru

last: Mircea

state: Vaud

address: Place du Vallon 18

department: Cardiology Department

country: Switzerland

institute: Centre Hospitalier Universitaire Vaudois

summary:
Background: Epicardial adipose tissue (EAT) has emerged as a key factor in the pathogenesis of cardiovascular diseases, including arrhythmias, coronary artery disease (CAD), and heart failure (HF). However, the molecular mechanisms linking EAT characteristics to cardiac pathology remain poorly understood.
Objectives: This study aimed to (1) characterize transcriptomic, metabolomic, and lipidomic differences in human hearts across varying levels of epicardial fat coverage (EpiFat Coverage, EFC), and (2) develop machine learning (ML) models to predict cardiovascular risk factors such as CAD, hypertension, and EFC class based on integrated multiomics data.
Methods: Thirty-two human donor hearts were analyzed using RNA sequencing, targeted metabolomics, and lipidomics. Donors were classified by BMI, EFC percentage, CAD status, and hypertension history. Differential expression analyses were performed using DESeq2, limma, and Lipidr, while ML classifiers (SVM, random forest, logistic regression, and LDA) and regressors were used to predict EFC, CAD, and hypertension.
Results: Distinct molecular signatures were identified for CAD, hypertension, and obesity-related EAT. CAD-associated genes included COL1A1, COL3A1, BGN, and SPP1, while hypertensive samples overexpressed PTGDR and BPIFB4. Overweight and obese EAT samples showed downregulated UCP1 expression. Integrating metabolomic and transcriptomic features improved model accuracy, achieving up to 99% ROC AUC for CAD and 88% for hypertension prediction. EFC classifiers reached 97% accuracy in distinguishing overweight from normal EAT coverage.
Conclusions: Integrating multiomics data with ML provides a powerful framework for identifying molecular determinants of EAT-related cardiovascular diseases. The predictive models developed here demonstrate strong potential for precision risk assessment of hypertension, CAD, and EAT burden, paving the way toward personalized cardiac health monitoring.

overall_design:
This was a prospective, non-randomized study, and the investigators were not blinded to the data. Donor hearts were categorized into normal, overweight, and obese groups based on body mass index (BMI). Accordingly, donor hearts from patients with a BMI less than 25 were classified as normal hearts (N=10, male=4, female=6). Similarly, donor hearts from patients with BMIs between 25 and 30 were classified as overweight hearts (N=8, male=4, female=4). Finally, donor hearts with a BMI of 30 or above were classified as obese hearts (N=14, male=6, female = 8). The donor hearts were also classified based on the anterior EAT surface area. ImageJ software was used to calculate the EAT surface area from photographed images, which was estimated as the percentage of the total epicardial area covered by fat. Accordingly, donor hearts with less than 75% EAT coverage were classified as normal hearts (N=11). Donor hearts with EAT coverage between 75% and 85% were classified as overweight hearts (N=9). Finally, donor hearts with EAT coverage exceeding 85% were classified as obese hearts (N=12).  These thresholds were chosen empirically, as the EFC biomarker is introduced for the first time.

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Submitter states that missing raw files are due to file loss.
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first: Stephen

last: Schwenderer

first: Eric

last: Rytkin

first: Tatiana

last: Efimova

first: Zoltan

last: Kutalik

first: Keith

last: Crandall

first: Kedar

last: Aras

first: Igor

last: Efimov


title: Phase I trial of intravenous VCN-01 oncolytic adenovirus and durvalumab in patients with head and neck metastatic squamous cell carcinoma refractory to immunotherapy

city: Madrid

first: Jaime

last: Martinez de Villarreal

state: Madrid

address: Melchor Fernández Almagro, 3

department: Molecular Oncology Programme

country: Spain

institute: CNIO

summary: VCN-01 is a hyaluronidase-expressing oncolytic adenovirus that increases immune checkpoint antibody tumor uptake in mice. VCN-01 was evaluated with durvalumab in recurrent/metastatic head and neck squamous cell carcinoma (R/M HNSCC) patients refractory to anti-PD-(L)1

overall_design: Patients (n=20) received intravenous VCN-01 (3.3E12 viral particles (vp), low dose (LD), or 1.0E13 vp, high dose (HD)), plus durvalumab (1500 mg/q4w) concomitantly (VCN-01 + durvalumab on day 1; Arm I) or sequentially (VCN-01 on day -14 + durvalumab on day 1; Arm II). Six patients were enrolled in Arm I LD, eight in Arm II LD, and six in Arm II HD.

first: Maria

last: Jove

first: Ricard

last: Mesía

first: Francisco X

last: Real

first: Jaime.

last: Martínez de Villarreal


title: Arginine methylationof BAF155 regualtes interactions with RNA processing machinery [ATAC-seq]

overall_design: ATAC-seq on cell lines following re-expression of BAF155 WT or BAF155 R1064K that cannot be methylated.


title: Single-nucleus multiomic profiling of hippocampus and frontal cortex in a C9orf72 knockout mouse model

city: Toronto

first: Paul

middle: M

last: McKeever

state: ON

address: 60 Leonard Ave., 4th floor - 4KD481

department: Tanz CRND

country: Canada

institute: University of Toronto

summary: This project contains single-nucleus multiomic sequencing data generated from hippocampal and frontal cortex tissue collected from wild-type, heterozygous, and C9orf72 knockout mice. Single-nucleus transcriptomic and chromatin accessibility profiles were generated using the 10x Genomics Chromium Single Cell Multiome ATAC + Gene Expression platform to simultaneously measure gene expression and chromatin accessibility within individual nuclei. The dataset was generated to investigate cell type-specific molecular and regulatory alterations associated with reduced or absent C9orf72 function in brain regions relevant to amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Libraries were prepared for paired gene expression and chromatin accessibility assays and sequenced on the Illumina NovaSeq 6000 platform.

overall_design: Hippocampal (n=12) and frontal cortex (n=14) tissue samples were collected from 3-month-old C9orf72 wild-type, heterozygous knockout, and homozygous knockout mice with balanced sex representation across genotypes. Nuclei were isolated from frozen tissue and processed using region-specific nuclei isolation workflows optimized at the time of sample preparation. Single-nucleus multiome libraries were generated using the 10x Genomics Chromium Single Cell Multiome ATAC + Gene Expression platform and sequenced on the Illumina NovaSeq 6000 or X-Plus platforms. Sequencing data were processed using Cell Ranger ARC to generate paired single-nucleus transcriptomic and chromatin accessibility count matrices for downstream multimodal integration and analysis.

first: Paul M.

first: Janice

last: Robertson


title: Genome-wide CRISPR screen identifies AMBRA1 as a potential biomarker of response to platinum-based therapies in oral squamous cell carcinomas [CRISPR Screen]

first: Ana

last: Sastre-Perona

address: Calle Paseo de la Castellana 261, INGEMM, Laboratorio de Epigenética, Hospital Universitario La Paz

institute: idiPAZ

summary: Oral Squamous Cell Carcinomas (OSCC) are among the most frequent and lethal cancers worldwide. Advanced stage tumors are still treated with standard chemotherapy, however, most of the patients develop chemotherapy resistance. To uncover new functional biomarkers of cisplatin response, we performed a synthetic lethality genome wide CRISPR/Cas9 screen in an oral squamous cell carcinoma cell line. This led to the discovery of AMBRA1, as a regulator of cisplatin sensitivity. In all tested OSCC cell lines and oral primary cultures, AMBRA1 knockout cells showed increased sensitivity to cisplatin treatment. Mechanistically, we demonstrated a new function of AMBRA1, where loss of AMBRA1 led to higher S phase, higher expression of genome instability markers, and higher DNA damage in basal conditions, thereby predisposing cancer cells to an increased sensitivity to cisplatin as well as to other platinum drugs. In summary, we uncovered AMBRA1 as a potential biomarker of response to platinum-based therapies in oral squamous cell carcinomas.

overall_design: CRISPR screen. Cells were infected with the library B (lentiCRISPR v2, 1000000048, addgene). Conditions: T0 cells collected before treatment, T7 cells that were cultured for 7 days, and T7 cisplatin treated cells at 50 uM concentration.

first: Lucía

last: Acero-Riaguas


title: Brown Fat-Specific RNA Labeling Reveals A Network of Inter-Organ Communication by Secreted microRNAs

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

type: Non-coding RNA profiling by high throughput sequencing

summary: Extracellular miRNAs are emerging as key regulators of organismal homeostasis. Here, using tissue-specific RNA labeling based on uracil phosphoribosyltransferase (UPRT)-mediated incorporation of 4-thiouracil (4TU) in male mice, we develop a roadmap of miRNA transfer from brown adipose tissue (BAT) to other tissues, where they can act to regulate energy metabolism. We demonstrate that BAT secretes miRNAs in both small extracellular vesicles (sEVs) and associated with plasma proteins, and that miRNAs in both compartments exhibit tissue-selective uptake in liver, muscle, and hypothalamus. Disruption of DICER in BAT leads to a significant depletion of multiple miRNAs in both BAT and distal tissues, including 80-90% decreases in the most abundant miRNAs in muscle. Target analyses, in vitro modeling, and PAR-CLIP analysis in muscle in vivo confirm that these BAT-secreted miRNAs directly interact with target mRNAs and alter mitochondrial function in recipient tissues. These findings provide a framework for understanding the role of BAT-secreted miRNAs in inter-organ communication.

overall_design: To label miRNAs in brown fat, UPRT mice (Tg(CAG-GFP,-Uprt)985Cdoe/J, strain #021469) crossed with UCP1;cre mice (Tg(Ucp1-cre)1Evdr/J, strain #024670) to generate UCP1;UPRT mice. Male (8-12 weeks old) mice were treated with 4TU (50mg/kg intraperitoneally) to 4TU-label BAT-miRNAs. Tissue RNA was extracted for biotinylation of 4TU-containing transcripts, which were then separated by streptavidin-pulldown for analysis by smRNA-seq.

first: Marsel

last: Lino

first: C

middle: R

last: Kahn


title: Genome-wide CRISPR screen identifies AMBRA1 as a potential biomarker of response to platinum-based therapies in oral squamous cell carcinomas [RNA-Seq]

overall_design: Compared control OSC20 cells with AMBRA1 deficiency and cisplatin treatment to identify differential expressed genes.


title: Systemic and Proximal Tubule Specific Knockout of Arhgef11 and Impact on Hypertension and Kidney Injury

city: Jackson

first: Bioinformatics

last: Core

state: MISSISSIPPI

address: 2500 N state street

institute: Molecular and Genomics Core Facility

summary: Hypertension is a progressive condition that predisposes patients to the development of chronic kidney disease (CKD). Previous genetic and animal studies utilizing the Dahl salt-sensitive (SS) rat, a genetic model of progressive hypertension and CKD, identified that Arhgef11 was playing a role in hypertension and CKD in the Dahl SS model. Arhgef11 is a Rho guanine nucleotide exchange factor involved in the regulation of the cytoskeleton, intracellular trafficking, protein-protein interactions, and transcription factor regulation.  Temporal evaluation of SS-WT and SS-Arhgef11-/- rats demonstrated that the loss of Arhgef11 attenuated hypertension and improved renal function. Transcriptome and proteomic studies lead to the hypothesis that dysregulation of these pathways in the kidney, particularly the proximal tubule, may alter sodium handling and ultimately lead to hypertension. Current rat studies confirmed previous work between SS-WT and SS-Arhgef11-/- and investigated early (week 4) transcriptional changes using single nuclei RNA sequencing, present before blood pressure differences are observed. Due to only being able to test systemic loss of Arhgef11 in the rat model, a global knockout (Arhgef11-/-(CMV)), as well as a proximal tubule-specific deletion (Arhgef11-/-(Sglt2)) were studied in the mouse. Studies utilized two models of experimental hypertension: Angiotensin II and deoxycorticosterone acetate (DOCA) + salt. Both models demonstrated a slight protective effect on blood pressure and kidney injury for DOCA experimental models, replicating the rat knockout data. However, the impact of the loss of Arhgef11 was dependent on the type of induced hypertension, with the large effect in the rat model likely explained by the highly permissive genetic background of the Dahl SS model.

