title: Inactivation of Hes1 in skeletal undifferentiated cells increases bone volume

city: Farmington

first: Ernesto

last: Canalis

state: CT

address: 263 Farmington Avenue

department: Orthopaedic Surgery

institute: UConn Health

summary: Leptin receptor positive (LepR+) cells are multipotent stromal cells that are a source of osteogenic and adipogenic cells. Inactivation of Notch receptor signaling in LepR+ cells causes an increase in bone mass in mature mice, but the target gene responsible was not identified. Because in LepR+ cells the expression of the Notch target gene Hes1 prevails over that of other genes, we explored the role of the Hes1 deletion in LepR+ cells. To this end, LepR-Cre;Hes1∆/∆ mice were compared to wild type littermates. Male and female 5-month-old LepR-Cre;Hes1∆/∆ mice exhibited an increase in bone volume/total volume (BV/TV) due to an increase in trabecular number; cortical bone was not affected. Bone histomorphometry demonstrated decreased osteoclast number and eroded surface, but no changes in osteoblast number or bone formation were noted. Neither osteogenesis nor adipogenesis were modified by the Hes1 deletion in bone marrow stromal cell cultures, although Tnfsf11 (encoding RANKL) was suppressed in osteogenic cultures of Hes1∆/∆ cells. Single cell RNA sequencing of femurs from 5-month-old LepR-Cre;Hes1∆/∆ and control mice revealed the presence of 23 cell clusters including clusters composed of hematological cells (myeloid, B cells and neutrophils), endothelial cells and osteoblasts. There were no substantial differences in gene expression, cluster distribution or trajectory finding between control and Hes1 inactivated cells. In conclusion, Hes1 inactivation in LepR+ cells results in an increase in bone mass secondary to a decrease in RANKL, osteoclast number and bone resorption, but HES1 has little influence on osteogenesis or adipogenesis in bone.

overall_design: Femurs isolated from 5-month-old C57BL/6 mice and subject to digestion then FACS sorted.

first: Canalis

last: Ernesto

first: Denker

last: Emily

first: Schilling

last: Lauren


title: Cell signaling pathways modulation in silica nanoparticle-saturated macrophages

status: Public on Apr 01 2026

city: Salt Lake City

first: Hamid

last: Ghandehari

state: Ut

address: 36 S Wasatch Dr

department: Molecular Pharmaceutics

country: USA

institute: Univeristy of Utah

type: Expression profiling by high throughput sequencing

summary: In this study, we studied RAW 264.7 macrophages saturated with silica nanoparticles (SNPs) of different size (50 and 100 nm), porosity (nonporous, mesoporous), density (solid, mesoporous, and hollow), and surface composition (hydrophobicity) at their maximum non-toxic concentrations to study the changes in gene expression, and immune signaling pathways by RNA sequencing, weighted gene co-expression network analysis (WGCNA), Hallmark and KEGG pathway analysis.

overall_design: RNA sequencing analysis of SNP-saturated (SNP100, SNP50, MSNP, HMSNP) RAW 264.7 macrophages

first: Sushanto Kumar

last: Saha

first: Philip

middle: J

last: Moos

first: Hamidreza


title: Epigenetic regulation of p53 represents a targetable dependency in synovial sarcoma

first: Li

last: Li

state: Utah

address: 201 PRESIDENTS CIRCLE

institute: University of Utah

summary: Synovial sarcoma is a deadly malignancy of soft-tissue with a predilection for adolescents and young adults that consistently associates with a t(X;18) chromosomal translocation and expression of the resultant fusion oncoprotein SS18::SSX. Here, the dependency on MDM2 that has been observed in multiple synovial sarcoma cell lines is presented. Very few synovial sarcomas in humans demonstrate TP53 mutation or loss, CDKN2A loss, or MDM2 gains, each common among other sarcoma types. Silencing of homologous Trp53 in a mouse model of SS18::SSX-expression-induced sarcomagenesis leads to a slightly reduced latency to tumorigenesis, but no increase in de-differentiated phenotypes, or nuclear pleiomorphism. Transcriptome analysis revealed minimal change in p53 target gene expression, suggesting that expression of the fusion alone was sufficient to impact these. Treatment of mice with the MDM2-p53-intereaction inhibitor, HDM201, was modestly successful at slowing tumor growth, alone. Combined treatment with HDM201 and the HDAC inhibitor panobinostat, known to be capable of derepressing Cdkn2a expression, synergized to curtail synovial sarcoma development.

overall_design: Gene expression profiling was performed on RNA-seq data generated from synovial sarcoma mouse tumors harboring distinct Trp53 genotypes (hSS2; Trp53-fl/fl and hSS2; Trp53-wt/wt). In addition, RNA-seq analysis was conducted on synovial sarcoma mouse tumors treated with HDM201, panobinostat, the combination therapy, or vehicle control. Tumors were harvested after two weeks of drug treatment for transcriptomic analysis.

first: Kevin

last: Jones

first: Jinxiu


title: Functional divergence of the Arg/N-degron pathway between the crop Brassica rapa and the model plant Arabidopsis thaliana

city: Maynooth

first: Emmanuelle

last: Graciet

state: Kildare

address: Biology Department

department: Biology

country: Ireland

institute: Maynooth University

summary: Comparison of the response to flg22 of Brassica rapa R-o-18 wild type and a N-degron pathway double mutant line for the E3 ligases PRT6.2 and PRT6.3 (Brprt6.2/3).

overall_design: Transcriptional differences between 3-day old seedlings of Brassica rapa R-o-18 (wild type) and the B. rapa prt6.2 prt6.3 double mutant upon 1 hour treatment with 1 uM flg22 (or mock control).

first: Brian

middle: C

last: Mooney

first: Pablo

last: Garcia

first: Shreenivas

last: Singh


title: Heterochronic activation of TGF-β signaling drives the diversity of the avian sterna

city: Fukuoka

first: Seung June

last: Kwon

state: Fukuoka

address: 744 Motooka, Nishi-ku

department: Graduate School of Systems Life Sciences

country: Japan

institute: Kyushu University

summary: Adaptive evolution has driven the diversification of vertebrate skeletal morphology, enabling a wide array of locomotor modes and lifestyles. In volant birds (carinates), the sternum develops a ventral keel that provides an attachment site for massive pectoral muscles essential for powered flight. In contrast, flightless ratites have lost both flight capability and the keel, resulting in a striking morphological contrast between their sterna. Here, we interrogated the cellular and molecular basis underlying this morphological divergence by using chicken embryos as a carinate model and emu embryos as a ratite model. Through a series of analyses including spatiotemporal transcriptomics and a spheroid culture system, we found that TGF-β signaling, which promotes proliferation of ventral sternal chondroprogenitors, is activated in both species until the stage when the left and right sternal progenitors meet; however, in chicken this activation persists beyond this stage, driving ventral extension of the keel primordium, whereas in emu it shuts off early, culminating in the absence of a protruding keel. Together, our findings suggest that skeletal morphological changes associated with behavioral transitions can arise from heterochrony in developmental signaling, thereby deepening our understanding of the evolutionary logic shaping skeletal diversification.

sample_organism:
Dromaius novaehollandiae
Gallus gallus

platform_organism:
Dromaius novaehollandiae
Gallus gallus

overall_design: RNA-Seq (combined with photo-isolation chemistry) profiling of chicken and emu sternal progenitors at developmental stage 24 and stage 36: dorsal and ventral. For each conditions, 4 biological replicates were prepared.

first: Yuji

last: Atsuta


title: Time-course transcriptome data of Actinoplanes sp. SE50/110 during the whole process of acarbose fermentation

city: Shanghai

first: Feifei

last: Cai

address: 800 Dongchuan RD. Minhang District, Shanghai, China

country: China

institute: Shanghai Jiao Tong University

summary: Metabolic engineering for high-value compounds like acarbose, a type 2 diabetes drug, requires systematic understanding of metabolic regulation. Here, we integrated multi-dimensional systems biology approach in Actinoplanes sp. SE50/110, a non-model bacterium producing acarbose. First, we reconstructed a substantially enhanced genome-scale metabolic model (iASE1267), which features an expanded set of genes, metabolites, and reactions, providing improved metabolic coverage. The model demonstrated high quality  with a MEMOTE  (metabolic model test suite) evaluation score of 80%, and showed significantly better phenotype simulation under various conditions. By using dual-objective OptRAM in-silico strain design approach on iASE1267 model, we identified two sets of static engineering strategies, overexpression of the 1-epi-valienol-1,7-diphosphate 1-adenylyltransferase AcbR and repression of an adenylosuccinate lyase; overexpression of a dTDP-glucose 4,6-dehydratase and repression of a 4-(cytidine 5'-diphospho)-2-methyl-D-erythritol kinase. Further, the dynamic flux pattern of time-course metabolic models revealed key time-dependent metabolic valves, L-aspartate oxidase (ASPO1), pyruvate carboxylase (PC), and pyruvate kinase (PYK). Additionally, we uncovered a core transcription-metabolism network by utilizing static modification sites as boundary markers, and identified two global negative transcriptional factors (TFs) within this network. Both the two TFs and the four metabolic genes have been experimentally validated with enhanced acarbose titer by 18–23%. This study establishes a framework linking static/dynamic modeling with transcriptional networks to decode metabolic-regulatory mechanisms in non-model bacteria, offering generalizable strategies for optimizing valuable microbial products.

overall_design: Transcriptome data encompassed 11 sampling points (8, 16, 20, 24, 32, 40, 48, 52, 56, 64,72 hr) over the whole 72-h fermentation period from Actinoplanes sp. SE50/110 ΔtreY cultured in fermentation medium.

first: Linquan

last: Bai

first: Zhuo

last: Wang


title: Transcriptome analysis uncovers PacC-mediated metabolic adaptation in the dermatophyte pathogen Tricophyton interdigitale

city: Ribeirão Preto

middle: Rodrigo

last: Sanches

state: SP

address: Av. Bandeirantes, 3900

department: Genetics

country: Brazil

institute: University of São Paulo

summary:
Purpose: We evaluated T. interdigitale H6 and PacC-1 mutant transcriptome using high-throughput RNA-sequencing (RNA-seq) technology aiming to identify metabolic pathways modulated by the transcription factor PacC.
Methods: We employed the next-generation sequencing (RNA-seq) approach to identify the central genes related to PacC in response to keratin.
Results: PacC acts as a central regulator of fungal adaptation and virulence in keratin-rich conditions, coordinating nutrient uptake, keratin degradation, and oxidative stress responses. Its mutation causes severe metabolic imbalance and cellular stress.
Conclusions: Our findings provide insights into a specific molecular function of PacC in a infection-like medium, highlighting PacC-dependent pH adaptation pathways as potential therapeutic targets in dermatophytoses.

overall_design: We examined at the transcriptomic level the effects of a pacC-1 mutant in Trichophyton interdigitale cultivated in keratin.

first: Joao

last: Neves-da-Rocha

first: Mayara

middle: I

last: Azevedo

middle: R

first: Antonio

last: Rossi

first: Nilce

middle: M

last: Martinez-Rossi


title: Effects of dietary human milk oligosaccharides (HMO) and Trichuiris muris  (Tm) infection on the caecum transcriptome in mice

city: Frederiksberg C

first: Andrew

last: Williams

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

summary: We examined how the adminsiration of prebiotic carbohyrdates (HMOs) and pathogen infection (Tm) interacted to modulate intestinal transcriptomic responses.

overall_design: Mice (n=6) were fed either a control diet or the same diet suppelemented with 3'-Sialyllactose (3'SL) in drinking water.  Mice were either left uninfected or trickle infected with Tm (3 doses of 20 eggs). Mice were terminated 35 days after the start of Tm trickle infection, and caecum tissues harvested and stored in RNAlater. Initially, the effects of 3'SL were assessed in healthy, uninfected mice. Subsequently, the effects of 3'SL were assessed in T. muris infected mice.


