title: Single-cell and spatial transcriptomics of A-P and D-V patterned human trunk embryoid model (hTEM)

city: Hong Kong

first: Tianming

last: Wu

state: Hong Kong

address: LKS Int Biomed Sci Bldg

department: School of Biomedical Sciences

institute: Chinese University of Hong Kong

summary: Human embryoid models enable mechanistic studies of development and disease. We generated trunk embryoids from human pluripotent stem cells that recapitulate posterior trunk formation at Carnegie stage (CS) 8-10, with patterned anterior-posterior (A-P) and dorsal-ventral (D-V) axes. These self-organizing structures comprise a ventral notochord, dorsal neural tube, floor plate and bilateral somites. Genetic and chemical perturbations of SHH signaling confirmed the notochord’s central role in D-V patterning. Moreover, VANGL1/2 loss-of-function mutations recapitulated mouse phenotypes, including axial truncation and somite segmentation failure. This model enables detailed study of key developmental events that underlie posterior trunk formation and provides a promising platform for human disease modeling.

overall_design: scRNA-seq of human trunk embryoid model v1 (hTEM.v1) at day 4/5/7, hTEM.v2 at day 5/7, hTEM.v3 at day 3/4/5/6/7 and day-6 hTEM.v3 derived from loss-of-function mutants including NOTO-LOF, SANT1 treatment (250 nM, days 4-6) and VANGL2-LOF. For spatial transcriptomics, Visium HD was applied onto hTEM.v2 (day7, transverse and longitudinal section) and hTEM.v3 (day 4 and day6.5, longitudinal section).

first: Hao

last: Yu

first: Brian

last: Wong

first: Ling

last: Xu

first: Joaquim

last: Vong

first: Stephen

last: Dalton


title: Identification of important genes for tooth development using single cell RNA-sequence datasets of sequential developing mouse molars

status: Public on Dec 24 2025

city: Sendai

first: Yuta

last: Chiba

state: Miyagi

address: 4-1 Seiryo-cho, Aoba-ku

country: Japan

institute: Tohoku University

type: Expression profiling by high throughput sequencing

summary: The organ development is dictated by the genes preferentially expressed in tissue or cell types uniquely. The clarification of gene expression profile and identification of specific genes in organ provide detailed understanding of organogenesis. Toward this purpose, the genome-wide analysis is a growing powerful tool for understanding development processes in organogenesis. Tooth is composed from enamel, dentin and cementum and these tissues are identical from other organs. The tooth-forming cell types are therefore unique and have complexed organization. The mechanisms of signal induction during tooth development is complicated because of the function of each cell types are still unclear. Single-cell RNA-sequence (scRNA-seq) is a suitable tool revealing gene expression of each cells. In this study, we approach the important genes in tooth development using scRNA-seq of sequential developing mouse molars. Our results show that the scRNA-seq highlight genes important for tooth development. These findings contribute resolving the mechanism of tooth development and establish the basis of tooth regeneration in future.

overall_design:
Examination of epithelial and mesenchymal cells in mouse molar.
NIDCD/NIDCR Genomics and Computational Biology Core [contributor]

first: Daniel

last: Martin


title: ILC2s navigate tissue redistribution during infection using stage-specific S1P receptors

status: Public on Dec 23 2025

city: New York

first: Yuefeng

last: Huang

state: NY

address: 701W 168th Street

department: Microbiology & Immunology

country: USA

institute: Columbia University

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Serine inhibits granulosa cell ferroptosis to maintain ovarian function

city: Nanchang

first: Haocheng

last: Gu

state: Jiangxi Province

address: Hongguantang Sub-district

country: China

institute: Nanchang University

summary: Cyclophosphamide (CTX) is a primary medicine for curing breast cancer which often caused premature ovarian insufficiency (POI). Our recent publication revealed that CTX induced POI by promoting the expression of SLC1A4, a transporter of serine efflux, in ovarian granulosa cells (GCs). Here, we reported that there was a closed connection between the reduction of serum serine and ovarian hypofunction in the breast cancer patients treated with CTX or women of childbearing age who were suffered from the staying-up-late. Additionally, we observed that dietary serine supplementation protected mice from CTX-induced POI without altering its anti-breast cancer. Furthermore, we demonstrated that the elevated serine promoted S1P synthesis, and in turn, inhibited the nuclear translocation of Nrf2 and consequent HO-1 expression, to suppress ferroptosis in GCs. Our study revealed that the chemotherapy-induced or idiopathic POI shared the same mechanisms, indicating that serine was a critical factor for maintaining ovarian function.

overall_design: Mouse ovarian granulosa cells were stimulated with cyclophosphamide for 24 hours, after which RNA was extracted to analyze gene expression differences between unstimulated and cyclophosphamide-stimulated ovarian granulosa cells.

first: Hongbo

last: Xin


title: Single nuclei RNA-sequencing of frontal cortex of a pig model of Angelman syndrome

city: College Station

first: Sarah

last: Christian

state: TX

address: 4467 TAMU

institute: Texas A&M University

summary: Angelman syndrome is a neurodevelopmental disorder caused by the loss of the maternal allele of the ubiquitin-protein ligase E3A (UBE3A) gene.  UBE3A is imprinted with maternal-allelic expression in neurons of the central nervous syndrome (CNS) and biallelically expressed in other cell types.  Consequently, in Angelman syndrome, UBE3A is absent in CNS neurons and reduced by half in other cells.   It is unclear how cell type-specific gene expression in the brain is dysregulated in Angelman syndrome.  Using single nuclei RNA-sequencing, we show that gene expression is dysregulated in neuronal subtypes in the frontal cortex of neonatal pigs with a UBE3A maternal deletion.  A total of 3,812 unique genes were dysregulated across ten cell-type clusters, with most of the dysregulated genes (3,154 genes) in excitatory neurons.

overall_design: Study design compares wildtype animals to UBE3A materal deletion animals. Replicates of four animals were used for each genotype and used in snRNA-sq.

first: Ashley

last: Coffell

first: Livia

last: Schuller

first: Scott

middle: V

last: Dindot


title: Global stabilization of the transcriptome in mitotic cells [PALseq]

city: Cambridge

first: Ekaterina

last: Khalizeva

state: MA

address: 455 Main St

department: Biology

institute: Whitehead Institute

summary: In the presence of cell division errors, mammalian cells can pause in mitosis for tens of hours with little to no transcription, while still requiring continued translation for viability. These unique aspects of mitosis require substantial adaptations to the core gene expression programs. During interphase, the homeostatic control of mRNA levels involves a constant balance of transcription and degradation, with a median mRNA half-life of ~2–4 hours. If such short mRNA half-lives persisted in mitosis, cells would be expected to rapidly deplete their transcriptome in the absence of new transcription. Here, we report that the transcriptome is globally stabilized during prolonged mitotic delays. Median mRNA half-lives are increased >4-fold in mitosis compared to interphase, thereby buffering mRNA levels in the absence of new synthesis. Moreover, the poly(A)-tail-length profile of mRNAs changes in mitosis, strongly suggesting a partial mitotic repression of deadenylation. In contrast, the machinery required for siRNA-mediated mRNA degradation remains active. We further show that mitotic mRNA stabilization is dependent on cytoplasmic poly(A)-binding proteins PABPC1&4. Depletion of PABPC1&4 and consequently reduced mRNA stability disrupts the maintenance of mitotic arrest, highlighting the critical physiological role of mitotic transcriptome buffering.

overall_design: RNA-seq data from transcription inhibition timecourses in HeLa cells arrested in mitosis, G2, or G1 using double thymidine block followed by STLC, RO3306, or STLC release respectively. One timecourse experiment only contained STLC-arrested cells without additional transcriptional inhibition. Also included are PAL-seq data from the STLC timecourse and the G2-vs-M timecourse in the presence of actinomycin D. RNA-seq data from HCT116 PABPC1&4-AID cells arrested in mitosis, with or without IAA-induced PABPC1&4 depletion (0 h and 4 h post-IAA addition)

first: Arash

last: Latifkar

first: Kehui

last: Xiang

first: Jimmy

last: Ly

first: Iain

middle: M

last: Cheeseman

first: David

middle: P

last: Bartel


title: Global stabilization of the transcriptome in mitotic cells [RNA-Seq]


title: Dietary High Fiber and N-Carbamylglutamate Enhance Sow Reproductive Performance via Modulating Lactobacilli, Lipid Metabolites, and the PI3K-Akt Signaling Pathway

city: Nanjing

first: Yaxu

last: Liang

state: 江苏省

address: 江苏省南京市玄武区南京农业大学

institute: Nanjing agricultural university

summary: Landrace x Yorkshire sows were selected to investigate the synergistic effects of high fiber diet and 0.05% NCG on reproductive performance through transcriptomic analysis of ileum and colon samples.

overall_design: The sows were randomly assigned to four dietary treatment groups (n = 100 per group) as follows: low-fiber group (LF; 3.73% crude fiber); low-fiber + NCG group (L+N; 3.73% crude fiber + 0.05% NCG); high-fiber group (HF; 7.46% crude fiber); high-fiber + NCG group (H+N; 7.46% crude fiber + 0.05% NCG). The experimental was initiated on the day of breeding and continued throughout the entire gestation period of 114 days.

first: Hongyang

last: Wang

first: Yongsong

last: Tan


title: Role of potato Pti5 in HR-mediated resistance to potato virus Y

city: Ljubljana

first: Maja

last: Križnik

address: Vecna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

summary: Pti5 is an ERF transcription factor that is differentially expressed in PVY-infected potato plants. The purpose of this dataset was to identify genes whose expression is altered by silencing the Pti5 gene in PVY-induced lesions.

overall_design: For RNA-Seq analysis of Pti5 downstream target gene expression, twenty tissue sections encompassing the lesions were sampled from PVYN-Wilga-inoculated leaves at 4 dpi and pooled.  Twenty tissue sections from mock-inoculated plants were pooled separately.


title: Ancestry-Linked IL-10 Signaling and Macrophage Activation Modulate Fibroblast Responses to Oxidative Stress in a PEG-Based Microphysiological System

city: College Park

first: Erika

middle: Taylor

last: Moore

state: Maryland

address: 3102 A. James Clark Hall

department: Bioengineering

institute: University of Maryland

summary: Fibroblast responses to injury are shaped by cytokine signaling and macrophage activation, yet the extent to which these pathways vary across individuals, and how ancestry-associated immune differences influence fibrosis risk, remains poorly understood. Here, we developed a poly(ethylene glycol) (PEG)-based hydrogel microphysiological system to model fibroblast–macrophage interactions following oxidative stress and integrate donor-specific immune signals using matched macrophages and serum. Circulating monocytes from individuals of self-reported African American ancestry exhibited higher expression of CCL4 and increased serum IL-10, whereas those from European ancestry donors showed elevated OXER1 expression. Within the hydrogel, oxidative stress reduced fibroblast number while inducing Ki67 and p16. Exogenous TGF-β1 enhanced fibroblast survival and collagen 3 production but did not independently increase α-smooth muscle actin (α-SMA). Anti-inflammatory macrophages promoted fibroblast activation through mechanisms resistant to TGF-β receptor inhibition. Incorporating donor-derived macrophages and serum revealed that cultures from individuals of European ancestry demonstrated higher fibroblast α-SMA and p16 expression, despite lower systemic IL-10 levels. Pharmacologic inhibition of IL-10 further increased α-SMA, particularly in European ancestry–derived cultures, identifying IL-10 as a key protective signal limiting fibroblast activation. This hydrogel system provides a platform for dissecting inter-individual immune variation and identifying mechanisms underlying ancestry-associated fibrosis risk.