overall_design: RNA was isolated from mouse kidney samples using phenol: chloroform extraction and PureLink RNA Mini Kit (Invitrogen) per the manufacturer’s instructions. RNA quantity (Qubit BR RNA Assay Kit; Invitrogen) and quality measures (RIN >8) (QIAxcel Advanced Bioanalyzer; Qiagen) were validated to confirm intact 18S/28S ribosomal RNA. Samples were then prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) per the manufacturer’s instructions and sequenced on the Illumina NextSeq 2000 platform using NextSeq™ 2000 P3 Reagent Kit (200 Cycles) with PE100 sequencing metrics.

first: Wenjie

last: Wu

first: Lavanya

last: Challagundla

first: Andrew

last: Milner

first: Michael

last: Garrett

first: Ashley

middle: C

last: Johnson


title: Narcissus papyraceus - expression quantification from the AmarylOmicBase study

city: Trois-Rivières

first: Karen

middle: Cristine

last: Goncalves dos Santos

address: 3351 boul des Forges

department: Departement de Chimie, Biochimie, Physique et Sciences Forensiques

institute: Université du Québec à Trois-Rivières

summary:
To facilitate new studies in the Amaryllidoideae subfamily, we present AmarylOmicBase, a unified transcriptomic database that integrates assemblies, annotations, and expression profiles from 39 studies, covering 27 species and 4 hybrid cultivars across 13 genera of Amaryllidoideae. The AmarylOmicBase (v2, https://doi.org/10.5281/zenodo.20349158) consists of de novo assemblies generated from published raw data using Trinity or IsoSeq workflows and provides standardized functional annotation and quantitative expression datasets.

Preprint - https://doi.org/10.1101/2025.11.24.690262

overall_design: Compilation of datasets previously published for this species, assembled into a single transcriptome.

first: Natacha

last: Merindol

first: Isabel

last: Desgagné-Penix


title: Narcissus pseudonarcissus - expression quantification from the AmarylOmicBase study

summary:
To facilitate new studies in the Amaryllidoideae subfamily, we present AmarylOmicBase, a unified transcriptomic database that integrates assemblies, annotations, and expression profiles from 39 studies, covering 29 species across 13 genera of Amaryllidoideae. The AmarylOmicBase includes both published and de novo assemblies generated from published raw data using Trinity or IsoSeq workflows and provides standardized functional annotation and quantitative expression datasets.

Preprint - https://doi.org/10.1101/2025.11.24.690262


title: CD36 aggravates ferroptosis in NK cells and dampens their anti-fibrotic activity in the liver

city: Jinzhou

first: wang

last: wenya

address: Sanjeon Songpa-ro

country: China

institute: JZMU

summary: Liver fibrosis is a major global health challenge, and it is an independent risk factor for the development of hepatocellular carcinoma (HCC). Several methods have been explored to improve liver fibrosis progression, but effective preventive and therapeutic strategies remain limited. Natural killer (NK) cells can limit the activation of hepatic stellate cells (HSCs), but they have exhibited impaired antifibrotic properties in liver fibrosis, and the underlying mechanisms are not well understood. In this study, we found that CD36 was markedly upregulated in NK cells from mice with liver fibrosis. The CD36 expression was negatively correlated with activation markers of NK cells. The CD36⁻ NK cells exhibited elevated cytotoxic cytokine production and enhanced antifibrotic activity against HSCs. The adoptive transfer of CD36⁻ NK cells alleviated liver fibrosis progression. Mechanistically, CD36 induced reactive oxygen species (ROS) and lipid peroxidation. These consequently triggered ferroptosis in NK cells. The blockage of CD36 or inhibition of ferroptosis in NK cells effectively restored their antifibrotic properties against HSCs. In summary, our findings demonstrated that the antifibrotic properties of NK cells were regulated by CD36. These results provide evidence that targeting CD36 could restore NK cell function for liver fibrosis immunotherapy.

overall_design: To investigate roles of CD36 in NK cells, we compared RNA-seq ananlysis for expression profile of CD36+NK cells vs CD36- NK cells in liver of fibrosis mice (biological triplicates).


title: Expression quantification from the AmarylOmicBase study (multiple species)

summary:
To facilitate new studies in the Amaryllidoideae subfamily, we present AmarylOmicBase, a unified transcriptomic database that integrates assemblies, annotations, and expression profiles from 39 studies, covering 27 Amaryllidoideae species and 4 hybrid cultivars across 13 genera of Amaryllidoideae. The AmarylOmicBase (v2, https://doi.org/10.5281/zenodo.20349158) includes de novo assemblies generated from published raw data using Trinity or IsoSeq workflows and provides standardized functional annotation (trinotate) and quantitative expression datasets.

Preprint - https://doi.org/10.1101/2025.11.24.690262

relation:
Reanalysis of: GSM3611855
Reanalysis of: GSM3611856
Reanalysis of: GSM3611857
Reanalysis of: GSM3611858
Reanalysis of: GSM3611859
Reanalysis of: GSM3611860
Reanalysis of: GSM3611861
Reanalysis of: GSM3611862

overall_design:
Assembly and annotation of dataset previously published for each species/hybrid cultivar

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The table below lists GEO and non-GEO accessions reused/reanalyzed for this study.
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title: Non-Temperature-Induced Antitumor Effects of Amplitude-Modulated Radiofrequency: Molecular and Functional Synergies with Radiotherapy

city: Berlin

first: Andranik

last: Ivanov

address: Chariteplatz 1

department: Core Unit Bioinformatics

country: Germany

institute: Berlin Institute of Health

summary: Background/Objectives: Amplitude-modulated radiofrequency (AMRF) fields have emerged as promising non-thermal strategies in oncology. While conventional hyper- thermia (HT) relies on thermal stress, the biological impact of AMRF, particularly in combination with radiotherapy (RT), remains insufficiently characterized. Methods: We assessed RF and AMRF, alone or with RT, using phenotypic analyses of proliferation, apop- tosis, and necrosis across four cancer cell lines (HT29, SW620, U343, U138). Transcriptomic profiling with Kyoto Encyclopedia of Genes and Genomes (KEGG), GO:BP and Reactome enrichment was performed in SW620 and U138 cells, selected for their strong phenotypic responses. Results: AMRF generally triggered broader cytotoxic effects than RF or HT, with AMRF+RT exhibiting the strongest necrotic responses. In SW620 cells, AMRF induced extensive transcriptional reprogramming involving immune modulation, extracellular matrix remodeling, and cell cycle regulation, whereas RF alone exhibited narrower and delayed effects. In contrast, U138 cells showed elevated apoptosis and necrosis but limited transcriptional changes, suggesting post-transcriptional or metabolic mechanisms rather than large-scale gene regulation. Conclusions: AMRF and AMRF+RT emerge as promising non-thermal anticancer modalities, expanding the biological impact of RF-based treatments and setting the grounds for further investigation in mechanistic and translational studies.

overall_design: Four cancer cell lines — two colorectal (HT29, SW620) and two glioblastoma (U343, U138) — were treated with radiofrequency (RF) or amplitude-modulated radiofrequency (AMRF) at 13.56 MHz and 42°C for 65 minutes, alone or in combination with 8 Gy gamma-radiation. Water bath controls at 37°C, 42°C, and 44°C, with and without radiation, were included to isolate non-temperature-induced effects from thermal responses. Proliferation, apoptosis, and necrosis were monitored over 96 hours using live-cell imaging. Based on initial phenotypic responses, SW620 and U138 were selected for RNA sequencing at 0 h and 24 h post-treatment, followed by gene set enrichment analysis across KEGG, GO:BP, and Reactome databases.


title: Leucojum aestivum - expression quantification from the AmarylOmicBase study


title: A contamination-adjusted tissue thrombopoietic framework identifies a clinically relevant CAF-myeloid niche in non-small cell lung cancer: a paired transcriptomic and survival study

city: Suzhou

first: Jiaqian

last: Qi

state: Jiangsu

address: No.188 Shizi Road

institute: The First Affiliated Hospital of Soochow University

summary: Platelet-related cancer biology is often studied through circulating markers, but tissue-centered thrombopoietic programs in lung cancer are difficult to distinguish from blood-contamination artifacts. In this study, paired bulk RNA-seq profiles were generated from human non-small cell lung cancer tumor tissues and matched adjacent non-tumor lung tissues. Sample identifiers beginning with C denote tumor tissue libraries, and identifiers beginning with N denote matched adjacent non-tumor tissue libraries; shared numeric suffixes indicate patient pairing. These data were used as the local discovery layer for a contamination-adjusted megakaryopoiesis-platelet tumor axis (MPTA) framework. The analysis combined paired differential expression, explicit contamination-aware score construction, public single-cell and spatial reference analyses, external cohort assessment, and local clinicopathologic and survival evaluation. The deposited sequencing data support the tumor-adjacent transcriptomic comparisons and locked tissue-centered MPTA score construction described in the manuscript.

overall_design: Bulk RNA-seq was performed on paired human non-small cell lung cancer tumor and matched adjacent non-tumor lung tissue specimens. Each library corresponds to one tissue sample. Tumor libraries are labeled with the prefix C, adjacent non-tumor libraries are labeled with the prefix N, and matched tumor-adjacent pairs share the same numeric suffix. This GEO submission batch includes C50/N50 and later sample identifiers available in the local manifest. The study design supports paired tumor-adjacent transcriptomic comparison, contamination-aware construction of the MPTA framework, and downstream integration with public reference datasets and local clinical outcome data.

first: Guocai

last: Mao

first: Jing

last: Li

last: Wang


title: Crinum x powellii - expression quantification from the AmarylOmicBase study


title: Shared and divergent transcriptional programs of oligodendrocyte differentiation across vertebrate species revealed by scRNA-seq analysis

city: Dalseong-gun

first: Tery

last: Yun

state: Daegu

address: 333 Technojungang-daero, Hyeonpung-eup

department: Department of Brain Sciences

country: South Korea

institute: DGIST

summary: Myelination is essential for neural function in the vertebrate central nervous system, yet the molecular details of how the oligodendrocyte differentiation program has evolved remains poorly understood. Here, we performed a cross-species single-cell transcriptomic analysis of oligodendrocyte lineage cells in the spinal cord of five vertebrate species: fugu, mudskipper, chicken, mouse, and human. Pseudotime trajectory analysis revealed a shared OPC to COP to MOL differentiation trajectory across all species. Among stage-specific DEGs, 302 high-shared genes were organized into four co-expression modules, with 46 evolutionary core genes enriched for oligodendrocyte differentiation and Wnt signaling. Notably, 184 amniote-exclusive genes were enriched for synaptic vesicle transport and locomotory behavior, predominantly at the OPC stage, compared with only 18 teleost-exclusive genes, indicating that amniotes have expanded the oligodendrocyte differentiation program at the progenitor stage.