title: RNA-seq of thymic DP cells from KANSL1-deficient mice and their control mice.

city: Beijing

first: xiaoyu

last: yi

state: Beijing

address: Taiping Road

institute: NCBA

summary: We report the application of RNA-sequence in WT and Kansl1-deleted mice DP thymocytes with 3 biological replicates.

overall_design: Double-positive (DP) thymocytes were isolated from Kansl1fl/fl CD4-Cre and littermate control mice, and total RNA was extracted for library construction and sequencing.

first: Xiaoyu

last: Yi

first: Chang

last: Lu

first: Ting

last: Li

first: Hao

last: Hong


title: SIRT1 is a therapeutic target of brain metabolic and developmental consequences of methionine synthase deficiency in inborn errors of cobalamin metabolism

city: Belfast

first: Yaser

last: Atlasi

address: Lisburn Road

department: Johnston Centre for Cancer Research

country: United Kingdom

institute: Queen's University Belfast

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Inborn errors of vitamin B12 metabolism (IECM) with impaired methionine synthase (MS) activity (encoded by MTR), manifest severe cognitive and neurological symptoms unresponsive to B12 therapy. We explored the effects of Mtr brain-selective deletion at postnatal stage in mouse, identified histone deacetylase SIRT1 as a target of innovative therapy and evaluated the SRT2104 SIRT1 pharmacological activator to reverse alterations. We observed hippocampal significant metabolomic, behavioral, epigenome-wide, and proteomic alterations with promoter hypermethylation of pyruvate dehydrogenase and an abolished expression of SIRT1. MS disrupted the SIRT1/Wnt axis, with decreased neurogenesis and increased astrocytosis associated with altered learning abilities in water maze. Treatment with SRT2104 reversed the alterations of TCA, neurogenesis/astrocytosis and cognition. Our data highlight the prominent role of SIRT1 in brain neurodevelopmental and metabolic alterations of IECM, and the SRT2104 SIRT1 pharmacological activator as a promising drug repurposing candidate to treat B12-IECM resistant neurological manifestations.

overall_design: H3K4me3 ChIPseq in WT and MTR-KO mice

first: Karim

last: Matmat

first: Ziad

last: Hassan

first: Grégory

last: Pourié

first: Snehaa Vivienne

last: Seal

first: Manon

last: Jeandel

first: Carole

last: Arnold

first: Sachin

last: Luharia

first: Rémy

last: Umoret

first: Ramia

last: Safar

first: Almut

last: Heinken

first: Jean-Marc

last: Alberto

first: Okan

last: Baspinar

first: Justine

last: Paoli

first: Sebastien

last: Hergalant

first: Pierre

last: Rouyer

first: Jean-Michel

last: Camadro

first: Laurent

last: Lignières

first: David

last: Coelho

first: Jean-Louis

last: Guéant*

first: Rosa-Maria

last: Guéant-Rodriguez


title: LncRNAs coordinate doxycycline-induced gene expression response in human iPSCs (ATAC-seq)

city: Boulder

first: Mingfeng

last: Liu

state: CO

address: 709 Mohawk Dr

institute: University of Colorado

summary: Long non-coding RNAs are known to regulate gene expression. However, less is understood about the temporal dynamics of lncRNA regulation, particularly how they influence early, middle, and late gene expression. To investigate this, we generated 17 genetically defined, Doxycycline-inducible lncRNA transgene hiPSC lines and performed high-density time-course RNA-seq and ATAC-seq. We observed that most lncRNA transgenes showed expected induction and subsequent changes in gene expression. However, the putative target genes of the different lncRNAs had substantial overlap, and control cell lines showed a similar set of induced genes, leading us to conclude that the substantial effect of doxycycline prevented identification of lncRNA-specific effects. Although doxycycline-induced gene expression changes have been reported previously, the large size of the current study allowed us to identify a highly reproducible doxycycline response gene signature (DRGS). We further observe that the DRGS occurs in most human cell lines tested with Dox exposure. Notably, the DRGS includes 18 endogenous lncRNAs that exhibit highly reproducible temporal regulation by Dox itself. Our results suggest these lncRNAs act synergistically as "co-response amplifiers" associated with the stress response; some are linked to different cell fates, such as epithelial-mesenchymal transition or nervous system development.

overall_design: The genomic integration strategy utilized the H11 safe harbor locus on chromosome 22. The Tet-On inducible expression cassette containing the target lncRNA was integrated through Cre-LoxP recombination (Lox2272/Lox511), followed by puromycin selection. Using this platform, we generated 17 lncRNA-expressing cell lines and one control cell line expressing mRNA for Green Fluorescent Protein (GFP). Next, we performed RNA-seq (0, 2, 4, 8, 16, 24, 48, and 96 hours, 3 replicates) and ATAC-seq (every 30 minutes from 0 to 2.5 hours, 3 replicates) after doxycycline induction.

first: Isabela

last: Pereira

first: Sajad

last: Sofi


title: The DoGA Consortium Atlas of Canine Enhancers and Promoters Across Tissues and Development

city: Stockholm

first: Carsten

last: Daub

address: Blickagången 16, 14152 Flemingsberg

department: Gastroenterology and Nutrition Unit (GUT)

country: Sweden

institute: Karolinska Institute

summary:
The domestic dog is a powerful genetic model for complex traits, disease and behaviours relevant to human biology, yet the canine genome still lacks a systematic transcription-defined atlas of regulatory elements. Existing resources have improved annotation but largely infer regulatory activity from chromatin features rather than directly mapping transcription initiation at promoters and enhancers. Here, we address this gap using 114 CAGE-seq libraries spanning 56 tissues and developmental stages from 9 dogs. We identify 68,446 promoters and 46,661 active enhancers, and define their tissue-enriched activity across the canine body.
Among comprehensive enhancer and promoter sets, 9,787 are classified as robust enhancers and 27,341 as robust promoters, thus indicating a subset with high confidence. Our results and data resources will facilitate additional future community efforts for gene discovery in disease, morphology, and behavior and improve the suitability of the dog as a model organism for human physiology and human diseases.

overall_design: The study focuses on the identification of enhancer and promoter elements across different dog breeds in different tissue samples. Additionally, the dataset includes six embryos, which are 30 days and 20-25 days old.

first: Isil

last: Takan

first: Matthias

last: Hortenhuber

first: Noora

last: Salokorpi

first: Rijja

last: Bokhari

first: Cesar

last: Araujo

first: Rasha

last: Aljelaify

first: Ileana

last: Quintero

first: Sini

last: Ezer

first: Faezeh

last: Mottaghitalab

first: Amitha

last: Raman

first: Fiona

last: Ross

first: Tarja

last: Jokinen

first: Pernilla

last: Syrja

first: Danika

last: Bannasch

first: Antti

last: Livanainen

first: Marjo

last: Hytonen

first: Juha

last: Kere

first: Hannes

last: Lohi


title: The deubiquitinase USP1 promotes the progression of AML by stabilizing ID1 [RNAseq_AML_shUSP1]

city: suzhou

first: yang

last: yang

address: zhongnan road

institute: soochow university

summary: Acute myeloid leukemia (AML) represents a clonal malignant disorder affecting the hematopoietic system, predominantly featuring abnormal clonal proliferation of myeloid precursor cells and linked to unfavorable prognosis. This investigation seeks to improve clinical outcomes through examing the mechanistic role ubiquitin-specific protease 1 (USP1) in AML. Data analysis from The Cancer Genome Atlas (TCGA) and TARGET databases demonstrated that USP1 exhibits high expression in AML, where increased show positive correlation with poor prognostic outcomes. In vitro studies using short hairpin RNA (shRNA) for USP1 knockdown showed significant suppression of AML cell proliferation and enhanced apoptosis. Additionally, in vivo investigations indicated that USP1 knockdown inhibited tumor growth and enhanced survival rates. The USP1 inhibitor SJB3-019A displayed similar effects on AML cells. Co-immunoprecipitation (CO-IP) coupled with mass spectrometry analysis indicated that USP1 associates with ID1, mediating its function via deubiquitination mechanisms. CUT&Tag findings additionally demonstrated that ID1 modulates target genes involved in AML. This investigation confirms that USP1 serves a critical role in facilitating the proliferation and survival of AML cells through ID1 stabilization. The findings suggest that the USP1 inhibitor SJB3-019A represents a promising new therapeutic approach for treating AML.

overall_design: mRNA profiles of CMK cells treated with short hairpin RNAs (shRNAs) targeting USP1 or negative control (shNC) were generated by RNA sequencing, in double, using Illumina NovaSeq6000.

first: Yang

last: Yang


title: Telomere recapping via gene therapy as a therapeutic strategy for cardio-renal syndromes type 4 [NX]

first: Danshu

last: Xie

address: No. 639, Zhizaoju Road

institute: Shanghai Jiaotong University, School of medicine

summary: Cardio-renal syndromes type 4 (CRS4) is defined as heart failure driven by chronic kidney disease (CKD). Cardiovascular mortality is the leading cause of mortality in advanced CKD patients. Current medical treatments exhibit limited efficacy. This study demonstrates that telomere shortening in cardiomyocytes is characteristic of CRS4. We engineered an adeno-associated virus9 (AAV9) gene therapy overexpressing catalytic inactive and nuclear localized human telomerase reverse transcriptase (modhTERT) under cardiac troponin T (cTnT) promotor. Overexpression of modhTERT recapped myocardial telomeres, reversed cardiac dysfunction, cardiac hypertrophy, cardiac fibrosis and mitochondrial dysfunction in two CRS4 animal models: 5/6 nephrectomy and Angiotensin II-high salt-uninephrectomy murine models.

overall_design: Sham mice (mice were sacrificed after sham operation for 16 weeks and injected with saline) Sham and injected with JV101 mice (mice were sacrificed after sham operation for 16 weeks and injected with JV101) NX mice (mice were sacrificed after 5/6 nephrectomy for 16 weeks and injected with saline) NX and injected with JV101 mice (mice were sacrificed after 5/6 nephrectomy for 16 weeks and injected with JV101) RNA-seq of isolated cardiomyocytes

first: Alex Chia Yu

last: Chang

first: Wei

last: Ding


title: Expression data of microRNAs captured by OAA from plasma of NSCLC patients treated with nivolumab

city: Maebashi

first: EIJI

last: Narusawa

address: Showa-machi, Maebashi, Gunma 371-8511,

institute: Department of General Surgical Science, Gunma University Graduate School of Medicine

summary: Background: Predictive biomarkers for immune checkpoint inhibitors (ICIs) in non-small cell lung cancer (NSCLC) are limited. High-mannose glycans, enriched in tumors, can be selectively captured using OAA1 (recombinant OAA), a novel lectin. This study investigates whether plasma microRNAs (miRNAs) enriched by OAA1 serve as predictive markers of response to anti-PD-1 therapy.  Methods: Pre-treatment plasma samples from 48 NSCLC patients treated with nivolumab were processed using OAA1 lectin columns. Levels of circulating miR-320a, miR-320b, and miR-3613-5p , which were identified as resistance associated miRNAs by microarray, were quantified with and without OAA1 enrichment. Associations with therapeutic response and overall survival were analyzed.  Results: The three miRNAs were significantly upregulated in patients with stable or progressive disease compared to partial responders, but only after OAA1 enrichment. ROC and survival analyses showed improved predictive and prognostic power with OAA1-enriched miRNAs. For example, miR-3613-5p’s AUC improved from 0.837 to 0.897, and its hazard ratio increased from 3.386 to 7.815.  Conclusion: OAA1-captured plasma miRNAs are associated with resistance to nivolumab and poor prognosis in NSCLC. This glycan-based enrichment strategy enhances the clinical value of circulating miRNAs and may complement tissue-based ICI biomarkers.