overall_design: In this study, monocytes from 24 human donors were analyzed for the expression of 269 inflammation-related genes to compare molecular profiles across sex and ancestry.

first: Nana

last: Owosu-Boaitey

last: Taylor Moore


title: Single-nuclei RNA-seq of meningioma

city: Heidelberg

first: Tang

last: Yiheng

address: Im Neuenheimer Feld 224

department: Department of Neuropathology

country: Germany

institute: Heidelberg University Hospital

summary: We applied single-nuclei RNA-seq to meningioma samples across grades and methylation classes, in order to characterize features of meningioma heterogeneity across subgroups. We identified an overall decrease in myeloid cell proportions from grade 1 to grade 3 meningiomas, as well as a phenotypic shift from microglia-like cells towards a myeloid-derived proliferative macrophage phenotype.

overall_design: Single-nuclei RNA-seq was performed on 26 meningioma samples across WHO grades and methylation classes.

first: Sybren

middle: N

last: Maas

first: Yiheng

last: Tang

first: Eric

last: Stutheit-Zhao

first: Ramin

last: Rahmanzade

first: Felix

last: Sahm


title: Spatial transcriptomic profiling (Visium) of meningioma

summary: We applied spatial transcriptomic profiling (10x Genomics Visium) to meningioma samples across grades and methylation classes, in order to characterize features of meningioma heterogeneity across subgroups. We identified an overall decrease in myeloid cell proportions from grade 1 to grade 3 meningiomas, as well as a phenotypic shift from microglia-like cells towards a myeloid-derived proliferative macrophage phenotype.

overall_design: Spatial transcriptomic profiling (10x Genomics Visium) was performed on 26 meningioma samples across WHO grades and methylation classes.


title: Single-cell atlas in the living fossil Yangtze sturgeon provides insight into the evolution of fish

city: Chengdu

first: Yeyu

last: Chen

state: --- Select One ---

address: The Fishery Institute of The Sichuan Academy of Agricultural Sciences, No.1611 Xiyuan Street

institute: Fisheries Research Institute, Sichuan Academy of Agricultural Sciences

summary: We constructed a fish cell atlas at the whole-body scale. We investigated the heterogeneity and functional diversity of cells in the digestive, immune and nervous systems. The tissue included heart, liver, spleen, head kidney, midkidney, pyloric caecum, stomach, duodenum (smallintestine), spiral intestine, rectum, skin, muscle, gill, brain, eye, gonad, and blood samples.

overall_design: We constructed a fish cell atlas by scRNA-seq, including heart, liver, spleen, head kidney, midkidney, pyloric caecum, stomach, duodenum (smallintestine), spiral intestine, rectum, skin, muscle, gill, brain, eye, gonad, and blood samples.


title: Integrative omics analysis elucidates the role of ANKRD9 in modulating chicken primary myoblast IMP metabolism via the purine metabolic pathway

city: Zhengzhou

first: Li

last: Yuanfang

address: No. 26 Longyuan East 7th Street, Zhengdong New District

institute: Harbin Institute of Technology Zhengzhou Research Institute

summary: With the continuous improvement of human dietary structure, the demand for high-quality chicken meat is steadily increasing. It is therefore crucial for breeders to enhance meat quality while maintaining muscle yield in broilers. Inosine monophosphate (IMP) is a key compound influencing meat flavour and quality. In this study, we used the Chinese local breed Gushi chicken breed as the research model and observed dynamic expression changes of the ankyrin repeat domain 9 (ANKRD9) gene in breast muscle tissues. By integrating transcriptomic and metabolomic analyses, we systematically investigated the role of ANKRD9 in chicken primary myoblasts. Our findings indicate that ANKRD9 may affect cell adhesion and IMP metabolism through regulation of the purine metabolic pathway. Further cellular experiments confirmed that ANKRD9 inhibits IMP metabolism in myoblasts. These results highlight the critical role of ANKRD9 in regulating IMP, a key flavour-related metabolite, and provide a potential molecular target and theoretical foundation for the breeding of high-quality broilers.

overall_design: RNA-seq expression profile of ANKRD9 overexpression and pcDNA3.1 in chicken primary myoblasts

first: Yuanfang

last: Li

first: Guoxi


title: RNA-seq of ISL1 overexpression during islet differentiation.

city: New York City

last: Hu

address: 430 East 67th Street

department: Developmental biology

institute: Sloan Kettering Institute

summary: This study aims to investigate the impact of ISL1 overexpression on hPSC-derived islet differentiation. hPSCs from four genotypes (WT, ISL1-/-, PDX1-/-, and PAX6-/-) were differentiated to pancreatic progenitors (day 11), transduced with ISL1-IRES2-BFP or BFP control lentivirus, and further differentiated to SC-islet (day 18). The BFP+ cells were isolated by flow cytometry sorting and subjected to RNA-seq to assess transcriptional responses to ISL1 overexpression across different genetic backgrounds.

overall_design: This study generated RNA-seq on 21 samples.  Cells were transduced with either ISL1-IRES2-BFP or BFP control on day 11 of islet differentiation and harvested on day 18. Most conditions were represented by three biological replicates. Three conditions, ISL1 overexpression in WT, BFP control overexpression in WT, and ISL1 overexpression in PDX1-/-, were represented by two biological replicates.

first: Danwei

last: Huangfu

first: Dingyu

last: Liu

first: Jiahui

last: Zhao


title: Uncovering Molecular Mechanisms of Milk Production in Indigenous Cattle through Transcriptome Profiling

city: Old Goa

first: Amiya

middle: Ranjan

last: Sahu

state: Goa

address: ICAR-Central Coastal Agricultural Research Institute

department: Animal Genetics and Breeding

country: India

summary: This study employed a transcriptomic approach to investigate the differential gene expression (DEG) profiles in peripheral blood mononuclear cells of high- and low-yielding animals within and between Gir and Shweta Kapila Indian cows.

overall_design: Twelve cows (6 from Gir and 6 from Sweta Kapila), in their second and third lactation, were selected for the study. On the basis of lactation record, individual cows within each breed were classified into high-yielding and low-yielding phenotypes (n=3 each). Total RNA were isolated from peripheral blood mononuclear cells and used for RNA Sequencing using Illumina NovaseqXplus.

middle: R

first: Satish

last: Kumar

first: Jaya

last: Bharati

first: Nibedita

last: Nayak

first: Shirish

last: Narnaware


title: Inosine monophosphate dehydrogenases are key players for functional embryo and seedling development in Arabidopsis

city: Kaiserslautern

first: Torsten

last: Möhlmann

address: Paul-Ehrlich-Str

institute: University of Kaiserslautern

summary: In plants, nucleotide de novo synthesis is required throughout development to energize biochemical reactions, provide DNA for cell division and RNAs for gene expression and translation. Inosine Monophosphate Dehydrogenases (IMPDH) are key enzymes in guanylate synthesis. We identify IMPDH2 from Arabidopsis as the major isoform, being enzymatically active in the plant cytosol and catalyzing the key enzymatic step in CTP biosynthesis. BIFC analysis suggests that IMPDH 1 nd 2 interact with thenmselves and with Cytidine Triphosphate Synthetase (CTPS) isoforms, by this connecting purone and pyrimidine metabolsim. Nucleotide quantification identifies IMPDH2 as bottleneck in guanylate biosynthesis, leading to nucleotide imbalance and limitation, causing reductions in ribosomal RNAs by reducing Target of Rapamycin (TOR) activity. Impaired photosynthesis and growth are consequences thereof. In contrast, overexpression of IMPDH supported growth and in strong lines lead to altered organ development presumably due to altered auxin metabolism during embryo development

overall_design: To analyze the lack of IMPDH2 on global gene expression , Col-0 (wild-type control) plants were compared to IMPDH2 T-DNA insertion line imphh2-0 at 4 and 8 days after germination. Plants were grown on soil at 120 µmol photons m-2 s-1, and samples were harvested after 3 hours of light  in three biological replicates.

first: Dörfer

last: Eva

first: Möhlmann

last: Torsten


title: Antibiotic-induced microbiota depletion impairs the pro-regenerative response to a biological scaffold

city: Baltimore

first: Christopher

last: Cherry

state: MD

address: 1800 Orleans St

institute: Johns Hopkins University

summary: Therapeutic biological scaffolds promote tissue repair primarily through the induction of type 2 immunity. However, systemic immunological factors, including aging, sex, and previous infections, can modulate this response. The gut microbiota is a well-established modulator of immune function across organ systems, yet its influence on type 2-mediated repair remains underexplored. Here, we establish a bidirectional relationship between the gut microbiota and biological scaffold-mediated tissue repair. Utilizing a conventionalized germ-free mouse, we demonstrate that scaffold implantation induces compositional and functional changes in the gut microbiome, particularly affecting amino acid biosynthesis. Additionally, in a model of antibiotic-induced microbiota depletion (AIMD), we show that dysbiosis disrupts key immune regulators of type 2 immunity, including reductions in eosinophils, pro-regenerative macrophages, and IL-4-producing CD4+ T cells. At 6 weeks post-scaffold implantation, we observed a significant decrease in myocytes with centrally located nuclei alongside an upregulation in pro-fibrotic gene expression with antibiotic treatment. These findings provide insights into the influence of the gut microbiota on type 2-mediated tissue repair.

overall_design: Mice were randomly assigned to either antibiotic treated or control groups, six mice per group. Each mouse was then given VML surgery treated with ECM with or without antibiotic treatment as described in the protocols sections.

first: Natalie

last: Rutkowski


title: A streamlined nanopore-compatible 5PSeq protocol for rapid phenotypic antimicrobial sensitivity testing (FigS4B-C_mixed_illumina)

city: Solna

first: Honglian

address: Tomtebodavägen 23

department: Department of Microbiology, Tumor and Cell Biology

country: Sweden

institute: Karolinska Institutet

summary: Antimicrobial resistance (AMR) poses a significant threat to public health. Rapid and accurate antimicrobial sensitivity testing is essential to guide effective treatment. Here, we present “simplified 5PSeq” (s5PSeq), a streamlined protocol for profiling 5’ monophosphorylated (5’P) mRNA degradation intermediates that reflect ribosome dynamics in vivo. By capturing antibiotic-induced, context-specific ribosome stalling events, s5PSeq provides a molecular proxy for bacterial growth inhibition—offering a molecular phenotypic readout without the need for culturing. s5PSeq reduces library preparation time to under four hours and incorporates a novel rRNA blocking strategy. We demonstrated its clinical utility by identifying erythromycin-resistant and sensitive Clostridioides difficile clinical isolates. Combining s5PSeq with real-time nanopore sequencing enables fast AMR diagnosis with as few as 3000 reads. In addition to simplifying the study of 5’P co-translational mRNA decay, our work suggests that utilizing information-rich phenotypic molecular readouts can significantly improve AMR diagnostics.

sample_organism:
Staphylococcus aureus
Enterococcus faecalis
Bacillus subtilis
Clostridioides difficile

overall_design: s5PSeq library using mixture of 100ng of total RNA extracted from exponetially growing (OD600=0.6-0.8)B.subtilis, S.aureus, E.faecalis and erythromycin treated C.difficile clinical isolates(resistant and sensitive respectively)

first: Susanne

last: Huch

first: Ryan

last: Hull

first: Fabricio

last: Garcia

first: Lilit

last: Nersisyan

first: Wei-Hua

last: Chen

first: Juan

last: Du

first: Vicent

last: Pelechano


title: A streamlined nanopore-compatible 5PSeq protocol for rapid phenotypic antimicrobial sensitivity testing (FigS4D-F_mixed_MinION)

last: Liu

platform_organism:
Staphylococcus aureus
Enterococcus faecalis
Bacillus subtilis
Clostridioides difficile

overall_design: s5PSeq library were prepared using 100ng extracted total RNA from exponetially growing (OD600=0.6-0.8) C.difficile clinical isolates that are resistant or sensitive to erythromycin. Bacteria cells are treated with erythromycin(1ug/ml) for 10min or without treatment. C.difficile RNA is mixed with equal amount of RNA from untreated B.subtilis, E.feacalis and S.aureus respectively.