sample_organism:
Gallus gallus
Takifugu obscurus
Periophthalmus magnuspinnatus

overall_design: Single-cell RNA sequencing (10x Genomics Chromium 3' v3) was performed on spinal cord tissue from fugu (Takifugu obscurus), mudskipper (Periophthalmus magnuspinnatus), and chicken (Gallus gallus). Two biological replicates were generated per species. Spinal cord tissue was dissected from juvenile fugu and mudskipper approximately one month post-hatching, and from chicken at embryonic days 10-11 (HH stage 36-37). Dissociated cells were FACS-sorted using propidium iodide exclusion prior to library preparation. Publicly available datasets were used for mouse (GSE Matson et al. 2022) and human (GSE188516).

first: Junhee

last: Park

first: Myungin

last: Baek


title: I-tRF-Asp promotes vascular remodeling in hypoxic pulmonary hypertension via hnRNPU phase separation which affects TCF7L2 alternative splicing.

city: Daqing

first: Hao

last: Yuan

address: 39 Xinyang Rd

institute: Harbin Medical University

summary: BACKGROUND: Pulmonary hypertension (PH) is a fatal disease characterized by pulmonary vascular remodeling, primarily driven by excessive proliferation of pulmonary arterial smooth muscle cells (PASMCs). While non-coding RNAs such as circular RNAs have been implicated in PH, the role of tRNA-derived small RNA (tsRNA) remains poorly understood. Among them, i-tRF-Asp represents a novel tsRNA whose function in hypoxic PH is unknown. This study aims to investigate whether i-tRF-Asp contributes to PASMC proliferation and vascular remodeling in hypoxic PH. METHODS: To elucidate the functional role of i-tRF-Asp, loss-of-function experiments were conducted in vitro using hypoxic mouse PASMCs (mPASMCs), alongside in vivo studies utilizing both SuHx (Sugen5416+hypoxia) induced pulmonary hypertension models in both adult male C57BL/6 mice and Sprague-Dawley rats. These models employed antisense oligonucleotide inhibitor and adeno-associated virus-mediated silencing. The underlying mechanisms were further explored via RNA immunoprecipitation, liquid-liquid phase separation assays, cell proliferation assessment, western blot, alternative splicing profiling and molecular dynamics simulation. RESULTS: Inhibition of i-tRF-Asp ameliorated hypoxia-induced pulmonary vascular remodeling, primarily through suppressing excessive proliferation of mPASMCs. Further analysis indicated that i-tRF-Asp facilitates liquid–liquid phase separation (LLPS) of hnRNPU. This process mediates selective recruitment of Tcf7l2 pre-mRNA and promotes alternative splicing, resulting in a pro-proliferative Tcf7l2 transcript variant that drives mPASMC proliferation. Furthermore, we have identified that the endonuclease ERN1 can upregulate the expression of i-tRF-Asp. CONCLUSION: The endoribonuclease ERN1 upregulates the expression of i-tRF-Asp, which in turn facilitates mPASMC proliferation and pulmonary vascular remodeling. This process is driven by hnRNPU LLPS-dependent alternative splicing of the long Tcf7l2 transcript isoform.

overall_design: To investigate the expression profiles of small RNAs, particularly tRNA-derived small RNAs (tsRNAs), in response to hypoxia, we performed Pandora-seq on primary mouse pulmonary artery smooth muscle cells (mPASMCs). The cells were divided into two groups: a normoxia control group (cultured under standard conditions) and a hypoxia group (treated with 3% O2 for 24 hours). Each group consists of three biological replicates (n=3 per group). By comparing the small RNA transcriptomes between these two groups, we aim to identify hypoxia-responsive tsRNAs involved in mPASMC proliferation and pulmonary vascular remodeling.


title: Transcriptome profiling of induced sputum identified up-regulated TNF-α/NF-κB signaling and down-regulated mitochondrial respiratory chain function in post-infectious Bronchiolitis obliterans

city: Frankfurt am Main

first: Ralf

last: Schubert

address: Theodor-Stern-Kai 7

institute: Goethe University Frankfurt

summary: Post-infectious bronchiolitis obliterans (PiBO) is a chronic lung disease that occurs after severe lower respiratory infections and leads to persistent inflammation and fibrotic changes in the small airways. In the present study, gene expression analysis was used to identify differentially expressed genes (DEGs) in sputum cells derived from PiBO patients compared to healthy controls. Clinical history, lung function parameters, and induced sputum samples were collected from nine patients with PiBO and eight healthy controls. Multiplex immunohistochemistry (mIHC) as well as mRNA sequencing (MACE-Seq) were performed. Evaluation of the biological targets was done by KEGG pathway enrichment analysis. PiBO patients showed significantly reduced lung function parameters, an increased neutrophil count, and an altered macrophage profile in sputum. Transcriptome analysis revealed significant upregulation of the TNFα-dependent NFκB signalling pathway, as well as significant downregulation of the oxidative phosphorylation (OXPHOS). Linear regression analyses and mIHC showed a shift in macrophage polarization that appears to be responsible for the dysregulated gene expression. Notably, expression of these DEGs significantly correlated with FEV₁ lung function. These findings indicate a central role of macrophages in the immunopathology of PiBO and contribute to our understanding of the molecular mechanism involved in the disease process.

overall_design: mRNA Sequencing by MACE-Seq of induced sputum samples from nine patients with PiBO and eight healthy controls.

first: Silvija

last: P. Jerkic

last: Naegele

first: Lucia

last: Gronau

first: Annika

last: Detring

first: Jordis

last: Trischler

first: Katharina

last: Blumchen

first: Björn

last: Rotter

first: Mohammed

last: Alkhatib

first: Margarete

last: Mijatovic

first: Adreas

last: Weigert

first: Andreas

first: Stefan

last: Zielen


title: Expression data from tomato fruit at three ripening stages (MG, Br, B10) in wild type lines (Alsa Craig, AC, and M82) and five tomato carotenoid mutants: apricot (at), yellow flesh (r), tangerine (t), Beta (B), and Delta (Del).

city: rome

first: SARAH

last: FRUSCIANTE

state: Roma

address: via anguillarese 301

department: SSPT (Department for Sustainability)

country: Italy

institute: ENEA -  Italian National Agency for new Technologies, Energy and Sustainable Economic Development

summary:
Carotenoids are essential natural compounds for human nutrition and play key roles in plants as photosynthetic pigments and as precursors of hormones and apocarotenoids. Tomato is a major model for carotenoid metabolism, where genetic variation strongly influences carotenoid composition during fruit ripening. Here we present an extensive biochemical and molecular characterization of five tomato carotenoid mutants—apricot (at), yellow flesh (r), tangerine (t), Delta (Del) and Beta (B)—across three ripening stages (mature green, breaker and red ripe). Gene-expression profiling (Affymetrix microarrays) was integrated with targeted isoprenoid metabolomics (carotenoids, chlorophylls, tocochromanols, quinones and ABA) and correlation-based analyses. Isoprenoid profiles showed strong, stage-dependent remodeling that extended beyond expected substrate/product changes and was accompanied by substantial transcriptional variation, often independent of the position of the mutated step in the pathway. The integrated analysis highlighted regulatory links between transcripts and metabolites and pointed to lycopene cyclization as a central node in isoprenoid network rewiring during ripening, improving our understanding of mechanisms controlling isoprenoid accumulation in tomato fruit.
Carotenoids are key bioactive compounds, and tomato is a major model to study how genetic variation shapes their accumulation during fruit ripening. We profiled five tomato carotenoid mutants (apricot at, yellow flesh r, tangerine t, Delta Del, Beta B) across three ripening stages using Affymetrix gene-expression arrays integrated with targeted isoprenoid metabolomics (carotenoids, chlorophylls, tocochromanols, quinones, ABA) and correlation analyses. The data reveal strong stage-dependent remodeling and highlight lycopene cyclization as a central hub in isoprenoid pathway rewiring during ripening.

overall_design: 63 Total samples were analyzed. We generated for each ripening stage (MG Mature Green, Br Breaker, B10 Breaker+10 days) the following comparisons: at MG>AC_MG; at Br>AC_Br; at FR>AC_FR; r MG>AC_MG; r Br>AC_Br; r FR>AC_FR; t MG>AC_MG; t Br>AC_Br; t FR>AC_FR; B MG>AC_MG; B Br>AC_Br; B FR>AC_FR; Del MG>M82_MG; Del Br>AC_M82; Del FR>M82_FR;

first: Sarah

last: Frusciante

first: Olivia

last: Demurtas

first: Giulia

last: Falcone

first: Giovanni

last: Giuliano


title: RNA Sequencing of the Long-Evans Rat Anterior Cingulate Cortex and Nucleus Accumbens Reveals Sex-Specific Developmental Changes and a Lingering Impact of Prenatal and Adolescent Alcohol Exposure in Females Only II

city: Binghamton

first: Anny

last: Gano

state: NY

address: 4400 Vestal Parkway East

institute: SUNY Binghamton

summary: Prenatal alcohol exposure through maternal drinking and adolescent alcohol intake are the two most common forms of early alcohol consumption, which may produce synergistic impacts on health. Yet, few preclinical studies have used double-hit models to examine how effects manifest across sex and lifespan. In this study, RNA-seq was used to analyze the effects of ethanol on the anterior cingulate cortex (ACC) of adult and adolescent male and female Long-Evans rats (n = 5+ per group, N = 144) that were exposed to ethanol during gestation, adolescence, or both. During prenatal exposure, dams received either ethanol liquid diet (PAE group: 2.2% v/v EtOH on gestational day [G]6-8, 4.5% on G9-10, and 6.7% on G11-20) or control diets (PF pair-fed, FCL free-choice liquid diet). In adolescence, offspring were exposed to alcohol (AAE: 11h of 10% EtOH in tap water, 1h water access, 12h of water deprivation daily from prenatal [P] day 27-41) or given ad libitum water access (VEH). Brains were collected on P42 (adolescence) and P90 (adulthood). Differentially expressed genes (DEGs) were identified via DESeq2, with the resulting p values adjusted using the Benjamini-Hochberg correction (≤ 0.05).

overall_design: Male and female Long Evans rats who received one of three prenatal ethanol conditions (Pair-Fed[PF], Free-Choice Liquid Diet [FCL] or Ethanol [PAE]) followed by one of two adolescent exposure conditions (water control [VEH] or alcohol [AAE]). Brains were collected either 24h after the final adolescent exposure (postnatal [P] day 42), or in adulthood without any challenge (P90). The Anterior Cingulate Cortex (ACC) was processed for all groups and is uploaded as a separate experiment. This submission is the nucleus accumbens (NAcc) for a select set of subgroups: hte PF group was excluded, so only male and female FCL-VEH/PAE-VEH were analyzed for adolescents, and only FCL-VEH/PAE-AAE were analyzed for adults.