overall_design: Paired pre-treatment and post-treatment blood samples collected from two NSCLC patients were utilized for microRNA isolation and RNA microarray as recently described. Briefly, miRNA was isolated from plasma by lectin column. RNA extraction was performed using the OAA-lectin column and the QIAzol® Lysis Reagent (Qiagen) followed by purification in the NucleoSpin® miRNA Plasma (MACHEREY-NAGEL GmbH & Co.). Biotinylated cRNA preparation was performed with the FlashTag™ Biotin HRS RNA Labeling Kit (Thermo Fisher Scientific, Walthmam, MA, USA) and the biotin-labeled sample were hybridized on GeneChip miRNA 4.0 Array. GeneChips were washed and stained in the Affymetrix GeneChips Fluidics Station 450. GeneChips were scanned using the Affymetrix GeneChip™ Scanner 3000 7G with AutoLoader.

first: Yukiko

last: Nakano

first: Eiji

first: Tadataka

last: Kamiyama

first: Takehiko

last: Yokobori

first: Yoshihiro

last: Taguchi


title: Role of MYOC A445V mutation on glaucomatous degeneration of human retinal ganglion cells.

city: Omaha

first: Iqbal

last: Ahmad

state: NE

address: 42nd St and Emile St

department: Ophthalmology and Visual Sciences

institute: University of Nebraska Medical Center

summary: Glaucoma is a group of diseases that results in the death of retinal ganglion cells (RGCs), leading to permanent blindness. Myocilin is one of the genetic factors associated with primary open angle glaucoma (POAG) with or without ocular hypertension. Using myocilin-dependent POAG patient-derived iPSC RGCs, we have shown that RGCs harboring the myocilin mutation (A445V) have dysregulated unfolded protein response with developmental and functional abnormalities, which may make them suscepetible to degeneration regardless of ocular hypertension.

overall_design: Patient-derived and gene-corrected iPSCs were differentiated into RGCs followed by differential gene expression analysis.

first: Subrata

last: Shil

first: Murali

last: Subramani

first: Matthew

last: J. van Hook

first: Fang

last: Qiu


title: Stromal Erbb3 shapes uterine gland morphogenesis

city: Cincinnati

first: Bo

last: Li

address: 240 Albert Sabin Way

institute: Cincinnati Children's Hospital Medical Center

summary: Uterine glands are critical for embryo implantation by secreting leukemia inhibitory factor. We show that stromal Erbb3 is required for uterine gland morphogenesis in mice, and its deletion causes implantation failure, impaired gland branching, and reduced LIF expression. Transcriptome analyses identify a stromal IGF1/IGF1R signaling axis that regulates epithelial FOXA2 expression and gland development.

overall_design: Endometrial tissues were collected from Erbb3^f/f (control) and Erbb3^d/d (stromal Erbb3-deleted) mice on day 3 of pregnancy. Single-cell suspensions were generated and processed using the 10x Genomics Chromium Flex Gene Expression workflow.  This design enables comparison of single-cell transcriptomes between control and Erbb3-deficient uteri.


title: Stromal Erbb3 shapes uterine gland morphogenesis [RNA-seq]

overall_design: RNA-seq profiling of day 3 mouse uterine stromal cells from Erbb3f/f and Erbb3d/d females.


title: ChemR23 prevents phenotypic switching of vascular smooth muscle cells into macrophage like foam cells in atherosclerosis.

city: Bern

first: Bryce

last: Evans

address: Murtenstrasse, 28, 365

department: DBMR

country: Switzerland

institute: Inselspital, Universitätsspital Bern

summary: Objective: Hematopoietic ChemR23 deficiency was shown to reduce atherosclerotic lesions by increasing M2 macrophages, but conflicting results in systemically deficient mice suggest a cell-specific function of ChemR23. Therefore, we aimed to study the role of ChemR23 particularly on vascular smooth muscle cells (VSMCs) in atherosclerosis. Methods and Results: Mice with a non-hematopoietic cell ChemR23 deficiency due to bone marrow transplantation of Apolipoprotein E deficient bone marrow into irradiated ChemR23e/e Apoe-/- double deficient recipient mice (Apoe-/- ►ChemR23e/e Apoe-/-) were fed a Western Diet for 6- or 12-weeks. Subsequent analysis revealed an increased lesion size and enhanced VSMC proliferation and VSMC foam cells in Apoe-/- ►ChemR23e/e Apoe-/- mice. Bulk RNA sequencing of adventitia-stripped aortas of Apoe-/- ►ChemR23e/e Apoe-/- mice exposed an increase in gene expression of synthetic VSMC markers such as Lgals3 and Cd68, while contractile genes were downregulated. Likewise, single-cell transcriptome data from advanced human atherosclerotic plaques uncovered the highest ChemR23 expression in contractile VSMCs while its expression in synthetic VSMCs was markedly reduced. In vitro, treatment of human aortic smooth muscle cells (HASMCs) with α-NETA, a small molecule inhibitor of ChemR23, increased synthetic gene expression but downregulated expression of TGFB, ABCA1, ABCG1 and SRB1. Further, α-NETA-treated HASMCs downregulated TGFB secretion, increased cholesterol uptake but decreased cholesterol efflux, and showed enhanced cell proliferation. Agonizing ChemR23 with its bona fide ligand chemerin 9 (C9) had no effect on synthetic gene expression but mitigated the effects of α-NETA on gene expression, cholesterol uptake, efflux, and cell proliferation. In vivo, both α-NETA and C9 treatment of Apoe-/- mice over 4 weeks WD revealed therapeutic potential. C9 reduced general inflammatory burden while α-NETA promoted an atheroprotective M2 macrophage phenotype. Conclusions: These findings reveal a critical role of ChemR23 in regulating VSMC phenotype switching thereby affecting atherosclerosis and suggest ChemR23 as a therapeutic target to either modulate inflammation (C9) or macrophage polarization (α-NETA) in atherosclerotic disease.

overall_design: Bulk RNA sequencing was performed on aortas from bone marrow–transplanted Apoe⁻/⁻►ChemR23e/eApoe⁻/⁻ and Apoe⁻/⁻►Apoe⁻/⁻ mice after 6 weeks of Western diet feeding. The aortas were dissected under a microscope, with the adventitia removed to preserve the media and intima. RNA was isolated from these layers, and sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA kit. Libraries were quality controlled, pooled, and sequenced on an Illumina NovaSeq 6000 platform, yielding paired-end reads. Data processing included alignment to the mouse reference genome with HiSat2, read counting with FeatureCounts, and differential gene expression analysis using DESeq2, followed by pathway enrichment analyses

first: Julia

last: Schulz

first: Anais

last: Yerly

first: Manovriti

last: Thakur

first: Nico

last: Angliker

first: Mark

last: Siegrist

first: Yvonne

last: Jansen

first: Yi

last: Yan

first: Sanne

middle: L

last: Maas

first: Christoph

last: Gold

first: Vasiliki

last: Triantafyllidou

first: Floriana

last: Farina

first: Batoul

last: Bayer

first: Christian

last: Weber

first: Justus

last: Wettich

first: Lars

last: Maegdefessel

first: Nadia

last: Sachs

first: Marc

last: Schindewolf

first: Drosos

last: Kotelis

first: Heidi

last: Noels

first: Donato

last: Santovito

first: Emiel

last: van der Vorst

last: Döring


title: Possible association between the microbiota in subgingival and atherosclerotic plaque in patients with carotid stenosis.

city: Halle (Saale)

first: Danny

last: Misiak

address: Kurt-Mothes-Str. 3a

department: Molecular Cell Biology

country: Germany

institute: Martin Luther University Halle-Wittenberg

summary: Bacterial DNA was detected in both subgingival and carotid plaque samples. The microbial composition differed between subgingival and carotid plaque communities. Alpha diversity analysis revealed significantly higher diversity in subgingival samples compared to carotid plaques (p = 0.039). Beta diversity analysis, including unweighted UniFrac analysis (p<0.001), linear discriminant analysis with effect size estimation, cladogram-based analysis, and principal component analysis, confirmed marked differences between the subgingival and carotid plaque microbiota. However, the study did reveal overlaps in a few individual cases.

overall_design: In this prospective cohort study, microbial samples from both subgingival sites and carotid plaques were collected from 25 hospitalized patients scheduled for carotid endarterectomy. Preoperative all patients underwent periodontal examination. The complex microbial composition was assessed using metagenomics sequencing of 16S rRNA gene targeting the V3/V4 regions.

first: Schulz

last: Susanne

first: Reichert

last: Stefan

first: Misiak

last: Danny


title: Intranasal delivery of SARS-CoV-2 triggers cellular and molecular alterations in the mouse trigeminal ganglion and brainstem: focus on the nociceptive pathways related to migraine

city: Paris

first: Frederic

last: Blond

address: 17 rue Moreau

country: France

institute: Institut de la Vision

summary: Headache disorders, including migraine, are common symptoms of COVID-19, which may result from the sensitization of the trigeminal ganglion (TG) and brainstem relay structures. Recent studies suggest that SARS-CoV-2 may invade trigeminal nerve endings in the nasal cavity. However, despite these insights, the precise underlying mechanisms remain poorly understood. Here, we investigated the cellular and molecular changes in the TG and brainstem with a special attention for the spinal trigeminal nucleus in K18-hACE2 mouse model infected with SARS-CoV-2. We first confirmed the expression of the cellular proteins playing a role in SARS-CoV-2 cell entry (ACE2, TMPRSS2 and NRP1) in both structures. In addition, we reported the expression of the viral nucleocapsid (N) and spike (S) proteins in TG and brainstem at 6 days post infection by multimodal approaches (RNA sequencing, RNAscope, and immunohistofluorescence). In the TG, SARS-CoV-2 proteins S and N were detected in nerve fibers as well as in transient receptor potential vanilloid 1 (TRPV1) and calcitonin gene-related peptide (CGRP) nociceptive neurons. Transcriptomics analysis of the TG from infected K18-hACE2 have revealed significant changes in gene expression, including Ccl2, Atf3, Cxcl10, Saa3, Plin4 genes. Additionally, increased immunoreactivity for ATF3 and Iba1 has been detected in the TG of these mice post-infection. In the brainstem, SARS-CoV-2 protein was exclusively found in neurons, with no detection in astrocytes or microglial cells, the latter exhibiting an activated form in K18-hACE2 infected mice. Bulk RNA-Seq analysis clearly confirmed a cytokine and chemokine storms, inflammasome activation (Gsdmd, Casp4/1, Nlrp3), molecular markers of neuronal activation (Jun, Fos, Fosb), neuronal injury (Atf3) and pain markers (Gfra1, Ntrk1, Ptgs2). We also shown that a significant number of infected neurons were found within, or in close contact to a dense network of CGRP-positive nociceptive nerve fibers in the trigeminal brainstem. Finally, we provided gene interaction networks and identified specific SARS-CoV-2 biomarkers Saa3, Cxcl10, Ccl2, Atf3 and Plin4 in TG and brainstem which could serve as potential indicators of disease severity. In conclusion, this study reports a robust set of transcriptomic and cellular changes triggered by SARS-CoV-2 in the TG and brainstem, offering a potential mechanistic explanation for sensory abnormalities, such as migraine, observed in COVID-19 patients.

overall_design: Male hemizygous transgenic mice expressing human ACE2 under the K18 promotor (B6.Cg-Tg(K18-ACE2)2Prlmn/J (K18-hACE2) were purchased from Jackson Laboratories via Charles River Laboratories (L'Arbresle, France), bred and maintained at Sorbonne University animal facilities.Viral infection was performed in a ABSL-3 facility (UMS28 Phenotyping small animal). Under xylazine/ketamine anesthesia (xylazine 10mg/kg, ketamine 100 mg/kg; 0.1ml/10g), male K18-hACE2 mice (11- to 22-week-old; n=25) were infected with 2.4 x 104 plaque-forming units (PFU) of SARS-CoV2 by intranasal inoculation (12-17l). K18 hACE2 mice (n=18) intranasally inoculated with an equal volume of HNE buffer (provider) were used as a mock-infection control.