title: Bradyzoite subtypes rule the crossroads of Toxoplasma development

city: Riverside

first: Emma

middle: H.

last: Wilson

state: California

address: 169 Aberdeen Dr, Multidisciplinary Research Building

department: Division of Biomedical Sciences

institute: University of California, Riverside School of Medicine

summary: Reactivation of toxoplasmosis is a significant health threat to chronically infected individuals, especially those who are or become immunocompromised.  An estimated one-third of the world population is infected with Toxoplasma, placing millions at risk.  The Toxoplasma cyst is the foundation of disease with its ingestion leading to infection and its reactivation, from slow replicating bradyzoites to fast replicating tachyzoites, leading to cell lysis in tissues such as the brain. There are no treatments that prevent or eliminate cysts in part due to our poor understanding of the mechanisms that underlie cyst formation and recrudescence.  In this study, we aimed to understand the biology of bradyzoites prior to recrudescence and the developmental pathways they initiate. We have discovered ME49EW cysts from infected mice harbor multiple bradyzoite subtypes that can be identified by their expression of distinct proteins. Sorting of these subtypes revealed they initiate distinct developmental pathways in animals and in primary astrocyte cell cultures.  Single bradyzoite RNA sequencing indicates 5 major bradyzoite subtypes occur within these cysts.  We further show that a crucial subtype comprising the majority of bradyzoites in chronically infected mice is absent from conventional in vitro models of bradyzoite development. Altogether this work establishes new foundational principles of Toxoplasma cyst development and reactivation that operate during the intermediate life cycle of Toxoplasma.

overall_design: Chronically infected mouse brains were harvested and bradyzoites were purified and subjected to scRNA-seq using 10X Genomics Chromium Next GEM platform.

middle: H

first: Michael

middle: W

last: White

first: Arzu

last: Ulu

first: Sandeep

last: Srivastava

first: Nala

last: Kachour

first: Brandon

last: Le


title: Nitroparaffin Transcriptional Profiles and Toxicokinetics Support Chemical-Specific Carcinogenicity Assessment

city: Durham

first: Rasim

last: Barutcu

state: NC

address: 6 Davis Drive

institute: ScitoVation

summary: The toxicological profiles of nitroparaffins—nitromethane (NM), nitroethane (NE), and 1-nitropropane (1NP)—remain incompletely characterized. This has led to reliance on read-across approaches, extrapolating carcinogenicity data from NM to NE and 1NP, though the validity of such extrapolations is uncertain. In this study, we examined the concentration-dependent transcriptional effects of NM, NE, and 1NP in primary rat hepatocytes to clarify their cellular impact and mechanisms of toxicity. We assessed cytotoxicity, differential gene expression, and pathway enrichment, and applied in vitro to in vivo extrapolation (IVIVE) to estimate systemic bioavailability and clearance rates. Cytotoxicity was observed at 3 mM for NM and NE but not up to 10 mM for 1NP. Transcriptomic profiling revealed minimal overlap in dysregulated genes and enriched pathways among the three compounds. NE elicited the broadest transcriptional response, whereas NM and 1NP showed more limited effects. IVIVE further indicated distinct systemic bioavailability and clearance, suggesting toxicokinetic differences. Taken together, these results demonstrate that structural similarity alone does not predict comparable toxicological behavior. Each nitroparaffin exhibited unique molecular activity and toxicokinetics, indicating that read-across within this class requires demonstrated concordance in both bioactivity and toxicokinetic profiles, which are currently absent for NE, NM and 1NP. Thus, reliance on read-across from NM to NE or 1NP may misrepresent health risks and carries significant regulatory implications.

overall_design: Transcriptional profiling of 1-nitropropane, nitromethane and nitroethane on primary rat hepatocytes.

first: A Rasim

first: Jamie

last: Scaglione

first: Marjory

last: Moreau

first: Elizabeth

last: Hofstetter

first: Todor

last: Antonijevic

first: Andrew

last: Maier

first: Pierre

last: Serfass

first: Leslie

last: Recio

first: Pamela

middle: J

last: Spencer


title: Neutrophil-induced lipoxygenase subtype promotes resolution of acute lung injury in mice (human version)

city: Boston

first: Toby

middle: Black

last: Lanser

state: Massachusetts

address: 60 Fenwood Road

department: Neurology

institute: Brigham and Women's Hospital

summary: Neutrophils are first responders to injury, playing a crucial role in mediating early inflammation. Recently, additional roles for neutrophils have been postulated in tissue repair and resolution of inflammation. Here, we identified a distinct subset of SiglecF+ neutrophils that emerged during mouse lung injury resolution that expressed 12/15-lipoxygenase. These SiglecF+ neutrophils demonstrated distinct anatomic distribution, morphology, gene expression and cell function compared to eosinophils and other neutrophil subsets. Notably, SiglecF+ neutrophils produced specialized pro-resolving mediators (SPMs) and macrophage colony-stimulating factor (M-CSF) that promoted monocyte differentiation into keratinocyte growth factor expressing-macrophages. Depletion of neutrophils hindered alveolar epithelial cell type II (AT2) repair, while adoptive transfer of SiglecF+ neutrophils accelerated epithelial restitution. Furthermore, TGF-b and GM-CSF, acting via AP-1/Jun, promoted SiglecF and 12/15-lipoxygenase expression in mouse neutrophils, and 15-lipoxygenase-1 in human neutrophils. Frequency of BAL 15-lipoxygenase+ neutrophils positively correlated with PaO2/FiO2 in ICU patients. Administration of 15-lipoxygenase-derived SPMs accelerated injury resolution and repair. Together, these findings uncover a pro-resolving subtype of neutrophils that play a pivotal role in the resolution of tissue injury.

overall_design: RNA-seq profiling of mouse neutrophils treated with either T+G or vehical control.

first: Luciana

last: Tavares

first: Thayse

last: Bruggemann

first: R

last: Cagnina

first: Robert

last: Nshimiyimana

first: et

last: al

first: Bruce

last: Levy


title: Neutrophil-induced lipoxygenase subtype promotes resolution of acute lung injury in mice

overall_design: RNA-seq profiling of mouse neutrophils  tread with either T+G or vehical control.


title: Aromatic Microbial Metabolite Hippuric Acid Potentiates Pro-Inflammatory Responses in Macrophages through TLR-MyD88 Signaling and Lipid Remodeling

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: The gut microbiome generates a diverse array of metabolites that actively shape host immunity, yet the pro-inflammatory potential of microbial metabolites remains incompletely understood. Using a non-targeted, liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based metabolomics, we identified hippuric acid, an aromatic gut microbe-derived metabolite, as a potent enhancer of pro-inflammatory responses in Escherichia coli infection model. Intraperitoneal administration of hippuric acid significantly heightened pro-inflammatory responses, promoted innate immune cell activation, and reduced survival in infected mice. Similar pro-inflammatory effects were observed in an LPS-induced inflammation model.  In vitro, hippuric acid selectively potentiated M1-like macrophage polarization (LPS + IFNγ) but had no effect on M2-like  polarization (IL-4). Hippuric acid further augmented responses to multiple myeloid differentiation primary response 88 (MyD88)-dependent toll-like receptor (TLR) ligands, but not to TRIF-dependent TLR3, or to cytosolic innate immune stimuli such as STING and NOD2 agonists, implicating TLR-MyD88 signaling as a likely mechanism of action. Genetic deletion of MyD88 abrogated the pro-inflammatory effects of hippuric acid both in vitro and in vivo, confirming its dependence on the MyD88 pathway. Transcriptomic and lipidomic analyses revealed that hippuric acid upregulated cholesterol biosynthesis and induced lipid accumulation. Pharmacological reduction of cellular cholesterol using fluvastatin or 25-hydroxycholesterol attenuated its pro-inflammatory effects. Notably, hippuric acid also enhanced pro-inflammatory responses in human macrophages, and its elevated levels correlated with increased sepsis mortality, underscoring its clinical relevance. Together, these findings identify hippuric acid as a previously unrecognized microbial-derived pro-inflammatory modulator that links gut microbial metabolism, lipid remodeling, and innate immune signaling, and offer new insights into its role in infection and inflammation.

overall_design: RNAseq for control and hippuric acid treatment, under untreated and LPS+IFNg treated conditions

first: Gauri

last: Mirji

first: Rahul

middle: S

last: Shinde


title: Single-cell RNA sequencing of neurogenic bladder resulting from pelvic nerve injury in rats

city: Wuhan

first: Jiaxin

last: Wang

address: No. 1037, Luoyu Road, Hongshan District, Wuhan City, Hubei Province

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: Neurogenic bladder (NB)-induced fibrosis is the major cause of irreversible bladder dysfunction, yet the underlying mechanisms remain undefined. Here, we performed single-cell RNA sequencing on bladder tissues collected from rats following bilateral pelvic nerve injury, and characterized the alterations in the bladder microenvironment post-injury.

overall_design: A rat model of neurogenic bladder was established via bilateral pelvic nerve injury (BPNI). Bladder tissues from control (sham-operated, n=3), 3-day post-injury (n=3), and 28-day post-injury groups (n=2) were processed for single-cell RNA sequencing using the 10X Genomics Chromium platform.

first: Lei

last: Zhang

first: Xinqi

last: Liu

first: Shuaixiang

last: Zheng

first: Lida

last: Ren

first: Jihong

first: Qing

last: Ling


title: Gene expression analysis of double conditional knockout mice for Sbno1 and Trp53

city: Otsu

first: Dai

last: Ihara

address: Tsukinowatyo Seta

department: Anatomy

institute: Shiga University of Medical Science

summary: We investigates gene expression profiles in double conditional knockout mice for Sbno1 and Trp53. To generate these knockouts in the developing forebrain, Sbno1 floxed mice, Trp53 floxed mice, and the Emx1-Cre driver line were utilized. RNA-seq was performed on the telencephalon at embryonic day 12.5 (E12.5) and the cerebral cortex at embryonic day 18.5 (E18.5) to elucidate the roles of Sbno1 and Trp53 in neural development.

overall_design: To generate double conditional knockout, we crossed Sbno1 floxed mice, Trp53 floxed mice, and the Emx1-Cre driver line. RNA-seq was performed on the telencephalon at embryonic day 12.5 (E12.5) and on the cerebral cortex at embryonic day 18.5 (E18.5). This design enabled us to investigate the roles of Sbno1 and Trp53 in neural development at different developmental stages.The raw data are at the BioProject (PRJDB37383).