first: Gano

last: Anny

first: Marquez-Wilkins

last: Esther M

first: Youngentob

last: Steven L

first: Favero

last: Carlita

first: Deak

last: Terrence


title: Homocysteine drives hippocampal blood-brain barrier disruption and cognitive decline under chronic stress via DNA hypomethylation of Cav1.2 [5mC-Seq]

city: Beijing

first: mao yang

last: Zhou

address: No. 27 Courtyard, Taiping Road, Haidian District, Beijing

institute: Academy of Military Medical Sciences

type: Methylation profiling by high throughput sequencing

summary: Chronic stress is a major risk factor for cognitive decline and blood-brain barrier (BBB) disruption, yet the underlying molecular mechanisms remain elusive. This study aimed to investigate the specific role of the metabolic intermediate homocysteine (Hcy) in chronic stress-induced BBB dysfunction and cognitive impairment. Methods: We utilized a rat model of chronic unpredictable mild stress (CUMS) and administered Vitamin B complex to lower Hcy levels in vivo. Regional Hcy accumulation, BBB permeability, and cognitive behaviors were assessed. In vitro, primary rat brain microvascular endothelial cells (BMECs) were exposed to Hcy to evaluate barrier-forming function, transcriptomic alterations, DNA methylation patterns, Cav1.2 expression, and reactive oxygen species (ROS) production. Results: CUMS selectively induced BBB hyperpermeability and significant Hcy accumulation predominantly within the rat hippocampus, which correlated intimately with cognitive deficits. Lowering Hcy levels via Vitamin B supplementation successfully restored hippocampal BBB integrity and alleviated cognitive impairment. In addition, elevated Hcy severely impaired the barrier function of BMECs. Mechanistically, Hcy reduced global DNA methylation in BMECs and specifically induced targeted DNA hypomethylation at the intro region of Cacna1c. This epigenetic shift caused the transcriptional derepression and overexpression of the Cav1.2 calcium channel. Upregulated Cav1.2 subsequently triggered a robust ROS burst, leading to tight junction degradation. Conclusions: Our findings unveil a novel metabolic-epigenetic axis where Hcy-driven Cacna1c hypomethylation directly disrupts BMEC function to dismantle the hippocampal BBB. Lowering Hcy or targeting this Hcy-Cav1.2 pathway establishes a promising therapeutic strategy for mitigating stress-related neurovascular damage and cognitive disorders.

overall_design: In our experiment, rats in the CUMS group were exposed to one of the following chronic unpredictable mild stressors: restraint for 8 h; food and water deprivation for 24 h; cage tilt at 45° for 24 h; wet bedding for 24 h; forced swimming in 4°C water for 3 min followed by towel drying; or continuous illumination for 24 h. These stressors were administered randomly each day over an 8-week period. To prevent habituation to any single stimulus, the same stressor was not applied on consecutive days. Non-stressed animals remained undisturbed in their home cages, except during routine cage cleaning procedures.Control and CUMS rats were dissected to isolate hippocampal tissues. The tissues were subjected to single-cell dissociation to generate a viable single-cell suspension. Brain endothelial cells were then isolated from the suspension using fluorescence-activated cell sorting (FACS) to obtain a purified cell population. Detailed procedures for single-cell dissociation and flow cytometry sorting are described in the protocols section.

first: Maoyang

first: Zhaoxin

last: Sun

first: Jinshan

last: Li

first: Fang

last: Xie

first: Xue

last: Wang

first: Zhaowei

first: Lingjia

last: Qian


title: RNA Sequencing of the Long-Evans Rat Anterior Cingulate Cortex and Nucleus Accumbens Reveals Sex-Specific Developmental Changes and a Lingering Impact of Prenatal and Adolescent Alcohol Exposure in Females Only I

summary: Prenatal alcohol exposure through maternal drinking and adolescent alcohol intake are the two most common forms of early alcohol consumption, which may produce synergistic impacts on health. Yet, few preclinical studies have used double-hit models to examine how effects manifest across sex and lifespan. In this study, RNA-seq was used to analyze the effects of ethanol on the anterior cingulate cortex (ACC) of adult and adolescent male and female Long-Evans rats (n = 5+ per group, N = 144) that were exposed to ethanol during gestation, adolescence, or both. During prenatal exposure, dams received either ethanol liquid diet (PAE group: 2.2% v/v EtOH on gestational day [G]6-8, 4.5% on G9-10, and 6.7% on G11-20) or control diets (PF pair-fed, FCL free-choice liquid diet). In adolescence, offspring were exposed to alcohol (AAE: 11h of 10% EtOH in tap water, 1h water access, 12h of water deprivation daily from prenatal [P] day 27-41) or given ad libitum water access (VEH). Brains were collected on P42 (adolescence) and P90 (adulthood). Differentially expressed genes (DEGs) were identified via DESeq2, with the resulting p values adjusted using the Benjamini-Hochberg correction (≤ 0.05). Surprisingly, there were minimal effects of any ethanol on males in adolescence, and none enduring in adulthood. In contrast, adult females with a double-hit history showed the most robust change: 4 genes were found to be downregulated (C3, Syt6, Spetex2l2, and Akap12) and 19 upregulated. These genes did not align to a specific pathway, yet more than one (i.e. C3, Akap12) were associated with immune function (e.g. complement system, glial function). It is interesting to note that these changes represent enduring alterations to baseline ACC state 48 days after the last ethanol exposure without a subsequent challenge. When examining ethanol-naïve controls, we found that between P42 and P90, both sexes were undergoing significant change. 451 DEGs were identified for males and 95 for females, yet only 36 DEGs overlapped between the sexes, demonstrating that even in the period of late adolescence (P42 onward), males and females were on different trajectories of development. Together, these findings form a foundation for examining sex-specific ACC development and female-specific vulnerability to damage from the double-hit ethanol model.

overall_design: RNA-seq profiling of the anterior cingulate cortex (ACC) of male and female Long Evans rats who received one of three prenatal ethanol conditions (Pair-Fed[PF], Free-Choice Liquid Diet [FCL] or Ethanol [PAE]) followed by one of two adolescent exposure conditions (water control [VEH] or alcohol [AAE]). Brains were collected either 24h after the final adolescent exposure (postnatal [P] day 42), or in adulthood without any challenge (P90). The nucleus accumbens (NAcc) was processed the same way with a select subset of groups and is available as a separate experiment.

first: Esther M

last: Marquez-Wilkins

first: Steven L

last: Youngentob

first: Carlita

last: Favero

first: Terrence

last: Deak


title: Treg-Derived IFN-γ Supports the Differentiation of Th1-Treg in tumor immunity and autoimmunity

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

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

summary: Tregs in tumors are functionally heterogeneous, and Th1-Tregs represent a highly suppressive subset. This study identifies Tregs themselves as a source of IFN-γ, which promotes Th1-Treg differentiation. Treg-derived IFN-γ acts in an autocrine manner to sustain T-bet expression and the Th1-Treg phenotype, while PF4 from Arg1(+) TAMs further amplifies this pathway by inducing Ifng expression in Tregs. Conditional deletion of Ifng in Foxp3(+) cells impaired Th1-Treg differentiation in both tumors and spleen, and a similar mechanism was observed in EAE. Overall, Treg-derived IFN-γ forms a positive feedback loop with other IFN-γ sources and TAM-derived PF4, driving the maintenance and accumulation of Th1-Tregs and reinforcing immunosuppression.

overall_design: Bulk RNA-seq analysis of gene expression profiles in PF4-treated YFP(-) CD4(+) CD25(+) cells from spleens of B16F10-bearing Foxp3-Cre/Tbx21-Flp/VeDTR(LF) mice (n = 5).

first: Ayumi

last: Kuratani

first: Masahiro

last: Yamamoto


title: Polycatechol-based iron predators disrupt fungal iron homeostasis to drive selective antifungal action

city: Shanghai

last: Liu

address: Dongchuan Road 500

institute: East china normal university

summary: Fungal infections pose a growing global health challenge, exacerbated by a scarcity of effective treatments and rising drug resistance. Although cationic polymers emerge as promising antifungal candidates owing to structural tunability, design flexibility, and resistance to proteolytic degradation, their clinical utility has been hampered by non-selective membrane-disruption mechanisms. Herein, we develop a class of polycatechols- termed fungal iron predators (FIPs), exhibit exceptional fungicidal activity and markedly low cytotoxicity. These FIPs can efficiently infiltrate fungal cells, selectively sequester labile irons, and disrupt iron homeostasis and metabolism. The ensuing iron starvation provokes severe mitochondrial dysfunction and energy collapse, culminating in fungal cell death. Through systemic optimization of cationic density and catechol stoichiometry, we obtained an FIP variant demonstrating potent antifungal activity with high selectivity toward fungi over mammalian cells, minimal propensity to induce resistance, and supplementary antioxidant properties. Remarkably, this FIP candidate shows robust therapeutic performance across multiple in vivo models of fungal infection. Critically, this work established a groundbreaking paradigm in polymer design: shifting the antifungal mechanism from traditional non-specific membrane disruption to targeted intracellular metabolic interference. The general applicability of this strategy across diverse cationic polymer backbones opens avenues for developing next generation of precision antifungal agents.

overall_design: To investigate the iron-sequestration mechanism of FIP, we performed transcriptomic analysis on C. albicans ATCC 10231. Logarithmic-phase cells (2x10^7 CFU/mL) were treated with 16 μg/mL of FIP at 30 °C for 3 h, with untreated cells as the blank control. Three biological replicates were performed for each group.

first: Mingrui

last: Cheng

first: Yuqi

last: Tao

first: Xingchen

first: Boyi

last: Wu

first: Wenjing

last: Ma

first: Xujiao

first: Jiaxu

last: Hong

first: Jingjing

last: Hu

first: Yiyun


title: Homocysteine drives hippocampal blood-brain barrier disruption and cognitive decline under chronic stress via DNA hypomethylation of Cav1.2

first: mao yang

last: Zhou

overall_design: Primary rat brain microvascular endothelial cells (BMECs) were isolated and cultured in vitro. Cells were treated with either vehicle control (solvent) or 100 µM homocysteine (Hcy) for 24 hours. Each group consisted of three biological replicates. Total RNA was extracted, and libraries were prepared for paired-end sequencing.

first: Maoyang

first: Zhaoxin

last: Sun

first: Jinshan

last: Li

first: Fang

last: Xie

first: Xue

first: Zhaowei

first: Lingjia


title: Single-cell RNA sequencing on the vein wall of female mouse deep vein thrombosis

city: Madison

first: Bo

state: WI

address: 1111 Highland Ave

institute: University of Wisconsin - Madison

summary: Deep vein thrombosis (DVT) is a common clinical problem, but its cellular and molecular mechanisms remain incompletely understood. We performed single-cell RNA sequencing (scRNA-seq) on the vein wall of female  C57BL/6J mice. Using the inferior vena cava (IVC) ligation model of DVT, we profiled the cellular heterogeneity and gene expression shifts occurring within the vein wall during the acute phase of thrombosis. This dataset provides a high-resolution map of the vascular response to acute venous thromboembolism.

overall_design: IVC ligation or sham surgery was performed on 8-week-old female C57BL/6J mice. After 24 hours, mice were euthanized and perfused with PBS, the vein wall was collected and analyzed using scRNAseq.

first: Huan

last: Yang

first: Ting


title: Brainstems of mice latently infected with HSV-1 exhibit sex-specific effects in neuro-inflammation and senescence

city: Stillwater

first: Clinton

last: Jones

state: Oklahoma

address: 250 McElroy Hall

department: Veterinary Pathobiology

institute: Oklahoma State University

summary: Following acute infection, herpes simplex virus type 1 (HSV-1) establishes life-long latency in neurons.  Although sensory neurons in trigeminal ganglia (TG) are primary sites for latency, brainstem is also an important site for latency.  For example, the principal sensory nucleus of the spinal trigeminal tract (Pr5) receives afferent inputs from TG and harbors latent HSV-1.  The locus coeruleus (LC), is indirectly linked to Pr5.  The latency associated transcript (LAT) locus is the only viral gene abundantly expressed during latency, and LAT mediates establishment and maintenance of latency.  Previous studies revealed senescent cells inflammation were detected in Pr5 and LC of aged mice and young mice latently infected with HSV-1 indicating HSV-1 influences senescence and inflammation during latency.  To expand our understanding of how HSV-1 influences senescence and inflammation in Pr5 and LC, NanoString studies in mice latently infected with wild-type HSV-1 and a LAT-null mutant (dLAT2903) were compared to age matched uninfected C57Bl/6 male and female mice.  Cellular genes that regulate neuron differentiation, axonal projection, and pro-inflammatory mediators were more prevalent in mice latently infected with wild-type (wt) HSV-1 and dLAT2903 versus uninfected mice.  Thus, HSV-1 latency in Pr5 and LC is not a static process.