first: Jian

last: Huang

first: Elodie

last: Reboussin

first: Lola

last: Bianchi

first: Christelle

last: Enond

first: Serban

last: Morosan

first: Isabelle

last: Malet

first: Stéphane

last: Fouquet

first: Eugénie

last: Genestant

first: William

last: Rostène

first: Christophe

last: Baudouin

last: Melik Parsadaniantz

last: Marot

first: Anne-Genevieve

last: Marcelin

first: Florence

last: Cayetanot

first: Xavier

last: Guillonneau

first: Laurence

last: Bodineau

last: Bourgeais-Rambur

first: Annabelle

last: Réaux-Le Goazigo


title: A fungal root endophyte functionally extends host immunity and mitigates natural immune variation in Arabidopsis

city: Köln

first: Natalie

last: Peltz

address: Bonner Str. 45

institute: University of Cologne

summary: Beneficial root-associated microbes can enhance plant resilience by complementing aspects of host immunity. The fungal root endophyte Serendipita indica (Si) is known to promote plant growth and confer broad stress tolerance. To assess how natural host genetic variation influences Si-mediated protection, we screened 47 Arabidopsis thaliana accessions for susceptibility to the fungal pathogen Bipolaris sorokiniana (Bs) with and without Si colonization. All accessions benefited from Si, indicating that endophyte-mediated disease mitigation occurs broadly across diverse host genotypes. A focused comparison of two genetically and geographically proximate Swedish accessions, T510 and T530, which displayed the most divergent protection scores, revealed substantial differences in Bs susceptibility. Transcriptome profiling under bi- and tripartite colonization showed conserved defense responses in both accessions. Bs infection downregulated growth- and development-related genes, consistent with a growth–immunity trade-off, with T530 exhibiting higher Bs colonization and a stronger transcriptional response than T510. Co-colonization with Si effectively suppressed pathogen growth and disease symptoms in both accessions. Comparative genomic and transcriptomic analyses identified four immune receptor genes, including the TIR-NLR ISI, present in T510 but absent in T530. An isi T-DNA insertion mutant phenocopied the heightened Bs susceptibility of T530, confirming that ISI contributes to root immunity, while Si-mediated protection remained intact despite increased pathogen susceptibility. Together, these findings demonstrate that fungal endophytes can mitigate the functional consequences of natural immune variation and enhance the resilience of genetically diverse plant populations.

overall_design: RNA-Seq analysis of root material from Col-0, T510 and T530 plants at 3 and 6 days post infection with either S. indica, B. sorokiniana, a mix of both, or water.

first: Laura

last: Armbruster

first: Christopher

last: Stephens

first: Vivien

last: Joisten-Rosenthal

first: Tim

last: Thomsen

first: Alex

middle: W

last: Yan

first: Nick

last: Dunken

first: Renan

last: Grando

first: Stan

last: Kopriva

first: Juliette

last: de Meaux

first: Gregor

last: Langen

first: Anna

first: Björn

last: Usadel

first: Alga

last: Zuccaro


title: KDM5C and KDM5D influence DNA methylation in adult mouse liver

city: Montreal

middle: K

last: Naumova

state: QC

address: 1001 Decarie Blvd

department: Obstetrics and Gynecology

country: Canada

institute: McGill University

type: Methylation profiling by high throughput sequencing

summary: Background. Several lines of evidence suggest that the sex-chromosome complement influences autosomal gene regulation and DNA methylation, however, the exact molecular mechanisms responsible for such effects remain elusive. X-linked epigenetic modifiers that escape X-chromosome inactivation, and hence have higher dosage in female cells, are the primary gene candidates for mediating the effects of X-dosage, whereas Y-linked paralogs may rescue such imbalance or have distinct effects on methylation. Methods. Here, we tested the impacts of mutations in mouse histone lysine 4 demethylases Kdm5c (X-linked) and Kdm5d (Y-linked) on DNA methylation in mouse liver. KDM5C and KDM5D demethylate H3K4me2/3 thereby facilitating DNA methylation of their target DNA regions. Therefore, loss of either Kdm5c or Kdm5d is expected to reduce DNA methylation at such regions. We hypothesized that Kdm5c gene dosage was responsible for the X-dosage dependent DNA methylation in mouse liver and compared DNA methylation patterns in heterozygous mutant Kdm5c+/- and wild type females using whole genome bisulfite sequencing (WGBS) and DSS. Results. We examined the impacts of mutations in Kdm5c or Kdm5d on genome-wide DNA methylation and found that they had different targets but tended to map close to H3K4me1-enriched regions. We also compared the Kdm5c and Kdm5d sensitive regions to regions with sex-chromosome complement dependent DNA methylation and found no overlaps. Conclusions. In summary, while Kdm5c and Kdm5d have multi-locus effects on DNA methylation in mouse liver, they are unlikely to be solely responsible for sex-chromosome complement effects on DNA methylation in adult mouse liver.

overall_design: Whole Genome Bisulfite Sequencing (WGBS) profiling of the methylomes of livers from adult (10-11 weeks old) Kdm5c and Kdm5d mutant mice in comparison to wild type littermates or control crosses.

first: Emily

last: Gibbons

first: Kathleen

last: Oros Klein

first: Shinya

last: Inoue

first: Tohru

last: Kimura

first: Celia

last: Greenwood


title: Affymetrix SNP array data of a new RUNX1 variant in familial leukemia

city: Perugia

first: Cristina

last: Mecucci

address: Piazzale Menghini n.9

department: Department of Medicine, Hematology and Bone Marrow Transplantation Unit

country: Italy

institute: University of Perugia

summary: Affymetrix SNP array data from autosomal dominant leukemia with a previously unpublished pathogenic RUNX1 variant in a Family affected by Friedreich Ataxia (FRDA).

overall_design: Copy number analysis  and SPNa  by CytoScan HD Affymetrix platform

first: Valentina

last: Pierini

first: Maria

last: Crocioni


title: PreciCE: Precision engineering of cell fates via data-driven multi-gene control of transcriptional networks

first: Jens

middle: Peter

last: Magnusson

address: Alfred Nobels Allé 8

department: Laboratory Medicine

institute: Karolinska Institutet

summary: The directed differentiation of stem cells into specific cell types is critical for regenerative medicine and cell-based applications. However, current methods for cell fate control are inefficient, imprecise, and rely on laborious trial-and-error. To address these limitations, we present a technology for data-driven multi-gene modulation of transcriptional networks. We develop bidirectional CRISPR-based tools based on dCas12a, Cas13d, and dCas9 for simultaneously activating and repressing many genes. Due to the vast combinatorial complexity of multi-gene regulation, we introduce a machine learning-based computational algorithm that uses single-cell RNA sequencing data to predict multi-gene perturbation sets for converting a starting cell type into a desired target cell type. By combining these technologies, we establish a unified workflow for data-driven cell fate engineering and demonstrate its efficacy in controlling early stem cell differentiation while suppressing alternative lineages through logic-based cell fate operations. This approach represents a significant advancement in the use of synthetic biology to engineer cell identity.

overall_design: Cultured human cells (HEK293T and iPSCs) were transfected with CRISPRa/i gene constructs that caused the simultaneous up- and downregulation of multiple genes. For some iPSC experiments, cells then underwent directed differentiation before analysis. Cells were FACS-sorted into 384-well plates and processed using Smart-seq3xpress, then sequenced using single-end or paired-end sequencing.

middle: P

first: Yusuf

last: Roohani

first: Daniel

last: Stauber

first: Yinglin

last: Situ

first: Paloma

last: Ruiz de Castroviejo Teba

first: Rickard

last: Sandberg

first: Jure

last: Leskovec

first: Lei

middle: S

last: Qi


title: Plant-specific function of H3K9me3 as a permissive chromatin mark during Arabidopsis seed germination

city: Seoul

first: Jae-Wook

last: Yoon

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

summary: Seed dormancy and germination are sequential phases, both tightly regulated by environmental and hormonal cues to ensure germination under favorable conditions. While hormonal and transcriptional regulators are well characterized, the epigenetic mechanisms governing these transitions are less understood. We profiled H3K4me3, H3K27me3, and H3K9me3 in the seeds of Arabidopsis thaliana Columbia-0 and Cape Verde Islands, representing shallow and deep dormancy, respectively, at freshly harvested (FH), after-ripened (AR), and germination-stimulated (GS) states. H3K4me3 and H3K9me3 co-localized in euchromatic, transcriptionally active regions, whereas H3K27me3 occupied repressive domains. Histone methylation landscapes were stable from FH to AR but showed a marked H3K9me3 increase from AR to GS in association with the activation of genes related to translation, energy metabolism, and cell division. Co-marking by H3K4me3 and H3K9me3 correlated with highest transcript levels. During dormancy release, AR-repressed genes, including DOG1, showed targeted reductions in H3K4me3 and H3K9me3 levels. These findings support a plant-specific role of H3K9me3 as an active or permissive chromatin mark promoting transcriptional reprogramming during germination.

overall_design: Histone H3K4me3, H3K9me3, and H3K27me3 ChIP-seq profiles of Arabidopsis seeds from the Col and Cvi ecotypes at each stage (FH, AR, and GS).

first: Min-Jeong

last: Kang

first: Hongshi

last: Jin

first: Yoo-Sun

last: Noh

first: Bosl


title: Activation of the aryl hydrocarbon receptor in human melanoma cells enhances cancer cell-intrinsic MHC-II expression

first: Zexian

last: Zeng

address: No.5 Yiheyuan Road, Haidian District, Beijing

institute: Peking University

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

overall_design: Refer to individual Series


title: ZIC2 affects oral squamous cell carcinoma stemness by regulating glycerophosphocholine metabolism via LYPLA2

city: Shijiazhuang City

first: Xingyue

last: Ma

state: Hebei

address: No. 383, Zhongshan East Road, Chang'an District, Shijiazhuang City, Hebei Province

institute: Stomatological Hospital of Hebei Medical University

summary: Oral squamous cell carcinoma (OSCC) is a common malignant tumor of the head and neck. Early-stage OSCC is mainly treated with surgery; for advanced cases, multidisciplinary treatments including surgery combined with adjuvant radiotherapy and chemotherapy are the main approaches. In our previous studies, we found through experiments and bioinformatics analysis that ZIC2 is highly expressed in OSCC and is associated with poor prognosis in patients. Subsequently, we constructed stable knockdown control (sh-NC) and experimental (sh-ZIC2) cell lines of ZIC2 using lentivirus, and conducted high throughput sequencing analysis to detect downstream differentially expressed genes, and performed enrichment analysis on the differentially expressed genes to identify related pathways.

overall_design: Stable cell lines of control group (sh-NC) and knockdown group (sh-ZIC2) were constructed in HN6 and SCC-9 cells, and three replicates were taken from each group, totaling 12 cell samples for high throughput sequencing.