first: Koki

last: Nukada

first: Katsushi

last: Yamaguchi

first: Shuji

last: Shigenobu

first: Yu

last: Katsuyama


title: Single-Cell Multiomic Atlas of Human Cortical Development in Down Syndrome - iPSC-derived Neural Xenografts snRNA-seq Dataset

city: London

first: Michael

last: Lattke

address: Hammersmith Hospital Campus, Du Cane Road

department: Brain Sciences

country: United Kingdom

institute: Imperial College London

summary: Down syndrome, caused by an extra copy of chromosome 21, is the most common genetic form of intellectual disability affecting up to 1 in 700 live births1-3. Yet, it remains unclear how the increased dosage of ~200 protein-coding genes on chromosome 21 affects brain development, particularly in the cerebral cortex—the area central to higher-level cognitive functions4-7. Here we generated a single-cell transcriptome and chromatin accessibility atlas from 30 human fetal cortical samples at mid gestation (10-20 weeks after conception), a critical period of cortical development8. We discovered an early global transcriptional network disruption, subtly altering ~600 genes involved in neural development and function, mostly in excitatory neurons accompanied by a significant reduction in RORB/FOXP1 expressing excitatory neurons. Multimodal network analyses predicted the chromosome 21 transcription factors BACH1, PKNOX1, and GABPA as key regulatory hubs controlling dozens of genes genetically linked to intellectual disability. Antisense-mediated normalization of the increased activity of these transcription factors in stem-cell-derived neural cells in vitro, which partially recapitulated molecular changes in the Down syndrome cortex, rescued expression of several of these predicted intellectual disability-associated targets. Finally, a humanized in vivo model replicates key molecular features of Down syndrome not recapitulated in neural cells in vitro. This resource defines the gene-regulatory landscape of the developing human cortex in Down syndrome, revealing early molecular and cellular signatures and candidate therapeutic targets, along with a human in vivo experimental platform for their preclinical testing.

overall_design: We performed  single-cell transcriptional profiling (Singleron Celescope technology) of iPSC-derived neural grafts (generated with approach from Real et al., 2018) from an individual with DS and from isogenic control iPSCs (CON, normal diploid karyotype; iPSC lines DS1 and DS2U from Weick et al., 2013, aquired from WiCell, UWWC1-DS1 and UWWC1-DS2U). We combined graft libraries generated with snRNA-seq with ibraries generated with the 10X-Multiome technology and compared grafts to fetal tissue and neural cells in vitro derived from the same iPSC line.

first: Vincenzo

last: De Paola


title: Single-Cell Multiomic Atlas of Human Cortical Development in Down Syndrome - Fetal Cortex Bulk RNA-seq Dataset

summary: Down syndrome, caused by an extra copy of chromosome 21, is the most common genetic form of intellectual disability, which affects up to 1 in 700 live births. Yet, how increased dosage of the ~200 protein-coding genes on human chromosome 21 affects cortical development and function remains unclear. Here we generated a single-cell transcriptome and chromatin accessibility atlas of the human foetal cortex at mid gestation (11-20 weeks after conception), a critical period of cortical development. We uncovered an early global transcriptional network disruption, subtly altering ~1000 genes involved in neural development and function primarily in excitatory neurons. These changes reflected clinical phenotypes like intellectual disability and epilepsy, were accompanied by a significant reduction in layer 4 neurons, and were driven by a network of transcription factors including chromosome 21 genes BACH1, PKNOX1, and GABPA. Finally, a xenograft model replicates key molecular features, offering an experimental platform for validating new therapeutic targets. This resource defines the gene-regulatory landscape of the developing human cortex in Down syndrome, revealing the earliest known molecular and cellular signatures of its neurological manifestations and novel candidate targets for therapeutic interventions.

overall_design: We performed bulk RNA-seq of  human brain samples from each 6 fetuses with DS and controls (CON, normal diploid karyotype), from surgical terminations of pregnancy spanning PCW 11 to 14, to complement our single nucleus Multiome (RNA/ATAC sequencing) dataset. One DS sample was excluded from the final analysis, as the data strongly diverged from all other samples, probably due to poor library quality.


title: Single-Cell Multiomic Atlas of Human Cortical Development in Down Syndrome - Neural Cells in vitro Basic Characterisation Bulk RNA-seq Dataset

overall_design: We performed bulk RNA-seq of from iPSC-derived human neural progenitors (iNPCs) and neurons (iNEU) in vitro from two individuals with Down syndrome (DS) and from isogenic control iPSCs (CON, normal diploid karyotype; iPSC lines DS1(DS) and DS2U(CON) from Weick et al., 2013, acquired from WiCell, UWWC1-DS1 and UWWC1-DS2U, and C13(DS) and C9 (CON) from Murray et al., 2015 and Alic et al. 2021, generated and provided by Dean Nizetic and Ivan Alic). Bulk RNA-seq was performed by Singleron using the Singleron AccuraCode technology. Changes in iNPC and iNEU in DS vs CON were then compared with our fetal brain tissue single nucleus Multiome (RNA/ATAC sequencing) dataset.


title: Single-Cell Multiomic Atlas of Human Cortical Development in Down Syndrome - Neural Progenitors in vitro - Treatment with Antisense Oligonucleotides for PKNOX1, BACH1 and GABPA (Bulk RNA-seq Dataset)

overall_design: We performed bulk RNA-seq of from iPSC-derived human neural progenitors (iNPCs) in vitro from an individual with DS and from isogenic control iPSCs (CON, normal diploid karyotype; C13(DS) and C9 (CON) from Murray et al., 2015 and Alic et al. 2021, generated and provided by Dean Nizetic and Ivan Alic). Progenitors were treated with antisense oligonucleotides (ASOs) to downregulate the transcription factors PKNOX1, BACH1 and GABPA, to assess consequences for the regulation of predicted downstream target genes. For ASO designs see related manuscript.


title: Single-Cell Multiomic Atlas of Human Cortical Development in Down Syndrome - iPSC-derived Neural Xenografts Multiome Dataset

overall_design: We performed combined single-cell transcriptional and chromatin accessibility profiling (10X Genomics Multiome technology) of iPSC-derived neural grafts (generated with approach from Real et al., 2018) from an individual with DS and from isogenic control iPSCs (CON, normal diploid karyotype; iPSC lines DS and DS2U from Weick et al., 2013, aquired from WiCell, UWWC1-DS1 and UWWC1-DS2U). We combined graft libraries with snRNA-seq libraries generated by Singleron and compared grafts to fetal tissue and neural cells in vitro, derived from the same iPSC line.


title: Revealing an unconventional JAK1/2-STAT3 branch in macrophage IFNγ signaling [ChIP-Seq]

city: Amsterdam

first: Josje

last: Huisman

state: Noord-Holland

address: Meibergdreef 9

department: Medical Biochemistry

country: Netherlands

institute: Amsterdam UMC

summary: Interferon-γ (IFNγ) is a key cytokine in immune activation and anti-viral responses that classically signals via JAK1/2-mediated STAT1 homodimers to drive macrophage activation. Here, we identify a non-canonical signaling component in which IFNγ also activates STAT3. Our results show that IFNγ activates STAT3 rapidly and directly through JAK1 and JAK2. We provide the first evidence that STAT3 can form heterodimers with STAT1 in this context and demonstrate that STAT3 is co-recruited to a subset of IFNγ-induced, STAT1-bound regulatory elements. While IFNγ directly activates STAT3, our results reveal that its contribution to gene regulation is limited, indicating that STAT1 easily substitutes the STAT1–STAT3 heterodimer for STAT1 homodimers when STAT3 is absent. These findings uncover STAT3 as a new unconventional player in macrophage IFNγ signaling, underscoring the complex and context-dependent nature of cytokine signaling networks.

overall_design: ChIP-seq of BMDMs stimulated with IFNγ, IFNy-IL6 or control conditions, targeting pSTAT1, pSTAT3, or Pol2.

first: Mees

last: Botman

first: Marten

middle: A

last: Hoeksema


title: Revealing an unconventional JAK1/2-STAT3 branch in macrophage IFNγ signaling [RNA-Seq]

overall_design: RNA-seq of STAT1 knockout (STAT1KO), STAT3 knockout (STAT3KO), and wild-type (WT) BMDMs under IFNγ, IL-6, IFNy-IL6-costimulation or no stimulation


title: Single-Cell Multiomic Atlas of Human Cortical Development in Down Syndrome

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

overall_design: Refer to individual Series


title: A New Form of Insulin Mutation Diabetes Defined by Zygosity, Stem Cell Models, and Population Data

city: Brussels

first: Yue

last: Tong

state: Brussels

address: Route de Lennik, 808

country: Belgium

institute: Université Libre de Bruxelles

summary: The heterozygous INS c.16C>T (insulin p.Arg6Cys, R6C) mutation has been described to cause monogenic diabetes, but its pathogenicity has recently been questioned. R6C preproinsulin exhibits impaired translocation into the endoplasmic reticulum (ER), potentially affecting insulin secretion. We explored why "one copy isn’t enough" for the R6C pathogenicity using integrative clinical, genetic, and functional approaches. Homozygous INS R6C individuals presented early-onset insulin-dependent diabetes, whereas heterozygous carriers showed variable or absent glycemic phenotypes. Population-level analysis revealed no significant enrichment of diabetes among heterozygous carriers. Heterozygous R6C induced pluripotent stem cell (iPSC)-derived β cells exhibited minimal defects, while homozygous R6C cells displayed preproinsulin accumulation and reduced insulin content and secretion. In vivo, homozygous R6C β cell transplants recapitulated human insulin deficiency and responded poorly to GLP-1 receptor agonist therapy. Transcriptionally, homozygous R6C β cells presented repression of translation, translocation and ER related pathways. Our findings establish R6C as a recessive pathogenic mutation, prompting a reassessment of the clinical interpretation of heterozygous R6C carriers. This study highlights the power of iPSC-based disease modeling and multi-modal variant classification frameworks for dissecting the functional consequences of rare genetic variants in human monogenic diabetes.

overall_design: We performed bulk-RNA sequencing on magnetic-activated cell sorting (MACS)-purified iPSC-derived stage 7 β-like cells.

first: Xiaoyan

last: Yi

first: Miriam

last: Cnop


title: Iron deficiency induces maturation-dependent loss of pancreatic β-cells.

city: Jette

first: Annelore

last: Van Mulders

address: Laarbeeklaan 103

department: Faculty Medicine & Pharmacy

institute: Vrije Universiteit Brussel (VUB)

summary: Pancreatic β-cells maintain glucose homeostasis by secreting insulin in response to rising blood glucose, a process fueled by mitochondrial ATP production. Iron, a core cofactor in the electron transport chain, is essential for this metabolic coupling. While the cytotoxic effects of iron overload are well known, the role of iron sufficiency during β-cell development remains unclear. Here, we identify a maturation-dependent requirement for iron in mouse and human β-cells. Using chemical chelation and genetic disruption of transferrin receptor (TFRC)-mediated uptake, we show that immature β-cells depend on iron during metabolic transition to functional maturity. Iron restriction at this stage impairs oxidative metabolism and compromises survival. In contrast, mature β-cells remain resilient to iron depletion, revealing a developmental switch in iron dependency. These findings establish iron as a key metabolic cue in β-cell development and suggest strategies to generate fully functional stem cell-derived β-cells for diabetes modeling and cell replacement therapy.

overall_design: To investigate the effect of Tfrc knockout in beta cells on the transcriptome pancreatic islet cells, islets from 3-week-old control and β-Tfrc-KO mice were isolated, dissociated, and subjected to single-cell RNA sequencing.