overall_design: Nine-week-old C57BL/6J mice were infected with ~2 x 10^5 PFU dLAT2903R or the LAT-/- mutant (dLAT2903) per eye without scarification. Five females and five males were infected with wt HSV-1 or dLAT2903, and another five mice of each sex were mock infected. Mice infected for 30 days were operationally defined as being latently infected. The Pr5 of the spinal trigeminal tract and LC were microdissected by Palkovit’s punch technique, using a mouse brain stereotaxic atlas as a reference. Bilateral micropunches were collected from 60-µm thick coronal sections based on stereotaxic coordinates. Punches collected from Pr5 and LC were preserved in RNAlater at -20°C until shipped. RNA isolated from the Pr5 and LC was hybridized to a mouse neuroinflammation panel (Catalog #XT-CSO-MNROI1-12) of target-specific fluorescent barcodes. The panel contained 770 genes, including 13 internal reference genes for data normalization. Subsequent quality control, normalization, and between-group comparisons for differential gene expression were done using the nSolver Analysis Software from NanoString Technologies.

first: Melanie

last: Whitmore

first: Kelly

last: Harrison

first: Hafez

last: Sadhegi

first: Bhuvana

last: Plakkot

first: UdayKiran

last: Venugopal

first: Chenoa

last: Turtle

first: Madhan

last: Subramanian


title: Transcriptomic profiling of primary mouse aortic smooth muscle cells treated with inflammatory macrophage-conditioned medium

last: Liu

summary: Inflammatory cell infiltration is a hallmark of many vascular diseases, but the specific molecular mechanisms by which macrophage-derived signals influence smooth muscle cell (SMC) phenotype remain poorly defined. This study utilized bulk RNA sequencing to elucidate the transcriptomic shifts driven by the inflammatory macrophage secretome.

overall_design: Primary mouse aortic SMCs were serum-starved and subsequently treated with conditioned media (CM) from either naïve or IFNγ/LPS-treated bone marrow-derived macrophages (BMDMs). RNA was extracted 24 hours post-treatment and subjected to bulk RNA sequencing


title: Glycosylation Orchestrates Megakaryocytic Fate of Hematopoietic Stem Cells via Wnt-Muc13 Signaling [scMultiome]

city: Milwaukee

first: Karin

last: Hoffmeister

address: 8727 Watertown Plank Road

institute: Versiti Blood Research Institute

summary: Hematopoietic stem and progenitor cells (HSPCs) sustain blood production through tightly regulated fate decisions. Disruption of this control underlies disorders such as myelodysplastic syndromes, myeloproliferative neoplasms, and inherited thrombocytopenias. While transcriptional and epigenetic regulation of HSPCs is well established, the contribution of glycosylation has remained largely unexplored. Here, we identify the glycosyltransferase B4GALT1 as a central regulator of hematopoiesis that integrates extrinsic niche cues with intrinsic transcriptional programs. B4GALT1 shapes the bone marrow microenvironment by generating complex glycan niches that support HSPC function. However, its deficiency produces oncogenic glycan signatures, disrupts HSPC niche integrity, and induces aberrant expression of Mucin 13 (MUC13). These changes expand stem and progenitor pools, enforce megakaryocyte lineage bias, and activate the Wnt–MUC13/β-catenin signaling axis, a pathway tightly linked to proliferation and malignant transformation. Consequently, B4GALT1 loss uncouples proliferation from self-renewal, altering key regulators of stem cell quiescence, lineage balance, and marrow homeostasis. Our findings define a previously unrecognized glycan-dependent regulatory axis that directs HSPC fate through coordinated transcriptional reprogramming, signaling modulation, and niche remodeling. This work establishes aberrant glycosylation as a driver of hematopoietic dysfunction and highlights B4GALT1 as a potential therapeutic target in stem cell–driven blood disorders.

overall_design: Bone marrow LSK cells were sorted by FACS using the Lineage-Sca-1+, cKit+ strategy for wild type and B4galt1 full knockout mice and analized using scRNAseq

first: Alejandro

last: Roisman

first: Leonardo

last: Rivadeneyra

first: Lindsey

last: Conroy

first: Natalia

last: Weich

first: Agata

last: Steenakers

first: Melissa

last: Lee-Sundlov

first: Simon

last: Glabere

first: Shikan

last: Zheng

first: Katelyn

middle: E

last: Rosenbalm

first: Mark

last: Zogg

first: George

middle: F

last: Steinhardt IV

first: Anthony

middle: J

last: Veltri

first: Joseph

middle: T

last: Lau

first: Monika

last: Zielonka

first: Jacek

first: Elisa

last: Fadda

first: Tongjun

last: Gu

first: Hartmut

last: Weiler

first: Ramon


title: Mitochondria-associated mRNAs restore ATP during oxidative stress via cytosolic translation

city: Charlestown

first: Kazuhide

last: Hayakawa

state: Massachusetts

address: MGH149 13th street, Room 2401

department: Radiology

institute: Massachusetts General Hospital

summary: Mitochondrial transplantation has been proposed as a strategy to restore cellular bioenergetics after oxidative injury, but the mechanisms governing ATP recovery remain unclear. Using placental mitochondria, we examined ATP restoration following H₂O₂-induced oxidative stress. Unmodified mitochondria modestly increased ATP under baseline conditions but failed to restore ATP after injury. In contrast, lipid-coated mitochondria (MitoCoat) and lipid-encapsulated mitochondria-associated mRNAs (MitoCoat-mRNA) significantly increased ATP levels in injured cells. Transcriptomic analyses revealed that ATP recovery occurred without normalization of canonical glycolytic or oxidative phosphorylation (OXPHOS) gene programs. Instead, unmodified mitochondria induced broad transcriptional responses associated with immune activation and cellular stress, whereas MitoCoat elicited a more restricted transcriptional profile. Notably, mitochondria-associated mRNAs alone restored ATP without detectable changes in host transcriptional programs. Removal of mitochondrial surface–associated ribosomes or inhibition of cytosolic but not mitochondrial translation attenuated ATP recovery. Restoration of key metabolic enzymes through cytosolic translation, including PFKP, pyruvate dehydrogenase, and ATP synthase subunit ATP5A, suggests that mitochondria-associated mRNAs promote recovery by re-establishing coupling between glycolysis and mitochondrial OXPHOS. Together, these findings identify encapsulated mitochondria-associated mRNAs as a potential strategy to restore cellular bioenergetics under oxidative stress.

overall_design: Astrocytes were first exposed to H₂O₂ for 30 minutes to induce oxidative stress and were subsequently treated 24 hours later. RNA sequencing was performed 6 hours after mitochondrial interventions after treatment with unmodified mitochondria, MitoCoat, or MitoCoat-mRNA.

first: Dong-Bin

last: Back

first: Gen

last: Hamanaka


title: Effects of nickel ion treatment on gene expression during osteogenic differentiation of mouse bone marrow mesenchymal stem cells

city: Guangzhou

first: Xi

last: Huang

state: Guangdong Province

address: Lingyuan West Road

department: Department of Periodontology

institute: Hospital of Stomatology, Sun Yat-sen University

summary: Nickel (Ni) is a ubiquitous environmental trace metal, yet its physiological roles and dose-dependent effects in skeletal biology remain poorly understood. Through comprehensive in vivo and in vitro experiments, we demonstrated that low-dose Ni (0.1 μM) significantly enhances matrix mineralization during osteogenic differentiation, whereas this pro-mineralization effect is markedly attenuated at higher concentrations. Although the inhibitory mechanism of high-dose nickel on osteogenesis has been largely attributed to oxidative stress, the molecular basis underlying the promotional effect of low-dose nickel remains unclear. To address this, we performed RNA-seq analysis on primary mouse bone marrow mesenchymal stem cells (mBMSCs) treated with 0.1 μM nickel following 7 days of osteogenic induction, aiming to elucidate the downstream signaling pathways responsible for its beneficial effects on bone mineralization.

overall_design: Mouse bone marrow mesenchymal stem cells (mBMSCs) were induced for osteogenic differentiation for 7 days in the presence or absence of low-dose nickel ions (0.1 μM). Three independent biological replicates were prepared for each condition (nickel-treated group and vehicle control group).

first: Xiaoxin

last: Ma


title: CXCL6 exacerbates metabolic dysfunction-associated steatohepatitis by suppressing LPIN1-mediated fatty acid oxidation in hepatocytes

city: Busan

first: Haeseung

last: Lee

address: 63 Beon-gil 2, Busandaehag-ro, Geumjeong-gu

department: College of Pharmacy

institute: Pusan National University

summary: Progression of hepatic steatosis to metabolic dysfunction-associated steatohepatitis (MASH) involves impaired fatty acid (FA) oxidation, which causes lipotoxicity and inflammation in hepatocytes. MASH is characterized by upregulation of the neutrophil-recruiting chemokine CXCL6. Although hepatocytes produce CXCL6, its direct contribution to MASH progression in hepatocytes, beyond neutrophil recruitment, remains unclear. Here, we show that Cxcl5, the murine homolog of human CXCL6, promotes steatosis-to-MASH transition when overexpressed in the mouse liver, whereas Cxcl5 deficiency protects against diet-induced MASH. Transcriptomic analysis of Cxcl5-deficient mice showed upregulation of FA metabolism genes. This is accompanied by reduced hepatic FA levels and increased Lipin-1 (LPIN1) expression, which activates PPARα. In vitro, recombinant mouse CXCL5 suppressed LPIN1 and PPARα expression in mouse hepatocytes, whereas Cxcl5-deficient hepatocytes exhibited elevated levels of both. Mechanistically, CXCL6 induced JNK activation, leading to inhibitory phosphorylation of the glucocorticoid receptor (GR). Luciferase assays demonstrated that CXCL6 attenuated GR-dependent LPIN1 promoter activation. Lpin1 knockdown reversed the protective phenotype in Cxcl5-deficient mice, indicating that LPIN1 suppression is essential for CXCL6-driven MASH progression. Human MASH samples consistently exhibited reduced hepatic LPIN1 expression and an inverse correlation between LPIN1 and CXCL6 expression. In conclusion, CXCL6 drives MASH progression by inhibiting GR-mediated LPIN1 transactivation in hepatocytes, impairing FA oxidation and promoting lipotoxicity.

overall_design: RNA-seq profiling of liver tissues from C57BL/6J mice subjected to diet-induced MASH under different dietary conditions.