first: Siyi

last: Li

first: Shuang

last: Mei

first: Xiangjun


title: Systematic identification of the functional lncRNAs during H7N9 avian influenza virus infection in mice

city: Yangzhou

first: Guoqing

last: Wang

state: Jiangsu province

address: 48 East Wenhui Road

institute: yangzhou university

type: Non-coding RNA profiling by high throughput sequencing

summary: Accumulating studies have identified the pivotal role of long non-coding RNAs (lncRNAs) in participating in host-virus interactions during virus infections. However, the regulatory roles of lncRNAs in influenza A virus (IAV) infection are still not fully elucidated. In this study, using high-throughput sequencing, we comprehensively compared the expression profiles of lncRNAs and mRNAs in mouse lungs infected either with the nonpathogenic parental (SDL124) H7N9 virus or its moderately pathogenic mouse-adapted (S8) variant. A total of 7636 significantly differentially expressed (SDE) lncRNAs were obtained in the S8-infected group compared to the mock group. As for the SDL124 group, 1042 SDE lncRNAs were identified. Subsequently, the mRNAs co-expressed with SDE lncRNAs were subjected to functional annotation and pathway enrichment analysis. The results indicated that the target mRNAs regulated by the S8 virus were mainly enriched in various immunological processes and exhibited a strong correlation with inflammatory-related signaling pathways. Moreover, 12 lncRNAs and 10 mRNAs co-expressed with SDE lncRNAs were selected and successfully verified by qPCR. Among these lncRNAs, NONMMUG032982.2 and NONMMUG032328.2 exhibited strong antiviral activity against IAV. Additionally, these two lncRNAs were chose for further in-depth bioinformatics analysis, including transcription factor prediction, coding capacity assessment, genomic location, construction of secondary structure, and prediction of potential interacting proteins. Taken together, these findings provide a cluster of lncRNAs probably associated with the virulence of IAV in mice and shed light on the anti-IAV effect of two functional lncRNAs, establishing molecular foundation for further exploring the regulatory mechanisms of lncRNAs in IAV infection.

overall_design: Systemically compared the expression profiles of lncRNAs and mRNAs in mouse lungs infected either with the nonpathogenic parental (SDL124) H7N9 virus or its moderately pathogenic mouse-adapted (S8) variant at 2 days post infection

first: Jiao

last: Hu

first: Xiufan

last: Liu


title: Activation of the aryl hydrocarbon receptor in human melanoma cells enhances cancer cell-intrinsic MHC-II expression [RNA-seq]

city: Beijing

summary: Cancer immunotherapy has revolutionized patient outcomes by enhancing immune responses, with major histocompatibility complex class II (MHC-II) playing a pivotal role. While MHC-II is classically expressed by professional antigen-presenting cells (pAPCs), emerging evidence highlights its expression by cancer cells, where it correlates with enhanced immune infiltration and favorable clinical outcomes. However, the regulatory mechanisms of cancer cell-intrinsic MHC-II remain unclear. Here, using genome-wide CRISPR-Cas9 screens, we identify the aryl hydrocarbon receptor (AhR) and its nuclear translocator (ARNT) as key regulators of MHC-II expression in human melanoma cells. The expression level and ligand-dependent activity of AhR and ARNT significantly correlate with cancer cell-intrinsic MHC-II expression. Multi-omics analyses reveal that this regulation is mediated through transcriptional activation of the MHC-II transactivator, CIITA, via binding of AhR-ARNT to its second promoter, pII. Our findings uncover a previously unrecognized regulatory axis for MHC-II expression in tumors, presenting new targets for enhancing immunotherapy.

overall_design: RNA-seq of A375 cells after CRISPR KO of AHR, ARNT or non-targeting control, and RNA-seq of WM115 cells after treatment of DMSO or FICZ.

first: Yiteng


title: Activation of the aryl hydrocarbon receptor in human melanoma cells enhances cancer cell-intrinsic MHC-II expression [Genome-wide CRISPR screen]

overall_design: Genome wide CRISPR screen on A375 and WM115 cells, targeting the lowest and highest ~10% of the population based on surface HLA-DR expression. Before sorting, WM115 cells were treated with 100 ng/mL IFNγ for 72 h.


title: Activation of the aryl hydrocarbon receptor in human melanoma cells enhances cancer cell-intrinsic MHC-II expression [ChIP-seq]

overall_design: ChIP-seq of HA-tag in SKMEL2 cells stably expressing 3×HA-RFP, 3×HA-AHR-RFP and 3×HA-ARNT-RFP.

first: Wenjin

last: Zheng


title: Activation of the aryl hydrocarbon receptor in human melanoma cells enhances cancer cell-intrinsic MHC-II expression [ATAC-seq]

overall_design: ATAC-seq of A375 cells after CRISPR KO of AHR, ARNT or non-targeting control.


title: C/EBPβ Deficiency Enhances Keratinocyte Apoptosis after UVB-Induced DNA Damage via Regulation of the Type I IFN and TNF Responses

city: RALEIGH

first: Dereje

last: Jima

state: NC

address: 850 Main Campus Drive

department: CHHE

institute: NCSU

summary: The epidermis is routinely subjected to DNA damage induced by solar (UVB) radiation. In addition to activating canonical DNA damage responses such as cycle cell checkpoints and DNA repair, UVB-induced DNA damage can also activate additional signaling pathways including inflammatory responses. The pathways activated downstream of UVB-induced DNA damage have a critical role in determining cellular survival to UVB radiation. Here we report that loss of CCAAT-enhancer/binding protein β (C/EBPβ) in mouse keratinocytes results in enhanced UVB-induced apoptosis through activation of extrinsic apoptosis genes cleaved caspase-8 and tBid. RNAseq and Ingenuity Pathway Analysis of UVB-treated C/EBPβ-/- primary keratinocytes revealed an enrichment of inflammatory signaling pathways, including the type I interferon (IFN-I) pathway as the most enriched pathway. Numerous IFN-I stimulated genes were up-regulated in UVB-treated C/EBPβ-/- keratinocytes, including genes that regulate extrinsic apoptosis. Inhibition of the interferon / receptor or the associated kinase Tyk2 greatly reduced cell death in UVB-exposed C/EBPβ deficient keratinocytes, demonstrating the dependence of IFN signaling in C/EBPβ regulated apoptosis. The apoptosis inducing cytokine, tumor necrosis factor alpha (TNF-α) was identified as one of the most significant upstream regulators activated in UVB exposed C/EBPβ-/- keratinocytes compared to UVB exposed wild type control. UVB exposed C/EBPβ-/- keratinocytes displayed increased expression of TNF-α and the enhanced apoptosis in C/EBPβ-/- keratinocytes was suppressed by a TNF-α neutralizing antibody. Our results indicate that loss of C/EBPβ enhances activation of a non-canonical UVB DNA damage response pathway involving interferon and TNF signaling to induce keratinocyte cell death.

overall_design: Total RNA was extracted  from UVB exposed wild type and C/EBPβ knockout primary mouse keratinocytes n=3 per group

first: Tobin

last: Emma

first: Sharma

last: Ayushma

first: Kros

last: Samantha

first: Jima

last: Dereje

first: Gray

last: Sophia

first: Hall

last: Jonathan


title: Transcriptome analysis of liver sinusoidal endothelial cells (LSECs) under palmitic acid treatment and IL-6/sIL-6R complex stimulation

city: Takatsuki, Osaka

first: Yasuhiko

last: Ueda

address: 2-7 Daigaku-machi

institute: Osaka Medical and Pharmaceutical University

summary: This study investigates the transcriptional changes in liver sinusoidal endothelial cells (LSECs) following palmitic acid (PA) treatment and IL-6/sIL-6R complex stimulation. LSECs were cultured with PA for 12 hours and subsequently stimulated with the IL-6/sIL-6R complex for 1 hour to assess trans-signaling activation and gene expression changes. RNA sequencing was performed on four experimental groups: Control, PA, Complex, and PA+Complex.

overall_design: RNA sequencing analysis of human liver sinusoidal endothelial cells under four different treatment conditions: (1) Control (untreated), (2) Palmitic acid treatment (PA), (3) IL-6/sIL-6R complex stimulation (Complex), and (4) Combined palmitic acid treatment and IL-6/sIL-6R complex stimulation (PA+Complex). Total of 12 samples were processed for RNA sequencing (n=3 per group).

first: Nao

last: Kawaguchi


title: MYST acetyltransferases are a targetable therapeutic vulnerability in SETBP1-mutant leukemia [CUT&Run]

city: Portland

first: Julia

last: Maxson

state: Oregon

address: 3181 SW Sam Jackson Park Rd

institute: Oregon Health and Science University

summary: Mutations in SET binding protein 1 (SETBP1) are associated with an adverse prognosis in myeloid malignancies. These mutations stabilize SETBP1 protein, driving increased expression of a progenitor-associated gene expression program through incompletely described mechanisms. A proteomic screen revealed interactions between SETBP1 and members of the MYST acetyltransferase complexes, including the catalytic subunits—KAT6A and KAT7. Mutant SETBP1 increases the localization of MYST complexes at known SETBP1 target genes, including the Hoxa cluster, where they drive increased histone acetylation and gene expression. Treatment of SETBP1D868N-expressing myeloid progenitors with MYST inhibitors reduced target gene expression. To establish the efficacy of MYST inhibition in vivo, we treated mice harboring a syngeneic SETBP1-mutant leukemia with the clinical-grade MYST inhibitor—PF-9363. This resulted in complete hematologic control and increased survival. MYST inhibition was also highly effective against a SETBP1-mutant PDX model. These studies identify MYST acetyltransferases as promising therapeutic targets in SETBP1-mutant malignancies.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: CUT&RUN on human cell line: Doxycycline-inducible SETBP1 expression in K562 cells. CUT&RUN on mouse primary cells: lentivirally transduced control (luciferase) or SETBP1D868N mutant into mouse bone marrow lineage-negative (Lin-) cells and GFP sorting positive cells.

first: Hanqian

last: Carlson

first: Thai

last: Nguyen


title: ANGPTL3 in podocytes contributes to pathogenesis of lupus nephritis by activating MSR1 in macrophage

city: Shanghai

last: Zhao

state: Shanghai

address: 399  Wanyuan Road

institute: Children’s Hospital of Fudan  University

summary: Lupus nephritis (LN), a severe complication of systemic lupus erythematosus (SLE), is driven by immune complex deposition and inflammatory renal injury. This study uncovers a novel mechanism in which podocyte-derived angiopoietin-like protein 3 (ANGPTL3) exacerbates LN pathogenesis through macrophage scavenger receptor 1 (MSR1)-mediated activation. Protein interaction screening revealed direct binding between ANGPTL3 and MSR1, a macrophage-enriched receptor. Clinical analyses demonstrated elevated glomerular expression of ANGPTL3 and MSR1 in LN patients, correlating with reduced renal function and histopathological damage. In vitro, ANGPTL3-overexpressing podocytes activated macrophages in an MSR1-dependent manner. RNA sequencing of ANGPTL3-stimulated bone marrow-derived macrophages (BMDMs) identified robust activation of interferon signaling pathways, with key genes (Tnip3, Isg20). Silencing Msr1 abolished these effects, suppressing interferon-related gene expression. In the pristane-induced lupus model, ANGPTL3 and MSR1 co-localized with infiltrating macrophages in injured glomeruli, mirroring human LN pathology. These findings establish the ANGPTL3-MSRI axis as a critical driver of macrophage activation and interferon signaling in LN, highlighting ANGPTL3 as a promising therapeutic target to mitigate immune-mediated renal injury in SLE.

overall_design: RNA-seq profiling of Wildtpye bone marrow-derived macrophages (BMDMs) and Msr1-silenced BMDMs treated with ANGPTL3-enriched supernatants.