first: Willem

last: Staels


title: Single-cell RNA sequencing profiles of schistosoma japonicum during reproductive development

city: Shanghai

first: SHAOYUN

last: CHENG

address: Songhu Road 2005

department: Department of Microbiology and Microbial Engineering, School of Life Science

institute: Fudan University

summary: Schistosomes are parasitic flatworms that require male-female pairing for sexual maturation and egg production, driving schistosomiasis pathology. However, the cellular dynamics underlying this process remain poorly understood. Here, we performed single-cell RNA sequencing on 104,671 cells from male and female Schistosoma japonicum across four developmental stages, identifying 76 distinct cell populations. Our transcriptomic atlas revealed developmental trajectories of multiple cell types, particularly within the reproductive and nervous systems. Notably, we discovered three male-specific neuron populations, including delta-3 neurons located in the gynecophoric canal. We identified the lsamp gene, co-expressed with nrps in delta-3 neurons, is essential for female sexual development. Loss of lsamp impaired axonal growth and disrupted the male ventral nerve network, reducing the targeted delivery of pheromone BATT precursors to delta-3 neurons and hindering female maturation. This work provides a high-resolution cellular landscape of schistosome sexual development and suggests new strategies to disrupt parasite reproduction and control schistosomiasis.

overall_design: scRNA-seq profiling of male and female S. japonicum across 4 time points (14dpi, 18dpi, 22dpi and 26dpi) throughout the reproductive development during their interplay.

first: Yanmin

last: You

first: Shaoyun

last: Cheng

first: Xu

last: Chen

first: Xi

first: Jipeng

last: Wang

first: Wei

last: Hu


title: In Vivo Dual RNA-Seq identifies a novel AB Toxin-like as a key effector of Leptospira interrogans barrier disruption (or host colonization)

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

summary: The ability to evade host immune responses and disrupt epithelial barriers is essential for microbial pathogenesis, yet the underlying mechanisms of these processes in extracellular pathogens remain poorly understood. Through in vivo dual RNA-Seq profiling, we reveal how Leptospira interrogans compromises cell barrier integrity and disseminates within its host. Unlike most pathogens that trigger a rapid immune response, L. interrogans employs a stealth strategy, delaying host recognition even as it establishes tissue colonization. Through our analysis, we identify a novel family of bacterial effectors, the Virulence-Modifying (VM) proteins, as key mediators of barrier disruption. These AB toxin-like proteins, also identified in other extracellular pathogens, induce intracellular calcium influx in epithelial cells, activating calmodulin and myosin light chain kinase to disrupt tight junctions. Mutants deficient in VM proteins show a loss of virulence in animals, underscoring their essential role in pathogenicity. This study uncovers a unique strategy by which an extracellular pathogen exploits host calcium signaling to breach epithelial barriers through a novel class of AB toxin-like proteins. These findings offer new possibilities for therapeutic targeting and our understanding of microbial pathogenesis.

sample_organism:
Leptospira interrogans
Mesocricetus auratus

overall_design: Here, we developed a dedicated protocol for dual RNA-Seq profiling of L. interrogans-infected hamsters, a model of human acute leptospirosis, to elucidate how this pathogen spreads and compromises cell barrier integrity. Golden Syrian hamsters were infected with 108 L. interrogans by intraperitoneal route.

first: Alexandre

last: Giraud-Gatineau

first: Georges

last: Haustant

first: Marc

last: Monot

first: Mathieu

last: Picardeau

first: Nadia

last: Benaroudj


title: Novel Crosstalk Between Mechanosensitive TRPV4 and NF-κB Inhibits Pulmonary Inflammation

city: Cleveland

first: Rachel

middle: G

last: Scheraga

state: Ohio

address: 2111 E. 96th Street NE4-254a

department: Inflammation and immunity

institute: Cleveland Clinic Foundation

summary: The NF-κB signaling pathway plays a critical role in activating macrophages in the pathogenesis of many pro-inflammatory diseases. Mounting evidence has pointed to the importance of tissue mechanical properties in modulating key cellular pro-inflammatory responses. Previous studies have highlighted the role of the mechanosensitive membrane cation channel transient receptor potential vanilloid 4 (TRPV4) in limiting macrophage pro-inflammatory responses and attenuating lung injury in bacterial pneumonia. Our current study demonstrates that alveolar macrophage TRPV4 suppresses pro-inflammatory gene expression following activation of multiple Toll-like receptors (e.g., TLR 1, 2, 4, and 9) in response to P. aeruginosa pneumonia in vivo and TLR agonists in vitro, highlighting the broad regulatory role of TRPV4 in modulating the inflammatory response. TRPV4 suppresses pro-inflammatory cytokines by dampening p65-dependent cytokine transcriptional activity, thereby implicating TRPV4 as a negative regulator of the NF-κB pathway. Upon stimulation with lipopolysaccharide (LPS), TRPV4 translocates to the plasma membrane, in part releasing p65 for nuclear translocation. In addition, TRPV4 was found to have sequence homology with IκBα largely within the TRPV4 ankyrin repeat domain (ANKRD), suggesting that TRPV4 may be acting as a mechanosensitive inhibitor of NF-κB. Further, TRPV4 ANKRD was proven to be critical for TRPV4 binding to the NF-κB pathway subunit, p65, in live cells. Given the diverse roles of TRPV4 and NF-κB/p65 in different cell types, we provide a specific example of novel mechanosensitive crosstalk in macrophages that have general consequences to a broad array of NF-κB dependent inflammatory and malignant diseases.

overall_design: BMDMs from 3 individual WT and 3 individual Trpv4 KO mice ± LPS (n=12 total samples)  were analyzed via 10X Genomic Sequencing.

first: Adam

last: Boulton

first: Megan

middle: E

last: Grund

first: Erica

last: Orsini

first: Susamma

last: Abraham

first: Ryan

last: Musich

first: Caitlin

last: Snyder


title: A streamlined nanopore-compatible 5PSeq protocol for rapid phenotypic antimicrobial sensitivity testing (Fig4_PromethION)

first: Honglian

last: Liu

overall_design: s5PSeq library were prepared using 200ng extracted total RNA from exponetially growing (OD600=0.6-0.8) C.difficile clinical isolates that are resistant or sensitive to erythromycin. Bacteria cells are treated with erythromycin(1ug/ml) for 10min or without treatment.

first: Susanne

last: Huch

last: Hull

first: Fabricio

last: Garcia

first: Lilit

last: Nersisyan

first: Wei-Hua

first: Juan

last: Du

first: Vicent

last: Pelechano


title: A streamlined nanopore-compatible 5PSeq protocol for rapid phenotypic antimicrobial sensitivity testing (Fig.4_MinION)

last: Chen


title: Deep targeted sequencing reveals genomic differences between primary and recurrent high-grade serous ovarian cancer

city: Incheon

first: Seong-Woo

last: Park

address: 265, Harmony-ro, Yeonsu-gu

country: South Korea

institute: Incheon National University

summary: High-grade ovarian cancer (HGSOC) is a highly fatal disease with frequent recurrence and high mortality rates, despite ongoing treatment advancements. Next-generation sequencing (NGS) is an experimental technique that can identify extensive genetic information, making it a key component of precision medicine. We conducted a study based on a sample of 108 patients retrospectively selected from Severance Hospital and Gangnam Severance Hospital. We aimed to identify genetic factors associated with HGSOC recurrence and survival using deep targeted sequencing. This study identified key genetic alterations associated with recurrence and survival in HGSOC and confirmed that somatic mutations are linked to disease prognosis. We expect that these findings will contribute to more precise prognosis prediction and the development of personalized therapeutic strategies for patients with recurrent ovarian cancer.

overall_design: Gene fusion profiling of primary and recurrent HGSOC patients by TSO500 targeted-sequencing. All sample was derived from tumor tissue.

first: Mi-Ryung

last: Han

first: Jae-Hoon

last: Kim

first: Young-Hoon

first: Jee-Whan

first: Yoo-Kyung

last: Lee

first: Han-Byoul

last: Cho

first: In-Ho


title: A streamlined nanopore-compatible 5PSeq protocol for rapid phenotypic antimicrobial sensitivity testing(Fig1_HT-5PSeq)

summary: Antimicrobial resistance (AMR) poses a significant threat to public health. Rapid and accurate antimicrobial sensitivity testing is essential to guide effective treatment. Here, we present “simplified 5PSeq” (s5PSeq), a streamlined protocol for profiling 5’ monophosphorylated (5’P) mRNA degradation intermediates that reflect ribosome dynamics in vivo. By capturing antibiotic-induced, context-specific ribosome stalling events, s5PSeq provides a molecular proxy for bacterial growth inhibition—offering a molecular phenotypic readout without the need for culturing. s5PSeq reduces library preparation time to under four hours and incorporates a novel rRNA blocking strategy. We demonstrated its clinical utility by identifying erythromycin-resistant and sensitive Clostridioides difficile clinical isolates. Combining s5PSeq with real-time nanopore sequencing enables fast AMR diagnosis with as few as 3000 reads. In addition to simplifying the study of 5’P co-translational mRNA decay, our work suggests that utilizing information-rich phenotypic molecular readouts can significantly improve AMR diagnostics.

sample_organism:
Bacillus subtilis
Lactiplantibacillus plantarum

overall_design: HT-5PSeq library of exponetially growing (OD600=0.6-0.8)b.subtilis and l.plantarum treated with different concentration of chloramphenicol(untreated, 1.6ug/ml, 8ug/ml, 40ug/ml) or erythromycin (untreated, 0.1ug/ml, 0.5ug/ml, 2.5ug/ml) for 10min.

first: Ryan


title: Nerve regeneration within a chitosan conduit after immediate and delayed nerve repair

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

country: Italy

institute: University of Turin

summary: Peripheral nerve injuries represent a significant clinical challenge due to their limited regenerative capacity. Surgical repair strategies include immediate nerve repair, performed shortly after injury, and delayed nerve repair, conducted after a prolonged period when primary intervention is not feasible. Understanding the molecular and genetic mechanisms underlying both strategies is essential for optimizing functional recovery. This study compares the transcriptional landscape of delayed and immediate nerve repair over time to elucidate key pathways involved in nerve regeneration. A rat model of sciatic nerve injury was used, where an 8-mm nerve gap was repaired using a chitosan conduit either immediately or after a 3-month delay. Regenerated nerves were collected at 7-, 14-, and 21-days post-repair. RNA sequencing was performed to analyze transcriptomic changes across time points, and differentially expressed genes were identified and subjected to Gene Ontology enrichment analysis to identify functional pathways and regulatory networks involved in nerve regeneration. Distinct transcriptional profiles were observed across time points after immediate and delayed repair when comparing regenerating nerves with a healthy nerve. At 7 days, both exhibited a robust inflammatory response with upregulation of genes related to cytokine signaling and myeloid cell activation. By 14 days, many pathways related to response to lipoprotein particles and phagocytosis were upregulated, with delayed repair showing downregulation of myelination-associated genes. At 21 days, immune response activation, phagocytosis and lipoprotein particle activated pathways remained upregulated in both conditions. These findings suggest that immediate repair induces a faster regenerative response, whereas delayed repair follows a slower trajectory but engages similar molecular pathways. Despite initial differences, both strategies eventually converge on key regenerative mechanisms. These insights emphasize the benefits of early intervention while highlighting the potential for delayed repair to achieve functional recovery. Future research will focus on enhancing delayed repair outcomes through targeted molecular approaches.

overall_design: Median nerves of adult female Rattus norvegicus were cut to obtain a 8 mm gap and repaired with a 10 mm chitosan conduit.  Two experimental groups were created: immediate repair (animals repaired immediately after injury) and delayed repair (repair carried out 3 months after injury). The nerves regenerated within the conduits were collected 7, 14, 21 days after repair. RNA was extracted and sent to Novogene SRL for Illumina Next-Generation sequencing.