first: Seonghwan

last: Hwang


title: Humanin and MOTS-c Attenuate Atrial Fibrillation by Suppressing Fibrosis and Mitochondrial Dysfunction in murine models

first: Ying

middle: ying

last: Liao

address: 150 Jimo Road，Pudongxin,Shanghai

institute: Shanghai East Hospital

summary: BACKGROUND: Atrial fibrillation (AF) is the most common clinical arrhythmia associated with mitochondrial dysfunction, oxidative stress, and atrial fibrosis. Mitochondrial-derived peptides (MDPs) including humanin (HN) and MOTS-c, demonstrated potent cytoprotective effects, but their role in AF remains elusive. METHODS: Public GEO database, immunohistochemistry and immunofluorescence were applied to determine their expressions in atrial tissues. Plasma peptide levels were measured in a clinical cohort. Murine AF models and primary rat cardiomyocytes and fibroblasts models were established by administration of angiotensin II (Ang II) and treated with (Gly14)-Humanin (HNG, an HN analogue) or MOTS-c. RESULTS: Both HN and MOTS-c gene expressions were significantly downregulated in human AF atrial tissue and negatively correlated with the extent of fibrosis. Plasma MOTS-c level decreased in AF patients and showed an inverse correlation with NT-proBNP. In vivo, administration of HNG or MOTS-c significantly reduced AF inducibility, attenuated atrial fibrosis and hypertrophy induced by Ang II. Furthermore, HNG or MOTS-c treatment improved mitochondrial ultrastructure, as well as downregulated the expressions of mitochondrial fission proteins (Drp1 and Fis1) and pro-inflammatory cytokines (IL-1β and IL-6) of atrial tissue in murine AF models. In primary cardiomyocytes, both peptides mitigated Ang II-induced oxidative stress. In addition, they directly inhibited Ang II-induced fibroblast activation, proliferation, and migration in vitro. Further RNA sequencing results suggested that HNG mainly affects cell adhesion pathways and MOTS-c acts on metabolic process of cardiac fibroblasts. CONCLUSIONS: The downregulation of HN and MOTS-c in human AF is associated with AF severity. Administration of HNG or MOTS-c effectively suppressing atrial fibrosis and mitochondrial dysfunction and prevents AF in murine models. Therefore, mitochondrial-derived peptides represent as the underappreciated contributor to AF therapy and potential biomarkers.

overall_design: In total, 12 RNA-seq samples were analyzed, including primary rat cardiac fibroblasts stimulated with Angiotensin II (AngII) alone, AngII combined with HNG treatment, and AngII combined with MOTS-c treatment, with four biological replicates per group.

first: Yingying

first: Jie

last: Xu

first: Yuheng

last: Jiao

first: Dihui

last: Cai

first: Yinyin

last: Shen

first: Xiaohui

last: Zhou

first: Wei

last: Han


title: UHRF2 regulating IFN-I in macrophages during VSV infection in macrophages

city: 上海

first: Qian

last: Zhang

state: 上海市

address: 盘山路7号

institute: Naval Medical University

summary:
Analyzing UHRF2 targets in macrophages during VSV infection
Cleavage under targets and tagmentation (CUT&Tag)-seq for regulator of IFN-I in primary mouse  macrophages during VSV infection

overall_design: Peritoneal macrophages infected with VSV RNA virus were subjected to CUT&Tag analysis of UHRF2 and IRF3.

first: Xuetao

last: Cao


title: Investigating response to PARP inhibition and androgen receptor pathway inhibition in C4-2B prostate cancer cells

city: Sacramento

first: Alan

last: Lombard

state: CA

address: 4500 2nd Avenue, Rm 4674

institute: University of California, Davis

summary: Use of PARP inhibitors (PARPi) has been shown effective in the management of selected patients with advanced prostate cancer. Still, it is incompletely understood how PARPi work and what mechanisms may enable adaptation and progression. This study utilized RNA-sequencing to understand response to PARP inhibition (olaparib) in regard to both intensity and duration of treatment. PARPi have also been shown to be effective when combined with androgen receptor (AR) pathway inhibitors (ARPi), but much remains unknown regarding the utility of combination regimens. We additionally performed RNA-sequencing to better define transcriptomic changes associated with either monotherapy PARPi (olaparib or talazoparib), monotherapy ARPi (abiraterone or enzalutamide), or combinations (abiraterone + olaparib, enzalutamide + talazoparib).

overall_design: We conducted two rounds of RNA-sequencing within this deposit. The first (LLG001-LLG018) tested response to either olaparib (1 or 5μM) for either 1 or 5 days in C4-2B cells. Vehicle treated cells at each timepoint served as control. The second (LLG037-LLG057) tested response to the following treatments in C4-2B cells after 5-days; abiraterone acetate (5μM), enzalutamide (20μM), olaparib (1μM), talazoparib (10nM), abiraterone acetate + olaparib, enzalutamide + talazoparib.

middle: P

first: Bryan

last: Correa Gonzalez

first: Akshaya

last: Karthikeyan


title: Small RNA profiling of Meloidogyne javanica-induced galls in Arabidopsis thaliana at 14 days post-infection [smallRNA-seq]

city: Toledo

first: Carolina

last: Escobar Lucas

state: Toledo

address: Avda Carlos III, s/n, Campus Fábrica de armas, Edificio Sabatini, laboratorio 08

department: Plant physiology

institute: University of Castilla-la Mancha

summary: This dataset contains the small RNA sequencing analysis of Arabidopsis thaliana roots during the maintenance stage of Meloidogyne javanica-induced galls. Small RNA populations were profiled in galls collected at 14 days post-infection (dpi) and in equivalent uninfected root tissues used as controls. Three independent biological replicates were analyzed per condition to characterize small RNA accumulation patterns associated with nematode feeding site maintenance.

overall_design: Galls induced by Meloidogyne javanica in Arabidopsis thaliana (Col-0) roots were collected at 14 days post-infection (dpi). Control samples consisted of non-infected root segments equivalent to the gall region. Three independent biological replicates were generated per condition. Total RNA was extracted from each replicate and used for small RNA library preparation and single-end sequencing on an Illumina HiSeq X platform.

first: Dominguez-Figueroa

last: Jose

first: Müller

last: Sebastian

first: Claudia Silva

last: Ana

first: Escobar

last: Carolina


title: Transcriptome profiling of Arabidopsis thaliana galls induced by Meloidogyne javanica at 14 days post-infection

summary: This study investigates transcriptional changes associated with the maintenance stage of nematode-induced feeding sites in Arabidopsis thaliana. RNA-seq analysis was performed on galls induced by Meloidogyne javanica at 14 days post-infection (dpi) and on equivalent non-infected root segments used as controls. Each condition included three independent biological replicates. These data were generated to characterize gene expression changes associated with gall development and maintenance.

overall_design: Galls induced by Meloidogyne javanica in Arabidopsis thaliana (Col-0) roots were collected at 14 days post-infection (dpi). Control samples consisted of non-infected root segments equivalent to the gall region. Three independent biological replicates were generated per condition. Total RNA was extracted from each replicate and used for strand-specific mRNA library preparation and paired-end sequencing on an Illumina HiSeq X platform.


title: Overexpression of KLF4 in SSc lung fibroblasts initiates dedifferentiation

city: Charleston

first: Deanna

last: Baker Frost

state: SC

address: 96 Jonathan Lucas St room 822

department: Medicine

institute: Medical University of South Carolina

summary: KLF4 was overexpressed by adenoviral infection in primary human SSc lung fibroblasts, RNA and protein were extracted, RNA sequencing and differential expression analysis "ad-KLF4 vs ad-Null" were performed to obtain gene and systems level analyses. Markers of alveolar, inflammatory and fibrotic fibroblasts were validated by qPCR and immunoblotting. Our results show that overexpression of KLF4 in SSc fibroblasts initiated dedifferentiation.

overall_design: Primary human SSc lung fibroblasts were infected with KLF4 adenovirus to overexpress KLF4.

first: Ludivine

last: RENAUD

first: Carol

last: FEGHALI-BOSTWICK

first: Sam

last: KOTZ

first: Avery

last: BUNDT


title: CELF2-dependent RNA regulation supports cortical architecture and synaptic stability during early brain development

city: San Antonio

first: Zhijie

middle: Jason

last: Liu

state: TEXAS

address: 7703 Floyd Curl Drive

department: Department of Molecular Medicine

institute: Universality of Texas Health Science Center at San Antonio

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

overall_design: Refer to individual Series


title: Sex disparity in systemic sclerosis-associated pulmonary fibrosis.

summary: Systemic sclerosis (SSc) is a fibrotic disease with high mortality and SSc-associated pulmonary fibrosis (SSc-PF) as the leading cause of death. SSc shows a significant sex disparity with a sex ratio of 1:3 men to women, yet SSc-PF is more severe in men. This study investigates gene expression differences between men and women with SSc-PF. Whole lung tissues from healthy donors and SSc-PF patients of both sexes were analyzed by RNA sequencing. Selected genes were validated by quantitative polymerase chain reaction (qPCR) and Western blotting analyses. Notably, in whole lung, genes related to extracellular matrix production, such as COL3A1, COL5A1, PDGFA, THBS1, and THBS2, were upregulated in females, while genes that are less-explicitly related to fibrosis, like GNB3, PCSK4, and PCSK7, were upregulated in males. Additionally, normal lung fibroblasts were treated with recombinant TGFβ to determine if there is a differential response in lung fibroblasts depending on sex. This study reveals differentially expressed genes that are unique to female and male SSc-PF patients and identifies potential sex-specific clinical targets.

overall_design: RNA sequencing analysis of total RNA extracted from whole lung tissue of male and female donors either (1) healthy or (2) with SSc-associated pulmonary fibrosis.

first: Audrey

last: GALIMBA


title: CELF2-dependent RNA regulation supports cortical architecture and synaptic stability during early brain development [snRNA-Seq]

summary: Neurodevelopment relies on precise post-transcriptional regulation to coordinate neuronal differentiation, migration, and circuit formation. The CUGBP Elav-like family member 2 (CELF2) is an RNA-binding protein with established roles in alternative splicing and mRNA regulation, yet its function in the developing brain remains poorly defined. Here, we investigated the role of CELF2 during early postnatal neurodevelopment using a constitutive Celf2 knockout mouse model. Celf2 knockout pups exhibited neonatal lethality accompanied by impaired neuronal maturation and disrupted cortical organization. Bulk RNA sequencing revealed widespread transcriptional dysregulation, while splicing analyses identified reduced exon inclusion in multiple neurodevelopmental transcripts following CELF2 loss. Notably, Camk2a transcript and protein levels were markedly reduced in knockout brains, consistent with CELF2 binding to the Camk2a 3′UTR. Functional studies in Caenorhabditis elegans demonstrated that expression of human CAMK2A partially rescued synaptic puncta deficits in unc-75 (CELF ortholog) mutants, supporting a conserved role for CELF-family proteins in synaptic maturation. Histological analyses revealed reductions in Nestin- and Doublecortin-positive immature neurons, thinning of upper cortical layers, and decreased CAMK2A expression. Single-nucleus RNA sequencing further revealed selective reductions in upper layer II/III excitatory neuron populations in the cortex. Together, these findings establish CELF2 as a critical post-transcriptional regulator required for neuronal maturation and architectural stability during early brain development and highlight how disruption of RNA regulatory programs may contribute to neurodevelopmental disorders.

overall_design: Single nuclei were isolated from postnatal day 0 (P0) mouse brains, with two hemibrains pooled per group (Celf2+/− and Celf2−/−). Dissected brain tissue was minced, homogenized, and lysed, followed by purification of nuclei via gradient ultracentrifugation. The purified nuclei were then resuspended and used for snRNA-seq library construction using the 10x Genomics platform.