title: Mesenchymal Stem Cells-derived Exosomes Inhibit Inflammatory Infiltration and Tissue Remodeling in Eosinophilic Chronic Rhinosinusitis

first: Boyu

last: Cai

address: 1279 Sanmen Road, Hongkou District

department: Department of ORL-HNS

institute: Shanghai Fourth People's Hospital Affiliated to Tongji University

summary: Exosomes generated from mesenchymal stem cells (MSCs-Exos) provide therapeutic promise for inflammatory diseases; however, their function in eosinophilic chronic rhinosinusitis (ECRS) is yet inadequately investigated. This research investigated the immunomodulatory and reparative properties of MSC-derived exosomes in a papain-induced mouse model of ECRS. MSCs-Exos were extracted and analyzed using transmission electron microscopy, NanoSight, and Western blotting. In vivo, intranasal delivery of MSCs-Exos mitigated ECRS symptoms, diminishing sneeze, epithelial hyperplasia, mucus hypersecretion, and collagen deposition. Histopathological and immunohistochemical evaluations demonstrated reduced expression of FXIII-A, Clca1, and iNOS, along with elevated E-cadherin levels, signifying inhibition of epithelial-mesenchymal transition and excessive mucus formation. Flow cytometry revealed that MSCs-Exos rebalanced Th1/Th2/Th17 responses by increasing Th1 (IFN-γ⁺) cell populations and decreasing Th2 (IL-4⁺) and Th17 (IL-17⁺) populations. RNA sequencing and bioinformatic analysis revealed the downregulation of type 2 inflammatory genes (Ccl24, Ccl11) and epithelial remodeling indicators (Clca1, Mmp12), with the enrichment of pathways associated with immune regulation (IL-10 signaling, Treg differentiation) and tissue healing. KEGG pathway analysis further indicated the involvement of IL-17, JAK-STAT, and TNF signaling regulation in the therapeutic effects. MSCs-Exos together alleviate ECRS by reestablishing immunological equilibrium, reducing inflammation, and preventing pathological remodeling, therefore establishing them as a viable cell-free treatment for chronic airway inflammatory conditions.

overall_design: RNA-seq  profiling of nasal mucosal tissues on the eosinophilic chronic rhinosinusitis (ECRS) mouse model before and after exosome therapy

first: Zhao

last: Wang

first: Maoxiang

last: Xu

first: Jiaojiao

last: Li

first: Danni

first: Fei

last: Tan


title: Peptide-based Wnt signal activation enables scalable production of clinical-grade patient-derived intestinal organoids for regenerative cell therapy

city: Tokyo

first: Tomohiro

last: Mizutani

address: 1-5-45 Yushima, Bunkyo-ku,

department: Department of Gastroenterology and Hepatology

institute: Institute of Science Tokyo

summary: Despite the clinical potential of intestinal organoids as a resource for regenerative cell therapy and bioengineering, the lack of reliable clinical-grade cultures has hampered further development. Here, we report the successful initiation and expansion of patient-derived intestinal organoids under a GMP-compliant protocol. Culture-, cost-, and time-efficiency improvements were achieved with organoid area-based passaging, one well plate culture, and the incorporation of Wnt activating peptide, PG-008. The peptide significantly enhanced organoid growth and stabilized patient-patient variability through intestinal stem cell (ISC) enrichment. Single cell RNA sequencing revealed that PG-008 resulted in remarkably pure culture consisting of ISCs and transit amplifying cells, suitable for rapid and consistent expansion. Intriguingly, our GMP-grade intestinal organoids contained LGR5+ ISCs, and injury-induced LGR5- regenerative ISCs, both enriched in peptide culture. Our study establishes clinical-grade intestinal organoids for further application, and a model facilitating in vitro investigations into regenerative stem cell induction and intestinal regeneration.

overall_design: Intestinal organoids were established from patient biopsies using GMP-compliant protocol, and cultured with recombinant Wnt3a protein or Wnt activating peptide PG-008. The organoids were expanded for four weeks, then dissociated into single cells and analyzed with scRNA-seq.

first: Hady

middle: Y

last: Sugihara


title: Cross-tissue single-cell atlas including central and peripheral immune tissues  in experimental autoimmune myasthenia gravis (EAMG)

city: Chongqing

first: Rui

last: Fan

state: Chongqing

address: 1st Youyi Road, Yuzhong District, Chongqing 400016, China

department: Neurology

institute: The First Affiliated Hospital of Chongqing Medical University

summary: Myasthenia gravis (MG) is an autoimmune disease with an incompletely understood mechanism and limited treatment options. MG is a systemic autoimmune disease, complex abnormal humoral and cellular immune responses play a crucial role in the pathogenesis of MG. The pathological changes involve not just individual immune tissues, but also complex interactions among multiple organs and systems. However, the majority of previous studies focused on abnormalities in peripheral blood and the thymus. With the development of high-throughput technology, several studies have unbiasedly revealed abnormal numbers and function of immune cells by single-cell RNA sequencing and, cytometry-of-time-flight/mass cytometry (CyTOF), indicated pivotal role of aberrant changes in innate immune cells, including monocytes and natural killer cell (NK), in the pathogenesis of MG. Nevertheless, these innate immune cells reside not only in blood, but also widely within the central and peripheral immune organ including bone marrow, thymus, spleen, and lymph nodes. But it is particularly difficult to collect these samples from patients and healthy control, hindering the comprehensive understanding of pathological mechanisms of MG. In the present study, single-cell sequencing technology was used to construct a cross-tissue single-cell atlas including bone marrow, thymus, spleen, lymph and whole blood in experimental autoimmune myasthenia gravis (EAMG) model

overall_design: Lennon score in the EAMG group were assessed, and rats with a clinical score ≥ 2, along with corresponding control rats, were selected for the experiment. The rats were anesthetized and placed in a biosafety cabinet, where blood was collected from the eyeball into EDTA-anticoagulated tubes. The spleen, thymus, lymph nodes, and tibias were dissected out and immediately placed in 5 mL of RPMI 1640 medium. The spleen, thymus, and lymph node tissues were thoroughly homogenized, then centrifuged at 300g for 5 minutes at room temperature. The supernatant was discarded, and after washing, the cell pellet was resuspended in PBS (HyClone, Marlborough, MA, USA) to form a single-cell suspension. GEXSCOPE red blood cell lysis buffer (Singleron Biotechnologies, Nanjing, China) was added to the cell suspension to remove red blood cells. The mixture was then centrifuged and resuspended in PBS. Trypan blue exclusion test was used to assess cell viability. We counted the cells using a TC20 automated cell counter (Bio-Rad, Hercules, CA, USA) and prepared a cell suspension with a final concentration of 1 × 10^5 cells/mL. The single-cell suspension was loaded onto a microfluidic device. The scRNA-seq library was constructed using the GEXSCOPE® Single Cell RNA Library Kit (Singleron Biotechnologies, Nanjing, China) and the Singleron Matrix® Automated Single Cell Processing System (Singleron Biotechnologies, Köln, Germany) based on the Singleron GEXSCOPE® protocol. After dilution to 4 nM, individual libraries were pooled for sequencing. The libraries were then sequenced on an Illumina HiSeq X with 150 bp paired-end reads (Illumina, San Diego, CA, USA).

first: Wenjun

last: Que

first: Dan

last: Lu

first: Linqi

last: Liu

first: Jing

last: Dong

first: Yaoqi

last: Gan

first: Zhihan

last: Zhang

first: Sisi

last: Jing

last: Xiao


title: MYST acetyltransferases are a targetable therapeutic vulnerability in SETBP1-mutant leukemia [RNA-Seq]

first: Julia

last: Maxson

overall_design: RNA-seq profiling of mouse bone marrow lineage-negative (Lin-) primary cells lentivirally transduced with control (luciferase) or SETBP1D868N mutant. To study MYST inhibitor effects, RNA-seq profiling was also performed on mouse bone marrow lineage-negative (Lin⁻) primary cells lentivirally transduced with the SETBP1D868N mutant followed by treatment with DMSO or PF-9363.

first: Hanqian

last: Carlson

first: Thai

last: Nguyen


title: Intracellular Aβ42 Sequestration by a Serine Protease Mitigates Neurotoxicity

city: hunan province

first: yang

last: meng

address: lusan

institute: hunan normal university

summary: The repeated failures in developing disease-modifying therapies for Alzheimer's disease (AD) by targeting extracellular Aβ have urged a complete reassessment of the cellular mechanisms underlying Aβ neurotoxicity. Emerging evidence suggests that intraneuronal Aβ accumulation represents an early pathogenic event in AD, preceding extracellular plaque formation and neuroinflammatory responses. However, whether targeting intracellular Aβ can halt disease progression and how this can be achieved remain unknown. While investigating the brain transcriptional responses to Aβ pathology, we identified a neuroprotective role for the serine protease Yip7 in a Drosophila AD model. Neuronal overexpression of yip7 alleviated multiple Aβ42- induced deficits, including declines in locomotor activity, impaired proteostasis, increased brain ageing and neuronal death, and reduced lifespan. Unlike canonical digestive proteases, Yip7 is not secreted but instead localizes to the endosomal/lysosomal compartments via a putative transmembrane domain initially predicted as a signal peptide. Crucially, Yip7’s neuroprotective function depends on its proper subcellular localization rather than the catalytic triad of serine proteases. Mechanistically, rather than directly eliminating Aβ, Yip7 increased neuronal retention of Aβ, supporting a model in which Yip7 reduces Aβ42 toxicity by limiting its degradation/secretion. Notably, yip7 overexpression also conferred protection in a Huntington's disease model, underscoring its broader relevance. Together, these findings introduce a novel concept that intracellular Aβ sequestration by a serine protease can mitigate neurotoxicity, and propose targeting intracellular amyloid as a promising therapeutic strategy for AD.

overall_design: Flies from Drosophila models with different genes were reared at 29°C and fed normally. Using Drosophila head transcriptome data to detect gene expression changes between wild-type and AD (Alzheimer’s disease) model flies.

first: Jingyun

last: Su

first: Xinfeng

last: Wang

first: Pa

last: Wu

first: Zongzhao

last: Zhai


title: Functional Requirement for Arginine Methylation of the Dicer Helicase Domain in 26G Endo-siRNA Pathway Activity and the Oocyte Meiotic Program

city: Houston

first: Nick

last: Newkirk

state: TX

department: Genetics and Epigenetics

institute: MD Anderson UTHealth Graduate School of Biomedical Sciences

summary: Spatiotemporal regulation of Dicer is critical for small RNA biogenesis, fertility, and early embryogenesis, yet, the mechanisms that modulate its activity, especially through the helicase domain, remain incompletely understood. Here, we identify regulatory roles for a non-traditional glycine-arginine-rich (GAR) motif, GRARR, in motif VI of the helicase domain. Mutations to conserved arginine residues of the GRARR motif impair maternal 26G endo-siRNA production and disrupt oocyte-to-embryo transition. We show that asymmetric di-methylation of Dicer R495 within this motif facilitates binding to ERI-5, a tandem-Tudor protein within the ERI Complex, likely potentiating 26G siRNA biogenesis, as deletion of eri-5 Tudor domains phenocopies Dicer GRARR mutants. Notably, these phenotypes are similar to those observed in Dicer phosphorylation mutants, implicating both arginine methylation and serine phosphorylation function in a coordinated mechanism. Our findings propose that a post-translational modification switch modulates Dicer conformation and effector engagement to control endo-siRNA production and oocyte-to-embryo transition.