first: Marina

last: García-Bejarano

first: Federica

last: Zen

first: Marwa

last: El Soury

first: Alessandro

last: Camandona

first: Jesús

last: M. de la Fuente

first: Isabelle

last: Perroteau

first: Giulia

last: Ronchi

first: Giovanna

last: Gambarotta


title: IFITM3 Deficiency Drives SARS-CoV-2 Adaptation While Preserving Variant-Specific Traits

city: Columbus

first: Jacob

last: Yount

state: OH

address: 460 W 12th Ave, BRT 790

department: Microbial Infection and Immunity

institute: The Ohio State University

summary: Here we investigated whether interferon-induced transmembrane protein 3 (IFITM3), a key antiviral protein deficient in certain human populations, affects interspecies adaptation of SARS-CoV-2. We found that SARS-CoV-2 Beta and Omicron variants passaged through IFITM3-deficient versus wild type mice exhibit enhanced replication and pathogenesis in this new host species. Enhancements were associated with amino acid substitutions in the viral genome, suggesting that IFITM3 limits accumulation of adaptive mutations. Mouse-adapted viruses enabled comparative studies of variants in mice. Beta caused lung dysfunction and altered cilia-associated gene programs, consistent with broad viral antigen distribution in the lungs. Omicron, which shows low pathogenicity and upper respiratory tract preference in humans, replicated to high nasal titers while exhibiting limited lung spread and reduced inflammatory responses compared to Beta. Our findings demonstrate that IFITM3 deficiency accelerates SARS-CoV-2 adaptation while preserving pre-existing variant-specific properties, highlighting that host adaptation enhances viral fitness without necessarily overriding intrinsic viral characteristics.

overall_design: RNA-seq profiling of WT (C57BL/6) mice infected with either MA10, mouse adapted Beta, or Omicron BA.4 SARS-CoV-2 strains (10^5 TCID50 instranasal) with mock animals serving as controls. RNA was extracted from lung homogenates at day 2 post infection.


title: A streamlined nanopore-compatible 5PSeq protocol for rapid phenotypic antimicrobial sensitivity testing

city: Solna

first: Honglian

last: Liu

address: Tomtebodavägen 23

institute: Karolinska Institutet

sample_organism:
Staphylococcus aureus
Enterococcus faecalis
Bacillus subtilis
Clostridioides difficile
Lactiplantibacillus plantarum


title: Neurons undergo IFNγ-driven persistent epigenetic shifts and synaptic remodeling in the inflamed brain [snRNA-Seq]

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

country: Switzerland

institute: University of Geneva Medical School

summary: Our study provides novel evidence that neuronal intrinsic epigenetic changes are established as a consequence of cytotoxic T cell-mediated immune attacks and persist long after the resolution of the inflammatory process and associate to long lasting synaptic loss

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single nuclear transcriptomes of neurons derived from  hippocampus, from sequential timepoints of viral déjà vu disease and corresponding control in a genetic background of NuTRAP transgenic mice

first: Shammas

last: Ghazal

first: Merkler

last: Doron


title: Neurons undergo IFNγ-driven persistent epigenetic shifts and synaptic remodeling in the inflamed brain [RNA-Seq]

overall_design: Single nuclear transcriptomes of sorted nuclei derived from  Brain hippocampal resections of Rasmussen encephalitis patients

first: Egarvari

last: Kristof


title: A streamlined nanopore-compatible 5PSeq protocol for rapid phenotypic antimicrobial sensitivity testing (Fig3_Illumina)

first: Susanne

last: Huch

last: Hull

first: Fabricio

last: Garcia

first: Lilit

last: Nersisyan

first: Wei-Hua

last: Chen

first: Juan

last: Du

first: Vicent

last: Pelechano


title: Single-Cell Multiomic Atlas of Human Cortical Development in Down Syndrome - Fetal Cortex Multiome Dataset

first: Michael

last: Lattke

overall_design: We performed combined single-cell transcriptional and chromatin accessibility profiling (10X Genomics Multiome technology) of human brain samples from fetuses with DS and controls (CON, normal diploid karyotype). We acquired 20 CON and 19 DS foetal brain samples from surgical terminations of pregnancy spanning PCW 10 to 20. After excluding two poorly preserved samples, we performed single nucleus RNA/ATAC sequencing. After excluding 3 samples with a large fraction of non-cortical cells and stringent quality controls, we retained 248,998 high-quality cells from 15 CON and 15 DS samples for final analyses.

first: Vincenzo

last: De Paola


title: RBPscan: A Quantitative, In Vivo Tool for Profiling RNA-Binding Protein Interactions IV

city: Québec

first: Dmitry

last: Kretov

state: Québec

department: Oncology Division

country: Canada

institute: CRCHU de Québec - Université Laval

summary: RNA-binding proteins (RBPs) are essential regulators of gene expression at post-transcriptional level, yet obtaining quantitative insights into RBP–RNA interactions in vivo remains a challenge. Here we developed RBPscan, a method that integrates RNA editing with massively parallel reporter assays (MPRAs) to profile RBP binding in vivo. RBPscan fuses the catalytic domain of ADAR to the RBP of interest, using RNA editing of a recorder mRNA as a readout of binding events. We demonstrate its utility in zebrafish embryos, human cells, and yeast, where it quantifies binding strength, resolves dissociation constants, identifies high-specificity motifs for a variety of RBPs, and links binding affinities to their impact on mRNA stability. RBPscan also provide positional information of conserved and novel Pumilio-binding sites in lncRNA NORAD. With its simplicity, scalability, and compatibility across systems, RBPscan offers a versatile tool for investigating RBP–RNA interactions and complements established methods for studying post-transcriptional regulatory networks.

sample_organism:
Danio rerio
Homo sapiens

platform_organism:
Danio rerio
Homo sapiens

overall_design: RBPscan analysis of drePum1 and hsaPum2 binding to various PREs was conducted in zebrafish embryos and HEK293T cells. Recorder mRNA contained 1,000 distinct PREs and other sequences. Each experiment was performed in three biological replicates.

first: Owen

last: Sanborn

first: Thora

last: McIssac

first: Elaine

last: Park

first: Imrat

last: Imrat

first: Samuel

last: Wu

first: Daniel

last: Cifuentes


title: Catalytic activity of nuclear METTL3 promotes functional m6A modifications that drive retinal development

city: Ann Arbor

first: Zhaowei

last: Han

state: Michigan

address: 1000 Wall St

department: Gilbert S. Omenn Department of Computational Medicine & Bioinformatics

institute: University of Michigan

summary: METTL3 catalyzes N6-methyladenosine (m6A) on mRNA, regulating RNA metabolism, but its role in early retinal development remains virtually unstudied. Using stem cell-derived 3D retinal organoids to model retinal progenitor cell (RPC) differentiation, we found that loss of METTL3 nuclear m6A enzymatic activity impairs formation of the Rx+ retinal anlage in vitro. Through dCas13b-FTO m6A engineering, we demonstrate that m6A modifications at the Six3 3'UTR control its stability. While Mettl3 loss altered histone modifications, direct METTL3 chromatin targets were not transcriptionally functional. Integration of transcriptome-wide m6A and protein-RNA mapping with a degron-based strategy revealed immediate effects of METTL3 degradation in RPCs, uncovering a regulatory interaction between METTL3 and its RNA target Ythdf1. We demonstrate uncoupling of chromatin accessibility from changes in retinal transcription and m6A modifications. In vivo studies of Mettl3-deficient RPCs showed altered cell cycle and impaired retinal ganglion cell generation. Our findings establish METTL3-dependent m6A modifications as an essential post-transcriptional layer that drives retinal development.

overall_design: CUT&RUN assay of day 4 retinal organoids of Rx:GFP line and Mettl3 KO line harboring Dox inducible HA-METTL3. METTL3 antibody (Abcam, Ab195352), H3K4me3 antibody (Millipore, 07-473) and H3K27me3 antibody (ActiveMotif, 39155) were used for this assay.

first: Jing

last: Xu

first: Rajesh

last: Rao


title: A streamlined nanopore-compatible 5PSeq protocol for rapid phenotypic antimicrobial sensitivity testing (Fig2_s5PSeq)

first: Honglian

last: Liu

overall_design: s5PSeq library using 200ng of total RNA extracted from exponetially growing (OD600=0.6-0.8)B.subtilis, C.difficile, S.aureus, E.faecalis

first: Susanne

last: Huch

first: Ryan

last: Hull

first: Fabricio

last: Garcia


title: RBPscan: A Quantitative, In Vivo Tool for Profiling RNA-Binding Protein Interactions II

overall_design: RBPscan analysis of drePum1 binding to different PREs was performed in zebrafish embryos. Recorder mRNA contained 1,000 different PREs as well as other sequences. The experiment was performed in three biological replicates for each concentration of drePum1.


title: RBPscan: A Quantitative, In Vivo Tool for Profiling RNA-Binding Protein Interactions I

overall_design: RBPscan analysis of the binding of various zebrafish and human RBPs to randomized 7-mer sequence motifs. The recorder mRNA contained a fully randomized 7-mer sequence in its 3'UTR. The experiment was performed in three biological replicates for each RBP.


title: RBPscan: A Quantitative, In Vivo Tool for Profiling RNA-Binding Protein Interactions.

overall_design: RBPscan analysis of drePum1 and hsaPum2 binding to NORAD RNA was performed in zebrafish embryos and HEK293T cells. Recorder mRNA contained tiled fragments spanning the sequence of human NORAD RNA.


title: RBPscan: A Quantitative, In Vivo Tool for Profiling RNA-Binding Protein Interactions III

overall_design: RBPscan analysis of the specificity and dynamics (dose- and time-dependency) of N22 peptide binding to the recorder mRNA, which contains three BoxB elements in its 3' UTR. Recorder mRNAs without BoxB sequences were used as controls. Each experiment was performed in three biological replicates.


title: Neurons undergo IFNγ-driven persistent epigenetic shifts and synaptic remodeling in the inflamed brain [ChIP-Seq]

first: Sylvain

last: LEMEILLE

overall_design: Histone mark deposition of neurons derived from two neuroanatomical structures, namely hippocampus and brainstem, from control conditions and sequential disease timepoints of CD8 T cell-mediated encephalitis diseas.

first: Shammas

last: Ghazal

first: Merkler

last: Doron


title: Kupffer cells control neonatal hepatic glucose metabolism via Igf1 signaling [3' scRNA-seq]

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: During perinatal development, liver metabolism is tightly regulated to ensure energy supply for the newborn. Before birth, glycogen is stored in hepatocytes and later metabolized to glucose, meeting the energy demands of the neonate. Shortly after birth, lipogenesis begins, driven by the transcriptional activation of enzymes involved in fatty acid oxidation. These processes are thought to be largely regulated by systemic insulin and glucagon levels. However, the role of liver-derived local factors in neonatal hepatocyte metabolism remains unexplored. Kupffer cells (KCs), the liver’s resident macrophages, colonize the fetal liver early in embryogenesis and support liver metabolism in adulthood. Yet, whether KCs influence neonatal hepatocyte metabolism is unknown. Here, using conditional knockout mouse models targeting macrophages, we demonstrate that yolk sac-derived KCs play a critical role in hepatocyte glycogen storage and function by regulating the TCA cycle - a role that monocyte-derived KC-like cells cannot substitute. Newborn pups lacking KCs mobilize glycogen more rapidly, a process regulated by insulin-like growth factor 1 (Igf1) production. Our findings reveal that macrophages are a major source of Igf1 at birth and that local Igf1 production by KCs is essential for balanced hepatocyte metabolism.