first: Zhang

last: Zhao

first: Chen

last: Lizhen

first: Jiang

last: Jing

first: Syed

last: Ishana


title: Mechanical-biochemical signaling accelerates scleral remodeling in myopia via the LaminA/C-Emerin-MKL1 axis

first: Bilian

last: Ke

address: No. 160 Pujian Road, Shanghai

institute: Renji Hospital, School of Medicine, Shanghai Jiao Tong University

summary: Scleral remodeling is the pathological basis of axial elongation during the progression of myopia. However, the mechanism underlying the onset and progression of scleral remodeling remains unclear. Here, based on reanalysis of single-cell RNA sequencing data, we showed that aberrant biomechanics in the sclera serve as signals that promote extracellular matrix (ECM) remodeling during the development of myopia via LaminA/C-Emerin-MKL1 axis, and followed by a decrease in collagen synthesis in scleral fibroblasts. Mice with lens-induced myopia (LIM) and guinea pigs with form-deprivation myopia (FDM) exhibited nuclear deformation and dysregulation of nuclear envelope (NE) proteins in sclera. We established a mechanical model to investigate the role of matrix stiffness in regulating collagen synthesis in human primary scleral fibroblasts. In contrast to stiff substrates, soft matrix attenuated the sequestration of LaminA/C and Emerin in the NE and impaired MKL1 nuclear accumulation and COL1A1 transcription. Interventions for MKL1 induced or inhibited the progression of myopia in vivo. We illustrate the therapeutic potential of a novel mechanointerference strategy that blocks scleral remodeling and myopia progression.

overall_design: Transcriptomic profiling (RNA-seq) of human primary scleral fibroblasts following siRNA-mediated knockdown of LaminA/C (LMNA) and Emerin (EMD) . The experiment aims to identify the downstream regulatory networks and pathways controlled by these nuclear envelope proteins in scleral fibroblasts, specifically investigating their role in mechanotransduction and extracellular matrix (ECM) homeostasis.

first: Yuying

first: Xin

first: Mingming

first: Xuetong

last: Wang

first: Wenzhe

last: Qian

first: Ting

first: Min

last: Li


title: CELF2-dependent RNA regulation supports cortical architecture and synaptic stability during early brain development [RNAseq]

overall_design: Total RNA was extracted from n=3 frozen postnatal day 0 (P0) mouse hemibrains per genotype using TRIzol reagent and further purified using a Qiagen RNA isolation kit. Poly(A)+ RNA libraries were prepared and sequenced on an Illumina platform.


title: Loss of maternal PADI6 disrupts DNA methylation and genomic imprinting maintenance in late preimplantation mouse embryos.

city: Napoli

first: Francesco

last: Cecere

state: Napoli

address: Via Posillipo 226

department: UOC Ricerca Clinica e Traslazionale

institute: AORN Santobono-Pausilipon

summary: The maternal-effect protein PADI6, which is part of the subcortical maternal complex, is involved in proper spindle assembly, organelle distribution, ribosome storage, and cytoplasmic lattice organization in mouse oocytes. In humans, variants of PADI6 are associated with female infertility and multilocus imprinting disturbance in offspring. Recently, it was demonstrated that PADI6 plays a role in the storage and cytoplasmic localization of epigenetic factors, including UHRF1 and DNMT1. Moreover, maternal PADI6 depletion leads to defective epigenetic reprogramming and zygotic genome activation but not to an imprinting defect in two-cell mouse embryos. These findings raise the possibility that imprinting disturbances arise later in development.

overall_design: By employing combined single-blastocyst RNAseq/BSseq and immunostaining validation in the embryos derived from Padi6P620A-mutant oocytes, we investigated the role of Padi6 in late preimplantation development. We demonstrated that embryos that overcame the two-cell stage block had a dramatic reduction in UHRF1 and DNMT1 protein levels, a decrease in H3K9me3, and whole-genome hypomethylation, including most imprinted loci and repetitive elements, at the blastocyst stage. Furthermore, these maternal mutant embryos showed deregulation of inner cell mass markers and defective blastocyst implantation, but no effect on trophoblast differentiation.

first: Carlo

last: Giaccari

first: Angela

last: Pagano

first: Emilia

last: D’Angelo

first: Abu

last: Saadat

first: Lucia

last: Mele

first: Paolo

last: Salerno

first: Giuseppe

last: Merla

first: Flavia

last: Cerrato

first: Andrea

last: Riccio


title: Loss of maternal PADI6 disrupts DNA methylation and genomic imprinting maintenance in late preimplantation mouse embryos


title: RNA-seq analysis of bEnd.3 cells with shRNA-mediated knockdown of Npc1 versus control

city: Henan

first: Ge

last: Gao

address: Xinxiang

institute: Henan Medical University

summary: This study aims to elucidate the transcriptional regulatory role of the Npc1 gene in bEnd.3 cells through transcriptome sequencing. We achieved stable knockdown of Npc1 in bEnd.3 cells using transposon-delivered shRNA, while the control group received non-targeting shRNA (n=3 biological replicates per group). Knockdown efficiency was validated by qRT-PCR (reduction >90%). Total RNA was extracted and sequenced on the DNBSEQ platform. Differential expression analysis revealed that differentially expressed genes were significantly enriched in pathways related to lipid metabolism and tight junction function, indicating that Npc1 plays a critical role in regulating these cellular processes in bEnd.3 cells. This dataset provides a resource for studying Npc1-dependent gene networks.

overall_design: RNA-seq profiling of wildtype bEnd.3 cells and  Npc1 knockdownb End.3 cells .

last: Yan

first: Jing

last: Kang

first: Liang

last: Qiao


title: EZH2 inhibition via GSK-126 mitigates EndMT and atherosclerosis in diabetes: A translational epigenetic approach.

city: Melbourne

first: Abdul Waheed

last: Khan

state: Vic

address: 99 Commercial Road

department: Diabetes

country: Australia

institute: Monash University

summary: Atherosclerosis drives cardiovascular morbidity in diabetes, with endothelial-to-mesenchymal transition (EndMT) as a key contributor. While epigenetic regulators are increasingly implicated in atherosclerotic progression, the specific role of Enhancer of Zeste Homolog 2 (EZH2), a histone methyltransferase, in EndMT in diabetes-associated atherosclerosis remains unclear. We show that EZH2-mediated H3K27 trimethylation is elevated in carotid plaques from diabetic patients and in aortic endothelium of diabetic Apoe-/- mice. Pharmacologic EZH2 inhibition with GSK-126 attenuated EndMT and reduced atherosclerotic burden in diabetic mice. In human aortic endothelial cells exposed to high glucose/TNF-α or serum from coronary artery disease patients, EZH2 blockade via GSK-126 or shRNA suppressed EndMT and reversed transcriptional programs assessed by RNA sequencing, including COL4A1 and NR2F2. These findings identify EZH2 as a driver of EndMT in diabetes-associated atherosclerosis and highlight EZH2 inhibition as a potential therapeutic strategy to limit vascular pathology.

overall_design: RNA‑sequencing was performed on human aortic endothelial cells cultured under three conditions: untreated control; combined EndMT‑inducing stimuli of TNF‑α (5 ng/mL) plus high glucose (25 mM); and the same TNF‑α + high‑glucose condition with GSK‑126 (5 µM). Biological replicates were collected for each group to enable transcriptomic comparison.

first: Misbah

last: Aziz

first: Karly

last: Sourris

first: Jairo

middle: A

last: Pinzon-Cortes

first: Tomasz

last: Block

first: Aozhi

last: Dai

first: Scott

middle: S

last: Maxwell

first: Jun

last: Okabe

first: Anna

last: Calkin

first: Mark

last: Cooper

first: Karin

last: Jandeleit-Dahm

first: Abdul

middle: W


title: Gastric mucosal transcriptomic responses to diet-induced obesity and calorie restriction in mice

city: Dallas

first: Jeffrey

middle: Marc

last: Zigman

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

summary: The transcriptional landscape of the gastric mucosa during diet-induced obesity (DIO) and calorie restriction (CR) is largely unexplored. Here, we profiled gastric mucosal gene expression changes induced in mice by DIO and CR and investigated the physiological role of Decidual Protein Induced by Progesterone 1 (Depp1) using newly-generated Depp1-knockout (KO) mice. RNA sequencing revealed that DIO predominantly induces a pro-inflammatory transcriptional signature, whereas CR upregulates genes involved in peptide transport and extracellular matrix organization and downregulates immunity-related genes. Among CR-induced genes, Depp1 showed the strongest positive correlation with ghrelin expression. qRT-PCR confirmed that Depp1 expression in the gastric mucosa was restricted to ghrelin cells and demonstrated that CR also induces Depp1 upregulation in other tissues, including kidney, lung, and liver. Hepatic Depp1 upregulation by CR was absent in ghrelin-KO mice. Notably, Depp1-knockout mice displayed normal metabolic and hormonal responses to CR, including the expected rise in circulating ghrelin. However, after 16 weeks of ad libitum high-fat diet feeding, male Depp1-KO mice exhibited greater increases in body weight, food intake, fat mass, and lean mass, as well as reduced glucose tolerance compared with wild-type littermates. These changes were accompanied by altered hepatic expression of the GHSR (ghrelin receptor) antagonist Leap2 and the gluconeogenic gene Pck1. Thus, while Depp1 is a CR-induced, ghrelin cell-regulated gene that modulates hepatic transcriptional responses, it is not required for short-term metabolic adaptation to CR. Instead, Depp1 plays a protective role against the full development of metabolic dysfunction during DIO through mechanisms that remain to be elucidated.

overall_design: RNA from scraped gastric mucosa tissue isolated from ad lib, standard chow fed mice (lean; n=4), mice subjected to a 7d acute-on-chronic CR protocol modeling starvation (CR; n=5), and mice fed a 42% high-fat diet (HFD) for 4w (DIO; n=5), with RIN ≥ 9 was used for library construction and pair-end sequencing (2 × 150 bp) on an Illumina NovaSeq X Plus (Novogene Co., Ltd.).

first: Sepideh

last: Sheybani-Deloui

first: Kripa

last: Shankar

first: Angie

middle: L

last: Bookout

first: Salil

last: Varshney

first: Omprakash

last: Singh

first: Connor

last: Lawrence

first: Jake

last: Tessnow

first: Aki

last: Uchida

first: Deepali

last: Gupta

first: Shota

last: Takemi

first: Sherri

last: Osborne-Lawrence


title: ChIP-Seq analysis of SIRT6 and KDM5C in pancreatic cancer cell line

city: Jinan, Shandong

first: Shuai

last: Leng

address: 105 Jiefang Road

institute: Central Hospital Affiliated to Shandong First Medical University

summary: Pancreatic cancer is among the deadliest malignant tumours, characterized by rapid progression, poor prognosis, and high mortality.SIRT6 and KDM5C plays an important role in tumorigenesis, development, and drug resistance .However, the precise molecular mechanisms through which SIRT6 and KDM5C inhibit tumorigenesis and metastasis in pancreatic cancer, as well as its role in cancer stem cells (CSCs), remain unclear.Collectively, our findings identify SIRT6 and KDM5C as key regulators of pancreatic cancer progression and suggest that they represent potential targets for early diagnosis and therapeutic intervention.

first: Wenqian

last: Yu


title: β-hydroxybutyrate-driven histone lysine β-hydroxybutyrylation promotes the immunostimulatory activity of monocyte-derived macrophages in rectal cancer

city: wuhan

first: Mingjie

last: Li

address: union hospital

institute: Huazhong University of Science and Technology

summary: Our previously reported phase II and phase III trials have demonstrated that short-course radiotherapy (SCRT) combined with neoadjuvant immunochemotherapy (SIC) has led to clinical benefits in locally advanced rectal cancer (LARC). Characterization of the molecular mechanisms underlying responses to SIC may lead to improved treatment strategies. Here, we prospectively collected and applied multi-omic analyses to paired pre- and post-treatment LARC specimens undergoing SIC.

overall_design:
To investigate the cellular and molecular contexture of the tumor immune microenvironment (TIME) following SIC treatment, we characterized stromal and immune cells isolated from tumor tissue specimens during SIC by high-throughput single-cell RNA sequencing (3 time points) (scRNA-seq).