overall_design: Hermaphrodite animals were shifted to 25C at the mid-L4 stage (after spermatogensis had completed) for 24 hours for oocytes to development, after which worms were collected, lysed and frozen in TRIzol at -80C for total RNA isolation. Total RNA was isolated from whole animals and prepared for small RNA sequencing using the TruSeq Small RNA Library Preparation Kit (Illumina)

first: Shin-Yu

last: Chen

first: Tokiko

last: Furuta

first: Leilei

last: Shi

first: Sabrina

last: Stratton

first: Hongyuan

last: Lin

first: Xiaodong

last: Cheng

first: Mark

last: Bedford

first: Swathi

last: Arur


title: Catabolism  of lignin-related methoxylated compounds in white-rot fungi utilizes a non-canonical extradiol dioxygenase

city: Golden

first: Davinia

last: Salvachua

address: 15013 Denver West Parkway

institute: National Renewable Energy Laboratory

summary: White-rot fungi (WRF) are the most effective lignin-degrading organisms in nature, making them essential to Earth’s carbon cycle. Lignin is a highly methoxylated, heterogeneous biopolymer derived from plants. However, the pathways WRF use to metabolize methoxylated aromatic compounds as carbon sources remain unidentified. Here, we employ a systems biology approach to elucidate the intracellular catabolism of vanillate – a monomethoxylated aromatic compound – in two white-rot fungi (WRF), Gelatoporia subvermispora and Trametes versicolor. We identified and biochemically validated a four-enzyme pathway that converts vanillate into β-ketoadipate – a metabolite that enters central carbon metabolism. This pathway deviates from typical bacterial pathways, where vanillate is initially demethylated and ring-cleaved by intradiol dioxygenases; instead, oxidative decarboxylation occurs prior to ring cleavage by extradiol dioxygenases. Thus, we conducted an in-depth investigation of ring cleavage and further downstream catabolism by the identified fungal enzymes using biochemical and structural approaches. This revealed non-canonical enzymes, including a highly substrate-specific extradiol dioxygenase and a metal-free, promiscuous reductase, the latter capable of acting on catabolic intermediates derived from both methoxylated and non-methoxylated aromatic compounds. This work emphasizes the potential of WRF and their enzymes to advance lignin valorization and enhance our understanding of their role during wood decay.

sample_organism:
Trametes versicolor
Gelatoporia subvermispora

overall_design: T. versicolor and G. subvermispora cultivations (6 per fungi) were conducted in M7 with cellobiose (5 g/L) and incubated statically at 28 °C, 75% humidity using a humidity-controlled incubator in the dark for 5 days (T. versicolor) or 12 days (G. subvermispora), then supplemented with filter-sterilized ascorbic acid (5 mM in water) and α-tocopherol (1 mM in ethanol). After 30 min, three flasks of each fungus were induced with vanillate (100 mM stock), for a final concentration of 2 mM. A second pulse of vanillate (100 mM stock) was added to the same flasks 12 h after the first pulse. For samples without vanillate, 2 pulses of autoclaved water (equal volume to the added vanillate solution) was added in lieu of vanillate solution at the same timepoints. Cultivations were harvested 12 h after the second pulse, corresponding to 6 days for T. versicolor and 13 days for G. subvermispora.

first: Alexa

last: Schwartz

first: Eugene

last: Kuatsjah

first: Irimpan

last: Mathews

first: Hugh

middle: D

last: Mitchell

first: Samuel

middle: O

last: Purvine

first: Elisabeth

last: Eder

first: David

last: Hoyt

first: Lye

last: Markillie

first: Meagan

last: Burnet

first: Sear

last: Woodsworth

first: Kelsey

last: Ramirez

first: Margan

last: Ingraham

first: Lummy

last: Monteiro

first: Ritimukta

last: Saranhi

first: John

middle: E

last: McGeehan


title: Cell-state specific drug-responses are associated with differences in signaling network wiring

city: Nijmegen

first: Klaas

last: Mulder

address: Geert Grooteplein 26

department: Molecular Developmental Biology

country: Netherlands

institute: Radboud University

summary: Intracellular signaling pathways form networks through which information is transmitted, often in the form of kinase-mediated phosphorylation events, to interpret extracellular signals and elicit appropriate cellular responses. Yet, even isogenic cells in an homogenous environment show heterogeneity in their intracellular “cell-state”, as well as their response to extracellular signals. Here, we aimed to better understand this relation between these phenomena by investigating how information flows through the EGF-receptor centered network upon targeted drug treatment, and how this is affected by cell-to-cell-state differences. Using single-cell ID-seq, we profiled the cell-state and signaling activity of primary human epidermal stem cells by measuring 69 (phospho-)proteins upon inhibition of the Erk/MAPK (p90RSK) and Akt/mTOR (p70S6K) routes downstream of the EGF pathway. We found that the effects of drug treatment propagated from the EGF-signalling pathway to other connected parts of the cellular signaling network, indicating altered signaling flow. We identified nine distinct cell-states that show pervasive state-dependent drug-responses for many (phospho-)proteins. Computational modeling of the signaling network using single-cell Comparative Network Reconstruction showed that many interactions between phospho-proteins (i.e. network wiring) were quantitatively different between cell-states. Furthermore, (phospho-)proteins with a cell-state dependent drug response, were more likely to be involved in interactions that showed a cell-state dependent strength. Overall, our results indicate that drug treatment response and signaling interactions between proteins are closely related and modulated by cell-state.

overall_design: scID-seq (DNA-tagged antibody measurements using HT-sequencing) of primary human epidermal keratinocytes treated with vehicle, p70S6K (PF4708671) or p90RSK (BI-D1870) inhibitors for 2 hours. Cell-hashing was used to allow pooling of treated samples prior to staining with the antibody panel and FACS-based single-cell distribution into 96-well PCR plates and library preparation.


title: Transcriptome of TACI KO and WT mouse marginal zone and follicular B cells

city: London

first: Victor

last: Tybulewicz

address: 1 Midland Road

institute: Francis Crick Institute

summary: The mature peripheral B cell compartment consists of follicular (FO) and marginal zone (MZ) B cells, which mature from transitional B cells in the spleen and mount T-dependent and T-independent antibody responses, respectively. TACI (Tnfrsf13b) is a member of the TNF-receptor superfamily expressed on mature and transitional B cells, with highest expression on MZ B cells and plasma cells, which is activated by the cytokines BAFF and APRIL. BAFF also stimulates the related receptor BAFFR, which provides signals that are essential for mature B-cell survival. Previous studies of TACI-/- mice have observed that TACI-deficiency leads to an expansion of mature B cells, and therefore it has long been thought that TACI is a negative regulator of mature B-cell survival. However, TACI-/- mice also have elevated levels of BAFF, therefore the B-cell hyperplasia phenotype in TACI-/- mice is most likely a cell-extrinsic effect due to increased BAFF-BAFFR signalling in TACI-/- B cells. To investigate the cell-intrinsic role of TACI, we generated mouse mixed bone marrow chimeras from TACI-/- and WT mice and studied the effect of TACI loss in vivo, without the confounding factor of increased BAFF. Here, we have analysed the transcriptomes of TACI KO and TACI WT marginal zone and follicular B cells by RNAseq.

overall_design: Mouse splenic follicular and marginal zone B cells of the genotype Tnfrsf13b-/- CD45.2+ (TACI KO), Tnfrsf13b+/+ CD45.2+ (TACI WT), or wildtype CD45.1+ were isolated by FACS from adult mixed bone marrow chimeras, with 6 biological repeats for each genotype, and analysed by RNAseq.

first: Daisy

middle: H

last: Luff

first: Stefan

last: Boeing


title: Serine metabolism ensures proper minor ZGA, regulating histone methylation and DNA integrity specifically male pronuclei of mouse zygotes

city: Sendai

first: Yohei

last: Hayashi

state: Miyagi

address: 4-1 Seiryo-machi, Aobaku

department: Institute of Development, Aging and Cancer

institute: Tohoku University

summary: Soon after fertilization, the zygotic epigenome undergoes a dramatic and rapid establishment process that is essential for the initiation of embryonic development. In such genome-wide epigenetic conversion, upstream regulation by metabolic pathways that supply essential substrates and cofactors is frequently observed in various cell types. However, the specific involvement of metabolic pathways in orchestrating epigenetic establishment within zygotes has remained largely unclear. In this study, we elucidated that the serine-glycine one-carbon (SGOC) metabolic pathway, which synthesizes S-Adenosylmethionine (SAM), a critical methyl group donor, has an essential role in regulating histone methylation in zygotes. Inhibition of the SGOC pathway led to pronounced zygotic arrest accompanied by disrupted histone methylations, specifically in the male pronuclei (PN). Notably, both zygotic arrest and disrupted histone methylation were rescued by inhibiting minor ZGA, indicating that minor ZGA regulated by the SGOC pathway functions upstream of histone methylation in the male PNs. SGOC pathway inhibition also caused the DNA damage exclusively in the male PN. Remarkably, enucleation of the male PN with impaired epigenome and DNA integrity rescued the zygotic arrest. Round spermatid injection-derived zygotes (ROSI-zygotes), which retain paternal histone methylations in the male PN, showed the greater resistance to CBR-induced paternal DNA damage than intracytoplasmic sperm injected zygotes (ICSI-zygotes). These findings demonstrate that the SGOC pathway safeguards paternal genome integrity in mouse zygotes by regulation of histone methylation via minor ZGA.

overall_design: To ivestigate the role of serine metabolic pathways in zygotic development, we  prepared 1 cell embryos from in vitro culture with the addition of DMSO (control), CBR-5884 (a inhibitor of serine metabolism) or CBR-5884+SAM (S-adenosylmethionine). We then performed RNA-seq analysis of 3 different conditions with 2 biological replicates.

first: Masatoshi

last: Ooga

first: Azusa

last: Inoue

first: Ayumu

last: Suzuki


title: DOT1L enhances BLM-induced pulmonary fibrosis by inducing endothelial-to-mesenchymal transition via H3K79me2 [ChIP-seq]

city: Guangzhou

first: Shu

last: Meng

state: Guangdong

address: No.9, XingDaoHuanBei Road, Guangzhou International Bio-island, Haizhu District

department: Department of Basic Science Research

institute: Guangzhou National Laboratory

summary: Endothelial-to-mesenchymal transition (EndoMT) have been reported to contribute to pulmonary fibrosis. Here, we showed that induction of EndoMT activated DOT1L expression and enhanced H3K79me2 level by TGFβ2 in human umbilical vein endothelial cells (HUVECs) in vitro. Using a bleomycin (BLM)-induced idiopathic pulmonary fibrosis (IPF) model, endothelial-lineage tracing reporter mice, and endothelial-specific Dot1L knockout mice, we confirmed that DOT1L mediates EndoMT and drives pulmonary fibrosis in vivo through H3K79 methylation. ChIP-seq revealed direct binding of SMAD2/3 to the DOT1L promoter and increased H3K79me2 deposition at fibrosis-related genes following TGFβ2 stimulation.

overall_design: HUVECs were collected at 24 h with TGFβ2 treatment or not, and ChIP-seq for SMAD2/3 was performed.

first: Yaofeng

last: Wang

first: Xing

last: Peng


title: Small RNA sequencing of circulating exosomes from SD rats

city: Guangzhou 510275

first: Weiyang

last: Fan

address: School of Life Sciences, Sun Yat-sen University, No. 135 Xingang West Road, Guangzhou

department: School of Life Sciences

institute: Sun Yat-sen University

summary: After total RNA was extracted by Trizol reagent kit (Invitrogen, Carlsbad, CA,USA), the RNA molecules in a size range of 18–30nt were enriched by polyacrylamide gelelectrophoresis(PAGE). Then the 3’ adapters were added and the 36-48nt RNAs were enriched. The 5’ adapters were then ligated to the RNAs as well. The ligation products were reverse transcribed by PCR amplification and the 140-160bp size PCR products were enriched to generate a cDNA library and sequenced using Illumina HiSeq Xten by Gene Denovo Biotechnology Co. (Guangzhou, China).

overall_design: Circulating exosomes were isolated from Naoxintong Capsule-treated (NXT-Exo) and saline-treated (Ctl-Exo) SD rats.