overall_design: P0 livers from the Spiflox Tnfrsf11aeGFPCre mouse model were digested to form single cell suspension then 50g spin step was berformed to enrich hepatocytes cells in the pellet and liver immune cells in the supernatant.the pups were WT(Spi1f/f Tnfrsf11aeGFP+/+) and KO (Spif/f Tnfrsf11aeGFPCre/+) .  3' counting scRNAseq was performed on the cells using SeqWell ^s3. ).  Full length scRNAseq libraries were generated via SmartSeq2.

first: Nikola

last: Makdissi

first: Daria

last: Hirschmann

first: Aleksej

last: Frolov

first: Nelli

last: Blank-Stein

first: Inaam

last: Sado

first: Fabian

last: Nikolka

first: Jingyuan

last: Cheng

first: Mohamed

last: Yaghmour

first: Philipp

last: Arnold

first: Christoph

last: Thiele

first: Felix

last: Meissner

first: Karsten

last: Hiller

first: Marc

last: Beyer

first: Elvira

last: Mass


title: Commercial nano-enabled fertilizer: unveiling its mechanisms of toxicity in non-target soil invertebrate species using a high-throughput transcriptomics approach

city: Aveiro

first: Susana

middle: Isabel Lopes

last: Gomes

address: Campus Universitário de Santiago, Departement of Biology, University of Aveiro

department: Biology

country: Portugal

institute: CESAM & University of Aveiro

summary: Nanoagrochemicals have the potential to increase agricultural productivity while being more environmentally friendly, compared to conventional agrochemicals. However, and given its early days, concerns regarding their risks to human health and environment remain to be investigated. The impact of the commercial nano enabled fertilizer WELGRO® Cu + Zn was previously assessed, and shown to induce a dose- response in the non-target soil living invertebrate Enchytraeus crypticus (Oligochaeta), both in terms of avoidance (2 days, EC50 ca. 300mg WELGRO/kg), and survival/reproduction in longer-term (56 days, EC50 ca. 630mg WELGRO/kg). New Approach Methodologies (NAMs) are on high demand, e.g. omics, allowing to move beyond standard hazards, providing insights in to the mechanism of toxicity of chemicals. The mechanisms of toxicity of WELGRO® are unknown, and in the present study we aimed to investigate it based on high-throughput transcriptomic analysis (4x44K microarray) measuring Differentially Expressed Genes (DEGs). The animals were exposed in the natural soil LUFA 2.2 for 2 and 21 days to WELGRO® (100, 500, 1000 mg WELGRO®/kg), the lower dose corresponding to realistic top soil concentrations, based on the recommended application rates). Results showed that gene transcription was clearly time-dependent. The impacts after immediate exposure (2d) were highest at lowest concentration (100 mg, DEGs = 582) and the opposite occurred for the longer exposure time (21d), at highest concentration (1000 mg, DEGs = 241). Regardless of the exposure period, ABC transporters were shut-down, leading to accumulation of waste products and further endoplasmic reticulum (ER) stress as cause of toxicity. DNA damage seems to also occur as part of the impact. Early exposure (2 days), affected neurotoxicity related pathways, although probably a transient/ reverted impact, as this was no longer observed after 21 days. WELGRO® is probably up-taken (at cellular level) by clathrin-mediated endocytosis, which takes more than 2 days to occur. This study provides insights into the mechanisms of toxicity of a commercially available nano enabled product, based on a realistic exposure scenario for a non-target species.

overall_design: Gene expression profile of Enchytraeus crypticus was analysed after 2 and 21 days of exposure to WELGRO, a nanoenabled commercial fertilizer, in three different concentrations: 100, 500 and 1000 mg WELGRO/kg soil. The exposure was performed in LUFA 2.2 soil. Three biological replicates per test treatment and control (un-spiked soil) were used.

middle: I

first: Janeck

last: Scott-Fordsmand

first: Mónica

last: Amorim


title: Functional Integration of Autologous Tissue-Engineered Grafts in a Pre-Clinical Esophageal Defect Model

first: George

middle: Thomas

last: Hall

address: Zayed Centre for Research, 20 Guilford Street

department: UCL Great Ormond Street Institute of Child Health

institute: University College London

summary: Congenital and acquired esophageal pathologies such as oesophageal atresia can leave large tissue deficits in patients were insufficient oesophagus exists to restore continuity. Currently, these require replacement by repurposing the stomach, colon or small bowel. The aim of this study was to develop a tissue engineered oesophagus as an alternative, produced using a clinically relevant timescale, and determine feasibility, safety of autologous transplantation of autologous grafts via a thoracic approach in a growing minipig model, together with assessment of function and integration.

overall_design: Five libraries of single-nucleus data and eleven of spatial transcriptomic data.  Single-nucleus data: Two libraries (Cher-Injected-nuclei, Cher-ReCell-nuclei) containing nuclei from single samples. The remaining three (P1, P2_R, P3) containing multiplexed nuclei from two samples each, as follows:  P1: AdeleInjectedCells & DollyRecellSN P2_R: FergieRecellSN & DollyInjectedCells P3: FergieInjectedCells & AdeleRecellSN   Spatial transcriptomic data:  Four native samples, with three from domestic pig (Native_1_ST, Native_2_ST, Native_3_ST) and one from a minipig which received a transplant (Cher_native_V). One pre-implant sample (Cher_ReCell_V) Six post-implant samples (Cher_Graft_V, Fergie_Graft_V, PVA, PVB, PVC, PVD)

middle: T


title: Kupffer cells control neonatal hepatic glucose metabolism via Igf1 signaling

first: Joachim

last: Schultze

first: Nikola

last: Makdissi

first: Daria

last: Hirschmann


title: Neurons undergo IFNγ-driven persistent epigenetic shifts and synaptic remodeling in the inflamed brain [ATAC-Seq]

first: Sylvain

last: LEMEILLE

overall_design: Chromatin accessibility of neurons derived from two neuroanatomical structures, namely hippocampus and brainstem, from control conditions and sequential disease timepoints of CD8 T cell-mediated encephalitis disease in a genetic background of NuTRAP transgenic and NuTRAP transgenic and IFNGR floxed mice

first: Shammas

last: Ghazal

first: Merkler

last: Doron


title: Apical and transcriptomic points of departure (aPOD and tPOD) of nine PFAS with different carbon chains and functional groups in zebrafish embryos

city: Ottawa

first: John

last: Stead

state: ON

address: 1125 Colonel By Drive

department: Department of Neuroscience

institute: Carleton University

summary: Per- and poly-fluoroalkyl substances (PFAS) are persistent environmental contaminants prevalent in industrial manufacturing processes and various consumer products. Human health consequences include reduced fertility, liver damage, thyroid disease, kidney disease, cancer, inflammation, hypertension, and obesity. In this study, various approaches were used to determine toxicological points of departure (PODs) for 9 PFAS (PFDS, PFDS, PFOA, PFOS, PFBA, PFBS, PFHxA, PFHxS, PFNA) in Zebrafish embryos exposed for 5 days from 4 to 120 hours post-fertilization. Apical PODs (aPODs) were assessed for developmental toxicity (based on mortality and malformation), behaviour (based in distance swum under light and dark conditions) and metabolism (based on NADH-dependent changes in alamarBlue fluorescence). Transcriptional PODs (tPODs) were determined using TempO-Seq S1500+ Zebrafish Surrogate Assay Panel applied to pools of 10 embryos. Count data were generated using the Omics data analysis framework for regulatory application (R-ODAF) pipeline, available at https://github.com/R-ODAF/R-ODAF_Health_Canada. Transcriptomic BMC modeling was performed using BMDExpress. PFAS toxicity was highest for PFAS with longer carbon chain length, and with a functional group of sulfonic acid compared with carboxylic acid. This toxicity ranking was similar across all aPODs and tPODs. This study demonstrates that for PFAS chemicals, transcriptional PODs can be used to reliably predict other aPOD estimates generated through assessments of metabolism, behaviour, or mortality/malformation.

overall_design: Zebrafish embryos were exposed for 5 days (from 4 to 120 hours post-fertilization) to one of nine PFAS chemicals (PFDS, PFDS, PFOA, PFOS, PFBA, PFBS, PFHxA, PFHxS, PFNA) in 0.1% DMSO (final concentration). PFAS concentrations (see concentration in metadata) are in micromolar units, with each PFAS used at 5 different concentrations (plus 0.1% DMSO controls). Following exposure, 10 embryos were pooled to generate a single sample per PFAS/concentration, with typically n=4 sample per group (see replicate in metadata). Samples were processed in two different batches (see processing_batch in metadata). For batch A, some zebrafish were from the Ottawa breeding facility, while others were a mixture of Ottawa and Montreal breeding facilities. These variables determined which samples were used as the control (0.1% DMSO only) group. 'control_mixed' (see chemical in metadata) was the contrast group for PFDS, PFDS, PFOA and PFOS. 'control_ottawa' was the contrast group for PFBA, PFBS, PFHxA and PFHxS. 'control_pfna' was the contrast group for PFNA. 'control_excluded' samples were outliers and not used in any contrast.

first: Hyojin

last: Lee

first: Andrew

last: Williams

first: Curry

last: Jory

first: Ella

last: Atlas

first: Eccles

last: Kristin

first: Jan

last: Mennigen

first: Carole

last: Yauk

first: Jason

last: O'Brien


title: HDAC1 has intrinsic protease activity and regulates transcription through clipping histone H3 N-terminal tail

city: Los Angeles

first: Yonghwan

last: Shin

state: CA

address: 1450 Biggy St

department: Biochemistry and Molecular Medicine

institute: University of Southern California

summary: Histone deacetylase 1 (HDAC1) has been mainly characterized as a factor removing acetyl groups from histone and non-histone proteins as well as inhibiting gene transcription. However, HDAC1 is also involved in positively regulating transcription of particular genes through as yet unknown mechanisms. Here we report the identification of an intrinsic protease activity residing in HDAC1 and capable of cleaving histone H3 between lysine 20 and alanine 21. Such HDAC1 protease activity toward H3 N-terminal tail (H3NT) depends on its stable association with nucleosomes and is required for bladder cancer cells to grow in an uncontrolled manner. Mechanistically, growth stimulatory genes are selectively activated by HDAC1-dependent H3NT proteolysis, and the levels of H3NT clipping are much higher in bladder cancer cells, serving as a cancer-specific chromatin signature. Moreover, artificial tethering of HDAC1 to target genes using CRISPR-dCas9 systems is sufficient for establishing H3NT proteolysis and achieving active transcriptional state in HDAC1-deficient cells, resulting in a higher proliferative capacity of cancer cells. Not only does this work establish HDAC1 as a new protease targeting H3NT, but our data also define a new mechanism underlying HDAC1-driven tumorigenesis by linking H3NT proteolysis to oncogenic gene expression program.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for LD611 cells  (shControl, and shHDAC1).

first: Woojin

last: An


title: Human Liver Epithelial Cell Chromatin Accessibility Response to HCoV-229E Infection

city: Richland

first: Lindsey

last: Anderson

state: WA

address: 3300 Stevens Dr

department: Biological Sciences Division

institute: Pacific Northwest National Laboratory

summary: The purpose of this experiment was to evaluate how wild-type Human coronavirus strain 229E (HCoV-229E) infection alters chromatin accessiblity in infected but not mock-infected samples.

overall_design: Human coronavirus 229E, UV-treated and mock-infected samples were collected in Huh7 human liver epithelial cells at 24 hours post infection. Samples were processed using Active Motif's Bulk ATAC-Seq kit (according to manufacturer's instructions) to generate bar coded library samples for RNA Seq analysis.