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Due to the requirements of the sequencing company and uncontrollable factors, our raw data cannot be provided
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title: RNA-Seq analysis SIRT6 or KDM5C knockdown effect on pancreatic cancer cell line

overall_design: siSIRT6,siKDM5C or controls were transfected into PANC-1 cells (n=3 for each group) for 48 hours. Total RNA was isolated using Trizol reagent (Invitrogen, USA). Agilent 2100 Bioanalyzer (Agilent Technologies, USA) was used to evaluate the RNA quality.


title: The trilineage coexistence observed during the differentiation of porcine extended pluripotent stem cells in LCDM medium

city: Nanjing

first: Lihua

last: Zhao

address: #101, Long mian road

institute: Nanjing Medical University

summary: Porcine extended pluripotent stem cells (pEPSCs) were cultured in LCDM medium for 96 hours. We performed single-cell RNA-sequencing (scRNA-seq) of pEPSC cultures. Following quality control, the 10× Genomics scRNA-seq dataset of 14,822 cells harvested at 96 h yielded 14,821 high-quality cells with a median of 2,595 genes detected per cellNetwork clustering analysis identified 8 distinct cell clusters.

overall_design: mRNA profiles of porcine extended pluripotent stem cells differentiated in LCDM medium for 96 hours.

first: Yanglin

last: Chen

first: Rongfeng

first: Xihe


title: Outer membrane remodeling via lipid-peptidoglycan crosstalk enables lipooligosaccharide-deficient colistin resistance

city: Richardson

first: Joseph

middle: Michael

last: Boll

address: 800 W Campbell

department: Biological Sciences

institute: University of Texas at Dallas

summary: Although several Acinetobacter baumannii lineages can acquire colistin resistance by eliminating LPS/LOS glycolipids, the widely used reference background ATCC 17978 is unable to access this trajectory under standard selection, suggesting that glycolipid essentiality is strongly context dependent. Here we show that this barrier is not absolute but instead reflects the structural state of the envelope. Disrupting phospholipid homeostasis, through loss of the Mla system, which mediates retrograde phospholipid transport, and the outer-membrane phospholipase PldA, which degrades mislocalized phospholipids, destabilizes lipid asymmetry and creates a fragile yet permissive state that enables the emergence of stable glycolipid-deficient, colistin-resistant variants.

overall_design: Differential gene expression in A. baumannii strain ATCC 17978: WT vs. Δmla ΔpldA; Δmla ΔpldA vs. LOS-deficient derivatives; and LOS-deficient cells ± colistin at OD600 of ~0.5 in triplicate.

first: Roberto

last: Olea-Ozuna

first: Berenice

last: Furlan

first: Hanling

last: Gong

first: Orietta

last: Massidda


title: Melatonin modulates inflammasome and antioxidant signaling in trophoblasts and decidual macrophages

city: Atlanta

first: Erica

last: Johnson

state: GA

address: 720 Westview Dr SW

department: Department of Microbiology, Biochemistry, and Immunology

institute: Morehouse School of Medicine

summary: This study investigates how melatonin regulates inflammatory and oxidative stress pathways at the maternal–fetal interface. We profiled transcriptomic responses in JEG-3 trophoblast-like cells and primary human decidual macrophages treated with melatonin at different doses. Cells were exposed to vehicle, 1 nM, or 1000 nM melatonin under defined inflammatory conditions. RNA-seq libraries were prepared using a strand-specific poly(A)-selected protocol and sequenced on a BGISEQ platform. Differential expression and pathway analyses focused on inflammasome and NRF2-related pathways. These data support a role for melatonin in modulating redox–inflammatory balance in placenta-relevant cell types.

overall_design: Bulk RNA-seq of JEG-3 trophoblast-like cells and primary human decidual macrophages treated with vehicle or melatonin (1 nM or 1000 nM). For each cell type and condition, biological replicates were profiled. Total RNA was extracted, poly(A)-selected, and used to prepare strand-specific mRNA libraries. Libraries were sequenced with paired-end reads on a BGISEQ platform. Gene-level counts were obtained and analyzed with DESeq2 to identify differentially expressed genes and enriched pathways

first: Tyana

last: Joseph

first: Toidi

last: Adekambi

first: Viviane

last: Schuch


title: MEK inhibition induces AXIN1 loss in colorectal cancer by mTOR associated suppression of protein synthesis [RiboSeq_HCT116]

city: Mannheim

first: Johanna

middle: Daniela

last: Schott

address: Franz-Volhard-Straße 6

department: Mannheim Institute for Innate Immunoscience

institute: Heidelberg University

summary: AXIN1 is a central regulatory hub of many oncogenic pathways in colorectal cancer (CRC). As the main scaffold protein and least abundant component of the beta-catenin destruction complex, changes in AXIN1 levels affect Wnt signaling output. We show that targeting the Ras-MAPK pathway by MEK1/2 inhibitors induces AXIN1 loss across a panel of CRC cell lines and patient-derived organoids. GSK3B inhibition similarly reduced AXIN1 levels, yet by distinct mechanisms. MEK1/2 causes a reduction of AXIN1 transcript levels, but neither affects protein stability nor post-translational modifications of AXIN1. In contrast, GSK3B inhibition induces rapid AXIN1 degradation. Prevention of AXIN1 loss by co-treatment with tankyrase inhibitors was much stronger for GSK3B than for MEK1/2 inhibition. Using isogenic CRC cell lines and murine intestinal organoids, we show that APC truncations strongly reduce basal AXIN1 levels, but do not alter dynamics of AXIN1 loss upon MEK1/2 inhibition. Polysome profiling and Ribo-Seq revealed that MEK1/2 inhibition reduces global protein synthesis via an mTOR dependent pathway. This translational repression is sufficient to cause significant AXIN1 loss, as treatment with mTOR inhibitors phenocopies the effect of MEK1/2 inhibitors. Our study demonstrates that AXIN1 protein homeostasis is critically controlled by Ras-MAPK signaling at the level of protein synthesis, and that MEK1/2 inhibitors cause AXIN1 loss by translational repression.

overall_design: To measure mRNA-specific changes in translation upon MEK1/2 inhibition, RiboSeq was performed in three biological replicates in HCT116 cells after 24 h of Trametinib or DMSO treatment. Ribosome-protected fragments (RPF) were generated by RNase I digest, while input (IN) material was treated with alkaline fragmentation.

first: Niyumi

last: Muthukumarana

first: Georg

last: Stoecklin

first: Tianzuo

last: Zhan


title: Marine Bacterium Stutzerimonas stutzeri Mitigates Parkinson's disease Pathology in C. elegans via Ferroptosis Modulation

city: LUCKNOW

first: SONIA

last: VERMA

state: UP

address: CSIR-Central Drug Research Institute

country: India

institute: CSIR-Central Drug Research Institute

summary: Parkinson's disease (PD) is a rapidly escalating neurodegenerative disorder marked by dopaminergic neurodegeneration, α-synuclein aggregation, and motor and non-motor impairments. Current therapies largely provide symptomatic relief and fail to prevent disease progression, underscoring the need for novel disease-modifying strategies. The marine biome has emerged as an unexplored reservoir of bioactive metabolites with neuroprotective potential, yet their therapeutic relevance in PD remains incompletely explored. Here, we report that Stutzerimonas stutzeri, a marine bacterium isolated from the Gulf of Mannar, exerts robust neuroprotective effects in Caenorhabditis elegans PD models. Dietary administration of S. stutzeri rescued dopaminergic neuronal loss, mitigated α-synuclein expression, and improved motor and sensory phenotypes. Mechanistic analyses revealed suppression of ferroptosis, evidenced by restoration of iron homeostasis, attenuation of lipid peroxidation, and recovery of ftn-1 expression. Our findings establish S. stutzeri as a previously unrecognized marine-derived therapeutic prospect for PD intervention and highlight ferroptosis modulation as a tractable therapeutic axis in neurodegeneration.

overall_design: For each condition (UA44 fed on either OP50 or S. stutzeri), worms were cultured in six independent biological replicates, with approximately 500 worms per replicate. On the third day of adulthood, three replicates were pooled, generating two pooled biological samples (>1500 worms each) per condition 38-41. Worm pellets were washed, snap-frozen, and processed at Biokart Genomics Lab (Bengaluru, India) for RNA isolation, sequencing, and analysis. Briefly, total RNA was extracted using the RNeasy Mini Kit (Qiagen), and integrity was verified (RNA Integrity Number > 7.0). Libraries were prepared with the NEBNext Ultra II RNA Library Prep Kit and sequenced on an Illumina HiSeq platform to obtain paired-end reads. RNA-Seq data was analyzed using the Galaxy platform 42. Quality assessment (FastQC) and trimming (Trimmomatic) were followed by alignment to the C. elegans ce11 genome (HISAT2) and quantification (featureCounts). Differential expression analysis was conducted using the LIMMA package after voom normalization. Genes with an adjusted p ≤ 0.05 and |log2 fold-change| ≥ 0.5 were considered significantly differentially expressed.

first: Simran

last: Singh

first: Anusree

last: Damodaran

first: Sanskriti

last: Goswami

first: Manjul

last: Lata

first: Mukesh

last: Pasupuleti

first: Sonia

last: Verma


title: MEK inhibition induces AXIN1 loss in colorectal cancer by mTOR associated suppression of protein synthesis


title: MEK inhibition induces AXIN1 loss in colorectal cancer by mTOR associated suppression of protein synthesis [RNASeq_HCT116]

overall_design: To compare changes in RNA expression upon MEK1/2 and GSK3 inhibition, HCT116 cells were treated with trametinib, CHIR-99021 or DMSO for 8 h, 24 h or 72 h, followed by extraction of total RNA and RNA-Seq.

first: Nachiyappan

last: Venkatachalam

first: Li

last: Wang


title: MEK inhibition induces AXIN1 loss in colorectal cancer by mTOR associated suppression of protein synthesis [RNASeq_SW480]

overall_design: To compare changes in RNA expression upon MEK1/2 and GSK3 inhibition, SW480 cells were treated with trametinib, CHIR-99021 or DMSO for 8 h, 24 h or 72 h, followed by extraction of total RNA and RNA-Seq.


title: Single cell transcriptome of the Mouse Neural Retina in Response to Sodium Iodate

city: Shanghai

first: Qingjian

last: Ou

address: NO.500, Zhennan Rd

department: Medical

institute: Tongji University

summary: Sodium iodate (SI) is a commonly used model for acute retinal injury in ophthalmology research, but the single-cell transcriptional landscape across its time course remains largely unknown. Here, we establish a single-cell transcriptomic atlas for neural retinas from mice subjected to SI treatment at 0, 3, and 7 days, with 2 biological replicates per time point.

overall_design: Single-cell RNA sequencing was performed on neural retinas from SI-treated mice at time points of 0, 3, and 7 days (n=2 per group) using an Illumina HiSeq 4000 system.

first: Zhenzhen

last: Zhao