first: Ziyan

last: Xu

first: Peibo

last: Li


title: Therapeutic Potential of ASO-Mediated KCNT1 Knockdown in KCNT1 Epileptic Encephalopathy

city: Boston

first: Timothy

last: Yu

state: MA

address: 300 Longwood Ave

institute: Boston Children's Hospital

summary: KCNT1-related epileptic encephalopathy, including Epilepsy of Infancy with Migrating Focal Seizures (EIMFS), is a severe neurodevelopmental disorder associated with refractory seizures, profound neurologic impairment, and premature death. It is caused by de novo genetic variants in KCNT1 which alter the function of Slack, an evolutionarily conserved sodium-gated potassium channel that modulates neuronal firing patterns and excitability. Pathogenic KCNT1 variants lead to overactive Slack channels, boosting total neuronal potassium currents by up to 40%, driving cortical hyperexcitability and causing seizures. Here we investigate antisense oligonucleotide (ASO)-mediated KCNT1 knockdown as a therapeutic strategy for patients with EIMFS. Intrathecal delivery of an experimental, non-allele-specific, KCNT1-targeting ASO by lumbar puncture in two patients with KCNT1 p.R474H, a severe, recurrent pathogenic variant, led to a significant reduction in seizure frequency and intensity, supporting the potential efficacy of suppression of KCNT1 expression as a therapeutic strategy for EIMFS. However, investigational treatment was also associated with development of ventricular enlargement or hydrocephalus in both patients, prompting in one case redirection of goals of care. This finding was not clearly related to EIMFS itself, drawing attention to an important possible toxicity of some intrathecal antisense oligonucleotides.

overall_design: RNA-seq of WT iPS-neurons with four treatment conditions: no treatment, Tofersen ASO, Tominersen ASO, and Valeriasen ASO


title: Loss of WWOX Drives Cutaneous Squamous Cell Carcinoma (cSCC) through Regulating EMT

city: Jerusalem

first: Rami

last: Aqeilan

address: Ein Kerem

country: Israel

institute: Hebrew University of Jerusalem

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

overall_design: Refer to individual Series


title: DOT1L enhances BLM-induced pulmonary fibrosis by inducing endothelial-to-mesenchymal transition via H3K79me2 [RNA-seq]

overall_design: HUVECs were collected at 24 h with TGFβ2 treatment or not (three replicates for each group). Total RNA were extracted and subjected to RNA-seq profiling.


title: p75 Neurotrophin Receptor Shapes the Dynamics of Adult Hippocampal Neurogenesis in Alzheimer's Disease

city: Heraklion

first: Matthieu

middle: David

last: Lavigne

address: Nikolaou Plastira 100

country: Greece

institute: IMBB-FORTH

summary: Background In the present study, we explore the intricate relationship between the adult hippocampal neurogenesis and the p75 pan-neurotrophin receptor (p75NTR), under physiological or neurodegenerative conditions, focusing on Alzheimer's Disease (AD). The hippocampal adult neurogenesis, the process of generating new neurons in the Dentate Gyrus (DG), is crucial for cognitive function and emotional resilience. Dysregulation of this process is strongly implicated in AD, a neurodegenerative disorder characterized by cognitive decline and memory impairment. p75NTR, known for its diverse functions in neuronal survival, differentiation and synaptic plasticity, emerges as a key player in modulating adult neurogenesis. In addition, its significant role in the context of AD has recently been revealed, although the exact mechanism of action remains elusive. Methods This study aims to address the connective relation of adult hippocampal neurogenesis and AD by investigating the role of the p75NTR in mouse and human neural stem cells under physiological and AD conditions. Results We firstly evaluated the impact of p75NTR in in vivo adult hippocampal neurogenesis, by performing 5-bromo-2′-deoxyuridine (BrdU) injections for detection of proliferation and immunohistochemistry analysis for key neurogenic markers in p75NTR knock-out (ko) mice, compared to the wildtype of 2-, 4-, and 6- months old mice, revealing the necessity of p75NTR, and defining its cell non-autonomous function to control neural stem cell fate. In order to investigate the role of p75NTR in AD, we have generated a mouse model by crossing the p75NTR ko mice with the 5xFAD mouse, an amyloid beta dependent mouse model of AD. Our data clearly indicate the importance of p75NTR expression for the proliferation and differentiation processes of adult neural stem cells (NSCs). Differential gene expression analysis confirmed the aforementioned properties. Finally, we investigate the p75NTR effects in human induced Pluripotent Stem Cells (hiPSCs)-derived NSCs, depicting receptor’s signaling and its dysregulation in the presence of toxic Amyloid- β in human neuronal cells. Conclusions By unraveling the pleiotropic mechanisms underlying p75NTR activation in adult neurogenesis, our research seeks to offer insights into novel mechanism of action for this neurotrophin receptor, providing potential therapeutic targets for addressing AD-related neurogenesis deficits.

overall_design: RNA-seq (3' mRNA-Seq FWD QuantSeq) profiling of hippocampal specimens of p75NTRko, 5xFAD, 5xFAD/p75NTRKO and WT mice of 2 months old, that have been dissected after BrdU injections.

first: Maria Anna

last: Papadopoulou

first: Electra

last: Tsagliotis

first: Konstantina

last: Michalaki

first: Ioannis

last: Charalampopoulos


title: Tfh scRNA-Seq

city: shanghai

first: GuoFeng

last: Fang

address: No. 1630 Dongfang Road, Pudong New Area

department: Shanghai Institute of Immunotherapy Innovation, Renji Hospital

institute: Shanghai Jiao Tong University School of Medicine

summary: Mice were intraperitoneally injected with LCMV on day 0. Simultaneously, wild-type SMARTA cells were intravenously injected. After 7 days, TFH cells were sorted and used for scRNA-seq analysis.

overall_design: C57BL/6 mice were intraperitoneally injected with 2 × 105 plaque-forming units (PFU) of the Armstrong strain of LCMV on day 0. Simultaneously, 2 × 105 wild-type SMARTA cells were intravenously injected. After 7 days, CD4+CD25–CD45.1+CXCR5+SLAM– TFH cells were sorted and used for scRNA-seq analysis.

first: Guotong

last: Fu

first: Guofeng

first: Tianyu

last: Lei


title: Persistent dopamine-dependent remodeling of the neural transcriptome in response to pregnancy and postpartum

city: New York

first: Jennifer

middle: C

last: Chan

state: New York

address: 1470 Madison Ave 9-201

department: Neuroscience

country: USA

institute: Icahn School of Medicine at Mount Sinai


title: Tfh and Th1 RNA-seq data

summary: RNA-seq analysis of FVD–CD4+CD45.1+Ly6C–PD1+ TFH and FVD–CD4+CD45.1+Ly6C+PD1– TH1 cells sorted by flow cytometry at 7 days post-LCMV infection, sequenced via Illumina NovaSeq 6000.

overall_design: RNA samples were isolated from freshly-isolated FVD–CD4+CD45.1+Ly6C–PD1+ TFH and FVD–CD4+CD45.1+Ly6C+PD1– TH1 SMARTA cells sorted from the spleens of CD45.2+ recipient mice (n = 3 biological replicates each group);


title: NeuID is a novel neuron-specific lncRNA that regulates neuronal function in Alzheimer’s disease

city: Göttingen

first: Andre

last: Fischer

state: NDS

address: Von-Siebold-Str. 3a

department: Epigenetics and Systems Medicine in Neurodegenerative Diseases

institute: DZNE Göttingen

summary: Non-coding RNAs are transcripts that do not encode proteins and comprise 98.5% of the human transcriptome. Among these, long non-coding RNAs (lncRNAs) have been implicated in various biological functions, including the control of gene expression and translation. The central nervous system (CNS) harbors a diverse array of lncRNA transcripts, yet the functions of many remain largely unexplored. In this study, we employed FANS with total RNA-sequencing and single-nuclei RNA sequencing approaches using human and mouse brain tissue to identify novel lncRNAs specific to neurons, and potentially associated with neurodegenerative diseases. We discovered a novel brain-specific lncRNA, the we named 'NeuID', that is specifically expressed in neuronal cells in the mouse and human brains. NeuID expression was found to be reduced in the brains of Alzheimer’s disease (AD) patients. Knockdown (KD) of NeuID resulted in the downregulation of synaptic plasticity genes. Additionally, NeuID KD led to decreased dendritic spine density and reduced neuronal network activity in MEA recordings. Furthermore, we demonstrate that NeuID interacts with EZH2, a component of the PRC2 complex, and mediates the h3k27me3 levels of Olig2 transcription factor. Notably, CRISPRa mediated overexpression of NeuID resulted in the rescue of functional impairment caused by AD-related pathological Aβ oligomers. Overall, our findings identify a novel brain and neuron-exclusive lncRNA that regulates neuronal function, is dysregulated in AD, and might be a potential therapeutic target against neuronal pathology in AD.

overall_design: RNA-seq profiling from primary hippocampal neurons treated with either control gapmers or NeuID gapmers to knockdown NeuID

first: Ranjit

last: Pradhan

first: Sadman

last: Sakib

first: Iga

last: Grzadzielewska

first: Eren

last: Diniz

first: Dennis

last: Krueger

first: Sophie

last: Schroeder

first: Susanne

last: Burkhardt

first: Anna-Lena

last: Schuetz

first: Jelena

last: Radulovic

first: Farahnaz

last: Sananbenesi

first: André


title: Multimodal profiling of oral squamous cell carcinoma identifies genomic alterations and expression programs associated with betel quid chewing

city: Boca Raton

first: Hansraj

last: Jangir

state: Florida

address: 777 glades

institute: Florida Atlantic University

summary: Betel quid (BQ) chewing is a profound risk for oral squamous cell carcinoma (OSCC) in Southeast Asia. To decipher contributory genomic abnormalities and transcriptional reprogramming in these malignancies, we conducted a multi-omics survey, including exome sequencing of tumor-normal pairs, alone with integrated single-cell and spatial transcriptomics of a set of tumors. In addition to enrichment of significantly altered genes (e.g mutations of TP53 and CHUK, copy gains of MAP3K13 and FADD, copy losses of CDKN2A) and mutational signatures associated with BQ chewing, we demonstrated frequently altered oncogenic pathways (Hippo and p53 signaling) and potential combination therapy opportunities linked to BQ use. Moreover, a shift of tumor microenvironment in BQ-related OSCC, characterized by extensive cell-cell crosstalk and induced tissue hypoxia, dendritic immunosuppression, and endothelial sprouting, was observed. Collectively, these differences in genomic landscape and tumor niche suggest that BQ-positive OSCC could be an etiological subtype different from their BQ-negative counterparts.

overall_design: Surgically resected oral cancer samples were analyzed by using scRNA-seq

first: Shih-Chi

last: Su

first: Lung-Ching

last: Chang

first: Shun-Fa

last: Yang


title: Multimodal profiling of oral squamous cell carcinoma identifies genomic alterations and expression programs associated with betel quid chewing [spatial transcriptomics]


title: Skin commensal Staphylococcus promotes systemic reconfiguration of Vγ6+ γδT cells

city: Bethesda

first: Verena

last: Link

address: 4 Memorial Drive

department: NIAID

institute: NIH

summary: Skin-resident Staphylococcus aureus, a common human commensal, can shape systemic immune responses without provoking inflammation in mice. This study demonstrates that topical skin colonization with live S. aureus robustly expands IL-17-producing Vγ6⁺ γδT17 cells both locally in the dermis and across distant tissues, including mucosal, lymphoid, and metabolic organs. This systemic reconfiguration is IL-1R-dependent yet independent of IL-23, TLR2, or the microbiota. Transcriptomic profiling reveals a transitional state in dermal Vγ6⁺ γδT cells, marked by changes in tissue-residency and migration-associated genes. Local proliferation, lymphatic trafficking and long-term recirculation sustain this response, even without systemic bacterial dissemination. These findings uncover a previously unrecognized allostatic process by which localized microbial signals recalibrate systemic immunological setpoints. The study expands our understanding of γδT17 cell dynamics and highlights their potential in tuning organismal fitness.

overall_design: Vγ6+ γδ T cells were FACsorted from ear skin of control mice (associated with media TSB) and topical associated mice (topical association with S. aureus (42F02)) 14 days following the first association.

first: Rao

last: Indira

first: van Dang

last: Eric

first: Belkaid

last: Yasmine