first: Amy

last: Sims

first: Hugh

last: Mitchell

first: Owen

last: Leiser

first: Tony

last: Chiang


title: Functional and molecular characterization of exosomes secreted from mesenchymal stromal cells exposed to IFNg in the presence of autophagy modulators tamoxifen and chloroquine

city: Fort Lauderdale

first: Vladimir

last: Beljanski

state: FL

address: 3300 S. University Drive

department: NSU MD

institute: Nova Southeastern Uni

type: Non-coding RNA profiling by high throughput sequencing

summary: Bone marrow mesenchymal stromal cells (MSCs) are therapeutic cells which adopt an immunomodulatory phenotype when exposed to pro-inflammatory cytokines and thus can be used for treatment of conditions associated with excessive inflammation. It was suggested recently that many therapeutic benefits of MSCs can be attributed to the secretion of exosomes, small membrane vesicles of endocytic origin. Exosome formation and release are impacted by the autophagy pathway, a homeostatic quality control mechanism that recycles proteins and organelles via lysosomal degradation. We hypothesized that the exposure of MSCs to autophagy modulators in the presence of a pro-inflammatory cytokine IFN may impact on exosome RNA content and immunomodulatory properties. To address this hypothesis, we treated MSCs with either tamoxifen (TX) or chloroquine (CQ) to stimulate or inhibit autophagy, respectively, in the presence of pro-inflammatory cytokine, IFN. Subsequently, we characterized exosomes from such cells and determined their functional and molecular properties. Exosomes’ immunoregulatory properties were evaluated ex-vivo using activated CD4 T cells and subsequent flow cytometry analysis to assess the effects of exosomes on CD4 T cell proliferation. We also performed small RNA sequencing to determine exosomal microRNA content. Subsequently, we performed functional analysis to determine potential effects of exosomal microRNAs on the expression of genes in target cells. Our data indicate that the exosomes isolated from MSCs treated with CQ+IFN possess higher capacity to decrease T cell proliferation. Small RNA sequencing of exosomal RNA revealed that, although similar microRNAs were found to be expressed in exosomes isolated from all treated cells, the treatments did affect the levels of multiple microRNAs. Analysis of putative gene targets revealed that most microRNA-target genes belong to either cancer or inflammation-related biological pathways. Overall, we conclude that the pre-treatment of MSCs with small molecules, in addition to pro-inflammatory cytokines, has a potential to additionally modulate biological targets of exosomes and thus biological effects of the latter.

overall_design: MSCs were grown in serum-free media and treated with IFNgamma in the presence or absence of tamoxifen (5 microM) or chloroquine (10 microM) for 48 h. Subsequently serum-free media was used to harvest MSC-secreted exosomes which were used to extract microRNAs which were subjected to deep sequencing. microRNA were then counted and following contrasts were created: 1. untreated vs. IFNgamma treated; 2. untreated vs. tamoxifene treated; 3. untreated vs chloroquine treated; 4. untreated vs. IFNgamma+tamoxifene treated; 5. untreated vs. IFNgamma+chloroquine treated.

first: Julia

middle: M

last: Hollweg

first: Renee

last: Potens

first: Tanner

last: Blaylock

first: Andres

middle: B

last: Irausquin

first: Nikhila

last: Paleati

first: Lubov

last: Nathanson


title: Stepwise evolution of root nodule symbiosis [DAP-seq]

city: Kunming

first: Dingjie

last: Wang

state: Yunnan

address: NO. 132 Lanhei Road

institute: Kunming Institute of Botany, Chinese Academy of Sciences

summary: Root nodule symbiosis (RNS) represents a significant phenotypic adaptation in plants to thrive in nitrogen-deficient environments. Recent findings propose a single gain of RNS at the crown of the nitrogen-fixing clade (NF clade). However, the genetic mechanisms underlying the origin and subsequent evolution of RNS remain largely unexplored. Here, we newly sequenced and assembled eleven genomes from the NF clade and studied genetic change along the evolution of RNS. Our results elucidated three key evolutionary stages leading to the formation of stable RNS between plants and symbiotic nitrogen-fixing bacteria.

overall_design: For cross species RNA-Seq analysis, we newly conducted RNA-Seq of the roots and nodules of five species (Coriaria nepalensis, Elaeagnus umbellata, Alnus trabeculosa, Chamaecrista pumila, Mimosa pudica), as well as the mycorrhizal and non-mycorrhizal roots of Populus deltoides x Populus euramericana cv. "Nanlin895". DNAaffinitypurificationsequencing (DAP-Seq) for transcription factor MtNIN and INPUT100 in Medicago truncatula.


title: Pre-cancerous Niche Remodelling Dictates Nascent Tumour Persistence

city: CAMBRIDGE

first: Maria

middle: Pilar

last: Alcolea

state: Cambridgeshire

address: Jeffrey Cheah Biomedical centre, Puddicombe way

department: Cambridge Stem Cell Institute

institute: University of Cambridge

summary: Interactions between mutant cells and their environment play a key role in determining cancer susceptibility. However, our understanding of how the pre-cancerous microenvironment contributes to early tumorigenesis remains limited. Here, we show that newly emerging tumours at their most incipient stages shape their microenvironment in a critical process that determines their survival. Analysis of nascent squamous tumours in the upper gastrointestinal tract of the mouse reveals that the stress response of early tumour cells instructs the underlying mesenchyme to form a supportive “pre-cancerous niche”, which dictates the long-term outcome of epithelial lesions. Stimulated fibroblasts beneath emerging tumours activate a wound healing response that triggers a dramatic remodelling of the underlying extracellular matrix, resulting in the formation of a fibronectin-rich stromal scaffold that promotes tumour growth. Functional heterotypic 3D culture assays and in vivo grafting experiments, combining carcinogen-free healthy epithelium and tumour derived stroma, demonstrate that the pre-cancerous niche alone is sufficient to confer tumour properties to normal epithelial cells. We propose a model where both mutations and the stromal response to genetic stress together define the likelihood of early tumours to persist and progress towards more advanced disease stages.

overall_design: scRNAseq of murine upper gastro-intestinal tract epithelial and stromal cells from early squamous tumours, morphologically normal (internal control) areas, and areas from age-matched (external control) animals.

first: Greta

last: Skrupskelyte

first: Jesus

last: Rojo Arias

first: Yiteng

last: Dang

first: Seungmin

last: Han

first: Harikrishnan

last: Ajith

first: Steffen

last: Rulands

first: Ben

middle: D

last: Simons

middle: P


title: Stepwise evolution of root nodule symbiosis [RNA-seq]

sample_organism: Populus deltoides x Populus x canadensis


title: Expression data from human lungs at cold ischemic time (CIT) and 2 hrs. after reperfusion (R2H)

city: Toronto

first: Mingyao

last: Liu

state: Ontario

address: 101 College Street

institute: University Health Network

summary:
Ischemia-reperfusion (IR) in lung transplantation activates genes in inate inflammation and cell death. Multiple programmed cell death (PCD) pathways have been proposed to be involved in IR injury in lung transplantation. However, the status of these pathways in human lung transplants remain unknown.
Study on the genes related PCD and their relationship with inflammation and signaling pathways in human lung transplants during IR.

overall_design: Lung tissue samples were collected at the end of cold ischemia (CIT) and at reperfusion 2 hours (H) at University Health Network in Toronto, Canada.

first: Yajin

last: Zhao

first: Lubiao

last: Liang

first: Jamie

last: Jeon

first: Shaf

last: Keshavjee


title: Stepwise evolution of root nodule symbiosis

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

platform_organism: Populus deltoides x Populus x canadensis

overall_design: Refer to individual Series


title: Novel Acinar Metaplastic States Uncovered in Exocrine Pancreas Disease

status: Public on Dec 22 2025

city: Boston

first: Sahar

last: Nissim

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Brigham and Women's Hospital

summary: We used single-cell RNA sequencing to profile mouse pancreas across models of acute pancreatitis (AP), recurrent acute pancreatitis (RAP), chronic pancreatitis (CP), and oncogenic Kras-driven acute pancreatitis (K-AP, abbreviated APK). We captured both whole-pancreas cell suspensions and FACS-enriched mKate2+ epithelial populations from defined timepoints spanning early injury, recurrent damage, chronic inflammation, and Kras-driven precursor lesion formation. These data characterize acinar and epithelial plasticity and associated microenvironmental remodeling across pancreatitis and Kras-mediated disease initiation. BACKGROUND & AIMS: In response to injury, pancreatic acinar cells undergo acinar-to-ductal metaplasia (ADM), marked by loss of acinar identity and acquisition of ductal features. While ADM can resolve to support tissue repair, it may also persist and serve as a precursor to pancreatic cancer. Whether diverse pancreatic stressors drive a shared or context-specific ADM program remains unclear. We sought to comprehensively define metaplastic responses to clinically relevant exocrine pancreas diseases known to increase cancer risk. METHODS: We profiled ADM and the surrounding microenvironment across mouse models of exocrine disease—including acute, recurrent, and chronic pancreatitis, as well as in the setting of oncogenic Kras—capturing over 300,000 single cells. To enable high-quality transcriptomic profiling in enzyme-rich tissue, we leveraged FixNCut, a method that preserves RNA integrity in the exocrine pancreas. Findings were validated in human pancreas tissue using CosMx spatial transcriptomics. RESULTS: We identify a conserved acinar response across disease contexts that gives rise to previously unrecognized distinct metaplastic states, including a “gateway” ADM population that precedes more advanced metaplastic states marked by complete loss of acinar identity. In pancreatic intraepithelial neoplasia (PanIN) precancerous lesions, we detect classical-like and basal-like states, suggesting that pancreatic cancer subtypes are specified much earlier than previously appreciated. In Kras-mutant tissue, we identify a second wave of inflammation and the emergence of an immunosuppressive niche, coinciding with PanIN formation. CONCLUSIONS: Our findings define a conserved program of acinar plasticity across exocrine pancreas diseases. We further link unresolved ADM to immune remodeling during precursor lesion formation and observe the emergence of pancreatic cancer subtypes in early PanIN lesions.

overall_design: Pancreatitis was induced in male mice at 8–9 weeks of age by intraperitoneal caerulein injection. For acute pancreatitis (AP), male C57BL/6 mice were injected with caerulein (0.1 μg/g diluted in saline) on two consecutive days once every hour for 8 hours. For recurrent acute pancreatitis (RAP), this 2-day injection protocol was repeated weekly for 6 weeks, and RAP samples (2x, 4x, 6x) were collected 3 days after the final injection. Kras(G12D) mice were generated by crossing Ptf1a-CreERT/+, CAGs-LSL-rtTA-IRES-mKate2/+, and LSL-KrasG12D alleles. One week before AP induction, KrasG12D mice (K-AP) received tamoxifen (0.25 mg/g in corn oil) by oral gavage for 3 consecutive days to activate Kras and mKate2. Chronic pancreatitis (CP) was induced in Ptf1a-CreERT/+, CAGs-LSL-rtTA-IRES-mKate2/+ mice using a 4-week caerulein protocol (0.25 μg/g, twice per day, 5 days per week). Pancreas tissue was collected at multiple timepoints after AP or K-AP (14 hr, 72 hr, 7 day, 14 day, 6 weeks, 12 weeks) and 72hr after the last injection for  CP or RAP protocols. Single-cell suspensions were prepared from whole pancreas, and for selected CP and K-AP timepoints, mKate2+ cells were enriched by FACS to obtain epithelial-only datasets before single-cell library preparation.

first: Aney

last: Katherine Jean

first: Jeong

last: Woo-Jeong

first: Nissim

last: Sahar